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Sample records for dynamic kinetic resolution

  1. Dynamic kinetic resolution of biaryl atropisomers by chiral dialkylaminopyridine catalysts.

    Science.gov (United States)

    Ma, Gaoyuan; Deng, Chao; Deng, Jun; Sibi, Mukund P

    2018-05-02

    The acylative dynamic kinetic resolution (DKR) of configurationally unstable biaryl atropisomers is achieved by using newly developed chiral dialkylaminopyridine catalysts with fluxional chirality. Various types of biaryl substrates containing phenolic structures were subjected to the DKR to obtain a range of acylated biaryl products with enantiomeric ratios up to 90 : 10.

  2. Recent Advances in Dynamic Kinetic Resolution by Chiral Bifunctional (Thiourea- and Squaramide-Based Organocatalysts

    Directory of Open Access Journals (Sweden)

    Pan Li

    2016-10-01

    Full Text Available The organocatalysis-based dynamic kinetic resolution (DKR process has proved to be a powerful strategy for the construction of chiral compounds. In this feature review, we summarized recent progress on the DKR process, which was promoted by chiral bifunctional (thiourea and squaramide catalysis via hydrogen-bonding interactions between substrates and catalysts. A wide range of asymmetric reactions involving DKR, such as asymmetric alcoholysis of azlactones, asymmetric Michael–Michael cascade reaction, and enantioselective selenocyclization, are reviewed and demonstrate the efficiency of this strategy. The (thiourea and squaramide catalysts with dual activation would be efficient for more unmet challenges in dynamic kinetic resolution.

  3. Dual enzymatic dynamic kinetic resolution by Thermoanaerobacter ethanolicus secondary alcohol dehydrogenase and Candida antarctica lipase B

    KAUST Repository

    Karume, Ibrahim

    2016-10-04

    The immobilization of Thermoanaerobacter ethanolicus secondary alcohol dehydrogenase (TeSADH) using sol–gel method enables its use to racemize enantiopure alcohols in organic media. Here, we report the racemization of enantiopure phenyl-ring-containing secondary alcohols using xerogel-immobilized W110A TeSADH in hexane rather than the aqueous medium required by the enzyme. We further showed that this racemization approach in organic solvent was compatible with Candida antarctica lipase B (CALB)-catalyzed kinetic resolution. This compatibility, therefore, allowed a dual enzymatic dynamic kinetic resolution of racemic alcohols using CALB-catalyzed kinetic resolution and W110A TeSADH-catalyzed racemization of phenyl-ring-containing alcohols.

  4. High resolution kinetic beam schemes in generalized coordinates for ideal quantum gas dynamics

    International Nuclear Information System (INIS)

    Shi, Yu-Hsin; Huang, J.C.; Yang, J.Y.

    2007-01-01

    A class of high resolution kinetic beam schemes in multiple space dimensions in general coordinates system for the ideal quantum gas is presented for the computation of quantum gas dynamical flows. The kinetic Boltzmann equation approach is adopted and the local equilibrium quantum statistics distribution is assumed. High-order accurate methods using essentially non-oscillatory interpolation concept are constructed. Computations of shock wave diffraction by a circular cylinder in an ideal quantum gas are conducted to illustrate the present method. The present method provides a viable means to explore various practical ideal quantum gas flows

  5. Large-scale ruthenium- and enzyme-catalyzed dynamic kinetic resolution of (rac-1-phenylethanol

    Directory of Open Access Journals (Sweden)

    Bäckvall Jan-E

    2007-12-01

    Full Text Available Abstract The scale-up of the ruthenium- and enzyme-catalyzed dynamic kinetic resolution (DKR of (rac-1-phenylethanol (2 is addressed. The immobilized lipase Candida antarctica lipase B (CALB was employed for the resolution, which shows high enantioselectivity in the transesterification. The ruthenium catalyst used, (η 5-C5Ph5RuCl(CO2 1, was shown to possess very high reactivity in the "in situ" redox racemization of 1-phenylethanol (2 in the presence of the immobilized enzyme, and could be used in 0.05 mol% with high efficiency. Commercially available isopropenyl acetate was employed as acylating agent in the lipase-catalyzed transesterifications, which makes the purification of the product very easy. In a successful large-scale DKR of 2, with 0.05 mol% of 1, (R-1-phenylethanol acetate (3 was obtained in 159 g (97% yield in excellent enantiomeric excess (99.8% ee.

  6. Kinetic and dynamic kinetic resolution of secondary alcohols with ionic-surfactant-coated Burkholderia cepacia lipase: substrate scope and enantioselectivity.

    Science.gov (United States)

    Kim, Cheolwoo; Lee, Jusuk; Cho, Jeonghun; Oh, Yeonock; Choi, Yoon Kyung; Choi, Eunjeong; Park, Jaiwook; Kim, Mahn-Joo

    2013-03-15

    Forty-four different secondary alcohols, which can be classified into several types (II-IX), were tested as the substrates of ionic surfactant-coated Burkholderia cepacia lipase (ISCBCL) to see its substrate scope and enantioselectivity in kinetic and dynamic kinetic resolution (KR and DKR). They include 6 boron-containing alcohols, 24 chiral propargyl alcohols, and 14 diarylmethanols. The results from the studies on KR indicate that ISCBCL accepted most of them with high enantioselectivity at ambient temperature and with useful to high enantioselectivity at elevated temperatures. In particular, ISCBCL displayed high enantioselectivity toward sterically demanding secondary alcohols (types VIII and IX) which have two bulky substituents at the hydroxymethine center. DKR reactions were performed by the combination of ISCBCL with a ruthenium-based racemization catalyst at 25-60 °C. Forty-one secondary alcohols were tested for DKR. About half of them were transformed into their acetates of high enantiopurity (>90% ee) with good yields (>80%). It is concluded that ISCBCL appears to be a superb enzyme for the KR and DKR of secondary alcohols.

  7. Development of dynamic kinetic resolution on large scale for (±-1-phenylethylamine

    Directory of Open Access Journals (Sweden)

    Lisa K. Thalén

    2010-09-01

    Full Text Available Candida antarctica lipase B (CALB and racemization catalyst 4 were combined in the dynamic kinetic resolution (DKR of (±-1-phenylethylamine (1. Several reaction parameters have been investigated to modify the method for application on multigram scale. A comparison of isopropyl acetate and alkyl methoxyacetates as acyl donors was carried out. It was found that lower catalyst loadings could be used to obtain (R-2-methoxy-N-(1-phenylethylacetamide (3 in good yield and high ee when alkyl methoxyacetates were used as acyl donors compared to when isopropyl acetate was used as the acyl donor. The catalyst loading could be decreased to 1.25 mol % Ru-catalyst 4 and 10 mg CALB per mmol 1 when alkyl methoxyacetates were used as the acyl donor.

  8. Development of dynamic kinetic resolution on large scale for (±)-1-phenylethylamine.

    Science.gov (United States)

    Thalén, Lisa K; Bäckvall, Jan-E

    2010-09-13

    Candida antarctica lipase B (CALB) and racemization catalyst 4 were combined in the dynamic kinetic resolution (DKR) of (±)-1-phenylethylamine (1). Several reaction parameters have been investigated to modify the method for application on multigram scale. A comparison of isopropyl acetate and alkyl methoxyacetates as acyl donors was carried out. It was found that lower catalyst loadings could be used to obtain (R)-2-methoxy-N-(1-phenylethyl)acetamide (3) in good yield and high ee when alkyl methoxyacetates were used as acyl donors compared to when isopropyl acetate was used as the acyl donor. The catalyst loading could be decreased to 1.25 mol % Ru-catalyst 4 and 10 mg CALB per mmol 1 when alkyl methoxyacetates were used as the acyl donor.

  9. Chemoenzymatic dynamic kinetic resolution of primary amines using a recyclable palladium nanoparticle catalyst together with lipases.

    Science.gov (United States)

    Gustafson, Karl P J; Lihammar, Richard; Verho, Oscar; Engström, Karin; Bäckvall, Jan-E

    2014-05-02

    A catalyst consisting of palladium nanoparticles supported on amino-functionalized siliceous mesocellular foam (Pd-AmP-MCF) was used in chemoenzymatic dynamic kinetic resolution (DKR) to convert primary amines to amides in high yields and excellent ee's. The efficiency of the nanocatalyst at temperatures below 70 °C enables reaction conditions that are more suitable for enzymes. In the present study, this is exemplified by subjecting 1-phenylethylamine (1a) and analogous benzylic amines to DKR reactions using two commercially available lipases, Novozyme-435 (Candida antartica Lipase B) and Amano Lipase PS-C1 (lipase from Burkholderia cepacia) as biocatalysts. The latter enzyme has not previously been used in the DKR of amines because of its low stability at temperatures over 60 °C. The viability of the heterogeneous Pd-AmP-MCF was further demonstrated in a recycling study, which shows that the catalyst can be reused up to five times.

  10. Recent Advances in Dynamic Kinetic Resolution by Chiral Bifunctional (Thio)urea- and Squaramide-Based Organocatalysts.

    Science.gov (United States)

    Li, Pan; Hu, Xinquan; Dong, Xiu-Qin; Zhang, Xumu

    2016-10-14

    The organocatalysis-based dynamic kinetic resolution (DKR) process has proved to be a powerful strategy for the construction of chiral compounds. In this feature review, we summarized recent progress on the DKR process, which was promoted by chiral bifunctional (thio)urea and squaramide catalysis via hydrogen-bonding interactions between substrates and catalysts. A wide range of asymmetric reactions involving DKR, such as asymmetric alcoholysis of azlactones, asymmetric Michael-Michael cascade reaction, and enantioselective selenocyclization, are reviewed and demonstrate the efficiency of this strategy. The (thio)urea and squaramide catalysts with dual activation would be efficient for more unmet challenges in dynamic kinetic resolution.

  11. MOLECULAR DYNAMICS SIMULATION OF KINETIC RESOLUTION OF RACEMIC ALCOHOL USING BURKHOLDERIA CEPACIA LIPASE IN ORGANIC SOLVENTS

    Directory of Open Access Journals (Sweden)

    A. C. Mathpati

    2018-03-01

    Full Text Available Lipases, a subclass of hydrolases, have gained a lot of importance as they can catalyze esterification, transesterification and hydrolysis reaction in non-aqueous media. Lipases are also widely used for kinetic resolution of racemic alcohols into enantiopure compounds. The lipase activity is affected by organic solvents due to changes in the conformational rigidity of enzymes, the active site, or altering the solvation of the transition state. The activity of lipases strongly depends on the logP value of solvents. Molecular dynamics (MD can help to understand the effect of solvents on lipase conformation as well as protein-ligand complex. In this work, MD simulations of Burkholderia cepacia lipase (BCL and complex between R and S conformation of acetylated form of 1-phenylethanol with BCL using gromacs have been carried in various organic solvents. The RMSD values were within the range of 0.15 to 0.20 nm and radius of gyration was found to be with 1.65 to 1.9 nm. Major changes in the B factor compared to reference structure were observed between residues 60 to 80, 120 to 150 and 240 to 260. Higher unfolding was observed in toluene and diethyl ether compared to hexane and acetonitrile. R acetylated complex was found to favorably bind BCL compared to S form. The predicted enantioselectivity were in good agreement with the experimental data.

  12. Chemoenzymatic Dynamic Kinetic Resolution: A Powerful Tool for the Preparation of Enantiomerically Pure Alcohols and Amines

    Science.gov (United States)

    2015-01-01

    Chemoenzymatic dynamic kinetic resolution (DKR) constitutes a convenient and efficient method to access enantiomerically pure alcohol and amine derivatives. This Perspective highlights the work carried out within this field during the past two decades and pinpoints important avenues for future research. First, the Perspective will summarize the more developed area of alcohol DKR, by delineating the way from the earliest proof-of-concept protocols to the current state-of-the-art systems that allows for the highly efficient and selective preparation of a wide range of enantiomerically pure alcohol derivatives. Thereafter, the Perspective will focus on the more challenging DKR of amines, by presenting the currently available homogeneous and heterogeneous methods and their respective limitations. In these two parts, significant attention will be dedicated to the design of efficient racemization methods as an important means of developing milder DKR protocols. In the final part of the Perspective, a brief overview of the research that has been devoted toward improving enzymes as biocatalysts is presented. PMID:25730714

  13. Merging Iron Catalysis and Biocatalysis-Iron Carbonyl Complexes as Efficient Hydrogen Autotransfer Catalysts in Dynamic Kinetic Resolutions

    KAUST Repository

    El-Sepelgy, Osama

    2016-09-29

    A dual catalytic iron/lipase system has been developed and applied in the dynamic kinetic resolution of benzylic and aliphatic secondary alcohols. A detailed study of the Knölker-type iron complexes demonstrated the hydrogen autotransfer of alcohols to proceed under mild reaction conditions and allowed the combination with the enzymatic resolution. Different racemic alcohols were efficiently converted to chiral acetates in good yields and with excellent enantioselectivities. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

  14. Merging Iron Catalysis and Biocatalysis-Iron Carbonyl Complexes as Efficient Hydrogen Autotransfer Catalysts in Dynamic Kinetic Resolutions

    KAUST Repository

    El-Sepelgy, Osama; Alandini, Nurtalya; Rueping, Magnus

    2016-01-01

    A dual catalytic iron/lipase system has been developed and applied in the dynamic kinetic resolution of benzylic and aliphatic secondary alcohols. A detailed study of the Knölker-type iron complexes demonstrated the hydrogen autotransfer of alcohols to proceed under mild reaction conditions and allowed the combination with the enzymatic resolution. Different racemic alcohols were efficiently converted to chiral acetates in good yields and with excellent enantioselectivities. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

  15. Stereoselective Preparation of N-Alkyl Dipeptide Analogues via Dynamic Kinetic Resolution of α-Halo Acyl Amino Esters

    International Nuclear Information System (INIS)

    Shin, Eun Kyoung; Chang, Ji Yeon; Kim, Hyun Jung; Kim, Yong Tae; Park, Yong Sun

    2006-01-01

    We have shown that dynamic kinetic resolution of α-bromo and α-chloro amides in nucleophilic substitution reaction can be successfully applied towards the preparation of various N-terminal functionalized dipeptide analogues. The stereochemical aspects of the results showed that stereoselectivity depends critically on the structures of amine nucleophiles. This mild and practical method can be run on a multi-gram scale without any special precautions and should be applicable to stereoselective syntheses of various peptidomimetics. Extension of this synthetic methodology to dynamic resolution of N-(α-haloacetyl) peptides in the stereospecific nucleophilic substitution (S N 2) could be an attractive synthetic strategy for asymmetric syntheses of peptide analogues. Recently it has been shown from our group that the chiral information of adjacent amino acid residue is efficiently transferred to the new C-N bond formation at α-halo carbon center for asymmetric syntheses of di-, tri- and tetrapeptide analogues. The α-halo stereogenic center of undergoes rapid epimerization in the presence of diisopropylethylamine (DIEA) and tetrabutylammonium iodide (TBAI), and (αS) reacts with the nucleophile preferentially to provide the dipeptide analogue (αR). The mechanistic investigation showed that this is a case of dynamic kinetic resolution, in which the stereoselectivity is determined by the difference in the diastereomeric transition state energies for the reaction with the nucleophiles. Herein we describe our recent progress to extend the scope of the methodology to stereoselective preparation of N-terminal functionalized dipeptide analogues with various amine nucleophiles

  16. Influence of the partial volume correction method on (18)F-fluorodeoxyglucose brain kinetic modelling from dynamic PET images reconstructed with resolution model based OSEM.

    Science.gov (United States)

    Bowen, Spencer L; Byars, Larry G; Michel, Christian J; Chonde, Daniel B; Catana, Ciprian

    2013-10-21

    Kinetic parameters estimated from dynamic (18)F-fluorodeoxyglucose ((18)F-FDG) PET acquisitions have been used frequently to assess brain function in humans. Neglecting partial volume correction (PVC) for a dynamic series has been shown to produce significant bias in model estimates. Accurate PVC requires a space-variant model describing the reconstructed image spatial point spread function (PSF) that accounts for resolution limitations, including non-uniformities across the field of view due to the parallax effect. For ordered subsets expectation maximization (OSEM), image resolution convergence is local and influenced significantly by the number of iterations, the count density, and background-to-target ratio. As both count density and background-to-target values for a brain structure can change during a dynamic scan, the local image resolution may also concurrently vary. When PVC is applied post-reconstruction the kinetic parameter estimates may be biased when neglecting the frame-dependent resolution. We explored the influence of the PVC method and implementation on kinetic parameters estimated by fitting (18)F-FDG dynamic data acquired on a dedicated brain PET scanner and reconstructed with and without PSF modelling in the OSEM algorithm. The performance of several PVC algorithms was quantified with a phantom experiment, an anthropomorphic Monte Carlo simulation, and a patient scan. Using the last frame reconstructed image only for regional spread function (RSF) generation, as opposed to computing RSFs for each frame independently, and applying perturbation geometric transfer matrix PVC with PSF based OSEM produced the lowest magnitude bias kinetic parameter estimates in most instances, although at the cost of increased noise compared to the PVC methods utilizing conventional OSEM. Use of the last frame RSFs for PVC with no PSF modelling in the OSEM algorithm produced the lowest bias in cerebral metabolic rate of glucose estimates, although by less than 5% in

  17. Kinetic investigation on enantioselective hydrolytic resolution of ...

    African Journals Online (AJOL)

    Kinetic investigation on enantioselective hydrolytic resolution of epichlorohydrin by crude epoxide hydrolase from domestic duck liver. X Ling, D Lu, J Wang, J Chen, L Ding, J Chen, H Chai, P Ouyang ...

  18. Catalytic Kinetic Resolution of Biaryl Compounds.

    Science.gov (United States)

    Ma, Gaoyuan; Sibi, Mukund P

    2015-08-10

    Biaryl compounds with axial chirality are very common in synthetic chemistry, especially in catalysis. Axially chiral biaryls are important due to their biological activities and extensive applications in asymmetric catalysis. Thus the development of efficient enantioselective methods for their synthesis has attracted considerable attention. This Minireview discusses the progress made in catalytic kinetic resolution of biaryl compounds and chronicles significant advances made recently in catalytic kinetic resolution of biaryl scaffolds. © 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Efficient Synthesis of Differentiated syn-1,2-Diol Derivatives by Asymmetric Transfer Hydrogenation-Dynamic Kinetic Resolution of α-Alkoxy-Substituted β-Ketoesters.

    Science.gov (United States)

    Monnereau, Laure; Cartigny, Damien; Scalone, Michelangelo; Ayad, Tahar; Ratovelomanana-Vidal, Virginie

    2015-08-10

    Asymmetric transfer hydrogenation was applied to a wide range of racemic aryl α-alkoxy-β-ketoesters in the presence of well-defined, commercially available, chiral catalyst Ru(II) -(N-p-toluenesulfonyl-1,2-diphenylethylenediamine) and a 5:2 mixture of formic acid and triethylamine as the hydrogen source. Under these conditions, dynamic kinetic resolution was efficiently promoted to provide the corresponding syn α-alkoxy-β-hydroxyesters derived from substituted aromatic and heteroaromatic aldehydes with a high level of diastereoselectivity (diastereomeric ratio (d.r.)>99:1) and an almost perfect enantioselectivity (enantiomeric excess (ee)>99 %). Additionally, after extensive screening of the reaction conditions, the use of Ru(II) - and Rh(III) -tethered precatalysts extended this process to more-challenging substrates that bore alkenyl-, alkynyl-, and alkyl substituents to provide the corresponding syn α-alkoxy-β-hydroxyesters with excellent enantiocontrol (up to 99 % ee) and good to perfect diastereocontrol (d.r.>99:1). Lastly, the synthetic utility of the present protocol was demonstrated by application to the asymmetric synthesis of chiral ester ethyl (2S)-2-ethoxy-3-(4-hydroxyphenyl)-propanoate, which is an important pharmacophore in a number of peroxisome proliferator-activated receptor α/γ dual agonist advanced drug candidates used for the treatment of type-II diabetes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Lipase-catalyzed asymmetric synthesis of naphtho[2,3-c]furan-1(3H)-one derivatives by a one-pot dynamic kinetic resolution/intramolecular Diels-Alder reaction: Total synthesis of (-)-himbacine.

    Science.gov (United States)

    Sugiyama, Koji; Kawanishi, Shinji; Oki, Yasuhiro; Kamiya, Marin; Hanada, Ryosuke; Egi, Masahiro; Akai, Shuji

    2018-04-01

    One-pot sequential reactions using the acyl moieties installed by enzymatic dynamic kinetic resolution of alcohols have been little investigated. In this work, the acryloyl moiety installed via the lipase/oxovanadium combo-catalyzed dynamic kinetic resolution of a racemic dienol [4-(cyclohex-1-en-1-yl)but-3-en-2-ol or 1-(cyclohex-1-en-1-yl)but-2-en-1-ol] with a (Z)-3-(phenylsulfonyl)acrylate underwent an intramolecular Diels-Alder reaction in a one-pot procedure to produce an optically active naphtho[2,3-c]furan-1(3H)-one derivative (98% ee). This method was successfully applied to the asymmetric total synthesis of (-)-himbacine. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Kinetic energy spectra, vertical resolution and dissipation in high-resolution atmospheric simulations.

    Science.gov (United States)

    Skamarock, W. C.

    2017-12-01

    We have performed week-long full-physics simulations with the MPAS global model at 15 km cell spacing using vertical mesh spacings of 800, 400, 200 and 100 meters in the mid-troposphere through the mid-stratosphere. We find that the horizontal kinetic energy spectra in the upper troposphere and stratosphere does not converge with increasing vertical resolution until we reach 200 meter level spacing. Examination of the solutions indicates that significant inertia-gravity waves are not vertically resolved at the lower vertical resolutions. Diagnostics from the simulations indicate that the primary kinetic energy dissipation results from the vertical mixing within the PBL parameterization and from the gravity-wave drag parameterization, with smaller but significant contributions from damping in the vertical transport scheme and from the horizontal filters in the dynamical core. Most of the kinetic energy dissipation in the free atmosphere occurs within breaking mid-latitude baroclinic waves. We will briefly review these results and their implications for atmospheric model configuration and for atmospheric dynamics, specifically that related to the dynamics associated with the mesoscale kinetic energy spectrum.

  2. Spectroscopy, Kinetics, and Dynamics of Combustion Radicals

    Energy Technology Data Exchange (ETDEWEB)

    Nesbitt, David J. [Research/Professor

    2013-08-06

    Spectroscopy, kinetics and dynamics of jet cooled hydrocarbon transients relevant to the DOE combustion mission have been explored, exploiting i) high resolution IR lasers, ii) slit discharge sources for formation of jet cooled radicals, and iii) high sensitivity detection with direct laser absorption methods and near the quantum shot noise limit. What makes this combination powerful is that such transients can be made under high concentrations and pressures characteristic of actual combustion conditions, and yet with the resulting species rapidly cooled (T ≈10-15K) in the slit supersonic expansion. Combined with the power of IR laser absorption methods, this provides novel access to spectral detection and study of many critical combustion species.

  3. Operational High Resolution Chemical Kinetics Simulation, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Numerical simulations of chemical kinetics are critical to addressing urgent issues in both the developed and developing world. Ongoing demand for higher resolution...

  4. Kinetics from Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Stelzl, Lukas S; Hummer, Gerhard

    2017-08-08

    Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

  5. Chemical kinetics and reaction dynamics

    CERN Document Server

    Houston, Paul L

    2006-01-01

    This text teaches the principles underlying modern chemical kinetics in a clear, direct fashion, using several examples to enhance basic understanding. It features solutions to selected problems, with separate sections and appendices that cover more technical applications.Each chapter is self-contained and features an introduction that identifies its basic goals, their significance, and a general plan for their achievement. This text's important aims are to demonstrate that the basic kinetic principles are essential to the solution of modern chemical problems, and to show how the underlying qu

  6. Fast Search and Adaptive Resolution for Complex Particle Kinetics

    Science.gov (United States)

    Larson, David J.

    2005-10-01

    A new plasma simulation algorithm, intended to bridge the gap between Eulerian fluid and kinetic regimes, is now being used for a variety of applications in ICF and weapon effects. The CPK method (Complex Particle Kinetic) concept [1] uses an ensemble of macro-particles with a Gaussian spatial profile and a Mawellian velocity distribution to represent particle distributions in phase space. Time evolution is modeled by a combination of Lagrangian motion and internal evolution within each individual macro-particle. Collisional particle-particle interactions [2] are facilitated by sorting particles into bins depending of the particle size. Different bin levels are connected by a linked list. Searching for neighboring particles is highly efficient because the search is limited to particles in neighboring bins with the possibility of interaction. The bin structure also allows the computation of various spatial moments at different resolutions. Combining the results of the moment calculations yields information on where and when increased resolution is necessary. We will present details of the particle binning process along with progress towards our goal of simulating the transition from continuum to fully kinetic physics. [1] D. W. Hewett, J. Comp. Phys. 189 (2003). [2] D. J. Larson, J. Comp. Phys. 188 (2003).

  7. Dynamics of asymmetric kinetic Ising systems revisited

    International Nuclear Information System (INIS)

    Huang, Haiping; Kabashima, Yoshiyuki

    2014-01-01

    The dynamics of an asymmetric kinetic Ising model is studied. Two schemes for improving the existing mean-field description are proposed. In the first scheme, we derive the formulas for instantaneous magnetization, equal-time correlation, and time-delayed correlation, considering the correlation between different local fields. To derive the time-delayed correlation, we emphasize that the small-correlation assumption adopted in previous work (Mézard and Sakellariou, 2011 J. Stat. Mech. L07001) is in fact not required. To confirm the prediction efficiency of our method, we perform extensive simulations on single instances with either temporally constant external driving fields or sinusoidal external fields. In the second scheme, we develop an improved mean-field theory for instantaneous magnetization prediction utilizing the notion of the cavity system in conjunction with a perturbative expansion approach. Its efficiency is numerically confirmed by comparison with the existing mean-field theory when partially asymmetric couplings are present. (paper)

  8. Detectors for high resolution dynamic pet

    International Nuclear Information System (INIS)

    Derenzo, S.E.; Budinger, T.F.; Huesman, R.H.

    1983-05-01

    This report reviews the motivation for high spatial resolution in dynamic positron emission tomography of the head and the technical problems in realizing this objective. We present recent progress in using small silicon photodiodes to measure the energy deposited by 511 keV photons in small BGO crystals with an energy resolution of 9.4% full-width at half-maximum. In conjunction with a suitable phototube coupled to a group of crystals, the photodiode signal to noise ratio is sufficient for the identification of individual crystals both for conventional and time-of-flight positron tomography

  9. Dynamic high resolution imaging of rats

    International Nuclear Information System (INIS)

    Miyaoka, R.S.; Lewellen, T.K.; Bice, A.N.

    1990-01-01

    A positron emission tomography with the sensitivity and resolution to do dynamic imaging of rats would be an invaluable tool for biological researchers. In this paper, the authors determine the biological criteria for dynamic positron emission imaging of rats. To be useful, 3 mm isotropic resolution and 2-3 second time binning were necessary characteristics for such a dedicated tomograph. A single plane in which two objects of interest could be imaged simultaneously was considered acceptable. Multi-layered detector designs were evaluated as a possible solution to the dynamic imaging and high resolution imaging requirements. The University of Washington photon history generator was used to generate data to investigate a tomograph's sensitivity to true, scattered and random coincidences for varying detector ring diameters. Intrinsic spatial uniformity advantages of multi-layered detector designs over conventional detector designs were investigated using a Monte Carlo program. As a result, a modular three layered detector prototype is being developed. A module will consist of a layer of five 3.5 mm wide crystals and two layers of six 2.5 mm wide crystals. The authors believe adequate sampling can be achieved with a stationary detector system using these modules. Economical crystal decoding strategies have been investigated and simulations have been run to investigate optimum light channeling methods for block decoding strategies. An analog block decoding method has been proposed and will be experimentally evaluated to determine whether it can provide the desired performance

  10. Influence of the interaction volume on the kinetic energy resolution of a velocity map imaging spectrometer

    International Nuclear Information System (INIS)

    Zhang Peng; Feng Zheng-Peng; Luo Si-Qiang; Wang Zhe

    2016-01-01

    We investigate the influence of the interaction volume on the energy resolution of a velocity map imaging spectrometer. The simulation results show that the axial interaction size has a significant influence on the resolution. This influence is increased for a higher kinetic energy. We further show that the radial interaction size has a minor influence on the energy resolution for the electron or ion with medium energy, but it is crucial for the resolution of the electron or ion with low kinetic energy. By tracing the flight trajectories we show how the electron or ion energy resolution is influenced by the interaction size. (paper)

  11. Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

    DEFF Research Database (Denmark)

    Toxvaerd, Søren

    2001-01-01

    Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

  12. Key factors of combustion from kinetics to gas dynamics

    CERN Document Server

    Rubtsov, Nikolai M

    2017-01-01

    This book summarizes the main advances in the mechanisms of combustion processes. It focuses on the analysis of kinetic mechanisms of gas combustion processes and experimental investigation into the interrelation of kinetics and gas dynamics in gas combustion. The book is complimentary to the one previously published, The Modes of Gaseous Combustion.

  13. Photon-Counting Microwave Kinetic Inductance Detectors (MKIDs) for High Resolution Far-Infrared Spectroscopy

    Data.gov (United States)

    National Aeronautics and Space Administration — We are developing ultrasensitive Microwave Kinetic Inductance Detectors (MKIDs) for high resolution far-infrared spectroscopy applications, with a long-term goal of...

  14. CATALYTIC KINETIC RESOLUTION OF 5-ALKOXY-2(5H)-FURANONES

    OpenAIRE

    FABER, WS; Kok, Johan C; DELANGE, B; FERINGA, BL; Faber, Wijnand S.; Lange, Ben de; Feringa, Bernard

    1994-01-01

    The kinetic resolution of racemic 5-alkoxy-2(5H)-furanones, using a chiral aminoalcohol catalyzed 1-4-addition of arylthiols, was examined. Using various butenolides it was shown that a gamma-alkoxy substituent appears to be essential to reach high enantioselectivities whereas electron-donating substituents in the arylthiols also increase the selectivity. Cinchona alkaloids are the preferred catalysts for the kinetic resolution, with quinine and quinidine leading to the most efficient and sel...

  15. Kinetic analysis of dynamic PET data

    Energy Technology Data Exchange (ETDEWEB)

    Knittel, B.

    1983-12-01

    Our goal is to quantify regional physiological processes such as blood flow and metabolism by means of tracer kinetic modeling and positron emission tomography (PET). Compartmental models are one way of characterizing the behavior of tracers in physiological systems. This paper describes a general method of estimating compartmental model rate constants from measurements of the concentration of tracers in blood and tissue, taken at multiple time intervals. A computer program which applies the method is described, and examples are shown for simulated and actual data acquired from the Donner 280-Crystal Positron Tomograph.

  16. Kinetic analysis of dynamic PET data

    International Nuclear Information System (INIS)

    Knittel, B.

    1983-12-01

    Our goal is to quantify regional physiological processes such as blood flow and metabolism by means of tracer kinetic modeling and positron emission tomography (PET). Compartmental models are one way of characterizing the behavior of tracers in physiological systems. This paper describes a general method of estimating compartmental model rate constants from measurements of the concentration of tracers in blood and tissue, taken at multiple time intervals. A computer program which applies the method is described, and examples are shown for simulated and actual data acquired from the Donner 280-Crystal Positron Tomograph

  17. Kinetic Energy from Supernova Feedback in High-resolution Galaxy Simulations

    Science.gov (United States)

    Simpson, Christine M.; Bryan, Greg L.; Hummels, Cameron; Ostriker, Jeremiah P.

    2015-08-01

    We describe a new method for adding a prescribed amount of kinetic energy to simulated gas modeled on a cartesian grid by directly altering grid cells’ mass and velocity in a distributed fashion. The method is explored in the context of supernova (SN) feedback in high-resolution (˜10 pc) hydrodynamic simulations of galaxy formation. Resolution dependence is a primary consideration in our application of the method, and simulations of isolated explosions (performed at different resolutions) motivate a resolution-dependent scaling for the injected fraction of kinetic energy that we apply in cosmological simulations of a 109 M⊙ dwarf halo. We find that in high-density media (≳50 cm-3) with coarse resolution (≳4 pc per cell), results are sensitive to the initial kinetic energy fraction due to early and rapid cooling. In our galaxy simulations, the deposition of small amounts of SN energy in kinetic form (as little as 1%) has a dramatic impact on the evolution of the system, resulting in an order-of-magnitude suppression of stellar mass. The overall behavior of the galaxy in the two highest resolution simulations we perform appears to converge. We discuss the resulting distribution of stellar metallicities, an observable sensitive to galactic wind properties, and find that while the new method demonstrates increased agreement with observed systems, significant discrepancies remain, likely due to simplistic assumptions that neglect contributions from SNe Ia and stellar winds.

  18. Oxidative kinetic resolution of racemic alcohols catalyzed by chiral ferrocenyloxazolinylphosphine-ruthenium complexes.

    Science.gov (United States)

    Nishibayashi, Yoshiaki; Yamauchi, Akiyoshi; Onodera, Gen; Uemura, Sakae

    2003-07-25

    Oxidative kinetic resolution of racemic secondary alcohols by using acetone as a hydrogen acceptor in the presence of a catalytic amount of [RuCl(2)(PPh(3))(ferrocenyloxazolinylphosphine)] (2) proceeds effectively to recover the corresponding alcohols in high yields with an excellent enantioselectivity. When 1-indanol is employed as a racemic alcohol, the oxidation proceeds quite smoothly even in the presence of 0.0025 mol % of the catalyst 2 to give an optically active 1-indanol in good yield with high enantioselectivity (up to 94% ee), where turnover frequency (TOF) exceeds 80,000 h(-1). From a practical viewpoint, the kinetic resolution is investigated in a large scale, optically pure (S)-1-indanol (75 g, 56% yield, >99% ee) being obtained from racemic 1-indanol (134 g) by employing this kinetic resolution method twice.

  19. The kinetics of crossflow dynamic membrane bioreactor | Li | Water SA

    African Journals Online (AJOL)

    Crossflow dynamic membrane bioreactor (CDMBR) kinetics was investigated by treating caprolactam wastewater over a period of 180 d. The removal efficiencies of organic substances and nitrogen averaged over 99% and 80%, respectively. The observed sludge yield was only 0.14 g SS·g-1 COD·d-1 at an SRT of 30 d ...

  20. Catalyst dynamics: consequences for classical kinetic descriptions of reactors

    DEFF Research Database (Denmark)

    Johannessen, Tue; Larsen, Jane Hvolbæk; Chorkendorff, Ib

    2001-01-01

    in situ studies and surface science investigations has brought added attention to the fact that catalysts may behave in a dynamic manner and reconstruct depending on the reaction conditions. This feature severely limits traditional kinetic descriptions. In the present paper, we present examples...

  1. Fractional neutron point kinetics equations for nuclear reactor dynamics

    International Nuclear Information System (INIS)

    Espinosa-Paredes, Gilberto; Polo-Labarrios, Marco-A.; Espinosa-Martinez, Erick-G.; Valle-Gallegos, Edmundo del

    2011-01-01

    The fractional point-neutron kinetics model for the dynamic behavior in a nuclear reactor is derived and analyzed in this paper. The fractional model retains the main dynamic characteristics of the neutron motion in which the relaxation time associated with a rapid variation in the neutron flux contains a fractional order, acting as exponent of the relaxation time, to obtain the best representation of a nuclear reactor dynamics. The physical interpretation of the fractional order is related with non-Fickian effects from the neutron diffusion equation point of view. The numerical approximation to the solution of the fractional neutron point kinetics model, which can be represented as a multi-term high-order linear fractional differential equation, is calculated by reducing the problem to a system of ordinary and fractional differential equations. The numerical stability of the fractional scheme is investigated in this work. Results for neutron dynamic behavior for both positive and negative reactivity and for different values of fractional order are shown and compared with the classic neutron point kinetic equations. Additionally, a related review with the neutron point kinetics equations is presented, which encompasses papers written in English about this research topic (as well as some books and technical reports) published since 1940 up to 2010.

  2. Recrystallization kinetics of nanostructured copper processed by dynamic plastic deformation

    DEFF Research Database (Denmark)

    Lin, Fengxiang; Zhang, Yubin; Pantleon, Wolfgang

    2012-01-01

    The recrystallization kinetics of nanostructured copper samples processed by dynamic plastic deformation was investigated by electron backscatter diffraction. It was found that the evolution of the recrystallized volume fraction as a function of annealing time has a very low slope (n=0.37) when...

  3. Inflationary dynamics of kinetically-coupled gauge fields

    DEFF Research Database (Denmark)

    Ferreira, Ricardo J. Z.; Ganc, Jonathan

    2015-01-01

    We investigate the inflationary dynamics of two kinetically-coupled massless U(1) gauge fields with time-varying kinetic-term coefficients. Ensuring that the system does not have strongly coupled regimes shrinks the parameter space. Also, we further restrict ourselves to systems that can be quant......We investigate the inflationary dynamics of two kinetically-coupled massless U(1) gauge fields with time-varying kinetic-term coefficients. Ensuring that the system does not have strongly coupled regimes shrinks the parameter space. Also, we further restrict ourselves to systems that can...... be quantized using the standard creation, annihilation operator algebra. This second constraint limits us to scenarios where the system can be diagonalized into the sum of two decoupled, massless, vector fields with a varying kinetic-term coefficient. Such a system might be interesting for magnetogenesis...... because of how the strong coupling problem generalizes. We explore this idea by assuming that one of the gauge fields is the Standard Model U(1) field and that the other dark gauge field has no particles charged under its gauge group. We consider whether it would be possible to transfer a magnetic field...

  4. Synthesis of Chiral Cyclic Carbonates via Kinetic Resolution of Racemic Epoxides and Carbon Dioxide

    Directory of Open Access Journals (Sweden)

    Xiao Wu

    2016-01-01

    Full Text Available The catalytic synthesis of cyclic carbonates using carbon dioxide as a C1-building block is a highly active area of research. Here, we review the catalytic production of enantiomerically enriched cyclic carbonates via kinetic resolution of racemic epoxides catalysed by metal-containing catalyst systems.

  5. Diels-Alder cycloaddition strategy for kinetic resolution of chiral pyrazolidinones.

    Science.gov (United States)

    Sibi, Mukund P; Kawashima, Keisuke; Stanley, Levi M

    2009-09-03

    A rare example of the application of a catalytic, enantioselective Diels-Alder cycloaddition to affect a kinetic resolution has been developed. Chiral pyrazolidinones are resolved with high selectivity through a process that utilizes a relay of stereochemical information from a permanent chiral center to a fluxional chiral center to enhance the inherent selectivity of the chiral Lewis acid catalyst.

  6. CATALYTIC KINETIC RESOLUTION OF 5-ALKOXY-2(5H)-FURANONES

    NARCIS (Netherlands)

    FABER, WS; Kok, Johan C; DELANGE, B; FERINGA, BL; Faber, Wijnand S.; Lange, Ben de; Feringa, Bernard

    1994-01-01

    The kinetic resolution of racemic 5-alkoxy-2(5H)-furanones, using a chiral aminoalcohol catalyzed 1-4-addition of arylthiols, was examined. Using various butenolides it was shown that a gamma-alkoxy substituent appears to be essential to reach high enantioselectivities whereas electron-donating

  7. Kinetic Resolution and Stereoselective Synthesis of 3-Substituted Aspartic Acids by Using Engineered Methylaspartate Ammonia Lyases

    NARCIS (Netherlands)

    Raj, Hans; Szymanski, Wiktor; Villiers, Jandré de; Puthan Veetil, Vinod; Quax, Wim J.; Shimamoto, Keiko; Janssen, Dick B.; Feringa, Ben L.; Poelarends, Gerrit J.

    2013-01-01

    Kinetic resolution and asymmetric synthesis of various valuable 3-substituted aspartic acids, which were obtained in fair to good yields with diastereomeric ratio values of up to >98:2 and enantiomeric excess values of up to >99 %, by using engineered methylaspartate ammonia lyases are described.

  8. Striking dynamics and kinetic properties of boxing and MMA gloves

    Directory of Open Access Journals (Sweden)

    Benjamin Lee

    2014-08-01

    Full Text Available With the growing popularity of Mixed Martial Arts (MMA as a competitive sport, questions regarding the dynamic response and properties of MMA gloves arise. High-energy impacts from punches are very similar to boxing yet MMA competition requires the use of 4 oz fingerless glove, compared to the larger full enclosure boxing glove. This work assessed the kinetic properties and strike dynamics of MMA gloves and compared findings with traditional boxing gloves. Gloves mounted on a molded fist were impacted repetitively on an instrumental anvil designed for impact, over a 5 hour period resulting in 10,000 continuous and consistent strikes. Kinetic data from impacts were sampled at the beginning of the data collection and subsequently every 30 minutes (every 1,000 strikes. MMA gloves produced 4-5 times greater peak force and 5 times faster load rate compared to the boxing glove. However, MMA gloves also showed signs of material fatigue, with peak force increasing by 35% and rate of loading increasing by 60% over the duration of the test. Boxing glove characteristics did deteriorate but to a lesser extent. In summary, the kinetic properties of MMA glove differed substantially from the boxing glove resulting in impacts characterized by higher peak forces and more rapid development of force. Material properties including stiffness and thickness play a role in the kinetic characteristics upon impact, and can be inferred to alter injury mechanisms of blunt force trauma.

  9. Kinetics of the Dynamical Information Shannon Entropy for Complex Systems

    International Nuclear Information System (INIS)

    Yulmetyev, R.M.; Yulmetyeva, D.G.

    1999-01-01

    Kinetic behaviour of dynamical information Shannon entropy is discussed for complex systems: physical systems with non-Markovian property and memory in correlation approximation, and biological and physiological systems with sequences of the Markovian and non-Markovian random noises. For the stochastic processes, a description of the information entropy in terms of normalized time correlation functions is given. The influence and important role of two mutually dependent channels of the entropy change, correlation (creation or generation of correlations) and anti-correlation (decay or annihilation of correlation) is discussed. The method developed here is also used in analysis of the density fluctuations in liquid cesium obtained from slow neutron scattering data, fractal kinetics of the long-range fluctuation in the short-time human memory and chaotic dynamics of R-R intervals of human ECG. (author)

  10. Electron and proton kinetics and dynamics in flaring atmospheres

    CERN Document Server

    Zharkova, Valentina

    2012-01-01

    This timely book presents new research results on high-energy particle physics related to solar flares, covering the theory and applications of the reconnection process in a clear and comprehensible way. It investigates particle kinetics and dynamics in flaring atmospheres and their diagnostics from spectral observations, while providing an analysis of the observation data and techniques and comparing various models. Written by an internationally acclaimed expert, this is vital reading for all solar, astro-, and plasma physicists working in the field.

  11. Mesoscopic dynamics of diffusion-influenced enzyme kinetics.

    Science.gov (United States)

    Chen, Jiang-Xing; Kapral, Raymond

    2011-01-28

    A particle-based mesoscopic model for enzyme kinetics is constructed and used to investigate the influence of diffusion on the reactive dynamics. Enzymes and enzyme-substrate complexes are modeled as finite-size soft spherical particles, while substrate, product, and solvent molecules are point particles. The system is evolved using a hybrid molecular dynamics-multiparticle collision dynamics scheme. Both the nonreactive and reactive dynamics are constructed to satisfy mass, momentum, and energy conservation laws, and reversible reaction steps satisfy detailed balance. Hydrodynamic interactions among the enzymes and complexes are automatically accounted for in the dynamics. Diffusion manifests itself in various ways, notably in power-law behavior in the evolution of the species concentrations. In accord with earlier investigations, regimes where the product production rate exhibits either monotonic or nonmonotonic behavior as a function of time are found. In addition, the species concentrations display both t(-1/2) and t(-3/2) power-law behavior, depending on the dynamical regime under investigation. For high enzyme volume fractions, cooperative effects influence the enzyme kinetics. The time dependent rate coefficient determined from the mass action rate law is computed and shown to depend on the enzyme concentration. Lifetime distributions of substrate molecules newly released in complex dissociation events are determined and shown to have either a power-law form for rebinding to the same enzyme from which they were released or an exponential form for rebinding to different enzymes. The model can be used and extended to explore a variety of issues related concentration effects and diffusion on enzyme kinetics.

  12. Mesoscopic dynamics of diffusion-influenced enzyme kinetics

    Science.gov (United States)

    Chen, Jiang-Xing; Kapral, Raymond

    2011-01-01

    A particle-based mesoscopic model for enzyme kinetics is constructed and used to investigate the influence of diffusion on the reactive dynamics. Enzymes and enzyme-substrate complexes are modeled as finite-size soft spherical particles, while substrate, product, and solvent molecules are point particles. The system is evolved using a hybrid molecular dynamics-multiparticle collision dynamics scheme. Both the nonreactive and reactive dynamics are constructed to satisfy mass, momentum, and energy conservation laws, and reversible reaction steps satisfy detailed balance. Hydrodynamic interactions among the enzymes and complexes are automatically accounted for in the dynamics. Diffusion manifests itself in various ways, notably in power-law behavior in the evolution of the species concentrations. In accord with earlier investigations, regimes where the product production rate exhibits either monotonic or nonmonotonic behavior as a function of time are found. In addition, the species concentrations display both t^{-1/2} and t^{-3/2} power-law behavior, depending on the dynamical regime under investigation. For high enzyme volume fractions, cooperative effects influence the enzyme kinetics. The time dependent rate coefficient determined from the mass action rate law is computed and shown to depend on the enzyme concentration. Lifetime distributions of substrate molecules newly released in complex dissociation events are determined and shown to have either a power-law form for rebinding to the same enzyme from which they were released or an exponential form for rebinding to different enzymes. The model can be used and extended to explore a variety of issues related concentration effects and diffusion on enzyme kinetics.

  13. Kinetics, dynamics and neutron noise in Molten Salt Reactors

    International Nuclear Information System (INIS)

    Pazsit, Imre

    2013-01-01

    Reactor kinetic and dynamic properties of Molten Salt Reactors (MSR) are investigated in a simple model, which allows closed compact analytical solutions to be obtained. The goal is to gain insight, rather than to produce high-quality quantitative data. Through an interpretation of the different terms in the basic equations, and by means of analytical solutions, various approximations are introduced and their validity discussed. The dynamical behaviour of MSRs and their response to small stationary perturbations is described and discussed in comparison with traditional systems. (author)

  14. Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron

    International Nuclear Information System (INIS)

    Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.

    2010-01-01

    Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.

  15. Dynamics of High-Resolution Networks

    DEFF Research Database (Denmark)

    Sekara, Vedran

    the unprecedented amounts of information collected by mobile phones to gain detailed insight into the dynamics of social systems. This dissertation presents an unparalleled data collection campaign, collecting highly detailed traces for approximately 1000 people over the course of multiple years. The availability...... are we all affected by an ever changing network structure? Answering these questions will enrich our understanding of ourselves, our organizations, and our societies. Yet, mapping the dynamics of social networks has traditionally been an arduous undertaking. Today, however, it is possible to use...... of such dynamic maps allows us to probe the underlying social network and understand how individuals interact and form lasting friendships. More importantly, these highly detailed dynamic maps provide us new perspectives at traditional problems and allow us to quantify and predict human life....

  16. Relevance and bio-catalytic strategies for the kinetic resolution of ketoprofen towards dexketoprofen.

    Science.gov (United States)

    Toledo, María Victoria; Briand, Laura Estefanía

    2017-11-10

    This review presents the most relevant investigations concerning the biocatalytic kinetic resolution of racemic ketoprofen to dexketoprofen for the last 22 years. The advantages related to the administration of the dex-enantiomer in terms of human health, the so called "chiral switch" in the pharmaceutical industry and the sustainability of biotransformations have been the driving forces to develop innovative technology to obtain dexketoprofen. In particular, the kinetic resolution of racemic ketoprofen through enantiomeric esterification and hydrolysis using lipases as biocatalysts are thoroughly revised and commented upon. In this context, the biocatalysts, acyl-acceptors (alcohols), reaction conditions, conversion, enantiomeric excess, and enantiomeric ratio among others are discussed. Moreover, the investigations concerning scaling up processes in order to obtain an optically pure enantiomer of the profen are presented. Finally, some guidelines about perspectives of the technology and research opportunities are given.

  17. Fluxionally chiral DMAP catalysts: kinetic resolution of axially chiral biaryl compounds.

    Science.gov (United States)

    Ma, Gaoyuan; Deng, Jun; Sibi, Mukund P

    2014-10-27

    Can organocatalysts that incorporate fluxional groups provide enhanced selectivity in asymmetric transformations? To address this issue, we have designed chiral 4-dimethylaminopyridine (DMAP) catalysts with fluxional chirality. These catalysts were found to be efficient in promoting the acylative kinetic resolution of secondary alcohols and axially chiral biaryl compounds with selectivity factors of up to 37 and 51, respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Simplification of lipase design in the enzymatic kinetic resolution of amines by saturation transfer difference NMR

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Marcio S.; Pietrobom, Daniel, E-mail: s.marcio@ufabc.edu.br [Universidade Federal do ABC (CCNH/UFABC), Santo André, SP (Brazil). Centro de Ciências Naturais e Humanas

    2016-07-01

    In this work, we demonstrate a nuclear magnetic resonance (NMR) method for racemic amide and lipase interaction as a first-pass design method in the enzymatic kinetic resolution of amines. As a novel adaptation of commonly used protein-ligand screening NMR methodologies, this approach relies upon a lipase-amide interaction wherein the time-consuming is reduced drastically and new insights are produced during the development of biocatalysis reactions. (author)

  19. Lipase-catalyzed highly enantioselective kinetic resolution of boron-containing chiral alcohols.

    Science.gov (United States)

    Andrade, Leandro H; Barcellos, Thiago

    2009-07-16

    The first application of enzymes as catalysts to obtain optically pure boron compounds is described. The kinetic resolution of boron-containing chiral alcohols via enantioselective transesterification catalyzed by lipases was studied. Aromatic, allylic, and aliphatic secondary alcohols containing a boronate ester or boronic acid group were resolved by lipase from Candida antartica (CALB), and excellent E values (E > 200) and high enantiomeric excesses (up to >99%) of both remaining substrates and acetylated product were obtained.

  20. Fouling Kinetics and Associated Dynamics of Structural Modifications

    DEFF Research Database (Denmark)

    Jacob, Jerome; Prádanos, Pedro; Calvo, J. I.

    1998-01-01

    It is shown that the fouling behaviour of microfiltration membranes does not agree within all the time ranges of any of the commonly used membrane blocking models (i.e. complete, standard, intermediate or cake blocking). The resulting experimental kinetics of flux decline do not fit to only one...... of these models, but according to a successive or simultaneous coexistence of two or more of them. This is studied by analysing the structural modifications associated with the fouling kinetics. To achieve this goal, here we analyse the dynamical changes on the structure of four microporous membranes made...... by Sartorius (ST02 and ST045, neutral) and Spectrum (SP02 and SP045, positively charged) when fouled by permeating a protein aqueous solution (bovine serum albumin (BSA) at 1 g l(-1)) under 10 kPa in a dead-end device. The structure after different fouling times is obtained by using an extended bubble point...

  1. Relativistic nuclear fluid dynamics and VUU kinetic theory

    International Nuclear Information System (INIS)

    Molitoris, J.J.; Hahn, D.; Alonso, C.; Collazo, I.; D'Alessandris, P.; McAbee, T.; Wilson, J.; Zingman, J.

    1987-01-01

    Relativistic kinetic theory may be used to understand hot dense hadronic matter. We address the questions of collective flow and pion production in a 3 D relativistic fluid dynamic model and in the VUU microscopic theory. The GSI/LBL collective flow and pion data point to a stiff equation of state. The effect of the nuclear equation of state on the thermodynamic parameters is discussed. The properties of dense hot hadronic matter are studied in Au + Au collisions from 0.1 to 10 GeV/nucleon. 22 refs., 5 figs

  2. Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

    Directory of Open Access Journals (Sweden)

    Nick D.L. Owens

    2016-01-01

    Full Text Available Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack a comprehensive understanding of transcript kinetics, which limits quantitative biology. This is an acute challenge in embryonic development, where rapid changes in gene expression dictate cell fate decisions. By ultra-high-frequency sampling of Xenopus embryos and absolute normalization of sequence reads, we present smooth gene expression trajectories in absolute transcript numbers. During a developmental period approximating the first 8 weeks of human gestation, transcript kinetics vary by eight orders of magnitude. Ordering genes by expression dynamics, we find that “temporal synexpression” predicts common gene function. Remarkably, a single parameter, the characteristic timescale, can classify transcript kinetics globally and distinguish genes regulating development from those involved in cellular metabolism. Overall, our analysis provides unprecedented insight into the reorganization of maternal and embryonic transcripts and redefines our ability to perform quantitative biology.

  3. Microwave Assisted Enzymatic Kinetic Resolution of (±-1-Phenyl-2-propyn-1-ol in Nonaqueous Media

    Directory of Open Access Journals (Sweden)

    Saravanan Devendran

    2014-01-01

    Full Text Available Kinetic resolution of 1-phenyl-2-propyn-1-ol, an important chiral synthon, was studied through trans-esterification with acyl acetate to investigate synergism between microwave irradiation and enzyme catalysis. Lipases from different microbial origins were employed for the kinetic resolution of (R/S-1-phenyl-2-propyn-1-ol, among which Candida antarctica lipase B, immobilized on acrylic resin (Novozym 435, was found to be the best catalyst in n-hexane as solvent. Vinyl acetate was the most effective among different acyl esters studied. The effect of various parameters was studied in a systematic manner. Definite synergism between microwave and enzyme was observed. The initial rate was improved around 1.28 times under microwave irradiation than conventional heating. Under optimum conditions, maximum conversion (48.78% and high enantiomeric excess (93.25% were obtained in 2 h. From modeling studies, it is concluded that the reaction follows the Ping-Pong bi-bi mechanism with dead end alcohol inhibition. Kinetic parameters were obtained by using nonlinear regression. This process is green, clean, and easily scalable as compared to the chemical process.

  4. Kinetic resolution and stereoselective synthesis of 3-substituted aspartic acids by using engineered methylaspartate ammonia lyases.

    Science.gov (United States)

    Raj, Hans; Szymanski, Wiktor; de Villiers, Jandré; Puthan Veetil, Vinod; Quax, Wim J; Shimamoto, Keiko; Janssen, Dick B; Feringa, Ben L; Poelarends, Gerrit J

    2013-08-19

    Enzymatic amino acid synthesis: Kinetic resolution and asymmetric synthesis of various valuable 3-substituted aspartic acids, which were obtained in fair to good yields with diastereomeric ratio values of up to >98:2 and enantiomeric excess values of up to >99 %, by using engineered methylaspartate ammonia lyases are described. These biocatalytic methodologies for the selective preparation of aspartic acid derivatives appear to be attractive alternatives for existing chemical methods. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. 3.5D dynamic PET image reconstruction incorporating kinetics-based clusters

    International Nuclear Information System (INIS)

    Lu Lijun; Chen Wufan; Karakatsanis, Nicolas A; Rahmim, Arman; Tang Jing

    2012-01-01

    Standard 3D dynamic positron emission tomographic (PET) imaging consists of independent image reconstructions of individual frames followed by application of appropriate kinetic model to the time activity curves at the voxel or region-of-interest (ROI). The emerging field of 4D PET reconstruction, by contrast, seeks to move beyond this scheme and incorporate information from multiple frames within the image reconstruction task. Here we propose a novel reconstruction framework aiming to enhance quantitative accuracy of parametric images via introduction of priors based on voxel kinetics, as generated via clustering of preliminary reconstructed dynamic images to define clustered neighborhoods of voxels with similar kinetics. This is then followed by straightforward maximum a posteriori (MAP) 3D PET reconstruction as applied to individual frames; and as such the method is labeled ‘3.5D’ image reconstruction. The use of cluster-based priors has the advantage of further enhancing quantitative performance in dynamic PET imaging, because: (a) there are typically more voxels in clusters than in conventional local neighborhoods, and (b) neighboring voxels with distinct kinetics are less likely to be clustered together. Using realistic simulated 11 C-raclopride dynamic PET data, the quantitative performance of the proposed method was investigated. Parametric distribution-volume (DV) and DV ratio (DVR) images were estimated from dynamic image reconstructions using (a) maximum-likelihood expectation maximization (MLEM), and MAP reconstructions using (b) the quadratic prior (QP-MAP), (c) the Green prior (GP-MAP) and (d, e) two proposed cluster-based priors (CP-U-MAP and CP-W-MAP), followed by graphical modeling, and were qualitatively and quantitatively compared for 11 ROIs. Overall, the proposed dynamic PET reconstruction methodology resulted in substantial visual as well as quantitative accuracy improvements (in terms of noise versus bias performance) for parametric DV

  6. The Palladium-Catalyzed Aerobic Kinetic Resolution of Secondary Alcohols: Reaction Development, Scope, and Applications

    KAUST Repository

    Ebner, Davidâ C.

    2009-12-07

    The first palladium-catalyzed enantioselective oxidation of secondary alcohols has been developed, utilizing the readily available diamine (-)-sparteine as a chiral ligand and molecular oxygen as the stoichiometric oxidant. Mechanistic insights regarding the role of the base and hydrogen-bond donors have resulted in several improvements to the original system. Namely, addition of cesium carbonate and tert-butyl alcohol greatly enhances reaction rates, promoting rapid resolutions. The use of chloroform as solvent allows the use of ambient air as the terminal oxidant at 23 degrees C, resulting in enhanced catalyst selectivity. These improved reaction conditions have permitted the successful kinetic resolution of benzylic, allylic, and cyclopropyl secondary alcohols to high enantiomeric excess with good-to-excellent selectivity factors. This catalyst system has also been applied to the desymmetrization of meso-diols, providing high yields of enantioenriched hydroxyketones.

  7. The Palladium-Catalyzed Aerobic Kinetic Resolution of Secondary Alcohols: Reaction Development, Scope, and Applications

    KAUST Repository

    Ebner, Davidâ C.; Bagdanoff, Jeffreyâ T.; Ferreira, Ericâ M.; McFadden, Ryanâ M.; Caspi, Danielâ D.; Trend, Raissaâ M.; Stoltz, Brianâ M.

    2009-01-01

    The first palladium-catalyzed enantioselective oxidation of secondary alcohols has been developed, utilizing the readily available diamine (-)-sparteine as a chiral ligand and molecular oxygen as the stoichiometric oxidant. Mechanistic insights regarding the role of the base and hydrogen-bond donors have resulted in several improvements to the original system. Namely, addition of cesium carbonate and tert-butyl alcohol greatly enhances reaction rates, promoting rapid resolutions. The use of chloroform as solvent allows the use of ambient air as the terminal oxidant at 23 degrees C, resulting in enhanced catalyst selectivity. These improved reaction conditions have permitted the successful kinetic resolution of benzylic, allylic, and cyclopropyl secondary alcohols to high enantiomeric excess with good-to-excellent selectivity factors. This catalyst system has also been applied to the desymmetrization of meso-diols, providing high yields of enantioenriched hydroxyketones.

  8. Kinetic studies of ICF target dynamics with ePLAS

    Science.gov (United States)

    Mason, R. J.

    2016-10-01

    The ePLAS code was recently used1 to show that a modeling change from artificial to real viscosity can result in a decrease of the predicted performance of ICF targets. This code typically follows either fluid or PIC electrons with fluid ions in self-consistent E - and B - fields computed by the Implicit Moment Method2. For the present study the ions have instead been run as PIC particles undergoing Krook-like self-collisions. The ePLAS collision model continually redistributes the ion particle properties toward a local Maxwellian, while conserving the mean density, momentum and energy. Whereas the use of real viscosity captures large Knudsen Number effects as the active target dimensions shrink below the ion mean-free-path, the new kinetic modeling can manifest additional effects such as collisional shock precursors3 from the escape and streaming of the fastest particle ions. In 2D cylindrical geometry we will explore how such kinetic shock extensions might affect shell and core compression dynamics in ICF target implosions.

  9. Kinetic and dynamic Delaunay tetrahedralizations in three dimensions

    Science.gov (United States)

    Schaller, Gernot; Meyer-Hermann, Michael

    2004-09-01

    We describe algorithms to implement fully dynamic and kinetic three-dimensional unconstrained Delaunay triangulations, where the time evolution of the triangulation is not only governed by moving vertices but also by a changing number of vertices. We use three-dimensional simplex flip algorithms, a stochastic visibility walk algorithm for point location and in addition, we propose a new simple method of deleting vertices from an existing three-dimensional Delaunay triangulation while maintaining the Delaunay property. As an example, we analyse the performance in various cases of practical relevance. The dual Dirichlet tessellation can be used to solve differential equations on an irregular grid, to define partitions in cell tissue simulations, for collision detection etc.

  10. Multi-scale method for the resolution of the neutronic kinetics equations

    International Nuclear Information System (INIS)

    Chauvet, St.

    2008-10-01

    In this PhD thesis and in order to improve the time/precision ratio of the numerical simulation calculations, we investigate multi-scale techniques for the resolution of the reactor kinetics equations. We choose to focus on the mixed dual diffusion approximation and the quasi-static methods. We introduce a space dependency for the amplitude function which only depends on the time variable in the standard quasi-static context. With this new factorization, we develop two mixed dual problems which can be solved with Cea's solver MINOS. An algorithm is implemented, performing the resolution of these problems defined on different scales (for time and space). We name this approach: the Local Quasi-Static method. We present here this new multi-scale approach and its implementation. The inherent details of amplitude and shape treatments are discussed and justified. Results and performances, compared to MINOS, are studied. They illustrate the improvement on the time/precision ratio for kinetics calculations. Furthermore, we open some new possibilities to parallelize computations with MINOS. For the future, we also introduce some improvement tracks with adaptive scales. (author)

  11. Detectors for high resolution dynamic positron emission tomography

    International Nuclear Information System (INIS)

    Derenzo, S.E.; Budinger, T.F.; Huesman, R.H.

    1985-01-01

    Tomography is the technique of producing a photographic image of an opaque specimen by transmitting a beam of x-rays or gamma rays through the specimen onto an adjacent photographic film. The image results from variations in thickness, density, and chemical composition, of the specimen. This technique is used to study the metabolism of the human brain. This article examines the design of equipment used for high resolution dynamic positron emission tomography. 27 references, 5 figures, 3 tables

  12. Energy resolution and efficiency of phonon-mediated kinetic inductance detectors for light detection

    International Nuclear Information System (INIS)

    Cardani, L.; Colantoni, I.; Coppolecchia, A.; Cruciani, A.; Vignati, M.; Bellini, F.; Casali, N.; Cosmelli, C.; Di Domizio, S.; Castellano, M. G.; Tomei, C.

    2015-01-01

    The development of sensitive cryogenic light detectors is of primary interest for bolometric experiments searching for rare events like dark matter interactions or neutrino-less double beta decay. Thanks to their good energy resolution and the natural multiplexed read-out, Kinetic Inductance Detectors (KIDs) are particularly suitable for this purpose. To efficiently couple KIDs-based light detectors to the large crystals used by the most advanced bolometric detectors, active surfaces of several cm 2 are needed. For this reason, we are developing phonon-mediated detectors. In this paper, we present the results obtained with a prototype consisting of four 40 nm thick aluminum resonators patterned on a 2 × 2 cm 2 silicon chip, and calibrated with optical pulses and X-rays. The detector features a noise resolution σ E  = 154 ± 7 eV and an (18 ± 2)% efficiency

  13. Energy resolution and efficiency of phonon-mediated kinetic inductance detectors for light detection

    Energy Technology Data Exchange (ETDEWEB)

    Cardani, L., E-mail: laura.cardani@roma1.infn.it [Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, 00185 Roma (Italy); Physics Department, Princeton University, Washington Road, 08544, Princeton, New Jersey (United States); Colantoni, I.; Coppolecchia, A. [Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, 00185 Roma (Italy); Cruciani, A.; Vignati, M.; Bellini, F.; Casali, N.; Cosmelli, C. [Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, 00185 Roma (Italy); INFN - Sezione di Roma, Piazzale Aldo Moro 2, 00185 Roma (Italy); Di Domizio, S. [Dipartimento di Fisica, Università degli Studi di Genova, Via Dodecaneso 33, 16146 Genova (Italy); INFN - Sezione di Genova, Via Dodecaneso 33, 16146 Genova (Italy); Castellano, M. G. [Istituto di Fotonica e Nanotecnologie - CNR, Via Cineto Romano 42, 00156 Roma (Italy); Tomei, C. [INFN - Sezione di Roma, Piazzale Aldo Moro 2, 00185 Roma (Italy)

    2015-08-31

    The development of sensitive cryogenic light detectors is of primary interest for bolometric experiments searching for rare events like dark matter interactions or neutrino-less double beta decay. Thanks to their good energy resolution and the natural multiplexed read-out, Kinetic Inductance Detectors (KIDs) are particularly suitable for this purpose. To efficiently couple KIDs-based light detectors to the large crystals used by the most advanced bolometric detectors, active surfaces of several cm{sup 2} are needed. For this reason, we are developing phonon-mediated detectors. In this paper, we present the results obtained with a prototype consisting of four 40 nm thick aluminum resonators patterned on a 2 × 2 cm{sup 2} silicon chip, and calibrated with optical pulses and X-rays. The detector features a noise resolution σ{sub E} = 154 ± 7 eV and an (18 ± 2)% efficiency.

  14. Flow chemistry and polymer-supported pseudoenantiomeric acylating agents enable parallel kinetic resolution of chiral saturated N-heterocycles

    Science.gov (United States)

    Kreituss, Imants; Bode, Jeffrey W.

    2017-05-01

    Kinetic resolution is a common method to obtain enantioenriched material from a racemic mixture. This process will deliver enantiopure unreacted material when the selectivity factor of the process, s, is greater than 1; however, the scalemic reaction product is often discarded. Parallel kinetic resolution, on the other hand, provides access to two enantioenriched products from a single racemic starting material, but suffers from a variety of practical challenges regarding experimental design that limit its applications. Here, we describe the development of a flow-based system that enables practical parallel kinetic resolution of saturated N-heterocycles. This process provides access to both enantiomers of the starting material in good yield and high enantiopurity; similar results with classical kinetic resolution would require selectivity factors in the range of s = 100. To achieve this, two immobilized quasienantiomeric acylating agents were designed for the asymmetric acylation of racemic saturated N-heterocycles. Using the flow-based system we could efficiently separate, recover and reuse the polymer-supported reagents. The amide products could be readily separated and hydrolysed to the corresponding amines without detectable epimerization.

  15. Kinetic Resolution of sec-Thiols via Enantioselective Oxidation with Rationally Engineered 5-(Hydroxymethyl)furfural Oxidase

    NARCIS (Netherlands)

    Pickl, Mathias; Swoboda, Alexander; Romero, Elvira; Winkler, Christoph; Binda, Claudia; Mattevi, Andrea; Faber, Kurt; Fraaije, Marco

    2018-01-01

    Various flavoprotein oxidases were recently shown to oxidize prim-thiols. Here we extend this reactivity towards sec-thiols via structure-guided engineering of 5-(hydroxymethyl)furfural oxidase (HMFO). The variants obtained were employed for the oxidative kinetic resolution of rac-sec-thiols

  16. Kinetic resolution of α-bromoamides: Experimental and theoretical investigation of highly enantioselective reactions catalyzed by haloalkane dehalogenases

    NARCIS (Netherlands)

    Westerbeek, Alja; Szymanski, Wiktor; Wijma, Hein J.; Marrink, Siewert; Feringa, Ben L.; Janssen, Dick B.

    2011-01-01

    Haloalkane dehalogenases from five sources were heterologously expressed in Escherichia coli, isolated, and tested for their ability to achieve kinetic resolution of racemic alpha-bromoamides, which are important intermediates used in the preparation of bioactive compounds. To explore the substrate

  17. Hydrodynamics in adaptive resolution particle simulations: Multiparticle collision dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Alekseeva, Uliana, E-mail: Alekseeva@itc.rwth-aachen.de [Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); German Research School for Simulation Sciences (GRS), Forschungszentrum Jülich, D-52425 Jülich (Germany); Winkler, Roland G., E-mail: r.winkler@fz-juelich.de [Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); Sutmann, Godehard, E-mail: g.sutmann@fz-juelich.de [Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation (IAS), Forschungszentrum Jülich, D-52425 Jülich (Germany); ICAMS, Ruhr-University Bochum, D-44801 Bochum (Germany)

    2016-06-01

    A new adaptive resolution technique for particle-based multi-level simulations of fluids is presented. In the approach, the representation of fluid and solvent particles is changed on the fly between an atomistic and a coarse-grained description. The present approach is based on a hybrid coupling of the multiparticle collision dynamics (MPC) method and molecular dynamics (MD), thereby coupling stochastic and deterministic particle-based methods. Hydrodynamics is examined by calculating velocity and current correlation functions for various mixed and coupled systems. We demonstrate that hydrodynamic properties of the mixed fluid are conserved by a suitable coupling of the two particle methods, and that the simulation results agree well with theoretical expectations.

  18. Breast MR imaging: correlation of high resolution dynamic MR findings with prognostic factors

    International Nuclear Information System (INIS)

    Lee, Shin Ho; Cho, Nariya; Chung, Hye Kyung; Kim, Seung Ja; Cho, Kyung Soo; Moon, Woo Kyung; Cho, Joo Hee

    2005-01-01

    We wanted to correlate the kinetic and morphologic MR findings of invasive breast cancer with the classical and molecular prognostic factors. Eighty-seven patients with invasive ductal carcinoma NOS underwent dynamic MR imaging at 1.5 T, and with using the T1-weighted 3D FLASH technique. The morphologic findings (shape, margin, internal enhancement of the mass or the enhancement distribution and the internal enhancement of any non-mass lesion) and the kinetic findings (the initial phase and the delayed phase of the time-signal. Intensity curve) were interpreted using a ACR BI-RADS-MRI lexicon. We correlate MR findings with histopathologic prognostic factors (tumor size, lymph node status and tumor grade) and the immunohistochemically detected biomarkers (ER, PR, ρ 53, c-erbB-2, EGFR and Ki-67). Univariate and multivariate statistical analyses were than performed. Among the MR findings, a spiculated margin, rim enhancement and washout were significantly correlated with the prognostic factors. A spiculated margin was independently associated with the established predictors of a good prognosis (a lower histologic and nuclear grade, positive ER and PR) and rim enhancement was associated with a poor prognosis (a higher histologic and nuclear grade, negative ER and PR). Wash out was a independent predictor of Ki-67 activity. Some of the findings of high resolution dynamic MR imaging were associated with the prognostic factors, and these findings may predict the prognosis of breast cancer

  19. Automotive exhaust gas conversion: from elementary step kinetics to prediction of emission dynamics

    NARCIS (Netherlands)

    Hoebink, J.H.B.J.; Harmsen, J.M.A.; Balenovic, M.; Backx, A.C.P.M.; Schouten, J.C.

