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Sample records for dynamic kinetic resolution

  1. Kinetic resolution and chemoenzymatic dynamic kinetic resolution of functionalized gamma-hydroxy amides.

    Science.gov (United States)

    Fransson, Ann-Britt L; Borén, Linnéa; Pàmies, Oscar; Bäckvall, Jan-E

    2005-04-01

    [reaction: see text] An efficient kinetic resolution of racemic gamma-hydroxy amides 1 was performed via Pseudomas cepacia lipase (PS-C)-catalyzed transesterification. The enzyme PS-C tolerates both variation in the chain length and different functionalities giving good to high enantioselectivity (E values of up to >250). The combination of enzymatic kinetic resolution with a ruthenium-catalyzed racemization led to a dynamic kinetic resolution. The use of 2,4-dimethyl-3-pentanol as a hydrogen source to suppress ketone formation in the dynamic kinetic resolution yields the corresponding acetates in good yield and good to high enantioselectivity (ee's up to 98%). The synthetic utility of this procedure was illustrated by the practical synthesis of the versatile intermediate gamma-lactone (R)-5-methyltetrahydrofuran-2-one.

  2. Oxazolidinone Synthesis through Halohydrin Dehalogenase-Catalyzed Dynamic Kinetic Resolution

    NARCIS (Netherlands)

    Mikleusevic, Ana; Hamersak, Zdenko; Salopek-Sondi, Branka; Tang, Lixia; Janssen, Dick B.; Elenkov, Maja Majeric

    2015-01-01

    An efficient dynamic kinetic resolution protocol using a single enzyme is described. Both the kinetic resolution and substrate racemization are catalyzed by halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC). The HheC-catalyzed reaction of epibromohydrin and

  3. Support influences in the Pd-catalyzed racemization and dynamic kinetic resolution of chiral benzylic amines

    NARCIS (Netherlands)

    Parvulescu, A.N.; Jacobs, P.A.; De Vos, D.E.

    2009-01-01

    The acid–base properties of the supports for Pd catalysts strongly affect their performance in racemization and dynamic kinetic resolution (DKR) of chiral benzylic amines. The need for a basic support was proven by comparing the racemization results obtained for Pd on silica, on LDH (layered double

  4. 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.

  5. Asymmetric Synthesis of Diverse Glycolic Acid Scaffolds via Dynamic Kinetic Resolution of α-Keto Esters

    Science.gov (United States)

    Steward, Kimberly M.; Corbett, Michael T.; Goodman, C. Guy; Johnson, Jeffrey S.

    2012-01-01

    The dynamic kinetic resolution of α-keto esters via asymmetric transfer hydrogenation has been developed as a technique for the highly stereoselective construction of structurally diverse β-substituted-α-hydroxy carboxylic acid derivatives. Through the development of a privileged m-terphenylsulfonamide for (arene)RuCl(monosulfonamide) complexes with a high affinity for selective α-keto ester reduction, excellent levels of chemo-, diastereo-, and enantiocontrol can be realized in the reduction of β-aryl- and β-chloro-α-keto esters. PMID:23186551

  6. Stereoselective nucleophilic fluoromethylation of aryl ketones: dynamic kinetic resolution of chiral α-fluoro carbanions.

    Science.gov (United States)

    Shen, Xiao; Miao, Wenjun; Ni, Chuanfa; Hu, Jinbo

    2014-01-13

    Although many methods are available for the synthesis of optically enriched monofluoromethyl secondary alcohols, synthesizing optically enriched monofluoromethyl tertiary alcohols remains a challenge. An efficient and easy-to-handle nucleophilic fluoromethylation protocol was developed. The current monofluoromethylation showed much higher facial selectivity than the corresponding difluoromethylation and proceeded via a different type of transition state. Excellent stereoselective control at the fluorinated carbon chiral center was found, an effect believed to be facilitated by the dynamic kinetic resolution of the chiral α-fluoro carbanions.

  7. 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.

  8. 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.

  9. 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

  10. Integration of reactive membrane extraction with lipase-hydrolysis dynamic kinetic resolution of naproxen 2,2,2-trifluoroethyl thioester in isooctane.

    Science.gov (United States)

    Lu, Chu-Hsun; Cheng, Yu-Chi; Tsai, Shau-Wei

    2002-07-20

    Lipases immobilized on polypropylene powders have been used as the biocatalyst in the enantioselective hydrolysis of (S)-naproxen from racemic naproxen thioesters in isooctane, in which trioctylamine was added to perform in situ racemization of the remaining (R)-thioester substrate. A detailed study of the kinetics for hydrolysis and racemization indicates that increasing the trioctylamine concentration can activate and stabilize the lipase as well as enhance the racemization and non-stereoselective hydrolysis of the thioester. Effects of the aqueous pH value and trioctylamine concentration on (S)-naproxen dissociation and partitioning in the aqueous phase as well as the transportation in a hollow fiber membrane were further investigated. Good agreements between the experimental data and theoretical results were obtained when the dynamic kinetic resolution process was integrated with a hollow fiber membrane to reactively extract the desired (S)-naproxen out of the reaction medium.

  11. Enzymatic dynamic kinetic resolution of racemic N-formyl- and N-carbamoyl-amino acids using immobilized L-N-carbamoylase and N-succinyl-amino acid racemase.

    Science.gov (United States)

    Soriano-Maldonado, Pablo; Las Heras-Vazquez, Francisco Javier; Clemente-Jimenez, Josefa María; Rodriguez-Vico, Felipe; Martínez-Rodríguez, Sergio

    2015-01-01

    Taking advantage of the catalytic promiscuity of L-carbamoylase from Geobacillus stearothermophilus CECT43 (BsLcar) and N-succinyl-amino acid racemase from Geobacillus kaustophilus CECT4264 (GkNSAAR), we have evaluated the production of different optically pure L-α-amino acids starting from different racemic N-formyl- and N-carbamoyl-amino acids using a dynamic kinetic resolution approach. The enzymes were immobilized on two different solid supports, resulting in improved stability of the enzymes in terms of thermostability and storage when compared to the enzymes in solution. The bienzymatic system retained up to 80% conversion efficiency after 20 weeks at 4 °C and up to 90% after 1 week at 45 °C. The immobilization process also resulted in a great enhancement of the activity of BsLcar toward N-formyl-tryptophan, showing for the first time that substrate specificity of L-carbamoylases can be influenced by this approach. The system was effective for the biosynthesis of natural and unnatural L-amino acids (enantiomeric excess (e.e.) >99.5%), such as L-methionine, L-alanine, L-tryptophan, L-homophenylalanine, L-aminobutyric acid, and L-norleucine, with a higher performance toward N-formyl-α-amino acid substrates. Biocatalyst reuse was studied, and after 10 reaction cycles, over 75% activity remained.

  12. Dynamic thermodynamic resolution: advantage by separation of equilibration and resolution.

    Science.gov (United States)

    Lee, Won Koo; Park, Yong Sun; Beak, Peter

    2009-02-17

    In the investigation of a chemical reaction, researchers typically survey variables such as time, temperature, and stoichiometry to optimize yields. This Account demonstrates how control of these variables, often in nontraditional ways, can provide significant improvements in enantiomeric ratios for asymmetric reactions. Dynamic thermodynamic resolution (DTR) offers a convenient method for the resolution of enantiomeric products in the course of a reaction. This process depends on an essential requirement: the equilibration of the penultimate diastereomers must be subject to external control. As a general case, the reaction of A(R), A(S) with B under the influence of the chiral species, L*, gives resolved products C(R) and C(S). In the first step of dynamic resolution under thermodynamic control, the enantiomeric reactants A(R) and A(S) and L* form the diastereomers A(R)/L* and A(S)/L*. The equilibrium between A(R) and A(S) can be rapid, slow, or not operative, and L* can represent a ligand, an auxiliary, or a crystallization process that provides a chiral environment. Second, the populations of the diastereomers are controlled, usually by thermal equilibration. Finally, the reaction of the diastereomers with a reagent B provides the enantiomeric products C(R) and C(S). The control of the diastereomeric equilibrium distinguishes DTR from other resolution techniques. By contrast, physical resolutions separate thermodynamically stable, nonequilibrating diastereomers, and dynamic kinetic resolutions utilize kinetic control for reactions of rapidly equilibrating diastereomers. The dynamic thermodynamic resolutions discussed in this Account illustrate cases of significantly improved enantioselectivities using this technique. Although many of the well-recognized cases come from organolithium chemistry, the principles are general, and we also present cases facilitated by other chemistries. This approach has been used to control enantioselectivities in a number of

  13. Kinetic distance and kinetic maps from molecular dynamics simulation

    CERN Document Server

    Noe, Frank

    2015-01-01

    Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine...

  14. 动态动力学拆分在手性药物合成中的应用%Application of Dynamic Kinetic Resolution in the Preparation of Chiral Drugs

    Institute of Scientific and Technical Information of China (English)

    林义; 吕力琼; 黄俊; 蒋成君

    2016-01-01

    动态动力学拆分是合成手性化合物最方便和最有效的方法之一,该方法的主要特征是用酶催化拆分和金属催化原位外消旋化未反应的底物,克服了经典动力学拆分最高产率只有50%的缺陷,理论上可以达到100%的收率。本文概述了动态动力学拆分技术在手性药物合成中的应用。%The dynamic kinetic resolution (DKR) of racemic compounds provides one of the most conve-nient and efficient routes to a wide range of chiral molecules. A key feature of this methodology is the use of metal catalysts for the in situ racemization of enzymatically unreactive enantiomers in the enzymatic resolu-tion of racemic substrates. It overcomes the limitation of the maximum 50% yield in the traditional kinetic resolution. In this way, all of the substrate could be converted into a single product isomer with a 100%theo-retical yield. In this review and the latest research progress as well as the application in preparation of chiral drugs are also presented.

  15. 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.

  16. High-resolution kinetic energy distributions via doppler shift measurements

    Science.gov (United States)

    Xu, Z.; Koplitz, B.; Buelow, S.; Baugh, D.; Wittig, C.

    1986-07-01

    In photolysis/probe experiments using pulsed sources, time delay produces both spatial and directional bias in the fragment distributions, thus enabling well-resolved kinetic energy distributions to be obtained from Doppler shift measurements. Data are presented for H-atoms detected using two-photon ionization, and high S/N and laser-limited kinetic energy resolution are demonstrated.

  17. Kinetic distance and kinetic maps from molecular dynamics simulation.

    Science.gov (United States)

    Noé, Frank; Clementi, Cecilia

    2015-10-13

    Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly interconverting states. Here, we build upon diffusion map theory and define a kinetic distance metric for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here, we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine. We find that the total kinetic variance (TKV) is an excellent indicator of model quality and can be used to rank different input feature sets.

  18. 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

  19. Modeling of Reactor Kinetics and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Matthew Johnson; Scott Lucas; Pavel Tsvetkov

    2010-09-01

    In order to model a full fuel cycle in a nuclear reactor, it is necessary to simulate the short time-scale kinetic behavior of the reactor as well as the long time-scale dynamics that occur with fuel burnup. The former is modeled using the point kinetics equations, while the latter is modeled by coupling fuel burnup equations with the kinetics equations. When the equations are solved simultaneously with a nonlinear equation solver, the end result is a code with the unique capability of modeling transients at any time during a fuel cycle.

  20. Lipase catalyse glycerolysis for kinetic resolution of racemates.

    Science.gov (United States)

    Dlugy, C; Wolfson, A

    2007-09-01

    Candida antarctica lipase B catalyzed kinetic resolution of representative secondary alcohols, esters, and amine was successfully performed using triacetin or glycerol as solvents and acyl donor/acceptor. High conversions and enantioselectivities were achieved and the product was easily separated by simple extraction with diethyl ether.

  1. Kinetic Resolution of Aryl Alkenylcarbinols Catalyzed by Fc-PIP

    Institute of Scientific and Technical Information of China (English)

    胡斌; 孟萌; 姜山山; 邓卫平

    2012-01-01

    An effective kinetic resolution of a variety of aryl alkenylcarbinols catalyzed by nonenzymatic acyl transfer catalyst Fe-PIP was developed, affording corresponding unreacted alcohols in good to excellent ee value up to 99% and with selectivity factors up to 24.

  2. The kinetic resolution of enantiomers by means of enzymatic reactions

    NARCIS (Netherlands)

    Otto, P.P.H.L.

    1990-01-01

    For conversions involving a single enzyme, and under certain limiting conditions, the process of kinetic resolution can be described with five variables, which can be determined experimentally. Their quantitative relations have been derived. If any three of these variables are known the other two ca

  3. GAS PHASE MOLECULAR DYNAMICS: HIGH-RESOLUTION SPECTROSCOPIC PROBES OF CHEMICAL DYNAMICS.

    Energy Technology Data Exchange (ETDEWEB)

    HALL, G.E.

    2006-05-30

    This research is carried out as part of the Gas Phase Molecular Dynamics group program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopic tools are developed and applied to problems in chemical dynamics. Recent topics have included the state-resolved studies of collision-induced electronic energy transfer, dynamics of barrierless unimolecular reactions, and the kinetics and spectroscopy of transient species.

  4. Catalytic Kinetic Resolution of Saturated N-Heterocycles by Enantioselective Amidation with Chiral Hydroxamic Acids.

    Science.gov (United States)

    Kreituss, Imants; Bode, Jeffrey W

    2016-12-20

    the amine products in high enantiopurity. The success of this process relied on identification of two cleavable acyl groups alongside implementation of flow-chemistry techniques to ensure reusability of the resolving agents. The work discussed in this Account has laid foundations for new catalyst design as well as development of desymmetrization and dynamic kinetic resolution processes. In the meantime, as all the requisite reagents are commercially available, we hope that hydroxamic acid promoted acylative kinetic resolution will become a method of choice for preparation of saturated N-heterocycles in enantiopure form.

  5. Dynamics of catalytic resolution of 2-lithio-N-Boc-piperidine by ligand exchange.

    Science.gov (United States)

    Beng, Timothy K; Tyree, William S; Parker, Trent; Su, Chicheung; Williard, Paul G; Gawley, Robert E

    2012-10-10

    The dynamics of the racemization and catalytic and stoichiometric dynamic resolution of 2-lithio-N-Boc-piperidine (7) have been investigated. The kinetic order in tetramethylethylenediamine (TMEDA) for both racemization and resolution of the title compound and the kinetic orders in two resolving ligands have been determined. The catalytic dynamic resolution is second order in TMEDA and 0.5 and 0.265 order in chiral ligands 8 and 10, respectively. The X-ray crystal structure of ligand 10 shows it to be an octamer. Dynamic NMR studies of the resolution process were carried out. Some of the requirements for a successful catalytic dynamic resolution by ligand exchange have been identified.

  6. Stereoelectronic basis for the kinetic resolution of N-heterocycles with chiral acylating reagents.

    Science.gov (United States)

    Hsieh, Sheng-Ying; Wanner, Benedikt; Wheeler, Philip; Beauchemin, André M; Rovis, Tomislav; Bode, Jeffrey W

    2014-06-10

    The kinetic resolution of N-heterocycles with chiral acylating agents reveals a previously unrecognized stereoelectronic effect in amine acylation. Combined with a new achiral hydroxamate, this effect makes possible the resolution of various N-heterocycles by using easily prepared reagents. A transition-state model to rationalize the stereochemical outcome of this kinetic resolution is also proposed.

  7. Acceleration-induced nonlocality: kinetic memory versus dynamic memory

    OpenAIRE

    Chicone, C.; Mashhoon, B.

    2001-01-01

    The characteristics of the memory of accelerated motion in Minkowski spacetime are discussed within the framework of the nonlocal theory of accelerated observers. Two types of memory are distinguished: kinetic and dynamic. We show that only kinetic memory is acceptable, since dynamic memory leads to divergences for nonuniform accelerated motion.

  8. Optimization of dynamic measurement of receptor kinetics by wavelet denoising.

    Science.gov (United States)

    Alpert, Nathaniel M; Reilhac, Anthonin; Chio, Tat C; Selesnick, Ivan

    2006-04-01

    The most important technical limitation affecting dynamic measurements with PET is low signal-to-noise ratio (SNR). Several reports have suggested that wavelet processing of receptor kinetic data in the human brain can improve the SNR of parametric images of binding potential (BP). However, it is difficult to fully assess these reports because objective standards have not been developed to measure the tradeoff between accuracy (e.g. degradation of resolution) and precision. This paper employs a realistic simulation method that includes all major elements affecting image formation. The simulation was used to derive an ensemble of dynamic PET ligand (11C-raclopride) experiments that was subjected to wavelet processing. A method for optimizing wavelet denoising is presented and used to analyze the simulated experiments. Using optimized wavelet denoising, SNR of the four-dimensional PET data increased by about a factor of two and SNR of three-dimensional BP maps increased by about a factor of 1.5. Analysis of the difference between the processed and unprocessed means for the 4D concentration data showed that more than 80% of voxels in the ensemble mean of the wavelet processed data deviated by less than 3%. These results show that a 1.5x increase in SNR can be achieved with little degradation of resolution. This corresponds to injecting about twice the radioactivity, a maneuver that is not possible in human studies without saturating the PET camera and/or exposing the subject to more than permitted radioactivity.

  9. Kinetics and dynamics of DNA hybridization.

    Science.gov (United States)

    Yin, Yandong; Zhao, Xin Sheng

    2011-11-15

    DNA hybridization, wherein strands of DNA form duplex or larger hybrids through noncovalent, sequence-specific interactions, is one of the most fundamental processes in biology. Developing a better understanding of the kinetic and dynamic properties of DNA hybridization will thus help in the elucidation of molecular mechanisms involved in numerous biochemical processes. Moreover, because DNA hybridization has been widely adapted in biotechnology, its study is invaluable to the development of a range of commercially important processes. In this Account, we examine recent studies of the kinetics and dynamics of DNA hybridization, including (i) intramolecular collision of random coil, single-stranded DNA (ssDNA), (ii) nucleic acid hairpin folding, and (iii) considerations of DNA hybridization from both a global view and a detailed base-by-base view. We also examine the spontaneous single-base-pair flipping in duplex DNA because of its importance to both DNA hybridization and repair. Intramolecular collision of random coil ssDNA, with chemical relaxation times ranging from hundreds of nanoseconds to a few microseconds, is investigated both theoretically and experimentally. The first passage time theory of Szabo, Schulten, and Schulten, which determines the average reaction time of the intrachain collision, was tested. Although it was found to provide an acceptable approximation, a more sophisticated theoretical treatment is desirable. Nucleic acid hairpin folding has been extensively investigated as an important model system of DNA hybridization. The relaxation time of hairpin folding and unfolding strongly depends on the stem length, and it may range from hundreds of microseconds to hundreds of milliseconds. The traditional two-state model has been revised to a multistate model as a result of new experimental observations and theoretical study, and partially folded intermediate states have been introduced to the folding energy landscape. On the other hand, new

  10. 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...

  11. 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.

  12. Dynamic and kinetic properties of Al-Li melts

    Science.gov (United States)

    Kiselev, A. I.

    2008-12-01

    The dynamic and kinetic properties of Al-Li melts are calculated. The liquid phase of this system is shown to be characterized by three states with different ion distributions and different degrees of electron localization.

  13. Mesoscopic dynamics of copolymer melts : From density dynamics to external potential dynamics using nonlocal kinetic coupling

    NARCIS (Netherlands)

    Maurits, N.M; Fraaije, J.G E M

    1997-01-01

    In this paper we apply nonlocal kinetic coupling to the dynamic mean-field density functional method, which is derived from generalized time-dependent Ginzburg-Landau theory. The method is applied to the mesoscopic dynamics of copolymer melts, which was previously simulated using a local coupling ap

  14. Mesoscopic dynamics of copolymer melts : From density dynamics to external potential dynamics using nonlocal kinetic coupling

    NARCIS (Netherlands)

    Maurits, NM; Fraaije, JGEM

    1997-01-01

    In this paper we apply nonlocal kinetic coupling to the dynamic mean-field density functional method, which is derived from generalized time-dependent Ginzburg-Landau theory. The method is applied to the mesoscopic dynamics of copolymer melts, which was previously simulated using a local coupling ap

  15. High-resolution infrared flash kinetic spectroscopy of OH radicals

    Energy Technology Data Exchange (ETDEWEB)

    Schiffman, A.; Nelson, D.D. Jr.; Robinson, M.S.; Nesbitt, D.J. (Univ. of Colorado, Boulder (United States) National Inst. of Standards and Tech., Boulder, CO (United States))

    1991-04-04

    A high-resolution infrared flash kinetic spectrometer is used for time- and frequency-resolved studies of the OH radical. OH is produced by 193-nm excimer laser photolysis of HNO{sub 3}/buffer gas mixtures in a 100-cm flow tube and is probed via weak fractional absorption of light from a widely tunable (2.35-3.59 {mu}m) single-mode ({Delta}{nu} {le} 2 MHz) color center laser. The IR absorption technique allows fast ({le}10{sup {minus}6} s), sensitive (<10{sup 9} radicals/cm{sup 3} per quantum state) detection of OH and is designed to permit determination of absolute OH number densities. The spectrometer is used to measure rate constants for the reactions of OH with ethane (k{sub 1}), propane (k{sub 2}), n-butane (k{sub 3}), and isobutane (k{sub 4}). The reliability of these measurements is tested on a variety of rotational, spin-orbit, and {lambda}-doublet states, with several buffer gases, and over more than an order of magnitude of alkane concentrations. The resulting rate constants are, in units of 10{sup {minus}12} cm{sup 3} molecule{sup {minus}1} s{sup {minus}1}, k{sub 1} = 0.243 {plus minus} 0.012, k{sub 2} = 1.02 {plus minus} 0.05, k{sub 3} = 2.35 {plus minus} 0.08, and k{sub 4} = 2.11 {plus minus} 0.09. The rate constants for the ethane, n-butane, and isobutane reactions agree with some previous determinations but are found to be between 10% and 25% lower than values currently used in atmospheric modeling; it is recommended that these values be revised to reflect the lower rates from this study. Current models of atmospheric air flow based on these rate constants, as well as those previously accepted values, are found to be inconsistent with daily changes in observed atmospheric alkane concentrations.

  16. Nonlinear Kinetic Dynamics of Magnetized Weibel Instability

    CERN Document Server

    Palodhi, L; Pegoraro, F

    2010-01-01

    Kinetic numerical simulations of the evolution of the Weibel instability during the full nonlinear regime are presented. The formation of strong distortions in the electron distribution function resulting in formation of strong peaks in it and their influence on the resulting electrostatic waves are shown.

  17. Generic Dynamic Scaling in Kinetic Roughening

    OpenAIRE

    Ramasco, José J.; López, Juan M.; Rodríguez, Miguel A.

    2000-01-01

    We study the dynamic scaling hypothesis in invariant surface growth. We show that the existence of power-law scaling of the correlation functions (scale invariance) does not determine a unique dynamic scaling form of the correlation functions, which leads to the different anomalous forms of scaling recently observed in growth models. We derive all the existing forms of anomalous dynamic scaling from a new generic scaling ansatz. The different scaling forms are subclasses of this generic scali...

  18. Quintessence dynamics with two scalar fields and mixed kinetic terms

    CERN Document Server

    van de Bruck, Carsten

    2009-01-01

    The dynamical properties of a model of dark energy in which two scalar fields are coupled by a non-canonical kinetic term are studied. We show that overall the addition of the coupling has only minor effects on the dynamics of the two-field system for both potentials studied, even preserving many of the features of the assisted quintessence scenario. The coupling of the kinetic terms enlarges the regions of stability of the critical points. When the potential is of an additive form, we find the kinetic coupling has an interesting effect on the dynamics of the fields as they approach the inflationary attractor, with the result that the combined equation of state of the scalar fields can approach -1 during the transition from a matter dominated universe to the recent period of acceleration.

  19. 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.

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

    DEFF Research Database (Denmark)

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

    2001-01-01

    The modelling of catalytic reactions/reactors has undergone great improvements since the introduction of empirical power-law kinetics in chemical reaction engineering and micro-kinetic models based on insight into the nature of elementary steps have appeared for many reactions. However, recent...... of the dynamical behaviour of some catalytic systems and discuss the corresponding Limitations in existing models for catalytic reactions and reactors. Catalytic reactors operated in non-steady-state are becoming more frequent in industry. The additional efforts needed to accurately simulate these types...... of reactors are discussed. Finally, we discuss the role of computational fluid dynamics (CFD) as a tool for detailed simulation of catalytic reactors....

  1. Potential of enzymatic kinetic resolution using solid substrates suspension: improved yield, productivity, substrate concentration, and recovery

    Science.gov (United States)

    Wolff; van Asperen V; Straathof; Heijnen

    1999-03-01

    In the literature the enzymatic kinetic resolution of a suspension of a solid substrate has largely been treated as a conventional kinetic resolution of a fully dissolved substrate. In this paper it is shown that this type of kinetic resolution is different in several important aspects. Quantitative models are developed for two types of such suspension processes. These models are used to compare the merits of these processes with the conventional kinetic resolution process where fully dissolved substrate is used. In the suspension processes the liquid phase concentration of substrate enantiomer that should be converted can be kept close to the maximum value, i.e., the solubility, when process conditions are properly chosen, whereas in a conventional process this concentration gradually decreases. Calculations show that this leads to a productivity that is about 6-fold higher in the suspension processes. Also, for enzymes with a low enantioselectivity, a severalfold increase in yield of remaining enantiopure substrate is predicted compared to the conventional kinetic resolution of dissolved enantiomers. Other potential advantages of using suspension reactions are that the initial substrate concentration may be higher (up to 25% (w/w)) and that the desired remaining substrate may be recovered by simply filtering off the solid crystals. Experimental evidence that these merits can be exploited is only partly given, using the few available examples from the literature.

  2. 4-wave dynamics in kinetic wave turbulence

    CERN Document Server

    Chibbaro, Sergio; Rondoni, Lamberto

    2016-01-01

    A general Hamiltonian wave system with quartic resonances is considered, in the standard kinetic limit of a continuum of weakly interacting dispersive waves with random phases. The evolution equation for the multimode characteristic function $Z$ is obtained within an "interaction representation" and a perturbation expansion in the small nonlinearity parameter. A frequency renormalization is performed to remove linear terms that do not appear in the 3-wave case. Feynman-Wyld diagrams are used to average over phases, leading to a first order differential evolution equation for $Z$. A hierarchy of equations, analogous to the Boltzmann hierarchy for low density gases is derived, which preserves in time the property of random phases and amplitudes. This amounts to a general formalism for both the $N$-mode and the 1-mode PDF equations for 4-wave turbulent systems, suitable for numerical simulations and for investigating intermittency.

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

    DEFF Research Database (Denmark)

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

    2001-01-01

    The modelling of catalytic reactions/reactors has undergone great improvements since the introduction of empirical power-law kinetics in chemical reaction engineering and micro-kinetic models based on insight into the nature of elementary steps have appeared for many reactions. However, recent...... of the dynamical behaviour of some catalytic systems and discuss the corresponding Limitations in existing models for catalytic reactions and reactors. Catalytic reactors operated in non-steady-state are becoming more frequent in industry. The additional efforts needed to accurately simulate these types...... 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...

  4. 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...

  5. Fractional neutron point kinetics equations for nuclear reactor dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Espinosa-Paredes, Gilberto, E-mail: gepe@xanum.uam.mx [Area de Ingenieria en Recursos Energeticos, Universidad Autonoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, Mexico, D.F. 09340 (Mexico); Polo-Labarrios, Marco-A. [Area de Ingenieria en Recursos Energeticos, Universidad Autonoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, Mexico, D.F. 09340 (Mexico); Espinosa-Martinez, Erick-G. [Retorno Quebec 6, Col. Burgos de Cuernavaca 62580, Temixco, Mor. (Mexico); Valle-Gallegos, Edmundo del [Escuela Superior de Fisica y Matematicas, Instituto Politecnico Nacional, Av. Instituto Politecnico Nacional s/n, Col. San Pedro Zacatenco, Mexico, D.F. 07738 (Mexico)

    2011-02-15

    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.

  6. Kinetic energy from supernova feedback in high-resolution galaxy simulations

    CERN Document Server

    Simpson, Christine M; Hummels, Cameron; Ostriker, Jeremiah P

    2014-01-01

    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 feedback in high-resolution hydrodynamic simulations of galaxy formation. In idealized tests at varying background densities and resolutions, we show convergence in behavior between models with different initial kinetic energy fractions at low densities and/or at high resolutions. We find that in high density media ($\\gtrsim$ 50 cm$^{-3}$) with coarse resolution ($\\gtrsim 4$ pc per cell), results are sensitive to the initial fraction of kinetic energy due to the early rapid cooling of thermal energy. We describe and test a resolution dependent scheme for adjusting this fraction that approximately replicates our high-resolution tests. We apply the method to a prompt supernova feedback model, meant to mimic Type II supernovae, in a cosmological simulation of a $10^9$ M...

  7. Kinetic Simulations of Plasmoid Chain Dynamics

    CERN Document Server

    Markidis, Stefano; Lapenta, Giovanni; Divin, Andrey; Goldman, Martin; Newman, David; Laure, Erwin

    2013-01-01

    The dynamics of a plasmoid chain is studied with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The plasmoid chain forms by spontaneous magnetic reconnection: the tearing instability rapidly disrupts the initial current sheet generating several small-scale plasmoids, that rapidly grow in size coalescing and kinking. The plasmoid kink is mainly driven by the coalescence process. It is found that the presence of guide field strongly influences the evolution of the plasmoid chain. Without a guide field, a main reconnection site dominates and smaller reconnection regions are included in larger ones, leading to an hierarchical structure of the plasmoid-dominated current sheet. On the contrary in presence of a guide field, plasmoids have approximately the same size and the hierarchical structure does not emerge, a strong core magnetic field develops in the center of the plasmoid...

  8. 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.

  9. Kinetic resolution of oxazinones: rational exploration of chemical space through the design of experiments.

    Science.gov (United States)

    Renzi, Polyssena; Kronig, Christel; Carlone, Armando; Eröksüz, Serap; Berkessel, Albrecht; Bella, Marco

    2014-09-08

    The organocatalytic kinetic resolution of 4-substituted oxazinones has been optimised (selectivity factor S up to 98, chiral oxazinone ee values up to 99.6 % (1 a-g) and product ee values up to 90 % (3 a-g)) in a rational way by applying the Design of Experiments (DoE) approach.

  10. Kinetic resolution of racemic carboxylic acids through asymmetric protolactonization promoted by chiral phosphonous acid diester.

    Science.gov (United States)

    Sakuma, Masayuki; Sakakura, Akira; Ishihara, Kazuaki

    2013-06-07

    Chiral phosphonium salts induce the kinetic resolution of racemic α-substituted unsaturated carboxylic acids through asymmetric protolactonization. Both the lactones and the recovered carboxylic acids are obtained with high enantioselectivities and high S (= kfast/kslow) values. Asymmetric protolactonization also leads to the desymmetrization of achiral carboxylic acids. Notably, chiral phosphonous acid diester not only induced the enantioselectivity but also promoted protolactonization.

  11. Parallel Kinetic Resolution of Racemic Aldehydes by Use of Asymmetric Horner-Wadsworth-Emmons Reactions

    DEFF Research Database (Denmark)

    Pedersen, Torben Møller; Jensen, Jakob Feldthusen; Humble, Rikke Eva

    2000-01-01

    A racemic aldehyde can undergo parallel kinetic resolution (PKR) by simultaneous reaction with two different chiral phosphonates, differing either in the structure of the chiral auxiliary or in the structure of the phosphoryl group (i.e., one (E)- and one (Z)-selective reagent). This strategy all...

  12. Diastereoselective Hydrogenation and Kinetic Resolution of Imines Using Rhodium/Diphosphine Catalyzed Hydrogenation.

    NARCIS (Netherlands)

    Lensink, Cornelis; Vries, Johannes G. de

    1993-01-01

    Kinetic resolution of racemic α-methylbenzyl amine can be achieved with 98% ee. of the remaining amine at 70% conversion using the Rhodium/2S,4S-BDPP catalyzed asymmetric hydrogenation of imines. The same catalyst will hydrogenate optically pure α-methylbenzyl amines with a diastereoselectivity of u

  13. Estimating kinetic parameters of complex catalytic reactions using a curve resolution based method

    NARCIS (Netherlands)

    Cruz, S.C.; Rothenberg, G.; Westerhuis, J.A.; Smilde, A.K.

    2008-01-01

    A Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) based algorithm is used to extract kinetic parameters from on-line FT - NIR data of a series of Heck reactions between iodobenzene and n-butyl acrylate (NBA), measured at different temperatures with different catalysts. Four

  14. Kinetic resolution of alkyne-substituted quaternary oxindoles via copper catalysed azide-alkyne cycloadditions.

    Science.gov (United States)

    Brittain, William D G; Buckley, Benjamin R; Fossey, John S

    2015-12-18

    The synthesis and kinetic resolution of quaternary oxindoles through copper catalysed azide-alkyne cycloadditions is presented. Selectivity factors (s) up to 22.1 ± 0.5 are reported. Enantioenriched alkynes and triazoles were obtained in ≥80% enantiomeric excess (e.e.).

  15. 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.

  16. Integrated modeling methodology for microtubule dynamics and Taxol kinetics with experimentally identifiable parameters.

    Science.gov (United States)

    Zhao, He; Sokhansanj, Bahrad A

    2007-10-01

    Microtubule dynamics play a critical role in cell function and stress response, modulating mitosis, morphology, signaling, and transport. Drugs such as paclitaxel (Taxol) can impact tubulin polymerization and affect microtubule dynamics. While theoretical methods have been previously proposed to simulate microtubule dynamics, we develop a methodology here that can be used to compare model predictions with experimental data. Our model is a hybrid of (1) a simple two-state stochastic formulation of tubulin polymerization kinetics and (2) an equilibrium approximation for the chemical kinetics of Taxol drug binding to microtubule ends. Model parameters are biologically realistic, with values taken directly from experimental measurements. Model validation is conducted against published experimental data comparing optical measurements of microtubule dynamics in cultured cells under normal and Taxol-treated conditions. To compare model predictions with experimental data requires applying a "windowing" strategy on the spatiotemporal resolution of the simulation. From a biological perspective, this is consistent with interpreting the microtubule "pause" phenomenon as at least partially an artifact of spatiotemporal resolution limits on experimental measurement.

  17. Dramatic Substituent Effect on the CCL-catalyzed Kinetic Resolution of 1-Aryl-2,3-allenols

    Institute of Scientific and Technical Information of China (English)

    XU, Dai-Wang(徐代旺); LI, Zu-Yi(李祖义); MA, Sheng-Ming(麻生明)

    2004-01-01

    Optically active 1-aryl-2,3-allenols were obtained via CCL-mediated kinetic resolution of the racemic allenols. The substitution pattern of the aromatic ring, regarding to both the type of the substituent and its position on the aromatic ring, was found to be critical for the kinetic resolution of 1-aryl-2,3-allenols.

  18. Resolution of structural heterogeneity in dynamic crystallography.

    Science.gov (United States)

    Ren, Zhong; Chan, Peter W Y; Moffat, Keith; Pai, Emil F; Royer, William E; Šrajer, Vukica; Yang, Xiaojing

    2013-06-01

    Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.

  19. Stochastic kinetic models: Dynamic independence, modularity and graphs

    CERN Document Server

    Bowsher, Clive G

    2010-01-01

    The dynamic properties and independence structure of stochastic kinetic models (SKMs) are analyzed. An SKM is a highly multivariate jump process used to model chemical reaction networks, particularly those in biochemical and cellular systems. We identify SKM subprocesses with the corresponding counting processes and propose a directed, cyclic graph (the kinetic independence graph or KIG) that encodes the local independence structure of their conditional intensities. Given a partition $[A,D,B]$ of the vertices, the graphical separation $A\\perp B|D$ in the undirected KIG has an intuitive chemical interpretation and implies that $A$ is locally independent of $B$ given $A\\cup D$. It is proved that this separation also results in global independence of the internal histories of $A$ and $B$ conditional on a history of the jumps in $D$ which, under conditions we derive, corresponds to the internal history of $D$. The results enable mathematical definition of a modularization of an SKM using its implied dynamics. Gra...