    2001-01-01

    Elementary step based kinetics show a high added value to describe the performance of catalytic exhaust gas converters under dynamic conditions, as demonstrated with a Euro test cycle. Combination of such kinetic models for individual global reactions covers the mutual interactions via common

  20. Dynamic Raman imaging system with high spatial and temporal resolution

    Science.gov (United States)

    Wang, Lei; Dai, Yinzhen; He, Hao; Lv, Ruiqi; Zong, Cheng; Ren, Bin

    2017-09-01

    There is an increasing need to study dynamic changing systems with significantly high spatial and temporal resolutions. In this work, we integrated point-scanning, line-scanning, and wide-field Raman imaging techniques into a single system. By using an Electron Multiplying CCD (EMCCD) with a high gain and high frame rate, we significantly reduced the time required for wide-field imaging, making it possible to monitor the electrochemical reactions in situ. The highest frame rate of EMCDD was ˜50 fps, and the Raman images for a specific Raman peak can be obtained by passing the signal from the sample through the Liquid Crystal Tunable Filter. The spatial resolutions of scanning imaging and wide-field imaging with a 100× objective (NA = 0.9) are 0.5 × 0.5 μm2 and 0.36 × 0.36 μm2, respectively. The system was used to study the surface plasmon resonance of Au nanorods, the surface-enhanced Raman scattering signal distribution for Au Nanoparticle aggregates, and dynamic Raman imaging of an electrochemical reacting system.

  1. Investigating sub-spine actin dynamics in rat hippocampal neurons with super-resolution optical imaging.

    Directory of Open Access Journals (Sweden)

    Vedakumar Tatavarty

    Full Text Available Morphological changes in dendritic spines represent an important mechanism for synaptic plasticity which is postulated to underlie the vital cognitive phenomena of learning and memory. These morphological changes are driven by the dynamic actin cytoskeleton that is present in dendritic spines. The study of actin dynamics in these spines traditionally has been hindered by the small size of the spine. In this study, we utilize a photo-activation localization microscopy (PALM-based single-molecule tracking technique to analyze F-actin movements with approximately 30-nm resolution in cultured hippocampal neurons. We were able to observe the kinematic (physical motion of actin filaments, i.e., retrograde flow and kinetic (F-actin turn-over dynamics of F-actin at the single-filament level in dendritic spines. We found that F-actin in dendritic spines exhibits highly heterogeneous kinematic dynamics at the individual filament level, with simultaneous actin flows in both retrograde and anterograde directions. At the ensemble level, movements of filaments integrate into a net retrograde flow of approximately 138 nm/min. These results suggest a weakly polarized F-actin network that consists of mostly short filaments in dendritic spines.

  2. Investigating sub-spine actin dynamics in rat hippocampal neurons with super-resolution optical imaging.

    Science.gov (United States)

    Tatavarty, Vedakumar; Kim, Eun-Ji; Rodionov, Vladimir; Yu, Ji

    2009-11-09

    Morphological changes in dendritic spines represent an important mechanism for synaptic plasticity which is postulated to underlie the vital cognitive phenomena of learning and memory. These morphological changes are driven by the dynamic actin cytoskeleton that is present in dendritic spines. The study of actin dynamics in these spines traditionally has been hindered by the small size of the spine. In this study, we utilize a photo-activation localization microscopy (PALM)-based single-molecule tracking technique to analyze F-actin movements with approximately 30-nm resolution in cultured hippocampal neurons. We were able to observe the kinematic (physical motion of actin filaments, i.e., retrograde flow) and kinetic (F-actin turn-over) dynamics of F-actin at the single-filament level in dendritic spines. We found that F-actin in dendritic spines exhibits highly heterogeneous kinematic dynamics at the individual filament level, with simultaneous actin flows in both retrograde and anterograde directions. At the ensemble level, movements of filaments integrate into a net retrograde flow of approximately 138 nm/min. These results suggest a weakly polarized F-actin network that consists of mostly short filaments in dendritic spines.

  3. Resolution of the diffusional paradox predicting infinitely fast kinetics on the nanoscale

    Science.gov (United States)

    Beke, D. L.; Erdélyi, Z.

    2006-01-01

    In our paper, we offer a natural resolution for a long-standing paradox in diffusion. We show that the growth rate of the diffusion zone (reaction layer) should not go to infinity with decreasing time (as 1/t ), just because the diffusion permeability of the interface is finite. Expression for the changeover thickness X* between the linear and parabolic regimes of the interface shift in phase separating binary A(B) systems is derived in the framework of a deterministic atomistic model for diffusion. X* lies typically between 0.01 and 300nm , depending on the composition dependence of the diffusion coefficient and the phase separation tendency of the alloy. While in ideal binary alloys with composition independent diffusivity, the deviation from the parabolic law practically cannot be observed, in real systems (where the diffusion coefficient can change several orders of magnitude with the composition), measurable deviations are expected as it was experimentally observed very recently in the Ni/Cu and Au/Ni systems. We also offer an atomistic explanation for the phenomenological interface transfer coefficient K . It measures the finite interface permeability (proportional to the jump frequency across the interface) and thus it controls the shift of the interface at short times (diffusion distances). Although it is almost exclusively accepted in the literature that linear growth kinetics are the result of interface reaction control, our results suggest that the linear or nonparabolic growth of a reaction layer on the nanoscale cannot be automatically interpreted by an interface reaction.

  4. Topological and kinetic determinants of the modal matrices of dynamic models of metabolism.

    Directory of Open Access Journals (Sweden)

    Bin Du

    Full Text Available Large-scale kinetic models of metabolism are becoming increasingly comprehensive and accurate. A key challenge is to understand the biochemical basis of the dynamic properties of these models. Linear analysis methods are well-established as useful tools for characterizing the dynamic response of metabolic networks. Central to linear analysis methods are two key matrices: the Jacobian matrix (J and the modal matrix (M-1 arising from its eigendecomposition. The modal matrix M-1 contains dynamically independent motions of the kinetic model near a reference state, and it is sparse in practice for metabolic networks. However, connecting the structure of M-1 to the kinetic properties of the underlying reactions is non-trivial. In this study, we analyze the relationship between J, M-1, and the kinetic properties of the underlying network for kinetic models of metabolism. Specifically, we describe the origin of mode sparsity structure based on features of the network stoichiometric matrix S and the reaction kinetic gradient matrix G. First, we show that due to the scaling of kinetic parameters in real networks, diagonal dominance occurs in a substantial fraction of the rows of J, resulting in simple modal structures with clear biological interpretations. Then, we show that more complicated modes originate from topologically-connected reactions that have similar reaction elasticities in G. These elasticities represent dynamic equilibrium balances within reactions and are key determinants of modal structure. The work presented should prove useful towards obtaining an understanding of the dynamics of kinetic models of metabolism, which are rooted in the network structure and the kinetic properties of reactions.

  5. Evidence for Dynamic Chemical Kinetics at Individual Molecular Ruthenium Catalysts.

    Science.gov (United States)

    Easter, Quinn T; Blum, Suzanne A

    2018-02-05

    Catalytic cycles are typically depicted as possessing time-invariant steps with fixed rates. Yet the true behavior of individual catalysts with respect to time is unknown, hidden by the ensemble averaging inherent to bulk measurements. Evidence is presented for variable chemical kinetics at individual catalysts, with a focus on ring-opening metathesis polymerization catalyzed by the second-generation Grubbs' ruthenium catalyst. Fluorescence microscopy is used to probe the chemical kinetics of the reaction because the technique possesses sufficient sensitivity for the detection of single chemical reactions. Insertion reactions in submicron regions likely occur at groups of many (not single) catalysts, yet not so many that their unique kinetic behavior is ensemble averaged. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Resolution enhancement in neural networks with dynamical synapses

    Directory of Open Access Journals (Sweden)

    C. C. Alan Fung

    2013-06-01

    Full Text Available Conventionally, information is represented by spike rates in the neural system. Here, we consider the ability of temporally modulated activities in neuronal networks to carry information extra to spike rates. These temporal modulations, commonly known as population spikes, are due to the presence of synaptic depression in a neuronal network model. We discuss its relevance to an experiment on transparent motions in macaque monkeys by Treue et al. in 2000. They found that if the moving directions of objects are too close, the firing rate profile will be very similar to that with one direction. As the difference in the moving directions of objects is large enough, the neuronal system would respond in such a way that the network enhances the resolution in the moving directions of the objects. In this paper, we propose that this behavior can be reproduced by neural networks with dynamical synapses when there are multiple external inputs. We will demonstrate how resolution enhancement can be achieved, and discuss the conditions under which temporally modulated activities are able to enhance information processing performances in general.

  7. Modal and Dynamic Analysis of a Vehicle with Kinetic Dynamic Suspension System

    Directory of Open Access Journals (Sweden)

    Bangji Zhang

    2016-01-01

    Full Text Available A novel kinetic dynamic suspension (KDS system is presented for the cooperative control of the roll and warp motion modes of off-road vehicles. The proposed KDS system consists of two hydraulic cylinders acting on the antiroll bars. Hence, the antiroll bars are not completely replaced by the hydraulic system, but both systems are installed. In this paper, the vibration analysis in terms of natural frequencies of different motion modes in frequency domain for an off-road vehicle equipped with different configurable suspension systems is studied by using the modal analysis method. The dynamic responses of the vehicle with different configurable suspension systems are investigated under different road excitations and maneuvers. The results of the modal and dynamic analysis prove that the KDS system can reduce the roll and articulation motions of the off-road vehicle without adding extra bounce stiffness and deteriorating the ride comfort. Furthermore, the roll stiffness is increased and the warp stiffness is decreased by the KDS system, which could significantly enhance handing performance and off-road capability.

  8. Dynamic range broadening for photomultipliers in kinetic spectrophotometry

    International Nuclear Information System (INIS)

    Rumas, V.K.

    1983-01-01

    The circuit of switching on a photomultiplier with prestage modulation developed for kinetic spectrophotometry purposes is described. Distinguishing features of the scheme are wide range of control pulse duration (40 nc - 2.5 mc) and direct transistor photostart by laser light pulse. In the case of PM prestage modulation for the second dynode modulation depth attains 400 while PM opening time constitutes 40 nc

  9. Microtubule dynamics. II. Kinetics of self-assembly

    DEFF Research Database (Denmark)

    Flyvbjerg, H.; Jobs, E.

    1997-01-01

    Inverse scattering theory describes the conditions necessary and sufficient to determine an unknown potential from known scattering data. No similar theory exists for when and how one may deduce the kinetics of an unknown chemical reaction from quantitative information about its final state and i...... to analyze the self-assembly of microtubules from tubulin are general, and many other reactions and processes may be studied as inverse problems with these methods when enough experimental data are available....

  10. Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles

    Directory of Open Access Journals (Sweden)

    Gengjie Jia

    2012-11-01

    Full Text Available Kinetic modeling of metabolic pathways has important applications in metabolic engineering, but significant challenges still remain. The difficulties faced vary from finding best-fit parameters in a highly multidimensional search space to incomplete parameter identifiability. To meet some of these challenges, an ensemble modeling method is developed for characterizing a subset of kinetic parameters that give statistically equivalent goodness-of-fit to time series concentration data. The method is based on the incremental identification approach, where the parameter estimation is done in a step-wise manner. Numerical efficacy is achieved by reducing the dimensionality of parameter space and using efficient random parameter exploration algorithms. The shift toward using model ensembles, instead of the traditional “best-fit” models, is necessary to directly account for model uncertainty during the application of such models. The performance of the ensemble modeling approach has been demonstrated in the modeling of a generic branched pathway and the trehalose pathway in Saccharomyces cerevisiae using generalized mass action (GMA kinetics.

  11. Iron oxide nanoparticle-based magnetic resonance method to monitor release kinetics from polymeric particles with high resolution.

    Science.gov (United States)

    Chan, Minnie; Schopf, Eric; Sankaranarayanan, Jagadis; Almutairi, Adah

    2012-09-18

    A new method to precisely monitor rapid release kinetics from polymeric particles using super paramagnetic iron oxide nanoparticles, specifically by measuring spin-spin relaxation time (T(2)), is reported. Previously, we have published the formulation of logic gate particles from an acid-sensitive poly-β-aminoester ketal-2 polymer. Here, a series of poly-β-aminoester ketal-2 polymers with varying hydrophobicities were synthesized and used to formulate particles. We attempted to measure fluorescence of released Nile red to determine whether the structural adjustments could finely tune the release kinetics in the range of minutes to hours; however, this standard technique did not differentiate each release rate of our series. Thus, a new method based on encapsulation of iron oxide nanoparticles was developed, which enabled us to resolve the release kinetics of our particles. Moreover, the kinetics matched the relative hydrophobicity order determined by octanol-water partition coefficients. To the best of our knowledge, this method provides the highest resolution of release kinetics to date.

  12. Textural kinetics: a novel dynamic contrast-enhanced (DCE)-MRI feature for breast lesion classification.

    Science.gov (United States)

    Agner, Shannon C; Soman, Salil; Libfeld, Edward; McDonald, Margie; Thomas, Kathleen; Englander, Sarah; Rosen, Mark A; Chin, Deanna; Nosher, John; Madabhushi, Anant

    2011-06-01

    Dynamic contrast-enhanced (DCE)-magnetic resonance imaging (MRI) of the breast has emerged as an adjunct imaging tool to conventional X-ray mammography due to its high detection sensitivity. Despite the increasing use of breast DCE-MRI, specificity in distinguishing malignant from benign breast lesions is low, and interobserver variability in lesion classification is high. The novel contribution of this paper is in the definition of a new DCE-MRI descriptor that we call textural kinetics, which attempts to capture spatiotemporal changes in breast lesion texture in order to distinguish malignant from benign lesions. We qualitatively and quantitatively demonstrated on 41 breast DCE-MRI studies that textural kinetic features outperform signal intensity kinetics and lesion morphology features in distinguishing benign from malignant lesions. A probabilistic boosting tree (PBT) classifier in conjunction with textural kinetic descriptors yielded an accuracy of 90%, sensitivity of 95%, specificity of 82%, and an area under the curve (AUC) of 0.92. Graph embedding, used for qualitative visualization of a low-dimensional representation of the data, showed the best separation between benign and malignant lesions when using textural kinetic features. The PBT classifier results and trends were also corroborated via a support vector machine classifier which showed that textural kinetic features outperformed the morphological, static texture, and signal intensity kinetics descriptors. When textural kinetic attributes were combined with morphologic descriptors, the resulting PBT classifier yielded 89% accuracy, 99% sensitivity, 76% specificity, and an AUC of 0.91.

  13. Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

    International Nuclear Information System (INIS)

    Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti

    2016-01-01

    Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

  14. Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti, E-mail: arti@iitm.ac.in [Department of Chemistry, Indian Institute of Technology, Madras, Chennai 600036 (India)

    2016-08-28

    Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

  15. Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

    Science.gov (United States)

    Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti

    2016-08-01

    Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

  16. Kinetic theory for electron dynamics near a positive ion

    International Nuclear Information System (INIS)

    Wrighton, Jeffrey M; Dufty, James W

    2008-01-01

    A theoretical description of time correlation functions for electron properties in the presence of a positive ion of charge number Z is given. The simplest case of an electron gas distorted by a single ion is considered. A semi-classical representation with a regularized electron–ion potential is used to obtain a linear kinetic theory that is asymptotically exact at short times. This Markovian approximation includes all initial (equilibrium) electron–electron and electron–ion correlations through renormalized pair potentials. The kinetic theory is solved in terms of single-particle trajectories of the electron–ion potential and a dielectric function for the inhomogeneous electron gas. The results are illustrated by a calculation of the autocorrelation function for the electron field at the ion. The dependence on charge number Z is shown to be dominated by the bound states of the effective electron–ion potential. On this basis, a very simple practical representation of the trajectories is proposed and shown to be accurate over a wide range including strong electron–ion coupling. This simple representation is then used for a brief analysis of the dielectric function for the inhomogeneous electron gas

  17. A High-Resolution Sensor Network for Monitoring Glacier Dynamics

    Science.gov (United States)

    Edwards, S.; Murray, T.; O'Farrell, T.; Rutt, I. C.; Loskot, P.; Martin, I.; Selmes, N.; Aspey, R.; James, T.; Bevan, S. L.; Baugé, T.

    2013-12-01

    Changes in Greenland and Antarctic ice sheets due to ice flow/ice-berg calving are a major uncertainty affecting sea-level rise forecasts. Latterly GNSS (Global Navigation Satellite Systems) have been employed extensively to monitor such glacier dynamics. Until recently however, the favoured methodology has been to deploy sensors onto the glacier surface, collect data for a period of time, then retrieve and download the sensors. This approach works well in less dynamic environments where the risk of sensor loss is low. In more extreme environments e.g. approaching the glacial calving front, the risk of sensor loss and hence data loss increases dramatically. In order to provide glaciologists with new insights into flow dynamics and calving processes we have developed a novel sensor network to increase the robustness of data capture. We present details of the technological requirements for an in-situ Zigbee wireless streaming network infrastructure supporting instantaneous data acquisition from high resolution GNSS sensors thereby increasing data capture robustness. The data obtained offers new opportunities to investigate the interdependence of mass flow, uplift, velocity and geometry and the network architecture has been specifically designed for deployment by helicopter close to the calving front to yield unprecedented detailed information. Following successful field trials of a pilot three node network during 2012, a larger 20 node network was deployed on the fast-flowing Helheim glacier, south-east Greenland over the summer months of 2013. The utilisation of dual wireless transceivers in each glacier node, multiple frequencies and four ';collector' stations located on the valley sides creates overlapping networks providing enhanced capacity, diversity and redundancy of data 'back-haul', even close to ';floor' RSSI (Received Signal Strength Indication) levels around -100 dBm. Data loss through radio packet collisions within sub-networks are avoided through the

  18. Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

    Science.gov (United States)

    Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

    2018-06-13

    An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

  19. Kinetic modeling and dynamic analysis of simultaneous saccharification and fermentation of cellulose to bioethanol

    International Nuclear Information System (INIS)

    Shadbahr, Jalil; Khan, Faisal; Zhang, Yan

    2017-01-01

    Highlights: • Deeper understanding of saccharification and fermentation process. • A new kinetic model for dynamic analysis of the simultaneous saccharification and fermentation. • Testing and validation of kinetic model. - Abstract: Kinetic modeling and dynamic analysis of the simultaneous saccharification and fermentation (SSF) of cellulose to ethanol was carried out in this study to determine the key reaction kinetics parameters and product inhibition features of the process. To obtain the more reliable kinetic parameters which can be applied for a wide range of operating conditions, batch SSF experiments were carried out at three enzyme loadings (10, 15 and 20 FPU/g cellulose) and two levels of initial concentrations of fermentable sugars (glucose and mannose). Results indicated that the maximum ethanol yield and concentration were achieved at high level of sugar concentrations with intermediate enzyme loading (15 FPU/g cellulose). Dynamic analysis of the acquired experimental results revealed that cellulase inhibition by cellobiose plays the most important role at high level of enzyme loading and low level of initial sugar concentrations. The inhibition of glucose becomes significant when high concentrations of sugars were present in the feedstock. Experimental results of SSF process also reveal that an efficient mixing between the phases helps to improve the ethanol yield significantly.

  20. Dynamic positron emission tomography image restoration via a kinetics-induced bilateral filter.

    Directory of Open Access Journals (Sweden)

    Zhaoying Bian

    Full Text Available Dynamic positron emission tomography (PET imaging is a powerful tool that provides useful quantitative information on physiological and biochemical processes. However, low signal-to-noise ratio in short dynamic frames makes accurate kinetic parameter estimation from noisy voxel-wise time activity curves (TAC a challenging task. To address this problem, several spatial filters have been investigated to reduce the noise of each frame with noticeable gains. These filters include the Gaussian filter, bilateral filter, and wavelet-based filter. These filters usually consider only the local properties of each frame without exploring potential kinetic information from entire frames. Thus, in this work, to improve PET parametric imaging accuracy, we present a kinetics-induced bilateral filter (KIBF to reduce the noise of dynamic image frames by incorporating the similarity between the voxel-wise TACs using the framework of bilateral filter. The aim of the proposed KIBF algorithm is to reduce the noise in homogeneous areas while preserving the distinct kinetics of regions of interest. Experimental results on digital brain phantom and in vivo rat study with typical (18F-FDG kinetics have shown that the present KIBF algorithm can achieve notable gains over other existing algorithms in terms of quantitative accuracy measures and visual inspection.

  1. Effects of different per translational kinetics on the dynamics of a core circadian clock model.

    Science.gov (United States)

    Nieto, Paula S; Revelli, Jorge A; Garbarino-Pico, Eduardo; Condat, Carlos A; Guido, Mario E; Tamarit, Francisco A

    2015-01-01

    Living beings display self-sustained daily rhythms in multiple biological processes, which persist in the absence of external cues since they are generated by endogenous circadian clocks. The period (per) gene is a central player within the core molecular mechanism for keeping circadian time in most animals. Recently, the modulation PER translation has been reported, both in mammals and flies, suggesting that translational regulation of clock components is important for the proper clock gene expression and molecular clock performance. Because translational regulation ultimately implies changes in the kinetics of translation and, therefore, in the circadian clock dynamics, we sought to study how and to what extent the molecular clock dynamics is affected by the kinetics of PER translation. With this objective, we used a minimal mathematical model of the molecular circadian clock to qualitatively characterize the dynamical changes derived from kinetically different PER translational mechanisms. We found that the emergence of self-sustained oscillations with characteristic period, amplitude, and phase lag (time delays) between per mRNA and protein expression depends on the kinetic parameters related to PER translation. Interestingly, under certain conditions, a PER translation mechanism with saturable kinetics introduces longer time delays than a mechanism ruled by a first-order kinetics. In addition, the kinetic laws of PER translation significantly changed the sensitivity of our model to parameters related to the synthesis and degradation of per mRNA and PER degradation. Lastly, we found a set of parameters, with realistic values, for which our model reproduces some experimental results reported recently for Drosophila melanogaster and we present some predictions derived from our analysis.

  2. Critical Analysis of Underground Coal Gasification Models. Part II: Kinetic and Computational Fluid Dynamics Models

    Directory of Open Access Journals (Sweden)

    Alina Żogała

    2014-01-01

    Originality/value: This paper presents state of art in the field of coal gasification modeling using kinetic and computational fluid dynamics approach. The paper also presents own comparative analysis (concerned with mathematical formulation, input data and parameters, basic assumptions, obtained results etc. of the most important models of underground coal gasification.

  3. Comparison of molecular dynamics and kinetic modeling of gas-surface interactions

    NARCIS (Netherlands)

    Frezzotti, A.; Gaastra - Nedea, S.V.; Markvoort, A.J.; Spijker, P.; Gibelli, L.

    2008-01-01

    The interaction of a dilute monatomic gas with a solid surface is studied byMolecular Dynamics (MD) simulations and by numerical solutions of a recently proposed kinetic model. Following previous investigations, the heat transport between parallel walls and Couette flow have been adopted as test

  4. Iridium-Catalyzed Dynamic Kinetic Isomerization: Expedient Synthesis of Carbohydrates from Achmatowicz Rearrangement Products.

    Science.gov (United States)

    Wang, Hao-Yuan; Yang, Ka; Bennett, Scott R; Guo, Sheng-rong; Tang, Weiping

    2015-07-20

    A highly stereoselective dynamic kinetic isomerization of Achmatowicz rearrangement products was discovered. This new internal redox isomerization provided ready access to key intermediates for the enantio- and diastereoselective synthesis of a series of naturally occurring sugars. The nature of the de novo synthesis also enables the preparation of both enantiomers. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Application of point kinetic model in the study of fluidized bed reactor dynamic

    International Nuclear Information System (INIS)

    Borges, Volnei; Vilhena, Marco Tullio de; Streck, Elaine E.

    1995-01-01

    In this work the dynamical behavior of the fluidized bed nuclear reactor is analysed. The main goal consist to study the effect of the acceleration term in the point kinetic equations. Numerical simulations are reported considering constant acceleration. (author). 7 refs, 4 figs

  6. Optically Controlled Electron-Transfer Reaction Kinetics and Solvation Dynamics : Effect of Franck-Condon States

    NARCIS (Netherlands)

    Gupta, Kriti; Patra, Aniket; Dhole, Kajal; Samanta, Alok Kumar; Ghosh, Swapan K.

    2017-01-01

    Experimental results for optically controlled electron-transfer reaction kinetics (ETRK) and nonequilibrium solvation dynamics (NESD) of Coumarin 480 in DMPC vesicle show their dependence on excitation wavelength λex. However, the celebrated Marcus theory and linear-response-theory-based approaches

  7. Palladium-Catalyzed Enantioselective C-H Olefination of Diaryl Sulfoxides through Parallel Kinetic Resolution and Desymmetrization.

    Science.gov (United States)

    Zhu, Yu-Chao; Li, Yan; Zhang, Bo-Chao; Zhang, Feng-Xu; Yang, Yi-Nuo; Wang, Xi-Sheng

    2018-03-07

    The first example of Pd II -catalyzed enantioselective C-H olefination with non-chiral or racemic sulfoxides as directing groups was developed. A variety of chiral diaryl sulfoxides were synthesized with high enantioselectivity (up to 99 %) through both desymmetrization and parallel kinetic resolution (PKR). This is the first report of Pd II -catalyzed enantioselective C(sp 2 )-H functionalization through PKR, and it represents a novel strategy to construct sulfur chiral centers. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Improved accuracy of quantitative parameter estimates in dynamic contrast-enhanced CT study with low temporal resolution

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sun Mo, E-mail: Sunmo.Kim@rmp.uhn.on.ca [Radiation Medicine Program, Princess Margaret Hospital/University Health Network, Toronto, Ontario M5G 2M9 (Canada); Haider, Masoom A. [Department of Medical Imaging, Sunnybrook Health Sciences Centre, Toronto, Ontario M4N 3M5, Canada and Department of Medical Imaging, University of Toronto, Toronto, Ontario M5G 2M9 (Canada); Jaffray, David A. [Radiation Medicine Program, Princess Margaret Hospital/University Health Network, Toronto, Ontario M5G 2M9, Canada and Department of Radiation Oncology, University of Toronto, Toronto, Ontario M5G 2M9 (Canada); Yeung, Ivan W. T. [Radiation Medicine Program, Princess Margaret Hospital/University Health Network, Toronto, Ontario M5G 2M9 (Canada); Department of Medical Physics, Stronach Regional Cancer Centre, Southlake Regional Health Centre, Newmarket, Ontario L3Y 2P9 (Canada); Department of Radiation Oncology, University of Toronto, Toronto, Ontario M5G 2M9 (Canada)

    2016-01-15

    Purpose: A previously proposed method to reduce radiation dose to patient in dynamic contrast-enhanced (DCE) CT is enhanced by principal component analysis (PCA) filtering which improves the signal-to-noise ratio (SNR) of time-concentration curves in the DCE-CT study. The efficacy of the combined method to maintain the accuracy of kinetic parameter estimates at low temporal resolution is investigated with pixel-by-pixel kinetic analysis of DCE-CT data. Methods: The method is based on DCE-CT scanning performed with low temporal resolution to reduce the radiation dose to the patient. The arterial input function (AIF) with high temporal resolution can be generated with a coarsely sampled AIF through a previously published method of AIF estimation. To increase the SNR of time-concentration curves (tissue curves), first, a region-of-interest is segmented into squares composed of 3 × 3 pixels in size. Subsequently, the PCA filtering combined with a fraction of residual information criterion is applied to all the segmented squares for further improvement of their SNRs. The proposed method was applied to each DCE-CT data set of a cohort of 14 patients at varying levels of down-sampling. The kinetic analyses using the modified Tofts’ model and singular value decomposition method, then, were carried out for each of the down-sampling schemes between the intervals from 2 to 15 s. The results were compared with analyses done with the measured data in high temporal resolution (i.e., original scanning frequency) as the reference. Results: The patients’ AIFs were estimated to high accuracy based on the 11 orthonormal bases of arterial impulse responses established in the previous paper. In addition, noise in the images was effectively reduced by using five principal components of the tissue curves for filtering. Kinetic analyses using the proposed method showed superior results compared to those with down-sampling alone; they were able to maintain the accuracy in the

  9. A quenched-flow system for measuring heterogeneous enzyme kinetics with sub-second time resolution

    DEFF Research Database (Denmark)

    Olsen, Johan Pelck; Kari, Jeppe; Borch, Kim

    2017-01-01

    of insoluble substrate. Perhaps for this reason, transient kinetics has rarely been reported for heterogeneous enzyme reactions. Here, we describe a quenched-flow system using peristaltic pumps and stirred substrate suspensions with a dead time below 100 ms. The general performance was verified by alkali...

  10. Investigation of nucleation kinetics in H2SO4 vapor through modeling of gas phase kinetics coupled with particle dynamics

    Science.gov (United States)

    Carlsson, Philip T. M.; Zeuch, Thomas

    2018-03-01

    We have developed a new model utilizing our existing kinetic gas phase models to simulate experimental particle size distributions emerging in dry supersaturated H2SO4 vapor homogeneously produced by rapid oxidation of SO2 through stabilized Criegee-Intermediates from 2-butene ozonolysis. We use a sectional method for simulating the particle dynamics. The particle treatment in the model is based on first principles and takes into account the transition from the kinetic to the diffusion-limited regime. It captures the temporal evolution of size distributions at the end of the ozonolysis experiment well, noting a slight underrepresentation of coagulation effects for larger particle sizes. The model correctly predicts the shape and the modes of the experimentally observed particle size distributions. The predicted modes show an extremely high sensitivity to the H2SO4 evaporation rates of the initially formed H2SO4 clusters (dimer to pentamer), which were arbitrarily restricted to decrease exponentially with increasing cluster size. In future, the analysis presented in this work can be extended to allow a direct validation of quantum chemically predicted stabilities of small H2SO4 clusters, which are believed to initiate a significant fraction of atmospheric new particle formation events. We discuss the prospects and possible limitations of the here presented approach.

  11. Improving estimation of kinetic parameters in dynamic force spectroscopy using cluster analysis

    Science.gov (United States)

    Yen, Chi-Fu; Sivasankar, Sanjeevi

    2018-03-01

    Dynamic Force Spectroscopy (DFS) is a widely used technique to characterize the dissociation kinetics and interaction energy landscape of receptor-ligand complexes with single-molecule resolution. In an Atomic Force Microscope (AFM)-based DFS experiment, receptor-ligand complexes, sandwiched between an AFM tip and substrate, are ruptured at different stress rates by varying the speed at which the AFM-tip and substrate are pulled away from each other. The rupture events are grouped according to their pulling speeds, and the mean force and loading rate of each group are calculated. These data are subsequently fit to established models, and energy landscape parameters such as the intrinsic off-rate (koff) and the width of the potential energy barrier (xβ) are extracted. However, due to large uncertainties in determining mean forces and loading rates of the groups, errors in the estimated koff and xβ can be substantial. Here, we demonstrate that the accuracy of fitted parameters in a DFS experiment can be dramatically improved by sorting rupture events into groups using cluster analysis instead of sorting them according to their pulling speeds. We test different clustering algorithms including Gaussian mixture, logistic regression, and K-means clustering, under conditions that closely mimic DFS experiments. Using Monte Carlo simulations, we benchmark the performance of these clustering algorithms over a wide range of koff and xβ, under different levels of thermal noise, and as a function of both the number of unbinding events and the number of pulling speeds. Our results demonstrate that cluster analysis, particularly K-means clustering, is very effective in improving the accuracy of parameter estimation, particularly when the number of unbinding events are limited and not well separated into distinct groups. Cluster analysis is easy to implement, and our performance benchmarks serve as a guide in choosing an appropriate method for DFS data analysis.

  12. Hydrolytic kinetic resolution of the enantiomers of the structural isomers trans-1-phenylpropene oxide and (2,3-epoxypropyl) benzene by yeast epoxide hydrolase

    CSIR Research Space (South Africa)

    Lotter, J

    2004-08-01

    Full Text Available Kinetic resolution of the enantiomers of trans-1-phenylpropene oxide and (2,3-epoxypropyl)benzene was achieved by yeasts from the genus Rhodotorula. The resolution of trans-1-phenylpropene oxide by Rhodotorula glutinis UOFS Y-0123 yielded (1R, 2R...

  13. Kinetic equations within the formalism of non-equilibrium thermo field dynamics

    International Nuclear Information System (INIS)

    Arimitsu, Toshihico

    1988-01-01

    After reviewing the real-time formalism of dissipative quantum field theory, i.e. non-equilibrium thermo field dynamics (NETFD), a kinetic equation, a self-consistent equation for the dissipation coefficient and a ''mass'' or ''chemical potential'' renormalization equation for non-equilibrium transient situations are extracted out of the two-point Green's function of the Heisenberg field, in their most general forms upon the basic requirements of NETFD. The formulation is applied to the electron-phonon system, as an example, where the gradient expansion and the quasi-particle approximation are performed. The formalism of NETFD is reinvestigated in connection with the kinetic equations. (orig.)

  14. High-resolution Statistics of Solar Wind Turbulence at Kinetic Scales Using the Magnetospheric Multiscale Mission

    Energy Technology Data Exchange (ETDEWEB)

    Chasapis, Alexandros; Matthaeus, W. H.; Parashar, T. N.; Maruca, B. A. [University of Delaware, Newark, DE (United States); Fuselier, S. A.; Burch, J. L. [Southwest Research Institute, San Antonio, TX (United States); Phan, T. D. [Space Sciences Laboratory, University of California, Berkeley, CA (United States); Moore, T. E.; Pollock, C. J.; Gershman, D. J. [NASA Goddard Space Flight Center, Greenbelt, MD (United States); Torbert, R. B. [University of New Hampshire, Durham, NH (United States); Russell, C. T.; Strangeway, R. J., E-mail: chasapis@udel.edu [University of California, Los Angeles, CA (United States)

    2017-07-20

    Using data from the Magnetospheric Multiscale (MMS) and Cluster missions obtained in the solar wind, we examine second-order and fourth-order structure functions at varying spatial lags normalized to ion inertial scales. The analysis includes direct two-spacecraft results and single-spacecraft results employing the familiar Taylor frozen-in flow approximation. Several familiar statistical results, including the spectral distribution of energy, and the sale-dependent kurtosis, are extended down to unprecedented spatial scales of ∼6 km, approaching electron scales. The Taylor approximation is also confirmed at those small scales, although small deviations are present in the kinetic range. The kurtosis is seen to attain very high values at sub-proton scales, supporting the previously reported suggestion that monofractal behavior may be due to high-frequency plasma waves at kinetic scales.

  15. A high resolution large dynamic range TDC circuit implementation

    International Nuclear Information System (INIS)

    Lei Wuhu; Liu Songqiu; Ye Weiguo; Han Hui; Li Pengyu

    2003-01-01

    Time measurement technology is usually used in nuclear experimentation. There are many methods of time measurement. The implementation method of Time to Digital Conversion (TDC) by means of electronic is a classical technology. The range and resolution of TDC is different according with different usage. A wide range and high resolution TDC circuit, including its theory and implementation way, is introduced in this paper. The test result is also given. (authors)

  16. A high resolution large dynamic range TDC circuit implementation

    International Nuclear Information System (INIS)

    Lei Wuhu; Liu Songqiu; Li Pengyu; Han Hui; Ye Yanlin

    2005-01-01

    Time measurement technology is usually used in nuclear experimentation. There are many methods of time measurement. The implementation method of Time to Digital Conversion (TDC) by means of electronics is a classical technology. The range and resolution of TDC is different according with different usage. A wide range and high resolution TDC circuit, including its theory and implementation way, is introduced in this paper. The test result is also given. (authors)

  17. Supercomputer algorithms for reactivity, dynamics and kinetics of small molecules

    International Nuclear Information System (INIS)

    Lagana, A.

    1989-01-01

    Even for small systems, the accurate characterization of reactive processes is so demanding of computer resources as to suggest the use of supercomputers having vector and parallel facilities. The full advantages of vector and parallel architectures can sometimes be obtained by simply modifying existing programs, vectorizing the manipulation of vectors and matrices, and requiring the parallel execution of independent tasks. More often, however, a significant time saving can be obtained only when the computer code undergoes a deeper restructuring, requiring a change in the computational strategy or, more radically, the adoption of a different theoretical treatment. This book discusses supercomputer strategies based upon act and approximate methods aimed at calculating the electronic structure and the reactive properties of small systems. The book shows how, in recent years, intense design activity has led to the ability to calculate accurate electronic structures for reactive systems, exact and high-level approximations to three-dimensional reactive dynamics, and to efficient directive and declaratory software for the modelling of complex systems

  18. Solving kinetic equations with adaptive mesh in phase space for rarefied gas dynamics and plasma physics (Invited)

    International Nuclear Information System (INIS)

    Kolobov, Vladimir; Arslanbekov, Robert; Frolova, Anna

    2014-01-01

    The paper describes an Adaptive Mesh in Phase Space (AMPS) technique for solving kinetic equations with deterministic mesh-based methods. The AMPS technique allows automatic generation of adaptive Cartesian mesh in both physical and velocity spaces using a Tree-of-Trees data structure. We illustrate advantages of AMPS for simulations of rarefied gas dynamics and electron kinetics on low temperature plasmas. In particular, we consider formation of the velocity distribution functions in hypersonic flows, particle kinetics near oscillating boundaries, and electron kinetics in a radio-frequency sheath. AMPS provide substantial savings in computational cost and increased efficiency of the mesh-based kinetic solvers

  19. Solving kinetic equations with adaptive mesh in phase space for rarefied gas dynamics and plasma physics (Invited)

    Energy Technology Data Exchange (ETDEWEB)

    Kolobov, Vladimir [CFD Research Corporation, Huntsville, AL 35805, USA and The University of Alabama in Huntsville, Huntsville, AL 35805 (United States); Arslanbekov, Robert [CFD Research Corporation, Huntsville, AL 35805 (United States); Frolova, Anna [Computing Center of the Russian Academy of Sciences, Moscow, 119333 (Russian Federation)

    2014-12-09

    The paper describes an Adaptive Mesh in Phase Space (AMPS) technique for solving kinetic equations with deterministic mesh-based methods. The AMPS technique allows automatic generation of adaptive Cartesian mesh in both physical and velocity spaces using a Tree-of-Trees data structure. We illustrate advantages of AMPS for simulations of rarefied gas dynamics and electron kinetics on low temperature plasmas. In particular, we consider formation of the velocity distribution functions in hypersonic flows, particle kinetics near oscillating boundaries, and electron kinetics in a radio-frequency sheath. AMPS provide substantial savings in computational cost and increased efficiency of the mesh-based kinetic solvers.

  20. Correlation between High Resolution Dynamic MR Features and Prognostic Factors in Breast Cancer

    International Nuclear Information System (INIS)

    Lee, Shin Ho; Cho, Nariya; Kim, Seung Ja; Cho, Kyung Soo; Ko, Eun Sook; Moon, Woo Kyung; Cha, Joo Hee

    2008-01-01

    To correlate high resolution dynamic MR features with prognostic factors in breast cancer. One hundred and ninety-four women with invasive ductal carcinomas underwent dynamic MR imaging using T1-weighted three dimensional fast low-angle shot (3D-FLASH) sequence within two weeks prior to surgery. Morphological and kinetic MR features were determined based on the breast imaging and reporting data system (BI-RADS) MR imaging lexicon. Histological specimens were analyzed for tumor size, axillary lymph node status, histological grade, expression of estrogen receptor (ER), expression of progesterone receptor (PR), and expression of p53, c-erbB-2, and Ki-67. Correlations between the MR features and prognostic factors were determined using the Pearson x 2 test, linear-by-linear association, and logistic regression analysis. By multivariate analysis, a spiculated margin was a significant, independent predictor of a lower histological grade (p < 0.001), and lower expression of Ki-67 (p = 0.007). Rim enhancement was significant, independent predictor of a higher histological grade (p < 0.001), negative expression of ER (p 0.001), negative expression of PR (p < 0.001) and a larger tumor size (p = 0.006). A washout curve may predict a higher level of Ki-67 (p = 0.05). Most of the parameters of the initial enhancement phase cannot predict the status of the prognostic factors. Only the enhancement ratio may predict a larger tumor size (p 0.05). Of the BI-RADS-MR features, a spiculated margin may predict favorable prognosis, whereas rim enhancement or washout may predict unfavorable prognosis of breast cancer

  1. Modeling and Classification of Kinetic Patterns of Dynamic Metabolic Biomarkers in Physical Activity.

    Directory of Open Access Journals (Sweden)

    Marc Breit

    2015-08-01

    Full Text Available The objectives of this work were the classification of dynamic metabolic biomarker candidates and the modeling and characterization of kinetic regulatory mechanisms in human metabolism with response to external perturbations by physical activity. Longitudinal metabolic concentration data of 47 individuals from 4 different groups were examined, obtained from a cycle ergometry cohort study. In total, 110 metabolites (within the classes of acylcarnitines, amino acids, and sugars were measured through a targeted metabolomics approach, combining tandem mass spectrometry (MS/MS with the concept of stable isotope dilution (SID for metabolite quantitation. Biomarker candidates were selected by combined analysis of maximum fold changes (MFCs in concentrations and P-values resulting from statistical hypothesis testing. Characteristic kinetic signatures were identified through a mathematical modeling approach utilizing polynomial fitting. Modeled kinetic signatures were analyzed for groups with similar behavior by applying hierarchical cluster analysis. Kinetic shape templates were characterized, defining different forms of basic kinetic response patterns, such as sustained, early, late, and other forms, that can be used for metabolite classification. Acetylcarnitine (C2, showing a late response pattern and having the highest values in MFC and statistical significance, was classified as late marker and ranked as strong predictor (MFC = 1.97, P < 0.001. In the class of amino acids, highest values were shown for alanine (MFC = 1.42, P < 0.001, classified as late marker and strong predictor. Glucose yields a delayed response pattern, similar to a hockey stick function, being classified as delayed marker and ranked as moderate predictor (MFC = 1.32, P < 0.001. These findings coincide with existing knowledge on central metabolic pathways affected in exercise physiology, such as β-oxidation of fatty acids, glycolysis, and glycogenolysis. The presented modeling

  2. Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models

    Directory of Open Access Journals (Sweden)

    Joseph A. Wayman

    2015-03-01

    Full Text Available Cell-free systems offer many advantages for the study, manipulation and modeling of metabolism compared to in vivo processes. Many of the challenges confronting genome-scale kinetic modeling can potentially be overcome in a cell-free system. For example, there is no complex transcriptional regulation to consider, transient metabolic measurements are easier to obtain, and we no longer have to consider cell growth. Thus, cell-free operation holds several significant advantages for model development, identification and validation. Theoretically, genome-scale cell-free kinetic models may be possible for industrially important organisms, such as E. coli, if a simple, tractable framework for integrating allosteric regulation with enzyme kinetics can be formulated. Toward this unmet need, we present an effective biochemical network modeling framework for building dynamic cell-free metabolic models. The key innovation of our approach is the integration of simple effective rules encoding complex allosteric regulation with traditional kinetic pathway modeling. We tested our approach by modeling the time evolution of several hypothetical cell-free metabolic networks. We found that simple effective rules, when integrated with traditional enzyme kinetic expressions, captured complex allosteric patterns such as ultrasensitivity or non-competitive inhibition in the absence of mechanistic information. Second, when integrated into network models, these rules captured classic regulatory patterns such as product-induced feedback inhibition. Lastly, we showed, at least for the network architectures considered here, that we could simultaneously estimate kinetic parameters and allosteric connectivity from synthetic data starting from an unbiased collection of possible allosteric structures using particle swarm optimization. However, when starting with an initial population that was heavily enriched with incorrect structures, our particle swarm approach could converge

  3. Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters.

    Science.gov (United States)

    Chiang, Austin W T; Liu, Wei-Chung; Charusanti, Pep; Hwang, Ming-Jing

    2014-01-15

    A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system's dynamics. We demonstrate our methodology on a prototype biological system of perfect adaptation dynamics, namely the chemotaxis model for Escherichia coli. Our results agreed well with those derived from experimental data and theoretical studies in the literature. Using this model system, we showed that there are motifs in kinetic parameters and that these motifs are governed by constraints of the specified system dynamics. A systematic approach based on enrichment statistical tests has been developed to elucidate the relationships between model parameters and the roles they play in affecting system dynamics of a prototype biological network. The proposed approach is generally applicable and therefore can find wide use in systems biology modeling research.

  4. A robust state-space kinetics-guided framework for dynamic PET image reconstruction

    International Nuclear Information System (INIS)

    Tong, S; Alessio, A M; Kinahan, P E; Liu, H; Shi, P

    2011-01-01

    Dynamic PET image reconstruction is a challenging issue due to the low SNR and the large quantity of spatio-temporal data. We propose a robust state-space image reconstruction (SSIR) framework for activity reconstruction in dynamic PET. Unlike statistically-based frame-by-frame methods, tracer kinetic modeling is incorporated to provide physiological guidance for the reconstruction, harnessing the temporal information of the dynamic data. Dynamic reconstruction is formulated in a state-space representation, where a compartmental model describes the kinetic processes in a continuous-time system equation, and the imaging data are expressed in a discrete measurement equation. Tracer activity concentrations are treated as the state variables, and are estimated from the dynamic data. Sampled-data H ∞ filtering is adopted for robust estimation. H ∞ filtering makes no assumptions on the system and measurement statistics, and guarantees bounded estimation error for finite-energy disturbances, leading to robust performance for dynamic data with low SNR and/or errors. This alternative reconstruction approach could help us to deal with unpredictable situations in imaging (e.g. data corruption from failed detector blocks) or inaccurate noise models. Experiments on synthetic phantom and patient PET data are performed to demonstrate feasibility of the SSIR framework, and to explore its potential advantages over frame-by-frame statistical reconstruction approaches.

  5. Is cancer a pure growth curve or does it follow a kinetics of dynamical structural transformation?

    Science.gov (United States)

    González, Maraelys Morales; Joa, Javier Antonio González; Cabrales, Luis Enrique Bergues; Pupo, Ana Elisa Bergues; Schneider, Baruch; Kondakci, Suleyman; Ciria, Héctor Manuel Camué; Reyes, Juan Bory; Jarque, Manuel Verdecia; Mateus, Miguel Angel O'Farril; González, Tamara Rubio; Brooks, Soraida Candida Acosta; Cáceres, José Luis Hernández; González, Gustavo Victoriano Sierra

    2017-03-07

    Unperturbed tumor growth kinetics is one of the more studied cancer topics; however, it is poorly understood. Mathematical modeling is a useful tool to elucidate new mechanisms involved in tumor growth kinetics, which can be relevant to understand cancer genesis and select the most suitable treatment. The classical Kolmogorov-Johnson-Mehl-Avrami as well as the modified Kolmogorov-Johnson-Mehl-Avrami models to describe unperturbed fibrosarcoma Sa-37 tumor growth are used and compared with the Gompertz modified and Logistic models. Viable tumor cells (1×10 5 ) are inoculated to 28 BALB/c male mice. Modified Gompertz, Logistic, Kolmogorov-Johnson-Mehl-Avrami classical and modified Kolmogorov-Johnson-Mehl-Avrami models fit well to the experimental data and agree with one another. A jump in the time behaviors of the instantaneous slopes of classical and modified Kolmogorov-Johnson-Mehl-Avrami models and high values of these instantaneous slopes at very early stages of tumor growth kinetics are observed. The modified Kolmogorov-Johnson-Mehl-Avrami equation can be used to describe unperturbed fibrosarcoma Sa-37 tumor growth. It reveals that diffusion-controlled nucleation/growth and impingement mechanisms are involved in tumor growth kinetics. On the other hand, tumor development kinetics reveals dynamical structural transformations rather than a pure growth curve. Tumor fractal property prevails during entire TGK.

  6. Growth Kinetics and Size Distribution Dynamics of Viscous Secondary Organic Aerosol

    Energy Technology Data Exchange (ETDEWEB)

    Zaveri, Rahul A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Atmospheric Science and Global Change Div. (ASGC); Shilling, John E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Atmospheric Science and Global Change Div. (ASGC); Zelenyuk, Alla [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical Sciences Div.; Liu, Jiumeng [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Atmospheric Science and Global Change Div. (ASGC); Bell, David M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical Sciences Div.; Paul Scherrer Inst. (PSI), Villigen (Switzerland). Lab. of Atmospheric Chemistry; D’Ambro, Emma L. [Univ. of Washington, Seattle, WA (United States). Dept. of Atmospheric Sciences and Dept. of Chemistry; Gaston, Cassandra J. [Univ. of Washington, Seattle, WA (United States). Dept. of Atmospheric Sciences; Univ. of Miami, Miami, FL (United States). Rosenstiel School of Marine and Atmospheric Science; Thornton, Joel A. [Univ. of Washington, Seattle, WA (United States). Dept. of Atmospheric Sciences and Dept. of Chemistry; Laskin, Alexander [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL); Purdue Univ., West Lafayette, IN (United States). Dept. of Chemistry; Lin, Peng [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL); Purdue Univ., West Lafayette, IN (United States). Dept. of Chemistry; Wilson, Jacqueline [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical Sciences Div.; Easter, Richard C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Atmospheric Science and Global Change Div. (ASGC); Wang, Jian [Brookhaven National Lab. (BNL), Upton, NY (United States). Environmental & Climate Sciences Dept.; Bertram, Allan K. [Univ. of British Columbia, Vancouver, BC (Canada). Dept. of Chemistry; Martin, Scot T. [Harvard Univ., Cambridge, MA (United States). School of Engineering and Applied Sciences (SEAS) and Dept. of Earth and Planetary Sciences; Seinfeld, John H. [California Inst. of Technology (CalTech), Pasadena, CA (United States). Div. of Chemistry and Chemical Engineering and Div. of Engineering and Applied Science; Worsnop, Douglas R. [Aerodyne Research, Billerica, MA (United States). Center for Aerosol and Cloud Chemistry

    2017-12-15

    Low bulk diffusivity inside viscous semisolid atmospheric secondary organic aerosol (SOA) can prolong equilibration time scale, but its broader impacts on aerosol growth and size distribution dynamics are poorly understood. In this article, we present quantitative insights into the effects of bulk diffusivity on the growth and evaporation kinetics of SOA formed under dry conditions from photooxidation of isoprene in the presence of a bimodal aerosol consisting of Aitken (ammonium sulfate) and accumulation (isoprene or α-pinene SOA) mode particles. Aerosol composition measurements and evaporation kinetics indicate that isoprene SOA is composed of several semivolatile organic compounds (SVOCs), with some reversibly reacting to form oligomers. Model analysis shows that liquid-like bulk diffusivities can be used to fit the observed evaporation kinetics of accumulation mode particles but fail to explain the growth kinetics of bimodal aerosol by significantly under-predicting the evolution of the Aitken mode. In contrast, the semisolid scenario successfully reproduces both evaporation and growth kinetics, with the interpretation that hindered partitioning of SVOCs into large viscous particles effectively promotes the growth of smaller particles that have shorter diffusion time scales. This effect has important implications for the growth of atmospheric ultrafine particles to climatically active sizes.

  7. New types of experimental data shape the use of enzyme kinetics for dynamic network modeling.

    Science.gov (United States)

    Tummler, Katja; Lubitz, Timo; Schelker, Max; Klipp, Edda

    2014-01-01

    Since the publication of Leonor Michaelis and Maude Menten's paper on the reaction kinetics of the enzyme invertase in 1913, molecular biology has evolved tremendously. New measurement techniques allow in vivo characterization of the whole genome, proteome or transcriptome of cells, whereas the classical enzyme essay only allows determination of the two Michaelis-Menten parameters V and K(m). Nevertheless, Michaelis-Menten kinetics are still commonly used, not only in the in vitro context of enzyme characterization but also as a rate law for enzymatic reactions in larger biochemical reaction networks. In this review, we give an overview of the historical development of kinetic rate laws originating from Michaelis-Menten kinetics over the past 100 years. Furthermore, we briefly summarize the experimental techniques used for the characterization of enzymes, and discuss web resources that systematically store kinetic parameters and related information. Finally, describe the novel opportunities that arise from using these data in dynamic mathematical modeling. In this framework, traditional in vitro approaches may be combined with modern genome-scale measurements to foster thorough understanding of the underlying complex mechanisms. © 2013 FEBS.

  8. Numerical simulation of stochastic point kinetic equation in the dynamical system of nuclear reactor

    International Nuclear Information System (INIS)

    Saha Ray, S.

    2012-01-01

    Highlights: ► In this paper stochastic neutron point kinetic equations have been analyzed. ► Euler–Maruyama method and Strong Taylor 1.5 order method have been discussed. ► These methods are applied for the solution of stochastic point kinetic equations. ► Comparison between the results of these methods and others are presented in tables. ► Graphs for neutron and precursor sample paths are also presented. -- Abstract: In the present paper, the numerical approximation methods, applied to efficiently calculate the solution for stochastic point kinetic equations () in nuclear reactor dynamics, are investigated. A system of Itô stochastic differential equations has been analyzed to model the neutron density and the delayed neutron precursors in a point nuclear reactor. The resulting system of Itô stochastic differential equations are solved over each time-step size. The methods are verified by considering different initial conditions, experimental data and over constant reactivities. The computational results indicate that the methods are simple and suitable for solving stochastic point kinetic equations. In this article, a numerical investigation is made in order to observe the random oscillations in neutron and precursor population dynamics in subcritical and critical reactors.

  9. Development and application of coupled system dynamics and game theory: A dynamic water conflict resolution method.

    Science.gov (United States)

    Zomorodian, Mehdi; Lai, Sai Hin; Homayounfar, Mehran; Ibrahim, Shaliza; Pender, Gareth

    2017-01-01

    the reservoirs using the mixed-strategy game and Markov chain methods. The two models were then evaluated against three performance indices: Reliability, Resilience and Vulnerability (R-R-V). The results showed that, while both models were well capable of dealing with conflict resolution over water resources in the Langat River basin, the second model achieved a substantially improved performance through its ability to deal with dynamicity, complexity and uncertainty in the river system.

  10. Development and application of coupled system dynamics and game theory: A dynamic water conflict resolution method.

    Directory of Open Access Journals (Sweden)

    Mehdi Zomorodian

    strategies for the reservoirs using the mixed-strategy game and Markov chain methods. The two models were then evaluated against three performance indices: Reliability, Resilience and Vulnerability (R-R-V. The results showed that, while both models were well capable of dealing with conflict resolution over water resources in the Langat River basin, the second model achieved a substantially improved performance through its ability to deal with dynamicity, complexity and uncertainty in the river system.

  11. Experimental methods of investigation of kinetics and dynamics of nuclear reactors

    International Nuclear Information System (INIS)

    Costa Oliveira, Jaime M.

    1969-03-01

    The author presents experimental methods used to study kinetic and dynamic properties of nuclear reactors. Kinetic methods aim at determining characteristic parameters of the behaviour in time of neutrons. Dynamic methods aim at establishing the relationships between the reactor behaviour and its internal and external causes (notably the measurement of transfer functions). The author proposes a classification with respect to the excitation type: periodic excitation (reactivity sinusoidal modulation, source sinusoidal modulation, periodic pulse excitation), non periodic excitation (reactivity monitoring, reactivity linear variation, reactivity variation according to any given law, removal of starting source), random excitation (random reactivity or source excitation), natural fluctuations (alpha-Rossi method, methods of reduced variance, probabilistic methods, correlation methods, spectral analysis method). He also addresses space and energy effects. Applications are reported for low power and power reactors

  12. Wetting kinetics of water nano-droplet containing non-surfactant nanoparticles: A molecular dynamics study

    International Nuclear Information System (INIS)

    Lu, Gui; Hu, Han; Sun, Ying; Duan, Yuanyuan

    2013-01-01

    In this Letter, dynamic wetting of water nano-droplets containing non-surfactant gold nanoparticles on a gold substrate is examined via molecular dynamics simulations. The results show that the addition of non-surfactant nanoparticles hinders the nano-second droplet wetting process, attributed to the increases in both surface tension of the nanofluid and friction between nanofluid and substrate. The droplet wetting kinetics decreases with increasing nanoparticle loading and water-particle interaction energy. The observed wetting suppression and the absence of nanoparticle ordering near the contact line of nano-sized droplets differ from the wetting behaviors reported from nanofluid droplets of micron size or larger

  13. Molecular theory of mass transfer kinetics and dynamics at gas-water interface

    International Nuclear Information System (INIS)

    Morita, Akihiro; Garrett, Bruce C

    2008-01-01

    The mass transfer mechanism across gas-water interface is studied with molecular dynamics (MD) simulation. The MD results provide a robust and qualitatively consistent picture to previous studies about microscopic aspects of mass transfer, including interface structure, free energy profiles for the uptake, scattering dynamics and energy relaxation of impinging molecules. These MD results are quantitatively compared with experimental uptake measurements, and we find that the apparent inconsistency between MD and experiment could be partly resolved by precise decomposition of the observed kinetics into elemental steps. Remaining issues and future perspectives toward constructing a comprehensive multi-scale description of interfacial mass transfer are summarized.

  14. Kinetic and dynamic probability-density-function descriptions of disperse turbulent two-phase flows

    Science.gov (United States)

    Minier, Jean-Pierre; Profeta, Christophe

    2015-11-01

    This article analyzes the status of two classical one-particle probability density function (PDF) descriptions of the dynamics of discrete particles dispersed in turbulent flows. The first PDF formulation considers only the process made up by particle position and velocity Zp=(xp,Up) and is represented by its PDF p (t ;yp,Vp) which is the solution of a kinetic PDF equation obtained through a flux closure based on the Furutsu-Novikov theorem. The second PDF formulation includes fluid variables into the particle state vector, for example, the fluid velocity seen by particles Zp=(xp,Up,Us) , and, consequently, handles an extended PDF p (t ;yp,Vp,Vs) which is the solution of a dynamic PDF equation. For high-Reynolds-number fluid flows, a typical formulation of the latter category relies on a Langevin model for the trajectories of the fluid seen or, conversely, on a Fokker-Planck equation for the extended PDF. In the present work, a new derivation of the kinetic PDF equation is worked out and new physical expressions of the dispersion tensors entering the kinetic PDF equation are obtained by starting from the extended PDF and integrating over the fluid seen. This demonstrates that, under the same assumption of a Gaussian colored noise and irrespective of the specific stochastic model chosen for the fluid seen, the kinetic PDF description is the marginal of a dynamic PDF one. However, a detailed analysis reveals that kinetic PDF models of particle dynamics in turbulent flows described by statistical correlations constitute incomplete stand-alone PDF descriptions and, moreover, that present kinetic-PDF equations are mathematically ill posed. This is shown to be the consequence of the non-Markovian characteristic of the stochastic process retained to describe the system and the use of an external colored noise. Furthermore, developments bring out that well-posed PDF descriptions are essentially due to a proper choice of the variables selected to describe physical systems

  15. Evaluations of high-resolution dynamically downscaled ensembles over the contiguous United States Climate Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Zobel, Zachary; Wang, Jiali; Wuebbles, Donald J.; Kotamarthi, V. Rao

    2018-02-01

    This study uses Weather Research and Forecast (WRF) model to evaluate the performance of six dynamical downscaled decadal historical simulations with 12-km resolution for a large domain (7200 x 6180 km) that covers most of North America. The initial and boundary conditions are from three global climate models (GCMs) and one reanalysis data. The GCMs employed in this study are the Geophysical Fluid Dynamics Laboratory Earth System Model with Generalized Ocean Layer Dynamics component, Community Climate System Model, version 4, and the Hadley Centre Global Environment Model, version 2-Earth System. The reanalysis data is from the National Centers for Environmental Prediction-US. Department of Energy Reanalysis II. We analyze the effects of bias correcting, the lateral boundary conditions and the effects of spectral nudging. We evaluate the model performance for seven surface variables and four upper atmospheric variables based on their climatology and extremes for seven subregions across the United States. The results indicate that the simulation’s performance depends on both location and the features/variable being tested. We find that the use of bias correction and/or nudging is beneficial in many situations, but employing these when running the RCM is not always an improvement when compared to the reference data. The use of an ensemble mean and median leads to a better performance in measuring the climatology, while it is significantly biased for the extremes, showing much larger differences than individual GCM driven model simulations from the reference data. This study provides a comprehensive evaluation of these historical model runs in order to make informed decisions when making future projections.

  16. Modeling Photo-Bleaching Kinetics to Create High Resolution Maps of Rod Rhodopsin in the Human Retina.

    Directory of Open Access Journals (Sweden)

    Martin Ehler

    Full Text Available We introduce and describe a novel non-invasive in-vivo method for mapping local rod rhodopsin distribution in the human retina over a 30-degree field. Our approach is based on analyzing the brightening of detected lipofuscin autofluorescence within small pixel clusters in registered imaging sequences taken with a commercial 488nm confocal scanning laser ophthalmoscope (cSLO over a 1 minute period. We modeled the kinetics of rhodopsin bleaching by applying variational optimization techniques from applied mathematics. The physical model and the numerical analysis with its implementation are outlined in detail. This new technique enables the creation of spatial maps of the retinal rhodopsin and retinal pigment epithelium (RPE bisretinoid distribution with an ≈ 50μm resolution.

  17. Modeling Photo-Bleaching Kinetics to Create High Resolution Maps of Rod Rhodopsin in the Human Retina

    Science.gov (United States)

    Ehler, Martin; Dobrosotskaya, Julia; Cunningham, Denise; Wong, Wai T.; Chew, Emily Y.; Czaja, Wojtek; Bonner, Robert F.

    2015-01-01

    We introduce and describe a novel non-invasive in-vivo method for mapping local rod rhodopsin distribution in the human retina over a 30-degree field. Our approach is based on analyzing the brightening of detected lipofuscin autofluorescence within small pixel clusters in registered imaging sequences taken with a commercial 488nm confocal scanning laser ophthalmoscope (cSLO) over a 1 minute period. We modeled the kinetics of rhodopsin bleaching by applying variational optimization techniques from applied mathematics. The physical model and the numerical analysis with its implementation are outlined in detail. This new technique enables the creation of spatial maps of the retinal rhodopsin and retinal pigment epithelium (RPE) bisretinoid distribution with an ≈ 50μm resolution. PMID:26196397

  18. Kinetic Resolution of sec-Thiols by Enantioselective Oxidation with Rationally Engineered 5-(Hydroxymethyl)furfural Oxidase.

    Science.gov (United States)

    Pickl, Mathias; Swoboda, Alexander; Romero, Elvira; Winkler, Christoph K; Binda, Claudia; Mattevi, Andrea; Faber, Kurt; Fraaije, Marco W

    2018-03-05

    Various flavoprotein oxidases were recently shown to oxidize primary thiols. Herein, this reactivity is extended to sec-thiols by using structure-guided engineering of 5-(hydroxymethyl)furfural oxidase (HMFO). The variants obtained were employed for the oxidative kinetic resolution of racemic sec-thiols, thus yielding the corresponding thioketones and nonreacted R-configured thiols with excellent enantioselectivities (E≥200). The engineering strategy applied went beyond the classic approach of replacing bulky amino acid residues with smaller ones, as the active site was additionally enlarged by a newly introduced Thr residue. This residue established a hydrogen-bonding interaction with the substrates, as verified in the crystal structure of the variant. These strategies unlocked HMFO variants for the enantioselective oxidation of a range of sec-thiols. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Novel approaches to estimating the turbulent kinetic energy dissipation rate from low- and moderate-resolution velocity fluctuation time series

    Directory of Open Access Journals (Sweden)

    M. Wacławczyk

    2017-11-01

    Full Text Available In this paper we propose two approaches to estimating the turbulent kinetic energy (TKE dissipation rate, based on the zero-crossing method by Sreenivasan et al. (1983. The original formulation requires a fine resolution of the measured signal, down to the smallest dissipative scales. However, due to finite sampling frequency, as well as measurement errors, velocity time series obtained from airborne experiments are characterized by the presence of effective spectral cutoffs. In contrast to the original formulation the new approaches are suitable for use with signals originating from airborne experiments. The suitability of the new approaches is tested using measurement data obtained during the Physics of Stratocumulus Top (POST airborne research campaign as well as synthetic turbulence data. They appear useful and complementary to existing methods. We show the number-of-crossings-based approaches respond differently to errors due to finite sampling and finite averaging than the classical power spectral method. Hence, their application for the case of short signals and small sampling frequencies is particularly interesting, as it can increase the robustness of turbulent kinetic energy dissipation rate retrieval.

  20. Dynamic Model of Basic Oxygen Steelmaking Process Based on Multizone Reaction Kinetics: Modeling of Decarburization

    Science.gov (United States)

    Rout, Bapin Kumar; Brooks, Geoffrey; Akbar Rhamdhani, M.; Li, Zushu; Schrama, Frank N. H.; Overbosch, Aart

    2018-03-01

    In a previous study by the authors (Rout et al. in Metall Mater Trans B 49:537-557, 2018), a dynamic model for the BOF, employing the concept of multizone kinetics was developed. In the current study, the kinetics of decarburization reaction is investigated. The jet impact and slag-metal emulsion zones were identified to be primary zones for carbon oxidation. The dynamic parameters in the rate equation of decarburization such as residence time of metal drops in the emulsion, interfacial area evolution, initial size, and the effects of surface-active oxides have been included in the kinetic rate equation of the metal droplet. A modified mass-transfer coefficient based on the ideal Langmuir adsorption equilibrium has been proposed to take into account the surface blockage effects of SiO2 and P2O5 in slag on the decarburization kinetics of a metal droplet in the emulsion. Further, a size distribution function has been included in the rate equation to evaluate the effect of droplet size on reaction kinetics. The mathematical simulation indicates that decarburization of the droplet in the emulsion is a strong function of the initial size and residence time. A modified droplet generation rate proposed previously by the authors has been used to estimate the total decarburization rate by slag-metal emulsion. The model's prediction shows that about 76 pct of total carbon is removed by reactions in the emulsion, and the remaining is removed by reactions at the jet impact zone. The predicted bath carbon by the model has been found to be in good agreement with the industrially measured data.

  1. Dynamic Model of Basic Oxygen Steelmaking Process Based on Multizone Reaction Kinetics: Modeling of Decarburization

    Science.gov (United States)

    Rout, Bapin Kumar; Brooks, Geoffrey; Akbar Rhamdhani, M.; Li, Zushu; Schrama, Frank N. H.; Overbosch, Aart

    2018-06-01

    In a previous study by the authors (Rout et al. in Metall Mater Trans B 49:537-557, 2018), a dynamic model for the BOF, employing the concept of multizone kinetics was developed. In the current study, the kinetics of decarburization reaction is investigated. The jet impact and slag-metal emulsion zones were identified to be primary zones for carbon oxidation. The dynamic parameters in the rate equation of decarburization such as residence time of metal drops in the emulsion, interfacial area evolution, initial size, and the effects of surface-active oxides have been included in the kinetic rate equation of the metal droplet. A modified mass-transfer coefficient based on the ideal Langmuir adsorption equilibrium has been proposed to take into account the surface blockage effects of SiO2 and P2O5 in slag on the decarburization kinetics of a metal droplet in the emulsion. Further, a size distribution function has been included in the rate equation to evaluate the effect of droplet size on reaction kinetics. The mathematical simulation indicates that decarburization of the droplet in the emulsion is a strong function of the initial size and residence time. A modified droplet generation rate proposed previously by the authors has been used to estimate the total decarburization rate by slag-metal emulsion. The model's prediction shows that about 76 pct of total carbon is removed by reactions in the emulsion, and the remaining is removed by reactions at the jet impact zone. The predicted bath carbon by the model has been found to be in good agreement with the industrially measured data.

  2. Ultrafast dynamics of laser-pulse excited semiconductors: non-Markovian quantum kinetic equations with nonequilibrium correlations

    Directory of Open Access Journals (Sweden)

    V.V.Ignatyuk

    2004-01-01

    Full Text Available Non-Markovian kinetic equations in the second Born approximation are derived for a two-zone semiconductor excited by a short laser pulse. Both collision dynamics and running nonequilibrium correlations are taken into consideration. The energy balance and relaxation of the system to equilibrium are discussed. Results of numerical solution of the kinetic equations for carriers and phonons are presented.

  3. Dynamic neuroanatomy at subcellular resolution in the zebrafish.

    Science.gov (United States)

    Faucherre, Adèle; López-Schier, Hernán

    2014-01-01

    Genetic means to visualize and manipulate neuronal circuits in the intact animal have revolutionized neurobiology. "Dynamic neuroanatomy" defines a range of approaches aimed at quantifying the architecture or subcellular organization of neurons over time during their development, regeneration, or degeneration. A general feature of these approaches is their reliance on the optical isolation of defined neurons in toto by genetically expressing markers in one or few cells. Here we use the afferent neurons of the lateral line as an example to describe a simple method for the dynamic neuroanatomical study of axon terminals in the zebrafish by laser-scanning confocal microscopy.

  4. Enzymatic Kinetic Resolution of 2-Piperidineethanol for the Enantioselective Targeted and Diversity Oriented Synthesis

    Directory of Open Access Journals (Sweden)

    Dario Perdicchia

    2015-12-01

    Full Text Available 2-Piperidineethanol (1 and its corresponding N-protected aldehyde (2 were used for the synthesis of several natural and synthetic compounds. The existence of a stereocenter at position 2 of the piperidine skeleton and the presence of an easily-functionalized group, such as the alcohol, set 1 as a valuable starting material for enantioselective synthesis. Herein, are presented both synthetic and enzymatic methods for the resolution of the racemic 1, as well as an overview of synthesized natural products starting from the enantiopure 1.

  5. Data Driven Approach for High Resolution Population Distribution and Dynamics Models

    Energy Technology Data Exchange (ETDEWEB)

    Bhaduri, Budhendra L [ORNL; Bright, Eddie A [ORNL; Rose, Amy N [ORNL; Liu, Cheng [ORNL; Urban, Marie L [ORNL; Stewart, Robert N [ORNL

    2014-01-01

    High resolution population distribution data are vital for successfully addressing critical issues ranging from energy and socio-environmental research to public health to human security. Commonly available population data from Census is constrained both in space and time and does not capture population dynamics as functions of space and time. This imposes a significant limitation on the fidelity of event-based simulation models with sensitive space-time resolution. This paper describes ongoing development of high-resolution population distribution and dynamics models, at Oak Ridge National Laboratory, through spatial data integration and modeling with behavioral or activity-based mobility datasets for representing temporal dynamics of population. The model is resolved at 1 km resolution globally and describes the U.S. population for nighttime and daytime at 90m. Integration of such population data provides the opportunity to develop simulations and applications in critical infrastructure management from local to global scales.

  6. Super-resolution optical microscopy for studying membrane structure and dynamics.

    Science.gov (United States)

    Sezgin, Erdinc

    2017-07-12

    Investigation of cell membrane structure and dynamics requires high spatial and temporal resolution. The spatial resolution of conventional light microscopy is limited due to the diffraction of light. However, recent developments in microscopy enabled us to access the nano-scale regime spatially, thus to elucidate the nanoscopic structures in the cellular membranes. In this review, we will explain the resolution limit, address the working principles of the most commonly used super-resolution microscopy techniques and summarise their recent applications in the biomembrane field.