  20. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-03-14

    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.

  2. Effect of temperature on Candida antartica lipase B activity in the kinetic resolution of acebutolol

    Science.gov (United States)

    Rajin, Mariani; Kamaruddin, A. H.

    2016-06-01

    Thermodynamic studies of free Candida antartica lipase B in kinetic resolution of acebutolol have been carried out to characterize the temperature effects towards enzyme stability and activity. A decreased in reaction rate was observed in temperature above 40oC. Thermodynamic studies on lipase deactivation exhibited a first-order kinetic pattern. The activation and deactivation energies were 39.63 kJ/mol and 54.90 kJ/mol, respectively. The enthalpy and entropy of the lipase deactivation were found to be 52.12 kJ/mol and -0.18 kJ/mol, respectively.

  3. Kinetic Energy-Based Temperature Computation in Non-Equilibrium Molecular Dynamics Simulation

    OpenAIRE

    Liu, Bin; Xu, Ran; He, Xiaoqiao

    2009-01-01

    The average kinetic energy is widely used to characterize temperature in molecular dynamics (MD) simulation. In this letter, the applicability of three types of average kinetic energy as measures of temperature is investigated, i.e., the total kinetic energy, kinetic energy without the centroid translation part, and thermal disturbance kinetic energy. Our MD simulations indicate that definitions of temperature based on the kinetic energy including rigid translational or rotational motion may ...

  4. Protein dynamics modulated electron transfer kinetics in early stage photosynthesis.

    Science.gov (United States)

    Kundu, Prasanta; Dua, Arti

    2013-01-28

    A recent experiment has probed the electron transfer kinetics in the early stage of photosynthesis in Rhodobacter sphaeroides for the reaction center of wild type and different mutants [Science 316, 747 (2007)]. By monitoring the changes in the transient absorption of the donor-acceptor pair at 280 and 930 nm, both of which show non-exponential temporal decay, the experiment has provided a strong evidence that the initial electron transfer kinetics is modulated by the dynamics of protein backbone. In this work, we present a model where the electron transfer kinetics of the donor-acceptor pair is described along the reaction coordinate associated with the distance fluctuations in a protein backbone. The stochastic evolution of the reaction coordinate is described in terms of a non-Markovian generalized Langevin equation with a memory kernel and Gaussian colored noise, both of which are completely described in terms of the microscopics of the protein normal modes. This model provides excellent fits to the transient absorption signals at 280 and 930 nm associated with protein distance fluctuations and protein dynamics modulated electron transfer reaction, respectively. In contrast to previous models, the present work explains the microscopic origins of the non-exponential decay of the transient absorption curve at 280 nm in terms of multiple time scales of relaxation of the protein normal modes. Dynamic disorder in the reaction pathway due to protein conformational fluctuations which occur on time scales slower than or comparable to the electron transfer kinetics explains the microscopic origin of the non-exponential nature of the transient absorption decay at 930 nm. The theoretical estimates for the relative driving force for five different mutants are in close agreement with the experimental estimates obtained using electrochemical measurements.

  5. Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.

    Science.gov (United States)

    Graziani, F R; Bauer, J D; Murillo, M S

    2014-09-01

    Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD

  6. Energy resolution and efficiency of phonon-mediated Kinetic Inductance Detectors for light detection

    OpenAIRE

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

  7. Use of a palladium(II)-catalyzed oxidative kinetic resolution in synthetic efforts toward bielschowskysin.

    Science.gov (United States)

    Meyer, Michael E; Phillips, John H; Ferreira, Eric M; Stoltz, Brian M

    2013-09-09

    Progress toward the cyclobutane core of bielshowskysin is reported. The core was thought to arise from a cyclopropane intermediate via a furan-mediated cyclopropane fragmentation, followed by a 1,4-Michael addition. The synthesis of the cyclopropane intermediate utilizes a Suzuki coupling reaction, an esterification with 2-diazoacetoacetic acid, and a copper catalyzed cyclopropanation. An alcohol intermediate within the synthetic route was obtained in high enantiopurity via a highly selective palladium(II)-catalyzed oxidative kinetic resolution (OKR).

  8. Direct Measurement of Single-Molecule DNA Hybridization Dynamics with Single-Base Resolution.

    Science.gov (United States)

    He, Gen; Li, Jie; Ci, Haina; Qi, Chuanmin; Guo, Xuefeng

    2016-07-25

    Herein, we report label-free detection of single-molecule DNA hybridization dynamics with single-base resolution. By using an electronic circuit based on point-decorated silicon nanowires as electrical probes, we directly record the folding/unfolding process of individual hairpin DNAs with sufficiently high signal-to-noise ratio and bandwidth. These measurements reveal two-level current oscillations with strong temperature dependence, enabling us to determine the thermodynamic and kinetic properties of hairpin DNA hybridization. More importantly, successive, stepwise increases and decreases in device conductance at low temperature on a microsecond timescale are successfully observed, indicating a base-by-base unfolding/folding process. The process demonstrates a kinetic zipper model for DNA hybridization/dehybridization at the single base-pair level. This measurement capability promises a label-free single-molecule approach to probe biomolecular interactions with fast dynamics.

  9. Agent dynamics in kinetic models of wealth exchange

    CERN Document Server

    Chatterjee, Arnab

    2010-01-01

    We study the dynamics of individual agents in some kinetic models of wealth exchange, particularly, the models with savings. For the model with uniform savings, agents perform simple random walks in the `"wealth space". On the other hand, we observe ballistic diffusion in the model with distributed savings. There is an associated skewness in the gain-loss distribution which explains the steady state behavior in such models. We find that in general an agent gains while interacting with an agent with a larger saving propensity.

  10. Dynamics of High-Resolution Networks

    DEFF Research Database (Denmark)

    Sekara, Vedran

    NETWORKS are everywhere. From the smallest confines of the cells within our bodies to the webs of social relations across the globe. Networks are not static, they constantly change, adapt, and evolve to suit new conditions. In order to understand the fundamental laws that govern networks we need...... 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...

  11. 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.

  12. Inflationary dynamics of kinetically-coupled gauge fields

    CERN Document Server

    Ferreira, Ricardo Z

    2014-01-01

    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 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 from the dark sector, generated perhaps before the coupling was turned on, to the visible sector. We also investigate wh...

  13. Kinetic modelling of runaway electrons in dynamic scenarios

    CERN Document Server

    Stahl, A; Papp, G; Landreman, M; Fülöp, T

    2016-01-01

    Improved understanding of runaway-electron formation and decay processes are of prime interest for the safe operation of large tokamaks, and the dynamics of the runaway electrons during dynamical scenarios such as disruptions are of particular concern. In this paper, we present kinetic modelling of scenarios with time-dependent plasma parameters; in particular, we investigate hot-tail runaway generation during a rapid drop in plasma temperature. With the goal of studying runaway-electron generation with a self-consistent electric-field evolution, we also discuss the implementation of a conservative collision operator and demonstrate its properties. An operator for avalanche runaway-electron generation, which takes the energy dependence of the scattering cross section and the runaway distribution into account, is investigated. We show that the simpler avalanche model of Rosenbluth & Putvinskii [Nucl. Fusion 37, 1355 (1997)] can give very inaccurate results for the avalanche growth rate (either lower or hig...

  14. Large Scale, High Resolution, Mantle Dynamics Modeling

    Science.gov (United States)

    Geenen, T.; Berg, A. V.; Spakman, W.

    2007-12-01

    To model the geodynamic evolution of plate convergence, subduction and collision and to allow for a connection to various types of observational data, geophysical, geodetical and geological, we developed a 4D (space-time) numerical mantle convection code. The model is based on a spherical 3D Eulerian fem model, with quadratic elements, on top of which we constructed a 3D Lagrangian particle in cell(PIC) method. We use the PIC method to transport material properties and to incorporate a viscoelastic rheology. Since capturing small scale processes associated with localization phenomena require a high resolution, we spend a considerable effort on implementing solvers suitable to solve for models with over 100 million degrees of freedom. We implemented Additive Schwartz type ILU based methods in combination with a Krylov solver, GMRES. However we found that for problems with over 500 thousend degrees of freedom the convergence of the solver degraded severely. This observation is known from the literature [Saad, 2003] and results from the local character of the ILU preconditioner resulting in a poor approximation of the inverse of A for large A. The size of A for which ILU is no longer usable depends on the condition of A and on the amount of fill in allowed for the ILU preconditioner. We found that for our problems with over 5×105 degrees of freedom convergence became to slow to solve the system within an acceptable amount of walltime, one minute, even when allowing for considerable amount of fill in. We also implemented MUMPS and found good scaling results for problems up to 107 degrees of freedom for up to 32 CPU¡¯s. For problems with over 100 million degrees of freedom we implemented Algebraic Multigrid type methods (AMG) from the ML library [Sala, 2006]. Since multigrid methods are most effective for single parameter problems, we rebuild our model to use the SIMPLE method in the Stokes solver [Patankar, 1980]. We present scaling results from these solvers for 3D

  15. STOCHASTIC KINETIC MODELS: DYNAMIC INDEPENDENCE, MODULARITY AND GRAPHS.

    Science.gov (United States)

    Bowsher, Clive G

    2010-08-01

    The dynamic properties and independence structure of stochastic kinetic models (SKMs) are analyzed. An SKM is a highly multivariate jump process used to model chemical reaction networks, particularly those in biochemical and cellular systems. We identify SKM subprocesses with the corresponding counting processes and propose a directed, cyclic graph (the kinetic independence graph or KIG) that encodes the local independence structure of their conditional intensities. Given a partition [A, D, B] of the vertices, the graphical separation A ⊥ B|D in the undirected KIG has an intuitive chemical interpretation and implies that A is locally independent of B given A ∪ D. It is proved that this separation also results in global independence of the internal histories of A and B conditional on a history of the jumps in D which, under conditions we derive, corresponds to the internal history of D. The results enable mathematical definition of a modularization of an SKM using its implied dynamics. Graphical decomposition methods are developed for the identification and efficient computation of nested modularizations. Application to an SKM of the red blood cell advances understanding of this biochemical system.

  16. Lipase-catalyzed kinetic resolution of (±)-1-(2-furyl) ethanol in nonaqueous media.

    Science.gov (United States)

    Devendran, Saravanan; Yadav, Ganapati D

    2014-06-01

    S-1-(2-Furyl) ethanol serves as an important chiral building block for the preparation of various natural products, fine chemicals, and is widely used in the chemical and pharmaceutical industries. In this work, lipase-catalyzed kinetic resolution of (R/S)-1-(2-furyl) ethanol using different acyl donors was investigated. Vinyl esters are good acyl donors vis-à-vis alkyl esters for kinetic resolution. Among them, vinyl acetate was found to be the best acyl donor. Different immobilized lipases such as Rhizomucor miehei lipase, Thermomyces lanuginosus lipase, and Candida antarctica lipase B were evaluated for this reaction, among which C. antarctica lipase B, immobilized on acrylic resin (Novozym 435), was found to be the best catalyst in n-heptane as solvent. The effect of various parameters was studied in a systematic manner. Maximum conversion of 47% and enantiomeric excess of the substrate (ees ) of 89% were obtained in 2 h using 5 mg of enzyme loading with an equimolar ratio of alcohol to vinyl acetate at 60 °C at a speed of 300 rpm in a batch reactor. From the analysis of progress curve and initial rate data, it was concluded that the reaction followed the ordered bi-bi mechanism with dead-end ester inhibition. Kinetic parameters were obtained by using nonlinear regression. This process is more economical, green, and easily scalable than the chemical processes.

  17. 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.

  18. Super-resolution optical microscopy of lipid plasma membrane dynamics.

    Science.gov (United States)

    Eggeling, Christian

    2015-01-01

    Plasma membrane dynamics are an important ruler of cellular activity, particularly through the interaction and diffusion dynamics of membrane-embedded proteins and lipids. FCS (fluorescence correlation spectroscopy) on an optical (confocal) microscope is a popular tool for investigating such dynamics. Unfortunately, its full applicability is constrained by the limited spatial resolution of a conventional optical microscope. The present chapter depicts the combination of optical super-resolution STED (stimulated emission depletion) microscopy with FCS, and why it is an important tool for investigating molecular membrane dynamics in living cells. Compared with conventional FCS, the STED-FCS approach demonstrates an improved possibility to distinguish free from anomalous molecular diffusion, and thus to give new insights into lipid-protein interactions and the traditional lipid 'raft' theory.

  19. Kinetic modelling of runaway electrons in dynamic scenarios

    Science.gov (United States)

    Stahl, A.; Embréus, O.; Papp, G.; Landreman, M.; Fülöp, T.

    2016-11-01

    Improved understanding of runaway-electron formation and decay processes are of prime interest for the safe operation of large tokamaks, and the dynamics of the runaway electrons during dynamical scenarios such as disruptions are of particular concern. In this paper, we present kinetic modelling of scenarios with time-dependent plasma parameters; in particular, we investigate hot-tail runaway generation during a rapid drop in plasma temperature. With the goal of studying runaway-electron generation with a self-consistent electric-field evolution, we also discuss the implementation of a collision operator that conserves momentum and energy and demonstrate its properties. An operator for avalanche runaway-electron generation, which takes the energy dependence of the scattering cross section and the runaway distribution into account, is investigated. We show that the simplified avalanche model of Rosenbluth and Putvinskii (1997 Nucl. Fusion 37 1355) can give inaccurate results for the avalanche growth rate (either lower or higher) for many parameters, especially when the average runaway energy is modest, such as during the initial phase of the avalanche multiplication. The developments presented pave the way for improved modelling of runaway-electron dynamics during disruptions or other dynamic events.

  20. 3.5D dynamic PET image reconstruction incorporating kinetics-based clusters.

    Science.gov (United States)

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

    2012-08-07

    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 and

  1. Origin of Kinetic Resolution of Hydroxy Esters through Catalytic Enantioselective Lactonization by Chiral Phosphoric Acids.

    Science.gov (United States)

    Changotra, Avtar; Sunoj, Raghavan B

    2016-08-05

    Kinetic resolution is a widely used strategy for separation and enrichment of enantiomers. Using density functional theory computations, the origin of how a chiral BINOL-phosphoric acid catalyzes the selective lactonization of one of the enantiomers of α-methyl γ-hydroxy ester is identified. In a stepwise mechanism, the stereocontrolling transition state for the addition of the hydroxyl group to the si face of the ester carbonyl in the case of the S isomer exhibits a network of more effective noncovalent interactions between the substrate and the chiral catalyst.

  2. 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.

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

    Science.gov (United States)

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

    2015-08-01

    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 cm2 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 cm2 silicon chip, and calibrated with optical pulses and X-rays. The detector features a noise resolution σE = 154 ± 7 eV and an (18 ± 2)% efficiency.

  4. Dynamic recrystallization behavior and kinetics of high strength steel

    Institute of Scientific and Technical Information of China (English)

    吴光亮; 周超洋; 刘新彬

    2016-01-01

    The dynamic recrystallization behavior of high strength steel during hot deformation was investigated. The hot compression test was conducted in the temperature range of 950−1150 °C under strain rates of 0.1, 1 and 5 s−1. It is observed that dynamic recrystallization (DRX) is the main flow softening mechanism and the flow stress increases with decreasing temperature and increasing strain rate. The relationship between material constants (Q, n, α and lnA) and strain is identified by the sixth order polynomial fit. The constitutive model is developed to predict the flow stress of the material incorporating the strain softening effect and verified. Moreover, the critical characteristics of DRX are extracted from the stress−strain curves under different deformation conditions by linear regression. The dynamic recrystallization volume fraction decreases with increasing strain rate at a constant temperature or decreasing deformation temperature under a constant strain rate. The kinetics of DRX increases with increasing deformation temperature or strain rate.

  5. Comparative kinetics of the snowball respect to other dynamical objects

    CERN Document Server

    Díaz, R A; Marin, F; Martínez, R; Diaz, Rodolfo A.; Gonzalez, Diego L.; Marin, Francisco

    2003-01-01

    We examine the kinetics of a snowball that is gaining mass while is rolling downhill. This dynamical system combines rotational effects with effects involving the variation of mass. In order to understand the consequences of both effects we compare its behavior with the one of some objects in which such effects are absent. Environmental conditions are also included. We conclude that the comparative velocity of the snowball is very sensitive to the hill profile and the retardation factors. We emphasize that the increase of mass (inertia), could surprisingly diminish the retardation effect due to the drag force. Additionally, when an exponential trajectory is assumed, the maximum velocity of the snowball can be reached at an intermediate step of the trip.

  6. High resolution, large dynamic range field map estimation

    Science.gov (United States)

    Dagher, Joseph; Reese, Timothy; Bilgin, Ali

    2013-01-01

    Purpose We present a theory and a corresponding method to compute high resolution field maps over a large dynamic range. Theory and Methods We derive a closed-form expression for the error in the field map value when computed from two echoes. We formulate an optimization problem to choose three echo times which result in a pair of maximally distinct error distributions. We use standard field mapping sequences at the prescribed echo times. We then design a corresponding estimation algorithm which takes advantage of the optimized echo times to disambiguate the field offset value. Results We validate our method using high resolution images of a phantom at 7T. The resulting field maps demonstrate robust mapping over both a large dynamic range, and in low SNR regions. We also present high resolution offset maps in vivo using both, GRE and MEGE sequences. Even though the proposed echo time spacings are larger than the well known phase aliasing cutoff, the resulting field maps exhibit a large dynamic range without the use of phase unwrapping or spatial regularization techniques. Conclusion We demonstrate a novel 3-echo field map estimation method which overcomes the traditional noise-dynamic range trade-off. PMID:23401245

  7. Upright, weight-bearing, dynamic-kinetic MRI of the spine: initial results.

    Science.gov (United States)

    Jinkins, J Randy; Dworkin, Jay S; Damadian, Raymond V

    2005-09-01

    The potential relative beneficial aspects of upright, weight-bearing (pMRI), dynamic-kinetic (kMRI) spinal imaging over that of recumbent MRI (rMRI) include the revelation of occult spinal disease dependent on true axial loading, the unmasking of kinetic-dependent spinal disease and the ability to scan the patient in the position of clinically relevant signs and symptoms. This imaging unit under study also demonstrated low claustrophobic potential and yielded comparatively high resolution images with little motion/magnetic susceptibility/chemical shift artifact. Overall, it was found that rMRI underestimated the presence and maximum degree of gravity-dependent spinal pathology and missed altogether pathology of a dynamic nature, factors that are optimally revealed with p/kMRI. Furthermore, p/kMRI enabled optimal linkage of the patient's clinical syndrome with the medical imaging abnormality responsible for the clinical presentation, thereby allowing for the first time an improvement at once in both imaging sensitivity and specificity.

  8. Upright, weight-bearing, dynamic-kinetic MRI of the spine: initial results

    Energy Technology Data Exchange (ETDEWEB)

    Jinkins, J. Randy [State University of New York, Department of Radiology, Downstate Medical Center, Brooklyn, NY (United States); Fonar Corporation, Melville, NY (United States); Dworkin, Jay S.; Damadian, Raymond V. [Fonar Corporation, Melville, NY (United States)

    2005-09-01

    The potential relative beneficial aspects of upright, weight-bearing (pMRI), dynamic-kinetic (kMRI) spinal imaging over that of recumbent MRI (rMRI) include the revelation of occult spinal disease dependent on true axial loading, the unmasking of kinetic-dependent spinal disease and the ability to scan the patient in the position of clinically relevant signs and symptoms. This imaging unit under study also demonstrated low claustrophobic potential and yielded comparatively high resolution images with little motion/magnetic susceptibility/chemical shift artifact. Overall, it was found that rMRI underestimated the presence and maximum degree of gravity-dependent spinal pathology and missed altogether pathology of a dynamic nature, factors that are optimally revealed with p/kMRI. Furthermore, p/kMRI enabled optimal linkage of the patient's clinical syndrome with the medical imaging abnormality responsible for the clinical presentation, thereby allowing for the first time an improvement at once in both imaging sensitivity and specificity. (orig.)

  9. Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics.

    Science.gov (United States)

    Zheng, Weihua; Andrec, Michael; Gallicchio, Emilio; Levy, Ronald M

    2009-08-27

    We present an approach to recover kinetics from a simplified protein folding model at different temperatures using the combined power of replica exchange (RE), a kinetic network, and effective stochastic dynamics. While RE simulations generate a large set of discrete states with the correct thermodynamics, kinetic information is lost due to the random exchange of temperatures. We show how we can recover the kinetics of a 2D continuous potential with an entropic barrier by using RE-generated discrete states as nodes of a kinetic network. By choosing the neighbors and the microscopic rates between the neighbors appropriately, the correct kinetics of the system can be recovered by running a kinetic simulation on the network. We fine-tune the parameters of the network by comparison with the effective drift velocities and diffusion coefficients of the system determined from short-time stochastic trajectories. One of the advantages of the kinetic network model is that the network can be built on a high-dimensional discretized state space, which can consist of multiple paths not consistent with a single reaction coordinate.

  10. New aspects of plasma sheet dynamics - MHD and kinetic theory

    Directory of Open Access Journals (Sweden)

    H. Wiechen

    Full Text Available Magnetic reconnection is a process of fundamental importance for the dynamics of the Earth's plasma sheet. In this context, the development of thin current sheets in the near-Earth plasma sheet is a topic of special interest because they could be a possible cause of microscopic fluctuations acting as collective non-idealness from a macroscopic point of view. Simulations of the near-Earth plasma sheet including boundary perturbations due to localized inflow through the northern (or southern plasma sheet boundary show developing thin current sheets in the near-Earth plasma sheet about 810 RE tailwards of the Earth. This location is largely independent from the localization of the perturbation. The second part of the paper deals with the problem of the macroscopic non-ideal consequences of microscopic fluctuations. A new model is presented that allows the quantitative calculation of macroscopic non-idealness without considering details of microscopic instabilities or turbulence. This model is only based on the assumption of a strongly fluctuating, mixing dynamics on microscopic scales in phase space. The result of this approach is an expression for anomalous non-idealness formally similar to the Krook resistivity but now describing the macroscopic consequences of collective microscopic fluctuations, not of collisions.

    Key words. Magnetospheric physics (plasma sheet · Space plasma physics (kinetic and MHD theory; magnetic reconnection

  11. Statistical theory for the kinetics and dynamics of roaming reactions.

    Science.gov (United States)

    Klippenstein, Stephen J; Georgievskii, Yuri; Harding, Lawrence B

    2011-12-22

    We present a statistical theory for the effect of roaming pathways on product branching fractions in both unimolecular and bimolecular reactions. The analysis employs a separation into three distinct steps: (i) the formation of weakly interacting fragments in the long-range/van der Waals region of the potential via either partial decomposition (for unimolecular reactants) or partial association (for bimolecular reactants), (ii) the roaming step, which involves the reorientation of the fragments from one region of the long-range potential to another, and (iii) the abstraction, addition, and/or decomposition from the long-range region to yield final products. The branching between the roaming induced channel(s) and other channels is obtained from a steady-state kinetic analysis for the two (or more) intermediates in the long-range region of the potential. This statistical theory for the roaming-induced product branching is illustrated through explicit comparisons with reduced dimension trajectory simulations for the decompositions of H(2)CO, CH(3)CHO, CH(3)OOH, and CH(3)CCH. These calculations employ high-accuracy analytic potentials obtained from fits to wide-ranging CASPT2 ab initio electronic structure calculations. The transition-state fluxes for the statistical theory calculations are obtained from generalizations of the variable reaction coordinate transition state theory approach. In each instance, at low energy the statistical analysis accurately reproduces the branching obtained from the trajectory simulations. At higher energies, e.g., above 1 kcal/mol, increasingly large discrepancies arise, apparently due to a dynamical biasing toward continued decomposition of the incipient molecular fragments (for unimolecular reactions). Overall, the statistical theory based kinetic analysis is found to provide a useful framework for interpreting the factors that determine the significance of roaming pathways in varying chemical environments.

  12. BioRef II—Neutron reflectometry with relaxed resolution for fast, kinetic measurements at HZB

    Science.gov (United States)

    Trapp, M.; Steitz, R.; Kreuzer, M.; Strobl, M.; Rose, M.; Dahint, R.

    2016-10-01

    We present an upgrade to the time-of-flight neutron reflectometer BioRef at the research reactor BER II of the Helmholtz-Zentrum Berlin für Materialien und Energie (HZB). Through the integration of an additional chopper into the existing setup, the available wavelength resolution is significantly extended. Now two distinct operation modes can be used: a high resolution mode with Δλ/λ ranging from 1% to 5%, which allows for the investigation of thick films up to 4000 Å, and a high flux mode with Δλ/λ = 7%-11%. In the high flux mode, reflectivity curves from 0.007 Å-1 to 0.2 Å-1 with three angular settings can be recorded in 7 min. For a single angular setting and its respective window in Q-space, a time resolution of even less than 4 min is reached. The different configurations are documented by respective measurements (a) on a Ni-Ti multilayer and (b) the swelling kinetics of a solid-supported phospholipid coating upon incubation in a polyelectrolyte solution.

  13. Characterization of dental composite curing kinetics using dynamic light scattering

    Science.gov (United States)

    Wells-Gray, Elaine M.; Kirkpatrick, Sean J.; Sakaguchi, Ron L.

    2009-02-01

    Polymer resin composites are a class of widely used restorative dental materials that undergo a complex polymerization curing process that has been the subject of substantial research. This study uses speckle correlation methods based on dynamic light scattering as a tool to monitor the rate and extent of dental composite polymerization during and after photo-curing. Thin disc-shaped samples (composite consisting of 50:50 BisGMA/TEGDMA resin, quartz silica filler particles, and camphorquinone as photo-initiator. A 633 nm HeNe laser beam was used to probe the top surface of the sample via a backscattered speckle pattern, while the bottom surface was illuminated with a halogen curing lamp (peak wavelength=470nm) to initiate the polymerization reaction. The speckle patterns were recorded with a CCD camera, and stored as a 'speckle cube' for post processing. Correlation values of the intensity fluctuation were calculated on a pixel-by-pixel basis for pairs of subsequent speckle images and then ensemble averaged. Results show a sharp decrease in correlation at the onset of curing, indicating a large amount of double bond conversion and movement within the composite. Correlation values then quickly increase, eventually reaching a plateau near unity, indicating cessation of molecular rearrangement. The kinetic behavior demonstrated by our correlation curves are in good agreement with curing data found in the literature, and demonstrate the usefulness of this technique for monitoring dental composite curing.

  14. Segmentation of dynamic PET images with kinetic spectral clustering

    Science.gov (United States)

    Mouysset, S.; Zbib, H.; Stute, S.; Girault, J. M.; Charara, J.; Noailles, J.; Chalon, S.; Buvat, I.; Tauber, C.

    2013-10-01

    Segmentation is often required for the analysis of dynamic positron emission tomography (PET) images. However, noise and low spatial resolution make it a difficult task and several supervised and unsupervised methods have been proposed in the literature to perform the segmentation based on semi-automatic clustering of the time activity curves of voxels. In this paper we propose a new method based on spectral clustering that does not require any prior information on the shape of clusters in the space in which they are identified. In our approach, the p-dimensional data, where p is the number of time frames, is first mapped into a high dimensional space and then clustering is performed in a low-dimensional space of the Laplacian matrix. An estimation of the bounds for the scale parameter involved in the spectral clustering is derived. The method is assessed using dynamic brain PET images simulated with GATE and results on real images are presented. We demonstrate the usefulness of the method and its superior performance over three other clustering methods from the literature. The proposed approach appears as a promising pre-processing tool before parametric map calculation or ROI-based quantification tasks.

  15. A high-resolution study of surfactant partitioning and kinetic limitations for two-component internally mixed aerosols

    Science.gov (United States)

    Suda, S. R.; Petters, M. D.

    2013-12-01

    Atmospheric aerosols serve as cloud condensation nuclei (CCN), altering cloud properties and ultimately affecting climate through their effect on the radiative balance. Aerosol CCN activity depends in part on aerosol composition and surfactant compounds are of particular interest because surfactants are enriched at the water/air interface, resulting in a radial concentration gradient within the aqueous droplet. Accurate treatment of the surfactant concentration gradient complicates the otherwise straightforward predictions of CCN activity for aerosols of known composition. To accurately evaluate predictions made by theory, laboratory studies investigating the relationship between critical supersaturation and dry diameter of particles that include surfactants require significant reduction in measurement uncertainty for both water-uptake and CCN measurements. Furthermore, uncertainties remain regarding kinetic limitations to surfactant partitioning that could result in deviation from predictions based on equilibrium thermodynamics. This study attempts to address some of these issues through high-resolution analysis of CCN activity of two-component mixed surfactant/non-surfactant aerosols at different internal mixing ratios performed with and without a water-uptake time delay to ascertain whether or not the observed effects are kinetically limited. We present new data for the aerosols consisting of 1) the ionic surfactant sodium dodecyl sulfate (SDS) with ammonium sulfate, 2) SDS with sodium chloride and 3) the strong non-ionic fluorosurfactant Zonyl with an organic proxy glucose. As a point of reference we also evaluated the mixture of ammonium sulfate with glucose. Aerosol activation diameters were determined using CCN analysis in conjunction with scanning mobility size classification and high sheath-to-aerosol flow ratios. This resulted in CCN-derived kappa values that could be determined within +/-5% relative error. To test whether dynamic surfactant partitioning

  16. 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.

  17. A Dynamical Resolution of the Sigma Term Puzzle

    CERN Document Server

    Ball, R D; Tigg, J; Ball, Richard D.; Forte, Stefano; Tigg, Jason

    1994-01-01

    We propose a resolution of the puzzle posed by the discrepancy between the pion-nucleon sigma term inferred from pion-nucleon scattering, and that deduced from baryon mass splittings using the Zweig rule. We show that there is a significant hypercharge-dependent dynamical contribution to baryon masses, not hitherto included in the analysis, which may be estimated using the scale Ward identity, and computed by solution of the Schwinger-Dyson equation for the quark self-energy. We find that the discrepancy is completely resolved without the need for any Zweig rule violation.

  18. 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.

  19. Acceleration of the KINETICS Integrated Dynamical/Chemical Computational Model Using MPI

    Science.gov (United States)

    Grossman, Max; Willacy, Karen; Allen, Mark

    2011-01-01

    Understanding the evolution of a planet's atmosphere not only provides a better theoretical understanding of planetary physics and the formation of planets, but also grants useful insight into Earth's own atmosphere. One of the tools used at JPL for the modeling of planetary atmospheres and protostellar disks is KINETICS. KINETICS can simulate years of complex dynamics and chemistry.

  20. Acceleration of the KINETICS Integrated Dynamical/Chemical Computational Model Using MPI

    Science.gov (United States)

    Grossman, Max; Willacy, Karen; Allen, Mark

    2011-01-01

    Understanding the evolution of a planet's atmosphere not only provides a better theoretical understanding of planetary physics and the formation of planets, but also grants useful insight into Earth's own atmosphere. One of the tools used at JPL for the modeling of planetary atmospheres and protostellar disks is KINETICS. KINETICS can simulate years of complex dynamics and chemistry.

  1. Exploring crystallization kinetics in natural rhyolitic melts using high resolution CT imagery of spherulites

    Science.gov (United States)

    Clow, T. W.; Befus, K. S.; Gardner, J. E.

    2014-12-01

    Little of our understanding of crystallization kinetics has been directly derived from studies of natural samples. We examine crystallization of rhyolitic melts by quantifying spherulite sizes and number densities in obsidian collected from Yellowstone caldera using high-resolution x-ray computed tomography (CT) imagery. Spherulites are spherical to ellipsoidal masses of intergrown alkali feldspar and quartz in a radiating, fibrous structure. They are thought to form in response to relatively rapid crystallization of melt in response to large amounts of undercooling. Recent research using compositional gradients that form outside of spherulites has suggested that they nucleate at 700 to 500 ˚C and their growth slows exponentially until it eventually ceases at ~400 ˚C. By quantifying spherulite textures, and using those temperature constraints, we derive new kinetic information regarding crystallization in natural rhyolitic systems. We find that spherulites range from 0.2 to 12.3 mm in diameter, and are 0.004 to 49.5 mm3 in volume. Such values generate number densities of 70 to 185 spherulites cm-3. Histograms of size display positively skewed distributions indicating small spherulites are far more abundant than larger ones. Those distributions imply nucleation rates change as a function of temperature. At higher temperatures where the melt is undercooled by 400-500 ˚C, nucleation is rare and growth is favored. With decreasing temperature, nucleation rates increase rapidly until cold enough temperatures are reached that diffusion limits crystallization and causes it to cease (undercoolings of ~650 ˚C). Assuming a cooling rate for the host obsidian of 10-5 ˚C s-1, then overall spherulite nucleation rates are 0.01 to 0.03 spherulites cm-3 hour-1.

  2. 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 its...... various initial concentrations of monomers. Distinct mathematical properties of the kinetics of the unknown reaction pathway are found. These properties are shown to restrict the kinetics to a single model that generalizes Oosawa's classical nucleation-polymerization model. The methods used here...

  3. Coarse Molecular Dynamics of a Peptide Fragment Free Energy, Kinetics, and Long-Time Dynamics Computations

    CERN Document Server

    Hummer, G; Hummer, Gerhard; Kevrekidis, Ioannis G.

    2002-01-01

    We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic and stochastic components of the peptide motion parametrized by an appropriate set of coarse variables. Techniques from traditional numerical analysis (Newton-Raphson, coarse projective integration) are thus enabled; these techniques help analyze important features of the free-energy landscape (coarse transition states, eigenvalues and eigenvectors, transition rates, etc.). Reverse integration of (irreversible) expected coarse variables backward in time can assist escape from free energy minima and trace low-dimensional free energy surfaces. To illustrate the ``coarse molecular dynamics'' approach, we combine multiple short (0.5-ps) replica simulations to map the free energy surface of the ``alanine dipeptide'' in water, and to determine the ~ 1/(1000 ps) rate of interconv...

  4. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    Energy Technology Data Exchange (ETDEWEB)

    Hall,G.E.; Sears, T.J.

    2009-04-03

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopy, augmented by theoretical and computational methods, is used to investigate the structure and collision dynamics of chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry. Applications and methods development are equally important experimental components of this work.

  5. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.

    Science.gov (United States)

    Votapka, Lane W; Amaro, Rommie E

    2015-10-01

    The kinetic rate constants of binding were estimated for four biochemically relevant molecular systems by a method that uses milestoning theory to combine Brownian dynamics simulations with more detailed molecular dynamics simulations. The rate constants found using this method agreed well with experimentally and theoretically obtained values. We predicted the association rate of a small charged molecule toward both a charged and an uncharged spherical receptor and verified the estimated value with Smoluchowski theory. We also calculated the kon rate constant for superoxide dismutase with its natural substrate, O2-, in a validation of a previous experiment using similar methods but with a number of important improvements. We also calculated the kon for a new system: the N-terminal domain of Troponin C with its natural substrate Ca2+. The kon calculated for the latter two systems closely resemble experimentally obtained values. This novel multiscale approach is computationally cheaper and more parallelizable when compared to other methods of similar accuracy. We anticipate that this methodology will be useful for predicting kinetic rate constants and for understanding the process of binding between a small molecule and a protein receptor.

  6. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.