  7. The effect of acquisition interval and spatial resolution on dynamic cardiac imaging with a stationary SPECT camera

    International Nuclear Information System (INIS)

    Roberts, J; Maddula, R; Clackdoyle, R; DiBella, E; Fu, Z

    2007-01-01

    The current SPECT scanning paradigm that acquires images by slow rotation of multiple detectors in body-contoured orbits around the patient is not suited to the rapid collection of tomographically complete data. During rapid image acquisition, mechanical and patient safety constraints limit the detector orbit to circular paths at increased distances from the patient, resulting in decreased spatial resolution. We consider a novel dynamic rotating slant-hole (DyRoSH) SPECT camera that can collect full tomographic data every 2 s, employing three stationary detectors mounted with slant-hole collimators that rotate at 30 rpm. Because the detectors are stationary, they can be placed much closer to the patient than is possible with conventional SPECT systems. We propose that the decoupling of the detector position from the mechanics of rapid image acquisition offers an additional degree of freedom which can be used to improve accuracy in measured kinetic parameter estimates. With simulations and list-mode reconstructions, we consider the effects of different acquisition intervals on dynamic cardiac imaging, comparing a conventional three detector SPECT system with the proposed DyRoSH SPECT system. Kinetic parameters of a two-compartment model of myocardial perfusion for technetium-99m-teboroxime were estimated. When compared to a conventional SPECT scanner for the same acquisition periods, the proposed DyRoSH system shows equivalent or reduced bias or standard deviation values for the kinetic parameter estimates. The DyRoSH camera with a 2 s acquisition period does not show any improvement compared to a DyRoSH camera with a 10 s acquisition period

  8. The effect of acquisition interval and spatial resolution on dynamic cardiac imaging with a stationary SPECT camera

    Science.gov (United States)

    Roberts, J.; Maddula, R.; Clackdoyle, R.; Di Bella, E.; Fu, Z.

    2007-08-01

    The current SPECT scanning paradigm that acquires images by slow rotation of multiple detectors in body-contoured orbits around the patient is not suited to the rapid collection of tomographically complete data. During rapid image acquisition, mechanical and patient safety constraints limit the detector orbit to circular paths at increased distances from the patient, resulting in decreased spatial resolution. We consider a novel dynamic rotating slant-hole (DyRoSH) SPECT camera that can collect full tomographic data every 2 s, employing three stationary detectors mounted with slant-hole collimators that rotate at 30 rpm. Because the detectors are stationary, they can be placed much closer to the patient than is possible with conventional SPECT systems. We propose that the decoupling of the detector position from the mechanics of rapid image acquisition offers an additional degree of freedom which can be used to improve accuracy in measured kinetic parameter estimates. With simulations and list-mode reconstructions, we consider the effects of different acquisition intervals on dynamic cardiac imaging, comparing a conventional three detector SPECT system with the proposed DyRoSH SPECT system. Kinetic parameters of a two-compartment model of myocardial perfusion for technetium-99m-teboroxime were estimated. When compared to a conventional SPECT scanner for the same acquisition periods, the proposed DyRoSH system shows equivalent or reduced bias or standard deviation values for the kinetic parameter estimates. The DyRoSH camera with a 2 s acquisition period does not show any improvement compared to a DyRoSH camera with a 10 s acquisition period.

  9. Viriato: a Fourier-Hermite spectral code for strongly magnetised fluid-kinetic plasma dynamics

    Science.gov (United States)

    Loureiro, Nuno; Dorland, William; Fazendeiro, Luis; Kanekar, Anjor; Mallet, Alfred; Zocco, Alessandro

    2015-11-01

    We report on the algorithms and numerical methods used in Viriato, a novel fluid-kinetic code that solves two distinct sets of equations: (i) the Kinetic Reduced Electron Heating Model equations [Zocco & Schekochihin, 2011] and (ii) the kinetic reduced MHD (KRMHD) equations [Schekochihin et al., 2009]. Two main applications of these equations are magnetised (Alfvnénic) plasma turbulence and magnetic reconnection. Viriato uses operator splitting to separate the dynamics parallel and perpendicular to the ambient magnetic field (assumed strong). Along the magnetic field, Viriato allows for either a second-order accurate MacCormack method or, for higher accuracy, a spectral-like scheme. Perpendicular to the field Viriato is pseudo-spectral, and the time integration is performed by means of an iterative predictor-corrector scheme. In addition, a distinctive feature of Viriato is its spectral representation of the parallel velocity-space dependence, achieved by means of a Hermite representation of the perturbed distribution function. A series of linear and nonlinear benchmarks and tests are presented, with focus on 3D decaying kinetic turbulence. Work partially supported by Fundação para a Ciência e Tecnologia via Grants UID/FIS/50010/2013 and IF/00530/2013.

  10. Investigation of Coal-biomass Catalytic Gasification using Experiments, Reaction Kinetics and Computational Fluid Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Battaglia, Francine [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Agblevor, Foster [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Klein, Michael [Univ. of Delaware, Newark, DE (United States); Sheikhi, Reza [Northeastern Univ., Boston, MA (United States)

    2015-12-31

    A collaborative effort involving experiments, kinetic modeling, and computational fluid dynamics (CFD) was used to understand co-gasification of coal-biomass mixtures. The overall goal of the work was to determine the key reactive properties for coal-biomass mixed fuels. Sub-bituminous coal was mixed with biomass feedstocks to determine the fluidization and gasification characteristics of hybrid poplar wood, switchgrass and corn stover. It was found that corn stover and poplar wood were the best feedstocks to use with coal. The novel approach of this project was the use of a red mud catalyst to improve gasification and lower gasification temperatures. An important results was the reduction of agglomeration of the biomass using the catalyst. An outcome of this work was the characterization of the chemical kinetics and reaction mechanisms of the co-gasification fuels, and the development of a set of models that can be integrated into other modeling environments. The multiphase flow code, MFIX, was used to simulate and predict the hydrodynamics and co-gasification, and results were validated with the experiments. The reaction kinetics modeling was used to develop a smaller set of reactions for tractable CFD calculations that represented the experiments. Finally, an efficient tool was developed, MCHARS, and coupled with MFIX to efficiently simulate the complex reaction kinetics.

  11. Kinetic and structural fragility—a correlation between structures and dynamics in metallic liquids and glasses

    International Nuclear Information System (INIS)

    Kelton, K F

    2017-01-01

    The liquid phase remains poorly understood. In many cases, the densities of liquids and their crystallized solid phases are similar, but since they are amorphous they lack the spatial order of the solid. Their dynamical properties change remarkably over a very small temperature range. At high temperatures, near their melting temperature, liquids flow easily under shear. However, only a few hundred degrees lower flow effectively ceases, as the liquid transforms into a solid-like glass. This temperature-dependent dynamical behavior is frequently characterized by the concept of kinetic fragility (or, generally, simply fragility). Fragility is believed to be an important quantity in glass formation, making it of significant practical interest. The microscopic origin of fragility remains unclear, however, making it also of fundamental interest. It is widely (although not uniformly) believed that the dynamical behavior is linked to the atomic structure of the liquid, yet experimental studies show that although the viscosity changes by orders of magnitude with temperature, the structural change is barely perceptible. In this article the concept of fragility is discussed, building to a discussion of recent results in metallic glass-forming liquids that demonstrate the presumed connection between structural and dynamical changes. In particular, it becomes possible to define a structural fragility parameter that can be linked with the kinetic fragility. (topical review)

  12. Marine Microorganisms as Source of Stereoselective Esterases and Ketoreductases: Kinetic Resolution of a Prostaglandin Intermediate

    KAUST Repository

    De Vitis, Valerio; Guidi, Benedetta; Contente, Martina Letizia; Granato, Tiziana Mariarita; Conti, Paola; Molinari, Francesco; Crotti, Elena; Mapelli, Francesca; Borin, Sara S.; Daffonchio, Daniele; Romano, Diego

    2014-01-01

    A screening among bacterial strains isolated from water-brine interface of the deep hypersaline anoxic basins (DHABs) of the Eastern Mediterranean was carried out for the biocatalytical resolution of racemic propyl ester of anti-2-oxotricyclo[2.2.1.0]heptan-7-carboxylic acid (R,S)-1, a key intermediate for the synthesis of d-cloprostenol. Bacillus horneckiae 15A gave highly stereoselective reduction of (R,S)-1, whereas Halomonas aquamarina 9B enantioselectively hydrolysed (R,S)-1; in both cases, enantiomerically pure unreacted (R)-1 could be easily recovered and purified at molar conversion below 57–58 %, showing the potential of DHAB extremophile microbiome and marine-derived enzymes in stereoselective biocatalysis.

  13. Marine Microorganisms as Source of Stereoselective Esterases and Ketoreductases: Kinetic Resolution of a Prostaglandin Intermediate

    KAUST Repository

    De Vitis, Valerio

    2014-09-30

    A screening among bacterial strains isolated from water-brine interface of the deep hypersaline anoxic basins (DHABs) of the Eastern Mediterranean was carried out for the biocatalytical resolution of racemic propyl ester of anti-2-oxotricyclo[2.2.1.0]heptan-7-carboxylic acid (R,S)-1, a key intermediate for the synthesis of d-cloprostenol. Bacillus horneckiae 15A gave highly stereoselective reduction of (R,S)-1, whereas Halomonas aquamarina 9B enantioselectively hydrolysed (R,S)-1; in both cases, enantiomerically pure unreacted (R)-1 could be easily recovered and purified at molar conversion below 57–58 %, showing the potential of DHAB extremophile microbiome and marine-derived enzymes in stereoselective biocatalysis.

  14. Universal Critical Dynamics in High Resolution Neuronal Avalanche Data

    Science.gov (United States)

    Friedman, Nir; Ito, Shinya; Brinkman, Braden A. W.; Shimono, Masanori; DeVille, R. E. Lee; Dahmen, Karin A.; Beggs, John M.; Butler, Thomas C.

    2012-05-01

    The tasks of neural computation are remarkably diverse. To function optimally, neuronal networks have been hypothesized to operate near a nonequilibrium critical point. However, experimental evidence for critical dynamics has been inconclusive. Here, we show that the dynamics of cultured cortical networks are critical. We analyze neuronal network data collected at the individual neuron level using the framework of nonequilibrium phase transitions. Among the most striking predictions confirmed is that the mean temporal profiles of avalanches of widely varying durations are quantitatively described by a single universal scaling function. We also show that the data have three additional features predicted by critical phenomena: approximate power law distributions of avalanche sizes and durations, samples in subcritical and supercritical phases, and scaling laws between anomalous exponents.

  15. Effects of Resolution on the Simulation of Boundary-layer Clouds and the Partition of Kinetic Energy to Subgrid Scales

    Directory of Open Access Journals (Sweden)

    Anning Cheng

    2010-02-01

    Full Text Available Seven boundary-layer cloud cases are simulated with UCLA-LES (The University of California, Los Angeles – large eddy simulation model with different horizontal and vertical gridspacing to investigate how the results depend on gridspacing. Some variables are more sensitive to horizontal gridspacing, while others are more sensitive to vertical gridspacing, and still others are sensitive to both horizontal and vertical gridspacings with similar or opposite trends. For cloud-related variables having the opposite dependence on horizontal and vertical gridspacings, changing the gridspacing proportionally in both directions gives the appearance of convergence. In this study, we mainly discuss the impact of subgrid-scale (SGS kinetic energy (KE on the simulations with coarsening of horizontal and vertical gridspacings. A running-mean operator is used to separate the KE of the high-resolution benchmark simulations into that of resolved scales of coarse-resolution simulations and that of SGSs. The diagnosed SGS KE is compared with that parameterized by the Smagorinsky-Lilly SGS scheme at various gridspacings. It is found that the parameterized SGS KE for the coarse-resolution simulations is usually underestimated but the resolved KE is unrealistically large, compared to benchmark simulations. However, the sum of resolved and SGS KEs is about the same for simulations with various gridspacings. The partitioning of SGS and resolved heat and moisture transports is consistent with that of SGS and resolved KE, which means that the parameterized transports are underestimated but resolved-scale transports are overestimated. On the whole, energy shifts to large-scales as the horizontal gridspacing becomes coarse, hence the size of clouds and the resolved circulation increase, the clouds become more stratiform-like with an increase in cloud fraction, cloud liquid-water path and surface precipitation; when coarse vertical gridspacing is used, cloud sizes do not

  16. The kinetics of dynamic recrystallization of a low carbon vanadium-nitride microalloyed steel

    International Nuclear Information System (INIS)

    Zhao, Baochun; Zhao, Tan; Li, Guiyan; Lu, Qiang

    2014-01-01

    Single-pass compression tests were performed on a Gleeble-3800 thermo-mechanical simulator to study the dynamic recrystallization behavior of a low carbon vanadium-nitride microalloyed steel at the temperature in the range from 900 °C to 1050 °C and strain rate in the range from 0.1 s −1 to 10 s −1 . Based on the flow curves from the tests, the effects of temperature and strain rate on the dynamic recrystallization behavior were analyzed. With the assistance of the process parameters, constitutive equations were used to obtain the activation energy and hot working equation. The strain hardening rate versus stress curves were used to determine the critical stress (strain) or the peak stress (strain). The dependence of the characteristic values on Zener–Hollomon was found. The dynamic recrystallization kinetics model of the tested steel was constructed and the validity was confirmed based on the experimental results

  17. Extracting a respiratory signal from raw dynamic PET data that contain tracer kinetics.

    Science.gov (United States)

    Schleyer, P J; Thielemans, K; Marsden, P K

    2014-08-07

    Data driven gating (DDG) methods provide an alternative to hardware based respiratory gating for PET imaging. Several existing DDG approaches obtain a respiratory signal by observing the change in PET-counts within specific regions of acquired PET data. Currently, these methods do not allow for tracer kinetics which can interfere with the respiratory signal and introduce error. In this work, we produced a DDG method for dynamic PET studies that exhibit tracer kinetics. Our method is based on an existing approach that uses frequency-domain analysis to locate regions within raw PET data that are subject to respiratory motion. In the new approach, an optimised non-stationary short-time Fourier transform was used to create a time-varying 4D map of motion affected regions. Additional processing was required to ensure that the relationship between the sign of the respiratory signal and the physical direction of movement remained consistent for each temporal segment of the 4D map. The change in PET-counts within the 4D map during the PET acquisition was then used to generate a respiratory curve. Using 26 min dynamic cardiac NH3 PET acquisitions which included a hardware derived respiratory measurement, we show that tracer kinetics can severely degrade the respiratory signal generated by the original DDG method. In some cases, the transition of tracer from the liver to the lungs caused the respiratory signal to invert. The new approach successfully compensated for tracer kinetics and improved the correlation between the data-driven and hardware based signals. On average, good correlation was maintained throughout the PET acquisitions.

  18. Extracting a respiratory signal from raw dynamic PET data that contain tracer kinetics

    International Nuclear Information System (INIS)

    Schleyer, P J; Thielemans, K; Marsden, P K

    2014-01-01

    Data driven gating (DDG) methods provide an alternative to hardware based respiratory gating for PET imaging. Several existing DDG approaches obtain a respiratory signal by observing the change in PET-counts within specific regions of acquired PET data. Currently, these methods do not allow for tracer kinetics which can interfere with the respiratory signal and introduce error. In this work, we produced a DDG method for dynamic PET studies that exhibit tracer kinetics. Our method is based on an existing approach that uses frequency-domain analysis to locate regions within raw PET data that are subject to respiratory motion. In the new approach, an optimised non-stationary short-time Fourier transform was used to create a time-varying 4D map of motion affected regions. Additional processing was required to ensure that the relationship between the sign of the respiratory signal and the physical direction of movement remained consistent for each temporal segment of the 4D map. The change in PET-counts within the 4D map during the PET acquisition was then used to generate a respiratory curve. Using 26 min dynamic cardiac NH 3 PET acquisitions which included a hardware derived respiratory measurement, we show that tracer kinetics can severely degrade the respiratory signal generated by the original DDG method. In some cases, the transition of tracer from the liver to the lungs caused the respiratory signal to invert. The new approach successfully compensated for tracer kinetics and improved the correlation between the data-driven and hardware based signals. On average, good correlation was maintained throughout the PET acquisitions. (paper)

  19. Practical considerations for high spatial and temporal resolution dynamic transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, Michael R. [Materials Science and Technology Division, Chemistry and Materials Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-356, Livermore, CA 94550 (United States)], E-mail: armstrong30@llnl.gov; Boyden, Ken [Materials Science and Technology Division, Chemistry and Materials Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-356, Livermore, CA 94550 (United States); Browning, Nigel D. [Materials Science and Technology Division, Chemistry and Materials Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-356, Livermore, CA 94550 (United States); Department of Chemical Engineering and Materials Science, University of California-Davis, One Shields Avenue, Davis, CA 95616 (United States); Campbell, Geoffrey H.; Colvin, Jeffrey D.; De Hope, William J.; Frank, Alan M. [Materials Science and Technology Division, Chemistry and Materials Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-356, Livermore, CA 94550 (United States); Gibson, David J.; Hartemann, Fred [N Division, Physics and Advanced Technologies Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-280, Livermore, CA 94550 (United States); Kim, Judy S. [Materials Science and Technology Division, Chemistry and Materials Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-356, Livermore, CA 94550 (United States); Department of Chemical Engineering and Materials Science, University of California-Davis, One Shields Avenue, Davis, CA 95616 (United States); King, Wayne E.; La Grange, Thomas B.; Pyke, Ben J.; Reed, Bryan W.; Shuttlesworth, Richard M.; Stuart, Brent C.; Torralva, Ben R. [Materials Science and Technology Division, Chemistry and Materials Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-356, Livermore, CA 94550 (United States)

    2007-04-15

    Although recent years have seen significant advances in the spatial resolution possible in the transmission electron microscope (TEM), the temporal resolution of most microscopes is limited to video rate at best. This lack of temporal resolution means that our understanding of dynamic processes in materials is extremely limited. High temporal resolution in the TEM can be achieved, however, by replacing the normal thermionic or field emission source with a photoemission source. In this case the temporal resolution is limited only by the ability to create a short pulse of photoexcited electrons in the source, and this can be as short as a few femtoseconds. The operation of the photo-emission source and the control of the subsequent pulse of electrons (containing as many as 5x10{sup 7} electrons) create significant challenges for a standard microscope column that is designed to operate with a single electron in the column at any one time. In this paper, the generation and control of electron pulses in the TEM to obtain a temporal resolution <10{sup -6} s will be described and the effect of the pulse duration and current density on the spatial resolution of the instrument will be examined. The potential of these levels of temporal and spatial resolution for the study of dynamic materials processes will also be discussed.

  20. Practical considerations for high spatial and temporal resolution dynamic transmission electron microscopy

    International Nuclear Information System (INIS)

    Armstrong, Michael R.; Boyden, Ken; Browning, Nigel D.; Campbell, Geoffrey H.; Colvin, Jeffrey D.; De Hope, William J.; Frank, Alan M.; Gibson, David J.; Hartemann, Fred; Kim, Judy S.; King, Wayne E.; La Grange, Thomas B.; Pyke, Ben J.; Reed, Bryan W.; Shuttlesworth, Richard M.; Stuart, Brent C.; Torralva, Ben R.

    2007-01-01

    Although recent years have seen significant advances in the spatial resolution possible in the transmission electron microscope (TEM), the temporal resolution of most microscopes is limited to video rate at best. This lack of temporal resolution means that our understanding of dynamic processes in materials is extremely limited. High temporal resolution in the TEM can be achieved, however, by replacing the normal thermionic or field emission source with a photoemission source. In this case the temporal resolution is limited only by the ability to create a short pulse of photoexcited electrons in the source, and this can be as short as a few femtoseconds. The operation of the photo-emission source and the control of the subsequent pulse of electrons (containing as many as 5x10 7 electrons) create significant challenges for a standard microscope column that is designed to operate with a single electron in the column at any one time. In this paper, the generation and control of electron pulses in the TEM to obtain a temporal resolution -6 s will be described and the effect of the pulse duration and current density on the spatial resolution of the instrument will be examined. The potential of these levels of temporal and spatial resolution for the study of dynamic materials processes will also be discussed

  1. Dynamic PET reconstruction using temporal patch-based low rank penalty for ROI-based brain kinetic analysis

    International Nuclear Information System (INIS)

    Kim, Kyungsang; Ye, Jong Chul; Son, Young Don; Cho, Zang Hee; Bresler, Yoram; Ra, Jong Beom

    2015-01-01

    Dynamic positron emission tomography (PET) is widely used to measure changes in the bio-distribution of radiopharmaceuticals within particular organs of interest over time. However, to retain sufficient temporal resolution, the number of photon counts in each time frame must be limited. Therefore, conventional reconstruction algorithms such as the ordered subset expectation maximization (OSEM) produce noisy reconstruction images, thus degrading the quality of the extracted time activity curves (TACs). To address this issue, many advanced reconstruction algorithms have been developed using various spatio-temporal regularizations. In this paper, we extend earlier results and develop a novel temporal regularization, which exploits the self-similarity of patches that are collected in dynamic images. The main contribution of this paper is to demonstrate that the correlation of patches can be exploited using a low-rank constraint that is insensitive to global intensity variations. The resulting optimization framework is, however, non-Lipschitz and non-convex due to the Poisson log-likelihood and low-rank penalty terms. Direct application of the conventional Poisson image deconvolution by an augmented Lagrangian (PIDAL) algorithm is, however, problematic due to its large memory requirements, which prevents its parallelization. Thus, we propose a novel optimization framework using the concave-convex procedure (CCCP) by exploiting the Legendre–Fenchel transform, which is computationally efficient and parallelizable. In computer simulation and a real in vivo experiment using a high-resolution research tomograph (HRRT) scanner, we confirm that the proposed algorithm can improve image quality while also extracting more accurate region of interests (ROI) based kinetic parameters. Furthermore, we show that the total reconstruction time for HRRT PET is significantly accelerated using our GPU implementation, which makes the algorithm very practical in clinical environments

  2. Stereoselectivity and substrate specificity in the kinetic resolution of methyl-substituted 1-oxaspiro[2.5]octanes by Rhodotorula glutinis epoxide hydrolase

    NARCIS (Netherlands)

    Weijers, C.A.G.M.; Meeuwse, P.; Herpers, R.L.J.M.; Franssen, M.C.R.; Sudhölter, E.J.R.

    2005-01-01

    [GRAPHICS] The kinetic resolution of a range of methyl-substituted 1-oxaspiro[2.5]octanes by yeast epoxide hydrolase (YEH) from Rhodotorula glutinis has been investigated. The structural determinants of substrate specificity and stereoselectivity of YEH toward these substrates appeared to be the

  3. Chemo-enzymatic Baeyer-Villiger oxidation of 4-methylcyclohexanone via kinetic resolution of racemic carboxylic acids: direct access to enantioenriched lactone.

    Science.gov (United States)

    Drożdż, Agnieszka; Chrobok, Anna

    2016-01-21

    A new method for the asymmetric chemo-enzymatic Baeyer-Villiger oxidation of prochiral 4-methylcyclohexanone to (R)-4-methylcaprolactone in the presence of (±)-4-methyloctanoic acid, Candida Antarctica lipase B and 30% aq. H2O2 has been developed. A mechanism for the asymmetric induction based on kinetic resolution of racemic carboxylic acids is proposed.

  4. Determination of the crystal-melt interface kinetic coefficient from molecular dynamics simulations

    International Nuclear Information System (INIS)

    Monk, J; Mendelev, M I; Yang, Y; Asta, M; Hoyt, J J; Sun, D Y

    2010-01-01

    The generation and dissipation of latent heat at the moving solid–liquid boundary during non-equilibrium molecular dynamics (MD) simulations of crystallization can lead to significant underestimations of the interface mobility. In this work we examine the heat flow problem in detail for an embedded atom description of pure Ni and offer strategies to obtain an accurate value of the kinetic coefficient, μ. For free-solidification simulations in which the entire system is thermostated using a Nose–Hoover or velocity rescaling algorithm a non-uniform temperature profile is observed and a peak in the temperature is found at the interface position. It is shown that if the actual interface temperature, rather than the thermostat set point temperature, is used to compute the kinetic coefficient then μ is approximately a factor of 2 larger than previous estimates. In addition, we introduce a layered thermostat method in which several sub-regions, aligned normal to the crystallization direction, are indepently thermostated to a desired undercooling. We show that as the number of thermostats increases (i.e., as the width of each independently thermostated layer decreases) the kinetic coefficient converges to a value consistent with that obtained using a single thermostat and the calculated interface temperature. Also, the kinetic coefficient was determined from an analysis of the equilibrium fluctuations of the solid–liquid interface position. We demonstrate that the kinetic coefficient obtained from the relaxation times of the fluctuation spectrum is equivalent to the two values obtained from free-solidification simulations provided a simple correction is made for the contribution of heat flow controlled interface motion. Finally, a one-dimensional phase field model that captures the effect of thermostats has been developed. The mesoscale model reproduces qualitatively the results from MD simulations and thus allows for an a priori estimate of the accuracy of a

  5. Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state

    Science.gov (United States)

    Min, Wei; Xie, X. Sunney; Bagchi, Biman

    2009-08-01

    Enzyme is a dynamic entity with diverse time scales, ranging from picoseconds to seconds or even longer. Here we develop a rate theory for enzyme catalysis that includes conformational dynamics as cycling on a two-dimensional (2D) reaction free energy surface involving an intrinsic reaction coordinate (X) and an enzyme conformational coordinate (Q). The validity of Michaelis-Menten (MM) equation, i.e., substrate concentration dependence of enzymatic velocity, is examined under a nonequilibrium steady state. Under certain conditions, the classic MM equation holds but with generalized microscopic interpretations of kinetic parameters. However, under other conditions, our rate theory predicts either positive (sigmoidal-like) or negative (biphasic-like) kinetic cooperativity due to the modified effective 2D reaction pathway on X-Q surface, which can explain non-MM dependence previously observed on many monomeric enzymes that involve slow or hysteretic conformational transitions. Furthermore, we find that a slow conformational relaxation during product release could retain the enzyme in a favorable configuration, such that enzymatic turnover is dynamically accelerated at high substrate concentrations. The effect of such conformation retainment in a nonequilibrium steady state is evaluated.

  6. A thermostatted kinetic theory model for event-driven pedestrian dynamics

    Science.gov (United States)

    Bianca, Carlo; Mogno, Caterina

    2018-06-01

    This paper is devoted to the modeling of the pedestrian dynamics by means of the thermostatted kinetic theory. Specifically the microscopic interactions among pedestrians and an external force field are modeled for simulating the evacuation of pedestrians from a metro station. The fundamentals of the stochastic game theory and the thermostatted kinetic theory are coupled for the derivation of a specific mathematical model which depicts the time evolution of the distribution of pedestrians at different exits of a metro station. The perturbation theory is employed in order to establish the stability analysis of the nonequilibrium stationary states in the case of a metro station consisting of two exits. A general sensitivity analysis on the initial conditions, the magnitude of the external force field and the number of exits is presented by means of numerical simulations which, in particular, show how the asymptotic distribution and the convergence time are affected by the presence of an external force field. The results show how, in evacuation conditions, the interaction dynamics among pedestrians can be negligible with respect to the external force. The important role of the thermostat term in allowing the reaching of the nonequilibrium stationary state is stressed out. Research perspectives are underlined at the end of paper, in particular for what concerns the derivation of frameworks that take into account the definition of local external actions and the introduction of the space and velocity dynamics.

  7. Kinetic modeling of particle dynamics in H− negative ion sources (invited)

    International Nuclear Information System (INIS)

    Hatayama, A.; Shibata, T.; Nishioka, S.; Ohta, M.; Yasumoto, M.; Nishida, K.; Yamamoto, T.; Miyamoto, K.; Fukano, A.; Mizuno, T.

    2014-01-01

    Progress in the kinetic modeling of particle dynamics in H − negative ion source plasmas and their comparisons with experiments are reviewed, and discussed with some new results. Main focus is placed on the following two topics, which are important for the research and development of large negative ion sources and high power H − ion beams: (i) Effects of non-equilibrium features of EEDF (electron energy distribution function) on H − production, and (ii) extraction physics of H − ions and beam optics

  8. Kinetic modeling of particle dynamics in H{sup −} negative ion sources (invited)

    Energy Technology Data Exchange (ETDEWEB)

    Hatayama, A., E-mail: akh@ppl.appi.keio.ac.jp; Shibata, T.; Nishioka, S.; Ohta, M.; Yasumoto, M.; Nishida, K.; Yamamoto, T. [Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522 (Japan); Miyamoto, K. [Naruto University of Education, 748 Nakashima, Takashima, Naruto-cho, Naruto-shi, Tokushima 772-8502 (Japan); Fukano, A. [Monozukuri Department, Tokyo Metropolitan College of Industrial Technology, Shinagawa, Tokyo 140-0011 (Japan); Mizuno, T. [Department of Management Science, College of Engineering, Tamagawa University, Machida, Tokyo 194-8610 (Japan)

    2014-02-15

    Progress in the kinetic modeling of particle dynamics in H{sup −} negative ion source plasmas and their comparisons with experiments are reviewed, and discussed with some new results. Main focus is placed on the following two topics, which are important for the research and development of large negative ion sources and high power H{sup −} ion beams: (i) Effects of non-equilibrium features of EEDF (electron energy distribution function) on H{sup −} production, and (ii) extraction physics of H{sup −} ions and beam optics.

  9. Wetting kinetics of nanodroplets on lyophilic nanopillar-arrayed surfaces: A molecular dynamics study

    Science.gov (United States)

    Zong, Diyuan; Yang, Zhen; Duan, Yuanyuan

    2017-10-01

    Wetting kinetics of water droplets on substrates with lyophilic nanopillars was investigated using molecular dynamics simulations. Early spreading of the droplet is hindered by the nanopillars because of the penetration of the liquid which induce an extra dissipation in the droplet. Droplet spreading is mainly controlled by liquid viscosity and surface tension and not dependent on solid wettability. Propagation of the fringe film is hindered by the enhanced solid wettability because of the energy barrier introduced by the interaction between water molecules and nanopillars which increase with solid wettability.

  10. Dynamic Model of Basic Oxygen Steelmaking Process Based on Multi-zone Reaction Kinetics: Model Derivation and Validation

    Science.gov (United States)

    Rout, Bapin Kumar; Brooks, Geoff; Rhamdhani, M. Akbar; Li, Zushu; Schrama, Frank N. H.; Sun, Jianjun

    2018-04-01

    A multi-zone kinetic model coupled with a dynamic slag generation model was developed for the simulation of hot metal and slag composition during the basic oxygen furnace (BOF) operation. The three reaction zones (i) jet impact zone, (ii) slag-bulk metal zone, (iii) slag-metal-gas emulsion zone were considered for the calculation of overall refining kinetics. In the rate equations, the transient rate parameters were mathematically described as a function of process variables. A micro and macroscopic rate calculation methodology (micro-kinetics and macro-kinetics) were developed to estimate the total refining contributed by the recirculating metal droplets through the slag-metal emulsion zone. The micro-kinetics involves developing the rate equation for individual droplets in the emulsion. The mathematical models for the size distribution of initial droplets, kinetics of simultaneous refining of elements, the residence time in the emulsion, and dynamic interfacial area change were established in the micro-kinetic model. In the macro-kinetics calculation, a droplet generation model was employed and the total amount of refining by emulsion was calculated by summing the refining from the entire population of returning droplets. A dynamic FetO generation model based on oxygen mass balance was developed and coupled with the multi-zone kinetic model. The effect of post-combustion on the evolution of slag and metal composition was investigated. The model was applied to a 200-ton top blowing converter and the simulated value of metal and slag was found to be in good agreement with the measured data. The post-combustion ratio was found to be an important factor in controlling FetO content in the slag and the kinetics of Mn and P in a BOF process.

  11. The Dynamic Range of Ultra-High Resolution Cryogenic Gamma-ray Spectrometers

    International Nuclear Information System (INIS)

    Ali, S; Terracol, S F; Drury, O B; Friedrich, S

    2005-01-01

    We are developing high-resolution cryogenic gamma-ray spectrometers for nuclear science and non-proliferation applications. The gamma-ray detectors are composed of a bulk superconducting Sn foil absorber attached to multilayer Mo/Cu transition-edge sensors (TES). The energy resolution achieved with a 1 x 1 x 0.25 mm 3 Sn absorber is 50 -90eV for γ-rays up to 100 keV and it decreases for large absorber sizes. We discuss the trade-offs between energy resolution and dynamic range, as well as development of TES arrays for higher count rates and better sensitivity

  12. The dynamic range of ultra-high-resolution cryogenic gamma-ray spectrometers

    Energy Technology Data Exchange (ETDEWEB)

    Ali, Shafinaz [Advanced Detector Group, Lawrence Livermore National Laboratory, 7000 East Avenue, L-270, Livermore, CA 94550 (United States); Terracol, Stephane F. [Advanced Detector Group, Lawrence Livermore National Laboratory, 7000 East Avenue, L-270, Livermore, CA 94550 (United States); Drury, Owen B. [Advanced Detector Group, Lawrence Livermore National Laboratory, 7000 East Avenue, L-270, Livermore, CA 94550 (United States); Friedrich, Stephan [Advanced Detector Group, Lawrence Livermore National Laboratory, 7000 East Avenue, L-270, Livermore, CA 94550 (United States)]. E-mail: friedrich1@llnl.gov

    2006-04-15

    We are developing high-resolution cryogenic gamma-ray spectrometers for nuclear science and non-proliferation applications. The gamma-ray detectors are composed of a bulk superconducting Sn foil absorber attached to a multilayer Mo/Cu transition-edge sensor (TES). The energy resolution of a detector with a 1x1x0.25 mm{sup 3} Sn absorber is 50-90 eV FWHM for {gamma}-rays up to 100 keV, and it decreases for larger absorbers. Here, we present the detector performance for different absorber volumes, and discuss the trade-offs between energy resolution and dynamic range.

  13. Sub-minute kinetics of human red cell fumarase: 1 H spin-echo NMR spectroscopy and 13 C rapid-dissolution dynamic nuclear polarization.

    Science.gov (United States)

    Shishmarev, Dmitry; Wright, Alan J; Rodrigues, Tiago B; Pileio, Giuseppe; Stevanato, Gabriele; Brindle, Kevin M; Kuchel, Philip W

    2018-03-01

    Fumarate is an important probe of metabolism in hyperpolarized magnetic resonance imaging and spectroscopy. It is used to detect the release of fumarase in cancer tissues, which is associated with necrosis and drug treatment. Nevertheless, there are limited reports describing the detailed kinetic studies of this enzyme in various cells and tissues. Thus, we aimed to evaluate the sub-minute kinetics of human red blood cell fumarase using nuclear magnetic resonance (NMR) spectroscopy, and to provide a quantitative description of the enzyme that is relevant to the use of fumarate as a probe of cell rupture. The fumarase reaction was studied using time courses of 1 H spin-echo and 13 C-NMR spectra. 1 H-NMR experiments showed that the fumarase reaction in hemolysates is sufficiently rapid to make its kinetics amenable to study in a period of approximately 3 min, a timescale characteristic of hyperpolarized 13 C-NMR spectroscopy. The rapid-dissolution dynamic nuclear polarization (RD-DNP) technique was used to hyperpolarize [1,4- 13 C]fumarate, which was injected into concentrated hemolysates. The kinetic data were analyzed using recently developed FmR α analysis and modeling of the enzymatic reaction using Michaelis-Menten equations. In RD-DNP experiments, the decline in the 13 C-NMR signal from fumarate, and the concurrent rise and fall of that from malate, were captured with high spectral resolution and signal-to-noise ratio, which allowed the robust quantification of fumarase kinetics. The kinetic parameters obtained indicate the potential contribution of hemolysis to the overall rate of the fumarase reaction when 13 C-NMR RD-DNP is used to detect necrosis in animal models of implanted tumors. The analytical procedures developed will be applicable to studies of other rapid enzymatic reactions using conventional and hyperpolarized substrate NMR spectroscopy. Copyright © 2018 John Wiley & Sons, Ltd.

  14. Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein-Ligand Residence Times.

    Science.gov (United States)

    Mollica, Luca; Theret, Isabelle; Antoine, Mathias; Perron-Sierra, Françoise; Charton, Yves; Fourquez, Jean-Marie; Wierzbicki, Michel; Boutin, Jean A; Ferry, Gilles; Decherchi, Sergio; Bottegoni, Giovanni; Ducrot, Pierre; Cavalli, Andrea

    2016-08-11

    Ligand-target residence time is emerging as a key drug discovery parameter because it can reliably predict drug efficacy in vivo. Experimental approaches to binding and unbinding kinetics are nowadays available, but we still lack reliable computational tools for predicting kinetics and residence time. Most attempts have been based on brute-force molecular dynamics (MD) simulations, which are CPU-demanding and not yet particularly accurate. We recently reported a new scaled-MD-based protocol, which showed potential for residence time prediction in drug discovery. Here, we further challenged our procedure's predictive ability by applying our methodology to a series of glucokinase activators that could be useful for treating type 2 diabetes mellitus. We combined scaled MD with experimental kinetics measurements and X-ray crystallography, promptly checking the protocol's reliability by directly comparing computational predictions and experimental measures. The good agreement highlights the potential of our scaled-MD-based approach as an innovative method for computationally estimating and predicting drug residence times.

  15. Photodissociation dynamics of propene at 157.6 nm: Kinetic energy distributions and branching ratios

    International Nuclear Information System (INIS)

    Lee, S.-H.; Lee, Y.-Y.; Lee, Yuan T.; Yang Xueming

    2003-01-01

    Photodissociation dynamics of propene at 157.6 nm has been investigated in a molecular beam apparatus using the photofragment translational spectroscopic technique combined with the vacuum ultraviolet ionization method. Eleven photofragments have been successfully detected and ascribed to eight (five binary and three triple) dissociation channels: namely, C 3 H 5 +H, C 3 H 4 +H+H, C 3 H 4 +H 2 , C 3 H 3 +H 2 +H, C 2 H 4 +CH 2 , C 2 H 3 +CH 3 , C 2 H 2 +CH 4 , and C 2 H 2 +CH 3 +H. Their branching ratios have been determined to be 1%, 7%, 2 H 2 +CH 3 +H channel. In addition, the averaged kinetic energy releases and the fractions in translational energy have also been determined from the measured kinetic energy distributions. For the binary dissociation channels, the fractions in translational energy are less than 18% except the C 3 H 5 +H channel, whereas they are more than 42% for the triple dissociation channels. An intriguing finding indicates that the C 2 H 4 +CH 2 channel has a nearly identical kinetic energy distribution and a similar branching ratio to the C 2 H 3 +CH 3 channel, although the former undergoes a three-center elimination process different from the C-C bond rupture occurring in the latter

  16. Dynamic Ureas with Fast and pH-Independent Hydrolytic Kinetics.

    Science.gov (United States)

    Cai, Kaimin; Ying, Hanze; Cheng, Jianjun

    2018-04-06

    Low cost, high performance hydrolysable polymers are of great importance in biomedical applications and materials industries. While many applications require materials to have a degradation profile insensitive to external pH to achieve consistent release profiles under varying conditions, hydrolysable chemistry techniques developed so far have pH-dependent hydrolytic kinetics. This work reports the design and synthesis of a new type of hydrolysable polymer that has identical hydrolysis kinetics from pH 3 to 11. The unprecedented pH independent hydrolytic kinetics of the aryl ureas were shown to be related to the dynamic bond dissociation controlled hydrolysis mechanism; the resulting hindered poly(aryl urea) can be degraded with a hydrolysis half-life of 10 min in solution. More importantly, these fast degradable hindered aromatic polyureas can be easily prepared by addition polymerization from commercially available monomers and are resistant to hydrolysis in solid form for months under ambient storage conditions. The combined features of good stability in solid state and fast hydrolysis at various pH values is unprecedented in polyurea material, and will have implications for materials design and applications, such as sacrificial coatings and biomaterials. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Simulation of the hot flow behaviour of a medium carbon microalloyed steel. Part 2. Dynamic recrystallization: onset and kinetics

    International Nuclear Information System (INIS)

    Cabrera, J.M.; Al Omar, A.; Prado, J.M.

    1997-01-01

    According to the part 1 of this work, in this second part the dynamic recrystallization of a commercial medium carbon microalloyed steel is characterized from the point of view of its onset and kinetics. For this purpose uniaxial hot compression tests were carried out over a range of five orders of magnitude in strain rate and 300 degree centigree of temperature. Experimental results are compared with those reported in the literature and the possible effect of dynamic precipitation is also analyzed. It is verified that the kinetics of dynamics recrystallization can balefully be described by the classical Avrami equation. (Author) 42 refs

  18. Kinetics of gamma quanta initiated difluoroethane chlorization in inert solvent in dynamic conditions

    International Nuclear Information System (INIS)

    Begishev, I.R.; Poluehktov, V.A.

    1979-01-01

    Studied is the kinetics of asymmetric difluoroethane chlorination under dynamic conditions where difluoroethane and chlorine are passed through liquid tetrachloromethane layer. It is shown that initiating chlorination of asymmetric difluoroethane by gamma quanta in the dose and temperature ranges of 2-50 rad/s and -30-100 deg C respectively brings to the significant increase of the reaction rate and unusually high trend for halogenated hydrocarbons, i.e. practically 1, 1, 1 - difluorochloroethane with quantitative yield is formed. In this case radiation chemical yield G=10 4 -10 5 is achieved. It is shown that the chlorination process under dynamic conditions, complicated by the transport of initial reagents from a gas phase to a liquid one and reaction products from a liquid phase to a gas one, is described satisfactorily by the model of ideal substitution reactor

  19. Simultaneous measurement of amyloid fibril formation by dynamic light scattering and fluorescence reveals complex aggregation kinetics.

    Directory of Open Access Journals (Sweden)

    Aaron M Streets

    Full Text Available An apparatus that combines dynamic light scattering and Thioflavin T fluorescence detection is used to simultaneously probe fibril formation in polyglutamine peptides, the aggregating subunit associated with Huntington's disease, in vitro. Huntington's disease is a neurodegenerative disorder in a class of human pathologies that includes Alzheimer's and Parkinson's disease. These pathologies are all related by the propensity of their associated protein or polypeptide to form insoluble, β-sheet rich, amyloid fibrils. Despite the wide range of amino acid sequence in the aggregation prone polypeptides associated with these diseases, the resulting amyloids display strikingly similar physical structure, an observation which suggests a physical basis for amyloid fibril formation. Thioflavin T fluorescence reports β-sheet fibril content while dynamic light scattering measures particle size distributions. The combined techniques allow elucidation of complex aggregation kinetics and are used to reveal multiple stages of amyloid fibril formation.

  20. Derivation of fluid dynamics from kinetic theory with the 14-moment approximation

    International Nuclear Information System (INIS)

    Denicol, G.S.; Molnar, E.; Niemi, H.; Rischke, D.H.

    2012-01-01

    We review the traditional derivation of the fluid-dynamical equations from kinetic theory according to Israel and Stewart. We show that their procedure to close the fluid-dynamical equations of motion is not unique. Their approach contains two approximations, the first being the so-called 14-moment approximation to truncate the single-particle distribution function. The second consists in the choice of equations of motion for the dissipative currents. Israel and Stewart used the second moment of the Boltzmann equation, but this is not the only possible choice. In fact, there are infinitely many moments of the Boltzmann equation which can serve as equations of motion for the dissipative currents. All resulting equations of motion have the same form, but the transport coefficients are different in each case. (orig.)

  1. Mechanistic basis for high stereoselectivity and broad substrate scope in the (salen)Co(III)-catalyzed hydrolytic kinetic resolution.

    Science.gov (United States)

    Ford, David D; Nielsen, Lars P C; Zuend, Stephan J; Musgrave, Charles B; Jacobsen, Eric N

    2013-10-16

    In the (salen)Co(III)-catalyzed hydrolytic kinetic resolution (HKR) of terminal epoxides, the rate- and stereoselectivity-determining epoxide ring-opening step occurs by a cooperative bimetallic mechanism with one Co(III) complex acting as a Lewis acid and another serving to deliver the hydroxide nucleophile. In this paper, we analyze the basis for the extraordinarily high stereoselectivity and broad substrate scope observed in the HKR. We demonstrate that the stereochemistry of each of the two (salen)Co(III) complexes in the rate-determining transition structure is important for productive catalysis: a measurable rate of hydrolysis occurs only if the absolute stereochemistry of each of these (salen)Co(III) complexes is the same. Experimental and computational studies provide strong evidence that stereochemical communication in the HKR is mediated by the stepped conformation of the salen ligand, and not the shape of the chiral diamine backbone of the ligand. A detailed computational analysis reveals that the epoxide binds the Lewis acidic Co(III) complex in a well-defined geometry imposed by stereoelectronic rather than steric effects. This insight serves as the basis of a complete stereochemical and transition structure model that sheds light on the reasons for the broad substrate generality of the HKR.

  2. Kinetic energy measurement of hydrogen in LHD peripheral plasma with a multi-wavelength-range fine-resolution spectrometer

    International Nuclear Information System (INIS)

    Fujii, Keisuke; Mizushiri, Keisuke; Nishioka, Tomomi; Shikama, Taiichi; Iwamae, Atsushi; Goto, Motoshi; Morita, Shigeru; Hasuo, Masahiro

    2010-01-01

    We have simultaneously measured high resolution emission spectra of the hydrogen atomic Balmer-α, -β, -γ lines and molecular Fulcher-α band for a LHD peripheral plasma generated under a central magnetic field strength of 0.4 T. It is found that the velocity distributions of excited atoms calculated from the Balmer-α, -β, and -γ line shapes show similar profiles to each other. The translational kinetic energy corresponding to the average velocity is about 13 eV, which is about 300 times larger than the rotational energy of hydrogen molecules estimated from the line intensities in the Fulcher-α band. The velocity distributions differ from Maxwellian and have a high velocity tail over 1x10 5 m/s. A correlation between the high velocity tail and the electron temperature and density is seen and suggesting the excited atoms having such high velocities to be generated by the charge exchange collisions from high velocity protons in the peripheral region.

  3. A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Fabrizio Marinelli

    2009-08-01

    Full Text Available Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.

  4. Analyzing the Molecular Kinetics of Water Spreading on Hydrophobic Surfaces via Molecular Dynamics Simulation.

    Science.gov (United States)

    Zhao, Lei; Cheng, Jiangtao

    2017-09-07

    In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation. The hydrophobic surfaces are composed of amorphous polytetrafluoroethylene (PTFE) with a static contact angle of ~112.4° for water. On the basis of the molecular kinetic theory (MKT), the influences of both viscous damping and solid-liquid retarding were analyzed in evaluating contact line friction, which characterizes the frictional force on the contact line. The unit displacement length on PTFE was estimated to be ~0.621 nm and is ~4 times as long as the bond length of C-C backbone. The static friction coefficient was found to be ~[Formula: see text] Pa·s, which is on the same order of magnitude as the dynamic viscosity of water, and increases with the droplet size. A nondimensional number defined by the ratio of the standard deviation of wetting velocity to the characteristic wetting velocity was put forward to signify the strength of the inherent contact line fluctuation and unveil the mechanism of enhanced energy dissipation in nanoscale, whereas such effect would become insignificant in macroscale. Moreover, regarding a liquid droplet on hydrophobic or superhydrophobic surfaces, an approximate solution to the base radius development was derived by an asymptotic expansion approach.

  5. High resolution neutron spectroscopy - a tool for the investigation of dynamics of polymers and soft matter

    International Nuclear Information System (INIS)

    Monkenbusch, M.; Richter, D.

    2007-01-01

    Neutron scattering, with the ability to vary the contrast of molecular items by hydrogen/deuterium exchanges, is an invaluable tool for soft matter research. Besides the structural information on the mesoscopic scale that is obtained by diffraction methods like small angle neutron scattering, the slow dynamics of molecular motion on mesoscopic scale is accessible by high resolution neutron spectroscopy. The basic features of neutron backscattering spectroscopy, and in particular neutron spin-echo spectroscopy, are presented, in combination with illustrations of results from polymer melt dynamics to protein dynamics which are obtained by these techniques. (authors)

  6. SYSTEM OF GUARANTEED RESOLUTION OF DYNAMIC CONFLICTS OF AIRCRAFTS IN REAL TIME

    Directory of Open Access Journals (Sweden)

    Svitlana Pavlova

    2017-03-01

    Full Text Available Purpose: The present work is devoted to improving of flight safety in civil aviation by creating and implementing a new system of resolution of dynamic conflict of aircrafts. The developed system is aimed at ensuring a guaranteed level of safety when resolution of rarefied conflict situations of aircraft in real-time. Methods: The proposed system is based on a new method of conflict resolution of aircraft on the basis of the theory of invariance. Results: The development of the system of conflict resolution of aircraft in real time and the implementation of the respective algorithms such control will ensure effective prevention of dangerous approaches. Discussion: The system is implemented as single unified equipment using satellite and radar navigation systems that will ensure the positioning of aircraft in real time. Provided that the system should be installed on all aircraft and integrated on board to properly ensure its functionality and interact with navigation systems.

  7. Towards high resolution mapping of 3-D mesoscale dynamics from observations

    Directory of Open Access Journals (Sweden)

    B. Buongiorno Nardelli

    2012-10-01

    Full Text Available The MyOcean R&D project MESCLA (MEsoSCaLe dynamical Analysis through combined model, satellite and in situ data was devoted to the high resolution 3-D retrieval of tracer and velocity fields in the oceans, based on the combination of in situ and satellite observations and quasi-geostrophic dynamical models. The retrieval techniques were also tested and compared with the output of a primitive equation model, with particular attention to the accuracy of the vertical velocity field as estimated through the Q vector formulation of the omega equation. The project focused on a test case, covering the region where the Gulf Stream separates from the US East Coast. This work demonstrated that innovative methods for the high resolution mapping of 3-D mesoscale dynamics from observations can be used to build the next generations of operational observation-based products.

  8. Super-resolution microscopy reveals cell wall dynamics and peptidoglycan architecture in ovococcal bacteria.

    Science.gov (United States)

    Wheeler, Richard; Mesnage, Stéphane; Boneca, Ivo G; Hobbs, Jamie K; Foster, Simon J

    2011-12-01

    Cell morphology and viability in Eubacteria is dictated by the architecture of peptidoglycan, the major and essential structural component of the cell wall. Although the biochemical composition of peptidoglycan is well understood, how the peptidoglycan architecture can accommodate the dynamics of growth and division while maintaining cell shape remains largely unknown. Here, we elucidate the peptidoglycan architecture and dynamics of bacteria with ovoid cell shape (ovococci), which includes a number of important pathogens, by combining biochemical analyses with atomic force and super-resolution microscopies. Atomic force microscopy analysis showed preferential orientation of the peptidoglycan network parallel to the short axis of the cell, with distinct architectural features associated with septal and peripheral wall synthesis. Super-resolution three-dimensional structured illumination fluorescence microscopy was applied for the first time in bacteria to unravel the dynamics of peptidoglycan assembly in ovococci. The ovococci have a unique peptidoglycan architecture and growth mode not observed in other model organisms. © 2011 Blackwell Publishing Ltd.

  9. xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

    International Nuclear Information System (INIS)

    McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

    2014-01-01

    A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP

  10. xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

    Energy Technology Data Exchange (ETDEWEB)

    McGreevy, Ryan; Singharoy, Abhishek [University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); Li, Qufei [The University of Chicago, Chicago, IL 60637 (United States); Zhang, Jingfen; Xu, Dong [University of Missouri, Columbia, MO 65211 (United States); Perozo, Eduardo [The University of Chicago, Chicago, IL 60637 (United States); Schulten, Klaus, E-mail: kschulte@ks.uiuc.edu [University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States)

    2014-09-01

    A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

  11. Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

    Science.gov (United States)

    Srinivas, Niranjan

    Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry. In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive. Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for

  12. Kinetic Behavior of on Various Cheeses under Constant and Dynamic Temperature

    Directory of Open Access Journals (Sweden)

    K. Kim

    2014-07-01

    Full Text Available In this study, we developed kinetic models to predict the growth of pathogenic Escherichia coli on cheeses during storage at constant and changing temperatures. A five-strain mixture of pathogenic E. coli was inoculated onto natural cheeses (Brie and Camembert and processed cheeses (sliced Mozzarella and sliced Cheddar at 3 to 4 log CFU/g. The inoculated cheeses were stored at 4, 10, 15, 25, and 30°C for 1 to 320 h, with a different storage time being used for each temperature. Total bacteria and E. coli cells were enumerated on tryptic soy agar and MacConkey sorbitol agar, respectively. E. coli growth data were fitted to the Baranyi model to calculate the maximum specific growth rate (μmax; log CFU/g/h, lag phase duration (LPD; h, lower asymptote (log CFU/g, and upper asymptote (log CFU/g. The kinetic parameters were then analyzed as a function of storage temperature, using the square root model, polynomial equation, and linear equation. A dynamic model was also developed for varying temperature. The model performance was evaluated against observed data, and the root mean square error (RMSE was calculated. At 4°C, E. coli cell growth was not observed on any cheese. However, E. coli growth was observed at 10°C to 30°C with a μmax of 0.01 to 1.03 log CFU/g/h, depending on the cheese. The μmax values increased as temperature increased, while LPD values decreased, and μmax and LPD values were different among the four types of cheese. The developed models showed adequate performance (RMSE = 0.176–0.337, indicating that these models should be useful for describing the growth kinetics of E. coli on various cheeses.

  13. Kinetic Behavior of Escherichia coli on Various Cheeses under Constant and Dynamic Temperature.

    Science.gov (United States)

    Kim, K; Lee, H; Gwak, E; Yoon, Y

    2014-07-01

    In this study, we developed kinetic models to predict the growth of pathogenic Escherichia coli on cheeses during storage at constant and changing temperatures. A five-strain mixture of pathogenic E. coli was inoculated onto natural cheeses (Brie and Camembert) and processed cheeses (sliced Mozzarella and sliced Cheddar) at 3 to 4 log CFU/g. The inoculated cheeses were stored at 4, 10, 15, 25, and 30°C for 1 to 320 h, with a different storage time being used for each temperature. Total bacteria and E. coli cells were enumerated on tryptic soy agar and MacConkey sorbitol agar, respectively. E. coli growth data were fitted to the Baranyi model to calculate the maximum specific growth rate (μ max; log CFU/g/h), lag phase duration (LPD; h), lower asymptote (log CFU/g), and upper asymptote (log CFU/g). The kinetic parameters were then analyzed as a function of storage temperature, using the square root model, polynomial equation, and linear equation. A dynamic model was also developed for varying temperature. The model performance was evaluated against observed data, and the root mean square error (RMSE) was calculated. At 4°C, E. coli cell growth was not observed on any cheese. However, E. coli growth was observed at 10°C to 30°C with a μ max of 0.01 to 1.03 log CFU/g/h, depending on the cheese. The μ max values increased as temperature increased, while LPD values decreased, and μ max and LPD values were different among the four types of cheese. The developed models showed adequate performance (RMSE = 0.176-0.337), indicating that these models should be useful for describing the growth kinetics of E. coli on various cheeses.

  14. Tracer kinetic modelling of tumour angiogenesis based on dynamic contrast-enhanced CT and MRI measurements

    Energy Technology Data Exchange (ETDEWEB)

    Brix, Gunnar [Federal Office for Radiation Protection, Department of Medical and Occupational Radiation Protection, Oberschleissheim (Germany); Bundesamt fuer Strahlenschutz (BfS), Abteilung fuer medizinischen und beruflichen Strahlenschutz, Oberschleissheim (Germany); Griebel, Juergen [Federal Office for Radiation Protection, Department of Medical and Occupational Radiation Protection, Oberschleissheim (Germany); Kiessling, Fabian [RWTH-Aachen University, Department of Experimental Molecular Imaging, Aachen (Germany); Wenz, Frederik [University Medical Center Mannheim, University of Heidelberg, Department of Radiation Oncology, Mannheim (Germany)

    2010-08-15

    Technical developments in both magnetic resonance imaging (MRI) and computed tomography (CT) have helped to reduce scan times and expedited the development of dynamic contrast-enhanced (DCE) imaging techniques. Since the temporal change of the image signal following the administration of a diffusible, extracellular contrast agent (CA) is related to the local blood supply and the extravasation of the CA into the interstitial space, DCE imaging can be used to assess tissue microvasculature and microcirculation. It is the aim of this review to summarize the biophysical and tracer kinetic principles underlying this emerging imaging technique offering great potential for non-invasive characterization of tumour angiogenesis. In the first part, the relevant contrast mechanisms are presented that form the basis to relate signal variations measured by serial CT and MRI to local tissue concentrations of the administered CA. In the second part, the concepts most widely used for tracer kinetic modelling of concentration-time courses derived from measured DCE image data sets are described in a consistent and unified manner to highlight their particular structure and assumptions as well as the relationships among them. Finally, the concepts presented are exemplified by the analysis of representative DCE data as well as discussed with respect to present and future applications in cancer diagnosis and therapy. Depending on the specific protocol used for the acquisition of DCE image data and the particular model applied for tracer kinetic analysis of the derived concentration-time courses, different aspects of tumour angiogenesis can be quantified in terms of well-defined physiological tissue parameters. DCE imaging offers promising prospects for improved tumour diagnosis, individualization of cancer treatment as well as the evaluation of novel therapeutic concepts in preclinical and early-stage clinical trials. (orig.)

  15. Gyrokinetic Electron and Fully Kinetic Ion Particle Simulation of Collisionless Plasma Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Yu Lin; Xueyi Wang; Liu Chen; Zhihong Lin

    2009-08-11

    Fully kinetic-particle simulations and hybrid simulations have been utilized for decades to investigate various fundamental plasma processes, such as magnetic reconnection, fast compressional waves, and wave-particle interaction. Nevertheless, due to disparate temporal and spatial scales between electrons and ions, existing fully kinetic-particle codes have to employ either unrealistically high electron-to-ion mass ratio, me/mi, or simulation domain limited to a few or a few ten's of the ion Larmor radii, or/and time much less than the global Alfven time scale in order to accommodate available computing resources. On the other hand, in the hybrid simulation, the ions are treated as fully kinetic particles but the electrons are treated as a massless fluid. The electron kinetic effects, e.g., wave-particle resonances and finite electron Larmor radius effects, are completely missing. Important physics, such as the electron transit time damping of fast compressional waves or the triggering mechanism of magnetic reconnection in collisionless plasmas is absent in the hybrid codes. Motivated by these considerations and noting that dynamics of interest to us has frequencies lower than the electron gyrofrequency, we planned to develop an innovative particle simulation model, gyrokinetic (GK) electrons and fully kinetic (FK) ions. In the GK-electron and FK-ion (GKe/FKi) particle simulation model, the rapid electron cyclotron motion is removed, while keeping finite electron Larmor radii, realistic me/mi ratio, wave-particle interactions, and off-diagonal components of electron pressure tensor. The computation power can thus be significantly improved over that of the full-particle codes. As planned in the project DE-FG02-05ER54826, we have finished the development of the new GK-electron and FK-ion scheme, finished its benchmark for a uniform plasma in 1-D, 2-D, and 3-D systems against linear waves obtained from analytical theories, and carried out a further convergence

  16. Gyrokinetic Electron and Fully Kinetic Ion Particle Simulation of Collisionless Plasma Dynamics

    International Nuclear Information System (INIS)

    Lin, Yu; Wang, Xueyi; Chen, Liu; Lin, Zhihong

    2009-01-01

    Fully kinetic-particle simulations and hybrid simulations have been utilized for decades to investigate various fundamental plasma processes, such as magnetic reconnection, fast compressional waves, and wave-particle interaction. Nevertheless, due to disparate temporal and spatial scales between electrons and ions, existing fully kinetic-particle codes have to employ either unrealistically high electron-to-ion mass ratio, me/mi, or simulation domain limited to a few or a few ten's of the ion Larmor radii, or/and time much less than the global Alfven time scale in order to accommodate available computing resources. On the other hand, in the hybrid simulation, the ions are treated as fully kinetic particles but the electrons are treated as a massless fluid. The electron kinetic effects, e.g., wave-particle resonances and finite electron Larmor radius effects, are completely missing. Important physics, such as the electron transit time damping of fast compressional waves or the triggering mechanism of magnetic reconnection in collisionless plasmas is absent in the hybrid codes. Motivated by these considerations and noting that dynamics of interest to us has frequencies lower than the electron gyrofrequency, we planned to develop an innovative particle simulation model, gyrokinetic (GK) electrons and fully kinetic (FK) ions. In the GK-electron and FK-ion (GKe/FKi) particle simulation model, the rapid electron cyclotron motion is removed, while keeping finite electron Larmor radii, realistic me/mi ratio, wave-particle interactions, and off-diagonal components of electron pressure tensor. The computation power can thus be significantly improved over that of the full-particle codes. As planned in the project DE-FG02-05ER54826, we have finished the development of the new GK-electron and FK-ion scheme, finished its benchmark for a uniform plasma in 1-D, 2-D, and 3-D systems against linear waves obtained from analytical theories, and carried out a further convergence test

  17. New approaches for the reliable in vitro assessment of binding affinity based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics.

    Science.gov (United States)

    Zeilinger, Markus; Pichler, Florian; Nics, Lukas; Wadsak, Wolfgang; Spreitzer, Helmut; Hacker, Marcus; Mitterhauser, Markus

    2017-12-01

    Resolving the kinetic mechanisms of biomolecular interactions have become increasingly important in early-phase drug development. Since traditional in vitro methods belong to dose-dependent assessments, binding kinetics is usually overlooked. The present study aimed at the establishment of two novel experimental approaches for the assessment of binding affinity of both, radiolabelled and non-labelled compounds targeting the A 3 R, based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics. A novel time-resolved competition assay was developed and applied to determine the K i of eight different A 3 R antagonists, using CHO-K1 cells stably expressing the hA 3 R. In addition, a new kinetic real-time cell-binding approach was established to quantify the rate constants k on and k off , as well as the dedicated K d of the A 3 R agonist [ 125 I]-AB-MECA. Furthermore, lipophilicity measurements were conducted to control influences due to physicochemical properties of the used compounds. Two novel real-time cell-binding approaches were successfully developed and established. Both experimental procedures were found to visualize the kinetic binding characteristics with high spatial and temporal resolution, resulting in reliable affinity values, which are in good agreement with values previously reported with traditional methods. Taking into account the lipophilicity of the A 3 R antagonists, no influences on the experimental performance and the resulting affinity were investigated. Both kinetic binding approaches comprise tracer administration and subsequent binding to living cells, expressing the dedicated target protein. Therefore, the experiments resemble better the true in vivo physiological conditions and provide important markers of cellular feedback and biological response.

  18. Reproducibility of intrarenal kinetics of Gd-DOTA with rabbits with dynamic MRI

    International Nuclear Information System (INIS)

    Grenier, N.; Broussin, J.; Barat, J.L.; Ducassou, D.

    1989-01-01

    Ten normal rabbits and seven rabbits with experimental acute renal failure by tubular necrosis were studied with dynamic MR to evaluate the reproducibility of intrarenal kinetics of Gd-DOTA. Sequential spin-echo sequences with short TR (200 msec)/TE (26 msec) were used yielding a 29 sec acquisition time. A usual semi-quantitative analysis of intrarenal contrast demonstrated the reproducilibity of some phases of the dynamic sequence in particular a drop in the signal within inner medulla between the third and the fourth minute after infusion. This effect, related to a high concentration of Gd-DOTA within the tubules was observed in 9 over 10 normal rabbits and in none of the rabbits with acute renal failure. The quantitative analysis calculation was based on relative signal intensity and contrast-to-noise ratio from the absolute signal intensity measure on regions-of-interest (ROI) on the cortex, outer medulla and inner medulla. No reproducibility of the variations with time of these parameters could be assessed. A gread number of factors of variations or error, mainly during the measurements of signal intensity with ROI, could explain this lack of reproducibility. At the present, dynamic MR is therefore not able to quantitatively evaluate the renal function. Only a semi-quantitative estimation of tubular concentration can be deduced [fr

  19. Many-body kinetics of dynamic nuclear polarization by the cross effect

    Science.gov (United States)

    Karabanov, A.; Wiśniewski, D.; Raimondi, F.; Lesanovsky, I.; Köckenberger, W.

    2018-03-01

    Dynamic nuclear polarization (DNP) is an out-of-equilibrium method for generating nonthermal spin polarization which provides large signal enhancements in modern diagnostic methods based on nuclear magnetic resonance. A particular instance is cross-effect DNP, which involves the interaction of two coupled electrons with the nuclear spin ensemble. Here we develop a theory for this important DNP mechanism and show that the nonequilibrium nuclear polarization buildup is effectively driven by three-body incoherent Markovian dissipative processes involving simultaneous state changes of two electrons and one nucleus. We identify different parameter regimes for effective polarization transfer and discuss under which conditions the polarization dynamics can be simulated by classical kinetic Monte Carlo methods. Our theoretical approach allows simulations of the polarization dynamics on an individual spin level for ensembles consisting of hundreds of nuclear spins. The insight obtained by these simulations can be used to find optimal experimental conditions for cross-effect DNP and to design tailored radical systems that provide optimal DNP efficiency.

  20. Kinetic modeling of the effect of solids retention time on methanethiol dynamics in anaerobic digestion.

    Science.gov (United States)

    Zhang, Dian; Strawn, Mary; Novak, John T; Wang, Zhi-Wu

    2018-07-01

    The highly volatile methanethiol (MT) with an extremely low odor threshold and distinctive putrid smell is often identified as a major odorous compound generated under anaerobic conditions. As an intermediate compound in the course of anaerobic digestion, the extent of MT emission is closely related to the time of anaerobic reaction. In this study, lab-scale anaerobic digesters were operated at solids retention time (SRTs) of 15, 20, 25, 30, 40 and 50 days to investigate the effect of SRT on MT emission. The experimental results demonstrated a bell-shaped curve of MT emission versus SRT with a peak around 20 days SRT. In order to understand this SRT effect, a kinetic model was developed to describe MT production and utilization dynamics in the course of anaerobic digestion and calibrated with the experimental results collected from this study. The model outcome revealed that the high protein content in the feed sludge together with the large maintenance coefficient of MT fermenters are responsible for the peak MT emission emergence in the range of typical SRT used for anaerobic digestion. A further analysis of the kinetic model shows that it can be extensively simplified with reasonable approximation to a form that anaerobic digestion practitioners could easily use to predict the MT and SRT relationship. Copyright © 2018 Elsevier Ltd. All rights reserved.

  1. Tracer kinetic model-driven registration for dynamic contrast-enhanced MRI time-series data.

    Science.gov (United States)

    Buonaccorsi, Giovanni A; O'Connor, James P B; Caunce, Angela; Roberts, Caleb; Cheung, Sue; Watson, Yvonne; Davies, Karen; Hope, Lynn; Jackson, Alan; Jayson, Gordon C; Parker, Geoffrey J M

    2007-11-01

    Dynamic contrast-enhanced MRI (DCE-MRI) time series data are subject to unavoidable physiological motion during acquisition (e.g., due to breathing) and this motion causes significant errors when fitting tracer kinetic models to the data, particularly with voxel-by-voxel fitting approaches. Motion correction is problematic, as contrast enhancement introduces new features into postcontrast images and conventional registration similarity measures cannot fully account for the increased image information content. A methodology is presented for tracer kinetic model-driven registration that addresses these problems by explicitly including a model of contrast enhancement in the registration process. The iterative registration procedure is focused on a tumor volume of interest (VOI), employing a three-dimensional (3D) translational transformation that follows only tumor motion. The implementation accurately removes motion corruption in a DCE-MRI software phantom and it is able to reduce model fitting errors and improve localization in 3D parameter maps in patient data sets that were selected for significant motion problems. Sufficient improvement was observed in the modeling results to salvage clinical trial DCE-MRI data sets that would otherwise have to be rejected due to motion corruption. Copyright 2007 Wiley-Liss, Inc.

  2. Modeling bubble dynamics and radical kinetics in ultrasound induced microalgal cell disruption.

    Science.gov (United States)

    Wang, Meng; Yuan, Wenqiao

    2016-01-01

    Microalgal cell disruption induced by acoustic cavitation was simulated through solving the bubble dynamics in an acoustical field and their radial kinetics (chemical kinetics of radical species) occurring in the bubble during its oscillation, as well as calculating the bubble wall pressure at the collapse point. Modeling results indicated that increasing ultrasonic intensity led to a substantial increase in the number of bubbles formed during acoustic cavitation, however, the pressure generated when the bubbles collapsed decreased. Therefore, cumulative collapse pressure (CCP) of bubbles was used to quantify acoustic disruption of a freshwater alga, Scenedesmus dimorphus, and a marine alga, Nannochloropsis oculata and compare with experimental results. The strong correlations between CCP and the intracellular lipid fluorescence density, chlorophyll-a fluorescence density, and cell particle/debris concentration were found, which suggests that the developed models could accurately predict acoustic cell disruption, and can be utilized in the scale up and optimization of the process. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Enantioselective Synthesis of Aminodiols by Sequential Rhodium-Catalysed Oxyamination/Kinetic Resolution: Expanding the Substrate Scope of Amidine-Based Catalysis.

    Science.gov (United States)

    Guasch, Joan; Giménez-Nueno, Irene; Funes-Ardoiz, Ignacio; Bernús, Miguel; Matheu, M Isabel; Maseras, Feliu; Castillón, Sergio; Díaz, Yolanda

    2018-03-26

    Regio- and stereoselective oxyamination of dienes through a tandem rhodium-catalysed aziridination-nucleophilic opening affords racemic oxazolidinone derivatives, which undergo a kinetic resolution acylation process with amidine-based catalysts (ABCs) to achieve s values of up to 117. This protocol was applied to the enantioselective synthesis of sphingosine. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Experimental evidence of the role of viscosity in the molecular kinetic theory of dynamic wetting.

    Science.gov (United States)

    Duvivier, D; Seveno, D; Rioboo, R; Blake, T D; De Coninck, J

    2011-11-01

    We report an experimental study of the dynamics of spontaneous spreading of aqueous glycerol drops on glass. For a range of glycerol concentrations, we follow the evolution of the radius and contact angle over several decades of time and investigate the influence of solution viscosity. The application of the molecular kinetic theory to the resulting data allows us to extract the coefficient of contact-line friction ζ, the molecular jump frequency κ(0), and the jump length λ for each solution. Our results show that the modified theory, which explicitly accounts for the effect of viscosity, can successfully be applied to droplet spreading. The viscosity affects the jump frequency but not the jump length. In combining these data, we confirm that the contact-line friction of the solution/air interface against the glass is proportional to the viscosity and exponentially dependent on the work of adhesion.

  5. Molecular kinetics. Ras activation by SOS: allosteric regulation by altered fluctuation dynamics.

    Science.gov (United States)

    Iversen, Lars; Tu, Hsiung-Lin; Lin, Wan-Chen; Christensen, Sune M; Abel, Steven M; Iwig, Jeff; Wu, Hung-Jen; Gureasko, Jodi; Rhodes, Christopher; Petit, Rebecca S; Hansen, Scott D; Thill, Peter; Yu, Cheng-Han; Stamou, Dimitrios; Chakraborty, Arup K; Kuriyan, John; Groves, Jay T

    2014-07-04

    Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras-guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average. Copyright © 2014, American Association for the Advancement of Science.

  6. Resistivity recovery simulations of electron-irradiated iron: Kinetic Monte Carlo versus cluster dynamics

    International Nuclear Information System (INIS)

    Dalla Torre, J.; Fu, C.-C.; Willaime, F.; Barbu, A.; Bocquet, J.-L.

    2006-01-01

    The isochronal resistivity recovery in high purity α-iron irradiated by electrons was successfully reproduced by a multiscale modelling approach. The stability and mobility of small self-defect clusters determined by ab initio methods were used as input data for an event based Kinetic Monte Carlo (KMC) model, used to explore the defect population evolution during the annealing and to extract the resistivity recovery peaks. In this paper, we investigate the possibility of using an efficient mesoscale model, the Cluster Dynamics (CD), instead of KMC in this approach. The comparison between the two methods for various CD initial conditions shows the importance of spatial correlations between defects, which are neglected in the CD model. However, using appropriate initial conditions, e.g. starting from the concentration of Frenkel pairs after the uncorrelated stage I E , the CD model captures the main characteristics of subsequent defect population evolution, and it can therefore be used for fast and semi-quantitative investigations

  7. Partial Overhaul and Initial Parallel Optimization of KINETICS, a Coupled Dynamics and Chemistry Atmosphere Model

    Science.gov (United States)

    Nguyen, Howard; Willacy, Karen; Allen, Mark

    2012-01-01

    KINETICS is a coupled dynamics and chemistry atmosphere model that is data intensive and computationally demanding. The potential performance gain from using a supercomputer motivates the adaptation from a serial version to a parallelized one. Although the initial parallelization had been done, bottlenecks caused by an abundance of communication calls between processors led to an unfavorable drop in performance. Before starting on the parallel optimization process, a partial overhaul was required because a large emphasis was placed on streamlining the code for user convenience and revising the program to accommodate the new supercomputers at Caltech and JPL. After the first round of optimizations, the partial runtime was reduced by a factor of 23; however, performance gains are dependent on the size of the data, the number of processors requested, and the computer used.

  8. A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics

    Directory of Open Access Journals (Sweden)

    van Gulik Walter M

    2006-12-01

    Full Text Available Abstract Background Dynamic modeling of metabolic reaction networks under in vivo conditions is a crucial step in order to obtain a better understanding of the (disfunctioning of living cells. So far dynamic metabolic models generally have been based on mechanistic rate equations which often contain so many parameters that their identifiability from experimental data forms a serious problem. Recently, approximative rate equations, based on the linear logarithmic (linlog format have been proposed as a suitable alternative with fewer parameters. Results In this paper we present a method for estimation of the kinetic model parameters, which are equal to the elasticities defined in Metabolic Control Analysis, from metabolite data obtained from dynamic as well as steady state perturbations, using the linlog kinetic format. Additionally, we address the question of parameter identifiability from dynamic perturbation data in the presence of noise. The method is illustrated using metabolite data generated with a dynamic model of the glycolytic pathway of Saccharomyces cerevisiae based on mechanistic rate equations. Elasticities are estimated from the generated data, which define the complete linlog kinetic model of the glycolysis. The effect of data noise on the accuracy of the estimated elasticities is presented. Finally, identifiable subset of parameters is determined using information on the standard deviations of the estimated elasticities through Monte Carlo (MC simulations. Conclusion The parameter estimation within the linlog kinetic framework as presented here allows the determination of the elasticities directly from experimental data from typical dynamic and/or steady state experiments. These elasticities allow the reconstruction of the full kinetic model of Saccharomyces cerevisiae, and the determination of the control coefficients. MC simulations revealed that certain elasticities are potentially unidentifiable from dynamic data only

  9. Nitrate denitrification with nitrite or nitrous oxide as intermediate products: Stoichiometry, kinetics and dynamics of stable isotope signatures.

    Science.gov (United States)

    Vavilin, V A; Rytov, S V

    2015-09-01

    A kinetic analysis of nitrate denitrification by a single or two species of denitrifying bacteria with glucose or ethanol as a carbon source and nitrite or nitrous oxide as intermediate products was performed using experimental data published earlier (Menyailo and Hungate, 2006; Vidal-Gavilan et al., 2013). Modified Monod kinetics was used in the dynamic biological model. The special equations were added to the common dynamic biological model to describe how isotopic fractionation between N species changes. In contrast to the generally assumed first-order kinetics, in this paper, the traditional Rayleigh equation describing stable nitrogen and oxygen isotope fractionation in nitrate was derived from the dynamic isotopic equations for any type of kinetics. In accordance with the model, in Vidal-Gavilan's experiments, the maximum specific rate of nitrate reduction was proved to be less for ethanol compared to glucose. Conversely, the maximum specific rate of nitrite reduction was proved to be much less for glucose compared to ethanol. Thus, the intermediate nitrite concentration was negligible for the ethanol experiment, while it was significant for the glucose experiment. In Menyailo's and Hungate's experiments, the low value of maximum specific rate of nitrous oxide reduction gives high intermediate value of nitrous oxide concentration. The model showed that the dynamics of nitrogen and oxygen isotope signatures are responding to the biological dynamics. Two microbial species instead of single denitrifying bacteria are proved to be more adequate to describe the total process of nitrate denitrification to dinitrogen. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. A study of pH-dependent photodegradation of amiloride by a multivariate curve resolution approach to combined kinetic and acid-base titration UV data.

    Science.gov (United States)

    De Luca, Michele; Ioele, Giuseppina; Mas, Sílvia; Tauler, Romà; Ragno, Gaetano

    2012-11-21

    Amiloride photostability at different pH values was studied in depth by applying Multivariate Curve Resolution Alternating Least Squares (MCR-ALS) to the UV spectrophotometric data from drug solutions exposed to stressing irradiation. Resolution of all degradation photoproducts was possible by simultaneous spectrophotometric analysis of kinetic photodegradation and acid-base titration experiments. Amiloride photodegradation showed to be strongly dependent on pH. Two hard modelling constraints were sequentially used in MCR-ALS for the unambiguous resolution of all the species involved in the photodegradation process. An amiloride acid-base system was defined by using the equilibrium constraint, and the photodegradation pathway was modelled taking into account the kinetic constraint. The simultaneous analysis of photodegradation and titration experiments revealed the presence of eight different species, which were differently distributed according to pH and time. Concentration profiles of all the species as well as their pure spectra were resolved and kinetic rate constants were estimated. The values of rate constants changed with pH and under alkaline conditions the degradation pathway and photoproducts also changed. These results were compared to those obtained by LC-MS analysis from drug photodegradation experiments. MS analysis allowed the identification of up to five species and showed the simultaneous presence of more than one acid-base equilibrium.

  11. Mucuna pruriens in Parkinson Disease: A Kinetic-Dynamic Comparison With Levodopa Standard Formulations.

    Science.gov (United States)

    Contin, Manuela; Lopane, Giovanna; Passini, Andrea; Poli, Ferruccio; Iannello, Carmelina; Guarino, Maria

    2015-01-01

    We compared levodopa (LD) kinetic-dynamic profile of a dose of LD/aromatic amino acid decarboxylase peripheral inhibitors versus a nominally equivalent dose of a commercial Mucuna pruriens (Mucuna) seeds extract in 2 patients with Parkinson disease chronically taking LD standard combined with self-prescribed Mucuna. Patients were challenged with a fasting morning dose of 100 mg LD/25 mg carbidopa (patient 1) or benserazide (patient 2) versus 100 mg LD from Mucuna capsules in 2 different sessions, after a 12-hour standard LD formulations' washout. They underwent kinetic-dynamic LD monitoring based on LD dose intake and simultaneous serial assessments of plasma drug concentrations and motor test performances. Quantitative analysis of LD in Mucuna capsules was also performed. Levodopa bioavailability was markedly lower after Mucuna administration compared with LD standard formulations: in patient 1, peak plasma LD concentration (Cmax) decreased from 2.0 to 1.0 mg/L and the area under the plasma concentration time curve from 137 to 33.6 mg/L per minute; in patient 2, Cmax was 0.7 mg/L after LD/benserazide and nearly undetectable after Mucuna. In patient 1, impaired LD bioavailability from Mucuna resulted in reduced duration and overall extent of drug response compared with LD/carbidopa. In patient 2, no significant subacute LD motor response was observed in either condition. Quantitative analysis of Mucuna formulation confirmed the 100 mg LD content for the utilized capsules. Our results show an impaired LD bioavailability from Mucuna preparation, as expected by the lacking aromatic amino acid decarboxylase inhibitors coadministration, which might explain the suggested lower dyskinetic potential of Mucuna compared with standard LD formulations.

  12. Dual enzymatic dynamic kinetic resolution by Thermoanaerobacter ethanolicus secondary alcohol dehydrogenase and Candida antarctica lipase B

    KAUST Repository

    Karume, Ibrahim; Musa, Musa M.; Bsharat, Odey; Takahashi, Masateru; Hamdan, Samir; El Ali, Bassam

    2016-01-01

    The immobilization of Thermoanaerobacter ethanolicus secondary alcohol dehydrogenase (TeSADH) using sol–gel method enables its use to racemize enantiopure alcohols in organic media. Here, we report the racemization of enantiopure phenyl

  13. xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.

    Science.gov (United States)

    McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

    2014-09-01

    X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

  14. Mapping the dissociative ionization dynamics of molecular nitrogen with attosecond resolution

    International Nuclear Information System (INIS)

    Klinker, M; González-Vázquez, J; Martin, F; Trabattoni, A; Sansone, G; Nisoli, M; Liu, C; Linguerri, R; Hochlaf, M; Klei, J; Vrakking, M J J; Calegari, F

    2015-01-01

    We wish to understand the processes underlying the ionization dynamics of N 2 as experimentally induced and studied by recording the kinetic energy release (KER) in a XUV-pump/IR-probe setup. To this end a theoretical model was developed describing the ionization process using Dyson Orbitals and, subsequently, the dissociation process using a large set of diabatic potential energy surfaces (PES) on which to propagate. From said set of PES, a small subset is extracted allowing for the identification of one and two photon processes chiefly responsible for the experimentally observed features. (paper)

  15. Quantitative dynamic ¹⁸FDG-PET and tracer kinetic analysis of soft tissue sarcomas.

    Science.gov (United States)

    Rusten, Espen; Rødal, Jan; Revheim, Mona E; Skretting, Arne; Bruland, Oyvind S; Malinen, Eirik

    2013-08-01

    To study soft tissue sarcomas using dynamic positron emission tomography (PET) with the glucose analog tracer [(18)F]fluoro-2-deoxy-D-glucose ((18)FDG), to investigate correlations between derived PET image parameters and clinical characteristics, and to discuss implications of dynamic PET acquisition (D-PET). D-PET images of 11 patients with soft tissue sarcomas were analyzed voxel-by-voxel using a compartment tracer kinetic model providing estimates of transfer rates between the vascular, non-metabolized, and metabolized compartments. Furthermore, standard uptake values (SUVs) in the early (2 min p.i.; SUVE) and late (45 min p.i.; SUVL) phases of the PET acquisition were obtained. The derived transfer rates K1, k2 and k3, along with the metabolic rate of (18)FDG (MRFDG) and the vascular fraction νp, was fused with the computed tomography (CT) images for visual interpretation. Correlations between D-PET imaging parameters and clinical parameters, i.e. tumor size, grade and clinical status, were calculated with a significance level of 0.05. The temporal uptake pattern of (18)FDG in the tumor varied considerably from patient to patient. SUVE peak was higher than SUVL peak for four patients. The images of the rate constants showed a systematic pattern, often with elevated intensity in the tumors compared to surrounding tissue. Significant correlations were found between SUVE/L and some of the rate parameters. Dynamic (18)FDG-PET may provide additional valuable information on soft tissue sarcomas not obtainable from conventional (18)FDG-PET. The prognostic role of dynamic imaging should be investigated.

  16. Dynamic PET of human liver inflammation: impact of kinetic modeling with optimization-derived dual-blood input function.

    Science.gov (United States)

    Wang, Guobao; Corwin, Michael T; Olson, Kristin A; Badawi, Ramsey D; Sarkar, Souvik

    2018-05-30

    The hallmark of nonalcoholic steatohepatitis is hepatocellular inflammation and injury in the setting of hepatic steatosis. Recent work has indicated that dynamic 18F-FDG PET with kinetic modeling has the potential to assess hepatic inflammation noninvasively, while static FDG-PET did not show a promise. Because the liver has dual blood supplies, kinetic modeling of dynamic liver PET data is challenging in human studies. The objective of this study is to evaluate and identify a dual-input kinetic modeling approach for dynamic FDG-PET of human liver inflammation. Fourteen human patients with nonalcoholic fatty liver disease were included in the study. Each patient underwent one-hour dynamic FDG-PET/CT scan and had liver biopsy within six weeks. Three models were tested for kinetic analysis: traditional two-tissue compartmental model with an image-derived single-blood input function (SBIF), model with population-based dual-blood input function (DBIF), and modified model with optimization-derived DBIF through a joint estimation framework. The three models were compared using Akaike information criterion (AIC), F test and histopathologic inflammation reference. The results showed that the optimization-derived DBIF model improved the fitting of liver time activity curves and achieved lower AIC values and higher F values than the SBIF and population-based DBIF models in all patients. The optimization-derived model significantly increased FDG K1 estimates by 101% and 27% as compared with traditional SBIF and population-based DBIF. K1 by the optimization-derived model was significantly associated with histopathologic grades of liver inflammation while the other two models did not provide a statistical significance. In conclusion, modeling of DBIF is critical for kinetic analysis of dynamic liver FDG-PET data in human studies. The optimization-derived DBIF model is more appropriate than SBIF and population-based DBIF for dynamic FDG-PET of liver inflammation. © 2018

  17. Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions

    International Nuclear Information System (INIS)

    Salmon, L.; Licinio, A.; Jensen, M.R.; Blackledge, M.; Ortega Roldan, J.L.; Van Nuland, N.; Lescop, E.

    2011-01-01

    We have recently presented a titration approach for the determination of residual dipolar couplings (RDCs) from experimentally inaccessible complexes. Here, we extend this approach to the measurement of 15 N spin relaxation rates and demonstrate that this can provide long-range structural, dynamic, and kinetic information about these elusive systems. (authors)

  18. Interplay between excitation kinetics and reaction-center dynamics in purple bacteria

    International Nuclear Information System (INIS)

    Caycedo-Soler, Felipe; RodrIguez, Ferney J; Quiroga, Luis; Johnson, Neil F

    2010-01-01

    Photosynthesis is arguably the fundamental process of life, since it enables energy from the Sun to enter the food chain on the Earth. It is a remarkable non-equilibrium process in which photons are converted to many-body excitations, which traverse a complex biomolecular membrane, where they are captured and fuel chemical reactions within a reaction center (RC) in order to produce nutrients. The precise nature of these dynamical processes-which lie at the interface between quantum and classical behavior and involve both noise and coordination-is still being explored. Here, we focus on a striking recent empirical finding concerning an illumination-driven transition in the biomolecular membrane architecture of the purple bacteria Rsp. photometricum. Using stochastic realizations to describe a hopping rate model for excitation transfer, we show numerically and analytically that this surprising shift in preferred architectures can be traced to the interplay between the excitation kinetics and the RC dynamics. The net effect is that the bacteria profit from efficient metabolism at low illumination intensities while using dissipation to avoid an oversupply of energy at high illumination intensities.

  19. Dynamics of entropy perturbations in assisted dark energy with mixed kinetic terms

    International Nuclear Information System (INIS)

    Karwan, Khamphee

    2011-01-01

    We study dynamics of entropy perturbations in the two-field assisted dark energy model. Based on the scenario of assisted dark energy, in which one scalar field is subdominant compared with the other in the early epoch, we show that the entropy perturbations in this two-field system tend to be constant on large scales in the early epoch and hence survive until the present era for a generic evolution of both fields during the radiation and matter eras. This behaviour of the entropy perturbations is preserved even when the fields are coupled via kinetic interaction. Since, for assisted dark energy, the subdominant field in the early epoch becomes dominant at late time, the entropy perturbations can significantly influence the dynamics of density perturbations in the universe. Assuming correlations between the entropy and curvature perturbations, the entropy perturbations can enhance the integrated Sachs-Wolfe (ISW) effect if the signs of the contributions from entropy perturbations and curvature perturbations are opposite after the matter era, otherwise the ISW contribution is suppressed. For canonical scalar field the effect of entropy perturbations on ISW effect is small because the initial value of the entropy perturbations estimated during inflation cannot be sufficiently large. However, in the case of k-essence, the initial value of the entropy perturbations can be large enough to affect the ISW effect to leave a significant imprint on the CMB power spectrum

  20. A three-state kinetic agent-based model to analyze tax evasion dynamics

    Science.gov (United States)

    Crokidakis, Nuno

    2014-11-01

    In this work we study the problem of tax evasion on a fully-connected population. For this purpose, we consider that the agents may be in three different states, namely honest tax payers, tax evaders and undecided, that are individuals in an intermediate class among honests and evaders. Every individual can change his/her state following a kinetic exchange opinion dynamics, where the agents interact by pairs with competitive negative (with probability q) and positive (with probability 1-q) couplings, representing agreement/disagreement between pairs of agents. In addition, we consider the punishment rules of the Zaklan econophysics model, for which there is a probability pa of an audit each agent is subject to in every period and a length of time k detected tax evaders remain honest. Our results suggest that below the critical point qc=1/4 of the opinion dynamics the compliance is high, and the punishment rules have a small effect in the population. On the other hand, for q>qc the tax evasion can be considerably reduced by the enforcement mechanism. We also discuss the impact of the presence of the undecided agents in the evolution of the system.

  1. FitEM2EM--tools for low resolution study of macromolecular assembly and dynamics.

    Directory of Open Access Journals (Sweden)

    Ziv Frankenstein

    Full Text Available Studies of the structure and dynamics of macromolecular assemblies often involve comparison of low resolution models obtained using different techniques such as electron microscopy or atomic force microscopy. We present new computational tools for comparing (matching and docking of low resolution structures, based on shape complementarity. The matched or docked objects are represented by three dimensional grids where the value of each grid point depends on its position with regard to the interior, surface or exterior of the object. The grids are correlated using fast Fourier transformations producing either matches of related objects or docking models depending on the details of the grid representations. The procedures incorporate thickening and smoothing of the surfaces of the objects which effectively compensates for differences in the resolution of the matched/docked objects, circumventing the need for resolution modification. The presented matching tool FitEM2EMin successfully fitted electron microscopy structures obtained at different resolutions, different conformers of the same structure and partial structures, ranking correct matches at the top in every case. The differences between the grid representations of the matched objects can be used to study conformation differences or to characterize the size and shape of substructures. The presented low-to-low docking tool FitEM2EMout ranked the expected models at the top.

  2. Transient Response Dynamic Module Modifications to Include Static and Kinetic Friction Effects

    Science.gov (United States)

    Misel, J. E.; Nenno, S. B.; Takahashi, D.

    1984-01-01

    A methodology that supports forced transient response dynamic solutions when both static and kinetic friction effects are included in a structural system model is described. Modifications that support this type of nonlinear transient response solution are summarized for the transient response dynamics (TRD) NASTRAN module. An overview of specific modifications for the NASTRAN processing subroutines, INITL, TRD1C, and TRD1D, are described with further details regarding inspection of nonlinear input definitions to define the type of nonlinear solution required, along with additional initialization requirements and specific calculation subroutines to successfully solve the transient response problem. The extension of the basic NASTRAN nonlinear methodology is presented through several stages of development to the point where constraint equations and residual flexibility effects are introduced into the finite difference Newmark-Beta recurrsion formulas. Particular emphasis is placed on cost effective solutions for large finite element models such as the Space Shuttle with friction degrees of freedom between the orbiter and payloads mounted in the cargo bay. An alteration to the dynamic finite difference equations of motion is discussed, which allows one to include friction effects at reasonable cost for large structural systems such as the Space Shuttle. Data are presented to indicate the possible impact of transient friction loads to the payload designer for the Space Shuttle. Transient response solution data are also included, which compare solutions without friction forces and those with friction forces for payloads mounted in the Space Shuttle cargo bay. These data indicate that payload components can be sensitive to friction induced loads.

  3. Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics.

    Science.gov (United States)

    Yang, Qian; Sing-Long, Carlos A; Reed, Evan J

    2017-08-01

    We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.

  4. Kinetics and dynamic modelling of batch anaerobic digestion of municipal solid waste in a stirred reactor

    International Nuclear Information System (INIS)

    Nopharatana, Annop; Pullammanappallil, Pratap C.; Clarke, William P.

    2007-01-01

    A series of batch, slurry anaerobic digestion experiments were performed where the soluble and insoluble fractions, and unwashed MSW were separately digested in a 200 l stirred stainless steel vessel at a pH of 7.2 and a temperature of 38 deg. C. It was found that 7% of the total MSW COD was readily soluble, of which 80% was converted to biogas; 50% of the insoluble fraction was solubilised, of this only 80% was converted to biogas. The rate of digesting the insoluble fraction was about four times slower than the rate of digesting the soluble fraction; 48% of the total COD was converted to biogas and 40% of the total nitrogen was converted to ammonia. Soluble and insoluble fractions were broken down simultaneously. The minimum time to convert 95% of the degradable fraction to biogas was 20 days. The lag phase for the degradation of insoluble fraction of MSW can be overcome by acclimatising the culture with the soluble fraction. The rate of digestion and the methane yield was not affected by particle size (within the range of 2-50 mm). A dynamic model was developed to describe batch digestion of MSW. The parameters of the model were estimated using data from the separate digestion of soluble and insoluble fractions and validated against data from the digestion of unwashed MSW. Trends in the specific aceticlastic and formate-utilising methanogenic activity were used to estimate initial methanogenic biomass concentration and bacterial death rate coefficient. The kinetics of hydrolysis of insoluble fraction could be adequately described by a Contois equation and the kinetics of acidogenesis, and aceticlastic and hydrogen utilising methanogenesis by Monod equations

  5. A model for plasticity kinetics and its role in simulating the dynamic behavior of Fe at high strain rates

    Energy Technology Data Exchange (ETDEWEB)

    Colvin, J D; Minich, R W; Kalantar, D H

    2007-03-29

    The recent diagnostic capability of the Omega laser to study solid-solid phase transitions at pressures greater than 10 GPa and at strain rates exceeding 10{sup 7} s{sup -1} has also provided valuable information on the dynamic elastic-plastic behavior of materials. We have found, for example, that plasticity kinetics modifies the effective loading and thermodynamic paths of the material. In this paper we derive a kinetics equation for the time-dependent plastic response of the material to dynamic loading, and describe the model's implementation in a radiation-hydrodynamics computer code. This model for plasticity kinetics incorporates the Gilman model for dislocation multiplication and saturation. We discuss the application of this model to the simulation of experimental velocity interferometry data for experiments on Omega in which Fe was shock compressed to pressures beyond the {alpha}-to-{var_epsilon} phase transition pressure. The kinetics model is shown to fit the data reasonably well in this high strain rate regime and further allows quantification of the relative contributions of dislocation multiplication and drag. The sensitivity of the observed signatures to the kinetics model parameters is presented.

  6. A study of static, kinetic, and dynamic visual acuity in 102 Japanese professional baseball players

    Directory of Open Access Journals (Sweden)

    Hoshina K

    2013-03-01

    Full Text Available Kohji Hoshina,1 Yuichi Tagami,2 Osamu Mimura,3 Hiroshi Edagawa,4 Masao Matsubara,5 Teiichi Nakayama6 1Hoshina Eye Clinic, Nishinomiya, Japan; 2Department of Ophthalmology, Kobe Century Memorial Hospital, Kobe, Japan; 3Department of Ophthalmology, Hyogo College of Medicine, Nishinomiya, Japan; 4Edagawa Eye Clinic, Tokyo, Japan; 5Department of Ophthalmology, Tokyo Women's Medical University Medical Center East, Tokyo, Japan; 6Ritsumeikan University, Kyoto, Japan Background: It seemed that visual functions might have some effects on the performance of baseball players. We measured static, kinetic, and dynamic visual acuity (SVA, KVA, and DVA, respectively of Japanese professional baseball players to ascertain whether there would be any difference in SVA, KVA, and DVA among player groups stratified according to their performance level. Methods: The subjects were 102 male professional baseball players with a mean age of 26 years who were members of a Japanese professional baseball club from 2000 to 2009. They were stratified into three groups according to their performance level: A (players who were on the roster of the top-level team all the time throughout the study period, B (players who were on the roster of the top-level team sometimes but not all the time, and C (players who were never on the roster of the top-level team. They were interviewed for the use of corrective visual aids, and examined for SVA, KVA, and DVA. The measurements of these parameters were compared among groups A, B, and C. We also investigated and analyzed the association of KVA or DVA with player position (pitchers or fielders and with hand dominance for batting. KVA was compared between the pitchers and the fielders because they each require different playing skills. DVA was compared between the right-handed and the left-handed batters. Results: There was no statistically significant difference among groups A, B, and C. There was a statistically significant difference in

  7. Computer-aided classification of lesions by means of their kinetic signatures in dynamic contrast-enhanced MR images

    Science.gov (United States)

    Twellmann, Thorsten; ter Haar Romeny, Bart

    2008-03-01

    The kinetic characteristics of tissue in dynamic contrast-enhanced magnetic resonance imaging data are an important source of information for the differentiation of benign and malignant lesions. Kinetic curves measured for each lesion voxel allow to infer information about the state of the local tissue. As a whole, they reflect the heterogeneity of the vascular structure within a lesion, an important criterion for the preoperative classification of lesions. Current clinical practice in analysis of tissue kinetics however is mainly based on the evaluation of the "most-suspect curve", which is only related to a small, manually or semi-automatically selected region-of-interest within a lesion and does not reflect any information about tissue heterogeneity. We propose a new method which exploits the full range of kinetic information for the automatic classification of lesions. Instead of breaking down the large amount of kinetic information to a single curve, each lesion is considered as a probability distribution in a space of kinetic features, efficiently represented by its kinetic signature obtained by adaptive vector quantization of the corresponding kinetic curves. Dissimilarity of two signatures can be objectively measured using the Mallows distance, which is a metric defined on probability distributions. The embedding of this metric in a suitable kernel function enables us to employ modern kernel-based machine learning techniques for the classification of signatures. In a study considering 81 breast lesions, the proposed method yielded an A z value of 0.89+/-0.01 for the discrimination of benign and malignant lesions in a nested leave-one-lesion-out evaluation setting.

  8. Kinetic analysis of dynamic 18F-fluoromisonidazole PET correlates with radiation treatment outcome in head-and-neck cancer

    Directory of Open Access Journals (Sweden)

    Paulsen Frank

    2005-12-01

    Full Text Available Abstract Background Hypoxia compromises local control in patients with head-and-neck cancer (HNC. In order to determine the value of [18F]-fluoromisonidazole (Fmiso with regard to tumor hypoxia, a patient study with dynamic Fmiso PET was performed. For a better understanding of tracer uptake and distribution, a kinetic model was developed to analyze dynamic Fmiso PET data. Methods For 15 HNC patients, dynamic Fmiso PET examinations were performed prior to radiotherapy (RT treatment. The data was analyzed using a two compartment model, which allows the determination of characteristic hypoxia and perfusion values. For different parameters, such as patient age, tumor size and standardized uptake value, the correlation to treatment outcome was tested using the Wilcoxon-Mann-Whitney U-test. Statistical tests were also performed for hypoxia and perfusion parameters determined by the kinetic model and for two different metrics based on these parameters. Results The kinetic Fmiso analysis extracts local hypoxia and perfusion characteristics of a tumor tissue. These parameters are independent quantities. In this study, different types of characteristic hypoxia-perfusion patterns in tumors could be identified. The clinical verification of the results, obtained on the basis of the kinetic analysis, showed a high correlation of hypoxia-perfusion patterns and RT treatment outcome (p = 0.001 for this initial patient group. Conclusion The presented study established, that Fmiso PET scans may benefit from dynamic acquisition and analysis by a kinetic model. The pattern of distribution of perfusion and hypoxia in the tissue is correlated to local control in HNC.

  9. Variations in calcite growth kinetics with surface topography: molecular dynamics simulations and process-based growth kinetics modelling

    NARCIS (Netherlands)

    Wolthers, M.; Di Tommaso, D.; Du, Zhimei; de Leeuw, Nora H.

    2013-01-01

    It is generally accepted that cation dehydration is the rate-limiting step to crystal growth from aqueous solution. Here we employ classical molecular dynamics simulations to show that the water exchange frequency at structurally distinct calcium sites in the calcite surface varies by about two

  10. Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

    International Nuclear Information System (INIS)

    Fogarty, Aoife C.; Potestio, Raffaello; Kremer, Kurt

    2015-01-01

    A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations

  11. Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

    Energy Technology Data Exchange (ETDEWEB)

    Fogarty, Aoife C., E-mail: fogarty@mpip-mainz.mpg.de; Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de; Kremer, Kurt, E-mail: kremer@mpip-mainz.mpg.de [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)

    2015-05-21

    A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.

  12. Incorporating human-water dynamics in a hyper-resolution land surface model

    Science.gov (United States)

    Vergopolan, N.; Chaney, N.; Wanders, N.; Sheffield, J.; Wood, E. F.

    2017-12-01

    The increasing demand for water, energy, and food is leading to unsustainable groundwater and surface water exploitation. As a result, the human interactions with the environment, through alteration of land and water resources dynamics, need to be reflected in hydrologic and land surface models (LSMs). Advancements in representing human-water dynamics still leave challenges related to the lack of water use data, water allocation algorithms, and modeling scales. This leads to an over-simplistic representation of human water use in large-scale models; this is in turn leads to an inability to capture extreme events signatures and to provide reliable information at stakeholder-level spatial scales. The emergence of hyper-resolution models allows one to address these challenges by simulating the hydrological processes and interactions with the human impacts at field scales. We integrated human-water dynamics into HydroBlocks - a hyper-resolution, field-scale resolving LSM. HydroBlocks explicitly solves the field-scale spatial heterogeneity of land surface processes through interacting hydrologic response units (HRUs); and its HRU-based model parallelization allows computationally efficient long-term simulations as well as ensemble predictions. The implemented human-water dynamics include groundwater and surface water abstraction to meet agricultural, domestic and industrial water demands. Furthermore, a supply-demand water allocation scheme based on relative costs helps to determine sectoral water use requirements and tradeoffs. A set of HydroBlocks simulations over the Midwest United States (daily, at 30-m spatial resolution for 30 years) are used to quantify the irrigation impacts on water availability. The model captures large reductions in total soil moisture and water table levels, as well as spatiotemporal changes in evapotranspiration and runoff peaks, with their intensity related to the adopted water management strategy. By incorporating human-water dynamics in

  13. A kinetic approach to model sorption dynamics of radionuclides in soils: from desire to operational application?

    Energy Technology Data Exchange (ETDEWEB)

    Martin-Garin, A.; Garcia-Sanchez, L.; Coppin, F. [Institut de Radioprotection et de Surete Nucleaire (France); Krimissa, M. [Electricite de France (France)

    2014-07-01

    The understanding of radionuclides (RN) behaviour and subsequent fluxes in the soil/solution/plant system is still a challenging question for realistic short, medium or long term risk assessments. Several years of researches have been devoted to improve the modeling of radionuclides migration in soils and their transfer to other compartments of the biosphere (eg. plants), as well as to constitute databases of model parameters (eg. distribution coefficient (K{sub d})). These works contributed to define, and then to extend, the domain of applicability of radioecological models, but they also helped to identify gaps and ways to improve them. However, these improvements have not been fully taken into account. Within this framework, the evolution of RN chemical speciation in time (often described as aging) was specifically addressed, as it control RN retention properties and bioavailability. Regarding soluble and RN solid speciation in soils, such processes generally lead to a shift from low to high K{sub d} values. Common explanations consist in the transfer of sorbed RN to non-(or less) exchangeable solid species, or in the lixiviation of the most available radionuclide fraction, both decreasing the reversibly sorbed RN fraction. Kinetics studies have examined such changes in K{sub d} value with time and various models have been proposed to fit the different evolutions. Among them, an empirical three-box model is often used to describe the kinetics of RN sorption when RN mostly occurs in the soil solution as a free ion (eg. Cs and Sr). This model assumes that the radionuclide may be sorbed either as a labile fraction, defining an exchangeable K{sub d}-like liquid/solid distribution, or sorbed as a less or non-exchangeable fraction. The last is estimated through its corresponding sorption and desorption rate constants, which describes a pseudo-first order reaction. Modeling of sorption dynamic is a way to link K{sub d} values derived from field-contaminated soils to

  14. Experimental research of kinetic and dynamic characteristics of temperature movements of machines

    Science.gov (United States)

    Parfenov, I. V.; Polyakov, A. N.

    2018-03-01

    Nowadays, the urgency of informational support of machines at different stages of their life cycle is increasing in the form of various experimental characteristics that determine the criteria for working capacity. The effectiveness of forming the base of experimental characteristics of machines is related directly to the duration of their field tests. In this research, the authors consider a new technique that allows reducing the duration of full-scale testing of machines by 30%. To this end, three new indicator coefficients were calculated in real time to determine the moments corresponding to the characteristic points. In the work, new terms for thermal characteristics of machine tools are introduced: kinetic and dynamic characteristics of the temperature movements of the machine. This allow taking into account not only the experimental values for the temperature displacements of the elements of the carrier system of the machine, but also their derivatives up to the third order, inclusively. The work is based on experimental data obtained in the course of full-scale thermal tests of a drilling-milling and boring CNC machine.

  15. SQERTSS: Dynamic rank based throttling of transition probabilities in kinetic Monte Carlo simulations

    International Nuclear Information System (INIS)

    Danielson, Thomas; Sutton, Jonathan E.; Hin, Céline; Virginia Polytechnic Institute and State University; Savara, Aditya

    2017-01-01

    Lattice based Kinetic Monte Carlo (KMC) simulations offer a powerful simulation technique for investigating large reaction networks while retaining spatial configuration information, unlike ordinary differential equations. However, large chemical reaction networks can contain reaction processes with rates spanning multiple orders of magnitude. This can lead to the problem of “KMC stiffness” (similar to stiffness in differential equations), where the computational expense has the potential to be overwhelmed by very short time-steps during KMC simulations, with the simulation spending an inordinate amount of KMC steps / cpu-time simulating fast frivolous processes (FFPs) without progressing the system (reaction network). In order to achieve simulation times that are experimentally relevant or desired for predictions, a dynamic throttling algorithm involving separation of the processes into speed-ranks based on event frequencies has been designed and implemented with the intent of decreasing the probability of FFP events, and increasing the probability of slow process events -- allowing rate limiting events to become more likely to be observed in KMC simulations. This Staggered Quasi-Equilibrium Rank-based Throttling for Steady-state (SQERTSS) algorithm designed for use in achieving and simulating steady-state conditions in KMC simulations. Lastly, as shown in this work, the SQERTSS algorithm also works for transient conditions: the correct configuration space and final state will still be achieved if the required assumptions are not violated, with the caveat that the sizes of the time-steps may be distorted during the transient period.

  16. Microbial Species Diversity, Community Dynamics, and Metabolite Kinetics of Water Kefir Fermentation

    Science.gov (United States)

    Laureys, David

    2014-01-01

    Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present were Lactobacillus casei/paracasei, Lactobacillus harbinensis, Lactobacillus hilgardii, Bifidobacterium psychraerophilum/crudilactis, Saccharomyces cerevisiae, and Dekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product. PMID:24532061

  17. Continuum kinetic methods for analyzing wave physics and distribution function dynamics in the turbulence dissipation challenge

    Science.gov (United States)

    Juno, J.; Hakim, A.; TenBarge, J.; Dorland, W.

    2015-12-01

    We present for the first time results for the turbulence dissipation challenge, with specific focus on the linear wave portion of the challenge, using a variety of continuum kinetic models: hybrid Vlasov-Maxwell, gyrokinetic, and full Vlasov-Maxwell. As one of the goals of the wave problem as it is outlined is to identify how well various models capture linear physics, we compare our results to linear Vlasov and gyrokinetic theory. Preliminary gyrokinetic results match linear theory extremely well due to the geometry of the problem, which eliminates the dominant nonlinearity. With the non-reduced models, we explore how the subdominant nonlinearities manifest and affect the evolution of the turbulence and the energy budget. We also take advantage of employing continuum methods to study the dynamics of the distribution function, with particular emphasis on the full Vlasov results where a basic collision operator has been implemented. As the community prepares for the next stage of the turbulence dissipation challenge, where we hope to do large 3D simulations to inform the next generation of observational missions such as THOR (Turbulence Heating ObserveR), we argue for the consideration of hybrid Vlasov and full Vlasov as candidate models for these critical simulations. With the use of modern numerical algorithms, we demonstrate the competitiveness of our code with traditional particle-in-cell algorithms, with a clear plan for continued improvements and optimizations to further strengthen the code's viability as an option for the next stage of the challenge.

  18. Evaluation of oxime efficacy in nerve agent poisoning: Development of a kinetic-based dynamic model

    International Nuclear Information System (INIS)

    Worek, Franz; Szinicz, Ladislaus; Eyer, Peter; Thiermann, Horst

    2005-01-01

    The widespread use of organophosphorus compounds (OP) as pesticides and the repeated misuse of highly toxic OP as chemical warfare agents (nerve agents) emphasize the necessity for the development of effective medical countermeasures. Standard treatment with atropine and the established acetylcholinesterase (AChE) reactivators, obidoxime and pralidoxime, is considered to be ineffective with certain nerve agents due to low oxime effectiveness. From obvious ethical reasons only animal experiments can be used to evaluate new oximes as nerve agent antidotes. However, the extrapolation of data from animal to humans is hampered by marked species differences. Since reactivation of OP-inhibited AChE is considered to be the main mechanism of action of oximes, human erythrocyte AChE can be exploited to test the efficacy of new oximes. By combining enzyme kinetics (inhibition, reactivation, aging) with OP toxicokinetics and oxime pharmacokinetics a dynamic in vitro model was developed which allows the calculation of AChE activities at different scenarios. This model was validated with data from pesticide-poisoned patients and simulations were performed for intravenous and percutaneous nerve agent exposure and intramuscular oxime treatment using published data. The model presented may serve as a tool for defining effective oxime concentrations and for optimizing oxime treatment. In addition, this model can be useful for the development of meaningful therapeutic animal models

  19. Microbial species diversity, community dynamics, and metabolite kinetics of water kefir fermentation.

    Science.gov (United States)

    Laureys, David; De Vuyst, Luc

    2014-04-01

    Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present were Lactobacillus casei/paracasei, Lactobacillus harbinensis, Lactobacillus hilgardii, Bifidobacterium psychraerophilum/crudilactis, Saccharomyces cerevisiae, and Dekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product.

  20. Method of Obtaining High Resolution Intrinsic Wire Boom Damping Parameters for Multi-Body Dynamics Simulations

    Science.gov (United States)

    Yew, Alvin G.; Chai, Dean J.; Olney, David J.

    2010-01-01

    The goal of NASA's Magnetospheric MultiScale (MMS) mission is to understand magnetic reconnection with sensor measurements from four spinning satellites flown in a tight tetrahedron formation. Four of the six electric field sensors on each satellite are located at the end of 60- meter wire booms to increase measurement sensitivity in the spin plane and to minimize motion coupling from perturbations on the main body. A propulsion burn however, might induce boom oscillations that could impact science measurements if oscillations do not damp to values on the order of 0.1 degree in a timely fashion. Large damping time constants could also adversely affect flight dynamics and attitude control performance. In this paper, we will discuss the implementation of a high resolution method for calculating the boom's intrinsic damping, which was used in multi-body dynamics simulations. In summary, experimental data was obtained with a scaled-down boom, which was suspended as a pendulum in vacuum. Optical techniques were designed to accurately measure the natural decay of angular position and subsequently, data processing algorithms resulted in excellent spatial and temporal resolutions. This method was repeated in a parametric study for various lengths, root tensions and vacuum levels. For all data sets, regression models for damping were applied, including: nonlinear viscous, frequency-independent hysteretic, coulomb and some combination of them. Our data analysis and dynamics models have shown that the intrinsic damping for the baseline boom is insufficient, thereby forcing project management to explore mitigation strategies.

  1. High-resolution dynamic pressure sensor array based on piezo-phototronic effect tuned photoluminescence imaging.

    Science.gov (United States)

    Peng, Mingzeng; Li, Zhou; Liu, Caihong; Zheng, Qiang; Shi, Xieqing; Song, Ming; Zhang, Yang; Du, Shiyu; Zhai, Junyi; Wang, Zhong Lin

    2015-03-24

    A high-resolution dynamic tactile/pressure display is indispensable to the comprehensive perception of force/mechanical stimulations such as electronic skin, biomechanical imaging/analysis, or personalized signatures. Here, we present a dynamic pressure sensor array based on pressure/strain tuned photoluminescence imaging without the need for electricity. Each sensor is a nanopillar that consists of InGaN/GaN multiple quantum wells. Its photoluminescence intensity can be modulated dramatically and linearly by small strain (0-0.15%) owing to the piezo-phototronic effect. The sensor array has a high pixel density of 6350 dpi and exceptional small standard deviation of photoluminescence. High-quality tactile/pressure sensing distribution can be real-time recorded by parallel photoluminescence imaging without any cross-talk. The sensor array can be inexpensively fabricated over large areas by semiconductor product lines. The proposed dynamic all-optical pressure imaging with excellent resolution, high sensitivity, good uniformity, and ultrafast response time offers a suitable way for smart sensing, micro/nano-opto-electromechanical systems.

  2. Dynamic placement of plasmonic hotspots for super-resolution surface-enhanced Raman scattering.

    Science.gov (United States)

    Ertsgaard, Christopher T; McKoskey, Rachel M; Rich, Isabel S; Lindquist, Nathan C

    2014-10-28

    In this paper, we demonstrate dynamic placement of locally enhanced plasmonic fields using holographic laser illumination of a silver nanohole array. To visualize these focused "hotspots", the silver surface was coated with various biological samples for surface-enhanced Raman spectroscopy (SERS) imaging. Due to the large field enhancements, blinking behavior of the SERS hotspots was observed and processed using a stochastic optical reconstruction microscopy algorithm enabling super-resolution localization of the hotspots to within 10 nm. These hotspots were then shifted across the surface in subwavelength (hotspots. Using this technique, we also show that such subwavelength shifting and localization of plasmonic hotspots has potential for imaging applications. Interestingly, illuminating the surface with randomly shifting SERS hotspots was sufficient to completely fill in a wide field of view for super-resolution chemical imaging.

  3. Full dynamic resolution low lower DA-Converters for flat panel displays

    Directory of Open Access Journals (Sweden)

    C. Saas

    2006-01-01

    Full Text Available It has been shown that stepwise charging can reduce the power dissipated in the source drivers of a flat panel display. However the solution presented only provided a dynamic resolution of 3 bits which is not sufficient for obtaining a full color resolution display. In this work a further development of the basic idea is presented. The stepwise charging is increased to 4 bits and supplemented by a current source to provide an output signal which represents an 8 bit value with sufficient accuracy. Within this work the application is an AM-OLED flat panel display, but the concept can easily be applied to other display technologies like TFT-LCD as well.

  4. An improved experimental scheme for simultaneous measurement of high-resolution zero electron kinetic energy (ZEKE) photoelectron and threshold photoion (MATI) spectra

    Science.gov (United States)

    Michels, François; Mazzoni, Federico; Becucci, Maurizio; Müller-Dethlefs, Klaus

    2017-10-01

    An improved detection scheme is presented for threshold ionization spectroscopy with simultaneous recording of the Zero Electron Kinetic Energy (ZEKE) and Mass Analysed Threshold Ionisation (MATI) signals. The objective is to obtain accurate dissociation energies for larger molecular clusters by simultaneously detecting the fragment and parent ion MATI signals with identical transmission. The scheme preserves an optimal ZEKE spectral resolution together with excellent separation of the spontaneous ion and MATI signals in the time-of-flight mass spectrum. The resulting improvement in sensitivity will allow for the determination of dissociation energies in clusters with substantial mass difference between parent and daughter ions.

  5. Validation of the Regional Climate Model ALARO with different dynamical downscaling approaches and different horizontal resolutions

    Science.gov (United States)

    Berckmans, Julie; Hamdi, Rafiq; De Troch, Rozemien; Giot, Olivier

    2015-04-01

    At the Royal Meteorological Institute of Belgium (RMI), climate simulations are performed with the regional climate model (RCM) ALARO, a version of the ALADIN model with improved physical parameterizations. In order to obtain high-resolution information of the regional climate, lateral bounary conditions (LBC) are prescribed from the global climate model (GCM) ARPEGE. Dynamical downscaling is commonly done in a continuous long-term simulation, with the initialisation of the model at the start and driven by the regularly updated LBCs of the GCM. Recently, more interest exists in the dynamical downscaling approach of frequent reinitializations of the climate simulations. For these experiments, the model is initialised daily and driven for 24 hours by the GCM. However, the surface is either initialised daily together with the atmosphere or free to evolve continuously. The surface scheme implemented in ALARO is SURFEX, which can be either run in coupled mode or in stand-alone mode. The regional climate is simulated on different domains, on a 20km horizontal resolution over Western-Europe and a 4km horizontal resolution over Belgium. Besides, SURFEX allows to perform a stand-alone or offline simulation on 1km horizontal resolution over Belgium. This research is in the framework of the project MASC: "Modelling and Assessing Surface Change Impacts on Belgian and Western European Climate", a 4-year project funded by the Belgian Federal Government. The overall aim of the project is to study the feedbacks between climate changes and land surface changes in order to improve regional climate model projections at the decennial scale over Belgium and Western Europe and thus to provide better climate projections and climate change evaluation tools to policy makers, stakeholders and the scientific community.

  6. Impact of the lateral boundary conditions resolution on dynamical downscaling of precipitation in mediterranean spain

    Energy Technology Data Exchange (ETDEWEB)

    Amengual, A.; Romero, R.; Homar, V.; Ramis, C.; Alonso, S. [Universitat de les Illes Balears, Grup de Meteorologia, Departament de Fisica, Palma de Mallorca (Spain)

    2007-10-15

    Conclusions on the General Circulation Models (GCMs) horizontal and temporal optimum resolution for dynamical downscaling of rainfall in Mediterranean Spain are derived based on the statistical analysis of mesoscale simulations of past events. These events correspond to the 165 heavy rainfall days during 1984-1993, which are simulated with the HIRLAM mesoscale model. The model is nested within the European Centre for Medium-Range Weather Forecasts atmospheric grid analyses. We represent the spectrum of GCMs resolutions currently applied in climate change research by using varying horizontal and temporal resolutions of these analyses. Three sets of simulations are designed using input data with 1 , 2 and 3 horizontal resolutions (available at 6 h intervals), and three additional sets are designed using 1 horizontal resolution with less frequent boundary conditions updated every 12, 24 and 48 h. The quality of the daily rainfall forecasts is verified against rain-gauge observations using correlation and root mean square error analysis as well as Relative Operating Characteristic curves. Spatial distribution of average precipitation fields are also computed and verified against observations. For the whole Mediterranean Spain, model skill is not appreciably improved when using enhanced spatial input data, suggesting that there is no clear benefit in using high resolution data from General Circulation Model for the regional downscaling of precipitation under the conditions tested. However, significant differences are found in verification scores when boundary conditions are interpolated less frequently than 12 h apart. The analysis is particularized for six major rain bearing flow regimes that affect the region, and differences in model performance are found among the flow types, with slightly better forecasts for Atlantic and cold front passage flows. A remarkable spatial variability in forecast quality is found in the domain, with an overall tendency for higher

  7. Dynamic frequency-domain interferometer for absolute distance measurements with high resolution

    International Nuclear Information System (INIS)

    Weng, Jidong; Liu, Shenggang; Ma, Heli; Tao, Tianjiong; Wang, Xiang; Liu, Cangli; Tan, Hua

    2014-01-01

    A unique dynamic frequency-domain interferometer for absolute distance measurement has been developed recently. This paper presents the working principle of the new interferometric system, which uses a photonic crystal fiber to transmit the wide-spectrum light beams and a high-speed streak camera or frame camera to record the interference stripes. Preliminary measurements of harmonic vibrations of a speaker, driven by a radio, and the changes in the tip clearance of a rotating gear wheel show that this new type of interferometer has the ability to perform absolute distance measurements both with high time- and distance-resolution

  8. Dynamic frequency-domain interferometer for absolute distance measurements with high resolution

    Science.gov (United States)

    Weng, Jidong; Liu, Shenggang; Ma, Heli; Tao, Tianjiong; Wang, Xiang; Liu, Cangli; Tan, Hua

    2014-11-01

    A unique dynamic frequency-domain interferometer for absolute distance measurement has been developed recently. This paper presents the working principle of the new interferometric system, which uses a photonic crystal fiber to transmit the wide-spectrum light beams and a high-speed streak camera or frame camera to record the interference stripes. Preliminary measurements of harmonic vibrations of a speaker, driven by a radio, and the changes in the tip clearance of a rotating gear wheel show that this new type of interferometer has the ability to perform absolute distance measurements both with high time- and distance-resolution.

  9. Inverse stochastic-dynamic models for high-resolution Greenland ice core records

    DEFF Research Database (Denmark)

    Boers, Niklas; Chekroun, Mickael D.; Liu, Honghu

    2017-01-01

    as statistical properties such as probability density functions, waiting times and power spectra, with no need for any external forcing. The crucial ingredients for capturing these properties are (i) high-resolution training data, (ii) cubic drift terms, (iii) nonlinear coupling terms between the 18O and dust......Proxy records from Greenland ice cores have been studied for several decades, yet many open questions remain regarding the climate variability encoded therein. Here, we use a Bayesian framework for inferring inverse, stochastic-dynamic models from 18O and dust records of unprecedented, subdecadal...

  10. Video-to-Video Dynamic Super-Resolution for Grayscale and Color Sequences

    Directory of Open Access Journals (Sweden)

    Elad Michael

    2006-01-01

    Full Text Available We address the dynamic super-resolution (SR problem of reconstructing a high-quality set of monochromatic or color super-resolved images from low-quality monochromatic, color, or mosaiced frames. Our approach includes a joint method for simultaneous SR, deblurring, and demosaicing, this way taking into account practical color measurements encountered in video sequences. For the case of translational motion and common space-invariant blur, the proposed method is based on a very fast and memory efficient approximation of the Kalman filter (KF. Experimental results on both simulated and real data are supplied, demonstrating the presented algorithms, and their strength.

  11. Analysis of blind identification methods for estimation of kinetic parameters in dynamic medical imaging

    Science.gov (United States)

    Riabkov, Dmitri

    Compartment modeling of dynamic medical image data implies that the concentration of the tracer over time in a particular region of the organ of interest is well-modeled as a convolution of the tissue response with the tracer concentration in the blood stream. The tissue response is different for different tissues while the blood input is assumed to be the same for different tissues. The kinetic parameters characterizing the tissue responses can be estimated by blind identification methods. These algorithms use the simultaneous measurements of concentration in separate regions of the organ; if the regions have different responses, the measurement of the blood input function may not be required. In this work it is shown that the blind identification problem has a unique solution for two-compartment model tissue response. For two-compartment model tissue responses in dynamic cardiac MRI imaging conditions with gadolinium-DTPA contrast agent, three blind identification algorithms are analyzed here to assess their utility: Eigenvector-based Algorithm for Multichannel Blind Deconvolution (EVAM), Cross Relations (CR), and Iterative Quadratic Maximum Likelihood (IQML). Comparisons of accuracy with conventional (not blind) identification techniques where the blood input is known are made as well. The statistical accuracies of estimation for the three methods are evaluated and compared for multiple parameter sets. The results show that the IQML method gives more accurate estimates than the other two blind identification methods. A proof is presented here that three-compartment model blind identification is not unique in the case of only two regions. It is shown that it is likely unique for the case of more than two regions, but this has not been proved analytically. For the three-compartment model the tissue responses in dynamic FDG PET imaging conditions are analyzed with the blind identification algorithms EVAM and Separable variables Least Squares (SLS). A method of

  12. Extended-Range High-Resolution Dynamical Downscaling over a Continental-Scale Domain

    Science.gov (United States)

    Husain, S. Z.; Separovic, L.; Yu, W.; Fernig, D.

    2014-12-01

    High-resolution mesoscale simulations, when applied for downscaling meteorological fields over large spatial domains and for extended time periods, can provide valuable information for many practical application scenarios including the weather-dependent renewable energy industry. In the present study, a strategy has been proposed to dynamically downscale coarse-resolution meteorological fields from Environment Canada's regional analyses for a period of multiple years over the entire Canadian territory. The study demonstrates that a continuous mesoscale simulation over the entire domain is the most suitable approach in this regard. Large-scale deviations in the different meteorological fields pose the biggest challenge for extended-range simulations over continental scale domains, and the enforcement of the lateral boundary conditions is not sufficient to restrict such deviations. A scheme has therefore been developed to spectrally nudge the simulated high-resolution meteorological fields at the different model vertical levels towards those embedded in the coarse-resolution driving fields derived from the regional analyses. A series of experiments were carried out to determine the optimal nudging strategy including the appropriate nudging length scales, nudging vertical profile and temporal relaxation. A forcing strategy based on grid nudging of the different surface fields, including surface temperature, soil-moisture, and snow conditions, towards their expected values obtained from a high-resolution offline surface scheme was also devised to limit any considerable deviation in the evolving surface fields due to extended-range temporal integrations. The study shows that ensuring large-scale atmospheric similarities helps to deliver near-surface statistical scores for temperature, dew point temperature and horizontal wind speed that are better or comparable to the operational regional forecasts issued by Environment Canada. Furthermore, the meteorological fields

  13. WRF high resolution dynamical downscaling of ERA-Interim for Portugal

    Energy Technology Data Exchange (ETDEWEB)

    Soares, Pedro M.M. [University of Lisbon, Instituto Dom Luiz, Lisbon (Portugal); Faculdade de Ciencias da Universidade de Lisboa, Lisbon (Portugal); Cardoso, Rita M.; Miranda, Pedro M.A.; Medeiros, Joana de [University of Lisbon, Instituto Dom Luiz, Lisbon (Portugal); Belo-Pereira, Margarida; Espirito-Santo, Fatima [Instituto de Meteorologia, Lisbon (Portugal)

    2012-11-15

    This study proposes a dynamically downscaled climatology of Portugal, produced by a high resolution (9 km) WRF simulation, forced by 20 years of ERA-Interim reanalysis (1989-2008), nested in an intermediate domain with 27 km of resolution. The Portuguese mainland is characterized by large precipitation gradients, with observed mean annual precipitation ranging from about 400 to over 2,200 mm, with a very wet northwest and rather dry southeast, largely explained by orographic processes. Model results are compared with all available stations with continuous records, comprising daily information in 32 stations for temperature and 308 for precipitation, through the computation of mean climatologies, standard statistical errors on daily to seasonally timescales, and distributions of extreme events. Results show that WRF at 9 km outperforms ERA-Interim in all analyzed variables, with good results in the representation of the annual cycles in each region. The biases of minimum and maximum temperature are reduced, with improvement of the description of temperature variability at the extreme range of its distribution. The largest gain of the high resolution simulations is visible in the rainiest regions of Portugal, where orographic enhancement is crucial. These improvements are striking in the high ranking percentiles in all seasons, describing extreme precipitation events. WRF results at 9 km compare favorably with published results supporting its use as a high-resolution regional climate model. This higher resolution allows a better representation of extreme events that are of major importance to develop mitigation/adaptation strategies by policy makers and downstream users of regional climate models in applications such as flash floods or heat waves. (orig.)

  14. Dynamic high-resolution ultrasound of the shoulder: How we do it

    Energy Technology Data Exchange (ETDEWEB)

    Corazza, Angelo, E-mail: angelcoraz@libero.it [Scuola di Specializzazione in Radiodiagnostica, Università degli Studi di Genova, Via Alberti 4, 16132 Genova (Italy); Orlandi, Davide, E-mail: theabo@libero.it [Scuola di Specializzazione in Radiodiagnostica, Università degli Studi di Genova, Via Alberti 4, 16132 Genova (Italy); Fabbro, Emanuele, E-mail: emanuele.fabbro@gmail.com [Scuola di Specializzazione in Radiodiagnostica, Università degli Studi di Genova, Via Alberti 4, 16132 Genova (Italy); Ferrero, Giulio, E-mail: giulio.ferrero@gmail.com [Scuola di Specializzazione in Radiodiagnostica, Università degli Studi di Genova, Via Alberti 4, 16132 Genova (Italy); Messina, Carmelo, E-mail: carmelomessina.md@gmail.com [Scuola di Specializzazione in Radiodiagnostica, Università degli Studi di Milano, Piazza Malan 2, 20097 San Donato Milanese (Italy); Sartoris, Riccardo, E-mail: riccardo.sartoris@hotmail.it [Scuola di Specializzazione in Radiodiagnostica, Università degli Studi di Genova, Via Alberti 4, 16132 Genova (Italy); Perugin Bernardi, Silvia, E-mail: silvy-86-@hotmail.it [Scuola di Specializzazione in Radiodiagnostica, Università degli Studi di Genova, Via Alberti 4, 16132 Genova (Italy); Arcidiacono, Alice, E-mail: a.arcidiacono84@gmail.com [Scuola di Specializzazione in Radiodiagnostica, Università degli Studi di Genova, Via Alberti 4, 16132 Genova (Italy); Silvestri, Enzo, E-mail: silvi.enzo@gmail.com [Dipartimento di Radiologia, Ospedale Evangelico Internazionale, Corso Solferino 29A, 16121 Genova (Italy); and others

    2015-02-15

    Highlights: • This paper shows how to apply US technique to image soft tissues around the shoulder. • Readers will learn to recognize normal US anatomy of tendons of the shoulder. • Readers will learn to apply dynamic maneuvers to improve rotator cuff visibility. - Abstract: Ultrasonography (US) is an established and well-accepted modality that can be used to evaluate articular and peri-articular structures around the shoulder. US has been proven to be useful in a wide range of rotator cuff diseases (tendon tears, tendinosis, and bursitis) as well as non-rotator cuff abnormalities (instability problems, synovial joint diseases, and nerve entrapment syndromes). Diagnostic accuracy of shoulder US when evaluating rotator cuff tears can reach 91–100% for partial and full thickness tears detection, respectively, having been reported to be as accurate as magnetic resonance imaging in experienced hands. US is cheap, readily available, capable to provide high-resolution images, and does not use ionizing radiations. In addition, US is the only imaging modality that allows performing dynamic evaluation of musculoskeletal structures, that may help to further increase diagnostic performance. In this setting, a standardized imaging protocol is essential for an exhaustive and efficient examination, also helping reducing the intrinsic dependence from operators of US. Furthermore, knowledge of pitfalls that can be encountered when examining the shoulder may help to avoid erroneous images interpretation. In this article we use detailed anatomic schemes and high-resolution US images to describe the normal US anatomy of soft tissues, articular, and para-articular structures located in and around the shoulder. Short video clips emphasizing the crucial role of dynamic maneuvers and dynamic real-time US examination of these structures are included as supplementary material.

  15. Dynamic high-resolution ultrasound of the shoulder: How we do it

    International Nuclear Information System (INIS)

    Corazza, Angelo; Orlandi, Davide; Fabbro, Emanuele; Ferrero, Giulio; Messina, Carmelo; Sartoris, Riccardo; Perugin Bernardi, Silvia; Arcidiacono, Alice; Silvestri, Enzo

    2015-01-01

    Highlights: • This paper shows how to apply US technique to image soft tissues around the shoulder. • Readers will learn to recognize normal US anatomy of tendons of the shoulder. • Readers will learn to apply dynamic maneuvers to improve rotator cuff visibility. - Abstract: Ultrasonography (US) is an established and well-accepted modality that can be used to evaluate articular and peri-articular structures around the shoulder. US has been proven to be useful in a wide range of rotator cuff diseases (tendon tears, tendinosis, and bursitis) as well as non-rotator cuff abnormalities (instability problems, synovial joint diseases, and nerve entrapment syndromes). Diagnostic accuracy of shoulder US when evaluating rotator cuff tears can reach 91–100% for partial and full thickness tears detection, respectively, having been reported to be as accurate as magnetic resonance imaging in experienced hands. US is cheap, readily available, capable to provide high-resolution images, and does not use ionizing radiations. In addition, US is the only imaging modality that allows performing dynamic evaluation of musculoskeletal structures, that may help to further increase diagnostic performance. In this setting, a standardized imaging protocol is essential for an exhaustive and efficient examination, also helping reducing the intrinsic dependence from operators of US. Furthermore, knowledge of pitfalls that can be encountered when examining the shoulder may help to avoid erroneous images interpretation. In this article we use detailed anatomic schemes and high-resolution US images to describe the normal US anatomy of soft tissues, articular, and para-articular structures located in and around the shoulder. Short video clips emphasizing the crucial role of dynamic maneuvers and dynamic real-time US examination of these structures are included as supplementary material

  16. Molecular dynamics study of kinetic boundary condition at an interface between a polyatomic vapor and its condensed phase

    OpenAIRE

    Ishiyama, Tatsuya; Yano, Takeru; Fujikawa, Shigeo

    2004-01-01

    The kinetic boundary condition for the Boltzmann equation at an interface between a polyatomic vapor and its liquid phase is investigated by the numerical method of molecular dynamics, with particular emphasis on the functional form of the evaporation part of the boundary condition, including the evaporation coefficient. The present study is an extension of a previous one for argon [Ishiyama, Yano, and Fujikawa, Phys. Fluids 16, 2899 (2004)] to water and methanol, typical examples of polyatom...

  17. Role of dynamical screening in excitation kinetics of biased quantum wells: Nonlinear absorption and ultrabroadband terahertz emission

    DEFF Research Database (Denmark)

    Turchinovich, Dmitry; Monozon, B. S.; Jepsen, Peter Uhd

    2006-01-01

    In this work we describe the ultrafast excitation kinetics of biased quantum well, arising from the optically induced dynamical screening of a bias electric field. The initial bia electric field inside the quantum well is screened by the optically excited polarized electron-hole pairs. This leads...... wells are in good agreement with our experimental observations [Turchinovich et al., Phys. Rev. B 68, 241307(R) (2003)], as well as in perfect compliance with qualitative considerations. ©2006 American Institute of Physics...

  18. Kinetics and dynamics of cyclosporine A in three hepatic cell culture systems

    NARCIS (Netherlands)

    Bellwon, P; Truisi, G L; Bois, Frederic Y; Wilmes, A; Schmidt, T.; Savary, C C; Parmentier, C.C.; Hewitt, P.G.; Schmal, O; Josse, R.; Richert, L.; Guillouzo, A; Mueller, S O; Jennings, P; Testai, E; Dekant, W.

    2015-01-01

    In vitro experiments have a high potential to improve current chemical safety assessment and reduce the number of animals used. However, most studies conduct hazard assessment alone, largely ignoring exposure and kinetic parameters. Therefore, in this study the kinetics of cyclosporine A (CsA) and

  19. Multivariate curve resolution applied to kinetic-spectroscopic data matrices: Dye determination in foods by means of enzymatic oxidation.

    Science.gov (United States)

    Boeris, Valeria; Arancibia, Juan A; Olivieri, Alejandro C

    2017-07-01

    In this work, the combination of chemometric techniques with kinetic-spectroscopic data allowed quantifying two dyes (tartrazine and carminic acid) in complex matrices as mustard, ketchup, asparagus soup powder, pumpkin soup powder, plum jam and orange-strawberry juice. Quantitative analysis was performed without the use of tedious sample pretreatment, due to the achievement of the second-order advantage. The results obtained showed an improvement in simplicity, speed and cost with respect to usual separation techniques, allowing to properly quantifying these dyes obtaining limits of detection below 0.6mgL -1 . In addition, to the best of our knowledge, is the first time that kinetic-spectroscopic data are obtained from the action of laccase for analytical purposes. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Inverse stochastic–dynamic models for high-resolution Greenland ice core records

    Directory of Open Access Journals (Sweden)

    N. Boers

    2017-12-01

    Full Text Available Proxy records from Greenland ice cores have been studied for several decades, yet many open questions remain regarding the climate variability encoded therein. Here, we use a Bayesian framework for inferring inverse, stochastic–dynamic models from δ18O and dust records of unprecedented, subdecadal temporal resolution. The records stem from the North Greenland Ice Core Project (NGRIP, and we focus on the time interval 59–22 ka b2k. Our model reproduces the dynamical characteristics of both the δ18O and dust proxy records, including the millennial-scale Dansgaard–Oeschger variability, as well as statistical properties such as probability density functions, waiting times and power spectra, with no need for any external forcing. The crucial ingredients for capturing these properties are (i high-resolution training data, (ii cubic drift terms, (iii nonlinear coupling terms between the δ18O and dust time series, and (iv non-Markovian contributions that represent short-term memory effects.

  1. Inverse stochastic-dynamic models for high-resolution Greenland ice core records

    Science.gov (United States)

    Boers, Niklas; Chekroun, Mickael D.; Liu, Honghu; Kondrashov, Dmitri; Rousseau, Denis-Didier; Svensson, Anders; Bigler, Matthias; Ghil, Michael

    2017-12-01

    Proxy records from Greenland ice cores have been studied for several decades, yet many open questions remain regarding the climate variability encoded therein. Here, we use a Bayesian framework for inferring inverse, stochastic-dynamic models from δ18O and dust records of unprecedented, subdecadal temporal resolution. The records stem from the North Greenland Ice Core Project (NGRIP), and we focus on the time interval 59-22 ka b2k. Our model reproduces the dynamical characteristics of both the δ18O and dust proxy records, including the millennial-scale Dansgaard-Oeschger variability, as well as statistical properties such as probability density functions, waiting times and power spectra, with no need for any external forcing. The crucial ingredients for capturing these properties are (i) high-resolution training data, (ii) cubic drift terms, (iii) nonlinear coupling terms between the δ18O and dust time series, and (iv) non-Markovian contributions that represent short-term memory effects.

  2. Temporal dynamics of motivation-cognitive control interactions revealed by high-resolution pupillometry

    Directory of Open Access Journals (Sweden)

    Kimberly Sarah Chiew

    2013-01-01

    Full Text Available Motivational manipulations, such as the presence of performance-contingent reward incentives, can have substantial influences on cognitive control. Previous evidence suggests that reward incentives may enhance cognitive performance specifically through increased preparatory, or proactive, control processes. The present study examined reward influences on cognitive control dynamics in the AX-Continuous Performance Task (AX-CPT, using high-resolution pupillometry. In the AX-CPT, contextual cues must be actively maintained over a delay in order to appropriately respond to ambiguous target probes. A key feature of the task is that it permits dissociable characterization of preparatory, proactive control processes (i.e., utilization of context and reactive control processes (i.e., target-evoked interference resolution. Task performance profiles suggested that reward incentives enhanced proactive control (context utilization. Critically, pupil dilation was also increased on reward incentive trials during context maintenance periods, suggesting trial-specific shifts in proactive control, particularly when context cues indicated the need to overcome the dominant target response bias. Reward incentives had both transient (i.e., trial-by-trial and sustained (i.e., block-based effects on pupil dilation, which may reflect distinct underlying processes. The transient pupillary effects were present even when comparing against trials matched in task performance, suggesting a unique motivational influence of reward incentives. These results suggest that pupillometry may be a useful technique for investigating reward motivational signals and their dynamic influence on cognitive control.

  3. High-resolution polypeptide structure and dynamics in anisotropic environments: The gramicidin channel

    Energy Technology Data Exchange (ETDEWEB)

    Cross, T.A.; Lee, K.C.; Ketchem, R.R.; Hu, W.; Lazo, N.D.; Huo, S. [Florida State Univ., Tallahassee, FL (United States)

    1994-12-01

    To understand the details of macromolecular function, high-resolution structural and dynamic detail is essential. The polypeptide fold of the gramicidin channel has been effectively modeled for the past 20 years, yet the functional changes in conductance and channel lifetime associated with amino acid substitutions cannot be predicted. To accomplish this goal, high-resolution electrostatic modeling and the precise orientation of all dipoles are required. Furthermore, an enhanced knowledge of the complex molecular environment of this membrane-bound peptide is needed. An aqueous environment is relatively uniform and achiral. The membrane environment is very heterogenous and chiral. A knowledge of the interactions, specific and nonspecific, between peptide and lipid will aid in developing a better understanding of this environment. To accomplish this goal, it is necessary to study the peptide in an extended lipid bilayer, rather than in a vesicular or micellar form. These latter environments are likely to possess increased dynamics, increased water penetration, and distorted interactions between the polypeptide and membrane surface. To perform NMR studies on bilayer bound peptides, solid state NMR methods are required, and for specific site information, isotopic labels are incorporated using solid phase peptide synthesis.

  4. Dynamic (4D) CT perfusion offers simultaneous functional and anatomical insights into pulmonary embolism resolution

    Energy Technology Data Exchange (ETDEWEB)

    Mirsadraee, Saeed, E-mail: saeed.mirsadraee@ed.ac.uk [Clinical Research Imaging Centre, Queen' s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ (United Kingdom); Reid, John H.; Connell, Martin [Clinical Research Imaging Centre, Queen' s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ (United Kingdom); MacNee, William; Hirani, Nikhil [The Queen' s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ (United Kingdom); Murchison, John T. [Department of Radiology, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA (United Kingdom); Beek, Edwin J. van [Clinical Research Imaging Centre, Queen' s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ (United Kingdom)

    2016-10-15

    Objective: Resolution and long-term functional effects of pulmonary emboli are unpredictable. This study was carried out to assess persisting vascular bed perfusion abnormalities and resolution of arterial thrombus in patients with recent pulmonary embolism (PE). Methods and materials: 26 Patients were prospectively evaluated by dynamic (4D) contrast enhanced CT perfusion dynamic pulmonary CT perfusion. Intermittent volume imaging was performed every 1.5–1.7 s during breath-hold and perfusion values were calculated by maximum-slope technique. Thrombus load (modified Miller score; MMS) and ventricular diameter were determined. Perfusion maps were visually scored and correlated with residual endoluminal filling defects. Results: The mean initial thrombus load was 13.1 ± 4.6 MMS (3–16), and 1.2 ± 2.1 MMS (0–8) at follow up. From the 24 CTPs with diagnostic quality perfusion studies, normal perfusion was observed in 7 (29%), and mildly-severely abnormal in 17 (71%). In 15 patients with no residual thrombus on follow up CTPA, normal perfusion was observed in 6, and abnormal perfusion in 9. Perfusion was abnormal in all patients with residual thrombus on follow up CTPA. Pulmonary perfusion changes were classified as reduced (n = 4), delayed (systemic circulation pattern; n = 5), and absent (no-flow; n = 5). The right ventricle was dilated in 12/25 (48%) at presentation, and normal in all 26 follow up scans. Weak correlation was found between initial ventricular dilatation and perfusion abnormality at follow up (r = 0.15). Conclusions: Most patients had substantial perfusion abnormality at 3–6 months post PE. Abnormal perfusion patterns were frequently observed in patients and in regions with no corresponding evidence of residual thrombus on CTPA. Some defects exhibit delayed, presumed systemic, enhancement (which we have termed ‘stunned’ lung). CT perfusion provides combined anatomical and functional information about PE resolution.

  5. Chemical kinetic insights into the ignition dynamics of n-hexane

    KAUST Repository

    Tingas, Alexandros

    2017-10-13

    Normal alkanes constitute a significant fraction of transportation fuels, and are the primary drivers of ignition processes in gasoline and diesel fuels. Low temperature ignition of n-alkanes is driven by a complex sequence of oxidation reactions, for which detailed mechanisms are still being developed. The current study explores the dynamics of low-temperature ignition of n-hexane/air mixtures, and identifies chemical pathways that characterize the combustion process. Two chemical kinetic mechanisms were selected as a comparative study in order to better understand the role of specific reaction sequences in ignition dynamics: one mechanism including a new third sequential O2 addition reaction pathways (recently proposed by Wang et al. 2017), while the other without (Zhang et al. 2015). The analysis is conducted by applying tools generated from the computational singular perturbation (CSP) approach to two distinct ignition phenomena: constant volume and compression ignition. In both cases, the role of the third sequential O2 addition reactions proves to be significant, although it is found to be much more pronounced in the constant volume cases compared to the HCCI. In particular, in the constant volume ignition case, reactions present in the third sequential O2 addition reaction pathways (e.g., KDHP  →  products + OH) contribute significantly to the explosivity of the mixture; when accounted for along with reactions P(OOH)2 + O2  →  OOP(OOH)2 and OOP(OOH)2  →  KDHP + OH, they decrease ignition delay time of the mixture by up to 40%. Under HCCI conditions, in the first-stage ignition, the third-O2 addition reactions contribute to the process, although their role decays with time and becomes negligible at the end of the first stage. The second ignition stage is dominated almost exclusively by hydrogen-related chemistry.