    Directory of Open Access Journals (Sweden)

    Lane W Votapka

    2015-10-01

    Full Text Available The kinetic rate constants of binding were estimated for four biochemically relevant molecular systems by a method that uses milestoning theory to combine Brownian dynamics simulations with more detailed molecular dynamics simulations. The rate constants found using this method agreed well with experimentally and theoretically obtained values. We predicted the association rate of a small charged molecule toward both a charged and an uncharged spherical receptor and verified the estimated value with Smoluchowski theory. We also calculated the kon rate constant for superoxide dismutase with its natural substrate, O2-, in a validation of a previous experiment using similar methods but with a number of important improvements. We also calculated the kon for a new system: the N-terminal domain of Troponin C with its natural substrate Ca2+. The kon calculated for the latter two systems closely resemble experimentally obtained values. This novel multiscale approach is computationally cheaper and more parallelizable when compared to other methods of similar accuracy. We anticipate that this methodology will be useful for predicting kinetic rate constants and for understanding the process of binding between a small molecule and a protein receptor.

  7. 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.

  8. Image derived input functions for dynamic High Resolution Research Tomograph PET brain studies.

    Science.gov (United States)

    Mourik, Jurgen E M; van Velden, Floris H P; Lubberink, Mark; Kloet, Reina W; van Berckel, Bart N M; Lammertsma, Adriaan A; Boellaard, Ronald

    2008-12-01

    The High Resolution Research Tomograph (HRRT) is a dedicated human brain positron emission tomography (PET) scanner. The aim of the present study was to validate the use of image derived input functions (IDIF) as an alternative for arterial sampling for HRRT human brain studies. To this end, IDIFs were extracted from 3D ordinary Poisson ordered subsets expectation maximization (OP-OSEM) and reconstruction based partial volume corrected (PVC) OP-OSEM images. IDIFs, either derived directly from regions of interest or further calibrated using manual samples taken during scans, were evaluated for dynamic [(11)C]flumazenil data (n=6). Results obtained with IDIFs were compared with those obtained using blood sampler input functions (BSIF). These comparisons included areas under the curve (AUC) for peak (0-3.3 min) and tail (3.3-55.0 min). In addition, slope, intercept and Pearson's correlation coefficient of tracer kinetic analysis results based on IDIF and BSIF were calculated for each subject. Good peak AUC ratios (0.83+/-0.21) between IDIF and BSIF were found for calibrated IDIFs extracted from OP-OSEM images. This combination of IDIFs and images also provided good slope values (1.07+/-0.11). Improved resolution, as obtained with PVC OP-OSEM, changed AUC ratios to 1.14+/-0.35 and, for tracer kinetic analysis, slopes changed to 0.95+/-0.13. For all reconstructions, non-calibrated IDIFs gave poorer results (>61+/-34% higher slopes) compared with calibrated IDIFs. The results of this study indicate that the use of IDIFs, extracted from OP-OSEM or PVC OP-OSEM images, is feasible for dynamic HRRT data, thereby obviating the need for online arterial sampling.

  9. Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

    Science.gov (United States)

    Plattner, Nuria; Doerr, Stefan; de Fabritiis, Gianni; Noé, Frank

    2017-10-01

    Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.

  10. Dynamic bilateral contrast-enhanced MR imaging of the breast: trade-off between spatial and temporal resolution.

    Science.gov (United States)

    Kuhl, Christiane K; Schild, Hans H; Morakkabati, Nuschin

    2005-09-01

    To investigate prospectively the trade-off between temporal and spatial resolution in dynamic contrast material-enhanced bilateral magnetic resonance (MR) imaging of the breast. Informed consent and institutional review board approval were obtained. An intraindividual comparative study was performed in 30 patients (mean age, 53 years; age range, 27-70 years) with a total of 54 enhancing lesions (28 benign and 26 malignant) who underwent dynamic MR imaging of the breast twice, once with a standard dynamic protocol (256 x 256 matrix, 69 seconds per acquisition) and once on a separate day with a modified dynamic protocol (400 x 512 matrix, 116 seconds per acquisition). Systematic qualitative analysis of morphologic features and region-of-interest-based analysis of enhancement kinetics were performed. A statistically significant difference (generalized linear modeling) in enhancement rates of benign versus malignant lesions was lost when moving from the standard to the modified dynamic protocol. Kinetic information on signal intensity time course patterns was preserved. Delineation of lesion margins and internal architecture was clearly superior with the modified dynamic protocol, which allowed identification of lesion features associated with high positive predictive value or high negative predictive value for breast cancer. Ten benign lesions classified as Breast Imaging Reporting and Data System (BI-RADS) category 3 with the standard protocol were correctly downgraded to BI-RADS category 2 with the modified protocol owing to visualization of internal septations. Thirteen malignant lesions categorized as BI-RADS category 3 or 4 with the standard protocol were correctly upgraded to BI-RADS category 4 or 5 with the modified protocol owing to visualization of spicules or rim enhancement. Receiver operating characteristic analysis revealed a significantly larger area under the curve for results obtained with the modified dynamic protocol. Increased spatial resolution

  11. 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.

  12. High-resolution hybrid simulations of kinetic plasma turbulence at proton scales

    CERN Document Server

    Franci, Luca; Matteini, Lorenzo; Verdini, Andrea; Hellinger, Petr

    2015-01-01

    We investigate properties of plasma turbulence from magneto-hydrodynamic (MHD) to sub-ion scales by means of two-dimensional, high-resolution hybrid particle-in-cell simulations. We impose an initial ambient magnetic field, perpendicular to the simulation box, and we add a spectrum of large-scale magnetic and kinetic fluctuations, with energy equipartition and vanishing correlation. Once the turbulence is fully developed, we observe a MHD inertial range, where the spectra of the perpendicular magnetic field and the perpendicular proton bulk velocity fluctuations exhibit power-law scaling with spectral indices of -5/3 and -3/2, respectively. This behavior is extended over a full decade in wavevectors and is very stable in time. A transition is observed around proton scales. At sub-ion scales, both spectra steepen, with the former still following a power law with a spectral index of ~-3. A -2.8 slope is observed in the density and parallel magnetic fluctuations, highlighting the presence of compressive effects ...

  13. High-Resolution Force Balance Analyses of Tidewater Glacier Dynamics

    Science.gov (United States)

    Enderlin, E. M.; Hamilton, G. S.; O'Neel, S.

    2015-12-01

    Changes in glacier velocity, thickness, and terminus position have been used to infer the dynamic response of tidewater glaciers to environmental perturbations, yet few analyses have attempted to quantify the associated variations in the glacier force balance. Where repeat high-resolution ice thickness and velocity estimates are available, force balance time series can be constructed to investigate the redistribution of driving and resistive forces associated with changes in terminus position. Comparative force balance analyses may, therefore, help us understand the variable dynamic response observed for glaciers in close proximity to each other. Here we construct force balance time series for Helheim Glacier, SE Greenland, and Columbia Glacier, SE Alaska, to investigate differences in dynamic sensitivity to terminus position change. The analysis relies on in situ and remotely sensed observations of ice thickness, velocity, and terminus position. Ice thickness time series are obtained from stereo satellite image-derived surface elevation and continuity-derived bed elevations that are constrained by airborne radar observations. Surface velocity time series are obtained from interferometric synthetic aperture radar (InSAR) observations. Approximately daily terminus positions are from a combination of satellite images and terrestrial time-lapse photographs. Helheim and Columbia glaciers are two of the best-studied Arctic tidewater glaciers with comprehensive high-resolution observational time series, yet we find that bed elevation uncertainties and poorly-constrained stress-coupling length estimates still hinder the analysis of spatial and temporal force balance variations. Here we use a new observationally-based method to estimate the stress-coupling length which successfully reduces noise in the derived force balance but preserves spatial variations that can be over-smoothed when estimating the stress-coupling length as a scalar function of the ice thickness

  14. High resolution dynamical mapping of social interactions with active RFID

    CERN Document Server

    Barrat, Alain; Colizza, Vittoria; Pinton, Jean-Francois; Broeck, Wouter Van den; Vespignani, Alessandro

    2008-01-01

    In this paper we present an experimental framework to gather data on face-to-face social interactions between individuals, with a high spatial and temporal resolution. We use active Radio Frequency Identification (RFID) devices that assess contacts with one another by exchanging low-power radio packets. When individuals wear the beacons as a badge, a persistent radio contact between the RFID devices can be used as a proxy for a social interaction between individuals. We present the results of a pilot study %recently performed during a conference, and a subsequent preliminary data analysis, that provides an assessment of our method and highlights its versatility and applicability in many areas concerned with human dynamics.

  15. 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.

  16. 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.

  17. Multiscale dynamics based on kinetic simulation of collisionless magnetic reconnection

    Science.gov (United States)

    Fujimoto, Keizo; Takamoto, Makoto

    2016-07-01

    Magnetic reconnection is a natural energy converter which allows explosive energy release of the magnetic field energy into plasma kinetic energy. The reconnection processes inherently involve multi-scale process. The breaking of the field lines takes place predominantly in a small region called the diffusion region formed near the x-line, while the fast plasma jets resulting from reconnection extend to a distance far beyond the ion kinetic scales from the x-line. There has been a significant gap in understanding of macro-scale and micro-scale processes. The macro-scale model of reconnection has been developed using the magnetohydrodynamics (MHD) equations, while the micro-scale processes around the x-line have been based on kinetic equations including the ion and electron inertia. The problem is that these two kinds of model have significant discrepancies. It has been believed without any guarantee that the microscopic model near the x-line would connect to the macroscopic model far downstream of the x-line. In order to bridge the gap between the macro and micro-scale processes, we have performed large-scale particle-in-cell simulations with the adaptive mesh refinement. The simulation results suggest that the microscopic processes around the x-line do not connect to the previous MHD model even in the region far downstream of the x-line. The slow mode shocks and the associated plasma acceleration do not appear at the exhaust boundary of kinetic reconnection. Instead, the ions are accelerated due to the Speiser motion in the current layer extending to a distance beyond the kinetic scales. The different acceleration mechanisms between the ions and electrons lead to the Hall current system in broad area of the exhaust. Therefore, the previous MHD model could be inappropriate for collisionless magnetic reconnection. Ref. K. Fujimoto & M. Takamoto, Phys. Plasmas, 23, 012903 (2016).

  18. Kinetic Resolution of 2-Chloro-1-(3,4-dichlorophenyl)ethanol by Lipase-Catalyzed Transesterification

    Institute of Scientific and Technical Information of China (English)

    WANG Ming-Hui; LI Ya-Feng; LIU Yong-Jun; ZHANG Shu-Sheng

    2007-01-01

    Kinetic resolution of racemic 2-chloro-l-(3,4-dichlorophenyl)ethanol was performed by free Alcaligene sp. lipase-catalyzed irreversible transesterification affording the (R)-isomer with≥95% ee and the (S)-isomer with ≥90% ee. The activity of lipase Alcaligene sp. strongly depends on the basicity of the reaction system, and an organic base such as triethylamine can enhance the activity of the lipase and enantioselectivity markedly.

  19. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    Energy Technology Data Exchange (ETDEWEB)

    Hall, G.E.

    2011-05-31

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

  20. 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.

  1. Wentzel-Kramers-Brillouin Approximation for Dynamic Systems with Kinetic Coupling in Entangled State Representations

    Institute of Scientific and Technical Information of China (English)

    范洪义

    2002-01-01

    We study the Wentzel-Kramers-Brillouin (WKB) approximation for dynamic systems with kinetic couplings inentangled state representations. The result shows that the kinetic coupling will affect the position of classicalturning points where the condition of using the WKB approximation breaks down. The modified WKB approx-imation formula is derived in the entangled state representation, for example, the common eigenvector of therelative coordinate and the total momentum of two particles. The corresponding Bohr-Sommerfeld quantizationrule is also derived.

  2. Emergence of Dynamic Cooperativity in the Stochastic Kinetics of Fluctuating Enzymes

    CERN Document Server

    Kumar, Ashutosh; Nandi, Mintu; Dua, Arti

    2016-01-01

    Dynamic cooperativity 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 cooperativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative cooperativity. For fewer enzymes, dynamic cooperativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, how...

  3. Collective relaxation dynamics and crystallization kinetics of the amorphous Biclotymol antiseptic.

    Science.gov (United States)

    Tripathi, Pragya; Romanini, Michela; Tamarit, Josep Lluis; Macovez, Roberto

    2015-11-10

    We employ dielectric spectroscopy to monitor the relaxation dynamics and crystallization kinetics of the Biclotymol antiseptic in its amorphous phase. The glass transition temperature of the material as determined by dielectric spectroscopy is Tg = 290 ± 1K. The primary (α) relaxation dynamics is observed to follow a Vogel-Fulcher-Tammann temperature dependence, with a kinetic fragility index m = 86 ± 13, which classifies Biclotymol as a relatively fragile glass former. A secondary relaxation is also observed, corresponding to an intramolecular dynamic process of the non-rigid Biclotymol molecule. The crystallization kinetics, measured at four different temperatures above the glass transition temperature, follows an Avrami behavior with exponent virtually equal to n = 2, indicating one-dimensional crystallization into needle-like crystallites, as experimentally observed, with a time-constant nucleation rate. The activation barrier for crystallization is found to be Ea = 115 ± 22 kJ mol(-1).

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

    Science.gov (United States)

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

    2016-08-28

    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.

  5. 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.

  6. Extracting Realistic Kinetics of Rare Activated Processes from Accelerated Molecular Dynamics Using Kramers' Theory.

    Science.gov (United States)

    Doshi, Urmi; Hamelberg, Donald

    2011-03-08

    The cis-trans isomerization of peptide bonds is very slow, occurring in hundreds of seconds. Kinetic studies of such processes using straightforward molecular dynamics are currently not possible. Here, we use Kramers' rate theory in the high friction regime in combination with accelerated molecular dynamics in explicit solvent to successfully retrieve the normal rate of cis to trans switching in the glycyl-prolyl dipeptide. Our approach bypasses the time-reweighting problem of the hyperdynamics scheme, wherein the addition of the bias potential alters the transition state regions and avoids an accurate estimation of kinetics. By performing accelerated molecular dynamics at a few different levels of acceleration, the rate of isomerization is enhanced as much as 10(10) to 10(11) times. Remarkably, the normal rates obtained by simply extrapolating to zero bias are within an order of experimental estimates. This provides validation from a kinetic standpoint of the ω torsional parameters of the AMBER force field that were recently revised by matching to experimentally measured equilibrium properties. We also provide a comparative analysis of the performance of the widely used water models, i.e., TIP3P and SPC/E, in estimating the kinetics of cis-trans isomerization. Furthermore, we show that the dynamic properties of bulk water can be corrected by adjusting the collision frequency in a Langevin thermostat, which then allows for better reproduction of cis-trans isomerization kinetics and a closer agreement of rates between experiments and simulations.

  7. 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

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

    Science.gov (United States)

    Breit, Marc; Netzer, Michael; Weinberger, Klaus M; Baumgartner, Christian

    2015-08-01

    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 modeling approach demonstrates high potential for dynamic biomarker identification and the investigation of kinetic mechanisms in disease or pharmacodynamics studies using MS data from longitudinal cohort studies.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    Paula S Nieto

    Full Text Available 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.

  11. Emergent kinetic constraints, ergodicity breaking, and cooperative dynamics in noisy quantum systems

    Science.gov (United States)

    Everest, B.; Marcuzzi, M.; Garrahan, J. P.; Lesanovsky, I.

    2016-11-01

    Kinetically constrained spin systems play an important role in understanding key properties of the dynamics of slowly relaxing materials, such as glasses. Recent experimental studies have revealed that manifest kinetic constraints govern the evolution of strongly interacting gases of highly excited atoms in a noisy environment. Motivated by this development we explore which types of kinetically constrained dynamics can generally emerge in quantum spin systems subject to strong noise and show how, in this framework, constraints are accompanied by conservation laws. We discuss an experimentally realizable case of a lattice gas, where the interplay between those and the geometry of the lattice leads to collective behavior and time-scale separation even at infinite temperature. This is in contrast to models of glass-forming substances which typically rely on low temperatures and the consequent suppression of thermal activation.

  12. 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.

  13. Determination of thermal inactivation kinetics of Listeria monocytogenes in chicken meat by isothermal and dynamic methods

    Science.gov (United States)

    The objective of this research is to determine the thermal inactivation kinetics of Listeria monocytogenes in chicken breast meat using both isothermal and dynamic conditions. A four-strain cocktail of L. monocytogenes was inoculated to chicken breast meat. Isothermal studies were performed by sub...

  14. Kinetic study of butanol production from various sugars by Clostridium acetobutylicum using a dynamic model

    NARCIS (Netherlands)

    Raganati, Francesca; Procentese, Alessandra; Olivieri, Giuseppe; Götz, Peter; Salatino, Piero; Marzocchella, Antonio

    2015-01-01

    This paper presents a kinetic dynamic model of acetone-butanol-ethanol production by Clostridium acetobutylicum DSM 792 developed with the biochemical networks simulator COPASI. This model is an evolution of previous models described in the literature, updated by including various mono-, di-,

  15. 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.

  16. Gelatinisation kinetics of corn and chickpea starches using DSC, RVA, and dynamic rheometry

    Science.gov (United States)

    The gelatinisation kinetics (non-isothermal) of corn and chickpea starches at different heating rates were calculated using differential scanning calorimetry (DSC), rapid visco analyser (RVA), and oscillatory dynamic rheometry. The data obtained from the DSC thermogram and the RVA profiles were fitt...