  6. Dynamics of Saturn’s 2010 Great White Spot from high-resolution Cassini ISS observations

    Science.gov (United States)

    Hueso, Ricardo; Sánchez-Lavega, A.; del Río-Gaztelurrutia, T.

    2012-10-01

    On December 5th 2010 a storm erupted in Saturn’s North Temperate latitudes which were experiencing early spring season. The storm quickly developed to a planet-wide disturbance of the Great White Spot type. The ISS instrument onboard Cassini acquired its first images of the storm on 23th December 2010 and performed repeated observations with a variety of spatial resolutions over the nearly 10 months period the storm continued active. Here we present an analysis of two of the image sequences with better spatial resolution of the mature storm when it was fully developed and very active. We used an image correlation algorithm to measure the cloud motions obtained from images separated 20 minutes and obtained 16,000 wind tracers in a domain of 60 degrees longitude per 20 degrees in latitude. Intense zonal and meridional motions accompanied the storm and reached values of 120 m/s in particular regions of the active storm. The storm released a chain of anticyclonic and cyclonic vortices at planetocentric latitudes of 36° and 32° respectively. The short time difference between the images results in estimated wind uncertainties of 15 m/s that did not allow to perform a complete analysis of the turbulence and kinetic spectrum of the motions. We identify locations of the updrafts and link those with the morphology in different observing filters. The global behaviour of the storm was examined in images separated by 10 hours confirming the intensity of the winds and the global behaviour of the vortices. Acknowledgments: This work was supported by the Spanish MICIIN project AYA2009-10701 with FEDER funds, by Grupos Gobierno Vasco IT-464-07 and by Universidad País Vasco UPV/EHU through program UFI11/55.

  7. Statistical dynamic image reconstruction in state-of-the-art high-resolution PET

    International Nuclear Information System (INIS)

    Rahmim, Arman; Cheng, J-C; Blinder, Stephan; Camborde, Maurie-Laure; Sossi, Vesna

    2005-01-01

    Modern high-resolution PET is now more than ever in need of scrutiny into the nature and limitations of the imaging modality itself as well as image reconstruction techniques. In this work, we have reviewed, analysed and addressed the following three considerations within the particular context of state-of-the-art dynamic PET imaging: (i) the typical average numbers of events per line-of-response (LOR) are now (much) less than unity (ii) due to the physical and biological decay of the activity distribution, one requires robust and efficient reconstruction algorithms applicable to a wide range of statistics and (iii) the computational considerations in dynamic imaging are much enhanced (i.e., more frames to be stored and reconstructed). Within the framework of statistical image reconstruction, we have argued theoretically and shown experimentally that the sinogram non-negativity constraint (when using the delayed-coincidence and/or scatter-subtraction techniques) is especially expected to result in an overestimation bias. Subsequently, two schemes are considered: (a) subtraction techniques in which an image non-negativity constraint has been imposed and (b) implementation of random and scatter estimates inside the reconstruction algorithms, thus enabling direct processing of Poisson-distributed prompts. Both techniques are able to remove the aforementioned bias, while the latter, being better conditioned theoretically, is able to exhibit superior noise characteristics. We have also elaborated upon and verified the applicability of the accelerated list-mode image reconstruction method as a powerful solution for accurate, robust and efficient dynamic reconstructions of high-resolution data (as well as a number of additional benefits in the context of state-of-the-art PET)

  8. Iteration scheme for implicit calculations of kinetic and equilibrium chemical reactions in fluid dynamics

    International Nuclear Information System (INIS)

    Ramshaw, J.D.; Chang, C.H.

    1995-01-01

    An iteration scheme for the implicit treatment of equilibrium chemical reactions in partial equilibrium flow has previously been described. Here we generalize this scheme to kinetic reactions as well as equilibrium reactions. This extends the applicability of the scheme to problems with kinetic reactions that are fast in regions of the flow field but slow in others. The resulting scheme thereby provides a single unified framework for the implicit treatment of an arbitrary number of coupled equilibrium and kinetic reactions in chemically reacting fluid flow. 10 refs., 2 figs

  9. Femtosecond laser spectroscopy of spins: Magnetization dynamics in thin magnetic films with spatio-temporal resolution

    International Nuclear Information System (INIS)

    Carpene, E.; Mancini, E.; Dallera, C.; Puppin, E.; De Silvestri, S.

    2010-01-01

    Based on the Magneto-Optical Kerr Effect (MOKE), we have developed an experimental set-up that allows us to fully characterize the magnetization dynamics in thin magnetic films by measuring all three real space components of the magnetization vector M. By means of the pump-probe technique it is possible to extract the time dependence of each individual projection with sub-picosecond resolution. This method has been exploited to investigate the temporal evolution of the magnetization (modulus and orientation) induced by an ultrashort laser pulse in thin epitaxial iron films. According to our results, we deduced that the initial, sub-picosecond demagnetization is established at the electronic level through electron-magnon excitations. The subsequent dynamics is characterized by a precessional motion on the 100 ps time scale, around an effective, time-dependent magnetic field. Following the full dynamics of M, the temporal evolution of the magneto-crystalline anisotropy constant can be unambiguously determined, providing the experimental evidence that the precession is triggered by the rapid, optically-induced misalignment between the magnetization vector and the effective magnetic field. These results suggest a possible pathway toward the ultrarapid switching of the magnetization.

  10. Measurement of Dynamic Urethral Pressures with a High Resolution Manometry System in Continent and Incontinent Women

    Science.gov (United States)

    Kirby, Anna C; Tan-Kim, Jasmine; Nager, Charles W.

    2015-01-01

    Objectives Female stress urinary incontinence (SUI) is caused by urethral dysfunction during dynamic conditions, but current technology has limitations in measuring urethral pressures under dynamic conditions. An 8-French high resolution manometry catheter (HRM) currently in clinical use in gastroenterology may accurately measure urethral pressures under dynamic conditions because it has a 25ms response rate and circumferential pressure sensors along the length of the catheter (ManoScan® ESO, Given Imaging). We evaluated the concordance, repeatability, and tolerability of this catheter. Methods We measured resting, cough, and strain maximum urethral closure pressures (MUCPs) using HRM and measured resting MUCPs with water perfusion side-hole catheter urethral pressure profilometry (UPP) in 37 continent and 28 stress incontinent subjects. Maneuvers were repeated after moving the HRM catheter along the urethral length to evaluate whether results depend on catheter positioning. Visual analog pain scores evaluated the comfort of HRM compared to UPP. Results The correlation coefficient for resting MUCPs measured by HRM vs. UPP was high (r = 0.79, prest, cough, and strain with HRM: r= 0.92, 0.89, and 0.89. Mean MUCPs (rest, cough, strain) were higher in continent than incontinent subjects (all p continent subjects during cough and strain maneuvers compared to rest. Conclusions This preliminary study shows that HRM is concordant with standard technology, repeatable, and well tolerated in the urethra. Incontinent women have more impairment of their urethral closure pressures during cough and strain than continent women. PMID:25185595

  11. Molecular dynamics study of the nanosized droplet spreading: The effect of the contact line forces on the kinetic energy dissipation

    International Nuclear Information System (INIS)

    Yoon, Hong Min; Kondaraju, Sasidhar; Lee, Jung Shin; Suh, Youngho; Lee, Joonho H.; Lee, Joon Sang

    2017-01-01

    Highlights: • Contact line forces, including friction and spreading forces are directly calculated. • Overall trends of variations in contact line forces during droplet spreading process show characteristics of contact line forces. • Detail relations of contact line forces and atomic kinetics in the contact line provide a clear evidence of the possible energy dissipation mechanism in droplet spreading process. - Abstract: Recent studies have revealed that contact line forces play an important role in the droplet spreading process. Despite their significance, the physics related to them has been studied only indirectly and the effect of contact line forces is still being disputed. We performed a molecular dynamics simulation and mimicked the droplet spreading process at the nanoscale. Based on the results of the simulation, the contact line forces were directly calculated. We found that the forces acting on the bulk and the contact line region showed different trends. Distinct positive and negative forces, contact line spreading, and friction forces were observed near the contact line. We also observed a strong dependency of the atomic kinetics in the contact line region on the variations in the contact line forces. The atoms of the liquid in the contact line region lost their kinetic energy due to the contact line friction force and became partially immobile on the solid surface. The results of the current study will be useful for understanding the role of the contact line forces on the kinetic energy dissipation in the contact line region.

  12. Molecular dynamics study of the nanosized droplet spreading: The effect of the contact line forces on the kinetic energy dissipation

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Hong Min [Department of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Kondaraju, Sasidhar [Department of Mechanical Science, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha 751013 (India); Lee, Jung Shin [Department of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Suh, Youngho; Lee, Joonho H. [Samsung Electronics, Mechatronics R& D Center, Hwaseong-si, Gyeonggi-do 445-330 (Korea, Republic of); Lee, Joon Sang, E-mail: joonlee@yonsei.ac.kr [Department of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2017-07-01

    Highlights: • Contact line forces, including friction and spreading forces are directly calculated. • Overall trends of variations in contact line forces during droplet spreading process show characteristics of contact line forces. • Detail relations of contact line forces and atomic kinetics in the contact line provide a clear evidence of the possible energy dissipation mechanism in droplet spreading process. - Abstract: Recent studies have revealed that contact line forces play an important role in the droplet spreading process. Despite their significance, the physics related to them has been studied only indirectly and the effect of contact line forces is still being disputed. We performed a molecular dynamics simulation and mimicked the droplet spreading process at the nanoscale. Based on the results of the simulation, the contact line forces were directly calculated. We found that the forces acting on the bulk and the contact line region showed different trends. Distinct positive and negative forces, contact line spreading, and friction forces were observed near the contact line. We also observed a strong dependency of the atomic kinetics in the contact line region on the variations in the contact line forces. The atoms of the liquid in the contact line region lost their kinetic energy due to the contact line friction force and became partially immobile on the solid surface. The results of the current study will be useful for understanding the role of the contact line forces on the kinetic energy dissipation in the contact line region.

  13. Effects of heterogeneity on recrystallization kinetics of nanocrystalline copper prepared by dynamic plastic deformation

    DEFF Research Database (Denmark)

    Lin, Fengxiang; Zhang, Yubin; Tao, Nairong

    2014-01-01

    to develop a heterogeneous structure, consisting of regions with different textures and microstructures. This heterogeneity within the deformed structure leads to the formation of severely clustered grains in partially recrystallized samples. The recrystallization kinetic curve shows an Avrami exponent less...... recrystallization kinetics. The hardness of the two samples was measured, and the mechanical properties before and after partial recrystallization of both samples are discussed based on the presence of structural heterogeneities on the macroscopic and the microscopic scale....

  14. Using Dynamic Contrast-Enhanced Magnetic Resonance Imaging Data to Constrain a Positron Emission Tomography Kinetic Model: Theory and Simulations

    Directory of Open Access Journals (Sweden)

    Jacob U. Fluckiger

    2013-01-01

    Full Text Available We show how dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI data can constrain a compartmental model for analyzing dynamic positron emission tomography (PET data. We first develop the theory that enables the use of DCE-MRI data to separate whole tissue time activity curves (TACs available from dynamic PET data into individual TACs associated with the blood space, the extravascular-extracellular space (EES, and the extravascular-intracellular space (EIS. Then we simulate whole tissue TACs over a range of physiologically relevant kinetic parameter values and show that using appropriate DCE-MRI data can separate the PET TAC into the three components with accuracy that is noise dependent. The simulations show that accurate blood, EES, and EIS TACs can be obtained as evidenced by concordance correlation coefficients >0.9 between the true and estimated TACs. Additionally, provided that the estimated DCE-MRI parameters are within 10% of their true values, the errors in the PET kinetic parameters are within approximately 20% of their true values. The parameters returned by this approach may provide new information on the transport of a tracer in a variety of dynamic PET studies.

  15. Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding.

    Science.gov (United States)

    Radford, Isolde H; Fersht, Alan R; Settanni, Giovanni

    2011-06-09

    Atomistic molecular dynamics simulations of the TZ1 beta-hairpin peptide have been carried out using an implicit model for the solvent. The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach. The Markov state model allowed for an unbiased identification of the metastable states of the system, and provided the basis for commitment probability calculations performed on the kinetic network. The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis. The combination of the two techniques allowed for a consistent and concise characterization of the dynamics of the peptide. The slowest relaxation process identified is the exchange between variably folded and denatured species, and the second slowest process is the exchange between two different subsets of the denatured state which could not be otherwise identified by simple inspection of the projected trajectory. The third slowest process is the exchange between a fully native and a partially folded intermediate state characterized by a native turn with a proximal backbone H-bond, and frayed side-chain packing and termini. The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.

  16. Joint reconstruction of dynamic PET activity and kinetic parametric images using total variation constrained dictionary sparse coding

    Science.gov (United States)

    Yu, Haiqing; Chen, Shuhang; Chen, Yunmei; Liu, Huafeng

    2017-05-01

    Dynamic positron emission tomography (PET) is capable of providing both spatial and temporal information of radio tracers in vivo. In this paper, we present a novel joint estimation framework to reconstruct temporal sequences of dynamic PET images and the coefficients characterizing the system impulse response function, from which the associated parametric images of the system macro parameters for tracer kinetics can be estimated. The proposed algorithm, which combines statistical data measurement and tracer kinetic models, integrates a dictionary sparse coding (DSC) into a total variational minimization based algorithm for simultaneous reconstruction of the activity distribution and parametric map from measured emission sinograms. DSC, based on the compartmental theory, provides biologically meaningful regularization, and total variation regularization is incorporated to provide edge-preserving guidance. We rely on techniques from minimization algorithms (the alternating direction method of multipliers) to first generate the estimated activity distributions with sub-optimal kinetic parameter estimates, and then recover the parametric maps given these activity estimates. These coupled iterative steps are repeated as necessary until convergence. Experiments with synthetic, Monte Carlo generated data, and real patient data have been conducted, and the results are very promising.

  17. Preclinical dynamic 18F-FDG PET - tumor characterization and radiotherapy response assessment by kinetic compartment analysis

    International Nuclear Information System (INIS)

    Roee, Kathrine; Aleksandersen, Thomas B.; Nilsen, Line B.; Hong Qu; Ree, Anne H.; Malinen, Eirik; Kristian, Alexandr; Seierstad, Therese; Olsen, Dag R.

    2010-01-01

    Background. Non-invasive visualization of tumor biological and molecular processes of importance to diagnosis and treatment response is likely to be critical in individualized cancer therapy. Since conventional static 18 F-FDG PET with calculation of the semi-quantitative parameter standardized uptake value (SUV) may be subject to many sources of variability, we here present an approach of quantifying the 18 F-FDG uptake by analytic two-tissue compartment modeling, extracting kinetic tumor parameters from dynamic 18 F-FDG PET. Further, we evaluate the potential of such parameters in radiotherapy response assessment. Material and methods. Male, athymic mice with prostate carcinoma xenografts were subjected to dynamic PET either untreated (n=8) or 24 h post-irradiation (7.5 Gy single dose, n=8). After 10 h of fasting, intravenous bolus injections of 10-15 MBq 18 F-FDG were administered and a 1 h dynamic PET scan was performed. 4D emission data were reconstructed using OSEM-MAP, before remote post-processing. Individual arterial input functions were extracted from the image series. Subsequently, tumor 18 F-FDG uptake was fitted voxel-by-voxel to a compartment model, producing kinetic parameter maps. Results. The kinetic model separated the 18 F-FDG uptake into free and bound tracer and quantified three parameters; forward tracer diffusion (k1), backward tracer diffusion (k2), and rate of 18 F-FDG phosphorylation, i.e. the glucose metabolism (k3). The fitted kinetic model gave a goodness of fit (r2) to the observed data ranging from 0.91 to 0.99, and produced parametrical images of all tumors included in the study. Untreated tumors showed homogeneous intra-group median values of all three parameters (k1, k2 and k3), whereas the parameters significantly increased in the tumors irradiated 24 h prior to 18 F-FDG PET. Conclusions. This study demonstrates the feasibility of a two-tissue compartment kinetic analysis of dynamic 18 F-FDG PET images. If validated, extracted

  18. Dynamic phase transition in the kinetic spin-3/2 Blume-Emery-Griffiths model in an oscillating field

    Energy Technology Data Exchange (ETDEWEB)

    Canko, Osman; Deviren, Bayram; Keskin, Mustafa [Department of Physics, Erciyes University, 38039 Kayseri (Turkey)

    2006-07-26

    The dynamic phase transitions are studied, within a mean-field approach, in the kinetic Blume-Emery-Griffiths model under the presence of a time varying (sinusoidal) magnetic field by using the Glauber-type stochastic dynamics. The behaviour of the time-dependence of the order parameters and the behaviour of the average order parameters in a period, which is also called the dynamic order parameters, as a function of reduced temperature, are investigated. The nature (continuous and discontinuous) of transition is characterized by studying the average order parameters in a period. The dynamic phase transition points are obtained and the phase diagrams are presented in the reduced magnetic field amplitude and reduced temperature plane. The phase diagrams exhibit one, two, or three dynamic tricritical points and a dynamic double critical end point, and besides a disordered and two ordered phases, seven coexistence phase regions exist, which strongly depend on interaction parameters. We also calculate the Liapunov exponent to verify the stability of solutions and the dynamic phase transition points.

  19. Dynamic phase transition in the kinetic spin-3/2 Blume-Emery-Griffiths model in an oscillating field

    International Nuclear Information System (INIS)

    Canko, Osman; Deviren, Bayram; Keskin, Mustafa

    2006-01-01

    The dynamic phase transitions are studied, within a mean-field approach, in the kinetic Blume-Emery-Griffiths model under the presence of a time varying (sinusoidal) magnetic field by using the Glauber-type stochastic dynamics. The behaviour of the time-dependence of the order parameters and the behaviour of the average order parameters in a period, which is also called the dynamic order parameters, as a function of reduced temperature, are investigated. The nature (continuous and discontinuous) of transition is characterized by studying the average order parameters in a period. The dynamic phase transition points are obtained and the phase diagrams are presented in the reduced magnetic field amplitude and reduced temperature plane. The phase diagrams exhibit one, two, or three dynamic tricritical points and a dynamic double critical end point, and besides a disordered and two ordered phases, seven coexistence phase regions exist, which strongly depend on interaction parameters. We also calculate the Liapunov exponent to verify the stability of solutions and the dynamic phase transition points

  20. Dynamic pressure sensor calibration techniques offering expanded bandwidth with increased resolution

    Science.gov (United States)

    Wisniewiski, David

    2015-03-01

    Advancements in the aerospace, defense and energy markets are being made possible by increasingly more sophisticated systems and sub-systems which rely upon critical information to be conveyed from the physical environment being monitored through ever more specialized, extreme environment sensing components. One sensing parameter of particular interest is dynamic pressure measurement. Crossing the boundary of all three markets (i.e. aerospace, defense and energy) is dynamic pressure sensing which is used in research and development of gas turbine technology, and subsequently embedded into a control loop used for long-term monitoring. Applications include quantifying the effects of aircraft boundary layer ingestion into the engine inlet to provide a reliable and robust design. Another application includes optimization of combustor dynamics by "listening" to the acoustic signature so that fuel-to-air mixture can be adjusted in real-time to provide cost operating efficiencies and reduced NOx emissions. With the vast majority of pressure sensors supplied today being calibrated either statically or "quasi" statically, the dynamic response characterization of the frequency dependent sensitivity (i.e. transfer function) of the pressure sensor is noticeably absent. The shock tube has been shown to be an efficient vehicle to provide frequency response of pressure sensors from extremely high frequencies down to 500 Hz. Recent development activity has lowered this starting frequency; thereby augmenting the calibration bandwidth with increased frequency resolution so that as the pressure sensor is used in an actual test application, more understanding of the physical measurement can be ascertained by the end-user.

  1. Detection and Extraction of Roads from High Resolution Satellites Images with Dynamic Programming

    Science.gov (United States)

    Benzouai, Siham; Smara, Youcef

    2010-12-01

    The advent of satellite images allows now a regular and a fast digitizing and update of geographic data, especially roads which are very useful for Geographic Information Systems (GIS) applications such as transportation, urban pollution, geomarketing, etc. For this, several studies have been conducted to automate roads extraction in order to minimize the manual processes [4]. In this work, we are interested in roads extraction from satellite imagery with high spatial resolution (at best equal to 10 m). The method is semi automatic and follows a linear approach where road is considered as a linear object. As roads extraction is a pattern recognition problem, it is useful, above all, to characterize roads. After, we realize a pre-processing by applying an Infinite Size Edge Filter -ISEF- and processing method based on dynamic programming concept, in particular, Fishler algorithm designed by F*.

  2. Galactic and stellar dynamics in the era of high resolution surveys

    Science.gov (United States)

    Boily, C. M.; Combes, F.; Hensler, G.; Spurzem, R.

    2008-12-01

    The conference Galactic and Stellar Dynamics in the Era of High Resolution Surveys took place at the European Doctoral College (EDC) in Strasbourg from 2008 March 16 to 20. The event was co-sponsored by the Astronomische Gesellschaft (AG) and the Société Fran\\c{c}aise d'Astronomie et d'Astrophysique (SF2A), a joint venture aiming to set a new trend of regular thematic meetings in specific areas of research. This special issue of the Astronomische Nachrichten is a compilation of the papers presented at the meeting. We give an outline of the meeting together with a short history of the relations of the two societies.

  3. Quantitative tradeoffs between spatial, temporal, and thermometric resolution of nonresonant Raman thermometry for dynamic experiments.

    Science.gov (United States)

    McGrane, Shawn D; Moore, David S; Goodwin, Peter M; Dattelbaum, Dana M

    2014-01-01

    The ratio of Stokes to anti-Stokes nonresonant spontaneous Raman can provide an in situ thermometer that is noncontact, independent of any material specific parameters or calibrations, can be multiplexed spatially with line imaging, and can be time resolved for dynamic measurements. However, spontaneous Raman cross sections are very small, and thermometric measurements are often limited by the amount of laser energy that can be applied without damaging the sample or changing its temperature appreciably. In this paper, we quantitatively detail the tradeoff space between spatial, temporal, and thermometric accuracy measurable with spontaneous Raman. Theoretical estimates are pinned to experimental measurements to form realistic expectations of the resolution tradeoffs appropriate to various experiments. We consider the effects of signal to noise, collection efficiency, laser heating, pulsed laser ablation, and blackbody emission as limiting factors, provide formulae to help choose optimal conditions and provide estimates relevant to planning experiments along with concrete examples for single-shot measurements.

  4. Distributed UAV-Swarm Real-Time Geomatic Data Collection Under Dynamically Changing Resolution Requirements

    Science.gov (United States)

    Almeida, Miguel; Hildmann, Hanno; Solmaz, Gürkan

    2017-08-01

    Unmanned Aerial Vehicles (UAVs) have been used for reconnaissance and surveillance missions as far back as the Vietnam War, but with the recent rapid increase in autonomy, precision and performance capabilities - and due to the massive reduction in cost and size - UAVs have become pervasive products, available and affordable for the general public. The use cases for UAVs are in the areas of disaster recovery, environmental mapping & protection and increasingly also as extended eyes and ears of civil security forces such as fire-fighters and emergency response units. In this paper we present a swarm algorithm that enables a fleet of autonomous UAVs to collectively perform sensing tasks related to environmental and rescue operations and to dynamically adapt to e.g. changing resolution requirements. We discuss the hardware used to build our own drones and the settings under which we validate the proposed approach.

  5. Two millennia of soil dynamics derived from ancient desert terraces using high resolution 3-D data

    Science.gov (United States)

    Filin, Sagi; Arav, Reuma; Avni, Yoav

    2017-04-01

    Large areas in the arid southern Levant are dotted with ancient terrace-based agriculture systems which were irrigated by runoff harvesting techniques. They were constructed and maintained between the 3rd - 9th centuries AD and abandoned in the 10th century AD. During their 600 years of cultivation, these terraces documented the gradual aggradation of alluvial soils, erosion processes within the drainage basins, as well as flashflood damage. From their abandonment and onwards, they documented 1000 years and more of land degradation and soil erosion processes. Examination of these installations presents an opportunity to study natural and anthropogenic induced changes over almost two millennia. On a global scale, such an analysis is unique as it is rare to find intact manifestations of anthropogenic influences over such time-scales because of landscape dynamics. It is also rare to find a near millennia documentation of soil erosion processes. We study in this paper the aggradation processes within intact agriculture plots in the region surrounding the world heritage Roman-Byzantine ancient city of Avdat, Negev Highlands. We follow the complete cycle of the historical desert agriculture, from the configuration pre-dating the first anthropogenic intervention, through the centuries of cultivation, and up to the present erosion phase, which spans over more than a millennium. We use high resolution 3-D laser scans to document the erosion and the environmental dynamics during these two millennia. The high-resolution data is then utilized to compute siltation rates as well as erosion rates. The long-term measures of soil erosion and land degradation we present here significantly improve our understanding of the mechanism of long-term environmental change acting in arid environments. For sustainable desert inhabitation, the study offers insights into better planning of modern agriculture in similar zones as well as insights on strategies needed to protect such historical

  6. Absorption Spectroscopy, Molecular Dynamics Calculations, and Multivariate Curve Resolution on the Phthalocyanine Aggregation

    International Nuclear Information System (INIS)

    Ajloo, Davood; Ghadamgahi, Maryam; Shaheri, Freshte; Zarei, Kobra

    2014-01-01

    Co(II)-tetrasulfonated phthalocyanine (CoTSP) is known to be aggregated to dimer at high concentration levels in water. A study on the aggregation of CoTSP using multivariate curve resolution analysis of the visible absorbance spectra over a concentration range of 30, 40 and 50 μM in the presence of dimethyl sulfoxide (DMSO), dimethyl formamide (DMF), acetonitrile (AN) and ethanol (EtOH) in the concentration range of 0 to 3.57 M is conducted. A hard modeling-based multivariate curve resolution method was applied to determine the dissociation constants of the CoTSP aggregates at various temperatures ranging from 25, 45 and 65 .deg. C and in the presence of various co-solvents. Dissociation constant for aggregation was increased and then decrease by temperature and concentration of phthalocyanine, respectively. Utilizing the vant Hoff relation, the enthalpy and entropy of the dissociation equilibriums were calculated. For the dissociation of both aggregates, the enthalpy and entropy changes were positive and negative, respectively. Molecular dynamics simulation of cosolvent effect on CoTSP aggregation was done to confirm spectroscopy results. Results of radial distribution function (RDF), root mean square deviation (RMSD) and distance curves confirmed more effect of polar solvent to decrease monomer formation

  7. Absorption Spectroscopy, Molecular Dynamics Calculations, and Multivariate Curve Resolution on the Phthalocyanine Aggregation

    Energy Technology Data Exchange (ETDEWEB)

    Ajloo, Davood; Ghadamgahi, Maryam; Shaheri, Freshte; Zarei, Kobra [Damghan Univ., Damghan (Iran, Islamic Republic of)

    2014-05-15

    Co(II)-tetrasulfonated phthalocyanine (CoTSP) is known to be aggregated to dimer at high concentration levels in water. A study on the aggregation of CoTSP using multivariate curve resolution analysis of the visible absorbance spectra over a concentration range of 30, 40 and 50 μM in the presence of dimethyl sulfoxide (DMSO), dimethyl formamide (DMF), acetonitrile (AN) and ethanol (EtOH) in the concentration range of 0 to 3.57 M is conducted. A hard modeling-based multivariate curve resolution method was applied to determine the dissociation constants of the CoTSP aggregates at various temperatures ranging from 25, 45 and 65 .deg. C and in the presence of various co-solvents. Dissociation constant for aggregation was increased and then decrease by temperature and concentration of phthalocyanine, respectively. Utilizing the vant Hoff relation, the enthalpy and entropy of the dissociation equilibriums were calculated. For the dissociation of both aggregates, the enthalpy and entropy changes were positive and negative, respectively. Molecular dynamics simulation of cosolvent effect on CoTSP aggregation was done to confirm spectroscopy results. Results of radial distribution function (RDF), root mean square deviation (RMSD) and distance curves confirmed more effect of polar solvent to decrease monomer formation.

  8. THE DYNAMICS OF PEACEFUL RESOLUTION OF THE GEORGIAN-ABKHAZ CONFLICT (BEFORE THE AUGUST 2008 EVENTS

    Directory of Open Access Journals (Sweden)

    А О Ласария

    2017-12-01

    Full Text Available In this article, research attention is paid to the structure and dynamics of the peaceful resolu-tion of ethnopolitical conflicts in the Caucasus region (on the example of the Georgian-Abkhaz confrontation. The study takes into account the factors that were the catalysts of the escalation of the ethnopolitical conflict in the territory of Abkhazia. The collapse of the USSR and the collapse of the ideology of internationalism led to the need to develop a completely new identity. Most of the elites and socio-political movements of the post-Soviet period have focused on the formation of ideological structures from national and historical roots. In the last decade of the 20th century, the tendencies towards the realization of the right to national self-determination (in Abkhazia and South Ossetia and on the other hand to maintain the territorial integrity of the state (for example, in post-Soviet Georgia acquired an antagonistic character. An important political goal is to identify conceptual aspects of the resolution of the Georgian-Abkhaz conflict, which can be used as a basis for elaborating mechanisms for regulating ethnopolitical conflicts in the Caucasus region.

  9. High resolution field study of sediment dynamics on a strongly heterogeneous bed

    Science.gov (United States)

    Bailly Du Bois, P.; Blanpain, O.; Lafite, R.; Cugier, P.; Lunven, M.

    2010-12-01

    Extensive field measurements have been carried out at several stations in a macrotidal inner continental shelf in the English Channel (around 25 m depth) during spring tide period. The strong tidal current measured (up to 1.6 m.s-1) allowed sediment dynamics on a bed characterised by a mixture of size with coarse grains to be dominant. Data acquired in such hydro-sedimentary conditions are scarce. A new instrument, the DYnamic Sediment Profile Imagery (DySPI) system, was specifically conceived and implemented in-situ to observe and measure, with a high temporal resolution, the dynamics of a strongly heterogeneous mixture of particles in a grain-size scale. The data collected covered: 1) grain size range (side scan sonar, video observations, Shipeck grab samples, DySPI images) and vertical sorting (stratigraphic sampling by divers) of sediment cover, 2) hydrodynamic features (acoustic Doppler velocimeter, acoustic Doppler profiler), 3) suspended load nature and dynamics (optical backscatter, chlorophyll fluorometer, particle size analyser, Niskin bottles, scanning electron microscopy), 4) sand and gravel bedload transport estimates (DySPI image processing), 5) transfer dynamics of fine grains within a coarse matrix and their depth of penetration (radionuclides measurements in stratigraphic samples). The four stations present different grain size vertical sorting from a quasi-permanent armouring to a homogenous distribution. The sediment cover condition is directly linked to hydrodynamic capacity and sediment availability. Fine grain ratio within deep sediment layers (up to 10 cm) is higher when the bed armouring is durable. However, fine sediments are not permanently depth trapped: deep layers are composed of few years-old radionuclide tracers fixed on fine grains and a vertical mixing coefficient has been evaluated for each sediment cover. Fine grain dynamics within a coarse matrix is inversely proportional to the robustness of the armour layer. For current

  10. Access to Optically Pure β-Hydroxy Esters via Non-Enzymatic Kinetic Resolution by a Planar-Chiral DMAP Catalyst

    Directory of Open Access Journals (Sweden)

    Alba E. Díazlvarez

    2014-09-01

    Full Text Available The development of new approaches to obtain optically pure β-hydroxy esters is an important area in synthetic organic chemistry since they are precursors of other high value compounds. Herein, the kinetic resolution of racemic β-hydroxy esters using a planar-chiral DMAP derivative catalyst is presented. Following this procedure, a range of aromatic β-hydroxy esters was obtained in excellent selectivities (up to s = 107 and high enantiomeric excess (up to 99% ee. Furthermore, the utility of the present method was demonstrated in the synthesis of (S-3-hydroxy-N-methyl-3-phenylpropanamide, a key intermediate for bioactive molecules such as fluoxetine, tomoxetine or nisoxetine, in its enantiomerically pure form.

  11. omega-Amino acid:pyruvate transaminase from Alcaligenes denitrificans Y2k-2: a new catalyst for kinetic resolution of beta-amino acids and amines.

    Science.gov (United States)

    Yun, Hyungdon; Lim, Seongyop; Cho, Byung-Kwan; Kim, Byung-Gee

    2004-04-01

    Alcaligenes denitrificans Y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed omega-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic beta-amino acid, and the corresponding structural gene (aptA) was cloned. The gene was functionally expressed in Escherichia coli BL21 by using an isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible pET expression system (9.6 U/mg), and the recombinant AptA was purified to show a specific activity of 77.2 U/mg for L-beta-amino-n-butyric acid (L-beta-ABA). The enzyme converts various beta-amino acids and amines to the corresponding beta-keto acids and ketones by using pyruvate as an amine acceptor. The apparent K(m) and V(max) for L-beta-ABA were 56 mM and 500 U/mg, respectively, in the presence of 10 mM pyruvate. In the presence of 10 mM L-beta-ABA, the apparent K(m) and V(max) for pyruvate were 11 mM and 370 U/mg, respectively. The enzyme exhibits high stereoselectivity (E > 80) in the kinetic resolution of 50 mM D,L-beta-ABA, producing optically pure D-beta-ABA (99% enantiomeric excess) with 53% conversion.

  12. ω-Amino Acid:Pyruvate Transaminase from Alcaligenes denitrificans Y2k-2: a New Catalyst for Kinetic Resolution of β-Amino Acids and Amines

    Science.gov (United States)

    Yun, Hyungdon; Lim, Seongyop; Cho, Byung-Kwan; Kim, Byung-Gee

    2004-01-01

    Alcaligenes denitrificans Y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed ω-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic β-amino acid, and the corresponding structural gene (aptA) was cloned. The gene was functionally expressed in Escherichia coli BL21 by using an isopropyl-β-d-thiogalactopyranoside (IPTG)-inducible pET expression system (9.6 U/mg), and the recombinant AptA was purified to show a specific activity of 77.2 U/mg for l-β-amino-n-butyric acid (l-β-ABA). The enzyme converts various β-amino acids and amines to the corresponding β-keto acids and ketones by using pyruvate as an amine acceptor. The apparent Km and Vmax for l-β-ABA were 56 mM and 500 U/mg, respectively, in the presence of 10 mM pyruvate. In the presence of 10 mM l-β-ABA, the apparent Km and Vmax for pyruvate were 11 mM and 370 U/mg, respectively. The enzyme exhibits high stereoselectivity (E > 80) in the kinetic resolution of 50 mM d,l-β-ABA, producing optically pure d-β-ABA (99% enantiomeric excess) with 53% conversion. PMID:15066855

  13. Dynamic phase transition in the kinetic spin-2 Blume-Emery-Griffiths model in an oscillating field

    Energy Technology Data Exchange (ETDEWEB)

    Ertas, Mehmet [Institute of Science, Erciyes University, 38039 Kayseri (Turkey); Canko, Osman [Department of Physics, Erciyes University, 38039 Kayseri (Turkey); Keskin, Mustafa [Department of Physics, Erciyes University, 38039 Kayseri (Turkey)], E-mail: keskin@erciyes.edu.tr

    2008-06-15

    We extend our recent paper [M. Keskin, O. Canko, M. Ertas, J. Exp. Theor. Phys. (Sov. Phys. JETP) 105 (2007) 1190.] to present a study, within a mean-field approach, the stationary states of the kinetic spin-2 Blume-Emery-Griffiths model in the presence of a time-dependent oscillating magnetic field by using the Glauber-type of stochastic dynamics. We found 20 fundamental types of dynamic phase diagrams where exhibit more complex and richer phase diagrams than our recent paper. Especially, the obtained dynamic phase diagrams show the dynamic triple, quadruple and dynamic double critical end points besides dynamic tricritical points that depending on interaction parameters. The phase diagrams also exhibit a disordered (d) and the ferromagnetic-2 (f{sub 2}) phases, and the f{sub 2}+d, f{sub 2}+fq, fq+d, f{sub 2}+f{sub 1}+fq and f{sub 2}+fq+d, where f{sub 1} are fq the ferromagnetic-1 and ferroquadrupolar or simply quadrupolar phases respectively, coexistence phase regions that strongly depend on interaction parameters.

  14. Multicritical dynamical phase diagrams of the kinetic Blume-Emery-Griffiths model with repulsive biquadratic coupling in an oscillating field

    Energy Technology Data Exchange (ETDEWEB)

    Temizer, Umuet [Department of Physics, Bozok University, 66100 Yozgat (Turkey); Kantar, Ersin [Institute of Science, Erciyes University, 38039 Kayseri (Turkey); Keskin, Mustafa [Department of Physics, Erciyes University, 38039 Kayseri (Turkey)], E-mail: keskin@erciyes.edu.tr; Canko, Osman [Department of Physics, Erciyes University, 38039 Kayseri (Turkey)

    2008-06-15

    We study, within a mean-field approach, the stationary states of the kinetic Blume-Emery-Griffiths model with repulsive biquadratic coupling under the presence of a time-varying (sinusoidal) magnetic field. We employ the Glauber-type stochastic dynamics to construct set of dynamic equations of motion. The behavior of the time dependence of the order parameters and the behavior of the average order parameters in a period, which is also called the dynamic order parameters, as functions of the reduced temperature are investigated. The dynamic phase transition points are calculated and phase diagrams are presented in the reduced magnetic field amplitude and reduced temperature plane. The dynamical transition from one regime to the other can be of first- or second order depending on the region in the phase diagram. According to the values of the crystal field interaction or single-ion anisotropy constant and biquadratic exchange constant, we find 20 fundamental types of phase diagrams which exhibit many dynamic critical points, such as tricritical points, zero-temperature critical points, double critical end points, critical end point, triple point and multicritical point. Moreover, besides a disordered and ordered phases, seven coexistence phase regions exist in the system.

  15. Dynamic phase transition in the kinetic spin-2 Blume-Emery-Griffiths model in an oscillating field

    International Nuclear Information System (INIS)

    Ertas, Mehmet; Canko, Osman; Keskin, Mustafa

    2008-01-01

    We extend our recent paper [M. Keskin, O. Canko, M. Ertas, J. Exp. Theor. Phys. (Sov. Phys. JETP) 105 (2007) 1190.] to present a study, within a mean-field approach, the stationary states of the kinetic spin-2 Blume-Emery-Griffiths model in the presence of a time-dependent oscillating magnetic field by using the Glauber-type of stochastic dynamics. We found 20 fundamental types of dynamic phase diagrams where exhibit more complex and richer phase diagrams than our recent paper. Especially, the obtained dynamic phase diagrams show the dynamic triple, quadruple and dynamic double critical end points besides dynamic tricritical points that depending on interaction parameters. The phase diagrams also exhibit a disordered (d) and the ferromagnetic-2 (f 2 ) phases, and the f 2 +d, f 2 +fq, fq+d, f 2 +f 1 +fq and f 2 +fq+d, where f 1 are fq the ferromagnetic-1 and ferroquadrupolar or simply quadrupolar phases respectively, coexistence phase regions that strongly depend on interaction parameters

  16. Dynamic phase transition in the kinetic spin-2 Blume-Emery-Griffiths model in an oscillating field

    Science.gov (United States)

    Ertaş, Mehmet; Canko, Osman; Keskin, Mustafa

    We extend our recent paper [M. Keskin, O. Canko, M. Ertaş, J. Exp. Theor. Phys. (Sov. Phys. JETP) 105 (2007) 1190.] to present a study, within a mean-field approach, the stationary states of the kinetic spin-2 Blume-Emery-Griffiths model in the presence of a time-dependent oscillating magnetic field by using the Glauber-type of stochastic dynamics. We found 20 fundamental types of dynamic phase diagrams where exhibit more complex and richer phase diagrams than our recent paper. Especially, the obtained dynamic phase diagrams show the dynamic triple, quadruple and dynamic double critical end points besides dynamic tricritical points that depending on interaction parameters. The phase diagrams also exhibit a disordered ( d) and the ferromagnetic-2 ( f2) phases, and the f2+ d, f2+ fq, fq+ d, f2+ f1+ fq and f2+ fq+ d, where f1 are fq the ferromagnetic-1 and ferroquadrupolar or simply quadrupolar phases respectively, coexistence phase regions that strongly depend on interaction parameters.

  17. Remotely Sensed High-Resolution Global Cloud Dynamics for Predicting Ecosystem and Biodiversity Distributions.

    Directory of Open Access Journals (Sweden)

    Adam M Wilson

    2016-03-01

    Full Text Available Cloud cover can influence numerous important ecological processes, including reproduction, growth, survival, and behavior, yet our assessment of its importance at the appropriate spatial scales has remained remarkably limited. If captured over a large extent yet at sufficiently fine spatial grain, cloud cover dynamics may provide key information for delineating a variety of habitat types and predicting species distributions. Here, we develop new near-global, fine-grain (≈1 km monthly cloud frequencies from 15 y of twice-daily Moderate Resolution Imaging Spectroradiometer (MODIS satellite images that expose spatiotemporal cloud cover dynamics of previously undocumented global complexity. We demonstrate that cloud cover varies strongly in its geographic heterogeneity and that the direct, observation-based nature of cloud-derived metrics can improve predictions of habitats, ecosystem, and species distributions with reduced spatial autocorrelation compared to commonly used interpolated climate data. These findings support the fundamental role of remote sensing as an effective lens through which to understand and globally monitor the fine-grain spatial variability of key biodiversity and ecosystem properties.

  18. Evaluations of high-resolution dynamically downscaled ensembles over the contiguous United States

    Science.gov (United States)

    Zobel, Zachary; Wang, Jiali; Wuebbles, Donald J.; Kotamarthi, V. Rao

    2018-02-01

    This study uses Weather Research and Forecast (WRF) model to evaluate the performance of six dynamical downscaled decadal historical simulations with 12-km resolution for a large domain (7200 × 6180 km) that covers most of North America. The initial and boundary conditions are from three global climate models (GCMs) and one reanalysis data. The GCMs employed in this study are the Geophysical Fluid Dynamics Laboratory Earth System Model with Generalized Ocean Layer Dynamics component, Community Climate System Model, version 4, and the Hadley Centre Global Environment Model, version 2-Earth System. The reanalysis data is from the National Centers for Environmental Prediction-US. Department of Energy Reanalysis II. We analyze the effects of bias correcting, the lateral boundary conditions and the effects of spectral nudging. We evaluate the model performance for seven surface variables and four upper atmospheric variables based on their climatology and extremes for seven subregions across the United States. The results indicate that the simulation's performance depends on both location and the features/variable being tested. We find that the use of bias correction and/or nudging is beneficial in many situations, but employing these when running the RCM is not always an improvement when compared to the reference data. The use of an ensemble mean and median leads to a better performance in measuring the climatology, while it is significantly biased for the extremes, showing much larger differences than individual GCM driven model simulations from the reference data. This study provides a comprehensive evaluation of these historical model runs in order to make informed decisions when making future projections.

  19. Estimating kinetic parameters from dynamic contrast-enhanced T(1)-weighted MRI of a diffusable tracer: standardized quantities and symbols

    DEFF Research Database (Denmark)

    Tofts, P.S.; Brix, G; Buckley, D.L.

    1999-01-01

    We describe a standard set of quantity names and symbols related to the estimation of kinetic parameters from dynamic contrast-enhanced T(1)-weighted magnetic resonance imaging data, using diffusable agents such as gadopentetate dimeglumine (Gd-DTPA). These include a) the volume transfer constant K......-limited conditions K(trans) equals the blood plasma flow per unit volume of tissue; under permeability-limited conditions K(trans) equals the permeability surface area product per unit volume of tissue. We relate these quantities to previously published work from our groups; our future publications will refer...

  20. Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations

    DEFF Research Database (Denmark)

    Costa, Rafael S.; Machado, Daniel; Rocha, Isabel

    2010-01-01

    , represent nowadays the limiting factor in the construction of such models. In this study, we compare four alternative modeling approaches based on Michaelis–Menten kinetics for the bi-molecular reactions and different types of simplified rate equations for the remaining reactions (generalized mass action......The construction of dynamic metabolic models at reaction network level requires the use of mechanistic enzymatic rate equations that comprise a large number of parameters. The lack of knowledge on these equations and the difficulty in the experimental identification of their associated parameters...

  1. In Vivo Optical Imaging for Targeted Drug Kinetics and Localization for Oral Surgery and Super-Resolution, Facilitated by Printed Phantoms

    Science.gov (United States)

    Bentz, Brian Z.

    Many human cancer cell types over-express folate receptors, and this provides an opportunity to develop targeted anti-cancer drugs. For these drugs to be effective, their kinetics must be well understood in vivo and in deep tissue where tumors occur. We demonstrate a method for imaging these parameters by incorporating a kinetic compartment model and fluorescence into optical diffusion tomography (ODT). The kinetics were imaged in a live mouse, and found to be in agreement with previous in vitro studies, demonstrating the validity of the method and its feasibility as an effective tool in preclinical drug development studies. Progress in developing optical imaging for biomedical applications requires customizable and often complex objects known as "phantoms" for testing and evaluation. We present new optical phantoms fabricated using inexpensive 3D printing methods with multiple materials, allowing for the placement of complex inhomogeneities in heterogeneous or anatomically realistic geometries, as opposed to previous phantoms which were limited to simple shapes formed by molds or machining. Furthermore, we show that Mie theory can be used to design the optical properties to match a target tissue. The phantom fabrication methods are versatile, can be applied to optical imaging methods besides diffusive imaging, and can be used in the calibration of live animal imaging data. Applications of diffuse optical imaging in the operating theater have been limited in part due to computational burden. We present an approach for the fast localization of arteries in the roof of the mouth that has the potential to reduce complications. Furthermore, we use the extracted position information to fabricate a custom surgical guide using 3D printing that could protect the arteries during surgery. The resolution of ODT is severely limited by the attenuation of high spatial frequencies. We present a super-resolution method achieved through the point localization of fluorescent

  2. Extracting a kinetic relation from the dynamics of a bistable chain

    International Nuclear Information System (INIS)

    Zhao, Qingze; Purohit, Prashant K

    2014-01-01

    We integrate Newton's second law for a chain of masses and bistable springs with a spinodal region with the goal of extracting a kinetic relation for propagating phase boundaries. Our numerical experiments correspond to the impact on a bar made of phase changing material. By reading off the spring extensions ahead and behind the phase boundaries in our numerical experiments, we compute a driving force and plot it as a function of the phase boundary velocity to get a kinetic relation. We then show that this kinetic relation results in solutions to Riemann problems in continuum bars that agree with the corresponding numerical experiments on the discrete mass–spring chain. We also integrate Langevin's equations of motion for the same chain of masses and springs to account for the presence of a heat bath at a fixed temperature. We find that the xt-plane looks similar to the purely mechanical numerical experiments at low temperatures but at high temperatures there is an increased incidence of random nucleation events. Using results from both impact and Riemann problems, we show that the kinetic relation is a function of the bath temperature. (paper)

  3. Neural estimation of kinetic rate constants from dynamic PET-scans

    DEFF Research Database (Denmark)

    Fog, Torben L.; Nielsen, Lars Hupfeldt; Hansen, Lars Kai

    1994-01-01

    A feedforward neural net is trained to invert a simple three compartment model describing the tracer kinetics involved in the metabolism of [18F]fluorodeoxyglucose in the human brain. The network can estimate rate constants from positron emission tomography sequences and is about 50 times faster ...

  4. Assessment of input function distortions on kinetic model parameters in simulated dynamic 82Rb PET perfusion studies

    International Nuclear Information System (INIS)

    Meyer, Carsten; Peligrad, Dragos-Nicolae; Weibrecht, Martin

    2007-01-01

    Cardiac 82 rubidium dynamic PET studies allow quantifying absolute myocardial perfusion by using tracer kinetic modeling. Here, the accurate measurement of the input function, i.e. the tracer concentration in blood plasma, is a major challenge. This measurement is deteriorated by inappropriate temporal sampling, spillover, etc. Such effects may influence the measured input peak value and the measured blood pool clearance. The aim of our study is to evaluate the effect of input function distortions on the myocardial perfusion as estimated by the model. To this end, we simulate noise-free myocardium time activity curves (TACs) with a two-compartment kinetic model. The input function to the model is a generic analytical function. Distortions of this function have been introduced by varying its parameters. Using the distorted input function, the compartment model has been fitted to the simulated myocardium TAC. This analysis has been performed for various sets of model parameters covering a physiologically relevant range. The evaluation shows that ±10% error in the input peak value can easily lead to ±10-25% error in the model parameter K 1 , which relates to myocardial perfusion. Variations in the input function tail are generally less relevant. We conclude that an accurate estimation especially of the plasma input peak is crucial for a reliable kinetic analysis and blood flow estimation

  5. Impact of human milk pasteurization on the kinetics of peptide release during in vitro dynamic term newborn digestion.

    Science.gov (United States)

    Deglaire, Amélie; De Oliveira, Samira C; Jardin, Julien; Briard-Bion, Valérie; Emily, Mathieu; Ménard, Olivia; Bourlieu, Claire; Dupont, Didier

    2016-07-01

    Holder pasteurization (62.5°C, 30 min) ensures sanitary quality of donor's human milk but also denatures beneficial proteins. Understanding whether this further impacts the kinetics of peptide release during gastrointestinal digestion of human milk was the aim of the present paper. Mature raw (RHM) or pasteurized (PHM) human milk were digested (RHM, n = 2; PHM, n = 3) by an in vitro dynamic system (term stage). Label-free quantitative peptidomics was performed on milk and digesta (ten time points). Ascending hierarchical clustering was conducted on "Pasteurization × Digestion time" interaction coefficients. Preproteolysis occurred in human milk (159 unique peptides; RHM: 91, PHM: 151), mostly on β-casein (88% of the endogenous peptides). The predicted cleavage number increased with pasteurization, potentially through plasmin activation (plasmin cleavages: RHM, 53; PHM, 76). During digestion, eight clusters resumed 1054 peptides from RHM and PHM, originating for 49% of them from β-casein. For seven clusters (57% of peptides), the kinetics of peptide release differed between RHM and PHM. The parent protein was significantly linked to the clustering (p-value = 1.4 E-09), with β-casein and lactoferrin associated to clusters in an opposite manner. Pasteurization impacted selectively gastric and intestinal kinetics of peptide release in term newborns, which may have further nutritional consequences. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Mechanical behavior and high-resolution EBSD investigation of the microstructural evolution in AISI 321 stainless steel under dynamic loading condition

    International Nuclear Information System (INIS)

    Tiamiyu, A.A.; Eskandari, M.; Sanayei, Mohsen; Odeshi, A.G.; Szpunar, J.A.

    2016-01-01

    The impact response of three regions (top, mid and center) across the thickness of AISI 321 austenitic stainless steel plate at high strain rates (>6000 s −1 ) was studied using the split Hopkinson pressure bar system. The result shows that texture and stored energy heterogeneity across plate thickness influenced the mechanical responses of the investigated steel in these regions. Microstructural evaluation using high-resolution electron backscattered diffraction (HR-EBSD) analysis showed that strengthening in AISI 321 steel originates from the evolution of strain-induced martensite and formation of nano-carbides in addition to plastic deformation by mechanical twinning and slip. This resulted in a desirable combination of high strength and good ductility (approx. 2000 MPa at 0.42 true strain). Phase transformation, dynamic recrystallization and formation of nano-carbides were confirmed within the adiabatic shear band (ASB) region. The average dynamic recrystallized (DRX) grain size in the shear band region is 0.28 µm in comparison to grain size of 15 µm outside the shear bands. The nano-sized grain inside the shear bands is proposed to form by rotational dynamic recrystallization. A comparative study of the alloy's behavior under dynamic and quasi-static compression shows that the stability of austenite is higher at high strain rates and lower at a low strain rate. The strength in the dynamically impacted specimen is compromised as a result of the suppressed evolution of strain-induced martensite and mechanical twin. Martensitic transformation under both loading conditions follows the FCC É£-austenite→BCC ά-martensite kinetic path and both phases obey the Kurdjumov-Sachs' {(111)É£||(110)ά and <−101>É£||<1–11>ά} orientation relationship.

  7. Mechanical behavior and high-resolution EBSD investigation of the microstructural evolution in AISI 321 stainless steel under dynamic loading condition

    Energy Technology Data Exchange (ETDEWEB)

    Tiamiyu, A.A., E-mail: ahmed.tiamiyu@usask.ca [Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Sask. (Canada); Eskandari, M. [Department of Materials Science & Engineering, Faculty of Engineering, Shahid Chamran University of Ahvaz, Ahvaz (Iran, Islamic Republic of); Sanayei, Mohsen; Odeshi, A.G.; Szpunar, J.A. [Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Sask. (Canada)

    2016-09-15

    The impact response of three regions (top, mid and center) across the thickness of AISI 321 austenitic stainless steel plate at high strain rates (>6000 s{sup −1}) was studied using the split Hopkinson pressure bar system. The result shows that texture and stored energy heterogeneity across plate thickness influenced the mechanical responses of the investigated steel in these regions. Microstructural evaluation using high-resolution electron backscattered diffraction (HR-EBSD) analysis showed that strengthening in AISI 321 steel originates from the evolution of strain-induced martensite and formation of nano-carbides in addition to plastic deformation by mechanical twinning and slip. This resulted in a desirable combination of high strength and good ductility (approx. 2000 MPa at 0.42 true strain). Phase transformation, dynamic recrystallization and formation of nano-carbides were confirmed within the adiabatic shear band (ASB) region. The average dynamic recrystallized (DRX) grain size in the shear band region is 0.28 µm in comparison to grain size of 15 µm outside the shear bands. The nano-sized grain inside the shear bands is proposed to form by rotational dynamic recrystallization. A comparative study of the alloy's behavior under dynamic and quasi-static compression shows that the stability of austenite is higher at high strain rates and lower at a low strain rate. The strength in the dynamically impacted specimen is compromised as a result of the suppressed evolution of strain-induced martensite and mechanical twin. Martensitic transformation under both loading conditions follows the FCC É£-austenite→BCC ά-martensite kinetic path and both phases obey the Kurdjumov-Sachs' {(111)É£||(110)ά and <−101>É£||<1–11>ά} orientation relationship.

  8. High resolution dynamical downscaling of air temperature and relative humidity: performance assessment of WRF for Portugal

    Science.gov (United States)

    Menezes, Isilda; Pereira, Mário; Moreira, Demerval; Carvalheiro, Luís; Bugalho, Lourdes; Corte-Real, João

    2017-04-01

    Air temperature and relative humidity are two of the atmospheric variables with higher impact on human and natural systems, contributing to define the stress/comfortable conditions, affecting the productivity and health of the individuals as well as diminishing the resilience to other environmental hazards. Atmospheric regional models, driven by large scale forecasts from global circulation models, are the best way to reproduce such environmental conditions in high space-time resolution. This study is focused on the performance assessment of the WRF mesoscale model to perform high resolution dynamical downscaling for Portugal with three two-way nested grids, at 60 km, 20 km and 5 km horizontal resolution. The simulations of WRF models were produced with different initial and boundary forcing conditions. The NCEP-FNL Operational Global Analysis data available on 1-degree by 1-degree grid every six hours and ERA-Interim reanalyses dataset were used to drive the models. Two alternative configurations of the WRF model, including planetary boundary, layer schemes, microphysics, land-surface models, radiation schemes, were used and tested within the 5 km spatial resolution domain. Simulations of air temperature and relative humidity were produced for January and July of 2016 and compared with the observed datasets provided by the Instituto Português do Mar e da Atmosfera (IPMA) for 83 weather stations. Different performance measures of bias, precision, and accuracy were used, namely normalized bias, standard deviation, mean absolute error, root mean square error, bias of root mean square error as well as correlation based measures (e.g., coefficient of determination) and goodness of fit measures (index of agreement). Main conclusions from the obtained results reveal: (i) great similarity between the spatial patterns of the simulated and observed fields; (ii) only small differences between simulations produced with ERA-Interim and NCEP-FNL, in spite of some differences

  9. Improving malignancy prediction in breast lesions with the combination of apparent diffusion coefficient and dynamic contrast-enhanced kinetic descriptors

    International Nuclear Information System (INIS)

    Nogueira, Luisa; Brandão, Sofia; Matos, Eduarda; Gouveia Nunes, Rita; Ferreira, Hugo Alexandre; Loureiro, Joana; Ramos, Isabel

    2015-01-01

    Aim: To assess how the joint use of apparent diffusion coefficient (ADC) and kinetic parameters (uptake phase and delayed enhancement characteristics) from dynamic contrast-enhanced (DCE) can boost the ability to predict breast lesion malignancy. Materials and methods: Breast magnetic resonance examinations including DCE and diffusion-weighted imaging (DWI) were performed on 51 women. The association between kinetic parameters and ADC were evaluated and compared between lesion types. Models with binary outcome of malignancy were studied using generalized estimating equations (GEE), (GEE), and using kinetic parameters and ADC values as malignancy predictors. Model accuracy was assessed using the corrected maximum quasi-likelihood under the independence confidence criterion (QICC). Predicted probability of malignancy was estimated for the best model. Results: ADC values were significantly associated with kinetic parameters: medium and rapid uptake phase (p<0.001) and plateau and washout curve types (p=0.004). Comparison between lesion type showed significant differences for ADC (p=0.001), early phase (p<0.001), and curve type (p<0.001). The predicted probabilities of malignancy for the first ADC quartile (≤1.17×10 −3  mm 2 /s) and persistent, plateau and washout curves, were 54.6%, 86.9%, and 97.8%, respectively, and for the third ADC quartile (≥1.51×10 −3  mm 2 /s) were 3.2%, 15.5%, and 54.8%, respectively. The predicted probability of malignancy was less than 5% for 18.8% of the lesions and greater than 33% for 50.7% of the lesions (24/35 lesions, corresponding to a malignancy rate of 68.6%). Conclusion: The best malignancy predictors were low ADCs and washout curves. ADC and kinetic parameters provide differentiated information on the microenvironment of the lesion, with joint models displaying improved predictive performance. -- Highlights: •ADC and kinetic parameters provide diverse information regarding lesion environment. •The best predictors

  10. High-Resolution Dynamical Downscaling Ensemble Projections of Future Extreme Temperature Distributions for the United States

    Science.gov (United States)

    Zobel, Zachary; Wang, Jiali; Wuebbles, Donald J.; Kotamarthi, V. Rao

    2017-12-01

    The aim of this study is to examine projections of extreme temperatures over the continental United States (CONUS) for the 21st century using an ensemble of high spatial resolution dynamically downscaled model simulations with different boundary conditions. The downscaling uses the Weather Research and Forecast model at a spatial resolution of 12 km along with outputs from three different Coupled Model Intercomparison Project Phase 5 global climate models that provide boundary conditions under two different future greenhouse gas (GHG) concentration trajectories. The results from two decadal-length time slices (2045-2054 and 2085-2094) are compared with a historical decade (1995-2004). Probability density functions of daily maximum/minimum temperatures are analyzed over seven climatologically cohesive regions of the CONUS. The impacts of different boundary conditions as well as future GHG concentrations on extreme events such as heat waves and days with temperature higher than 95°F are also investigated. The results show that the intensity of extreme warm temperature in future summer is significantly increased, while the frequency of extreme cold temperature in future winter decreases. The distribution of summer daily maximum temperature experiences a significant warm-side shift and increased variability, while the distribution of winter daily minimum temperature is projected to have a less significant warm-side shift with decreased variability. Using "business-as-usual" scenario, 5-day heat waves are projected to occur at least 5-10 times per year in most CONUS and ≥95°F days will increase by 1-2 months by the end of the century.

  11. High-Resolution Monitoring of Himalayan Glacier Dynamics Using Unmanned Aerial Vehicles

    Science.gov (United States)

    Immerzeel, W.; Kraaijenbrink, P. D. A.; Shea, J.; Shrestha, A. B.; Pellicciotti, F.; Bierkens, M. F.; de Jong, S. M.

    2014-12-01

    Himalayan glacier tongues are commonly debris covered and play an important role in modulating the glacier response to climate . However, they remain relatively unstudied because of the inaccessibility of the terrain and the difficulties in field work caused by the thick debris mantles. Observations of debris-covered glaciers are therefore limited to point locations and airborne remote sensing may bridge the gap between scarce, point field observations and coarse resolution space-borne remote sensing. In this study we deploy an Unmanned Airborne Vehicle (UAV) on two debris covered glaciers in the Nepalese Himalayas: the Lirung and Langtang glacier during four field campaigns in 2013 and 2014. Based on stereo-imaging and the structure for motion algorithm we derive highly detailed ortho-mosaics and digital elevation models (DEMs), which we geometrically correct using differential GPS observations collected in the field. Based on DEM differencing and manual feature tracking we derive the mass loss and the surface velocity of the glacier at a high spatial resolution and accuracy. We also assess spatiotemporal changes in supra-glacial lakes and ice cliffs based on the imagery. On average, mass loss is limited and the surface velocity is very small. However, the spatial variability of melt rates is very high, and ice cliffs and supra-glacial ponds show mass losses that can be an order of magnitude higher than the average. We suggest that future research should focus on the interaction between supra-glacial ponds, ice cliffs and englacial hydrology to further understand the dynamics of debris-covered glaciers. Finally, we conclude that UAV deployment has large potential in glaciology and it represents a substantial advancement over methods currently applied in studying glacier surface features.

  12. Assessments of the kinetic and dynamic transient behavior of sub-critical systems (ADS) in comparison to critical reactor systems

    International Nuclear Information System (INIS)

    Schikorr, W.M.

    2001-01-01

    The neutron kinetic and the reactor dynamic behavior of Accelerator Driven Systems (ADS) is significantly different from those of conventional power reactor systems currently in use for the production of power. It is the objective of this study to examine and to demonstrate the intrinsic differences of the kinetic and dynamic behavior of accelerator driven systems to typical plant transient initiators in comparison to the known, kinetic and dynamic behavior of critical thermal and fast reactor systems. It will be shown that in sub-critical assemblies, changes in reactivity or in the external neutron source strength lead to an asymptotic power level essentially described by the instantaneous power change (i.e. prompt jump). Shutdown of ADS operating at high levels of sub-criticality, (i.e. k eff ∼0.99), without the support of reactivity control systems (such as control or safety rods), may be problematic in case the ability of cooling of the core should be impaired (i.e. loss of coolant flow). In addition, the dynamic behavior of sub-critical systems to typical plant transients such as protected or unprotected loss of flow (LOF) or heat sink (LOH) transients are not necessarily substantially different from the plant dynamic behavior of critical systems if the reactivity feedback coefficients of the ADS design are unfavorable. As expected, the state of sub-criticality and the temperature feedback coefficients, such as Doppler and coolant temperature coefficient, play dominant roles in determining the course and direction of plant transients. Should the combination of these safety coefficients be very unfavorable, not much additional margin in safety may be gained by making a critical system only sub-critical (i.e. k eff ∼0.95). A careful optimization procedure between the selected operating level of sub-criticality, the safety reactivity coefficients and the possible need for additional reactivity control systems seems, therefore, advisable during the early

  13. Motion robust high resolution 3D free-breathing pulmonary MRI using dynamic 3D image self-navigator.

    Science.gov (United States)

    Jiang, Wenwen; Ong, Frank; Johnson, Kevin M; Nagle, Scott K; Hope, Thomas A; Lustig, Michael; Larson, Peder E Z

    2018-06-01

    To achieve motion robust high resolution 3D free-breathing pulmonary MRI utilizing a novel dynamic 3D image navigator derived directly from imaging data. Five-minute free-breathing scans were acquired with a 3D ultrashort echo time (UTE) sequence with 1.25 mm isotropic resolution. From this data, dynamic 3D self-navigating images were reconstructed under locally low rank (LLR) constraints and used for motion compensation with one of two methods: a soft-gating technique to penalize the respiratory motion induced data inconsistency, and a respiratory motion-resolved technique to provide images of all respiratory motion states. Respiratory motion estimation derived from the proposed dynamic 3D self-navigator of 7.5 mm isotropic reconstruction resolution and a temporal resolution of 300 ms was successful for estimating complex respiratory motion patterns. This estimation improved image quality compared to respiratory belt and DC-based navigators. Respiratory motion compensation with soft-gating and respiratory motion-resolved techniques provided good image quality from highly undersampled data in volunteers and clinical patients. An optimized 3D UTE sequence combined with the proposed reconstruction methods can provide high-resolution motion robust pulmonary MRI. Feasibility was shown in patients who had irregular breathing patterns in which our approach could depict clinically relevant pulmonary pathologies. Magn Reson Med 79:2954-2967, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  14. Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data.

    Science.gov (United States)

    Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

    2017-05-07

    A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

  15. Dynamical scaling, domain-growth kinetics, and domain-wall shapes of quenched two-dimensional anisotropic XY models

    DEFF Research Database (Denmark)

    Mouritsen, Ole G.; Praestgaard, Eigil

    1988-01-01

    obeys dynamical scaling and the shape of the dynamical scaling function pertaining to the structure factor is found to depend on P. Specifically, this function is described by a Porod-law behavior, q-ω, where ω increases with the wall softness. The kinetic exponent, which describes how the linear domain...... infinite to zero temperature as well as to nonzero temperatures below the ordering transition. The continuous nature of the spin variables causes the domain walls to be ‘‘soft’’ and characterized by a finite thickness. The steady-state thickness of the walls can be varied by a model parameter, P. At zero...... size varies with time, R(t)∼tn, is for both models at zero temperature determined to be n≃0.25, independent of P. At finite temperatures, the growth kinetics is found to cross over to the Lifshitz-Allen-Cahn law characterized by n≃0.50. The results support the idea of two separate zero...

  16. Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data

    Science.gov (United States)

    Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

    2017-05-01

    A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

  17. Dynamic phase transitions and dynamic phase diagrams in the kinetic spin-5/2 Blume–Capel model in an oscillating external magnetic field: Effective-field theory and the Glauber-type stochastic dynamics approach

    International Nuclear Information System (INIS)

    Ertaş, Mehmet; Keskin, Mustafa; Deviren, Bayram

    2012-01-01

    Using an effective field theory with correlations, we study a kinetic spin-5/2 Blume–Capel model with bilinear exchange interaction and single-ion crystal field on a square lattice. The effective-field dynamic equation is derived by employing the Glauber transition rates. First, the phases in the kinetic system are obtained by solving this dynamic equation. Then, the thermal behavior of the dynamic magnetization, the hysteresis loop area and correlation are investigated in order to characterize the nature of the dynamic transitions and to obtain dynamic phase transition temperatures. Finally, we present the phase diagrams in two planes, namely (T/zJ, h 0 /zJ) and (T/zJ, D/zJ), where T absolute temperature, h 0 , the amplitude of the oscillating field, D, crystal field interaction or single-ion anisotropy constant and z denotes the nearest-neighbor sites of the central site. The phase diagrams exhibit four fundamental phases and ten mixed phases which are composed of binary, ternary and tetrad combination of fundamental phases, depending on the crystal field interaction parameter. Moreover, the phase diagrams contain a dynamic tricritical point (T), a double critical end point (B), a multicritical point (A) and zero-temperature critical point (Z). - Highlights: ► The effective-field theory is used to study the kinetic spin-5/2 Ising Blume–Capel model. ► Time variations of average order parameter have been studied to find phases in the system. ► The dynamic magnetization, hysteresis loop area and correlation have been calculated. ► The dynamic phase boundaries of the system depend on D/zJ. ► The dynamic phase diagrams are presented in the (T/zJ, h 0 /zJ) and (D/zJ, T/zJ) planes.

  18. Dynamic phase transitions and dynamic phase diagrams in the kinetic spin-5/2 Blume-Capel model in an oscillating external magnetic field: Effective-field theory and the Glauber-type stochastic dynamics approach

    Energy Technology Data Exchange (ETDEWEB)

    Ertas, Mehmet [Department of Physics, Erciyes University, 38039 Kayseri (Turkey); Keskin, Mustafa, E-mail: keskin@erciyes.edu.tr [Department of Physics, Erciyes University, 38039 Kayseri (Turkey); Deviren, Bayram [Department of Physics, Nevsehir University, 50300 Nevsehir (Turkey)

    2012-04-15

    Using an effective field theory with correlations, we study a kinetic spin-5/2 Blume-Capel model with bilinear exchange interaction and single-ion crystal field on a square lattice. The effective-field dynamic equation is derived by employing the Glauber transition rates. First, the phases in the kinetic system are obtained by solving this dynamic equation. Then, the thermal behavior of the dynamic magnetization, the hysteresis loop area and correlation are investigated in order to characterize the nature of the dynamic transitions and to obtain dynamic phase transition temperatures. Finally, we present the phase diagrams in two planes, namely (T/zJ, h{sub 0}/zJ) and (T/zJ, D/zJ), where T absolute temperature, h{sub 0}, the amplitude of the oscillating field, D, crystal field interaction or single-ion anisotropy constant and z denotes the nearest-neighbor sites of the central site. The phase diagrams exhibit four fundamental phases and ten mixed phases which are composed of binary, ternary and tetrad combination of fundamental phases, depending on the crystal field interaction parameter. Moreover, the phase diagrams contain a dynamic tricritical point (T), a double critical end point (B), a multicritical point (A) and zero-temperature critical point (Z). - Highlights: Black-Right-Pointing-Pointer The effective-field theory is used to study the kinetic spin-5/2 Ising Blume-Capel model. Black-Right-Pointing-Pointer Time variations of average order parameter have been studied to find phases in the system. Black-Right-Pointing-Pointer The dynamic magnetization, hysteresis loop area and correlation have been calculated. Black-Right-Pointing-Pointer The dynamic phase boundaries of the system depend on D/zJ. Black-Right-Pointing-Pointer The dynamic phase diagrams are presented in the (T/zJ, h{sub 0}/zJ) and (D/zJ, T/zJ) planes.

  19. Correction of the kinetic blur and representation of heart dynamics in nuclear imagery

    International Nuclear Information System (INIS)

    Ignaszewski, A.; Vaillant, D.; Sabatier, J.P.; Fernandez, Y.