  17. Kinetic Cooperativity, Loop Dynamics, and Allostery from NMR and MD simulations

    Science.gov (United States)

    Bruschweiler, Rafael

    The hallmark of glucokinase (GCK), which catalyzes the phosphorylation of glucose during glycolysis, is its kinetic cooperativity whose understanding at atomic detail has remained open since its discovery over 40 years ago. I will discuss how the origin of kinetic cooperativity is rooted in intramolecular protein dynamics using NMR relaxation data of 17 isoleucines distributed over all parts of GCK. Residues of glucose-free GCK located in the small domain display a distinct exchange behavior involving multiple conformers that are substantially populated, whereas in the glucose-bound form these dynamic processes are quenched. The conformational exchange process directly competes with the enzymatic turnover at physiological glucose concentrations, thereby generating the sigmoidal rate dependence that defines kinetic cooperativity. The flexible nature of protein loops and the timescales of their dynamics are critical for many biologically important events at the molecular level, such as protein interaction and recognition processes. Based on a library of proteins, rules about loop dynamics in terms of amplitude and timescales can be derived using molecular dynamics (MD) simulations and NMR data. These rules have been implemented in the new web server ToeLoop (for Timescales Of Every Loop) that permits the prediction of loop dynamics based on an average 3D protein structure (http://spin.ccic.ohio-state.edu/index.php/loop/index).

  18. Watching coherent molecular structural dynamics during photoreaction: beyond kinetic description

    CERN Document Server

    Lemke, Henrik T; Hartsock, Robert; van Driel, Tim Brandt; Chollet, Matthieu; Glownia, J M; Song, Sanghoon; Zhu, Diling; Pace, Elisabetta; Nielsen, Martin M; Benfatto, Maurizio; Gaffney, Kelly J; Collet, Eric; Cammarata, Marco

    2015-01-01

    A deep understanding of molecular photo-transformations occurring is challenging because of the complex interaction between electronic and nuclear structure. The initially excited electronic energy dissipates into electronic and structural reconfigurations often in less than a billionth of a second. Molecular dynamics induced by photoexcitation have been very successfully studied with femtosecond optical spectroscopies, but electronic and nuclear dynamics are often very difficult to disentangle. X-ray based spectroscopies can reduce the ambiguity between theoretical models and experimental data, but it is only with the recent development of bright ultrafast X-ray sources, that key information during transient molecular processes can be obtained on their intrinsic timescale. We use Free Electron Laser (FEL) based time-resolved X-ray Absorption Near Edge Structure (XANES) measurements around the Iron K-edge of a spin crossover prototypical compound. We reveal its transformation from the ligand-located electroni...

  19. Low-Temperature Kinetics and Dynamics with Coulomb Crystals

    Science.gov (United States)

    Heazlewood, Brianna R.; Softley, Timothy P.

    2015-04-01

    Coulomb crystals-as a source of translationally cold, highly localized ions-are being increasingly utilized in the investigation of ion-molecule reaction dynamics in the cold regime. To develop a fundamental understanding of ion-molecule reactions, and to challenge existing models that describe the rates, product branching ratios, and temperature dependence of such processes, investigators need to exercise full control over the experimental reaction parameters. This requires not only state selection of the reactants, but also control over the collision process (e.g., the collisional energy and angular momentum) and state-selective product detection. The combination of Coulomb crystals in ion traps with cold neutral-molecule sources is enabling the measurement of state-selective reaction rates in a diverse range of systems. With the development of appropriate product detection techniques, we are moving toward the ultimate goal of examining low-energy, state-to-state ion-molecule reaction dynamics.

  20. 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

  1. Kinetic theories for spin models for cooperative relaxation dynamics

    Science.gov (United States)

    Pitts, Steven Jerome

    The facilitated kinetic Ising models with asymmetric spin flip constraints introduced by Jackle and co-workers [J. Jackle, S. Eisinger, Z. Phys. B 84, 115 (1991); J. Reiter, F. Mauch, J. Jackle, Physica A 184, 458 (1992)] exhibit complex relaxation behavior in their associated spin density time correlation functions. This includes the growth of relaxation times over many orders of magnitude when the thermodynamic control parameter is varied, and, in some cases, ergodic-nonergodic transitions. Relaxation equations for the time dependence of the spin density autocorrelation function for a set of these models are developed that relate this autocorrelation function to the irreducible memory function of Kawasaki [K. Kawasaki, Physica A 215, 61 (1995)] using a novel diagrammatic series approach. It is shown that the irreducible memory function in a theory of the relaxation of an autocorrelation function in a Markov model with detailed balance plays the same role as the part of the memory function approximated by a polynomial function of the autocorrelation function with positive coefficients in schematic simple mode coupling theories for supercooled liquids [W. Gotze, in Liquids, Freezing and the Glass Transition, D. Levesque, J. P. Hansen, J. Zinn-Justin eds., 287 (North Holland, New York, 1991)]. Sets of diagrams in the series for the irreducible memory function are summed which lead to approximations of this type. The behavior of these approximations is compared with known results from previous analytical calculations and from numerical simulations. For the simplest one dimensional model, relaxation equations that are closely related to schematic extended mode coupling theories [W. Gotze, ibid] are also derived using the diagrammatic series. Comparison of the results of these approximate theories with simulation data shows that these theories improve significantly on the results of the theories of the simple schematic mode coupling theory type. The potential

  2. On the origins of kinetic resolution of cyclohexane-1,2-diols through stereoselective acylation by chiral tetrapeptides.

    Science.gov (United States)

    Shinisha, C B; Sunoj, Raghavan B

    2009-08-06

    The relative energies of cyclohexane-1,2-diols and chiral tetrapeptide (2 (Boc) or 3 (Moc)) complexes calculated using DFT indicate a thermodynamic preference for chiral recognition toward (1R,2R)(e,e)-alpha isomer. The barrier for stereoselective acyl transfer is identified as lower for trans-(1R,2R)-cyclohexane-1,2-diol, leading to the kinetic resolution (KR) of trans-(1S,2S)-cyclohexane-1,2-diol. The prediction is in concert with the reported experiments for trans-diols, while that for hitherto unknown cis-diol demands experimental verification. It is proposed that desymmetrization would enable the resolution of cis-(1R,2S)-2-hydroxycyclohexyl acetate.

  3. High-resolution kinetics and modeling of hydrogen peroxide degradation in live cells

    DEFF Research Database (Denmark)

    Altintas, Ali; Davidsen, Kristian; Garde, Christian

    2016-01-01

    - and intra-cellular peroxide we have developed a mathematical model that describes two distinct kinetic processes, an initial rapid degradation in the first 10–20 min followed by a slower process. Using this model, a qualitative comparison allowed us to assign the dependence of temporal events to genetic...

  4. Kinetic theory and quasilinear theories of jet dynamics

    CERN Document Server

    Bouchet, F; Tangarife, T

    2016-01-01

    We review progress that has been made to constructa theory for the jet formation and maintenance in planetary atmospheres. The theory is built in the regime where velocityfluctuations around the base jet are very small compared to the zonaljet velocity itself. Such situations are frequent in many naturaljets, for instance in the atmosphere of outer planets, the most prominentexample being probably Jupiter's troposphere jets. As discussed inother chapters of this book, fluctuations close to Jupiter zonaljets are smaller than the zonal jets themselves. In such a regime, it is natural and often justified to treat the non-zonalpart of the dynamics with a quasi-linear approximation: at leadingorder the dynamics of the non-zonal flow is described by theequation linearized close to the quasi-stationary zonal jets. The theory, based on a multi-scale method called stochastic averaging, share similarities with Stochastic Structural Stability Theory (S3T) and with second order closure(CE2), also discussed in other chapt...

  5. Dynamic Model of Heat Inactivation Kinetics for Bacterial Adaptation▿

    Science.gov (United States)

    Corradini, Maria G.; Peleg, Micha

    2009-01-01

    The Weibullian-log logistic (WeLL) inactivation model was modified to account for heat adaptation by introducing a logistic adaptation factor, which rendered its “rate parameter” a function of both temperature and heating rate. The resulting model is consistent with the observation that adaptation is primarily noticeable in slow heat processes in which the cells are exposed to sublethal temperatures for a sufficiently long time. Dynamic survival patterns generated with the proposed model were in general agreement with those of Escherichia coli and Listeria monocytogenes as reported in the literature. Although the modified model's rate equation has a cumbersome appearance, especially for thermal processes having a variable heating rate, it can be solved numerically with commercial mathematical software. The dynamic model has five survival/adaptation parameters whose determination will require a large experimental database. However, with assumed or estimated parameter values, the model can simulate survival patterns of adapting pathogens in cooked foods that can be used in risk assessment and the establishment of safe preparation conditions. PMID:19201963

  6. Quantitative nucleation and growth kinetics of gold nanoparticles via model-assisted dynamic spectroscopic approach.

    Science.gov (United States)

    Zhou, Yao; Wang, Huixuan; Lin, Wenshuang; Lin, Liqin; Gao, Yixian; Yang, Feng; Du, Mingming; Fang, Weiping; Huang, Jiale; Sun, Daohua; Li, Qingbiao

    2013-10-01

    Lacking of quantitative experimental data and/or kinetic models that could mathematically depict the redox chemistry and the crystallization issue, bottom-to-up formation kinetics of gold nanoparticles (GNPs) remains a challenge. We measured the dynamic regime of GNPs synthesized by l-ascorbic acid (representing a chemical approach) and/or foliar aqueous extract (a biogenic approach) via in situ spectroscopic characterization and established a redox-crystallization model which allows quantitative and separate parameterization of the nucleation and growth processes. The main results were simplified as the following aspects: (I) an efficient approach, i.e., the dynamic in situ spectroscopic characterization assisted with the redox-crystallization model, was established for quantitative analysis of the overall formation kinetics of GNPs in solution; (II) formation of GNPs by the chemical and the biogenic approaches experienced a slow nucleation stage followed by a growth stage which behaved as a mixed-order reaction, and different from the chemical approach, the biogenic method involved heterogeneous nucleation; (III) also, biosynthesis of flaky GNPs was a kinetic-controlled process favored by relatively slow redox chemistry; and (IV) though GNPs formation consists of two aspects, namely the redox chemistry and the crystallization issue, the latter was the rate-determining event that controls the dynamic regime of the whole physicochemical process.

  7. Cosmological dynamics of scalar fields with kinetic corrections: Beyond the exponential potential

    CERN Document Server

    Dutta, Jibitesh; Tamanini, Nicola

    2016-01-01

    We expand the dynamical systems investigation of cosmological scalar fields characterised by kinetic corrections presented in [N. Tamanini, Phys. Rev. D 89 (2014) 083521]. In particular we do not restrict the analysis to exponential potentials only, but we consider arbitrary scalar field potentials and derive general results regarding the corresponding cosmological dynamics. Two specific potentials are then used as examples to show how these models can be employed not only to describe dark energy, but also to achieve dynamical crossing of the phantom barrier at late times. Stability and viability issues at the classical level are also discussed.

  8. Dynamics of Zonal Flows: Failure of Wave-Kinetic Theory, and New Geometrical Optics Approximations

    CERN Document Server

    Parker, Jeffrey B

    2016-01-01

    The self-organization of turbulence into regular zonal flows can be fruitfully investigated with quasilinear methods and statistical descriptions. A wave kinetic equation that assumes asymptotically large-scale zonal flows is pathological. From an exact description of quasilinear dynamics emerges two better geometrical optics approximations. These involve not only the mean flow shear but also the second and third derivative of the mean flow. One approximation takes the form of a new wave kinetic equation, but is only valid when the zonal flow is quasi-static and wave action is conserved.

  9. Reactive molecular dynamics simulation and chemical kinetic modeling of pyrolysis and combustion of n-dodecane

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Quan-De [College of Chemistry, Sichuan University, Chengdu (China); Wang, Jing-Bo; Li, Juan-Qin; Tan, Ning-Xin; Li, Xiang-Yuan [College of Chemical Engineering, Sichuan University, Chengdu (China)

    2011-02-15

    The initiation mechanisms and kinetics of pyrolysis and combustion of n-dodecane are investigated by using the reactive molecular dynamics (ReaxFF MD) simulation and chemical kinetic modeling. From ReaxFF MD simulations, we find the initiation mechanisms of pyrolysis of n-dodecane are mainly through two pathways, (1) the cleavage of C-C bond to form smaller hydrocarbon radicals, and (2) the dehydrogenation reaction to form an H radical and the corresponding n-C{sub 12}H{sub 25} radical. Another pathway is the H-abstraction reactions by small radicals including H, CH{sub 3}, and C{sub 2}H{sub 5}, which are the products after the initiation reaction of n-dodecane pyrolysis. ReaxFF MD simulations lead to reasonable Arrhenius parameters compared with experimental results based on first-order kinetic analysis of n-dodecane pyrolysis. The density/pressure effects on the pyrolysis of n-dodecane are also analyzed. By appropriate mapping of the length and time from macroscopic kinetic modeling to ReaxFF MD, a simple comparison of the conversion of n-dodecane from ReaxFF MD simulations and that from kinetic modeling is performed. In addition, the oxidation of n-dodecane is studied by ReaxFF MD simulations. We find that formaldehyde molecule is an important intermediate in the oxidation of n-dodecane, which has been confirmed by kinetic modeling, and ReaxFF leads to reasonable reaction pathways for the oxidation of n-dodecane. These results indicate that ReaxFF MD simulations can give an atomistic description of the initiation mechanism and product distributions of pyrolysis and combustion for hydrocarbon fuels, and can be further used to provide molecular based robust kinetic reaction mechanism for chemical kinetic modeling of hydrocarbon fuels. (author)

  10. Polyoxometalate complexes for oxidative kinetic resolution of secondary alcohols: unique effects of chiral environment, immobilization and aggregation.

    Science.gov (United States)

    Shi, Lei; Wang, Yizhan; Li, Bao; Wu, Lixin

    2014-06-28

    In this paper, the chiral surfactants bearing two long alkyl chains with hydroxyl groups at their terminals were synthesized and employed to encapsulate a catalytically efficient polyoxometalate through electrostatic interaction. The obtained chiral surfactant-encapsulated polyoxometalate complexes, in which a defined chiral microenvironment surrounds the inorganic cluster, were covalently immobilized into the silica matrix via a sol-gel process. Kinetic resolution of racemic aromatic alcohols was selected as the model reaction to evaluate the chiral supramolecular hybrid catalysts. Up to 89% enantiomeric excess was obtained by varying the reaction conditions. Importantly, the change of loading values of the chiral surfactant-encapsulated polyoxometalates leads to mutative inner microstructures ranging from uniform dispersion to subsequent formation of nanocrystalline domains in the silica matrix. Such a structural evolution differentiates the density and stability of the chiral microenvironment, resulting in a regular change of enantioselectivity of the prepared asymmetric catalysts. Moreover, the fixation of the chiral microenvironment surrounding the polyoxometalates by covalent immobilization was proved to have a promoting effect on enantioselectivity. The present research uncovers the unique effect of immobilization on the kinetic resolution. The strategy helps to understand the influencing factors of enantioselectivity, and provides a convenient and efficient approach for the construction of supramolecular asymmetric catalysts based on chiral surfactant-encapsulated polyoxometalate complexes.

  11. 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.

  12. Differential kinetic dynamics and heating of ions in the turbulent solar wind

    CERN Document Server

    Valentini, F; Stabile, S; Pezzi, O; Servidio, S; De Marco, R; Marcucci, F; Bruno, R; Lavraud, B; De Keyser, J; Consolini, G; Brienza, D; Sorriso-Valvo, L; Retinò, A; Vaivads, A; Salatti, M; Veltri, P

    2016-01-01

    The solar wind plasma is a fully ionized and turbulent gas ejected by the outer layers of the solar corona at very high speed, mainly composed by protons and electrons, with a small percentage of helium nuclei and a significantly lower abundance of heavier ions. Since particle collisions are practically negligible, the solar wind is typically not in a state of thermodynamic equilibrium. Such a complex system must be described through self-consistent and fully nonlinear models, taking into account its multi-species composition and turbulence. We use a kinetic hybrid Vlasov-Maxwell numerical code to reproduce the turbulent energy cascade down to ion kinetic scales, in typical conditions of the uncontaminated solar wind plasma, with the aim of exploring the differential kinetic dynamics of the dominant ion species, namely protons and alpha particles. We show that the response of different species to the fluctuating electromagnetic fields is different. In particular, a significant differential heating of alphas w...

  13. Nonlinear Stochastic Dynamics of Complex Systems, I: A Chemical Reaction Kinetic Perspective with Mesoscopic Nonequilibrium Thermodynamics

    CERN Document Server

    Qian, Hong

    2016-01-01

    We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity, but population wise with statistical rate laws in their syntheses, degradations, spatial diffusion, individual state transitions, and interactions. Such a formal kinetic system in a small volume $V$, like a single cell, can be rigorously treated in terms of a Markov process describing its nonlinear kinetics as well as nonequilibrium thermodynamics at a mesoscopic scale. We introduce notions such as open, driven chemical systems, entropy production, free energy dissipation, etc. Then in the macroscopic limit, we illustrate how two new "laws", in terms of a generalized free energy of the mesoscopic stochastic dynamics, emerge. Detailed balance and complex balance are two special classes of "simple" nonlinear kinetics. Phase transition is intrinsically related to multi-stability...

  14. Macroscopic dynamics of incoherent soliton ensembles: soliton-gas kinetics and direct numerical modeling

    CERN Document Server

    Carbone, Francesco; El, Gennady

    2015-01-01

    We undertake a detailed comparison of the results of direct numerical simulations of the integrable soliton gas dynamics with the analytical predictions inferred from the exact solutions of the relevant kinetic equation for solitons. We use the KdV soliton gas as a simplest analytically accessible model yielding major insight into the general properties of soliton gases in integrable systems. Two model problems are considered: (i) the propagation of a `trial' soliton through a one-component `cold' soliton gas consisting of randomly distributed solitons of approximately the same amplitude; and (ii) collision of two cold soliton gases of different amplitudes (soliton gas shock tube problem) leading to the formation of an incoherend dispersive shock wave. In both cases excellent agreement is observed between the analytical predictions of the soliton gas kinetics and the direct numerical simulations. Our results confirm relevance of the kinetic equation for solitons as a quantitatively accurate model for macrosco...

  15. DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results

    Directory of Open Access Journals (Sweden)

    Gizzatkulov Nail M

    2010-08-01

    Full Text Available Abstract Background Systems biology research and applications require creation, validation, extensive usage of mathematical models and visualization of simulation results by end-users. Our goal is to develop novel method for visualization of simulation results and implement it in simulation software package equipped with the sophisticated mathematical and computational techniques for model development, verification and parameter fitting. Results We present mathematical simulation workbench DBSolve Optimum which is significantly improved and extended successor of well known simulation software DBSolve5. Concept of "dynamic visualization" of simulation results has been developed and implemented in DBSolve Optimum. In framework of the concept graphical objects representing metabolite concentrations and reactions change their volume and shape in accordance to simulation results. This technique is applied to visualize both kinetic response of the model and dependence of its steady state on parameter. The use of the dynamic visualization is illustrated with kinetic model of the Krebs cycle. Conclusion DBSolve Optimum is a user friendly simulation software package that enables to simplify the construction, verification, analysis and visualization of kinetic models. Dynamic visualization tool implemented in the software allows user to animate simulation results and, thereby, present them in more comprehensible mode. DBSolve Optimum and built-in dynamic visualization module is free for both academic and commercial use. It can be downloaded directly from http://www.insysbio.ru.

  16. Development of patient collation system by kinetic analysis for chest dynamic radiogram with flat panel detector

    Science.gov (United States)

    Tsuchiya, Yuichiro; Kodera, Yoshie

    2006-03-01

    In the picture archiving and communication system (PACS) environment, it is important that all images be stored in the correct location. However, if information such as the patient's name or identification number has been entered incorrectly, it is difficult to notice the error. The present study was performed to develop a system of patient collation automatically for dynamic radiogram examination by a kinetic analysis, and to evaluate the performance of the system. Dynamic chest radiographs during respiration were obtained by using a modified flat panel detector system. Our computer algorithm developed in this study was consisted of two main procedures, kinetic map imaging processing, and collation processing. Kinetic map processing is a new algorithm to visualize a movement for dynamic radiography; direction classification of optical flows and intensity-density transformation technique was performed. Collation processing consisted of analysis with an artificial neural network (ANN) and discrimination for Mahalanobis' generalized distance, those procedures were performed to evaluate a similarity of combination for the same person. Finally, we investigated the performance of our system using eight healthy volunteers' radiographs. The performance was shown as a sensitivity and specificity. The sensitivity and specificity for our system were shown 100% and 100%, respectively. This result indicated that our system has excellent performance for recognition of a patient. Our system will be useful in PACS management for dynamic chest radiography.

  17. Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics

    Science.gov (United States)

    Li, Dong; Shao, Lin; Chen, Bi-Chang; Zhang, Xi; Zhang, Mingshu; Moses, Brian; Milkie, Daniel E.; Beach, Jordan R.; Hammer, John A.; Pasham, Mithun; Kirchhausen, Tomas; Baird, Michelle A.; Davidson, Michael W.; Xu, Pingyong; Betzig, Eric

    2015-01-01

    Super-resolution fluorescence microscopy is distinct among nanoscale imaging tools in its ability to image protein dynamics in living cells. Structured illumination microscopy (SIM) stands out in this regard because of its high speed and low illumination intensities, but typically offers only a twofold resolution gain. We extended the resolution of live-cell SIM through two approaches: ultrahigh numerical aperture SIM at 84-nanometer lateral resolution for more than 100 multicolor frames, and nonlinear SIM with patterned activation at 45- to 62-nanometer resolution for approximately 20 to 40 frames. We applied these approaches to image dynamics near the plasma membrane of spatially resolved assemblies of clathrin and caveolin, Rab5a in early endosomes, and a-actinin, often in relationship to cortical actin. In addition, we examined mitochondria, actin, and the Golgi apparatus dynamics in three dimensions. PMID:26315442

  18. Volumetric analysis of syringomyelia following hindbrain decompression for Chiari malformation Type I: syringomyelia resolution follows exponential kinetics

    Science.gov (United States)

    Coumans, Jean-Valery; Walcott, Brian P.; Butler, William E.; Nahed, Brian V.; Kahle, Kristopher T.

    2013-01-01

    Object Resolution of syringomyelia is common following hindbrain decompression for Chiari malformation, yet little is known about the kinetics governing this process. The authors sought to establish the volumetric rate of syringomyelia resolution. Methods A retrospective cohort of patients undergoing hindbrain decompression for a Chiari malformation Type I with preoperative cervical or thoracic syringomyelia was identified. Patients were included in the study if they had at least 3 neuroimaging studies that detailed the entirety of their preoperative syringomyelia over a minimum of 6 months postoperatively. The authors reconstructed the MR images in 3 dimensions and calculated the volume of the syringomyelia. They plotted the syringomyelia volume over time and constructed regression models using the method of least squares. The Akaike information criterion and Bayesian information criterion were used to calculate the relative goodness of fit. The coefficients of determination R2 (unadjusted and adjusted) were calculated to describe the proportion of variability in each individual data set accounted for by the statistical model. Results Two patients were identified as meeting inclusion criteria. Plots of the least-squares best fit were identified as 4.01459e−0.0180804x and 13.2556e−0.00615859x. Decay of the syringomyelia followed an exponential model in both patients (R2 = 0.989582 and 0.948864). Conclusions Three-dimensional analysis of syringomyelia resolution over time enables the kinetics to be estimated. This technique is yet to be validated in a large cohort. Because syringomyelia is the final common pathway for a number of different pathological processes, it is possible that this exponential only applies to syringomyelia related to treatment of Chiari malformation Type I. PMID:21882909

  19. Multivariate curve resolution-alternating least squares and kinetic modeling applied to near-infrared data from curing reactions of epoxy resins: mechanistic approach and estimation of kinetic rate constants.

    Science.gov (United States)

    Garrido, M; Larrechi, M S; Rius, F X

    2006-02-01

    This study describes the combination of multivariate curve resolution-alternating least squares with a kinetic modeling strategy for obtaining the kinetic rate constants of a curing reaction of epoxy resins. The reaction between phenyl glycidyl ether and aniline is monitored by near-infrared spectroscopy under isothermal conditions for several initial molar ratios of the reagents. The data for all experiments, arranged in a column-wise augmented data matrix, are analyzed using multivariate curve resolution-alternating least squares. The concentration profiles recovered are fitted to a chemical model proposed for the reaction. The selection of the kinetic model is assisted by the information contained in the recovered concentration profiles. The nonlinear fitting provides the kinetic rate constants. The optimized rate constants are in agreement with values reported in the literature.

  20. 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

  1. Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.

    Science.gov (United States)

    Buchner, Ginka S; Murphy, Ronan D; Buchete, Nicolae-Viorel; Kubelka, Jan

    2011-08-01

    The problem of spontaneous folding of amino acid chains into highly organized, biologically functional three-dimensional protein structures continues to challenge the modern science. Understanding how proteins fold requires characterization of the underlying energy landscapes as well as the dynamics of the polypeptide chains in all stages of the folding process. In recent years, important advances toward these goals have been achieved owing to the rapidly growing interdisciplinary interest and significant progress in both experimental techniques and theoretical methods. Improvements in the experimental time resolution led to determination of the timescales of the important elementary events in folding, such as formation of secondary structure and tertiary contacts. Sensitive single molecule methods made possible probing the distributions of the unfolded and folded states and following the folding reaction of individual protein molecules. Discovery of proteins that fold in microseconds opened the possibility of atomic-level theoretical simulations of folding and their direct comparisons with experimental data, as well as of direct experimental observation of the barrier-less folding transition. The ultra-fast folding also brought new questions, concerning the intrinsic limits of the folding rates and experimental signatures of barrier-less "downhill" folding. These problems will require novel approaches for even more detailed experimental investigations of the folding dynamics as well as for the analysis of the folding kinetic data. For theoretical simulations of folding, a main challenge is how to extract the relevant information from overwhelmingly detailed atomistic trajectories. New theoretical methods have been devised to allow a systematic approach towards a quantitative analysis of the kinetic network of folding-unfolding transitions between various configuration states of a protein, revealing the transition states and the associated folding pathways at

  2. 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.

  3. Some fundamental problems for an energy conserving adaptive resolution molecular dynamics scheme

    OpenAIRE

    Site, L. Delle

    2007-01-01

    Adaptive resolution molecular dynamics (MD) schemes allow for changing the number of degrees of freedom on the fly and preserve the free exchange of particles between regions of different resolution. There are two main alternatives on how to design the algorithm to switch resolution using auxiliary ''switching'' functions; force based and potential energy based approach. In this work we show that, in the framework of classical MD, the latter presents fundamental conceptual problems which make...

  4. Multi-Volume High Resolution RGB-D Mapping with Dynamic Volume Placement

    OpenAIRE

    Salvato, Michael; Finman, Ross; Leonard, John

    2015-01-01

    We present a novel RGB-D mapping system for generating 3D maps over spatially extended regions with higher resolution than current methods using multiple, dynamically placed mapping volumes. Our method takes in RGB-D frames and dynamically assigns multiple mapping volumes to the environment, exchanging mapping volumes between the CPU and GPU. Mapping volumes are added or removed as needed to allow for spatially extended, high resolution mapping. Our system is designed to maximize the resoluti...

  5. Asymptotic Solutions of the Kinetic Boltzmann Equation, Multicomponent Non-equilibrium Gas Dynamics and Turbulence

    CERN Document Server

    Serov, S A

    2013-01-01

    In the article correct method for the kinetic Boltzmann equation asymptotic solution is formulated, the Hilbert's and Enskog's methods are discussed. The equations system of multicomponent non-equilibrium gas dynamics is derived, that corresponds to the first order in the approximate (asymptotic) method for solution of the system of kinetic Boltzmann equations. It is shown, that the velocity distribution functions of particles, obtained by the proposed method and by Enskog's method, within Enskog's approach, are equivalent up to the infinitesimal first order terms of the asymptotic expansion, but, generally speaking, differ in the next order. Interpretation of turbulent gas flow is proposed, as stratified on components gas flow, which is described by the derived equations system of multicomponent non-equilibrium gas dynamics.

  6. Molecular dynamical studies of the dissociation of a diatomic molecular crystal. II. Equilibrium kinetics

    Science.gov (United States)

    Trevino, S. F.; Tsai, D. H.

    1984-07-01

    The properties of a molecular dynamical model undergoing equilibrium chemical reactions are reported. It is shown that the kinetics of the modeled reaction is consistent with established thermodynamic considerations. Further, at constant pressure, the relation between the Arrhenius energy of reaction ΔE, the potential energy change upon dissociation Δɛ, and the work done due to the volume change PΔV, viz, -ΔE=-(Δɛ+PΔV), is satisfied.

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

    OpenAIRE

    Laureys, David; De Vuyst, Luc

    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...

  8. Dynamic kinetic cross-coupling strategy for the asymmetric synthesis of axially chiral heterobiaryls.

    Science.gov (United States)

    Ros, Abel; Estepa, Beatriz; Ramírez-López, Pedro; Álvarez, Eleuterio; Fernández, Rosario; Lassaletta, José M

    2013-10-23

    A dynamic kinetic asymmetric transformation (DYKAT) technique has been designed for the synthesis of 2'-substituted 2-aryl pyridines/isoquinolines and related heterobiaryls. In this way, the Pd(0)-catalyzed coupling of racemic 2-triflates with aryl boroxines using a TADDOL-derived phosphoramidite as the ligand provides the corresponding coupling products with good to excellent enantioselectivities. Structural studies support that the formation of configurationally labile oxidative addition palladacycles is the key for the success of the methodology.

  9. Nonequilibrium dynamical phase transition of 3D kinetic Ising/Heisenberg spin system

    Institute of Scientific and Technical Information of China (English)

    Shao Yuan-Zhi; Lai J. K. L.; Shek C. H.; Lin Guang-Ming; Lan Tu

    2004-01-01

    We have studied the nonequilibrium dynamic phase transitions of both three-dimensional (3D) kinetic Ising and Heisenberg spin systems in the presence of a perturbative magnetic field by Monte Carlo simulation. The feature of the phase transition is characterized by studying the distribution of the dynamical order parameter.In the case of anisotropic Ising spin system (ISS), the dynamic transition is discontinuous and continuous under low and high temperatures respectively, which indicates the existence of a tri-critical point (TCP) on the phase boundary separating low-temperature order phase and high-temperature disorder phase. The TCP shifts towards the higher temperature region with the decrease of frequency, I.e. TTCp=1.33×exp(-ω/30.7). In the case of the isotropic Heisenberg spin system (HSS), however, the situation on dynamic phase transition of HSS is quite different from that of ISS in that no stable dynamical phase transition was observed in kinetic HSS after a threshold time. The evolution of magnetization in the HSS driven by a symmetrical external field after a certain duration always tends asymptotically to a disorder state no matter what an initial state the system starts with. The threshold time τ depends upon the amplitude H0,reduced temperature T/TC and the frequency ωas τ=C·ωα·H-β0·(T/TC)-γ.

  10. Kinetics of SiHCl3 chemical vapor deposition and fluid dynamic simulations.

    Science.gov (United States)

    Cavallotti, Carlo; Masi, Maurizio

    2011-09-01

    Though most of the current silicon photovoltaic technology relies on trichlorosilane (SiHCl3) as a precursor gas to deposit Si, only a few studies have been devoted to the investigation of its gas phase and surface kinetics. In the present work we propose a new kinetic mechanism apt to describe the gas phase and surface chemistry active during the deposition of Si from SiHCl3. Kinetic constants of key reactions were either taken from the literature or determined through ab initio calculations. The capability of the mechanism to reproduce experimental data was tested through the implementation of the kinetic scheme in a fluid dynamic model and in the simulation of both deposition and etching of Si in horizontal reactors. The results of the simulations show that the reactivity of HCl is of key importance in order to control the Si deposition rate. When HCl reaches a critical concentration in the gas phase it starts etching the Si surface, so that the net deposition rate is the net sum of the adsorption rate of the gas phase precursors and the etching rate due to HCl. In these conditions the possibility to further deposit Si is directly related to the rate of consumption of HCl through its reaction with SiHCl3 to give SiCl4. The proposed reaction mechanism was implemented in a 3D fluid dynamic model of a simple Siemens reactor. The simulation results indicate that the proposed interpretation of the growth process applies also to this class of reactors, which operate in what can be defined as a mixed kinetic-transport controlled regime.

  11. 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.

  12. Downscaling time series of MERIS full resolution data to monitor vegetation seasonal dynamics

    NARCIS (Netherlands)

    Zurita Milla, R.; Kaiser, G.; Clevers, J.G.P.W.; Schneider, W.; Schaepman, M.E.

    2009-01-01

    Monitoring vegetation dynamics is fundamental for improving Earth system models and for increasing our understanding of the terrestrial carbon cycle and the interactions between biosphere and climate. Medium spatial resolution sensors, like MERIS, exhibit a significant potential to study these dynam

  13. Surface Plasmon Resonance Analysis of Antifungal Azoles Binding to CYP3A4 with Kinetic Resolution of Multiple Binding Orientations†

    Science.gov (United States)

    Pearson, Josh T.; Hill, John J.; Swank, Jennifer; Isoherranen, Nina; Kunze, Kent L.; Atkins, William M.

    2008-01-01

    The heme-containing Cytochrome P450s (CYPs) are a major enzymatic determinant of drug clearance and drug-drug interactions. The CYP3A4 isoform is inhibited by antifungal imidazoles or triazoles, which form low spin heme iron complexes via formation of a nitrogen-ferric iron coordinate bond. However, CYP3A4 also slowly oxidizes the antifungal itraconazole (ITZ) at a site that is ∼ 25 Å from the triazole nitrogens, suggesting that large antifungal azoles can adopt multiple orientations within the CYP3A4 active site. Here, we report a surface plasmon resonance (SPR) analysis with kinetic resolution of two binding modes of ITZ, and the related drug ketoconazole (KTZ). SPR reveals a very slow off-rate for one binding orientation. Multiphasic binding kinetics are observed and one of the two binding components resolved by curve-fitting exhibits ‘equilibrium overshoot’. Pre-loading of CYP3A4 with the heme ligand imidazole abolishes this component of the antifungal azole binding trajectories, and it eliminates the conspicuously slow off-rate. The fractional populations of CYP3A4 complexes corresponding to different drug orientations can be manipulated by altering the duration of the pulse of drug exposure. UV-vis difference absorbance titrations yield low spin spectra and KD values that are consistent with the high affinity complex resolved by SPR. These results demonstrate that ITZ and KTZ bind in multiple orientations, including a catalytically productive mode and a slowly-dissociating inhibitory mode. Most importantly, they provide the first example of an SPR-based method for the kinetic characterization of drug binding to any human CYP, including mechanistic insight not available from other methods. PMID:16700545

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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)

    2015-09-30

    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.

  19. 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.

  20. Viriato: A Fourier-Hermite spectral code for strongly magnetized fluid-kinetic plasma dynamics

    Science.gov (United States)

    Loureiro, N. F.; Dorland, W.; Fazendeiro, L.; Kanekar, A.; Mallet, A.; Vilelas, M. S.; Zocco, A.

    2016-09-01

    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 (KREHM) equations (Zocco and Schekochihin, 2011) (which reduce to the standard Reduced-MHD equations in the appropriate limit) and (ii) the kinetic reduced MHD (KRMHD) equations (Schekochihin et al., 2009). Two main applications of these equations are magnetized (Alfvénic) plasma turbulence and magnetic reconnection. Viriato uses operator splitting (Strang or Godunov) 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 composed of the combination of a total variation diminishing (TVD) third order Runge-Kutta method for the time derivative with a 7th order upwind scheme for the fluxes. 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, including a detailed analysis of 2D and 3D Orszag-Tang-type decaying turbulence, both in fluid and kinetic regimes.