    1975-01-01

    In heart cavity studies the simplicity and harmlessness nuclear imagery are great advantages, but it is necessary to improve on the data obtainable by this technique. The usual image is faulty, owing to the presence of a kinetic softness, and deficient because it fails to account for the mobility of the walls. An attempt was made to correct the kinetic softness on an image and to reconstitute the film of a heart cycle, an aim achieved by combining a computer with the camera. The examination conditions generally adopted include storage of all data and a reconstitution of the entire cycle is programmed taking a multiple time unit of 20ms; this supplies a sequence of images which when observed in succession resembles the heat contractility film [fr

  20. Cardiovascular coupling analysis with high-resolution joint symbolic dynamics in patients suffering from acute schizophrenia

    International Nuclear Information System (INIS)

    Schulz, Steffen; Tupaika, Nadine; Voss, Andreas; Berger, Sandy; Bär, Karl-Jürgen; Haueisen, Jens

    2013-01-01

    Besides the well-known cardiac risk factors for schizophrenia, increasing concerns have been raised regarding the cardiac side-effects of antipsychotic medications. A bivariate analysis of autonomic regulation, based on cardiovascular coupling, can provide additional information about heart rate (HR) and blood pressure regulatory patterns within the complex interactions of the cardiovascular system. We introduce a new high-resolution coupling analysis method (HRJSD) based on joint symbolic dynamics (JSD), which is characterized by three symbols, a threshold (individual dynamic variability, physiological) for time series transformation and eight coupling pattern families. This is based on a redundancy reduction strategy used to quantify and characterize cardiovascular couplings. In this study, short-term (30 min) HR and systolic blood pressure (SP) time series of 42 unmedicated (UNMED) and 42 medicated patients (MED) suffering from acute schizophrenia were analysed to establish the suitability of the new method for quantifying the effects of antipsychotics on cardiovascular couplings. We were able to demonstrate that HRJSD, applying the threshold based on spontaneous baroreflex sensitivity (BRS) estimation, revealed eight significant pattern families that were able to quantify the anti-cholinergic effects of antipsychotics and the related changes of cardiovascular regulation (coupling) in MED in comparison to UNMED. This was in contrast to the simple JSD, BRS (sequence method) and only partly to standard linear HR variability indices. HRJSD provides strong evidence that autonomic regulation in MED seems to be, to some extent, predominated by invariable HR responses in combination with alternating SP values in contrast to UNMED, indicating an impairment of the baroreflex control feedback loop in MED. Surrogate data analysis was applied to test for the significance and nonlinearity of cardiovascular couplings in the original data due to medical treatment with

  1. Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models

    Science.gov (United States)

    2015-03-03

    based whole-cell models of E. coli [6]. Conversely , highly abstracted kinetic frameworks, such as the cybernetic framework, represented a paradigm shift...metabolic objective function has been the optimization of biomass formation [18], although other metabolic objectives have also been estimated [19...experimental data. Toward these questions, we explored five hypothetical cell-free networks. Each network shared the same enzymatic connectivity, but

  2. The onset of fluid-dynamical behavior in relativistic kinetic theory

    Science.gov (United States)

    Noronha, Jorge; Denicol, Gabriel S.

    2017-11-01

    In this proceedings we discuss recent findings regarding the large order behavior of the Chapman-Enskog expansion in relativistic kinetic theory. It is shown that this series in powers of the Knudsen number has zero radius of convergence in the case of a Bjorken expanding fluid described by the Boltzmann equation in the relaxation time approximation. This divergence stems from the presence of non-hydrodynamic modes, which give non-perturbative contributions to the Knudsen series.

  3. Opinion dynamics: kinetic modelling with mass media, application to the Scottish independence referendum

    OpenAIRE

    Boudin , Laurent; Salvarani , Francesco

    2016-01-01

    International audience; We consider a kinetic model describing some mechanisms of opinion formation in the framework of referendums, by allowing that the individuals, who can interact between themselves and modify their opinion by means of spontaneous self-thinking, are moreover under the influence of mass media. After proving the main properties of the model, such as existence of solutions and conservation properties, we study, at the numerical level, both the transient and the asymptotic re...

  4. Recent Insight into the Kinetic Mechanisms and Conformational Dynamics of Y-Family DNA Polymerases

    OpenAIRE

    Maxwell, Brian A.; Suo, Zucai

    2014-01-01

    The kinetic mechanisms by which DNA polymerases catalyze DNA replication and repair have long been areas of active research. Recently discovered Y-family DNA polymerases catalyze the bypass of damaged DNA bases that would otherwise block replicative DNA polymerases and stall replication forks. Unlike DNA polymerases from the five other families, the Y-family DNA polymerases have flexible, solvent-accessible active sites that are able to tolerate various types of damaged template bases and all...

  5. Dynamic hysteresis behaviors in the kinetic Ising system on triangular lattice

    Science.gov (United States)

    Kantar, Ersin; Ertaş, Mehmet

    2018-04-01

    We studied dynamic hysteresis behaviors of the spin-1 Blume-Capel (BC) model in a triangular lattice by means of the effective-field theory (EFT) with correlations and using Glauber-type stochastic dynamics. The effects of the exchange interaction (J), crystal field (D), temperature (T) and oscillating frequency (w) on the hysteresis behaviors of the BC model in a triangular lattice are investigated in detail. Results are compared with some other dynamic studies and quantitatively good agreement is found.

  6. Candida Rugosa Lipase-catalyzed Kinetic Resolution of 3-(Isobutyryloxy)methyl 4-[2-(Difluoromethoxy)phenyl]-2-methyl-5,5-dioxo-1,4-dihydrobenzothieno[3,2-b]pyridine-3-carboxylate

    NARCIS (Netherlands)

    Sobolev, A.; Zhalubovskis, R.; Franssen, M.C.R.; Vigante, B.; Chekavichus, B.; Duburs, G.; Groot, de Æ.

    2004-01-01

    The lipase-catalyzed kinetic resolution of 3-(isobutyryloxy)methyl 4-[2-(difluoromethoxy)phenyl]-2-methyl-5,5-dioxo-1,4-dihydrobenzothieno[3,2-b]pyridine-3-carboxylate has been performed. The most enantioselective reaction (E = 28) was transesterification with n-butanol in water-saturated toluene at

  7. CubeSats in Hydrology: Ultra-High Resolution Insights into Vegetation Dynamics and Terrestrial Evaporation

    KAUST Repository

    McCabe, Matthew; Aragon, B.; Houborg, Rasmus; Mascaro, J.

    2017-01-01

    Satellite-based remote sensing has generally necessitated a trade-off between spatial resolution and temporal frequency, affecting the capacity to observe fast hydrological processes and rapidly changing land surface conditions. An avenue for overcoming these spatiotemporal restrictions is the concept of using constellations of satellites, as opposed to the mission focus exemplified by the more conventional space-agency approach to earth observation. Referred to as CubeSats, these platforms offer the potential to provide new insights into a range of earth system variables and processes. Their emergence heralds a paradigm shift from single-sensor launches to an operational approach that envisions tens to hundreds of small, lightweight and comparatively inexpensive satellites placed into a range of low earth orbits. Although current systems are largely limited to sensing in the optical portion of the electromagnetic spectrum, we demonstrate the opportunity and potential that CubeSats present the hydrological community via the retrieval of vegetation dynamics and terrestrial evaporation and foreshadow future sensing capabilities.

  8. Sub-Airy disk angular resolution with high dynamic range in the near-infrared

    Directory of Open Access Journals (Sweden)

    Richichi A.

    2011-07-01

    Full Text Available Lunar occultations (LO are a simple and effective high angular resolution method, with minimum requirements in instrumentation and telescope time. They rely on the analysis of the diffraction fringes created by the lunar limb. The diffraction phenomen occurs in space, and as a result LO are highly insensitive to most of the degrading effects that limit the performance of traditional single telescope and long-baseline interferometric techniques used for direct detection of faint, close companions to bright stars. We present very recent results obtained with the technique of lunar occultations in the near-IR, showing the detection of companions with very high dynamic range as close as few milliarcseconds to the primary star. We discuss the potential improvements that could be made, to increase further the current performance. Of course, LO are fixed-time events applicable only to sources which happen to lie on the Moon’s apparent orbit. However, with the continuously increasing numbers of potential exoplanets and brown dwarfs beign discovered, the frequency of such events is not negligible. I will list some of the most favorable potential LO in the near future, to be observed from major observatories.

  9. Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique

    Science.gov (United States)

    Shadrack Jabes, B.; Krekeler, C.; Klein, R.; Delle Site, L.

    2018-05-01

    We employ the Grand Canonical Adaptive Resolution Simulation (GC-AdResS) molecular dynamics technique to test the spatial locality of the 1-ethyl 3-methyl imidazolium chloride liquid. In GC-AdResS, atomistic details are kept only in an open sub-region of the system while the environment is treated at coarse-grained level; thus, if spatial quantities calculated in such a sub-region agree with the equivalent quantities calculated in a full atomistic simulation, then the atomistic degrees of freedom outside the sub-region play a negligible role. The size of the sub-region fixes the degree of spatial locality of a certain quantity. We show that even for sub-regions whose radius corresponds to the size of a few molecules, spatial properties are reasonably reproduced thus suggesting a higher degree of spatial locality, a hypothesis put forward also by other researchers and that seems to play an important role for the characterization of fundamental properties of a large class of ionic liquids.

  10. The neural dynamics of competition resolution for language production in the prefrontal cortex.

    Science.gov (United States)

    Bourguignon, Nicolas J; Ohashi, Hiroki; Nguyen, Don; Gracco, Vincent L

    2018-03-01

    Previous research suggests a pivotal role of the prefrontal cortex (PFC) in word selection during tasks of confrontation naming (CN) and verb generation (VG), both of which feature varying degrees of competition between candidate responses. However, discrepancies in prefrontal activity have also been reported between the two tasks, in particular more widespread and intense activation in VG extending into (left) ventrolateral PFC, the functional significance of which remains unclear. We propose that these variations reflect differences in competition resolution processes tied to distinct underlying lexico-semantic operations: Although CN involves selecting lexical entries out of limited sets of alternatives, VG requires exploration of possible semantic relations not readily evident from the object itself, requiring prefrontal areas previously shown to be recruited in top-down retrieval of information from lexico-semantic memory. We tested this hypothesis through combined independent component analysis of functional imaging data and information-theoretic measurements of variations in selection competition associated with participants' performance in overt CN and VG tasks. Selection competition during CN engaged the anterior insula and surrounding opercular tissue, while competition during VG recruited additional activity of left ventrolateral PFC. These patterns remained after controlling for participants' speech onset latencies indicative of possible task differences in mental effort. These findings have implications for understanding the neural-computational dynamics of cognitive control in language production and how it relates to the functional architecture of adaptive behavior. © 2017 Wiley Periodicals, Inc.

  11. CubeSats in Hydrology: Ultra-High Resolution Insights into Vegetation Dynamics and Terrestrial Evaporation

    KAUST Repository

    McCabe, Matthew

    2017-12-01

    Satellite-based remote sensing has generally necessitated a trade-off between spatial resolution and temporal frequency, affecting the capacity to observe fast hydrological processes and rapidly changing land surface conditions. An avenue for overcoming these spatiotemporal restrictions is the concept of using constellations of satellites, as opposed to the mission focus exemplified by the more conventional space-agency approach to earth observation. Referred to as CubeSats, these platforms offer the potential to provide new insights into a range of earth system variables and processes. Their emergence heralds a paradigm shift from single-sensor launches to an operational approach that envisions tens to hundreds of small, lightweight and comparatively inexpensive satellites placed into a range of low earth orbits. Although current systems are largely limited to sensing in the optical portion of the electromagnetic spectrum, we demonstrate the opportunity and potential that CubeSats present the hydrological community via the retrieval of vegetation dynamics and terrestrial evaporation and foreshadow future sensing capabilities.

  12. Dosimetric and qualitative analysis of kinetic properties of millennium 80 multileaf collimator system for dynamic intensity modulated radiotherapy treatments

    Directory of Open Access Journals (Sweden)

    Bhardwaj Anup

    2007-01-01

    Full Text Available The aim of this paper is to analyze the positional accuracy, kinetic properties of the dynamic multileaf collimator (MLC and dosimetric evaluation of fractional dose delivery for the intensity modulated radiotherapy (IMRT for step and shoot and sliding window (dynamic techniques of Varian multileaf collimator millennium 80. Various quality assurance tests such as accuracy in leaf positioning and speed, stability of dynamic MLC output, inter and intra leaf transmission, dosimetric leaf separation and multiple carriage field verification were performed. Evaluation of standard field patterns as pyramid, peaks, wedge, chair, garden fence test, picket fence test and sweeping gap output was done. Patient dose quality assurance procedure consists of an absolute dose measurement for all fields at 5 cm depth on solid water phantom using 0.6cc water proof ion chamber and relative dose verification using Kodak EDR-2 films for all treatment fields along transverse and coronal direction using IMRT phantom. The relative dose verification was performed using Omni Pro IMRT film verification software. The tests performed showed acceptable results for commissioning the millennium 80 MLC and Clinac DHX for dynamic and step and shoot IMRT treatments.

  13. Expanding the linear dynamic range for quantitative liquid chromatography-high resolution mass spectrometry utilizing natural isotopologue signals

    International Nuclear Information System (INIS)

    Liu, Hanghui; Lam, Lily; Yan, Lin; Chi, Bert; Dasgupta, Purnendu K.

    2014-01-01

    Highlights: • Less abundant isotopologue ions were utilized to decrease detector saturation. • A 25–50 fold increase in the upper limit of dynamic range was demonstrated. • Linear dynamic range was expanded without compromising mass resolution. - Abstract: The linear dynamic range (LDR) for quantitative liquid chromatography–mass spectrometry can be extended until ionization saturation is reached by using a number of target isotopologue ions in addition to the normally used target ion that provides the highest sensitivity. Less abundant isotopologue ions extend the LDR: the lower ion abundance decreases the probability of ion detector saturation. Effectively the sensitivity decreases and the upper limit of the LDR increases. We show in this paper that the technique is particularly powerful with a high resolution time of flight mass spectrometer because the data for all ions are automatically acquired, and we demonstrated this for four small organic molecules; the upper limits of LDRs increased by 25–50 times

  14. Brownian dynamics of aggregation kinetics of hard spheres with flexibele bounds

    NARCIS (Netherlands)

    Rzepiela, A.A.; Opheusden, van J.; Vliet, van T.

    2001-01-01

    Brownian dynamics (BD) simulations have been performed on the aggregation dynamics of colloidal particles within the context of a ball-and-string model. Particles are treated as hard spheres that can bind irreversibly through a string attached to their surface. The model is set up to mimic some

  15. Satellite microwave remote sensing of North Eurasian inundation dynamics: development of coarse-resolution products and comparison with high-resolution synthetic aperture radar data

    International Nuclear Information System (INIS)

    Schroeder, R; Rawlins, M A; McDonald, K C; Podest, E; Zimmermann, R; Kueppers, M

    2010-01-01

    Wetlands are not only primary producers of atmospheric greenhouse gases but also possess unique features that are favourable for application of satellite microwave remote sensing to monitoring their status and trend. In this study we apply combined passive and active microwave remote sensing data sets from the NASA sensors AMSR-E and QuikSCAT to map surface water dynamics over Northern Eurasia. We demonstrate our method on the evolution of large wetland complexes for two consecutive years from January 2006 to December 2007. We apply river discharge measurements from the Ob River along with land surface runoff simulations derived from the Pan-Arctic Water Balance Model during and after snowmelt in 2006 and 2007 to interpret the abundance of widespread flooding along the River Ob in early summer of 2007 observed in the remote sensing products. The coarse-resolution, 25 km, surface water product is compared to a high-resolution, 30 m, inundation map derived from ALOS PALSAR (Advanced Land Observation Satellite phased array L-band synthetic aperture radar) imagery acquired for 11 July 2006, and extending along a transect in the central Western Siberian Plain. We found that the surface water fraction derived from the combined AMSR-E/QuikSCAT data sets closely tracks the inundation mapped using higher-resolution ALOS PALSAR data.

  16. Transforming SWAT for continental-scale high-resolution modeling of floodplain dynamics: opportunities and challenges

    Science.gov (United States)

    Rajib, A.; Merwade, V.; Liu, Z.; Lane, C.; Golden, H. E.; Tavakoly, A. A.; Follum, M. L.

    2017-12-01

    There have been many initiatives to develop frameworks for continental-scale modeling and mapping floodplain dynamics. The choice of a model for such needs should be governed by its suitability to be executed in high performance cyber platforms, ability to integrate supporting hydraulic/hydrodynamic tools, and ability to assimilate earth observations. Furthermore, disseminating large volume of outputs for public use and interoperability with similar frameworks should be considered. Considering these factors, we have conducted a series of modeling experiments and developed a suite of cyber-enabled platforms that have transformed Soil and Water Assessment Tool (SWAT) into an appropriate model for use in a continental-scale, high resolution, near real-time flood information framework. Our first experiment uses a medium size watershed in Indiana, USA and attempts burning-in a high resolution, National Hydrography Dataset Plus(NHDPlus) into the SWAT model. This is crucial with a view to make the outputs comparable with other global/national initiatives. The second experiment is built upon the first attempt to add a modified landscape representation in the model which differentiates between the upland and floodplain processes. Our third experiment involves two separate efforts: coupling SWAT with a hydrodynamic model LISFLOOD-FP and a new generation, low complexity hydraulic model AutoRoute. We have executed the prototype "loosely-coupled" models for the Upper Mississippi-Ohio River Basin in the USA, encompassing 1 million square km drainage area and nearly 0.2 million NHDPlus river reaches. The preliminary results suggest reasonable accuracy for both streamflow and flood inundation. In this presentation, we will also showcase three cyber-enabled platforms, including SWATShare to run and calibrate large scale SWAT models online using high performance computational resources, HydroGlobe to automatically extract and assimilate multiple remotely sensed earth observations in

  17. High-Resolution Denitrification Kinetics in Pasture Soils Link N2O Emissions to pH, and Denitrification to C Mineralization.

    Directory of Open Access Journals (Sweden)

    Md Sainur Samad

    Full Text Available Denitrification in pasture soils is mediated by microbial and physicochemical processes leading to nitrogen loss through the emission of N2O and N2. It is known that N2O reduction to N2 is impaired by low soil pH yet controversy remains as inconsistent use of soil pH measurement methods by researchers, and differences in analytical methods between studies, undermine direct comparison of results. In addition, the link between denitrification and N2O emissions in response to carbon (C mineralization and pH in different pasture soils is still not well described. We hypothesized that potential denitrification rate and aerobic respiration rate would be positively associated with soils. This relationship was predicted to be more robust when a high resolution analysis is performed as opposed to a single time point comparison. We tested this by characterizing 13 different temperate pasture soils from northern and southern hemispheres sites (Ireland and New Zealand using a fully automated-high-resolution GC detection system that allowed us to detect a wide range of gas emissions simultaneously. We also compared the impact of using different extractants for determining pH on our conclusions. In all pH measurements, soil pH was strongly and negatively associated with both N2O production index (IN2O and N2O/(N2O+N2 product ratio. Furthermore, emission kinetics across all soils revealed that the denitrification rates under anoxic conditions (NO+N2O+N2 μmol N/h/vial were significantly associated with C mineralization (CO2 μmol/h/vial measured both under oxic (r2 = 0.62, p = 0.0015 and anoxic (r2 = 0.89, p<0.0001 conditions.

  18. A faster, high resolution, mtPA-GFP-based mitochondrial fusion assay acquiring kinetic data of multiple cells in parallel using confocal microscopy.

    Science.gov (United States)

    Lovy, Alenka; Molina, Anthony J A; Cerqueira, Fernanda M; Trudeau, Kyle; Shirihai, Orian S

    2012-07-20

    Mitochondrial fusion plays an essential role in mitochondrial calcium homeostasis, bioenergetics, autophagy and quality control. Fusion is quantified in living cells by photo-conversion of matrix targeted photoactivatable GFP (mtPAGFP) in a subset of mitochondria. The rate at which the photoconverted molecules equilibrate across the entire mitochondrial population is used as a measure of fusion activity. Thus far measurements were performed using a single cell time lapse approach, quantifying the equilibration in one cell over an hour. Here, we scale up and automate a previously published live cell method based on using mtPAGFP and a low concentration of TMRE (15 nm). This method involves photoactivating a small portion of the mitochondrial network, collecting highly resolved stacks of confocal sections every 15 min for 1 hour, and quantifying the change in signal intensity. Depending on several factors such as ease of finding PAGFP expressing cells, and the signal of the photoactivated regions, it is possible to collect around 10 cells within the 15 min intervals. This provides a significant improvement in the time efficiency of this assay while maintaining the highly resolved subcellular quantification as well as the kinetic parameters necessary to capture the detail of mitochondrial behavior in its native cytoarchitectural environment. Mitochondrial dynamics play a role in many cellular processes including respiration, calcium regulation, and apoptosis. The structure of the mitochondrial network affects the function of mitochondria, and the way they interact with the rest of the cell. Undergoing constant division and fusion, mitochondrial networks attain various shapes ranging from highly fused networks, to being more fragmented. Interestingly, Alzheimer's disease, Parkinson's disease, Charcot Marie Tooth 2A, and dominant optic atrophy have been correlated with altered mitochondrial morphology, namely fragmented networks. Often times, upon fragmentation

  19. High-resolution dynamic angiography using flat-panel volume CT: feasibility demonstration for neuro and lower limb vascular applications

    International Nuclear Information System (INIS)

    Mehndiratta, Amit; Rabinov, James D.; Grasruck, Michael; Liao, Eric C.; Crandell, David; Gupta, Rajiv

    2015-01-01

    This paper evaluates a prototype flat-panel volume CT (fpVCT) for dynamic in vivo imaging in a variety of neurovascular and lower limb applications. Dynamic CTA was performed on 12 patients (neuro = 8, lower limb = 4) using an fpVCT with 120 kVp, 50 mA, rotation time varying from 8 to 19 s, and field of view of 25 x 25 x 18 cm 3 . Four-dimensional data sets (i.e. 3D images over time) were reconstructed and reviewed. Dynamic CTA demonstrated sufficient spatio-temporal resolution to elucidate first-pass and recirculation dynamics of contrast bolus through neurovasclar pathologies and phasic blood flow though lower-limb vasculature and grafts. The high spatial resolution of fpVCT resulted in reduced partial volume and metal beam-hardening artefacts. This facilitated assessment of vascular lumen in the presence of calcified plaque and evaluation of fractures, especially in the presence of fixation hardware. Evaluation of arteriovenous malformation using dynamic fpVCT angiography was of limited utility. Dynamic CTA using fpVCT can visualize time-varying phenomena in neuro and lower limb vascular applications and has sufficient diagnostic imaging quality to evaluate a number of pathologies affecting these regions. (orig.)

  20. High-resolution dynamic angiography using flat-panel volume CT: feasibility demonstration for neuro and lower limb vascular applications

    Energy Technology Data Exchange (ETDEWEB)

    Mehndiratta, Amit [Massachusetts General Hospital, Department of Radiology, Harvard Medical School, Boston, MA (United States); University of Oxford, Institute of Biomedical Engineering and Keble College, Oxford (United Kingdom); Indian Institute of Technology Delhi and All India Institute of Medical Science, Centre for Biomedical Engineering, New Delhi (India); Rabinov, James D. [Massachusetts General Hospital, Interventional Neuroradiology, Harvard Medical School, Boston, MA (United States); Grasruck, Michael [Siemens Medical Solutions, Forchheim (Germany); Liao, Eric C. [Massachusetts General Hospital, Department of Plastic and Reconstructive Surgery and Center for Regenerative Medicine, Harvard Medical School, Boston, MA (United States); Crandell, David [Spaulding Rehabilitation Hospital, Department of Physical Medicine and Rehabilitation, Harvard Medical School, Charlestown, MA (United States); Gupta, Rajiv [Massachusetts General Hospital, Department of Radiology, Harvard Medical School, Boston, MA (United States)

    2015-07-15

    This paper evaluates a prototype flat-panel volume CT (fpVCT) for dynamic in vivo imaging in a variety of neurovascular and lower limb applications. Dynamic CTA was performed on 12 patients (neuro = 8, lower limb = 4) using an fpVCT with 120 kVp, 50 mA, rotation time varying from 8 to 19 s, and field of view of 25 x 25 x 18 cm{sup 3}. Four-dimensional data sets (i.e. 3D images over time) were reconstructed and reviewed. Dynamic CTA demonstrated sufficient spatio-temporal resolution to elucidate first-pass and recirculation dynamics of contrast bolus through neurovasclar pathologies and phasic blood flow though lower-limb vasculature and grafts. The high spatial resolution of fpVCT resulted in reduced partial volume and metal beam-hardening artefacts. This facilitated assessment of vascular lumen in the presence of calcified plaque and evaluation of fractures, especially in the presence of fixation hardware. Evaluation of arteriovenous malformation using dynamic fpVCT angiography was of limited utility. Dynamic CTA using fpVCT can visualize time-varying phenomena in neuro and lower limb vascular applications and has sufficient diagnostic imaging quality to evaluate a number of pathologies affecting these regions. (orig.)

  1. Contrast kinetics of the malignant breast tumour - border versus centre enhancement on dynamic midfield MRI

    DEFF Research Database (Denmark)

    Marklund, M.; Torp-Pedersen, S.; Bentzon, N.

    2008-01-01

    receptor negative tumours. CONCLUSION: The border/centre enhancement difference in malignant breast tumours is easily visualized on midfield dynamic magnetic resonance mammography. The dynamic behaviour is significantly correlated to histological features and receptor status of the tumours Udgivelsesdato......PURPOSE: To quantify the border versus centre enhancement of malignant breast tumours on dynamic magnetic resonance mammography. MATERIALS AND METHODS: Fifty-two women diagnosed with primary breast cancer underwent dynamic magnetic resonance mammography (Omniscan 0.2 mmol/kg bodyweight......) on a midfield scanner (0.6 T), prior to surgery. The following five variables were recorded from the border and centre regions of the tumours: Early Enhancement, Time to Peak, Wash-in rate, Wash-out rate and Area under Curve. Information on histology type, oestrogen and progesterone receptor status...

  2. Photodissociation dynamics of formyl fluoride (HFCO) at 193 nm: Branching ratios and distributions of kinetic energy

    International Nuclear Information System (INIS)

    Lee, H.; Wu, C.-Y.; Yang, S.K.; Lee, Y.-P.

    2005-01-01

    Following photodissociation of formyl fluoride (HFCO) at 193 nm, we detected products with fragmentation translational spectroscopy utilizing a tunable vacuum ultraviolet beam from a synchrotron for ionization. Among three primary dissociation channels observed in this work, the F-elimination channel HFCO→HCO+F dominates, with a branching ratio ∼0.66 and an average release of kinetic energy ∼55 kJ mol -1 ; about 17% of HCO further decomposes to H+CO. The H-elimination channel HFCO→FCO+H has a branching ratio ∼0.28 and an average release of kinetic energy ∼99 kJ mol -1 ; about 21% of FCO further decomposes to F+CO. The F-elimination channel likely proceeds via the S 1 surface whereas the H-elimination channel proceeds via the T 1 surface; both channels exhibit moderate barriers for dissociation. The molecular HF-elimination channel HFCO→HF+CO, correlating with the ground electronic surface, has a branching ratio of only ∼0.06; the average translational release of 93 kJ mol -1 , ∼15% of available energy, implies that the fragments are highly internally excited. Detailed mechanisms of photodissociation are discussed

  3. Quantification of in vivo metabolic kinetics of hyperpolarized pyruvate in rat kidneys using dynamic 13C MRSI.

    Science.gov (United States)

    Xu, Tao; Mayer, Dirk; Gu, Meng; Yen, Yi-Fen; Josan, Sonal; Tropp, James; Pfefferbaum, Adolf; Hurd, Ralph; Spielman, Daniel

    2011-10-01

    With signal-to-noise ratio enhancements on the order of 10,000-fold, hyperpolarized MRSI of metabolically active substrates allows the study of both the injected substrate and downstream metabolic products in vivo. Although hyperpolarized [1-(13)C]pyruvate, in particular, has been used to demonstrate metabolic activities in various animal models, robust quantification and metabolic modeling remain important areas of investigation. Enzyme saturation effects are routinely seen with commonly used doses of hyperpolarized [1-(13)C]pyruvate; however, most metrics proposed to date, including metabolite ratios, time-to-peak of metabolic products and single exchange rate constants, fail to capture these saturation effects. In addition, the widely used small-flip-angle excitation approach does not correctly model the inflow of fresh downstream metabolites generated proximal to the target slice, which is often a significant factor in vivo. In this work, we developed an efficient quantification framework employing a spiral-based dynamic spectroscopic imaging approach. The approach overcomes the aforementioned limitations and demonstrates that the in vivo (13)C labeling of lactate and alanine after a bolus injection of [1-(13)C]pyruvate is well approximated by saturatable kinetics, which can be mathematically modeled using a Michaelis-Menten-like formulation, with the resulting estimated apparent maximal reaction velocity V(max) and apparent Michaelis constant K(M) being unbiased with respect to critical experimental parameters, including the substrate dose, bolus shape and duration. Although the proposed saturatable model has a similar mathematical formulation to the original Michaelis-Menten kinetics, it is conceptually different. In this study, we focus on the (13)C labeling of lactate and alanine and do not differentiate the labeling mechanism (net flux or isotopic exchange) or the respective contribution of various factors (organ perfusion rate, substrate transport

  4. Adsorption kinetics and dynamics of small organic molecules on a silica wafer: Butane, pentane, nonane, thiophene, and methanol adsorption on SiO2/Si(1 1 1)

    International Nuclear Information System (INIS)

    Funk, S.; Goering, J.; Burghaus, U.

    2008-01-01

    The adsorption kinetics (by thermal desorption spectroscopy) and adsorption dynamics (by molecular beam scattering) have been determined for a number of alkanes, methanol, thiophene, and water on a silica wafer-SiO 2 /Si(1 1 1). No indications for bond activation were present, i.e., all probe molecules adsorb molecularly obeying 1st order kinetics. The coverage-dependent heat of adsorption has been determined accordingly. The adsorption dynamics are precursor-mediated with Kisliuk-like shapes of the adsorption probabilities at low impact energies and adsorbate-assisted adsorption at large impact energies

  5. Crystallization-induced dynamic resolution R-epimer from 25-OCH3-PPD epimeric mixture.

    Science.gov (United States)

    Zhang, Sainan; Tang, Yun; Cao, Jiaqing; Zhao, Chen; Zhao, Yuqing

    2015-11-15

    25-OCH3-PPD is a promising antitumor dammarane sapogenin isolated from the total saponin-hydrolyzed extract of Panax ginseng berry and Panax notoginseng leaves. 20(R)-25-OCH3-PPD was more potent as an anti-cancer agent than 20(S)-25-OCH3-PPD and epimeric mixture of 25-OCH3-PPD. This paper describes the rapid separation process of the R-epimer of 25-OCH3-PPD from its epimeric mixture by crystallization-induced dynamic resolution (CIDR). The optimized CIDR process was based on single factor analysis and nine well-planned orthogonal design experiments (OA9 matrix). A rapid and sensitive reverse phase high-performance liquid chromatographic (HPLC) method with evaporative light-scattering detector (ELSD) was developed and validated for the quantitation of 25-OCH3-PPD epimeric mixture and crystalline product. Separation and quantitation were achieved with a silica column using a mobile phase consisting of methanol and water (87:13, v/v) at a flow rate of 1.0mL/min. The ELSD detection was performed at 50°C and 3L/min. Under conditions involving 3mL of 95% ethanol, 8% HCl, and a hermetically sealed environment for 72h, the maximum production of 25(R)-OCH3-PPD was achieved with a chemical purity of 97% and a total yield of 87% through the CIDR process. The 25(R)-OCH3-PPD was nearly completely separated from the 220mg 25-OCH3-PPD epimeric mixture. Overall, a simple and steady small-batch purification process for the large-scale production of 25(R)-OCH3-PPD from 25-OCH3-PPD epimeric mixture was developed. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. The dynamics of cyclone clustering in re-analysis and a high-resolution climate model

    Science.gov (United States)

    Priestley, Matthew; Pinto, Joaquim; Dacre, Helen; Shaffrey, Len

    2017-04-01

    Extratropical cyclones have a tendency to occur in groups (clusters) in the exit of the North Atlantic storm track during wintertime, potentially leading to widespread socioeconomic impacts. The Winter of 2013/14 was the stormiest on record for the UK and was characterised by the recurrent clustering of intense extratropical cyclones. This clustering was associated with a strong, straight and persistent North Atlantic 250 hPa jet with Rossby wave-breaking (RWB) on both flanks, pinning the jet in place. Here, we provide for the first time an analysis of all clustered events in 36 years of the ERA-Interim Re-analysis at three latitudes (45˚ N, 55˚ N, 65˚ N) encompassing various regions of Western Europe. The relationship between the occurrence of RWB and cyclone clustering is studied in detail. Clustering at 55˚ N is associated with an extended and anomalously strong jet flanked on both sides by RWB. However, clustering at 65(45)˚ N is associated with RWB to the south (north) of the jet, deflecting the jet northwards (southwards). A positive correlation was found between the intensity of the clustering and RWB occurrence to the north and south of the jet. However, there is considerable spread in these relationships. Finally, analysis has shown that the relationships identified in the re-analysis are also present in a high-resolution coupled global climate model (HiGEM). In particular, clustering is associated with the same dynamical conditions at each of our three latitudes in spite of the identified biases in frequency and intensity of RWB.

  7. Insight derived from molecular dynamics simulations into molecular motions, thermodynamics and kinetics of HIV-1 gp120.

    Directory of Open Access Journals (Sweden)

    Peng Sang

    Full Text Available Although the crystal structures of the HIV-1 gp120 core bound and pre-bound by CD4 are known, the details of dynamics involved in conformational equilibrium and transition in relation to gp120 function have remained elusive. The homology models of gp120 comprising the N- and C-termini and loops V3 and V4 in the CD4-bound and CD4-unbound states were built and subjected to molecular dynamics (MD simulations to investigate the differences in dynamic properties and molecular motions between them. The results indicate that the CD4-bound gp120 adopted a more compact and stable conformation than the unbound form during simulations. For both the unbound and bound gp120, the large concerted motions derived from essential dynamics (ED analyses can influence the size/shape of the ligand-binding channel/cavity of gp120 and, therefore, were related to its functional properties. The differences in motion direction between certain structural components of these two forms of gp120 were related to the conformational interconversion between them. The free energy calculations based on the metadynamics simulations reveal a more rugged and complex free energy landscape (FEL for the unbound than for the bound gp120, implying that gp120 has a richer conformational diversity in the unbound form. The estimated free energy difference of ∼-6.0 kJ/mol between the global minimum free energy states of the unbound and bound gp120 indicates that gp120 can transform spontaneously from the unbound to bound states, revealing that the bound state represents a high-probability "ground state" for gp120 and explaining why the unbound state resists crystallization. Our results provide insight into the dynamics-and-function relationship of gp120, and facilitate understandings of the thermodynamics, kinetics and conformational control mechanism of HIV-1 gp120.

  8. General problems arising from the analogical resolution of the kinetic equations of nuclear reactors (1961); Problemes generaux poses par la resolution analogique des equations cinetiques des reacteurs nucleaires (1961)

    Energy Technology Data Exchange (ETDEWEB)

    Caillet, C [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1961-07-01

    The author reviews precisely the analogical techniques used for the resolution of the kinetic equations of nuclear reactors. Prior to this, he recalls the reasons which oblige physicians and engineers, even today, to use electronic machines in this domain. The author then considers the technological problems posed by the range of values which the various nuclear parameters adopt. In each case, he shows that a compromise is possible allowing an optimum precision. He compares the results to those obtained by arithmetic calculation and uses the examples chosen in a critical analysis of the present possibilities of the two methods of calculation. (author) [French] L'auteur cherche a faire un point aussi exact que possible des techniques analogiques utilisees pour resoudre les equations cinetiques des reacteurs nucleaires. Il rappelle auparavant les raisons pour lesquelles physiciens et ingenieurs sont obliges, encore aujourd'hui, de faire appel aux machines electroniques dans ce domaine. Puis il etudie les problemes technologiques que souleve le champ des valeurs prises par les differents parametres nucleaires. Dans chacun des cas, il montre l'existence d'un compromis qui permet d'atteindre une precision optimum. Il compare les resultats obtenus a ceux provenant de calculateurs arithmetiques et profite des exemples choisis pour faire une analyse critique des possibilites actuelles offertes par les deux modes de calcul. (auteur)

  9. Comparison of quasi-static and dynamic squats: a three-dimensional kinematic, kinetic and electromyographic study of the lower limbs.

    Science.gov (United States)

    Clément, Julien; Hagemeister, Nicola; Aissaoui, Rachid; de Guise, Jacques A

    2014-01-01

    Numerous studies have described 3D kinematics, 3D kinetics and electromyography (EMG) of the lower limbs during quasi-static or dynamic squatting activities. One study compared these two squatting conditions but only at low speed on healthy subjects, and provided no information on kinetics and EMG of the lower limbs. The purpose of the present study was to contrast simultaneous recordings of 3D kinematics, 3D kinetics and EMG of the lower limbs during quasi-stat ic and fast-dynamic squats in healthy and pathological subjects. Ten subjects were recruited: five healthy and five osteoarthritis subjects. A motion-capture system, force plate, and surface electrodes respectively recorded 3D kinematics, 3D kinetics and EMG of the lower limbs. Each subject performed a quasi-static squat and several fast-dynamic squats from 0° to 70° of knee flexion. The two squatting conditions were compared for positions where quasi-static and fast-dynamic knee flexion-extension angles were similar. Mean differences between quasi-static and fast-dynamic squats were 1.5° for rotations, 1.9 mm for translations, 2.1% of subjects' body weight for ground reaction forces, 6.6 Nm for torques, 11.2 mm for center of pressure, and 6.3% of maximum fast-dynamic electromyographic activities for EMG. Some significant differences (psquats were small. 69.5% of compared data were equivalent. In conclusion, this study showed that quasi-static and fast-dynamic squatting activities are comparable in terms of 3D kinematics, 3D kinetics and EMG, although some reservations still remain. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Experimental kinetic parameters in the thermo-fluid-dynamic modelling of coal combustion

    International Nuclear Information System (INIS)

    Migliavacca, G.; Perini, M.; Parodi, E.

    2001-01-01

    The designing and the optimisation of modern and efficient combustion systems are nowadays frequently based on calculation tools for mathematical modelling, which are able to predict the evolution of the process starting from the first principles of physics. Otherwise, in many cases, specific experimental parameters are needed to describe the specific nature of the materials considered in the calculations. It is especially true in the modelling of coal combustion, which is a complex process strongly dependent on the chemical and physical features of the fuel. This paper describes some experimental techniques used to estimate the fundamental kinetic parameters of coal combustion and shows how this data may be introduced in a model calculation to predict the pollutant emissions from a real scale combustion plant [it

  11. Wastewater treatment using photo-impinging streams cyclone reactor: Computational fluid dynamics and kinetics modeling

    Energy Technology Data Exchange (ETDEWEB)

    Royaee, Sayed Javid; Shafeghat, Amin [Research Institute of Petroleum Industry, Tehran (Iran, Islamic Republic of); Sohrabi, Morteza [Amirkabir University of Technology, Tehran (Iran, Islamic Republic of)

    2014-02-15

    A photo impinging streams cyclone reactor has been used as a novel apparatus in photocatalytic degradation of organic compounds using titanium dioxide nanoparticles in wastewater. The operating parameters, including catalyst loading, pH, initial phenol concentration and light intensity have been optimized to increase the efficiency of the photocatalytic degradation process within this photoreactor. The results have demonstrated a higher efficiency and an increased performance capability of the present reactor in comparison with the conventional processes. In the next step, residence time distribution (RTD) of the slurry phase within the reactor was measured using the impulse tracer method. A CFD-based model for predicting the RTD was also developed which compared well with the experimental results. The RTD data was finally applied in conjunction with the phenol degradation kinetic model to predict the apparent rate coefficient for such a reaction.

  12. Structural and dynamical properties of solvated electrons; a study of kinetic spectroscopy using pulse radiolysis

    International Nuclear Information System (INIS)

    Huis, C. van

    1977-01-01

    In this thesis the pulse radiolysis experiments of hexamethyl-phosphortriamide (HMPA), propanol-1, 3-methylpentane and mixtures of propanol-1 and 3-methylpentane are reported. In the pulse radiolysis of HMPA, carried out at room temperature, the high yield of esub(s) - (G=2) and the very high wavelength of the maximum absorption (max= 2200 nm) in the esub(s) - absorption spectrum are explained by considering the aprotic nature and the molecular structure of this compound. In the experiment with propanol-1 (temperature range 93deg-123degK) a temporal shift to lower wavelengths in the time range of 10 s-10 ms is observed. In further experiments biphenyl was used as electron scavenger. It was concluded that after the electron pulse the following sequence of events takes place: 1) electron redistribution in times shorter than 1 s; 2) dipole reorientation during 10 s-10 ms; 3) recombination of a part of the solvated electrons; 4) a reaction of the solvated electrons with the neighbouring propanol-1 molecules. In the experiments with 3-methylpentane at 103deg-113degK an esub(s) - absorption band with third order decay kinetics was observed. This is attributed to geminate recombination. The activation energy of the recombination process was 0.4 eV. The experiments with mixtures of propanol-1 and 3-methylpentane were carried out at 103degK. At low propanol-1 concentrations the build-up at 500 nm obeys first order kinetics, whereas at high concentrations this build-up can be split up into three first order components, as was measured in pure propanol-1. The half-lives of the three components were in the ratio of 1:10:100. In the last chapter theoretical models for the electron redistribution and the matric relaxation are discussed and compared with the experiments

  13. Research on Dynamic Modeling and Application of Kinetic Contact Interface in Machine Tool

    Directory of Open Access Journals (Sweden)

    Dan Xu

    2016-01-01

    Full Text Available A method is presented which is a kind of combining theoretic analysis and experiment to obtain the equivalent dynamic parameters of linear guideway through four steps in detail. From statics analysis, vibration model analysis, dynamic experiment, and parameter identification, the dynamic modeling of linear guideway is synthetically studied. Based on contact mechanics and elastic mechanics, the mathematic vibration model and the expressions of basic mode frequency are deduced. Then, equivalent stiffness and damping of guideway are obtained in virtue of single-freedom-degree mode fitting method. Moreover, the investigation above is applied in a certain gantry-type machining center; and through comparing with simulation model and experiment results, both availability and correctness are validated.

  14. Superfluid kinetic equation approach to the dynamics of the 3He A-B phase boundary

    International Nuclear Information System (INIS)

    Palmeri, J.

    1990-01-01

    The dynamics of the A-B phase boundary is studied using a nonequilibrium theory inspired by the microscopic approach to flux flow in type-II superconductors, namely a generalized two-fluid model consisting of coupled dynamical equations for the superfluid order parameter and the quasiparticle fluid. The interface mobility is obtained to lowest order in the front velocity in three different dynamical regimes: the gapless, hydrodynamic, and ballistic. Experiments have so far only been performed in the ballistic regime, and in this regime we find that, if only Andreev scattering processes are accounted for in the interface mobility, then the theoretical predictions for the terminal velocity of the planar interface are too big by a factor ∼2. From this we conclude that there may be other important contributions to the interface mobility in the ballistic regime, and we discuss a few possibilities

  15. Intramolecular diffusive motion in alkane monolayers studied by high-resolution quasielastic neutron scattering and molecular dynamics simulations

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Criswell, L.; Fuhrmann, D

    2004-01-01

    Molecular dynamics simulations of a tetracosane (n-C24H50) monolayer adsorbed on a graphite basal-plane surface show that there are diffusive motions associated with the creation and annihilation of gauche defects occurring on a time scale of similar to0.1-4 ns. We present evidence...... that these relatively slow motions are observable by high-energy-resolution quasielastic neutron scattering (QNS) thus demonstrating QNS as a technique, complementary to nuclear magnetic resonance, for studying conformational dynamics on a nanosecond time scale in molecular monolayers....

  16. Chemical Kinetics, Heat Transfer, and Sensor Dynamics Revisited in a Simple Experiment

    Science.gov (United States)

    Sad, Maria E.; Sad, Mario R.; Castro, Alberto A.; Garetto, Teresita F.

    2008-01-01

    A simple experiment about thermal effects in chemical reactors is described, which can be used to illustrate chemical reactor models, the determination and validation of their parameters, and some simple principles of heat transfer and sensor dynamics. It is based in the exothermic reaction between aqueous solutions of sodium thiosulfate and…

  17. Time-resolved PIV technique for high temporal resolution measurement of mechanical prosthetic aortic valve fluid dynamics.

    Science.gov (United States)

    Kaminsky, R; Morbiducci, U; Rossi, M; Scalise, L; Verdonck, P; Grigioni, M

    2007-02-01

    Prosthetic heart valves (PHVs) have been used to replace diseased native valves for more than five decades. Among these, mechanical PHVs are the most frequently implanted. Unfortunately, these devices still do not achieve ideal behavior and lead to many complications, many of which are related to fluid mechanics. The fluid dynamics of mechanical PHVs are particularly complex and the fine-scale characteristics of such flows call for very accurate experimental techniques. Adequate temporal resolution can be reached by applying time-resolved PIV, a high-resolution dynamic technique which is able to capture detailed chronological changes in the velocity field. The aim of this experimental study is to investigate the evolution of the flow field in a detailed time domain of a commercial bileaflet PHV in a mock-loop mimicking unsteady conditions, by means of time-resolved 2D Particle Image Velocimetry (PIV). The investigated flow field corresponded to the region immediately downstream of the valve plane. Spatial resolution as in "standard" PIV analysis of prosthetic valve fluid dynamics was used. The combination of a Nd:YLF high-repetition-rate double-cavity laser with a high frame rate CMOS camera allowed a detailed, highly temporally resolved acquisition (up to 10000 fps depending on the resolution) of the flow downstream of the PHV. Features that were observed include the non-homogeneity and unsteadiness of the phenomenon and the presence of large-scale vortices within the field, especially in the wake of the valve leaflets. Furthermore, we observed that highly temporally cycle-resolved analysis allowed the different behaviors exhibited by the bileaflet valve at closure to be captured in different acquired cardiac cycles. By accurately capturing hemodynamically relevant time scales of motion, time-resolved PIV characterization can realistically be expected to help designers in improving PHV performance and in furnishing comprehensive validation with experimental data

  18. Dynamic PET simulator via tomographic emission projection for kinetic modeling and parametric image studies.

    Science.gov (United States)

    Häggström, Ida; Beattie, Bradley J; Schmidtlein, C Ross

    2016-06-01

    To develop and evaluate a fast and simple tool called dpetstep (Dynamic PET Simulator of Tracers via Emission Projection), for dynamic PET simulations as an alternative to Monte Carlo (MC), useful for educational purposes and evaluation of the effects of the clinical environment, postprocessing choices, etc., on dynamic and parametric images. The tool was developed in matlab using both new and previously reported modules of petstep (PET Simulator of Tracers via Emission Projection). Time activity curves are generated for each voxel of the input parametric image, whereby effects of imaging system blurring, counting noise, scatters, randoms, and attenuation are simulated for each frame. Each frame is then reconstructed into images according to the user specified method, settings, and corrections. Reconstructed images were compared to MC data, and simple Gaussian noised time activity curves (GAUSS). dpetstep was 8000 times faster than MC. Dynamic images from dpetstep had a root mean square error that was within 4% on average of that of MC images, whereas the GAUSS images were within 11%. The average bias in dpetstep and MC images was the same, while GAUSS differed by 3% points. Noise profiles in dpetstep images conformed well to MC images, confirmed visually by scatter plot histograms, and statistically by tumor region of interest histogram comparisons that showed no significant differences (p dynamic PET and parametric images, and demonstrated that it generates both images and subsequent parametric images with very similar noise properties to those of MC images, in a fraction of the time. They believe dpetstep to be very useful for generating fast, simple, and realistic results, however since it uses simple scatter and random models it may not be suitable for studies investigating these phenomena. dpetstep can be downloaded free of cost from https://github.com/CRossSchmidtlein/dPETSTEP.

  19. Probing the hydrogen equilibrium and kinetics in zeolite imidazolate frameworks via molecular dynamics and quasi-elastic neutron scattering experiments.

    Science.gov (United States)

    Pantatosaki, Evangelia; Jobic, Hervé; Kolokolov, Daniil I; Karmakar, Shilpi; Biniwale, Rajesh; Papadopoulos, George K

    2013-01-21

    The problem of simulating processes involving equilibria and dynamics of guest sorbates within zeolitic imidazolate frameworks (ZIF) by means of molecular dynamics (MD) computer experiments is of growing importance because of the promising role of ZIFs as molecular "traps" for clean energy applications. A key issue for validating such an atomistic modeling attempt is the possibility of comparing the MD results, with real experiments being able to capture analogous space and time scales to the ones pertained to the computer experiments. In the present study, this prerequisite is fulfilled through the quasi-elastic neutron scattering technique (QENS) for measuring self-diffusivity, by elaborating the incoherent scattering signal of hydrogen nuclei. QENS and MD experiments were performed in parallel to probe the hydrogen motion, for the first time in ZIF members. The predicted and measured dynamics behaviors show considerable concentration variation of the hydrogen self-diffusion coefficient in the two topologically different ZIF pore networks of this study, the ZIF-3 and ZIF-8. Modeling options such as the flexibility of the entire matrix versus a rigid framework version, the mobility of the imidazolate ligand, and the inclusion of quantum mechanical effects in the potential functions were examined in detail for the sorption thermodynamics and kinetics of hydrogen and also of deuterium, by employing MD combined with Widom averaging towards studying phase equilibria. The latter methodology ensures a rigorous and efficient way for post-processing the dynamics trajectory, thereby avoiding stochastic moves via Monte Carlo simulation, over the large number of configurational degrees of freedom a nonrigid framework encompasses.

  20. Comparison of elastic-viscous-plastic and viscous-plastic dynamics models using a high resolution Arctic sea ice model

    Energy Technology Data Exchange (ETDEWEB)

    Hunke, E.C. [Los Alamos National Lab., NM (United States); Zhang, Y. [Naval Postgraduate School, Monterey, CA (United States)

    1997-12-31

    A nonlinear viscous-plastic (VP) rheology proposed by Hibler (1979) has been demonstrated to be the most suitable of the rheologies commonly used for modeling sea ice dynamics. However, the presence of a huge range of effective viscosities hinders numerical implementations of this model, particularly on high resolution grids or when the ice model is coupled to an ocean or atmosphere model. Hunke and Dukowicz (1997) have modified the VP model by including elastic waves as a numerical regularization in the case of zero strain rate. This modification (EVP) allows an efficient, fully explicit discretization that adapts well to parallel architectures. The authors present a comparison of EVP and VP dynamics model results from two 5-year simulations of Arctic sea ice, obtained with a high resolution sea ice model. The purpose of the comparison is to determine how differently the two dynamics models behave, and to decide whether the elastic-viscous-plastic model is preferable for high resolution climate simulations, considering its high efficiency in parallel computation. Results from the first year of this experiment (1990) are discussed in detail in Hunke and Zhang (1997).

  1. Random Forests Are Able to Identify Differences in Clotting Dynamics from Kinetic Models of Thrombin Generation.

    Science.gov (United States)

    Arumugam, Jayavel; Bukkapatnam, Satish T S; Narayanan, Krishna R; Srinivasa, Arun R

    2016-01-01

    Current methods for distinguishing acute coronary syndromes such as heart attack from stable coronary artery disease, based on the kinetics of thrombin formation, have been limited to evaluating sensitivity of well-established chemical species (e.g., thrombin) using simple quantifiers of their concentration profiles (e.g., maximum level of thrombin concentration, area under the thrombin concentration versus time curve). In order to get an improved classifier, we use a 34-protein factor clotting cascade model and convert the simulation data into a high-dimensional representation (about 19000 features) using a piecewise cubic polynomial fit. Then, we systematically find plausible assays to effectively gauge changes in acute coronary syndrome/coronary artery disease populations by introducing a statistical learning technique called Random Forests. We find that differences associated with acute coronary syndromes emerge in combinations of a handful of features. For instance, concentrations of 3 chemical species, namely, active alpha-thrombin, tissue factor-factor VIIa-factor Xa ternary complex, and intrinsic tenase complex with factor X, at specific time windows, could be used to classify acute coronary syndromes to an accuracy of about 87.2%. Such a combination could be used to efficiently assay the coagulation system.

  2. Coarse-grained molecular dynamics modeling of the kinetics of lamellar block copolymer defect annealing

    Science.gov (United States)

    Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.

    2016-01-01

    State-of-the-art block copolymer (BCP)-directed self-assembly (DSA) methods still yield defect densities orders of magnitude higher than is necessary in semiconductor fabrication despite free-energy calculations that suggest equilibrium defect densities are much lower than is necessary for economic fabrication. This disparity suggests that the main problem may lie in the kinetics of defect removal. This work uses a coarse-grained model to study the rates, pathways, and dependencies of healing a common defect to give insight into the fundamental processes that control defect healing and give guidance on optimal process conditions for BCP-DSA. It is found that bulk simulations yield an exponential drop in defect heal rate above χN˜30. Thin films show no change in rate associated with the energy barrier below χN˜50, significantly higher than the χN values found previously for self-consistent field theory studies that neglect fluctuations. Above χN˜50, the simulations show an increase in energy barrier scaling with 1/2 to 1/3 of the bulk systems. This is because thin films always begin healing at the free interface or the BCP-underlayer interface, where the increased A-B contact area associated with the transition state is minimized, while the infinitely thick films cannot begin healing at an interface.

  3. Random Forests Are Able to Identify Differences in Clotting Dynamics from Kinetic Models of Thrombin Generation.

    Directory of Open Access Journals (Sweden)

    Jayavel Arumugam

    Full Text Available Current methods for distinguishing acute coronary syndromes such as heart attack from stable coronary artery disease, based on the kinetics of thrombin formation, have been limited to evaluating sensitivity of well-established chemical species (e.g., thrombin using simple quantifiers of their concentration profiles (e.g., maximum level of thrombin concentration, area under the thrombin concentration versus time curve. In order to get an improved classifier, we use a 34-protein factor clotting cascade model and convert the simulation data into a high-dimensional representation (about 19000 features using a piecewise cubic polynomial fit. Then, we systematically find plausible assays to effectively gauge changes in acute coronary syndrome/coronary artery disease populations by introducing a statistical learning technique called Random Forests. We find that differences associated with acute coronary syndromes emerge in combinations of a handful of features. For instance, concentrations of 3 chemical species, namely, active alpha-thrombin, tissue factor-factor VIIa-factor Xa ternary complex, and intrinsic tenase complex with factor X, at specific time windows, could be used to classify acute coronary syndromes to an accuracy of about 87.2%. Such a combination could be used to efficiently assay the coagulation system.

  4. Kinetics and dynamics of near-resonant vibrational energy transfer in gas ensembles of atmospheric interest

    Science.gov (United States)

    McCaffery, Anthony J.

    2018-03-01

    This study of near-resonant, vibration-vibration (V-V) gas-phase energy transfer in diatomic molecules uses the theoretical/computational method, of Marsh & McCaffery (Marsh & McCaffery 2002 J. Chem. Phys. 117, 503 (doi:10.1063/1.1489998)) The method uses the angular momentum (AM) theoretical formalism to compute quantum-state populations within the component molecules of large, non-equilibrium, gas mixtures as the component species proceed to equilibration. Computed quantum-state populations are displayed in a number of formats that reveal the detailed mechanism of the near-resonant V-V process. Further, the evolution of quantum-state populations, for each species present, may be followed as the number of collision cycles increases, displaying the kinetics of evolution for each quantum state of the ensemble's molecules. These features are illustrated for ensembles containing vibrationally excited N2 in H2, O2 and N2 initially in their ground states. This article is part of the theme issue `Modern theoretical chemistry'.

  5. Kinetic and dynamic aspects of soil-plant-snail transfer of cadmium in the field

    International Nuclear Information System (INIS)

    Gimbert, Frederic; Mench, Michel; Coeurdassier, Michael; Badot, Pierre-Marie; Vaufleury, Annette de

    2008-01-01

    The proper use of bioaccumulation in the assessment of environmental quality involves accounting for chemical fluxes in organisms. Cadmium (Cd) accumulation kinetics in a soil-plant-snail food chain were therefore investigated in the field under different soil contamination (from 0 to 40 mg kg -1 ), soil pH (6 and 7) and season. Allowing for an accurate and sensitive assessment of Cd transfer to snails, toxicokinetics appears an interesting tool in the improvement of risk assessment procedures and a way to quantify metal bioavailability for a defined target. On the basis of uptake fluxes, snails proved to be sensitive enough to distinguish moderate soil contaminations. The soil pH did not appear, in the range studied, as a modulating parameter of the Cd transfer from soil to snail whereas the season, by influencing the snail mass, may modify the internal concentrations. The present data specifying a time integrated assessment of environmental factors on metal bioavailability and transfer to terrestrial snails should ensure their rational use in environmental biomonitoring. - Toxicokinetics and uptake fluxes can be used to describe the environment contamination by Cd, its bioavailability and transfer to Helix aspersa snails in the field

  6. A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics

    Science.gov (United States)

    Byun, Hye Suk; El-Naggar, Mohamed Y.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2017-10-01

    Kinetic Monte Carlo (KMC) simulations are used to study long-time dynamics of a wide variety of systems. Unfortunately, the conventional KMC algorithm is not scalable to larger systems, since its time scale is inversely proportional to the simulated system size. A promising approach to resolving this issue is the synchronous parallel KMC (SPKMC) algorithm, which makes the time scale size-independent. This paper introduces a formal derivation of the SPKMC algorithm based on local transition-state and time-dependent Hartree approximations, as well as its scalable parallel implementation based on a dual linked-list cell method. The resulting algorithm has achieved a weak-scaling parallel efficiency of 0.935 on 1024 Intel Xeon processors for simulating biological electron transfer dynamics in a 4.2 billion-heme system, as well as decent strong-scaling parallel efficiency. The parallel code has been used to simulate a lattice of cytochrome complexes on a bacterial-membrane nanowire, and it is broadly applicable to other problems such as computational synthesis of new materials.

  7. Dynamic PET simulator via tomographic emission projection for kinetic modeling and parametric image studies

    Energy Technology Data Exchange (ETDEWEB)

    Häggström, Ida, E-mail: haeggsti@mskcc.org [Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York 10065 and Department of Radiation Sciences, Umeå University, Umeå 90187 (Sweden); Beattie, Bradley J.; Schmidtlein, C. Ross [Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York 10065 (United States)

    2016-06-15

    Purpose: To develop and evaluate a fast and simple tool called dPETSTEP (Dynamic PET Simulator of Tracers via Emission Projection), for dynamic PET simulations as an alternative to Monte Carlo (MC), useful for educational purposes and evaluation of the effects of the clinical environment, postprocessing choices, etc., on dynamic and parametric images. Methods: The tool was developed in MATLAB using both new and previously reported modules of PETSTEP (PET Simulator of Tracers via Emission Projection). Time activity curves are generated for each voxel of the input parametric image, whereby effects of imaging system blurring, counting noise, scatters, randoms, and attenuation are simulated for each frame. Each frame is then reconstructed into images according to the user specified method, settings, and corrections. Reconstructed images were compared to MC data, and simple Gaussian noised time activity curves (GAUSS). Results: dPETSTEP was 8000 times faster than MC. Dynamic images from dPETSTEP had a root mean square error that was within 4% on average of that of MC images, whereas the GAUSS images were within 11%. The average bias in dPETSTEP and MC images was the same, while GAUSS differed by 3% points. Noise profiles in dPETSTEP images conformed well to MC images, confirmed visually by scatter plot histograms, and statistically by tumor region of interest histogram comparisons that showed no significant differences (p < 0.01). Compared to GAUSS, dPETSTEP images and noise properties agreed better with MC. Conclusions: The authors have developed a fast and easy one-stop solution for simulations of dynamic PET and parametric images, and demonstrated that it generates both images and subsequent parametric images with very similar noise properties to those of MC images, in a fraction of the time. They believe dPETSTEP to be very useful for generating fast, simple, and realistic results, however since it uses simple scatter and random models it may not be suitable for

  8. Dynamic PET simulator via tomographic emission projection for kinetic modeling and parametric image studies

    International Nuclear Information System (INIS)

    Häggström, Ida; Beattie, Bradley J.; Schmidtlein, C. Ross

    2016-01-01

    Purpose: To develop and evaluate a fast and simple tool called dPETSTEP (Dynamic PET Simulator of Tracers via Emission Projection), for dynamic PET simulations as an alternative to Monte Carlo (MC), useful for educational purposes and evaluation of the effects of the clinical environment, postprocessing choices, etc., on dynamic and parametric images. Methods: The tool was developed in MATLAB using both new and previously reported modules of PETSTEP (PET Simulator of Tracers via Emission Projection). Time activity curves are generated for each voxel of the input parametric image, whereby effects of imaging system blurring, counting noise, scatters, randoms, and attenuation are simulated for each frame. Each frame is then reconstructed into images according to the user specified method, settings, and corrections. Reconstructed images were compared to MC data, and simple Gaussian noised time activity curves (GAUSS). Results: dPETSTEP was 8000 times faster than MC. Dynamic images from dPETSTEP had a root mean square error that was within 4% on average of that of MC images, whereas the GAUSS images were within 11%. The average bias in dPETSTEP and MC images was the same, while GAUSS differed by 3% points. Noise profiles in dPETSTEP images conformed well to MC images, confirmed visually by scatter plot histograms, and statistically by tumor region of interest histogram comparisons that showed no significant differences (p < 0.01). Compared to GAUSS, dPETSTEP images and noise properties agreed better with MC. Conclusions: The authors have developed a fast and easy one-stop solution for simulations of dynamic PET and parametric images, and demonstrated that it generates both images and subsequent parametric images with very similar noise properties to those of MC images, in a fraction of the time. They believe dPETSTEP to be very useful for generating fast, simple, and realistic results, however since it uses simple scatter and random models it may not be suitable for

  9. Coarse-grained molecular dynamics modeling of the kinetics of lamellar BCP defect annealing

    Science.gov (United States)

    Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.

    2015-03-01

    Directed self-assembly of block copolymers (BCPs) is a process that has received great interest in the field of nanomanufacturing in the past decade, and great strides towards forming high quality aligned patterns have been made. But state of the art methods still yield defectivities orders of magnitude higher than is necessary in semi-conductor fabrication even though free energy calculations suggest that equilibrium defectivities are much lower than is necessary for economic semi-conductor fabrication. This disparity suggests that the main problem may lie in the kinetics of defect removal. This work uses a coarse-grained model to study the rates, pathways, and dependencies of healing a common defect to give insight into the fundamental processes that control defect healing and give guidance on optimal process conditions for BCP-DSA. It is found that infinitely thick films yield an exponential drop in defect heal rate above χN ~ 30. Below χN ~ 30, the rate of transport was similar to the rate at which the transition state was reached so that the overall rate changed only slightly. The energy barrier in periodic simulations increased with 0.31 χN on average. Thin film simulations show no change in rate associated with the energy barrier below χN ~ 50, and then show an increase in energy barrier scaling with 0.16χN. Thin film simulations always begin to heal at either the free interface or the BCP-underlayer interface where the increased A-B contact area associated with the transition state will be minimized, while the infinitely thick films must start healing in the bulk where the A-B contact area is increased. It is also found that cooperative chain movement is required for the defect to start healing.

  10. Absolute quantitation of myocardial blood flow with 201Tl and dynamic SPECT in canine: optimisation and validation of kinetic modelling

    International Nuclear Information System (INIS)

    Iida, Hidehiro; Kim, Kyeong-Min; Nakazawa, Mayumi; Sohlberg, Antti; Zeniya, Tsutomu; Hayashi, Takuya; Watabe, Hiroshi; Eberl, Stefan; Tamura, Yoshikazu; Ono, Yukihiko

    2008-01-01

    201 Tl has been extensively used for myocardial perfusion and viability assessment. Unlike 99m Tc-labelled agents, such as 99m Tc-sestamibi and 99m Tc-tetrofosmine, the regional concentration of 201 Tl varies with time. This study is intended to validate a kinetic modelling approach for in vivo quantitative estimation of regional myocardial blood flow (MBF) and volume of distribution of 201 Tl using dynamic SPECT. Dynamic SPECT was carried out on 20 normal canines after the intravenous administration of 201 Tl using a commercial SPECT system. Seven animals were studied at rest, nine during adenosine infusion, and four after beta-blocker administration. Quantitative images were reconstructed with a previously validated technique, employing OS-EM with attenuation-correction, and transmission-dependent convolution subtraction scatter correction. Measured regional time-activity curves in myocardial segments were fitted to two- and three-compartment models. Regional MBF was defined as the influx rate constant (K 1 ) with corrections for the partial volume effect, haematocrit and limited first-pass extraction fraction, and was compared with that determined from radio-labelled microspheres experiments. Regional time-activity curves responded well to pharmacological stress. Quantitative MBF values were higher with adenosine and decreased after beta-blocker compared to a resting condition. MBFs obtained with SPECT (MBF SPECT ) correlated well with the MBF values obtained by the radio-labelled microspheres (MBF MS ) (MBF SPECT = -0.067 + 1.042 x MBF MS , p 201 Tl and dynamic SPECT. (orig.)

  11. Diagnostic value of kinetic analysis using dynamic FDG PET in immunocompetent patients with primary CNS lymphoma

    International Nuclear Information System (INIS)

    Nishiyama, Yoshihiro; Yamamoto, Yuka; Monden, Toshihide; Sasakawa, Yasuhiro; Satoh, Katashi; Ohkawa, Motoomi; Kawai, Nobuyuki

    2007-01-01

    The purpose of this study was to investigate the accumulation of FDG in immunocompetent patients with primary central nervous system (CNS) lymphoma using qualitative and quantitative PET images and to compare baseline with follow-up PET after therapy. Twelve immunocompetent patients with CNS lymphoma were examined. Dynamic emission data were acquired for 60 min immediately following injection of FDG. In seven patients, repeated PET studies were performed after treatment. Applying a three-compartment five-parameter model, K 1 , k 2 , k 3 , k 4 , vascular fraction (V B ) and cerebral metabolic rate of glucose (CMR Glc ) were obtained. We evaluated the FDG uptake visually using qualitative and parametric images and quantitatively using parametric images. A total of 12 lesions were identified in ten patients with newly diagnosed CNS lymphoma. On visual analysis, ten lesions showed an increase on qualitative images, eight showed an increase on K 1 images, 12 showed an increase on k 3 images and ten showed an increase on CMR Glc images. On quantitative analysis, k 2 , k 3 and CMR Glc values of the lesion were significantly different from those of the normal grey matter (p 3 and CMR Glc images. The K 1 , k 2 , k 3 and CMR Glc values after treatment were significantly different from those obtained before treatment (p 3 , using dynamic FDG PET might be helpful for diagnosis of CNS lymphoma and for monitoring therapeutic assessment. (orig.)

  12. Dynamic phase transition in the kinetic spin-32 Blume-Capel model: Phase diagrams in the temperature and crystal-field interaction plane

    Energy Technology Data Exchange (ETDEWEB)

    Keskin, Mustafa [Department of Physics, Erciyes University, 38039 Kayseri (Turkey)]. E-mail: keskin@erciyes.edu.tr; Canko, Osman [Department of Physics, Erciyes University, 38039 Kayseri (Turkey); Deviren, Bayram [Department of Physics, Erciyes University, 38039 Kayseri (Turkey)

    2007-06-15

    We analyze, within a mean-field approach, the stationary states of the kinetic spin-32 Blume-Capel (BC) model by the Glauber-type stochastic dynamics and subject to a time-dependent oscillating external magnetic field. The dynamic phase transition (DPT) points are obtained by investigating the behavior of the dynamic magnetization as a function of temperature and as well as calculating the Liapunov exponent. Phase diagrams are constructed in the temperature and crystal-field interaction plane. We find five fundamental types of phase diagrams for the different values of the reduced magnetic field amplitude parameter (h) in which they present a disordered, two ordered phases and the coexistences phase regions. The phase diagrams also exhibit a dynamic double-critical end point for 0dynamic tricritical point for 1.44dynamic tricritical points for h>5.06.

  13. Coupling of the computational fluid dynamics code ANSYS CFX with the 3D neutron kinetic core model DYN3D

    International Nuclear Information System (INIS)

    Kliem, S.; Grahn, A.; Rohde, U.; Schuetze, J.; Frank, Th.

    2010-01-01

    The computational fluid dynamics code ANSYS CFX has been coupled with the neutron-kinetic core model DYN3D. ANSYS CFX calculates the fluid dynamics and related transport phenomena in the reactors coolant and provides the corresponding data to DYN3D. In the fluid flow simulation of the coolant, the core itself is modeled within the porous body approach. DYN3D calculates the neutron kinetics and the fuel behavior including the heat transfer to the coolant. The physical data interface between the codes is the volumetric heat release rate into the coolant. In the prototype that is currently available, the coupling is restricted to single-phase flow problems. In the time domain an explicit coupling of the codes has been implemented so far. Steady-state and transient verification calculations for two small-size test problems confirm the correctness of the implementation of the prototype coupling. The first test problem was a mini-core consisting of nine real-size fuel assemblies with quadratic cross section. Comparison was performed with the DYN3D stand-alone code. In the steady state, the effective multiplication factor obtained by the DYN3D/ANSYS CFX codes hows a deviation of 9.8 pcm from the DYN3D stand-alone solution. This difference can be attributed to the use of different water property packages in the two codes. The transient test case simulated the withdrawal of the control rod from the central fuel assembly at hot zero power in the same mini-core. Power increase during the introduction of positive reactivity and power reduction due to fuel temperature increase are calculated in the same manner by the coupled and the stand-alone codes. The maximum values reached during the power rise differ by about 1 MW at a power level of 50 MW. Beside the different water property packages, these differences are caused by the use of different flow solvers. The same calculations were carried for a mini-core with seven real-size fuel assemblies with hexagonal cross section in

  14. Studies of pyrolysis kinetics of sewage sludge obtained from dynamic experiments; Estudio cinetico de la pirolisis de fangos mediante experimentos dinamicos

    Energy Technology Data Exchange (ETDEWEB)

    Arauzo, J; Gonzalo, A; Sanchez, J L [Universidad de Zaragoza, Madrid (Spain). Inst. de Investigacion en Ingenieria de Aragon. Grupo de Procesos Termoquimicos; Resende, F L.P. [University of Michigan, Ann Arbor, MI (United States). Dept. of Chemical Engineering; Rocha, J D [Universidade Estadual de Campinas (UNICAMP), Campinas, SP (Brazil). Nucleo Interdisciplinar de Planejamento Energetico (NIPE); Mesa Perez, J M [Universidade Estadual de Campinas (UNICAMP), Campinas, SP (Brazil). Fac. de Engenharia Agricola

    2004-07-01

    In this work, a pyrolysis model is presented in order to describe the pyrolysis kinetics of sewage sludge. Data were obtained from dynamic experiments, at heating rates of 5 to 20 deg C/min and in a temperature range of 40 to 900 deg C. A simple first order or near first order can predict reasonably well the final conversion reached, but, in what concerns the weight loss rate, a simple model cannot predict the peaks obtained in the weight loss rate. As it is shown, the best fit has been obtained by a model which takes into account four fractions which decompose independently following a first order kinetics. (author)

  15. Dynamics and regulation at the tip : a high resolution view on microtubele assembly

    NARCIS (Netherlands)

    Munteanu, Laura

    2008-01-01

    Microtubules are highly dynamic protein polymers that and are essential for intracellular organization and fundamental processes like transport and cell division. In cells, a wide family of microtubule-associated proteins (MAPs) tightly regulates microtubule dynamics. The work presented in this

  16. Dynamic rupture scenarios from Sumatra to Iceland - High-resolution earthquake source physics on natural fault systems

    Science.gov (United States)

    Gabriel, Alice-Agnes; Madden, Elizabeth H.; Ulrich, Thomas; Wollherr, Stephanie

    2017-04-01

    Capturing the observed complexity of earthquake sources in dynamic rupture simulations may require: non-linear fault friction, thermal and fluid effects, heterogeneous fault stress and fault strength initial conditions, fault curvature and roughness, on- and off-fault non-elastic failure. All of these factors have been independently shown to alter dynamic rupture behavior and thus possibly influence the degree of realism attainable via simulated ground motions. In this presentation we will show examples of high-resolution earthquake scenarios, e.g. based on the 2004 Sumatra-Andaman Earthquake, the 1994 Northridge earthquake and a potential rupture of the Husavik-Flatey fault system in Northern Iceland. The simulations combine a multitude of representations of source complexity at the necessary spatio-temporal resolution enabled by excellent scalability on modern HPC systems. Such simulations allow an analysis of the dominant factors impacting earthquake source physics and ground motions given distinct tectonic settings or distinct focuses of seismic hazard assessment. Across all simulations, we find that fault geometry concurrently with the regional background stress state provide a first order influence on source dynamics and the emanated seismic wave field. The dynamic rupture models are performed with SeisSol, a software package based on an ADER-Discontinuous Galerkin scheme for solving the spontaneous dynamic earthquake rupture problem with high-order accuracy in space and time. Use of unstructured tetrahedral meshes allows for a realistic representation of the non-planar fault geometry, subsurface structure and bathymetry. The results presented highlight the fact that modern numerical methods are essential to further our understanding of earthquake source physics and complement both physic-based ground motion research and empirical approaches in seismic hazard analysis.

  17. The nonlinear dynamics of family problem solving in adolescence: the predictive validity of a peaceful resolution attractor.

    Science.gov (United States)

    Dishion, Thomas J; Forgatch, Marion; Van Ryzin, Mark; Winter, Charlotte

    2012-07-01

    In this study we examined the videotaped family interactions of a community sample of adolescents and their parents. Youths were assessed in early to late adolescence on their levels of antisocial behavior. At age 16-17, youths and their parents were videotaped interacting while completing a variety of tasks, including family problem solving. The interactions were coded and compared for three developmental patterns of antisocial behavior: early onset, persistent; adolescence onset; and typically developing. The mean duration of conflict bouts was the only interaction pattern that discriminated the 3 groups. In the prediction of future antisocial behavior, parent and youth reports of transition entropy and conflict resolution interacted to account for antisocial behavior at age 18-19. Families with low entropy and peaceful resolutions predicted low levels of youth antisocial behavior at age 18-19. These findings suggest the need to study both attractors and repellers to understand family dynamics associated with health and social and emotional development.

  18. Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling.

    Science.gov (United States)

    Huang, Yu-Ming M; Huber, Gary A; Wang, Nuo; Minteer, Shelley D; McCammon, J Andrew

    2018-02-01

    Malate dehydrogenase (MDH) and citrate synthase (CS) are two pacemaking enzymes involved in the tricarboxylic acid (TCA) cycle. Oxaloacetate (OAA) molecules are the intermediate substrates that are transferred from the MDH to CS to carry out sequential catalysis. It is known that, to achieve a high flux of intermediate transport and reduce the probability of substrate leaking, a MDH-CS metabolon forms to enhance the OAA substrate channeling. In this study, we aim to understand the OAA channeling within possible MDH-CS metabolons that have different structural orientations in their complexes. Three MDH-CS metabolons from native bovine, wild-type porcine, and recombinant sources, published in recent work, were selected to calculate OAA transfer efficiency by Brownian dynamics (BD) simulations and to study, through electrostatic potential calculations, a possible role of charges that drive the substrate channeling. Our results show that an electrostatic channel is formed in the metabolons of native bovine and recombinant porcine enzymes, which guides the oppositely charged OAA molecules passing through the channel and enhances the transfer efficiency. However, the channeling probability in a suggested wild-type porcine metabolon conformation is reduced due to an extended diffusion length between the MDH and CS active sites, implying that the corresponding arrangements of MDH and CS result in the decrease of electrostatic steering between substrates and protein surface and then reduce the substrate transfer efficiency from one active site to another. © 2017 The Protein Society.

  19. High resolution polarimeter-interferometer system for fast equilibrium dynamics and MHD instability studies on Joint-TEXT tokamak (invited)

    Energy Technology Data Exchange (ETDEWEB)

    Chen, J.; Zhuang, G., E-mail: ge-zhuang@hust.edu.cn; Li, Q.; Liu, Y.; Gao, L.; Zhou, Y. N.; Jian, X.; Xiong, C. Y.; Wang, Z. J. [State Key Laboratory of Advanced Electromagnetic Engineering and Technology, Huazhong University of Science and Technology, Wuhan 430074 (China); Brower, D. L.; Ding, W. X. [Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095 (United States)

    2014-11-15

    A high-performance Faraday-effect polarimeter-interferometer system has been developed for the J-TEXT tokamak. This system has time response up to 1 μs, phase resolution < 0.1° and minimum spatial resolution ∼15 mm. High resolution permits investigation of fast equilibrium dynamics as well as magnetic and density perturbations associated with intrinsic Magneto-Hydro-Dynamic (MHD) instabilities and external coil-induced Resonant Magnetic Perturbations (RMP). The 3-wave technique, in which the line-integrated Faraday angle and electron density are measured simultaneously by three laser beams with specific polarizations and frequency offsets, is used. In order to achieve optimum resolution, three frequency-stabilized HCOOH lasers (694 GHz, >35 mW per cavity) and sensitive Planar Schottky Diode mixers are used, providing stable intermediate-frequency signals (0.5–3 MHz) with S/N > 50. The collinear R- and L-wave probe beams, which propagate through the plasma poloidal cross section (a = 0.25–0.27 m) vertically, are expanded using parabolic mirrors to cover the entire plasma column. Sources of systematic errors, e.g., stemming from mechanical vibration, beam non-collinearity, and beam polarization distortion are individually examined and minimized to ensure measurement accuracy. Simultaneous density and Faraday measurements have been successfully achieved for 14 chords. Based on measurements, temporal evolution of safety factor profile, current density profile, and electron density profile are resolved. Core magnetic and density perturbations associated with MHD tearing instabilities are clearly detected. Effects of non-axisymmetric 3D RMP in ohmically heated plasmas are directly observed by polarimetry for the first time.

  20. High resolution mapping of riffle-pool dynamics based on ADCP and close-range remote sensing data

    Science.gov (United States)

    Salmela, Jouni; Kasvi, Elina; Alho, Petteri

    2017-04-01

    Present development of mobile laser scanning (MLS) and close-range photogrammetry with unmanned aerial vehicle (UAV) enable us to create seamless digital elevation models (DEMs) of the riverine environment. Remote-controlled flow measurement platforms have also improved spatio-temporal resolution of the flow field data. In this study, acoustic Doppler current profiler (ADCP) attached to remote-controlled mini-boat, UAV-based bathymetry and MLS techniques were utilized to create the high-resolution DEMs of the river channel. These high-resolution measurements can be used in many fluvial applications such as computational fluid dynamics, channel change detection, habitat mapping or hydro-electric power plant planning. In this study we aim: 1) to analyze morphological changes of river channel especially riffle and pool formations based on fine-scale DEMs and ADCP measurements, 2) to analyze flow fields and their effect on morphological changes. The interest was mainly focused on reach-scale riffle-pool dynamics within two-year period of 2013 and 2014. The study was performed in sub-arctic meandering Pulmankijoki River located in Northern Finland. The river itself has shallow and clear water and sandy bed sediment. Discharge remains typically below 10 m3s-1 most of the year but during snow melt period in spring the discharge may exceed 70 m3s-1. We compared DEMs and ADCP measurements to understand both magnitude and spatio-temporal change of the river bed. Models were accurate enough to study bed form changes and locations and persistence of riffles and pools. We analyzed their locations with relation to flow during the peak and low discharge. Our demonstrated method has improved significantly spatio-temporal resolution of riverine DEMs compared to other cross-sectional and photogrammetry based models. Together with flow field measurements we gained better understanding of riverbed-water interaction

  1. Dynamic Resolution in GPU-Accelerated Volume Rendering to Autostereoscopic Multiview Lenticular Displays

    Directory of Open Access Journals (Sweden)

    Daniel Ruijters

    2008-09-01

    Full Text Available The generation of multiview stereoscopic images of large volume rendered data demands an enormous amount of calculations. We propose a method for hardware accelerated volume rendering of medical data sets to multiview lenticular displays, offering interactive manipulation throughout. The method is based on buffering GPU-accelerated direct volume rendered visualizations of the individual views from their respective focal spot positions, and composing the output signal for the multiview lenticular screen in a second pass. This compositing phase is facilitated by the fact that the view assignment per subpixel is static, and therefore can be precomputed. We decoupled the resolution of the individual views from the resolution of the composited signal, and adjust the resolution on-the-fly, depending on the available processing resources, in order to maintain interactive refresh rates. The optimal resolution for the volume rendered views is determined by means of an analysis of the lattice of the output signal for the lenticular screen in the Fourier domain.

  2. Kinetics of Quality Changes of Pangasius Fillets at Stable and Dynamic Temperatures, Simulating Downstream Cold Chain Conditions

    Directory of Open Access Journals (Sweden)

    Nga Mai

    2017-01-01

    Full Text Available This study was about the quality changes of Pangasius fillets during storage under simulated temperature conditions of downstream cold chain. Sensory, chemical, and microbiological analyses were conducted over storage time and bacterial growth was modelled. Sensory quality index (QI, at five stable (1, 4, 9, 15, and 19 ± 1°C and three dynamic temperatures, progressed faster at higher temperatures, especially with sooner temperature abuses. Total volatile basic nitrogen remained under the acceptable limit throughout all the storage conditions. Total viable psychrotrophic counts (TVC were around 5.68 ± 0.24 log CFU g−1 at the beginning and exceeded the limit of 6 log CFU g−1 after 216, 96, 36, 16, and 7 h at 1, 4, 9, 15, and 19 ± 1°C, respectively. Meanwhile, Pseudomonas counts started at 3.81 ± 0.53 log CFU g−1 and reached 4.60–6.36 log CFU g−1 by the time of TVC rejection. Since lower shelf lives were given by TVC rather than QI, it should be appropriate to base the product shelf life on the TVC acceptable limit. Kinetics models based on the Baranyi and Roberts and square root models, developed for TVC and Pseudomonas spp., gave acceptable bacterial estimations at dynamic temperatures, with over 80% of observed counts within the acceptable simulation zone, revealing promising model applicability as a supporting tool for cold chain management. However, further improvement and validation of the models are needed.

  3. Spatio-temporal image correlation spectroscopy and super-resolution microscopy to quantify molecular dynamics in T cells.

    Science.gov (United States)

    Ashdown, George W; Owen, Dylan M

    2018-02-02

    Many cellular processes are regulated by the spatio-temporal organisation of signalling complexes, cytoskeletal components and membranes. One such example is at the T cell immunological synapse where the retrograde flow of cortical filamentous (F)-actin from the synapse periphery drives signalling protein microclusters towards the synapse centre. The density of this mesh however, makes visualisation and analysis of individual actin fibres difficult due to the resolution limit of conventional microscopy. Recently, super-resolution methods such as structured illumination microscopy (SIM) have surpassed this resolution limit. Here, we apply SIM to better visualise the dense cortical actin meshwork in T cell synapses formed against activating, antibody-coated surfaces and image under total-internal reflection fluorescence (TIRF) illumination. To analyse the observed molecular flows, and the relationship between them, we apply spatio-temporal image correlation spectroscopy (STICS) and its cross-correlation variant (STICCS). We show that the dynamic cortical actin mesh can be visualised with unprecedented detail and that STICS/STICCS can output accurate, quantitative maps of molecular flow velocity and directionality from such data. We find that the actin flow can be disrupted using small molecule inhibitors of actin polymerisation. This combination of imaging and quantitative analysis may provide an important new tool for researchers to investigate the molecular dynamics at cellular length scales. Here we demonstrate the retrograde flow of F-actin which may be important for the clustering and dynamics of key signalling proteins within the plasma membrane, a phenomenon which is vital to correct T cell activation and therefore the mounting of an effective immune response. Copyright © 2018. Published by Elsevier Inc.

  4. Trajectory Calculations for Bergman Cyclization Predict H/D Kinetic Isotope Effects Due to Nonstatistical Dynamics in the Product.

    Science.gov (United States)

    Doubleday, Charles; Boguslav, Mayla; Howell, Caronae; Korotkin, Scott D; Shaked, David

    2016-06-22

    An unusual H/D kinetic isotope effect (KIE) is described, in which isotopic selectivity arises primarily from nonstatistical dynamics in the product. In DFT-based quasiclassical trajectories of Bergman cyclization of (Z)-3-hexen-1,5-diyne (1) at 470 K, the new CC bond retains its energy, and 28% of nascent p-benzyne recrosses back to the enediyne on a vibrational time scale. The competing process of intramolecular vibrational redistribution (IVR) in p-benzyne is too slow to prevent this. Deuteration increases the rate of IVR, which decreases the fraction of recrossing and increases the yield of statistical (trapable) p-benzyne, 2. Trapable yields for three isotopomers of 2 range from 72% to 86%. The resulting KIEs for Bergman cyclization differ substantially from KIEs predicted by transition state theory, which suggests that IVR in this reaction can be studied by conventional KIEs. Leakage of vibrational zero point energy (ZPE) into the reaction coordinate was probed by trajectories in which initial ZPE in the CH/CD stretching modes was reduced by 25%. This did not change the predicted KIEs.

  5. Periodicity in tumor vasculature targeting kinetics of ligand-functionalized nanoparticles studied by dynamic contrast enhanced magnetic resonance imaging and intravital microscopy

    DEFF Research Database (Denmark)

    Hak, Sjoerd; Cebulla, Jana; Huuse, Else Marie

    2014-01-01

    In the past two decades advances in the development of targeted nanoparticles have facilitated their application as molecular imaging agents and targeted drug delivery vehicles. Nanoparticle-enhanced molecular imaging of the angiogenic tumor vasculature has been of particular interest. Not only...... because angiogenesis plays an important role in various pathologies, but also since endothelial cell surface receptors are directly accessible for relatively large circulating nanoparticles. Typically, nanoparticle targeting towards these receptors is studied by analyzing the contrast distribution...... kinetics. These kinetics will not only depend on nanoparticle characteristics, but also on receptor binding and recycling. In this study, we monitored the in vivo targeting kinetics of αvβ3-integrin specific nanoparticles with intravital microscopy and dynamic contrast enhanced magnetic resonance imaging...

  6. Self-Consistent System of Equations for a Kinetic Description of the Low-Pressure Discharges Accounting for the Nonlocal and Collisionless Electron Dynamics

    International Nuclear Information System (INIS)

    Kaganovich, Igor D.; Polomarov, Oleg

    2003-01-01

    In low-pressure discharges, when the electron mean free path is larger or comparable with the discharge length, the electron dynamics is essentially non-local. Moreover, the electron energy distribution function (EEDF) deviates considerably from a Maxwellian. Therefore, an accurate kinetic description of the low-pressure discharges requires knowledge of the non-local conductivity operator and calculation of the non-Maxwellian EEDF. The previous treatments made use of simplifying assumptions: a uniform density profile and a Maxwellian EEDF. In the present study a self-consistent system of equations for the kinetic description of nonlocal, non-uniform, nearly collisionless plasmas of low-pressure discharges is derived. It consists of the nonlocal conductivity operator and the averaged kinetic equation for calculation of the non-Maxwellian EEDF. The importance of accounting for the non-uniform plasma density profile on both the current density profile and the EEDF is demonstrated

  7. An efficient non hydrostatic dynamical care far high-resolution simulations down to the urban scale

    International Nuclear Information System (INIS)

    Bonaventura, L.; Cesari, D.

    2005-01-01

    Numerical simulations of idealized stratified flows aver obstacles at different spatial scales demonstrate the very general applicability and the parallel efficiency of a new non hydrostatic dynamical care far simulation of mesoscale flows aver complex terrain

  8. Improving the off-axis spatial resolution and dynamic range of the NIF X-ray streak cameras (invited)

    Energy Technology Data Exchange (ETDEWEB)

    MacPhee, A. G., E-mail: macphee2@llnl.gov; Hatch, B. W.; Bell, P. M.; Bradley, D. K.; Datte, P. S.; Landen, O. L.; Palmer, N. E.; Piston, K. W.; Rekow, V. V. [Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, California 94551-0808 (United States); Dymoke-Bradshaw, A. K. L.; Hares, J. D. [Kentech Instruments Ltd., Isis Building, Howbery Park, Wallingford, Oxfordshire OX10 8BD (United Kingdom); Hassett, J. [Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, California 94551-0808 (United States); Department of Electrical and Computer Engineering, University of Rochester, Rochester, New York 14627 (United States); Meadowcroft, A. L. [AWE Aldermaston, Reading, Berkshire RG7 4PR (United Kingdom); Hilsabeck, T. J.; Kilkenny, J. D. [General Atomics, P.O. Box 85608, San Diego, California 92186-5608 (United States)

    2016-11-15

    We report simulations and experiments that demonstrate an increase in spatial resolution of the NIF core diagnostic x-ray streak cameras by at least a factor of two, especially off axis. A design was achieved by using a corrector electron optic to flatten the field curvature at the detector plane and corroborated by measurement. In addition, particle in cell simulations were performed to identify the regions in the streak camera that contribute the most to space charge blurring. These simulations provide a tool for convolving synthetic pre-shot spectra with the instrument function so signal levels can be set to maximize dynamic range for the relevant part of the streak record.

  9. Dynamic functional coupling of high resolution EEG potentials related to unilateral internally triggered one-digit movements.

    Science.gov (United States)

    Urbano, A; Babiloni, C; Onorati, P; Babiloni, F

    1998-06-01

    Between-electrode cross-covariances of delta (0-3 Hz)- and theta (4-7 Hz)-filtered high resolution EEG potentials related to preparation, initiation. and execution of human unilateral internally triggered one-digit movements were computed to investigate statistical dynamic coupling between these potentials. Significant (P planning, starting, and performance of unilateral movement. The involvement of these cortical areas is supported by the observation that averaged spatially enhanced delta- and theta-bandpassed potentials were computed from the scalp regions where task-related electrical activation of primary sensorimotor areas and supplementary motor area was roughly represented.

  10. Quantitative analysis of localized stresses in irradiated stainless steels using high resolution electron backscatter diffraction and molecular dynamics modeling

    International Nuclear Information System (INIS)

    Johnson, D.C.; Kuhr, B.; Farkas, D.; Was, G.S.

    2016-01-01

    Quantitative measurements of stress near dislocation channel–grain boundary (DC–GB) interaction sites were made using high resolution electron backscatter diffraction (HREBSD) and have been compared with molecular dynamics (MD) simulations. Tensile stress normal to the grain boundary was significantly elevated at discontinuous DC–GB intersections with peak magnitudes roughly an order of magnitude greater than at sites where slip transfer occurred. These results constitute the first measurement of stress amplification at DC–GB intersections and provide support to the theory that high normal stress at the grain boundary may be a key driver for the initiation of irradiation assisted stress corrosion cracks.

  11. Improving the off-axis spatial resolution and dynamic range of the NIF X-ray streak cameras (invited).

    Science.gov (United States)

    MacPhee, A G; Dymoke-Bradshaw, A K L; Hares, J D; Hassett, J; Hatch, B W; Meadowcroft, A L; Bell, P M; Bradley, D K; Datte, P S; Landen, O L; Palmer, N E; Piston, K W; Rekow, V V; Hilsabeck, T J; Kilkenny, J D

    2016-11-01

    We report simulations and experiments that demonstrate an increase in spatial resolution of the NIF core diagnostic x-ray streak cameras by at least a factor of two, especially off axis. A design was achieved by using a corrector electron optic to flatten the field curvature at the detector plane and corroborated by measurement. In addition, particle in cell simulations were performed to identify the regions in the streak camera that contribute the most to space charge blurring. These simulations provide a tool for convolving synthetic pre-shot spectra with the instrument function so signal levels can be set to maximize dynamic range for the relevant part of the streak record.

  12. Dynamic phase transition in the kinetic spin-1 Blume-Capel model: Phase diagrams in the temperature and crystal-field interaction plane

    International Nuclear Information System (INIS)

    Keskin, M.; Canko, O.; Temizer, U.

    2007-01-01

    Within a mean-field approach, the stationary states of the kinetic spin-1 Blume-Capel model in the presence of a time-dependent oscillating external magnetic field is studied. The Glauber-type stochastic dynamics is used to describe the time evolution of the system and obtain the mean-field dynamic equation of motion. The dynamic phase-transition points are calculated and phase diagrams are presented in the temperature and crystal-field interaction plane. According to the values of the magnetic field amplitude, three fundamental types of phase diagrams are found: One exhibits a dynamic tricritical point, while the other two exhibit a dynamic zero-temperature critical point

  13. Production of solar radiation bankable datasets from high-resolution solar irradiance derived with dynamical downscaling Numerical Weather prediction model

    Directory of Open Access Journals (Sweden)

    Yassine Charabi

    2016-11-01

    Full Text Available A bankable solar radiation database is required for the financial viability of solar energy project. Accurate estimation of solar energy resources in a country is very important for proper siting, sizing and life cycle cost analysis of solar energy systems. During the last decade an important progress has been made to develop multiple solar irradiance database (Global Horizontal Irradiance (GHI and Direct Normal Irradiance (DNI, using satellite of different resolution and sophisticated models. This paper assesses the performance of High-resolution solar irradiance derived with dynamical downscaling Numerical Weather Prediction model with, GIS topographical solar radiation model, satellite data and ground measurements, for the production of bankable solar radiation datasets. For this investigation, NWP model namely Consortium for Small-scale Modeling (COSMO is used for the dynamical downscaling of solar radiation. The obtained results increase confidence in solar radiation data base obtained from dynamical downscaled NWP model. The mean bias of dynamical downscaled NWP model is small, on the order of a few percents for GHI, and it could be ranked as a bankable datasets. Fortunately, these data are usually archived in the meteorological department and gives a good idea of the hourly, monthly, and annual incident energy. Such short time-interval data are valuable in designing and operating the solar energy facility. The advantage of the NWP model is that it can be used for solar radiation forecast since it can estimate the weather condition within the next 72–120 hours. This gives a reasonable estimation of the solar radiation that in turns can be used to forecast the electric power generation by the solar power plant.

  14. Reaction dynamics of the four-centered elimination CH2OH + --> CHO + +H2: Measurement of kinetic energy release distribution and classical trajectory calculation

    Science.gov (United States)

    Lee, Tae Geol; Park, Seung C.; Kim, Myung Soo

    1996-03-01

    Mass-analyzed ion kinetic energy (MIKE) spectrum of CHO+ generated in the unimolecular dissociation of CH2OH+ was measured. Kinetic energy release distribution (KERD) was evaluated by analyzing the spectrum according to the algorithm developed previously. The average kinetic energy release evaluated from the distribution was extraordinarily large, 1.63 eV, corresponding to 75% of the reverse barrier of the reaction. A global analytical potential energy surface was constructed such that the experimental energetics was represented and that various features in the ab initio potential energy surface were closely reproduced. Classical trajectory calculation was carried out with the global analytical potential energy surface to investigate the causes for the extraordinarily large kinetic energy release. Based on the detailed dynamical calculations, it was found that the strained bending forces at the transition state and strengthening of the CO bond from double to triple bond character were mainly responsible for such a significant kinetic energy release. In addition, the dissociation products H2 and CHO+ ion were found to be rotationally excited in the trajectory calculations. This was attributed to the asymmetry of the transition state and the release of asymmetric bending forces. Also, the bending vibrational modes of CHO+ and the H2 stretching mode, which are coupled with the bending coordinates, were found to be moderately excited.

  15. Flow-Induced New Channels of Energy Exchange in Multi-Scale Plasma Dynamics - Revisiting Perturbative Hybrid Kinetic-MHD Theory.

    Science.gov (United States)

    Shiraishi, Junya; Miyato, Naoaki; Matsunaga, Go

    2016-05-10

    It is found that new channels of energy exchange between macro- and microscopic dynamics exist in plasmas. They are induced by macroscopic plasma flow. This finding is based on the kinetic-magnetohydrodynamic (MHD) theory, which analyses interaction between macroscopic (MHD-scale) motion and microscopic (particle-scale) dynamics. The kinetic-MHD theory is extended to include effects of macroscopic plasma flow self-consistently. The extension is realised by generalising an energy exchange term due to wave-particle resonance, denoted by δ WK. The first extension is generalisation of the particle's Lagrangian, and the second one stems from modification to the particle distribution function due to flow. These extensions lead to a generalised expression of δ WK, which affects the MHD stability of plasmas.

  16. Two Monthly Continuous Dynamic Model Based on Nash Bargaining Theory for Conflict Resolution in Reservoir System.

    Science.gov (United States)

    Homayounfar, Mehran; Zomorodian, Mehdi; Martinez, Christopher J; Lai, Sai Hin

    2015-01-01

    So far many optimization models based on Nash Bargaining Theory associated with reservoir operation have been developed. Most of them have aimed to provide practical and efficient solutions for water allocation in order to alleviate conflicts among water users. These models can be discussed from two viewpoints: (i) having a discrete nature; and (ii) working on an annual basis. Although discrete dynamic game models provide appropriate reservoir operator policies, their discretization of variables increases the run time and causes dimensionality problems. In this study, two monthly based non-discrete optimization models based on the Nash Bargaining Solution are developed for a reservoir system. In the first model, based on constrained state formulation, the first and second moments (mean and variance) of the state variable (water level in the reservoir) is calculated. Using moment equations as the constraint, the long-term utility of the reservoir manager and water users are optimized. The second model is a dynamic approach structured based on continuous state Markov decision models. The corresponding solution based on the collocation method is structured for a reservoir system. In this model, the reward function is defined based on the Nash Bargaining Solution. Indeed, it is used to yield equilibrium in every proper sub-game, thereby satisfying the Markov perfect equilibrium. Both approaches are applicable for water allocation in arid and semi-arid regions. A case study was carried out at the Zayandeh-Rud river basin located in central Iran to identify the effectiveness of the presented methods. The results are compared with the results of an annual form of dynamic game, a classical stochastic dynamic programming model (e.g. Bayesian Stochastic Dynamic Programming model, BSDP), and a discrete stochastic dynamic game model (PSDNG). By comparing the results of alternative methods, it is shown that both models are capable of tackling conflict issues in water allocation

  17. Two Monthly Continuous Dynamic Model Based on Nash Bargaining Theory for Conflict Resolution in Reservoir System.

    Directory of Open Access Journals (Sweden)

    Mehran Homayounfar

    Full Text Available So far many optimization models based on Nash Bargaining Theory associated with reservoir operation have been developed. Most of them have aimed to provide practical and efficient solutions for water allocation in order to alleviate conflicts among water users. These models can be discussed from two viewpoints: (i having a discrete nature; and (ii working on an annual basis. Although discrete dynamic game models provide appropriate reservoir operator policies, their discretization of variables increases the run time and causes dimensionality problems. In this study, two monthly based non-discrete optimization models based on the Nash Bargaining Solution are developed for a reservoir system. In the first model, based on constrained state formulation, the first and second moments (mean and variance of the state variable (water level in the reservoir is calculated. Using moment equations as the constraint, the long-term utility of the reservoir manager and water users are optimized. The second model is a dynamic approach structured based on continuous state Markov decision models. The corresponding solution based on the collocation method is structured for a reservoir system. In this model, the reward function is defined based on the Nash Bargaining Solution. Indeed, it is used to yield equilibrium in every proper sub-game, thereby satisfying the Markov perfect equilibrium. Both approaches are applicable for water allocation in arid and semi-arid regions. A case study was carried out at the Zayandeh-Rud river basin located in central Iran to identify the effectiveness of the presented methods. The results are compared with the results of an annual form of dynamic game, a classical stochastic dynamic programming model (e.g. Bayesian Stochastic Dynamic Programming model, BSDP, and a discrete stochastic dynamic game model (PSDNG. By comparing the results of alternative methods, it is shown that both models are capable of tackling conflict issues in

  18. Dynamic perfusion CT: Optimizing the temporal resolution for the calculation of perfusion CT parameters in stroke patients

    Energy Technology Data Exchange (ETDEWEB)

    Kaemena, Andreas [Department of Radiology, Charite-Medical University Berlin, Augustenburger Platz 1, D-13353 Berlin (Germany)], E-mail: andreas.kaemena@charite.de; Streitparth, Florian; Grieser, Christian; Lehmkuhl, Lukas [Department of Radiology, Charite-Medical University Berlin, Augustenburger Platz 1, D-13353 Berlin (Germany); Jamil, Basil [Department of Radiotherapy, Charite-Medical University Berlin, Schumannstr. 20/21, D-10117 Berlin (Germany); Wojtal, Katarzyna; Ricke, Jens; Pech, Maciej [Department of Radiology, Charite-Medical University Berlin, Augustenburger Platz 1, D-13353 Berlin (Germany)

    2007-10-15

    Purpose: To assess the influence of different temporal sampling rates on the accuracy of the results from cerebral perfusion CTs in patients with an acute ischemic stroke. Material and methods: Thirty consecutive patients with acute stroke symptoms received a dynamic perfusion CT (LightSpeed 16, GE). Forty millilitres of iomeprol (Imeron 400) were administered at an injection rate of 4 ml/s. After a scan delay of 7 s, two adjacent 10 mm slices at 80 kV and 190 mA were acquired in a cine mode technique with a cine duration of 49 s. Parametric maps for the blood flow (BF), blood volume (BV) and mean transit time (MTT) were calculated for temporal sampling intervals of 0.5, 1, 2, 3 and 4 s using GE's Perfusion 3 software package. In addition to the quantitative ROI data analysis, a visual perfusion map analysis was performed. Results: The perfusion analysis proved to be technically feasible with all patients. The calculated perfusion values revealed significant differences with regard to the BF, BV and MTT, depending on the employed temporal resolution. The perfusion contrast between ischemic lesions and healthy brain tissue decreased continuously at the lower temporal resolutions. The visual analysis revealed that ischemic lesions were best depicted with sampling intervals of 0.5 and 1 s. Conclusion: We recommend a temporal scan resolution of two images per second for the best detection and depiction of ischemic areas.

  19. Mapping groundwater dynamics using multiple sources of exhaustive high resolution data

    NARCIS (Netherlands)

    Finke, P.A.; Brus, D.J.; Bierkens, M.F.P.; Hoogland, T.; Knotters, M.; Vries, de F.

    2004-01-01

    Existing groundwater table (GWT) class maps, available at full coverage for the Netherlands at 1:50,000 scale, no longer satisfy user demands. Groundwater levels have changed due to strong human impact, so the maps are partially outdated. Furthermore, a more dynamic description of groundwater table

  20. Observations of movement dynamics of flying insects using high resolution lidar

    DEFF Research Database (Denmark)

    Kirkeby, Carsten Thure; Wellenreuther, Maren; Brydegaard, Mikkel

    2016-01-01

    insects (wing size cross-section) moved across the field and clustered near the light trap around 22:00 local time, while larger insects (wing size >2.5 mm2 in cross-section) were most abundant near the lidar beam before 22:00 and then moved towards the light trap between 22:00 and 23:30. We......Insects are fundamental to ecosystem functioning and biodiversity, yet the study of insect movement, dispersal and activity patterns remains a challenge. Here we present results from a novel high resolution laser-radar (lidar) system for quantifying flying insect abundance recorded during one...

  1. Quasiclassical Theory of Spin Dynamics in Superfluid ^3He: Kinetic Equations in the Bulk and Spin Response of Surface Majorana States

    Science.gov (United States)

    Silaev, M. A.

    2018-06-01

    We develop a theory based on the formalism of quasiclassical Green's functions to study the spin dynamics in superfluid ^3He. First, we derive kinetic equations for the spin-dependent distribution function in the bulk superfluid reproducing the results obtained earlier without quasiclassical approximation. Then, we consider spin dynamics near the surface of fully gapped ^3He-B-phase taking into account spin relaxation due to the transitions in the spectrum of localized fermionic states. The lifetimes of longitudinal and transverse spin waves are calculated taking into account the Fermi-liquid corrections which lead to a crucial modification of fermionic spectrum and spin responses.

  2. Effective-field theory for dynamic phase diagrams of the kinetic spin-3/2 Blume–Capel model under a time oscillating longitudinal field

    Energy Technology Data Exchange (ETDEWEB)

    Ertaş, Mehmet [Department of Physics, Erciyes University, 38039 Kayseri (Turkey); Kocakaplan, Yusuf [Institute of Science, Erciyes University, 38039 Kayseri (Turkey); Keskin, Mustafa, E-mail: keskin@erciyes.edu.tr [Department of Physics, Erciyes University, 38039 Kayseri (Turkey)

    2013-12-15

    Dynamic phase diagrams are presented for the kinetic spin-3/2 Blume–Capel model under a time oscillating longitudinal field by use of the effective-field theory with correlations. The dynamic equation of the average magnetization is obtained for the square lattice by utilizing the Glauber-type stochastic process. Dynamic phase diagrams are presented in the reduced temperature and the magnetic field amplitude plane. We also investigated the effect of longitudinal field frequency. Finally, the discussion and comparison of the phase diagrams are given. - Highlights: • Dynamic behaviors in the spin-3/2 Blume–Capel system is investigated by the effective-field theory based on the Glauber-type stochastic dynamics. • The dynamic phase transitions and dynamic phase diagrams are obtained. • The effects of the longitudinal field frequency on the dynamic phase diagrams of the system are investigated. • Dynamic phase diagrams exhibit several ordered phases, coexistence phase regions and several critical points as well as a re-entrant behavior.

  3. Effective-field theory for dynamic phase diagrams of the kinetic spin-3/2 Blume–Capel model under a time oscillating longitudinal field

    International Nuclear Information System (INIS)

    Ertaş, Mehmet; Kocakaplan, Yusuf; Keskin, Mustafa

    2013-01-01

    Dynamic phase diagrams are presented for the kinetic spin-3/2 Blume–Capel model under a time oscillating longitudinal field by use of the effective-field theory with correlations. The dynamic equation of the average magnetization is obtained for the square lattice by utilizing the Glauber-type stochastic process. Dynamic phase diagrams are presented in the reduced temperature and the magnetic field amplitude plane. We also investigated the effect of longitudinal field frequency. Finally, the discussion and comparison of the phase diagrams are given. - Highlights: • Dynamic behaviors in the spin-3/2 Blume–Capel system is investigated by the effective-field theory based on the Glauber-type stochastic dynamics. • The dynamic phase transitions and dynamic phase diagrams are obtained. • The effects of the longitudinal field frequency on the dynamic phase diagrams of the system are investigated. • Dynamic phase diagrams exhibit several ordered phases, coexistence phase regions and several critical points as well as a re-entrant behavior

  4. Population dynamics of the murine lymphokine activated killer system: precursor frequency and kinetics of maturation and renewal.

    Science.gov (United States)

    Owen-Schaub, L B; Hemstreet, G P; Hemingway, L L; Abraham, S R; DeBault, L E

    1987-11-01

    The proliferation kinetics and population renewal of recombinant interleukin-2 (rIL-2)-induced murine lymphokine activated killers (LAK) arising from splenic precursors was studied. Extensive proliferation has been shown to accompany the de novo generation of LAK cytotoxicity. In this report, a thymidine 'hot pulse' suicide technique was employed to examine the sensitivity of LAK progenitors during various time periods following culture initiation. Hot pulse during the first 24 hr of culture resulted in a 30-35% reduction in lytic activity when assayed on day 5. Pulse periods between days 1 and 4 resulted in almost complete inhibition (90-95%) of lytic function when assayed on day 5. Proliferation of LAK progenitors was documented by limiting dilution analysis comparison of splenic precursors and functionally mature LAK cultures. These studies showed a 75- to 80-fold enrichment of LAK progenitors after 3 days culture in rIL-2. By flow cytometric cell cycle analysis, we demonstrated that the number of cells in the S/G2/M phase increased with the length of rIL-2 culture and represented approximately 40% of the cells by day 4. Finally, we used the rate of decay of lytic activity following irradiation as a factor to define the mean life span of a cytotoxic effector in the absence of cellular input. An exponential decrease to approximately 50% of controls was observed within 8-9 hr after irradiation. Taken together, these results suggest that the LAK system is highly dynamic and requires continuous cellular proliferation for its maintenance.

  5. Kinetic Analysis of Dynamic Positron Emission Tomography Data using Open-Source Image Processing and Statistical Inference Tools.

    Science.gov (United States)

    Hawe, David; Hernández Fernández, Francisco R; O'Suilleabháin, Liam; Huang, Jian; Wolsztynski, Eric; O'Sullivan, Finbarr

    2012-05-01

    In dynamic mode, positron emission tomography (PET) can be used to track the evolution of injected radio-labelled molecules in living tissue. This is a powerful diagnostic imaging technique that provides a unique opportunity to probe the status of healthy and pathological tissue by examining how it processes substrates. The spatial aspect of PET is well established in the computational statistics literature. This article focuses on its temporal aspect. The interpretation of PET time-course data is complicated because the measured signal is a combination of vascular delivery and tissue retention effects. If the arterial time-course is known, the tissue time-course can typically be expressed in terms of a linear convolution between the arterial time-course and the tissue residue. In statistical terms, the residue function is essentially a survival function - a familiar life-time data construct. Kinetic analysis of PET data is concerned with estimation of the residue and associated functionals such as flow, flux, volume of distribution and transit time summaries. This review emphasises a nonparametric approach to the estimation of the residue based on a piecewise linear form. Rapid implementation of this by quadratic programming is described. The approach provides a reference for statistical assessment of widely used one- and two-compartmental model forms. We illustrate the method with data from two of the most well-established PET radiotracers, (15)O-H(2)O and (18)F-fluorodeoxyglucose, used for assessment of blood perfusion and glucose metabolism respectively. The presentation illustrates the use of two open-source tools, AMIDE and R, for PET scan manipulation and model inference.

  6. Study on a hidden protein-DNA binding in salmon sperm DNA sample by dynamic kinetic capillary isoelectric focusing

    International Nuclear Information System (INIS)

    Liang Liang; Dou Peng; Dong Mingming; Ke Xiaokang; Bian Ningsheng; Liu Zhen

    2009-01-01

    Nuclease P1 is an important enzyme that hydrolyzes RNA or single-stranded DNA into nucleotides, and complete digestion is an essential basis for assays based on this enzyme. To digest a doubled-stranded DNA, the enzyme is usually combined with heat denaturing, which breaks doubled-stranded DNA into single strands. This paper presents an un-expected phenomenon that nuclease P1, in combination with heat denaturing, fails to completely digest a DNA sample extracted from salmon sperm. Under the experimental conditions used, at which nuclease P1 can completely digest calf thymus DNA, the digestion yield of salmon sperm DNA was only 89.5%. Spectrometric measurement indicated that a total protein of 4.7% is present in the DNA sample. To explain the reason for this phenomenon, the dynamic kinetic capillary isoelectric focusing (DK-CIEF) approach proposed previously, which allows for the discrimination of different types of protein-DNA interactions and the measurement of the individual dissociation rate constants, was modified and applied to examine possible protein-DNA interactions involved. It was found that a non-specific DNA-protein binding occurs in the sample, the dissociation rate constant for which was measured to be 7.05 ± 0.83 x 10 -3 s -1 . The formation of DNA-protein complex was suggested to be the main reason for the incomplete digestion of the DNA sample. The modified DK-CIEF approach can be applied as general DNA samples, with the advantages of fast speed and low sample consumption.

  7. Dynamics of Transformation from Platinum Icosahedral Nanoparticles to Larger FCC Crystal at Millisecond Time Resolution

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Wenpei [Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Materials Science and Engineering and Fredrick Seitz Materials Research Lab.; Wu, Jianbo [Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Materials Science and Engineering, Fredrick Seitz Materials Research Lab. and Dept. of Chemical and Biomolecular Engineering; Shanghai Jiao Tong Univ. (China). School of Materials Science and Engineering; Yoon, Aram [Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Materials Science and Engineering and Fredrick Seitz Materials Research Lab.; Lu, Ping [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Qi, Liang [Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Materials Science and Engineering; Wen, Jianguo [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials and Electron Microscopy Center; Miller, Dean J. [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials and Electron Microscopy Center; Mabon, James C. [Univ. of Illinois at Urbana-Champaign, IL (United States). Fredrick Seitz Materials Research Lab.; Wilson, William L. [Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Materials Science and Engineering and Fredrick Seitz Materials Research Lab.; Yang, Hong [Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Chemical and Biomolecular Engineering; Zuo, Jian-Min [Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Materials Science and Engineering and Fredrick Seitz Materials Research Lab.

    2017-12-08

    Atomic motion at grain boundaries is essential to microstructure development, growth and stability of catalysts and other nanostructured materials. However, boundary atomic motion is often too fast to observe in a conventional transmission electron microscope (TEM) and too slow for ultrafast electron microscopy. We report on the entire transformation process of strained Pt icosahedral nanoparticles (ICNPs) into larger FCC crystals, captured at 2.5 ms time resolution using a fast electron camera. Results show slow diffusive dislocation motion at nm/s inside ICNPs and fast surface transformation at μm/s. By characterizing nanoparticle strain, we show that the fast transformation is driven by inhomogeneous surface stress. And interaction with pre-existing defects led to the slowdown of the transformation front inside the nanoparticles. Particle coalescence, assisted by oxygen-induced surface migration at T ≥ 300°C, also played a critical role. Thus by studying transformation in the Pt ICNPs at high time and spatial resolution, we obtain critical insights into the transformation mechanisms in strained Pt nanoparticles.

  8. High-resolution and large dynamic range nanomechanical mapping in tapping-mode atomic force microscopy

    International Nuclear Information System (INIS)

    Sahin, Ozgur; Erina, Natalia

    2008-01-01

    High spatial resolution imaging of material properties is an important task for the continued development of nanomaterials and studies of biological systems. Time-varying interaction forces between the vibrating tip and the sample in a tapping-mode atomic force microscope contain detailed information about the elastic, adhesive, and dissipative response of the sample. We report real-time measurement and analysis of the time-varying tip-sample interaction forces with recently introduced torsional harmonic cantilevers. With these measurements, high-resolution maps of elastic modulus, adhesion force, energy dissipation, and topography are generated simultaneously in a single scan. With peak tapping forces as low as 0.6 nN, we demonstrate measurements on blended polymers and self-assembled molecular architectures with feature sizes at 1, 10, and 500 nm. We also observed an elastic modulus measurement range of four orders of magnitude (1 MPa to 10 GPa) for a single cantilever under identical feedback conditions, which can be particularly useful for analyzing heterogeneous samples with largely different material components.

  9. Interactive desktop analysis of high resolution simulations: application to turbulent plume dynamics and current sheet formation

    International Nuclear Information System (INIS)

    Clyne, John; Mininni, Pablo; Norton, Alan; Rast, Mark

    2007-01-01

    The ever increasing processing capabilities of the supercomputers available to computational scientists today, combined with the need for higher and higher resolution computational grids, has resulted in deluges of simulation data. Yet the computational resources and tools required to make sense of these vast numerical outputs through subsequent analysis are often far from adequate, making such analysis of the data a painstaking, if not a hopeless, task. In this paper, we describe a new tool for the scientific investigation of massive computational datasets. This tool (VAPOR) employs data reduction, advanced visualization, and quantitative analysis operations to permit the interactive exploration of vast datasets using only a desktop PC equipped with a commodity graphics card. We describe VAPORs use in the study of two problems. The first, motivated by stellar envelope convection, investigates the hydrodynamic stability of compressible thermal starting plumes as they descend through a stratified layer of increasing density with depth. The second looks at current sheet formation in an incompressible helical magnetohydrodynamic flow to understand the early spontaneous development of quasi two-dimensional (2D) structures embedded within the 3D solution. Both of the problems were studied at sufficiently high spatial resolution, a grid of 504 2 by 2048 points for the first and 1536 3 points for the second, to overwhelm the interactive capabilities of typically available analysis resources

  10. High spatial resolution three-dimensional mapping of vegetation spectral dynamics using computer vision and hobbyist unmanned aerial vehicles

    Science.gov (United States)

    Dandois, J. P.; Ellis, E. C.

    2013-12-01

    High spatial resolution three-dimensional (3D) measurements of vegetation by remote sensing are advancing ecological research and environmental management. However, substantial economic and logistical costs limit this application, especially for observing phenological dynamics in ecosystem structure and spectral traits. Here we demonstrate a new aerial remote sensing system enabling routine and inexpensive aerial 3D measurements of canopy structure and spectral attributes, with properties similar to those of LIDAR, but with RGB (red-green-blue) spectral attributes for each point, enabling high frequency observations within a single growing season. This 'Ecosynth' methodology applies photogrammetric ''Structure from Motion'' computer vision algorithms to large sets of highly overlapping low altitude (USA. Ecosynth canopy height maps (CHMs) were strong predictors of field-measured tree heights (R2 0.63 to 0.84) and were highly correlated with a LIDAR CHM (R 0.87) acquired 4 days earlier, though Ecosynth-based estimates of aboveground biomass densities included significant errors (31 - 36% of field-based estimates). Repeated scanning of a 0.25 ha forested area at six different times across a 16 month period revealed ecologically significant dynamics in canopy color at different heights and a structural shift upward in canopy density, as demonstrated by changes in vertical height profiles of point density and relative RGB brightness. Changes in canopy relative greenness were highly correlated (R2 = 0.88) with MODIS NDVI time series for the same area and vertical differences in canopy color revealed the early green up of the dominant canopy species, Liriodendron tulipifera, strong evidence that Ecosynth time series measurements capture vegetation structural and spectral dynamics at the spatial scale of individual trees. Observing canopy phenology in 3D at high temporal resolutions represents a breakthrough in forest ecology. Inexpensive user-deployed technologies for

  11. Dynamic phase transition in the kinetic spin-32 Blume-Capel model: Phase diagrams in the temperature and crystal-field interaction plane

    International Nuclear Information System (INIS)

    Keskin, Mustafa; Canko, Osman; Deviren, Bayram

    2007-01-01

    We analyze, within a mean-field approach, the stationary states of the kinetic spin-32 Blume-Capel (BC) model by the Glauber-type stochastic dynamics and subject to a time-dependent oscillating external magnetic field. The dynamic phase transition (DPT) points are obtained by investigating the behavior of the dynamic magnetization as a function of temperature and as well as calculating the Liapunov exponent. Phase diagrams are constructed in the temperature and crystal-field interaction plane. We find five fundamental types of phase diagrams for the different values of the reduced magnetic field amplitude parameter (h) in which they present a disordered, two ordered phases and the coexistences phase regions. The phase diagrams also exhibit a dynamic double-critical end point for 0 5.06

  12. Comparison of morphological and kinetic parameters in distinction of benign and malignant breast lesions in dynamic contrast enhanced magnetic resonance imaging

    Directory of Open Access Journals (Sweden)

    Direnç Özlem Aksoy

    2013-12-01

    Full Text Available Objective: To evaluate the value of qualitative morphologicaland kinetic data and quantitative kinetic data indistinction of malignancy in dynamic contrast enhancedmagnetic resonance imaging (DCE-MRI of the breast.Methods: DCE-MRIs of 49 subjects were evaluated.Morphological and contrast enhancement parameters of95 lesions were recorded in these subjects. Post-contrastkinetic behavior of these lesions were also investigated.Among the quantitative parameters, relative enhancements(E1, E2, Epeak, time-to-peak (Tpeak, slope ofcurve (Slope, signal enhancement ratio (SER, and maximumintensity time ratio (MITR were calculated. Theseresults were compared with the pathological diagnosis.Results: Spiculated contour (100%, rim enhancement(97.87%, irregular shape (95.74%, and irregular margin(91.49% were the most specific morphological featuresof malignancy in mass lesions. In non-mass lesions, focalzone (91.49% was the most specific feature of malignancy.74.5% of the benign lesions showed type 1, 77.1%of the malignant lesions showed type 2 and 3 curves accordingto the kinetic curve evaluation. All quantitativeparameters except Epeak were found to be statisticallysignificant in distinction of malignancy.Conclusion: None of the morphological features of thebenign lesions were found to be significantly specific.More specific features can be described for malignantlesions. Early behavior of the kinetic curve is not usefulfor diagnosis of malignancy but the intermediate and latebehavior gives useful information. Quantitative data involvedin this study might be promising.Key words: Morphological, kinetic, breast lesions, magnetic resonance imaging, dynamic

  13. The (kinetic) theory of active particles applied to learning dynamics. Comment on "Collective learning modeling based on the kinetic theory of active particles" by D. Burini et al.

    Science.gov (United States)

    Nieto, J.

    2016-03-01

    The learning phenomena, their complexity, concepts, structure, suitable theories and models, have been extensively treated in the mathematical literature in the last century, and [4] contains a very good introduction to the literature describing the many approaches and lines of research developed about them. Two main schools have to be pointed out [5] in order to understand the two -not exclusive- kinds of existing models: the stimulus sampling models and the stochastic learning models. Also [6] should be mentioned as a survey where two methods of learning are pointed out, the cognitive and the social, and where the knowledge looks like a mathematical unknown. Finally, as the authors do, we refer to the works [9,10], where the concept of population thinking was introduced and which motivate the game theory rules as a tool (both included in [4] to develop their theory) and [7], where the ideas of developing a mathematical kinetic theory of perception and learning were proposed.

  14. Dynamic patterns and ecological impacts of declining ocean pH in a high-resolution multi-year dataset.

    Science.gov (United States)

    Wootton, J Timothy; Pfister, Catherine A; Forester, James D

    2008-12-02

    Increasing global concentrations of atmospheric CO(2) are predicted to decrease ocean pH, with potentially severe impacts on marine food webs, but empirical data documenting ocean pH over time are limited. In a high-resolution dataset spanning 8 years, pH at a north-temperate coastal site declined with increasing atmospheric CO(2) levels and varied substantially in response to biological processes and physical conditions that fluctuate over multiple time scales. Applying a method to link environmental change to species dynamics via multispecies Markov chain models reveals strong links between in situ benthic species dynamics and variation in ocean pH, with calcareous species generally performing more poorly than noncalcareous species in years with low pH. The models project the long-term consequences of these dynamic changes, which predict substantial shifts in the species dominating the habitat as a consequence of both direct effects of reduced calcification and indirect effects arising from the web of species interactions. Our results indicate that pH decline is proceeding at a more rapid rate than previously predicted in some areas, and that this decline has ecological consequences for near shore benthic ecosystems.

  15. High-resolution dynamic imaging and quantitative analysis of lung cancer xenografts in nude mice using clinical PET/CT.

    Science.gov (United States)

    Wang, Ying Yi; Wang, Kai; Xu, Zuo Yu; Song, Yan; Wang, Chu Nan; Zhang, Chong Qing; Sun, Xi Lin; Shen, Bao Zhong

    2017-08-08

    Considering the general application of dedicated small-animal positron emission tomography/computed tomography is limited, an acceptable alternative in many situations might be clinical PET/CT. To estimate the feasibility of using clinical PET/CT with [F-18]-fluoro-2-deoxy-D-glucose for high-resolution dynamic imaging and quantitative analysis of cancer xenografts in nude mice. Dynamic clinical PET/CT scans were performed on xenografts for 60 min after injection with [F-18]-fluoro-2-deoxy-D-glucose. Scans were reconstructed with or without SharpIR method in two phases. And mice were sacrificed to extracting major organs and tumors, using ex vivo γ-counting as a reference. Strikingly, we observed that the image quality and the correlation between the all quantitive data from clinical PET/CT and the ex vivo counting was better with the SharpIR reconstructions than without. Our data demonstrate that clinical PET/CT scanner with SharpIR reconstruction is a valuable tool for imaging small animals in preclinical cancer research, offering dynamic imaging parameters, good image quality and accurate data quatification.

  16. High Resolution Angle Resolved Photoemission Studies on Quasi-Particle Dynamics in Graphite

    Energy Technology Data Exchange (ETDEWEB)

    Leem, C.S.

    2010-06-02

    We obtained the spectral function of the graphite H point using high resolution angle resolved photoelectron spectroscopy (ARPES). The extracted width of the spectral function (inverse of the photo-hole lifetime) near the H point is approximately proportional to the energy as expected from the linearly increasing density of states (DOS) near the Fermi energy. This is well accounted by our electron-phonon coupling theory considering the peculiar electronic DOS near the Fermi level. And we also investigated the temperature dependence of the peak widths both experimentally and theoretically. The upper bound for the electron-phonon coupling parameter is 0.23, nearly the same value as previously reported at the K point. Our analysis of temperature dependent ARPES data at K shows that the energy of phonon mode of graphite has much higher energy scale than 125K which is dominant in electron-phonon coupling.

  17. A new look at stress: abscisic acid patterns and dynamics at high-resolution.

    Science.gov (United States)

    Jones, Alexander M

    2016-04-01

    Abscisic acid (ABA) is a key phytohormone promoting abiotic stress tolerance as well as developmental processes such as seed dormancy. A spatiotemporal map of ABA concentrations would greatly advance our understanding of the cell type and timing of ABA action. Organ and tissue-level ABA measurements, as well as indirect in vivo measurements such as cell-specific transcriptional analysis of ABA metabolic enzymes and ABA-responsive promoters, have all contributed to current views of the localization and timing of ABA accumulations. Recently developed Förster resonance energy transfer (FRET) biosensors for ABA that sense ABA levels directly promise to add unprecedented resolution to in vivo ABA spatiotemporal mapping and expand our knowledge of the mechanisms controlling ABA levels in space and time. © 2015 Carnegie Institution for Science New Phytologist © 2015 New Phytologist Trust.

  18. Determination of dynamic characteristics of multi-layer carbon plastic structures of high-resolution scanner

    Directory of Open Access Journals (Sweden)

    В. Н. Маслей

    2017-10-01

    Full Text Available The comparative analysis results for the numerical determination of the dynamic characteristics of multi-layer carbon-fiber plates of the space vehicle scanner design by various types of finite element approximation of the physico-mechanical properties of the composite material are presented. Using the topological structure of the construction of reinforcing layers material in the plate package plane, experimental data for the elastic and mass characteristics of homogeneous carbon-fiber fibers, equivalent structural and orthotropic stiffness and elastic characteristics of the material of composite plates are determined.

  19. Improved resolution and reliability in dynamic PET using Bayesian regularization of MRTM2

    DEFF Research Database (Denmark)

    Agn, Mikael; Svarer, Claus; Frokjaer, Vibe G.

    2014-01-01

    This paper presents a mathematical model that regularizes dynamic PET data by using a Bayesian framework. We base the model on the well known two-parameter multilinear reference tissue method MRTM2 and regularize on the assumption that spatially close regions have similar parameters. The developed...... model is compared to the conventional approach of improving the low signal-to-noise ratio of PET data, i.e., spatial filtering of each time frame independently by a Gaussian kernel. We show that the model handles high levels of noise better than the conventional approach, while at the same time...

  20. Stark mapping of H2 Rydberg states in the strong-field regime with dynamical resolution

    International Nuclear Information System (INIS)

    Glab, W.L.; Qin, K.

    1993-01-01

    We have acquired spectra of high Rydberg states of molecular hydrogen in a static external field, in the energy region from below the energy at which field ionization becomes classically possible (E c ) to well above this energy. Simultaneous spectra of ionization and dissociation were acquired, thereby allowing direct information on the excited-state decay dynamics to be obtained. We have found that states with energies below E c undergo field-induced predissociation, while states with energies well above E c decay predominantly by field ionization. Field ionization and dissociation compete effectively as decay channels for states with energies in a restricted region just above E c . Comparison of our ionization spectra to the results of a single-channel quantum-defect theory Stark calculation shows quantitative agreement except near curve crossings, indicating that inclusion of different core rotational state channels will be required to properly account for coupling between the Stark states. Several states in the spectra undergo pronounced changes in their dynamical properties over a narrow range of field values, which we interpret as being due to interference cancellation of the ionization rates for these states

  1. Improved High Resolution Models of Subduction Dynamics: Use of transversely isotropic viscosity with a free-surface

    Science.gov (United States)

    Liu, X.; Gurnis, M.; Stadler, G.; Rudi, J.; Ratnaswamy, V.; Ghattas, O.

    2017-12-01

    Dynamic topography, or uncompensated topography, is controlled by internal dynamics, and provide constraints on the buoyancy structure and rheological parameters in the mantle. Compared with other surface manifestations such as the geoid, dynamic topography is very sensitive to shallower and more regional mantle structure. For example, the significant dynamic topography above the subduction zone potentially provides a rich mine for inferring the rheological and mechanical properties such as plate coupling, flow, and lateral viscosity variations, all critical in plate tectonics. However, employing subduction zone topography in the inversion study requires that we have a better understanding of the topography from forward models, especially the influence of the viscosity formulation, numerical resolution, and other factors. One common approach to formulating a fault between the subducted slab and the overriding plates in viscous flow models assumes a thin weak zone. However, due to the large lateral variation in viscosity, topography from free-slip numerical models typically has artificially large magnitude as well as high-frequency undulations over subduction zone, which adds to the difficulty in making comparisons between model results and observations. In this study, we formulate a weak zone with the transversely isotropic viscosity (TI) where the tangential viscosity is much smaller than the viscosity in the normal direction. Similar with isotropic weak zone models, TI models effectively decouple subducted slabs from the overriding plates. However, we find that the topography in TI models is largely reduced compared with that in weak zone models assuming an isotropic viscosity. Moreover, the artificial `tooth paste' squeezing effect observed in isotropic weak zone models vanishes in TI models, although the difference becomes less significant when the dip angle is small. We also implement a free-surface condition in our numerical models, which has a smoothing

  2. High-resolution inelastic X-ray scattering to study the high-frequency atomic dynamics of disordered systems

    International Nuclear Information System (INIS)

    Monaco, G.

    2008-01-01

    The use of momentum-resolved inelastic X-ray scattering with meV energy resolution to study the high-frequency atomic dynamics in disordered systems is here reviewed. The typical realization of this experiment is described together with some common models used to interpret the measured spectra and to extract parameters of interest for the investigation of disordered systems. With the help of some selected examples, the present status of the field is discussed. Particular attention is given to those results which are still open for discussion or controversial, and which will require further development of the technique to be fully solved. Such an instrumental development seems nowadays possible at the light of recently proposed schemes for advanced inelastic X-ray scattering spectrometers. (author)

  3. Phosphotyrosine-mediated LAT assembly on membranes drives kinetic bifurcation in recruitment dynamics of the Ras activator SOS.

    Science.gov (United States)

    Huang, William Y C; Yan, Qingrong; Lin, Wan-Chen; Chung, Jean K; Hansen, Scott D; Christensen, Sune M; Tu, Hsiung-Lin; Kuriyan, John; Groves, Jay T

    2016-07-19

    The assembly of cell surface receptors with downstream signaling molecules is a commonly occurring theme in multiple signaling systems. However, little is known about how these assemblies modulate reaction kinetics and the ultimate propagation of signals. Here, we reconstitute phosphotyrosine-mediated assembly of extended linker for the activation of T cells (LAT):growth factor receptor-bound protein 2 (Grb2):Son of Sevenless (SOS) networks, derived from the T-cell receptor signaling system, on supported membranes. Single-molecule dwell time distributions reveal two, well-differentiated kinetic species for both Grb2 and SOS on the LAT assemblies. The majority fraction of membrane-recruited Grb2 and SOS both exhibit fast kinetics and single exponential dwell time distributions, with average dwell times of hundreds of milliseconds. The minor fraction exhibits much slower kinetics, extending the dwell times to tens of seconds. Considering this result in the context of the multistep process by which the Ras GEF (guanine nucleotide exchange factor) activity of SOS is activated indicates that kinetic stabilization from the LAT assembly may be important. This kinetic proofreading effect would additionally serve as a stochastic noise filter by reducing the relative probability of spontaneous SOS activation in the absence of receptor triggering. The generality of receptor-mediated assembly suggests that such effects may play a role in multiple receptor proximal signaling processes.

  4. High Resolution and Large Dynamic Range Resonant Pressure Sensor Based on Q-Factor Measurement

    Science.gov (United States)

    Gutierrez, Roman C. (Inventor); Stell, Christopher B. (Inventor); Tang, Tony K. (Inventor); Vorperian, Vatche (Inventor); Wilcox, Jaroslava (Inventor); Shcheglov, Kirill (Inventor); Kaiser, William J. (Inventor)

    2000-01-01

    A pressure sensor has a high degree of accuracy over a wide range of pressures. Using a pressure sensor relying upon resonant oscillations to determine pressure, a driving circuit drives such a pressure sensor at resonance and tracks resonant frequency and amplitude shifts with changes in pressure. Pressure changes affect the Q-factor of the resonating portion of the pressure sensor. Such Q-factor changes are detected by the driving/sensing circuit which in turn tracks the changes in resonant frequency to maintain the pressure sensor at resonance. Changes in the Q-factor are reflected in changes of amplitude of the resonating pressure sensor. In response, upon sensing the changes in the amplitude, the driving circuit changes the force or strength of the electrostatic driving signal to maintain the resonator at constant amplitude. The amplitude of the driving signals become a direct measure of the changes in pressure as the operating characteristics of the resonator give rise to a linear response curve for the amplitude of the driving signal. Pressure change resolution is on the order of 10(exp -6) torr over a range spanning from 7,600 torr to 10(exp -6) torr. No temperature compensation for the pressure sensor of the present invention is foreseen. Power requirements for the pressure sensor are generally minimal due to the low-loss mechanical design of the resonating pressure sensor and the simple control electronics.

  5. High-resolution dynamic downscaling of CMIP5 output over the Tropical Andes

    Science.gov (United States)

    Reichler, Thomas; Andrade, Marcos; Ohara, Noriaki

    2015-04-01

    Our project is targeted towards making robust predictions of future changes in climate over the tropical part of the South American Andes. This goal is challenging, since tropical lowlands, steep mountains, and snow covered subarctic surfaces meet over relatively short distances, leading to distinct climate regimes within the same domain and pronounced spatial gradients in virtually every climate quantity. We use an innovative approach to solve this problem, including several quadruple nested versions of WRF, a systematic validation strategy to find the version of WRF that best fits our study region, spatial resolutions at the kilometer scale, 20-year-long simulation periods, and bias-corrected output from various CMIP5 simulations that also include the multi-model mean of all CMIP5 models. We show that the simulated changes in climate are consistent with the results from the global climate models and also consistent with two different versions of WRF. We also discuss the expected changes in snow and ice, derived from off-line coupling the regional simulations to a carefully calibrated snow and ice model.

  6. Dynamic electrostatic force microscopy technique for the study of electrical properties with improved spatial resolution

    International Nuclear Information System (INIS)

    Maragliano, C; Heskes, D; Stefancich, M; Chiesa, M; Souier, T

    2013-01-01

    The need to resolve the electrical properties of confined structures (CNTs, quantum dots, nanorods, etc) is becoming increasingly important in the field of electronic and optoelectronic devices. Here we propose an approach based on amplitude modulated electrostatic force microscopy to obtain measurements at small tip–sample distances, where highly nonlinear forces are present. We discuss how this improves the lateral resolution of the technique and allows probing of the electrical and surface properties. The complete force field at different tip biases is employed to derive the local work function difference. Then, by appropriately biasing the tip–sample system, short-range forces are reconstructed. The short-range component is then separated from the generic tip–sample force in order to recover the pure electrostatic contribution. This data can be employed to derive the tip–sample capacitance curve and the sample dielectric constant. After presenting a theoretical model that justifies the need for probing the electrical properties of the sample in the vicinity of the surface, the methodology is presented in detail and verified experimentally. (paper)

  7. DYNAMIC SOFTWARE TESTING MODELS WITH PROBABILISTIC PARAMETERS FOR FAULT DETECTION AND ERLANG DISTRIBUTION FOR FAULT RESOLUTION DURATION

    Directory of Open Access Journals (Sweden)

    A. D. Khomonenko

    2016-07-01

    Full Text Available Subject of Research.Software reliability and test planning models are studied taking into account the probabilistic nature of error detection and discovering. Modeling of software testing enables to plan the resources and final quality at early stages of project execution. Methods. Two dynamic models of processes (strategies are suggested for software testing, using error detection probability for each software module. The Erlang distribution is used for arbitrary distribution approximation of fault resolution duration. The exponential distribution is used for approximation of fault resolution discovering. For each strategy, modified labeled graphs are built, along with differential equation systems and their numerical solutions. The latter makes it possible to compute probabilistic characteristics of the test processes and states: probability states, distribution functions for fault detection and elimination, mathematical expectations of random variables, amount of detected or fixed errors. Evaluation of Results. Probabilistic characteristics for software development projects were calculated using suggested models. The strategies have been compared by their quality indexes. Required debugging time to achieve the specified quality goals was calculated. The calculation results are used for time and resources planning for new projects. Practical Relevance. The proposed models give the possibility to use the reliability estimates for each individual module. The Erlang approximation removes restrictions on the use of arbitrary time distribution for fault resolution duration. It improves the accuracy of software test process modeling and helps to take into account the viability (power of the tests. With the use of these models we can search for ways to improve software reliability by generating tests which detect errors with the highest probability.

  8. Using High-Resolution Data to Assess Land Use Impact on Nitrate Dynamics in East African Tropical Montane Catchments

    Science.gov (United States)

    Jacobs, Suzanne R.; Weeser, Björn; Guzha, Alphonce C.; Rufino, Mariana C.; Butterbach-Bahl, Klaus; Windhorst, David; Breuer, Lutz

    2018-03-01

    Land use change alters nitrate (NO3-N) dynamics in stream water by changing nitrogen cycling, nutrient inputs, uptake and hydrological flow paths. There is little empirical evidence of these processes for East Africa. We collected a unique 2 year high-resolution data set to assess the effects of land use (i.e., natural forest, smallholder agriculture and commercial tea plantations) on NO3-N dynamics in three subcatchments within a headwater catchment in the Mau Forest Complex, Kenya's largest tropical montane forest. The natural forest subcatchment had the lowest NO3-N concentrations (0.44 ± 0.043 mg N L-1) with no seasonal variation. NO3-N concentrations in the smallholder agriculture (1.09 ± 0.11 mg N L-1) and tea plantation (2.13 ± 0.19 mg N L-1) subcatchments closely followed discharge patterns, indicating mobilization of NO3-N during the rainy seasons. Hysteresis patterns of rainfall events indicate a shift from subsurface flow in the natural forest to surface runoff in agricultural subcatchments. Distinct peaks in NO3-N concentrations were observed during rainfall events after a longer dry period in the forest and tea subcatchments. The high-resolution data set enabled us to identify differences in NO3-N transport of catchments under different land use, such as enhanced NO3-N inputs to the stream during the rainy season and higher annual export in agricultural subcatchments (4.9 ± 0.3 to 12.0 ± 0.8 kg N ha-1 yr-1) than in natural forest (2.6 ± 0.2 kg N ha-1 yr-1). This emphasizes the usefulness of our monitoring approach to improve the understanding of land use effects on riverine N exports in tropical landscapes, but also the need to apply such methods in other regions.

  9. Solid-State NMR on bacterial cells: selective cell wall signal enhancement and resolution improvement using dynamic nuclear polarization

    International Nuclear Information System (INIS)

    Takahashi, Hiroki; Bardet, Michel; De Paepe, Gael; Hediger, Sabine; Ayala, Isabel; Simorre, Jean-Pierre

    2013-01-01

    Dynamic nuclear polarization (DNP) enhanced solid-state nuclear magnetic resonance (NMR) has recently emerged as a powerful technique for the study of material surfaces. In this study, we demonstrate its potential to investigate cell surface in intact cells. Using Bacillus subtilis bacterial cells as an example, it is shown that the polarizing agent 1-(TEMPO-4-oxy)-3-(TEMPO-4-amino)propan-2-ol (TOTAPOL) has a strong binding affinity to cell wall polymers (peptidoglycan). This particular interaction is thoroughly investigated with a systematic study on extracted cell wall materials, disrupted cells, and entire cells, which proved that TOTAPOL is mainly accumulating in the cell wall. This property is used on one hand to selectively enhance or suppress cell wall signals by controlling radical concentrations and on the other hand to improve spectral resolution by means of a difference spectrum. Comparing DNP-enhanced and conventional solid-state NMR, an absolute sensitivity ratio of 24 was obtained on the entire cell sample. This important increase in sensitivity together with the possibility of enhancing specifically cell wall signals and improving resolution really opens new avenues for the use of DNP-enhanced solid-state NMR as an on-cell investigation tool. (authors)

  10. Solid-state NMR on bacterial cells: selective cell wall signal enhancement and resolution improvement using dynamic nuclear polarization.

    Science.gov (United States)

    Takahashi, Hiroki; Ayala, Isabel; Bardet, Michel; De Paëpe, Gaël; Simorre, Jean-Pierre; Hediger, Sabine

    2013-04-03

    Dynamic nuclear polarization (DNP) enhanced solid-state nuclear magnetic resonance (NMR) has recently emerged as a powerful technique for the study of material surfaces. In this study, we demonstrate its potential to investigate cell surface in intact cells. Using Bacillus subtilis bacterial cells as an example, it is shown that the polarizing agent 1-(TEMPO-4-oxy)-3-(TEMPO-4-amino)propan-2-ol (TOTAPOL) has a strong binding affinity to cell wall polymers (peptidoglycan). This particular interaction is thoroughly investigated with a systematic study on extracted cell wall materials, disrupted cells, and entire cells, which proved that TOTAPOL is mainly accumulating in the cell wall. This property is used on one hand to selectively enhance or suppress cell wall signals by controlling radical concentrations and on the other hand to improve spectral resolution by means of a difference spectrum. Comparing DNP-enhanced and conventional solid-state NMR, an absolute sensitivity ratio of 24 was obtained on the entire cell sample. This important increase in sensitivity together with the possibility of enhancing specifically cell wall signals and improving resolution really opens new avenues for the use of DNP-enhanced solid-state NMR as an on-cell investigation tool.

  11. Toolbox for Urban Mobility Simulation: High Resolution Population Dynamics for Global Cities

    Science.gov (United States)

    Bhaduri, B. L.; Lu, W.; Liu, C.; Thakur, G.; Karthik, R.

    2015-12-01

    In this rapidly urbanizing world, unprecedented rate of population growth is not only mirrored by increasing demand for energy, food, water, and other natural resources, but has detrimental impacts on environmental and human security. Transportation simulations are frequently used for mobility assessment in urban planning, traffic operation, and emergency management. Previous research, involving purely analytical techniques to simulations capturing behavior, has investigated questions and scenarios regarding the relationships among energy, emissions, air quality, and transportation. Primary limitations of past attempts have been availability of input data, useful "energy and behavior focused" models, validation data, and adequate computational capability that allows adequate understanding of the interdependencies of our transportation system. With increasing availability and quality of traditional and crowdsourced data, we have utilized the OpenStreetMap roads network, and has integrated high resolution population data with traffic simulation to create a Toolbox for Urban Mobility Simulations (TUMS) at global scale. TUMS consists of three major components: data processing, traffic simulation models, and Internet-based visualizations. It integrates OpenStreetMap, LandScanTM population, and other open data (Census Transportation Planning Products, National household Travel Survey, etc.) to generate both normal traffic operation and emergency evacuation scenarios. TUMS integrates TRANSIMS and MITSIM as traffic simulation engines, which are open-source and widely-accepted for scalable traffic simulations. Consistent data and simulation platform allows quick adaption to various geographic areas that has been demonstrated for multiple cities across the world. We are combining the strengths of geospatial data sciences, high performance simulations, transportation planning, and emissions, vehicle and energy technology development to design and develop a simulation

  12. Numerical modeling of permafrost dynamics in Alaska using a high spatial resolution dataset

    Directory of Open Access Journals (Sweden)

    E. E. Jafarov

    2012-06-01

    Full Text Available Climate projections for the 21st century indicate that there could be a pronounced warming and permafrost degradation in the Arctic and sub-Arctic regions. Climate warming is likely to cause permafrost thawing with subsequent effects on surface albedo, hydrology, soil organic matter storage and greenhouse gas emissions.

    To assess possible changes in the permafrost thermal state and active layer thickness, we implemented the GIPL2-MPI transient numerical model for the entire Alaska permafrost domain. The model input parameters are spatial datasets of mean monthly air temperature and precipitation, prescribed thermal properties of the multilayered soil column, and water content that are specific for each soil class and geographical location. As a climate forcing, we used the composite of five IPCC Global Circulation Models that has been downscaled to 2 by 2 km spatial resolution by Scenarios Network for Alaska Planning (SNAP group.

    In this paper, we present the modeling results based on input of a five-model composite with A1B carbon emission scenario. The model has been calibrated according to the annual borehole temperature measurements for the State of Alaska. We also performed more detailed calibration for fifteen shallow borehole stations where high quality data are available on daily basis. To validate the model performance, we compared simulated active layer thicknesses with observed data from Circumpolar Active Layer Monitoring (CALM stations. The calibrated model was used to address possible ground temperature changes for the 21st century. The model simulation results show widespread permafrost degradation in Alaska could begin between 2040–2099 within the vast area southward from the Brooks Range, except for the high altitude regions of the Alaska Range and Wrangell Mountains.

  13. Total Synthesis and Stereochemical Assignment of Delavatine A: Rh-Catalyzed Asymmetric Hydrogenation of Indene-Type Tetrasubstituted Olefins and Kinetic Resolution through Pd-Catalyzed Triflamide-Directed C-H Olefination.

    Science.gov (United States)

    Zhang, Zhongyin; Wang, Jinxin; Li, Jian; Yang, Fan; Liu, Guodu; Tang, Wenjun; He, Weiwei; Fu, Jian-Jun; Shen, Yun-Heng; Li, Ang; Zhang, Wei-Dong

    2017-04-19

    Delavatine A (1) is a structurally unusual isoquinoline alkaloid isolated from Incarvillea delavayi. The first and gram-scale total synthesis of 1 was accomplished in 13 steps (the longest linear sequence) from commercially available starting materials. We exploited an isoquinoline construction strategy and developed two reactions, namely Rh-catalyzed asymmetric hydrogenation of indene-type tetrasubstituted olefins and kinetic resolution of β-alkyl phenylethylamine derivatives through Pd-catalyzed triflamide-directed C-H olefination. The substrate scope of the first reaction covered unfunctionalized olefins and those containing polar functionalities such as sulfonamides. The kinetic resolution provided a collection of enantioenriched indane- and tetralin-based triflamides, including those bearing quaternary chiral centers. The selectivity factor (s) exceeded 100 for a number of substrates. These reactions enabled two different yet related approaches to a key intermediate 28 in excellent enantiopurity. In the synthesis, the triflamide served as not only an effective directing group for C-H bond activation but also a versatile functional group for further elaborations. The relative and absolute configurations of delavatine A were unambiguously assigned by the syntheses of the natural product and its three stereoisomers. Their cytotoxicity against a series of cancer cell lines was evaluated.

  14. Measurement of dynamic urethral pressures with a high-resolution manometry system in continent and incontinent women.

    Science.gov (United States)

    Kirby, Anna C; Tan-Kim, Jasmine; Nager, Charles W

    2015-01-01

    Female stress urinary incontinence is caused by urethral dysfunction during dynamic conditions, but current technology has limitations in measuring urethral pressures under these conditions. An 8-French high-resolution manometry (HRM) catheter currently in clinical use in gastroenterology may accurately measure urethral pressures under dynamic conditions because it has a 25-millisecond response rate and circumferential pressure sensors along the length of the catheter (ManoScan ESO; Given Imaging, Yoqneam, Israel). We evaluated the concordance, repeatability, and tolerability of this catheter. We measured resting, cough, and strain maximum urethral closure pressures (MUCPs) using HRM and measured resting MUCPs with water-perfusion side-hole catheter urethral pressure profilometry (UPP) in 37 continent and 28 stress-incontinent subjects. Maneuvers were repeated after moving the HRM catheter along the urethral length to evaluate whether results depend on catheter positioning. Visual analog pain scores evaluated the comfort of HRM compared to UPP. The correlation coefficient for resting MUCPs measured by HRM versus UPP was high (r = 0.79, P rest, cough, and strain with HRM: r = 0.92, 0.89, and 0.89. Mean MUCPs (rest, cough, and strain) were higher in continent than in incontinent subjects (all P continent subjects during cough and strain maneuvers compared to rest. This preliminary study shows that HRM is concordant with standard technology, repeatable, and well tolerated in the urethra. Incontinent women have more impairment of their urethral closure pressures during cough and strain than continent women.

  15. Analysis of stationary fuel cell dynamic ramping capabilities and ultra capacitor energy storage using high resolution demand data

    Science.gov (United States)

    Meacham, James R.; Jabbari, Faryar; Brouwer, Jacob; Mauzey, Josh L.; Samuelsen, G. Scott

    Current high temperature fuel cell (HTFC) systems used for stationary power applications (in the 200-300 kW size range) have very limited dynamic load following capability or are simply base load devices. Considering the economics of existing electric utility rate structures, there is little incentive to increase HTFC ramping capability beyond 1 kWs -1 (0.4% s -1). However, in order to ease concerns about grid instabilities from utility companies and increase market adoption, HTFC systems will have to increase their ramping abilities, and will likely have to incorporate electrical energy storage (EES). Because batteries have low power densities and limited lifetimes in highly cyclic applications, ultra capacitors may be the EES medium of choice. The current analyses show that, because ultra capacitors have a very low energy storage density, their integration with HTFC systems may not be feasible unless the fuel cell has a ramp rate approaching 10 kWs -1 (4% s -1) when using a worst-case design analysis. This requirement for fast dynamic load response characteristics can be reduced to 1 kWs -1 by utilizing high resolution demand data to properly size ultra capacitor systems and through demand management techniques that reduce load volatility.

  16. Investigating Forest Harvest Effects on DOC Concentration and Quality: An In Situ, High Resolution Approach to Quantifying DOC Export Dynamics

    Science.gov (United States)

    Jollymore, A. J.; Johnson, M. S.; Hawthorne, I.

    2013-12-01

    Justification: Forest harvest effects on water quality can signal alterations in hydrologic and ecologic processes incurred as a result of forest harvest activities. Organic matter (OM), specifically dissolved organic carbon (DOC), plays a number of important roles mediating UV-light penetration, redox reactivity and microbial activity within aquatic ecosystems. Quantification of DOC is typically pursued via grab sampling followed by chemical or spectrophotometric analysis, limiting the temporal resolution obtained as well as the accuracy of export calculations. The advent of field-deployable sensors capable of measuring DOC concentration and certain quality characteristics in situ provides the ability to observe dynamics at temporal scales necessary for accurate calculation of DOC flux, as well as the observation of dynamic changes in DOC quality on timescales impossible to observe through grab sampling. Methods: This study utilizes a field deployable UV-Vis spectrophotometer (spectro::lyzer, s::can, Austria) to investigate how forest harvest affects DOC export. The sensor was installed at an existing hydrologic monitoring site at the outlet of a headwater stream draining a small (91 hectare) second growth Douglasfir-dominated catchment near Campbell River on Vancouver Island, British Columbia. Measurement began late in 2009, prior to forest harvest and associated activities such as road building (which commenced in October 2010 and ended in early 2011), and continues to present. During this time - encompassing the pre, during and post-harvest conditions - the absorbance spectrum of stream water from 200 to 750 nm was measured. DOC concentration and spectroscopic indices related to DOC quality (including SUVA, which relates to the concentration of aromatic carbon, and spectral slope) were subsequently calculated for each spectra obtained at 30-minute intervals. Results and conclusions: High frequency measurements of DOC show that overall export of OM increased in

  17. Monitoring vegetation dynamics with medium resolution MODIS-EVI time series at sub-regional scale in southern Africa

    Science.gov (United States)

    Dubovyk, Olena; Landmann, Tobias; Erasmus, Barend F. N.; Tewes, Andreas; Schellberg, Jürgen

    2015-06-01

    Currently there is a lack of knowledge on spatio-temporal patterns of land surface dynamics at medium spatial scale in southern Africa, even though this information is essential for better understanding of ecosystem response to climatic variability and human-induced land transformations. In this study, we analysed vegetation dynamics across a large area in southern Africa using the 14-years (2000-2013) of medium spatial resolution (250 m) MODIS-EVI time-series data. Specifically, we investigated temporal changes in the time series of key phenometrics including overall greenness, peak and timing of annual greenness over the monitoring period and study region. In order to specifically capture spatial and per pixel vegetation changes over time, we calculated trends in these phenometrics using a robust trend analysis method. The results showed that interannual vegetation dynamics followed precipitation patterns with clearly differentiated seasonality. The earliest peak greenness during 2000-2013 occurred at the end of January in the year 2000 and the latest peak greenness was observed at the mid of March in 2012. Specifically spatial patterns of long-term vegetation trends allowed mapping areas of (i) decrease or increase in overall greenness, (ii) decrease or increase of peak greenness, and (iii) shifts in timing of occurrence of peak greenness over the 14-year monitoring period. The observed vegetation decline in the study area was mainly attributed to human-induced factors. The obtained information is useful to guide selection of field sites for detailed vegetation studies and land rehabilitation interventions and serve as an input for a range of land surface models.

  18. From Particles and Point Clouds to Voxel Models: High Resolution Modeling of Dynamic Landscapes in Open Source GIS

    Science.gov (United States)

    Mitasova, H.; Hardin, E. J.; Kratochvilova, A.; Landa, M.

    2012-12-01

    Multitemporal data acquired by modern mapping technologies provide unique insights into processes driving land surface dynamics. These high resolution data also offer an opportunity to improve the theoretical foundations and accuracy of process-based simulations of evolving landforms. We discuss development of new generation of visualization and analytics tools for GRASS GIS designed for 3D multitemporal data from repeated lidar surveys and from landscape process simulations. We focus on data and simulation methods that are based on point sampling of continuous fields and lead to representation of evolving surfaces as series of raster map layers or voxel models. For multitemporal lidar data we present workflows that combine open source point cloud processing tools with GRASS GIS and custom python scripts to model and analyze dynamics of coastal topography (Figure 1) and we outline development of coastal analysis toolbox. The simulations focus on particle sampling method for solving continuity equations and its application for geospatial modeling of landscape processes. In addition to water and sediment transport models, already implemented in GIS, the new capabilities under development combine OpenFOAM for wind shear stress simulation with a new module for aeolian sand transport and dune evolution simulations. Comparison of observed dynamics with the results of simulations is supported by a new, integrated 2D and 3D visualization interface that provides highly interactive and intuitive access to the redesigned and enhanced visualization tools. Several case studies will be used to illustrate the presented methods and tools and demonstrate the power of workflows built with FOSS and highlight their interoperability.Figure 1. Isosurfaces representing evolution of shoreline and a z=4.5m contour between the years 1997-2011at Cape Hatteras, NC extracted from a voxel model derived from series of lidar-based DEMs.

  19. A regional-scale, high resolution dynamical malaria model that accounts for population density, climate and surface hydrology.

    Science.gov (United States)

    Tompkins, Adrian M; Ermert, Volker

    2013-02-18

    The relative roles of climate variability and population related effects in malaria transmission could be better understood if regional-scale dynamical malaria models could account for these factors. A new dynamical community malaria model is introduced that accounts for the temperature and rainfall influences on the parasite and vector life cycles which are finely resolved in order to correctly represent the delay between the rains and the malaria season. The rainfall drives a simple but physically based representation of the surface hydrology. The model accounts for the population density in the calculation of daily biting rates. Model simulations of entomological inoculation rate and circumsporozoite protein rate compare well to data from field studies from a wide range of locations in West Africa that encompass both seasonal endemic and epidemic fringe areas. A focus on Bobo-Dioulasso shows the ability of the model to represent the differences in transmission rates between rural and peri-urban areas in addition to the seasonality of malaria. Fine spatial resolution regional integrations for Eastern Africa reproduce the malaria atlas project (MAP) spatial distribution of the parasite ratio, and integrations for West and Eastern Africa show that the model grossly reproduces the reduction in parasite ratio as a function of population density observed in a large number of field surveys, although it underestimates malaria prevalence at high densities probably due to the neglect of population migration. A new dynamical community malaria model is publicly available that accounts for climate and population density to simulate malaria transmission on a regional scale. The model structure facilitates future development to incorporate migration, immunity and interventions.

  20. Temporal dynamics of selective attention and conflict resolution during cross-dimensional go-nogo decisions

    Directory of Open Access Journals (Sweden)

    Moschner Carsten

    2007-08-01

    Full Text Available Abstract Background Decision-making is a fundamental capacity which is crucial to many higher-order psychological functions. We recorded event-related potentials (ERPs during a visual target-identification task that required go-nogo choices. Targets were identified on the basis of cross-dimensional conjunctions of particular colors and forms. Color discriminability was manipulated in three conditions to determine the effects of color distinctiveness on component processes of decision-making. Results Target identification was accompanied by the emergence of prefrontal P2a and P3b. Selection negativity (SN revealed that target-compatible features captured attention more than target-incompatible features, suggesting that intra-dimensional attentional capture was goal-contingent. No changes of cross-dimensional selection priorities were measurable when color discriminability was altered. Peak latencies of the color-related SN provided a chronometric measure of the duration of attention-related neural processing. ERPs recorded over the frontocentral scalp (N2c, P3a revealed that color-overlap distractors, more than form-overlap distractors, required additional late selection. The need for additional response selection induced by color-overlap distractors was severely reduced when color discriminability decreased. Conclusion We propose a simple model of cross-dimensional perceptual decision-making. The temporal synchrony of separate color-related and form-related choices determines whether or not distractor processing includes post-perceptual stages. ERP measures contribute to a comprehensive explanation of the temporal dynamics of component processes of perceptual decision-making.

  1. All-in-one light-tunable borated phosphors with chemical and luminescence dynamical control resolution.

    Science.gov (United States)

    Lin, Chun Che; Liu, Yun-Ping; Xiao, Zhi Ren; Wang, Yin-Kuo; Cheng, Bing-Ming; Liu, Ru-Shi

    2014-06-25

    Single-composition white-emitting phosphors with superior intrinsic properties upon excitation by ultraviolet light-emitting diodes are important constituents of next-generation light sources. Borate-based phosphors, such as NaSrBO3:Ce(3+) and NaCaBO3:Ce(3+), have stronger absorptions in the near-ultraviolet region as well as better chemical/physical stability than oxides. Energy transfer effects from sensitizer to activator caused by rare-earth ions are mainly found in the obtained photoluminescence spectra and lifetime. The interactive mechanisms of multiple dopants are ambiguous in most cases. We adjust the doping concentration in NaSrBO3:RE (RE = Ce(3+), Tb(3+), Mn(2+)) to study the energy transfer effects of Ce(3+) to Tb(3+) and Mn(2+) by comparing the experimental data and theoretical calculation. The vacuum-ultraviolet experimental determination of the electronic energy levels for Ce(3+) and Tb(3+) in the borate host regarding the 4f-5d and 4f-4f configurations are described. Evaluation of the Ce(3+)/Mn(2+) intensity ratios as a function of Mn(2+) concentration is based on the analysis of the luminescence dynamical process and fluorescence lifetime measurements. The results closely agree with those directly obtained from the emission spectra. Density functional calculations are performed using the generalized gradient approximation plus an on-site Coulombic interaction correction scheme to investigate the forbidden mechanism of interatomic energy transfer between the NaSrBO3:Ce(3+) and NaSrBO3:Eu(2+) systems. Results indicate that the NaSrBO3:Ce(3+), Tb(3+), and Mn(2+) phosphors can be used as a novel white-emitting component of UV radiation-excited devices.

  2. Headwater sediment dynamics in a debris flow catchment constrained by high-resolution topographic surveys

    Science.gov (United States)

    Loye, Alexandre; Jaboyedoff, Michel; Theule, Joshua Isaac; Liébault, Frédéric

    2016-06-01

    Debris flows have been recognized to be linked to the amounts of material temporarily stored in torrent channels. Hence, sediment supply and storage changes from low-order channels of the Manival catchment, a small tributary valley with an active torrent system located exclusively in sedimentary rocks of the Chartreuse Massif (French Alps), were surveyed periodically for 16 months using terrestrial laser scanning (TLS) to study the coupling between sediment dynamics and torrent responses in terms of debris flow events, which occurred twice during the monitoring period. Sediment transfer in the main torrent was monitored with cross-section surveys. Sediment budgets were generated seasonally using sequential TLS data differencing and morphological extrapolations. Debris production depends strongly on rockfall occurring during the winter-early spring season, following a power law distribution for volumes of rockfall events above 0.1 m3, while hillslope sediment reworking dominates debris recharge in spring and autumn, which shows effective hillslope-channel coupling. The occurrence of both debris flow events that occurred during the monitoring was linked to recharge from previous debris pulses coming from the hillside and from bedload transfer. Headwater debris sources display an ambiguous behaviour in sediment transfer: low geomorphic activity occurred in the production zone, despite rainstorms inducing debris flows in the torrent; still, a general reactivation of sediment transport in headwater channels was observed in autumn without new debris supply, suggesting that the stored debris was not exhausted. The seasonal cycle of sediment yield seems to depend not only on debris supply and runoff (flow capacity) but also on geomorphic conditions that destabilize remnant debris stocks. This study shows that monitoring the changes within a torrent's in-channel storage and its debris supply can improve knowledge on recharge thresholds leading to debris flow.

  3. Dynamical influence of gravity waves generated by the Vestfjella Mountains in Antarctica: radar observations, fine-scale modelling and kinetic energy budget analysis

    Directory of Open Access Journals (Sweden)

    Joel Arnault

    2012-02-01

    Full Text Available Gravity waves generated by the Vestfjella Mountains (in western Droning Maud Land, Antarctica, southwest of the Finnish/Swedish Aboa/Wasa station have been observed with the Moveable atmospheric radar for Antarctica (MARA during the SWEDish Antarctic Research Programme (SWEDARP in December 2007/January 2008. These radar observations are compared with a 2-month Weather Research Forecast (WRF model experiment operated at 2 km horizontal resolution. A control simulation without orography is also operated in order to separate unambiguously the contribution of the mountain waves on the simulated atmospheric flow. This contribution is then quantified with a kinetic energy budget analysis computed in the two simulations. The results of this study confirm that mountain waves reaching lower-stratospheric heights break through convective overturning and generate inertia gravity waves with a smaller vertical wavelength, in association with a brief depletion of kinetic energy through frictional dissipation and negative vertical advection. The kinetic energy budget also shows that gravity waves have a strong influence on the other terms of the budget, i.e. horizontal advection and horizontal work of pressure forces, so evaluating the influence of gravity waves on the mean-flow with the vertical advection term alone is not sufficient, at least in this case. We finally obtain that gravity waves generated by the Vestfjella Mountains reaching lower stratospheric heights generally deplete (create kinetic energy in the lower troposphere (upper troposphere–lower stratosphere, in contradiction with the usual decelerating effect attributed to gravity waves on the zonal circulation in the upper troposphere–lower stratosphere.

  4. WE-FG-206-06: Dual-Input Tracer Kinetic Modeling and Its Analog Implementation for Dynamic Contrast-Enhanced (DCE-) MRI of Malignant Mesothelioma (MPM)

    Energy Technology Data Exchange (ETDEWEB)

    Lee, S; Rimner, A; Hayes, S; Hunt, M; Deasy, J; Zauderer, M; Rusch, V; Tyagi, N [Memorial Sloan Kettering Cancer Center, New York, NY (United States)

    2016-06-15

    Purpose: To use dual-input tracer kinetic modeling of the lung for mapping spatial heterogeneity of various kinetic parameters in malignant MPM Methods: Six MPM patients received DCE-MRI as part of their radiation therapy simulation scan. 5 patients had the epitheloid subtype of MPM, while one was biphasic. A 3D fast-field echo sequence with TR/TE/Flip angle of 3.62ms/1.69ms/15° was used for DCE-MRI acquisition. The scan was collected for 5 minutes with a temporal resolution of 5-9 seconds depending on the spatial extent of the tumor. A principal component analysis-based groupwise deformable registration was used to co-register all the DCE-MRI series for motion compensation. All the images were analyzed using five different dual-input tracer kinetic models implemented in analog continuous-time formalism: the Tofts-Kety (TK), extended TK (ETK), two compartment exchange (2CX), adiabatic approximation to the tissue homogeneity (AATH), and distributed parameter (DP) models. The following parameters were computed for each model: total blood flow (BF), pulmonary flow fraction (γ), pulmonary blood flow (BF-pa), systemic blood flow (BF-a), blood volume (BV), mean transit time (MTT), permeability-surface area product (PS), fractional interstitial volume (vi), extraction fraction (E), volume transfer constant (Ktrans) and efflux rate constant (kep). Results: Although the majority of patients had epitheloid histologies, kinetic parameter values varied across different models. One patient showed a higher total BF value in all models among the epitheloid histologies, although the γ value was varying among these different models. In one tumor with a large area of necrosis, the TK and ETK models showed higher E, Ktrans, and kep values and lower interstitial volume as compared to AATH and DP and 2CX models. Kinetic parameters such as BF-pa, BF-a, PS, Ktrans values were higher in surviving group compared to non-surviving group across most models. Conclusion: Dual-input tracer

  5. New GOES High-Resolution Magnetic Measurements and their Contribution to Understanding Magnetospheric Particle Dynamics

    Science.gov (United States)

    Redmon, R. J.; Loto'aniu, P. T. M.; Boudouridis, A.; Chi, P. J.; Singer, H. J.; Kress, B. T.; Rodriguez, J. V.; Abdelqader, A.; Tilton, M.

    2017-12-01

    studies, we find that the wave amplitude of poloidal oscillations is amplified at low altitudes but attenuated on the ground, confirming the theoretical predictions of wave propagation from the magnetosphere to the ground. We include examples of GOES-16 particle flux and magnetic field observations illustrating complex particle dynamics.

  6. Single-molecule resolution of protein dynamics on polymeric membrane surfaces: the roles of spatial and population heterogeneity.

    Science.gov (United States)

    Langdon, Blake B; Mirhossaini, Roya B; Mabry, Joshua N; Sriram, Indira; Lajmi, Ajay; Zhang, Yanxia; Rojas, Orlando J; Schwartz, Daniel K

    2015-02-18

    Although polymeric membranes are widely used in the purification of protein pharmaceuticals, interactions between biomolecules and membrane surfaces can lead to reduced membrane performance and damage to the product. In this study, single-molecule fluorescence microscopy provided direct observation of bovine serum albumin (BSA) and human monoclonal antibody (IgG) dynamics at the interface between aqueous buffer and polymeric membrane materials including regenerated cellulose and unmodified poly(ether sulfone) (PES) blended with either polyvinylpyrrolidone (PVP), polyvinyl acetate-co-polyvinylpyrrolidone (PVAc-PVP), or polyethylene glycol methacrylate (PEGM) before casting. These polymer surfaces were compared with model surfaces composed of hydrophilic bare fused silica and hydrophobic trimethylsilane-coated fused silica. At extremely dilute protein concentrations (10(-3)-10(-7) mg/mL), protein surface exchange was highly dynamic with protein monomers desorbing from the surface within ∼1 s after adsorption. Protein oligomers (e.g., nonspecific dimers, trimers, or larger aggregates), although less common, remained on the surface for 5 times longer than monomers. Using newly developed super-resolution methods, we could localize adsorption sites with ∼50 nm resolution and quantify the spatial heterogeneity of the various surfaces. On a small anomalous subset of the adsorption sites, proteins adsorbed preferentially and tended to reside for significantly longer times (i.e., on "strong" sites). Proteins resided for shorter times overall on surfaces that were more homogeneous and exhibited fewer strong sites (e.g., PVAc-PVP/PES). We propose that strong surface sites may nucleate protein aggregation, initiated preferentially by protein oligomers, and accelerate ultrafiltration membrane fouling. At high protein concentrations (0.3-1.0 mg/mL), fewer strong adsorption sites were observed, and surface residence times were reduced. This suggests that at high concentrations

  7. Integrating real-time and manual monitored data to predict hillslope soil moisture dynamics with high spatio-temporal resolution using linear and non-linear models

    Science.gov (United States)

    Spatio-temporal variability of soil moisture (') is a challenge that remains to be better understood. A trade-off exists between spatial coverage and temporal resolution when using the manual and real-time ' monitoring methods. This restricted the comprehensive and intensive examination of ' dynamic...

  8. Dynamic inundation mapping of Hurricane Harvey flooding in the Houston metro area using hyper-resolution modeling and quantitative image reanalysis

    Science.gov (United States)

    Noh, S. J.; Lee, J. H.; Lee, S.; Zhang, Y.; Seo, D. J.

    2017-12-01

    Hurricane Harvey was one of the most extreme weather events in Texas history and left significant damages in the Houston and adjoining coastal areas. To understand better the relative impact to urban flooding of extreme amount and spatial extent of rainfall, unique geography, land use and storm surge, high-resolution water modeling is necessary such that natural and man-made components are fully resolved. In this presentation, we reconstruct spatiotemporal evolution of inundation during Hurricane Harvey using hyper-resolution modeling and quantitative image reanalysis. The two-dimensional urban flood model used is based on dynamic wave approximation and 10 m-resolution terrain data, and is forced by the radar-based multisensor quantitative precipitation estimates. The model domain includes Buffalo, Brays, Greens and White Oak Bayous in Houston. The model is simulated using hybrid parallel computing. To evaluate dynamic inundation mapping, we combine various qualitative crowdsourced images and video footages with LiDAR-based terrain data.

  9. Measuring dynamic and kinetic information in the previously inaccessible supra-τ(c) window of nanoseconds to microseconds by solution NMR spectroscopy.

    Science.gov (United States)

    Ban, David; Sabo, T Michael; Griesinger, Christian; Lee, Donghan

    2013-09-26

    Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool that has enabled experimentalists to characterize molecular dynamics and kinetics spanning a wide range of time-scales from picoseconds to days. This review focuses on addressing the previously inaccessible supra-tc window (defined as τ(c) supra-τ(c) supra-τ(c) window. In the second section, the current state of the art for RD is analyzed, as well as the considerable progress toward pushing the sensitivity of RD further into the supra-τ(c) scale by up to a factor of two (motion up to 25 μs). From the data obtained with these techniques and methodology, the importance of the supra-τ(c) scale for protein function and molecular recognition is becoming increasingly clearer as the connection between motion on the supra-τ(c) scale and protein functionality from the experimental side is further strengthened with results from molecular dynamics simulations.

  10. Supporting interpretation of dynamic simulation. Application to chemical kinetic models; Aides a l`interpretation de simulations dynamiques. Application aux modeles de cinetique chimique

    Energy Technology Data Exchange (ETDEWEB)

    Braunschweig, B

    1998-04-22

    Numerous scientific and technical domains make constant use of dynamical simulations. Such simulators are put in the hands of a growing number of users. This phenomenon is due both to the extraordinary increase in computing performance, and to better graphical user interfaces which make simulation models easy to operate. But simulators are still computer programs which produce series of numbers from other series of numbers, even if they are displayed graphically. This thesis presents new interaction paradigms between a dynamical simulator and its user. The simulator produces a self-made interpretation of its results, thanks to a dedicated representation of its domain with objects. It shows dominant cyclic mechanisms identified by their instantaneous loop gain estimates, it uses a notion of episodes for splitting the simulation into homogeneous time intervals, and completes this by animations which rely on the graphical structure of the system. These new approaches are demonstrated with examples from chemical kinetics, because of the energic and exemplary characteristics of the encountered behaviors. They are implemented in the Spike software, Software Platform for Interactive Chemical Kinetics Experiments. Similar concepts are also shown in two other domains: interpretation of seismic wave propagation, and simulation of large projects. (author) 95 refs.

  11. Improved performance of Yarrowia lipolytica lipase-catalyzed kinetic resolution of (R,S)-2-octanol by an integrated strategy of interfacial activation, bioimprinting and immobilization.

    Science.gov (United States)

    Liu, Ying; Guo, Chen; Sun, Xi-Tong; Liu, Chun-Zhao

    2013-08-01

    Yarrowia lipolytica lipase (YLL) demonstrated an (R)-enantiopreference for efficient resolution of (R,S)-2-octanol. The activity, enantioselectivity, the ratio of substrate to enzyme, acetaldehyde tolerance, and operational stability of YLL were improved by an integrated strategy of interfacial activation, bioimprinting, and immobilization. In comparison with the control, both the enzymatic activity and enantioselectivity increased by a factor of 8.85 and 2.75 by the integrated strategy, respectively. Fifty-one percentage of conversion with 220 of enantioselectivity was obtained using the immobilized YLL prepared by the integrated strategy at a ratio of 104 of substrate to enzyme loaded. The immobilized YLL retained 97% of its initial activity without a decrease in enantioselectivity after 10 successive reuse cycles. Together these results will result in a promising strategy with the YYL for efficient resolution of (R,S)-2-octanol in practice. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. Viral Transmission Dynamics at Single-Cell Resolution Reveal Transiently Immune Subpopulations Caused by a Carrier State Association.

    Directory of Open Access Journals (Sweden)

    William Cenens

    2015-12-01

    Full Text Available Monitoring the complex transmission dynamics of a bacterial virus (temperate phage P22 throughout a population of its host (Salmonella Typhimurium at single cell resolution revealed the unexpected existence of a transiently immune subpopulation of host cells that emerged from peculiarities preceding the process of lysogenization. More specifically, an infection event ultimately leading to a lysogen first yielded a phage carrier cell harboring a polarly tethered P22 episome. Upon subsequent division, the daughter cell inheriting this episome became lysogenized by an integration event yielding a prophage, while the other daughter cell became P22-free. However, since the phage carrier cell was shown to overproduce immunity factors that are cytoplasmically inherited by the P22-free daughter cell and further passed down to its siblings, a transiently resistant subpopulation was generated that upon dilution of these immunity factors again became susceptible to P22 infection. The iterative emergence and infection of transiently resistant subpopulations suggests a new bet-hedging strategy by which viruses could manage to sustain both vertical and horizontal transmission routes throughout an infected population without compromising a stable co-existence with their host.

  13. Greenhouse Gas Dynamics in a Salt-Wedge Estuary Revealed by High Resolution Cavity Ring-Down Spectroscopy Observations.

    Science.gov (United States)

    Tait, Douglas R; Maher, Damien T; Wong, WeiWen; Santos, Isaac R; Sadat-Noori, Mahmood; Holloway, Ceylena; Cook, Perran L M

    2017-12-05

    Estuaries are an important source of greenhouse gases to the atmosphere, but uncertainties remain in the flux rates and production pathways of greenhouse gases in these dynamic systems. This study performs simultaneous high resolution measurements of the three major greenhouse gases (carbon dioxide, methane, and nitrous oxide) as well as carbon stable isotope ratios of carbon dioxide and methane, above and below the pycnocline along a salt wedge estuary (Yarra River estuary, Australia). We identified distinct zones of elevated greenhouse gas concentrations. At the tip of salt wedge, average CO 2 and N 2 O concentrations were approximately five and three times higher than in the saline mouth of the estuary. In anaerobic bottom waters, the natural tracer radon ( 222 Rn) revealed that porewater exchange was the likely source of the highest methane concentrations (up to 1302 nM). Isotopic analysis of CH 4 showed a dominance of acetoclastic production in fresh surface waters and hydrogenotrophic production occurring in the saline bottom waters. The atmospheric flux of methane (in CO 2 equivalent units) was a major (35-53%) contributor of atmospheric radiative forcing from the estuary, while N 2 O contributed <2%. We hypothesize that the release of bottom water gases when stratification episodically breaks down will release large pulses of greenhouse gases to the atmosphere.

  14. Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Agarwal, Animesh, E-mail: animesh@zedat.fu-berlin.de; Delle Site, Luigi, E-mail: dellesite@fu-berlin.de [Institute for Mathematics, Freie Universität Berlin, Berlin (Germany)

    2015-09-07

    Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.

  15. Characterising Dynamic Instability in High Water-Cut Oil-Water Flows Using High-Resolution Microwave Sensor Signals

    Science.gov (United States)

    Liu, Weixin; Jin, Ningde; Han, Yunfeng; Ma, Jing

    2018-06-01

    In the present study, multi-scale entropy algorithm was used to characterise the complex flow phenomena of turbulent droplets in high water-cut oil-water two-phase flow. First, we compared multi-scale weighted permutation entropy (MWPE), multi-scale approximate entropy (MAE), multi-scale sample entropy (MSE) and multi-scale complexity measure (MCM) for typical nonlinear systems. The results show that MWPE presents satisfied variability with scale and anti-noise ability. Accordingly, we conducted an experiment of vertical upward oil-water two-phase flow with high water-cut and collected the signals of a high-resolution microwave resonant sensor, based on which two indexes, the entropy rate and mean value of MWPE, were extracted. Besides, the effects of total flow rate and water-cut on these two indexes were analysed. Our researches show that MWPE is an effective method to uncover the dynamic instability of oil-water two-phase flow with high water-cut.

  16. Resolution-of-identity stochastic time-dependent configuration interaction for dissipative electron dynamics in strong fields.

    Science.gov (United States)

    Klinkusch, Stefan; Tremblay, Jean Christophe

    2016-05-14

    In this contribution, we introduce a method for simulating dissipative, ultrafast many-electron dynamics in intense laser fields. The method is based on the norm-conserving stochastic unraveling of the dissipative Liouville-von Neumann equation in its Lindblad form. The N-electron wave functions sampling the density matrix are represented in the basis of singly excited configuration state functions. The interaction with an external laser field is treated variationally and the response of the electronic density is included to all orders in this basis. The coupling to an external environment is included via relaxation operators inducing transition between the configuration state functions. Single electron ionization is represented by irreversible transition operators from the ionizing states to an auxiliary continuum state. The method finds its efficiency in the representation of the operators in the interaction picture, where the resolution-of-identity is used to reduce the size of the Hamiltonian eigenstate basis. The zeroth-order eigenstates can be obtained either at the configuration interaction singles level or from a time-dependent density functional theory reference calculation. The latter offers an alternative to explicitly time-dependent density functional theory which has the advantage of remaining strictly valid for strong field excitations while improving the description of the correlation as compared to configuration interaction singles. The method is tested on a well-characterized toy system, the excitation of the low-lying charge transfer state in LiCN.

  17. Resolution-of-identity stochastic time-dependent configuration interaction for dissipative electron dynamics in strong fields

    Energy Technology Data Exchange (ETDEWEB)

    Klinkusch, Stefan; Tremblay, Jean Christophe [Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, D-14195 Berlin (Germany)

    2016-05-14

    In this contribution, we introduce a method for simulating dissipative, ultrafast many-electron dynamics in intense laser fields. The method is based on the norm-conserving stochastic unraveling of the dissipative Liouville-von Neumann equation in its Lindblad form. The N-electron wave functions sampling the density matrix are represented in the basis of singly excited configuration state functions. The interaction with an external laser field is treated variationally and the response of the electronic density is included to all orders in this basis. The coupling to an external environment is included via relaxation operators inducing transition between the configuration state functions. Single electron ionization is represented by irreversible transition operators from the ionizing states to an auxiliary continuum state. The method finds its efficiency in the representation of the operators in the interaction picture, where the resolution-of-identity is used to reduce the size of the Hamiltonian eigenstate basis. The zeroth-order eigenstates can be obtained either at the configuration interaction singles level or from a time-dependent density functional theory reference calculation. The latter offers an alternative to explicitly time-dependent density functional theory which has the advantage of remaining strictly valid for strong field excitations while improving the description of the correlation as compared to configuration interaction singles. The method is tested on a well-characterized toy system, the excitation of the low-lying charge transfer state in LiCN.

  18. Spatial-Temporal Dynamics of High-Resolution Animal Networks: What Can We Learn from Domestic Animals?

    Directory of Open Access Journals (Sweden)

    Shi Chen

    Full Text Available Animal social network is the key to understand many ecological and epidemiological processes. We used real-time location system (RTLS to accurately track cattle position, analyze their proximity networks, and tested the hypothesis of temporal stationarity and spatial homogeneity in these networks during different daily time periods and in different areas of the pen. The network structure was analyzed using global network characteristics (network density, subgroup clustering (modularity, triadic property (transitivity, and dyadic interactions (correlation coefficient from a quadratic assignment procedure at hourly level. We demonstrated substantial spatial-temporal heterogeneity in these networks and potential link between indirect animal-environment contact and direct animal-animal contact. But such heterogeneity diminished if data were collected at lower spatial (aggregated at entire pen level or temporal (aggregated at daily level resolution. The network structure (described by the characteristics such as density, modularity, transitivity, etc. also changed substantially at different time and locations. There were certain time (feeding and location (hay that the proximity network structures were more consistent based on the dyadic interaction analysis. These results reveal new insights for animal network structure and spatial-temporal dynamics, provide more accurate descriptions of animal social networks, and allow more accurate modeling of multiple (both direct and indirect disease transmission pathways.

  19. Relaxation dynamics and transformation kinetics of deeply supercooled water: Temperature, pressure, doping, and proton/deuteron isotope effects.

    Science.gov (United States)

    Lemke, Sonja; Handle, Philip H; Plaga, Lucie J; Stern, Josef N; Seidl, Markus; Fuentes-Landete, Violeta; Amann-Winkel, Katrin; Köster, Karsten W; Gainaru, Catalin; Loerting, Thomas; Böhmer, Roland

    2017-07-21

    Above its glass transition, the equilibrated high-density amorphous ice (HDA) transforms to the low-density pendant (LDA). The temperature dependence of the transformation is monitored at ambient pressure using dielectric spectroscopy and at elevated pressures using dilatometry. It is found that near the glass transition temperature of deuterated samples, the transformation kinetics is 300 times slower than the structural relaxation, while for protonated samples, the time scale separation is at least 30 000 and insensitive to doping. The kinetics of the HDA to LDA transformation lacks a proton/deuteron isotope effect, revealing that this process is dominated by the restructuring of the oxygen network. The x-ray diffraction experiments performed on samples at intermediate transition stages reflect a linear combination of the LDA and HDA patterns implying a macroscopic phase separation, instead of a local intermixing of the two amorphous states.

  20. Relaxation dynamics and transformation kinetics of deeply supercooled water: Temperature, pressure, doping, and proton/deuteron isotope effects

    Science.gov (United States)

    Lemke, Sonja; Handle, Philip H.; Plaga, Lucie J.; Stern, Josef N.; Seidl, Markus; Fuentes-Landete, Violeta; Amann-Winkel, Katrin; Köster, Karsten W.; Gainaru, Catalin; Loerting, Thomas; Böhmer, Roland

    2017-07-01

    Above its glass transition, the equilibrated high-density amorphous ice (HDA) transforms to the low-density pendant (LDA). The temperature dependence of the transformation is monitored at ambient pressure using dielectric spectroscopy and at elevated pressures using dilatometry. It is found that near the glass transition temperature of deuterated samples, the transformation kinetics is 300 times slower than the structural relaxation, while for protonated samples, the time scale separation is at least 30 000 and insensitive to doping. The kinetics of the HDA to LDA transformation lacks a proton/deuteron isotope effect, revealing that this process is dominated by the restructuring of the oxygen network. The x-ray diffraction experiments performed on samples at intermediate transition stages reflect a linear combination of the LDA and HDA patterns implying a macroscopic phase separation, instead of a local intermixing of the two amorphous states.

  1. New signal acquisition and processing system for the execution of initial criticality after refueling and physical tests at low power in Angra-2, with the incorporation of the real time resolution of the inverse point kinetic equation - IPK

    Energy Technology Data Exchange (ETDEWEB)

    Júnior, Décio Brandes M.F.; Oliveira, Mônica Georgia N.; Silva, Cristiano da, E-mail: deciobr@eletronuclear.gov.br, E-mail: mongeor@eletronuclear.gov.br, E-mail: cdsilva@eletronuclear.gov.br [Eletrobrás Termonuclear S.A. (ELETRONUCLEAR), Angra dos Reis, RJ (Brazil). Departamento DDD.O - Física de Reatores

    2017-07-01

    The goal of this work is present the new System of Acquisition and Signal Processing for the execution of the initial criticality after refueling and physical tests at low power with the incorporation of the real time resolution of Inverse Point Kinetic Equations (IPK). The system was developed using cRIO 9082 hardware (compactRIO), which is a programmable logic controller (PLC) and, the National Lab's LabVIEW programming language. The developed system enabled a better visualization and monitoring interface of the neutron flux evolution during the first criticality of cycle and following the low power physical tests, which allows the Reactor Physics Group and Reactor Operators of Angra 2 guide faster and accurately the reactivity variations at physical tests. The digital reactivity meter developed reinforces in Angra-2 the set of operational practices of reactivity management. (author)

  2. Asymmetric aminolytic kinetic resolution of racemic epoxides using recyclable chiral polymeric Co(III)-salen complexes: a protocol for total utilization of racemic epoxide in the synthesis of (R)-Naftopidil and (S)-Propranolol.

    Science.gov (United States)

    Kumar, Manish; Kureshy, Rukhsana I; Shah, Arpan K; Das, Anjan; Khan, Noor-ul H; Abdi, Sayed H R; Bajaj, Hari C

    2013-09-20

    Chiral polymeric Co(III) salen complexes with chiral ((R)/(S)-BINOL, diethyl tartrate) and achiral (piperazine and trigol) linkers with varying stereogenic centers were synthesized for the first time and used as catalysts for aminolytic kinetic resolution (AKR) of a variety of terminal epoxides and glycidyl ethers to get enantio-pure epoxides (ee, 99%) and N-protected β-amino alcohols (ee, 99%) with quantitative yield in 16 h at RT under optimized reaction conditions. This protocol was also used for the synthesis of two enantiomerically pure drug molecules (R)-Naftopidil (α1-blocker) and (S)-Propranolol (β-blocker) as a key step via AKR of single racemic naphthylglycidyl ether with Boc-protected isoproylamine with 100% epoxide utilization at 1 g level. The catalyst 1 was successfully recycled for a number of times.

  3. New signal acquisition and processing system for the execution of initial criticality after refueling and physical tests at low power in Angra-2, with the incorporation of the real time resolution of the inverse point kinetic equation - IPK

    International Nuclear Information System (INIS)

    Júnior, Décio Brandes M.F.; Oliveira, Mônica Georgia N.; Silva, Cristiano da

    2017-01-01

    The goal of this work is present the new System of Acquisition and Signal Processing for the execution of the initial criticality after refueling and physical tests at low power with the incorporation of the real time resolution of Inverse Point Kinetic Equations (IPK). The system was developed using cRIO 9082 hardware (compactRIO), which is a programmable logic controller (PLC) and, the National Lab's LabVIEW programming language. The developed system enabled a better visualization and monitoring interface of the neutron flux evolution during the first criticality of cycle and following the low power physical tests, which allows the Reactor Physics Group and Reactor Operators of Angra 2 guide faster and accurately the reactivity variations at physical tests. The digital reactivity meter developed reinforces in Angra-2 the set of operational practices of reactivity management. (author)

  4. Measuring Dynamic and Kinetic Information in the Previously Inaccessible Supra-tc Window of Nanoseconds to Microseconds by Solution NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Donghan Lee

    2013-09-01

    Full Text Available Nuclear Magnetic Resonance (NMR spectroscopy is a powerful tool that has enabled experimentalists to characterize molecular dynamics and kinetics spanning a wide range of time-scales from picoseconds to days. This review focuses on addressing the previously inaccessible supra-τc window (defined as τc < supra-τc < 40 μs; in which τc is the overall tumbling time of a molecule from the perspective of local inter-nuclear vector dynamics extracted from residual dipolar couplings (RDCs and from the perspective of conformational exchange captured by relaxation dispersion measurements (RD. The goal of the first section is to present a detailed analysis of how to extract protein dynamics encoded in RDCs and how to relate this information to protein functionality within the previously inaccessible supra-τc window. In the second section, the current state of the art for RD is analyzed, as well as the considerable progress toward pushing the sensitivity of RD further into the supra-τc scale by up to a factor of two (motion up to 25 ms. From the data obtained with these techniques and methodology, the importance of the supra-τ c scale for protein function and molecular recognition is becoming increasingly clearer as the connection between motion on the supra-τc scale and protein functionality from the experimental side is further strengthened with results from molecular dynamics simulations.

  5. A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics

    NARCIS (Netherlands)

    Nikerel, I.E.; Van Winden, W.; Van Gulik, W.M.; Heijnen, J.J.

    2006-01-01

    Background: Dynamic modeling of metabolic reaction networks under in vivo conditions is a crucial step in order to obtain a better understanding of the (dis)functioning of living cells. So far dynamic metabolic models generally have been based on mechanistic rate equations which often contain so

  6. Development of High-Resolution Dynamic Dust Source Function - A Case Study with a Strong Dust Storm in a Regional Model

    Science.gov (United States)

    Kim, Dongchul; Chin, Mian; Kemp, Eric M.; Tao, Zhining; Peters-Lidard, Christa D.; Ginoux, Paul

    2017-01-01

    A high-resolution dynamic dust source has been developed in the NASA Unified-Weather Research and Forecasting (NU-WRF) model to improve the existing coarse static dust source. In the new dust source map, topographic depression is in 1-km resolution and surface bareness is derived using the Normalized Difference Vegetation Index (NDVI) data from Moderate Resolution Imaging Spectroradiometer (MODIS). The new dust source better resolves the complex topographic distribution over the Western United States where its magnitude is higher than the existing, coarser resolution static source. A case study is conducted with an extreme dust storm that occurred in Phoenix, Arizona in 0203 UTC July 6, 2011. The NU-WRF model with the new high-resolution dynamic dust source is able to successfully capture the dust storm, which was not achieved with the old source identification. However the case study also reveals several challenges in reproducing the time evolution of the short-lived, extreme dust storm events.

  7. Development of High-Resolution Dynamic Dust Source Function -A Case Study with a Strong Dust Storm in a Regional Model.

    Science.gov (United States)

    Kim, Dongchul; Chin, Mian; Kemp, Eric M; Tao, Zhining; Peters-Lidard, Christa D; Ginoux, Paul

    2017-06-01

    A high-resolution dynamic dust source has been developed in the NASA Unified-Weather Research and Forecasting (NU-WRF) model to improve the existing coarse static dust source. In the new dust source map, topographic depression is in 1-km resolution and surface bareness is derived using the Normalized Difference Vegetation Index (NDVI) data from Moderate Resolution Imaging Spectroradiometer (MODIS). The new dust source better resolves the complex topographic distribution over the Western United States where its magnitude is higher than the existing, coarser resolution static source. A case study is conducted with an extreme dust storm that occurred in Phoenix, Arizona in 02-03 UTC July 6, 2011. The NU-WRF model with the new high-resolution dynamic dust source is able to successfully capture the dust storm, which was not achieved with the old source identification. However the case study also reveals several challenges in reproducing the time evolution of the short-lived, extreme dust storm events.

  8. Transient analysis of carbon monoxide transport phenomena and adsorption kinetics in HT-PEMFC during dynamic current extraction

    International Nuclear Information System (INIS)

    Raj, Kamal Abdul Rasheedj; Chan, Siew Hwa

    2015-01-01

    Highlights: • Increasing the fuel cell temperature reduces outlet CO concentration. • Increasing the CO inlet (initial) concentration increases outlet CO concentration. • Increasing current density step and dwell time increases outlet CO concentration. • Increasing in the CL and GDL porosities reduces outlet CO concentration. - Abstract: This paper investigates the transport phenomena of carbon monoxide (CO) and adsorption kinetics, in a high-temperature proton exchange membrane fuel cell (HT-PEMFC) during step-wise current extraction (step-change in current extraction). Step-wise current extraction is a common process done to accommodate a sudden power surge during an operation. Since HT-PEMFCs are capable of handling high impurity of CO, hydrogen fuel that is contaminated with trace amount of CO is usually considered for commercial benefits. Thus, a transient three-dimensional isothermal anodic electro-kinetic numerical model is developed to determine the effect of operating parameters such as fuel cell temperature, CO inlet (initial) concentration, step-change of current density and dwell time on the transport phenomena of CO and adsorption kinetics. In addition, geometrical factors such as the catalyst layer (CL) and gas diffusion layer (GDL) porosity are also varied as well. The results show that the above-mentioned operating parameters can affect the maximum CO concentration at the CL, especially at the outlet of the channel. Specifically, a reduction of fuel cell temperature can significantly increase the CO concentration near the outlet, while increasing CO inlet (initial) concentration, step-change amplitude of current density and current density dwell time can cause an increase in CO concentration at the outlet, albeit to different extent. In addition, the increase in the porosity of CL and GDL, results in the reduction of the maximum CO concentration at the outlet, albeit to different extent. In addition, the CO and hydrogen surface coverage

  9. Static and Dynamic Reservoir Characterization Using High Resolution P-Wave Velocity Data in Delhi Field, la

    Science.gov (United States)

    Hussain, S.; Davis, T.

    2012-12-01

    Static and dynamic reservoir characterization was done on high resolution P-wave seismic data in Delhi Field, LA to study the complex stratigraphy of the Holt-Bryant sands and to delineate the CO2 flow path. The field is undergoing CO2 injection for enhanced oil recovery. The seismic data was bandwidth extended by Geotrace to decrease the tuning thickness effect. Once the authenticity of the added frequencies in the data was determined, the interpretation helped map thin Tuscaloosa and Paluxy sands. Cross-equalization was done on the baseline and monitor surveys to remove the non-repeatable noise in the data. Acoustic impedance (AI) inversion was done on the baseline and monitor surveys to map the changes in AI with CO2 injection in the field. Figure 1 shows the AI percentage change at Base Paluxy. The analysis helped identify areas that were not being swept by CO2. Figure 2 shows the CO2 flow paths in Tuscaloosa formation. The percentage change of AI with CO2 injection and pressure increase corresponded with the fluid substitution modeling results. Time-lapse interpretation helped in delineating the channels, high permeability zones and the bypassed zones in the reservoir.; Figure 1: P-impedance percentage difference map with a 2 ms window centered at the base of Paluxy with the production data from June 2010 overlain; the black dashed line is the oil-water contact; notice the negative impedance change below the OWC. The lighter yellow color shows area where Paluxy is not being swept completely. ; Figure 2: P-impedance percentage difference map at TUSC 7 top; the white triangles are TUSC 7 injectors and the white circles are TUSC 7 producers; the black polygons show the flow paths of CO2.

  10. High-resolution dynamical downscaling of re-analysis data over the Kerguelen Islands using the WRF model

    Science.gov (United States)

    Fonseca, Ricardo; Martín-Torres, Javier

    2018-03-01

    We have used the Weather Research and Forecasting (WRF) model to simulate the climate of the Kerguelen Islands (49° S, 69° E) and investigate its inter-annual variability. Here, we have dynamically downscaled 30 years of the Climate Forecast System Reanalysis (CFSR) over these islands at 3-km horizontal resolution. The model output is found to agree well with the station and radiosonde data at the Port-aux-Français station, the only location in the islands for which observational data is available. An analysis of the seasonal mean WRF data showed a general increase in precipitation and decrease in temperature with elevation. The largest seasonal rainfall amounts occur at the highest elevations of the Cook Ice Cap in winter where the summer mean temperature is around 0 °C. Five modes of variability are considered: conventional and Modoki El Niño-Southern Oscillation (ENSO), Indian Ocean Dipole (IOD), Subtropical IOD (SIOD) and Southern Annular Mode (SAM). It is concluded that a key mechanism by which these modes impact the local climate is through interaction with the diurnal cycle in particular in the summer season when it has a larger magnitude. One of the most affected regions is the area just to the east of the Cook Ice Cap extending into the lower elevations between the Gallieni and Courbet Peninsulas. The WRF simulation shows that despite the small annual variability, the atmospheric flow in the Kerguelen Islands is rather complex which may also be the case for the other islands located in the Southern Hemisphere at similar latitudes.

  11. Kinetic Typography

    DEFF Research Database (Denmark)

    van Leeuwen, Theo; Djonov, Emilia

    2014-01-01

    After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images.......After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images....

  12. Quantification of photoinduced bending of dynamic molecular crystals: from macroscopic strain to kinetic constants and activation energies.

    Science.gov (United States)

    Chizhik, Stanislav; Sidelnikov, Anatoly; Zakharov, Boris; Naumov, Panče; Boldyreva, Elena

    2018-02-28

    Photomechanically reconfigurable elastic single crystals are the key elements for contactless, timely controllable and spatially resolved transduction of light into work from the nanoscale to the macroscale. The deformation in such single-crystal actuators is observed and usually attributed to anisotropy in their structure induced by the external stimulus. Yet, the actual intrinsic and external factors that affect the mechanical response remain poorly understood, and the lack of rigorous models stands as the main impediment towards benchmarking of these materials against each other and with much better developed soft actuators based on polymers, liquid crystals and elastomers. Here, experimental approaches for precise measurement of macroscopic strain in a single crystal bent by means of a solid-state transformation induced by light are developed and used to extract the related temperature-dependent kinetic parameters. The experimental results are compared against an overarching mathematical model based on the combined consideration of light transport, chemical transformation and elastic deformation that does not require fitting of any empirical information. It is demonstrated that for a thermally reversible photoreactive bending crystal, the kinetic constants of the forward (photochemical) reaction and the reverse (thermal) reaction, as well as their temperature dependence, can be extracted with high accuracy. The improved kinematic model of crystal bending takes into account the feedback effect, which is often neglected but becomes increasingly important at the late stages of the photochemical reaction in a single crystal. The results provide the most rigorous and exact mathematical description of photoinduced bending of a single crystal to date.

  13. A study on the kinetic behavior of Listeria monocytogenes in ice cream stored under static and dynamic chilling and freezing conditions.

    Science.gov (United States)

    Gougouli, M; Angelidis, A S; Koutsoumanis, K

    2008-02-01

    The kinetic behavior of Listeria monocytogenes in 2 commercial ice cream products (A and B) that were inoculated and stored under static chilling (4 to 16 degrees C), static freezing (-5 to -33 degrees C), dynamic chilling, and dynamic chilling-freezing conditions was studied, simulating conditions of the aging process and of normal or abuse conditions during distribution and storage. The ice cream products A and B had different compositions but similar pH (6.50 and 6.67, respectively) and water activity (0.957 and 0.965, respectively) values. For both chilling and freezing conditions, the kinetic behavior of the pathogen was similar in the 2 products, indicating that the pH and water activity, together with temperature, were the main factors controlling growth. Under chilling conditions, L. monocytogenes grew well at all temperatures tested. Under freezing conditions, no significant changes in the population of the pathogen were observed throughout a 90-d storage period for either of the inoculum levels tested (10(3) and 10(6) cfu/g). Growth data from chilled storage conditions were fitted to a mathematical model, and the calculated maximum specific growth rate was modeled as a function of temperature by using a square root model. The model was further validated under dynamic chilling and dynamic chilling-freezing conditions by using 4 different storage temperature scenarios. Under dynamic chilling conditions, the model accurately predicted the growth of the pathogen in both products, with 99.5% of the predictions lying within the +/- 20% relative error zone. The results from the chilling-freezing storage experiments showed that the pathogen was able to initiate growth within a very short time after a temperature upshift from freezing to chilling temperatures. This indicates that the freezing conditions did not cause a severe stress in L. monocytogenes cells capable of leading to a significant "additional" lag phase during the subsequent growth of the pathogen at

  14. Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori

    Science.gov (United States)

    Wang, Liang-Wei; Liu, Yu-Nan; Lyu, Ping-Chiang; Jackson, Sophie E.; Hsu, Shang-Te Danny

    2015-09-01

    Understanding the mechanism by which a polypeptide chain thread itself spontaneously to attain a knotted conformation has been a major challenge in the field of protein folding. HP0242 is a homodimeric protein from Helicobacter pylori with intertwined helices to form a unique pseudo-knotted folding topology. A tandem HP0242 repeat has been constructed to become the first engineered trefoil-knotted protein. Its small size renders it a model system for computational analyses to examine its folding and knotting pathways. Here we report a multi-parametric study on the folding stability and kinetics of a library of HP0242 variants, including the trefoil-knotted tandem HP0242 repeat, using far-UV circular dichroism and fluorescence spectroscopy. Equilibrium chemical denaturation of HP0242 variants shows the presence of highly populated dimeric and structurally heterogeneous folding intermediates. Such equilibrium folding intermediates retain significant amount of helical structures except those at the N- and C-terminal regions in the native structure. Stopped-flow fluorescence measurements of HP0242 variants show that spontaneous refolding into knotted structures can be achieved within seconds, which is several orders of magnitude faster than previously observed for other knotted proteins. Nevertheless, the complex chevron plots indicate that HP0242 variants are prone to misfold into kinetic traps, leading to severely rolled-over refolding arms. The experimental observations are in general agreement with the previously reported molecular dynamics simulations. Based on our results, kinetic folding pathways are proposed to qualitatively describe the complex folding processes of HP0242 variants.

  15. Comparison of the results of the fifth dynamic AER benchmark-a benchmark for coupled thermohydraulic system/three-dimensional hexagonal kinetic core models

    International Nuclear Information System (INIS)

    Kliem, S.

    1998-01-01

    The fifth dynamic benchmark was defined at seventh AER-Symposium, held in Hoernitz, Germany in 1997. It is the first benchmark for coupled thermohydraulic system/three-dimensional hexagonal neutron kinetic core models. In this benchmark the interaction between the components of a WWER-440 NPP with the reactor core has been investigated. The initiating event is a symmetrical break of the main steam header at the end of the first fuel cycle and hot shutdown conditions with one control rod group stucking. This break causes an overcooling of the primary circuit. During this overcooling the scram reactivity is compensated and the scrammed reactor becomes re critical. The calculation was continued until the highly-borated water from the high pressure injection system terminated the power excursion. Each participant used own best-estimate nuclear cross section data. Only the initial subcriticality at the beginning of the transient was given. Solutions were received from Kurchatov Institute Russia with the code BIPR8/ATHLET, VTT Energy Finland with HEXTRAN/SMABRE, NRI Rez Czech Republic with DYN3/ATHLET, KFKI Budapest Hungary with KIKO3D/ATHLET and from FZR Germany with the code DYN3D/ATHLET.In this paper the results are compared. Beside the comparison of global results, the behaviour of several thermohydraulic and neutron kinetic parameters is presented to discuss the revealed differences between the solutions.(Authors)

  16. How Four Scientists Integrate Thermodynamic and Kinetic Theory, Context, Analogies, and Methods in Protein-Folding and Dynamics Research: Implications for Biochemistry Instruction.

    Science.gov (United States)

    Jeffery, Kathleen A; Pelaez, Nancy; Anderson, Trevor R

    2018-01-01

    To keep biochemistry instruction current and relevant, it is crucial to expose students to cutting-edge scientific research and how experts reason about processes governed by thermodynamics and kinetics such as protein folding and dynamics. This study focuses on how experts explain their research into this topic with the intention of informing instruction. Previous research has modeled how expert biologists incorporate research methods, social or biological context, and analogies when they talk about their research on mechanisms. We used this model as a guiding framework to collect and analyze interview data from four experts. The similarities and differences that emerged from analysis indicate that all experts integrated theoretical knowledge with their research context, methods, and analogies when they explained how phenomena operate, in particular by mapping phenomena to mathematical models; they explored different processes depending on their explanatory aims, but readily transitioned between different perspectives and explanatory models; and they explained thermodynamic and kinetic concepts of relevance to protein folding in different ways that aligned with their particular research methods. We discuss how these findings have important implications for teaching and future educational research. © 2018 K. A. Jeffery et al. CBE—Life Sciences Education © 2018 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  17. Carcinoma of the uterine cervix. High-resolution turbo spin-echo MR imaging with contrast-enhanced dynamic scanning and T2-weighting

    International Nuclear Information System (INIS)

    Abe, Y.; Yamashita, Y.; Namimoto, T.; Takahashi, M.; Katabuchi, H.; Tanaka, N.; Okamura, H.

    1998-01-01

    Purpose: To compare high-resolution contrast-enhanced (Gd-DTPA) dynamic MR imaging with T2-weighted turbo spin-echo (TSE) imaging in the evaluation of uterine cervical carcinoma. Material and Methods: Thirty-two patients with cervical carcinoma underwent MR imaging on a 1.5 T superconductive unit to have the extension of the disease assessed before treatment. A phased-array coil was used in all patients. In 25 patients, surgical confirmation of the diagnosis was obtained after imaging. Radiation therapy was selected for the remaining 7 patients with advanced carcinoma. Qualitative and quantitative image analyses were also performed. Results: The cervical carcinomas showed maximum contrast in the cervical stroma and myometrium in the early dynamic phase. The tumor/cervical-stroma contrast in the early dynamic phase obtained with the T1-weighted TSE technique (contrast-to-noise ratio 22.6) was significantly higher than that obtained in T2-weighted TSE imaging (contrast-to-noise ratio 4.3). In the evaluation of parametrial invasion, the accuracy of T2-weighted imaging was 71.8% and contrast-enhanced dynamic imaging 81.2%. Conclusion: High-resolution contrast-enhanced (Gd-DTPA) dynamic MR imaging in cervical cancer offers improved tumor/cervical-stroma contrast and provides useful information on parametrial invasion. (orig.)

  18. Impact of respiratory motion correction and spatial resolution on lesion detection in PET: a simulation study based on real MR dynamic data

    Science.gov (United States)

    Polycarpou, Irene; Tsoumpas, Charalampos; King, Andrew P.; Marsden, Paul K.

    2014-02-01

    The aim of this study is to investigate the impact of respiratory motion correction and spatial resolution on lesion detectability in PET as a function of lesion size and tracer uptake. Real respiratory signals describing different breathing types are combined with a motion model formed from real dynamic MR data to simulate multiple dynamic PET datasets acquired from a continuously moving subject. Lung and liver lesions were simulated with diameters ranging from 6 to 12 mm and lesion to background ratio ranging from 3:1 to 6:1. Projection data for 6 and 3 mm PET scanner resolution were generated using analytic simulations and reconstructed without and with motion correction. Motion correction was achieved using motion compensated image reconstruction. The detectability performance was quantified by a receiver operating characteristic (ROC) analysis obtained using a channelized Hotelling observer and the area under the ROC curve (AUC) was calculated as the figure of merit. The results indicate that respiratory motion limits the detectability of lung and liver lesions, depending on the variation of the breathing cycle length and amplitude. Patients with large quiescent periods had a greater AUC than patients with regular breathing cycles and patients with long-term variability in respiratory cycle or higher motion amplitude. In addition, small (less than 10 mm diameter) or low contrast (3:1) lesions showed the greatest improvement in AUC as a result of applying motion correction. In particular, after applying motion correction the AUC is improved by up to 42% with current PET resolution (i.e. 6 mm) and up to 51% for higher PET resolution (i.e. 3 mm). Finally, the benefit of increasing the scanner resolution is small unless motion correction is applied. This investigation indicates high impact of respiratory motion correction on lesion detectability in PET and highlights the importance of motion correction in order to benefit from the increased resolution of future

  19. Impact of respiratory motion correction and spatial resolution on lesion detection in PET: a simulation study based on real MR dynamic data

    International Nuclear Information System (INIS)

    Polycarpou, Irene; Tsoumpas, Charalampos; King, Andrew P; Marsden, Paul K

    2014-01-01

    The aim of this study is to investigate the impact of respiratory motion correction and spatial resolution on lesion detectability in PET as a function of lesion size and tracer uptake. Real respiratory signals describing different breathing types are combined with a motion model formed from real dynamic MR data to simulate multiple dynamic PET datasets acquired from a continuously moving subject. Lung and liver lesions were simulated with diameters ranging from 6 to 12 mm and lesion to background ratio ranging from 3:1 to 6:1. Projection data for 6 and 3 mm PET scanner resolution were generated using analytic simulations and reconstructed without and with motion correction. Motion correction was achieved using motion compensated image reconstruction. The detectability performance was quantified by a receiver operating characteristic (ROC) analysis obtained using a channelized Hotelling observer and the area under the ROC curve (AUC) was calculated as the figure of merit. The results indicate that respiratory motion limits the detectability of lung and liver lesions, depending on the variation of the breathing cycle length and amplitude. Patients with large quiescent periods had a greater AUC than patients with regular breathing cycles and patients with long-term variability in respiratory cycle or higher motion amplitude. In addition, small (less than 10 mm diameter) or low contrast (3:1) lesions showed the greatest improvement in AUC as a result of applying motion correction. In particular, after applying motion correction the AUC is improved by up to 42% with current PET resolution (i.e. 6 mm) and up to 51% for higher PET resolution (i.e. 3 mm). Finally, the benefit of increasing the scanner resolution is small unless motion correction is applied. This investigation indicates high impact of respiratory motion correction on lesion detectability in PET and highlights the importance of motion correction in order to benefit from the increased resolution of future

  20. Ejecta cloud from the AIDA space project kinetic impact on the secondary of a binary asteroid: I. mechanical environment and dynamical model

    Science.gov (United States)

    Yu, Yang; Michel, Patrick; Schwartz, Stephen R.; Naidu, Shantanu P.; Benner, Lance A. M.

    2017-01-01

    An understanding of the post-impact dynamics of ejecta clouds are crucial to the planning of a kinetic impact mission to an asteroid, and also has great implications for the history of planetary formation. The purpose of this article is to track the evolution of ejecta produced by AIDA mission, which targets for kinetic impact the secondary of near-Earth binary asteroid (65803) Didymos on 2022, and to feedback essential informations to AIDA's ongoing phase-A study. We present a detailed dynamic model for the simulation of an ejecta cloud from a binary asteroid that synthesizes all relevant forces based on a previous analysis of the mechanical environment. We apply our method to gain insight into the expected response of Didymos to the AIDA impact, including the subsequent evolution of debris and dust. The crater scaling relations from laboratory experiments are employed to approximate the distributions of ejecta mass and launching speed. The size distribution of fragments is modeled with a power law fitted from observations of real asteroid surface. A full-scale demonstration is simulated using parameters specified by the mission. We report the results of the simulation, which include the computed spread of the ejecta cloud and the recorded history of ejecta accretion and escape. The violent period of the ejecta evolution is found to be short, and is followed by a stage where the remaining ejecta is gradually cleared. Solar radiation pressure proves to be efficient in cleaning dust-size ejecta, and the simulation results after two weeks shows that large debris on polar orbits (perpendicular to the binary orbital plane) has a survival advantage over smaller ejecta and ejecta that keeps to low latitudes.

  1. High-resolution He beam scattering as a tool for the investigation of the structural and dynamical properties of surface soliton dislocations

    International Nuclear Information System (INIS)

    El-Batanouny, M.; Martini, K.M.

    1986-01-01

    We discuss the applicability of high-resolution-He-beam/surface scattering to the investigation of the structural and dynamic properties of soliton-like surface misfit dislocations and associated phase transitions. We present evidence, based on recent He diffraction measurements, for the existence of double-sine-Gordon soliton-like dislocations on the reconstructed Au(111) surface. 18 refs., 3 figs., 1 tab

  2. The dynamics of particle disks. III - Dense and spinning particle disks. [development of kinetic theory for planetary rings

    Science.gov (United States)

    Araki, Suguru

    1991-01-01

    The kinetic theory of planetary rings developed by Araki and Tremaine (1986) and Araki (1988) is extended and refined, with a focus on the implications of finite particle size: (1) nonlocal collisions and (2) finite filling factors. Consideration is given to the derivation of the equations for the local steady state, the low-optical-depth limit, and the steady state at finite filling factors (including the effects of collision inelasticity, spin degrees of freedom, and self-gravity). Numerical results are presented in extensive graphs and characterized in detail. The importance of distinguishing effects (1) and (2) at low optical depths is stressed, and the existence of vertical density profiles with layered structures at high filling factors is demonstrated.

  3. Dynamical and many-body correlation effects in the kinetic energy spectra of isotopes produced in nuclear multifragmentation

    Science.gov (United States)

    Souza, S. R.; Donangelo, R.; Lynch, W. G.; Tsang, M. B.

    2018-03-01

    The properties of the kinetic energy spectra of light isotopes produced in the breakup of a nuclear source and during the de-excitation of its products are examined. The initial stage, at which the hot fragments are created, is modeled by the statistical multifragmentation model, whereas the Weisskopf-Ewing evaporation treatment is adopted to describe the subsequent fragment de-excitation, as they follow their classical trajectories dictated by the Coulomb repulsion among them. The energy spectra obtained are compared to available experimental data. The influence of the fusion cross section entering into the evaporation treatment is investigated and its influence on the qualitative aspects of the energy spectra turns out to be small. Although these aspects can be fairly well described by the model, the underlying physics associated with the quantitative discrepancies remains to be understood.

  4. Absorption of calcium ions on oxidized graphene sheets and study its dynamic behavior by kinetic and isothermal models

    Directory of Open Access Journals (Sweden)

    Mahmoud Fathy

    2016-07-01

    Full Text Available Abstract Sorption of calcium ion from the hard underground water using novel oxidized graphene (GO sheets was studied in this paper. Physicochemical properties and microstructure of graphene sheets were investigated using Raman spectrometer, thermogravimetry analyzer, transmission electron microscope, scanning electron microscope. The kinetics adsorption of calcium on graphene oxide sheets was examined using Lagergren first and second orders. The results show that the Lagergren second-order was the best-fit model that suggests the conception process of calcium ion adsorption on the Go sheets. For isothermal studies, the Langmuir and Freundlich isotherm models were used at temperatures ranging between 283 and 313 K. Thermodynamic parameters resolved at 283, 298 and 313 K indicating that the GO adsorption was exothermic spontaneous process. Finally, the graphene sheets show high partiality toward calcium particles and it will be useful in softening and treatment of hard water.

  5. CFD analysis of the dynamic behaviour of a fuel rod subchannel in a supercritical water reactor with point kinetics

    International Nuclear Information System (INIS)

    Ampomah-Amoako, Emmanuel; Akaho, Edward H.K.; Nyarko, Benjamin J.B.; Ambrosini, Walter

    2013-01-01

    Highlights: • The analysis of flow stability of nuclear fuel subchannels with supercritical water is presented. • The results obtained by a CFD code are compared with those of a system code. • The model includes also heat conduction in the fuel rod and point neutron kinetics. - Abstract: The paper presents the analysis by a CFD code of coupled neutronic–thermal hydraulic instabilities in a subchannel slice belonging to a square lattice assembly. The work represents a further phase in the assessment of the suitability of CFD codes for studies of flow stability of supercritical fluids; the research started in previous work with the analysis of bare 2D circular pipes and already addressed 3D subchannel slices with no allowance for heat conduction or neutronic effects. In the present phase, a more realistic system is considered, dealing with a slice of a fuel assembly subchannel containing the regions of the pellet, the gap and the cladding and including also the effect of inlet and outlet throttling. The adopted neutronic model is a point kinetics one, including six delayed neutron groups with global Doppler and fluid density feedbacks. The response of the model to perturbations applied starting from a steady-state condition at the rated power is compared with that of a similar model developed for a 1D system code. Upward, horizontal and downward flow orientations are addressed making use of a uniform power profile and changing relevant parameters as the gap equivalent conductance and the density reactivity coefficient. A bottom-peaked power profile is also considered in the case of vertical upward flow. Though the adopted model can still be considered simple in comparison with actual details of fuel assemblies, the obtained results demonstrate the potential of the adopted methodology for more accurate analyses to be made with larger computational resources

  6. Low energy ion-molecule reaction dynamics and chemiionization kinetics: Progress report, February 1, 1985-January 31, 1988