  1. Generalized and Stability Rational Functions for Dynamic Systems of Reactor Kinetics

    Directory of Open Access Journals (Sweden)

    Ahmed E. Aboanber

    2013-01-01

    Full Text Available The base of reactor kinetics dynamic systems is a set of coupled stiff ordinary differential equations known as the point reactor kinetics equations. These equations which express the time dependence of the neutron density and the decay of the delayed neutron precursors within a reactor are first order nonlinear and essentially describe the change in neutron density within the reactor due to a change in reactivity. Outstanding the particular structure of the point kinetic matrix, a semianalytical inversion is performed and generalized for each elementary step resulting eventually in substantial time saving. Also, the factorization techniques based on using temporarily the complex plane with the analytical inversion is applied. The theory is of general validity and involves no approximations. In addition, the stability of rational function approximations is discussed and applied to the solution of the point kinetics equations of nuclear reactor with different types of reactivity. From the results of various benchmark tests with different types of reactivity insertions, the developed generalized Padé approximation (GPA method shows high accuracy, high efficiency, and stable character of the solution.

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

    Science.gov (United States)

    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.

  3. Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex.

    Science.gov (United States)

    Salim, Nilshad; Lamichhane, Rajan; Zhao, Rui; Banerjee, Tuhina; Philip, Jane; Rueda, David; Feig, Andrew L

    2012-03-07

    Kissing hairpin interactions form when the loop residues of two hairpins have Watson-Crick complementarity. In a unimolecular context, kissing interactions are important for tertiary folding and pseudoknot formation, whereas in a bimolecular context, they provide a basis for molecular recognition. In some cases, kissing complexes can be a prelude to strand displacement reactions where the two hairpins resolve to form a stable extended intermolecular duplex. The kinetics and thermodynamics of kissing-complex formation and their subsequent strand-displacement reactions are poorly understood. Here, biophysical techniques including isothermal titration calorimetry, surface plasmon resonance, and single-molecule fluorescence have been employed to probe the factors that govern the stability of kissing complexes and their subsequent structural rearrangements. We show that the general understanding of RNA duplex formation can be extended to kissing complexes but that kissing complexes display an unusual level of stability relative to simple duplexes of the same sequence. These interactions form and break many times at room temperature before becoming committed to a slow, irreversible forward transition to the strand-displaced form. Furthermore, using smFRET we show that the primary difference between stable and labile kissing complexes is based almost completely on their off rates. Both stable and labile complexes form at the same rate within error, but less stable species dissociate rapidly, allowing us to understand how these complexes can help generate specificity along a folding pathway or during a gene regulation event. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. 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.

  5. Classifying the expansion kinetics and critical surface dynamics of growing cell populations

    CERN Document Server

    Block, M; Drasdo, D

    2006-01-01

    Based on a cellular automaton model the growth kinetics and the critical surface dynamics of cell monolayers is systematically studied by variation of the cell migration activity, the size of the proliferation zone and the cell cycle time distribution over wide ranges. The model design avoids lattice artifacts and ensures high performance. The monolayer expansion velocity derived from our simulations can be interpreted as a generalization of the velocity relationship for a traveling front in the Fisher-Kolmogorov-Petrovskii-Piskounov (FKPP) equation that is frequently used to model tumor growth phenomena by continuum models. The critical surface dynamics corresponds to the Kardar-Parisi-Zhang (KPZ) universality class for all parameters and model variations studied. While the velocity agrees quantitatively with experimental observations by Bru et al, the critical surface dynamics is in contrast to their interpretation as generic molecular-beam-epitaxy-like growth.

  6. Kinetic theory of correlated fluids: from dynamic density functional to Lattice Boltzmann methods.

    Science.gov (United States)

    Marconi, Umberto Marini Bettolo; Melchionna, Simone

    2009-07-07

    Using methods of kinetic theory and liquid state theory we propose a description of the nonequilibrium behavior of molecular fluids, which takes into account their microscopic structure and thermodynamic properties. The present work represents an alternative to the recent dynamic density functional theory, which can only deal with colloidal fluids and is not apt to describe the hydrodynamic behavior of a molecular fluid. The method is based on a suitable modification of the Boltzmann transport equation for the phase space distribution and provides a detailed description of the local structure of the fluid and its transport coefficients. Finally, we propose a practical scheme to solve numerically and efficiently the resulting kinetic equation by employing a discretization procedure analogous to the one used in the Lattice Boltzmann method.

  7. Oenological prefermentation practices strongly impact yeast population dynamics and alcoholic fermentation kinetics in Chardonnay grape must.

    Science.gov (United States)

    Albertin, Warren; Miot-Sertier, Cécile; Bely, Marina; Marullo, Philippe; Coulon, Joana; Moine, Virginie; Colonna-Ceccaldi, Benoit; Masneuf-Pomarede, Isabelle

    2014-05-16

    Yeast species of Hanseniaspora and Candida genus are predominant during the early stages of winemaking, while species of Metschnikowia, Pichia, Zygoascus, Issatchenkia, Torulaspora and other genera are present at lower population levels. The impact of common oenological practices on yeast dynamics during the prefermentative stage and the early stage of alcoholic fermentation (AF) remains elusive. In this work, the effect of four prefermentative oenological practices (clarification degree, temperature, sulphite and starter yeast addition) on yeast dynamics was evaluated in a Chardonnay grape must. The growth curves of four genus or species, namely Saccharomyces spp., Hanseniaspora spp., Candida zemplinina and Torulaspora delbrueckii, were followed by quantitative PCR. The fermentation kinetics were also recorded, as well as the production of acetic acid. Variance analysis allowed determining the effect of each practice and their interaction factors, as well as their relative importance on yeast dynamics and fermentation kinetics. Our experimental design showed that the population dynamics of the four species were differently impacted by the oenological practices, with some species being more sensitive than others to the clarification degree (C. zemplinina), sulphite addition (Saccharomyces spp.), starter yeast inoculation (Hanseniaspora spp.) or prefermentation temperature (T. delbrueckii). Significant interaction effects between practices were revealed, highlighting the interest of experimental design allowing interaction analysis, as some factors may buffer the effect of other ones. Hanseniaspora genus showed atypical behaviour: growth dynamics showed a decrease during AF that we interpreted as early cellular lysis. In conclusion, this study provides new insights on the impact of common oenological practices on the dynamics of non-Saccharomyces yeast that will be useful for a better management of mixed fermentation between S. cerevisiae and non

  8. Practical Considerations for High Spatial and Temporal Resolution Dynamic Transmission Electron Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, M; Boyden, K; Browning, N D; Campbell, G H; Colvin, J D; DeHope, B; Frank, A M; Gibson, D J; Hartemann, F; Kim, J S; King, W E; LaGrange, T B; Pyke, B J; Reed, B W; Shuttlesworth, R M; Stuart, B C; Torralva, B R

    2006-05-01

    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 5 x 10{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.

  9. 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.

    2014-08-01

    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 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.

  10. A Bayesian spatial temporal mixtures approach to kinetic parametric images in dynamic positron emission tomography.

    Science.gov (United States)

    Zhu, W; Ouyang, J; Rakvongthai, Y; Guehl, N J; Wooten, D W; El Fakhri, G; Normandin, M D; Fan, Y

    2016-03-01

    Estimation of parametric maps is challenging for kinetic models in dynamic positron emission tomography. Since voxel kinetics tend to be spatially contiguous, the authors consider groups of homogeneous voxels together. The authors propose a novel algorithm to identify the groups and estimate kinetic parameters simultaneously. Uncertainty estimates for kinetic parameters are also obtained. Mixture models were used to fit the time activity curves. In order to borrow information from spatially nearby voxels, the Potts model was adopted. A spatial temporal model was built incorporating both spatial and temporal information in the data. Markov chain Monte Carlo was used to carry out parameter estimation. Evaluation and comparisons with existing methods were carried out on cardiac studies using both simulated data sets and a pig study data. One-compartment kinetic modeling was used, in which K1 is the parameter of interest, providing a measure of local perfusion. Based on simulation experiments, the median standard deviation across all image voxels, of K1 estimates were 0, 0.13, and 0.16 for the proposed spatial mixture models (SMMs), standard curve fitting, and spatial K-means methods, respectively. The corresponding median mean squared biases for K1 were 0.04, 0.06, and 0.06 for abnormal region of interest (ROI); 0.03, 0.03, and 0.04 for normal ROI; and 0.007, 0.02, and 0.05 for the noise region. SMM is a fully Bayesian algorithm which determines the optimal number of homogeneous voxel groups, voxel group membership, parameter estimation, and parameter uncertainty estimation simultaneously. The voxel membership can also be used for classification purposes. By borrowing information from spatially nearby voxels, SMM substantially reduces the variability of parameter estimates. In some ROIs, SMM also reduces mean squared bias.

  11. 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 con

  12. Nonequilibrium Dynamical Phase Transition of a Three-Dimensional Kinetic Heisenberg Spin System

    Institute of Scientific and Technical Information of China (English)

    邵元智; 林光明; 蓝图; J.K.L Lai; C.H.Shek

    2002-01-01

    We systematically investigate the dynamical response of a three-dimensional kinetic isotropic Heisenberg spin system (ISS) to an external driving field by Monte Carlo numerical simulation. The dynamical response of the isotropic HSS differs obviously from those of the anisotropic Ising spin system in which no realstable ordered state and relevant dynamical phase transition were observed in the kinetic ISS. There is a threshold time after which the magnetization m(t) in the ISS driven by a symmetrical external field always tends asymptotically to a disorder state regardless of the initial state of the system. The threshold time depends on the reduced temperature T/TC of the investigated spin system, amplitude H0 and frequency of the external field, i.e. γ = C. ωα . H0-β. (T/TC)-γ.C is a constant equal to 0.0302 for a three-dimensional lattice and exponents а = 1.18 ± 0.01, β = 1.81 ± 0.01and γ = 1.68 ± 0.01.

  13. Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics.

    Science.gov (United States)

    Zhang, Yuwei; Song, Ping; Fu, Qiang; Ruan, Mingbo; Xu, Weilin

    2014-06-25

    Understanding the microscopic elementary process of chemical reactions, especially in condensed phase, is highly desirable for improvement of efficiencies in industrial chemical processes. Here we show an approach to gaining new insights into elementary reactions in condensed phase by combining quantum chemical calculations with a single-molecule analysis. Elementary chemical reactions in liquid-phase, revealed from quantum chemical calculations, are studied by tracking the fluorescence of single dye molecules undergoing a reversible redox process. Statistical analyses of single-molecule trajectories reveal molecular reaction kinetics and dynamics of elementary reactions. The reactivity dynamic fluctuations of single molecules are evidenced and probably arise from either or both of the low-frequency approach of the molecule to the internal surface of the SiO2 nanosphere or the molecule diffusion-induced memory effect. This new approach could be applied to other chemical reactions in liquid phase to gain more insight into their molecular reaction kinetics and the dynamics of elementary steps.

  14. A COMPARATIVE ANALYSIS OF DISPUTE RESOLUTION DYNAMICS IN ASIA

    Directory of Open Access Journals (Sweden)

    Pawel Voronin

    2014-01-01

    Full Text Available China’s rise to prominence in the international community following the end of the Cold War, the growth in economic power and population numbers project that China will become the leading world power within several decades, regardless of the course its government takes. The article aimes to contribute to answering the question whether this rise will be peaceful through a comparative analysis of resolved and unresolved territorial disputes between China and groups of neighbouring states between 1986 and 2013. While previous studies have focused rather exclusively on Chinese behaviour, this text will examine both sides of the dispute and the behavior of the parties in light of regional dynamics

  15. New planetary boundary layer parametrization in ECHAM5-HAM: Dynamical refinement of the vertical resolution

    Science.gov (United States)

    Siegenthaler-Le Drian, C.; Spichtinger, P.; Lohmann, U.

    2010-09-01

    Marine stratocumulus-capped boundary layers exhibit a strong net cooling impact on the Earth-Atmosphere system. Moreover, they are highly persistent over subtropical oceans. Therefore climate models need to represent them well in order to make reliable projections of future climate. One of the reasons for the absence of stratocumuli in the general circulation model ECHAM5-HAM (Roeckner et al., 2003; Stier et al., 2005) is due to the limited vertical resolution. In the current model version, no vertical sub-grid scale variability of clouds is taken into account, such that clouds occupy the full vertical layer. Around the inversion on top of the planetary boundary layer (PBL), conserved variables often have a steep gradient, which in a GCM may produce large discretization errors (Bretherton and Park, 2009). This inversion has a large diurnal cycle and varies with location around the globe, which is difficult to represent in a classical, coarse Eulerian approach. Furthermore, Lenderink and Holtslag (2000) and Lock (2001) showed that an inconsistent numerical representation between the entrainment parametrization and the other schemes, particularly with the vertical advection can lead to the occurrence of 'numerical entrainment'. The problem can be resolved by introducing a dynamical inversion as introduced by Grenier and Bretherton (2001) and Lock (2001). As these features can be seen in our version of ECHAM5-HAM, our implementation is aimed to reduce the numerical entrainment and to better represent stratocumuli in ECHAM5-HAM. To better resolve stratocumulus clouds, their inversion and the interaction between the turbulent diffusion and the vertical advection, the vertical grid is dynamically refined. The new grid is based on the reconstruction of the profiles of variables experiencing a sharp gradient (temperature, mixing ratio) applying the method presented in Grenier and Bretherton (2001). In typical stratocumulus regions, an additional grid level is thus

  16. Sensitive high-resolution white light Schlieren technique with a large dynamic range for the investigation of ablation dynamics

    NARCIS (Netherlands)

    Vogel, Alfred; Apitz, Ingo; Freidank, Sebastian; Dijkink, R.J.

    2006-01-01

    We developed a modified Hoffman contrast technique with a 12 ns pulsed incoherent extended white-light source that enables an easily interpretable visualization of ablation plumes with high resolution, a large dynamic range, and color information. By comparison, a conventional dark-field setup with

  17. The non-equilibrium thermodynamics and kinetics of focal adhesion dynamics.

    Directory of Open Access Journals (Sweden)

    Joseph E Olberding

    Full Text Available BACKGROUND: We consider a focal adhesion to be made up of molecular complexes, each consisting of a ligand, an integrin molecule, and associated plaque proteins. Free energy changes drive the binding and unbinding of these complexes and thereby controls the focal adhesion's dynamic modes of growth, treadmilling and resorption. PRINCIPAL FINDINGS: We have identified a competition among four thermodynamic driving forces for focal adhesion dynamics: (i the work done during the addition of a single molecular complex of a certain size, (ii the chemical free energy change associated with the addition of a molecular complex, (iii the elastic free energy change associated with deformation of focal adhesions and the cell membrane, and (iv the work done on a molecular conformational change. We have developed a theoretical treatment of focal adhesion dynamics as a nonlinear rate process governed by a classical kinetic model. We also express the rates as being driven by out-of-equilibrium thermodynamic driving forces, and modulated by kinetics. The mechanisms governed by the above four effects allow focal adhesions to exhibit a rich variety of behavior without the need to introduce special constitutive assumptions for their response. For the reaction-limited case growth, treadmilling and resorption are all predicted by a very simple chemo-mechanical model. Treadmilling requires symmetry breaking between the ends of the focal adhesion, and is achieved by driving force (i above. In contrast, depending on its numerical value (ii causes symmetric growth, resorption or is neutral, (iii causes symmetric resorption, and (iv causes symmetric growth. These findings hold for a range of conditions: temporally-constant force or stress, and for spatially-uniform and non-uniform stress distribution over the FA. The symmetric growth mode dominates for temporally-constant stress, with a reduced treadmilling regime. SIGNIFICANCE: In addition to explaining focal adhesion

  18. Evaporative cooling of microscopic water droplets in vacuo: Molecular dynamics simulations and kinetic gas theory.

    Science.gov (United States)

    Schlesinger, Daniel; Sellberg, Jonas A; Nilsson, Anders; Pettersson, Lars G M

    2016-03-28

    In the present study, we investigate the process of evaporative cooling of nanometer-sized droplets in vacuum using molecular dynamics simulations with the TIP4P/2005 water model. The results are compared to the temperature evolution calculated from the Knudsen theory of evaporation which is derived from kinetic gas theory. The calculated and simulation results are found to be in very good agreement for an evaporation coefficient equal to unity. Our results are of interest to experiments utilizing droplet dispensers as well as to cloud micro-physics.

  19. 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

    Recrystallization and mechanical behavior of nanocrystalline copper prepared by dynamic plastic deformation (DPD) and DPD with additional cold-rolling (DPD+CR) were investigated, with an emphasis on the effects of heterogeneity within the deformation microstructure. The DPD sample was found...... than 1, which is explained using a two-stage kinetics model incorporating the heterogeneity. The heterogeneity of the DPD sample is largely reduced by applying additional rolling. This change in deformation path leads to a more random distribution of the recrystallized grains and more conventional...

  20. 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.

  1. Improved ambiguity resolution for URTK with dynamic atmosphere constraints

    Science.gov (United States)

    Tang, Weiming; Liu, Wenjian; Zou, Xuan; Li, Zongnan; Chen, Liang; Deng, Chenlong; Shi, Chuang

    2016-12-01

    Raw observation processing method with prior knowledge of ionospheric delay could strengthen the ambiguity resolution (AR), but it does not make full use of the relatively longer wavelength of wide-lane (WL) observation. Furthermore, the accuracy of calculated atmospheric delays from the regional augmentation information has quite different in quality, while the atmospheric constraint used in the current methods is usually set to an empirical value. A proper constraint, which matches the accuracy of calculated atmospheric delays, can most effectively compensate the residual systematic biases caused by large inter-station distances. Therefore, the standard deviation of the residual atmospheric parameters should be fine-tuned. This paper presents an atmosphere-constrained AR method for undifferenced network RTK (URTK) rover, whose ambiguities are sequentially fixed according to their wavelengths. Furthermore, this research systematically analyzes the residual atmospheric error and finds that it mainly varies along the positional relationship between the rover and the chosen reference stations. More importantly, its ionospheric part of certain location will also be cyclically influenced every day. Therefore, the standard deviation of residual ionospheric error can be modeled by a daily repeated cosine or other functions with the help of data one day before, and applied by rovers as pseudo-observation. With the data collected at 29 stations from a continuously operating reference station network in Guangdong Province (GDCORS) in China, the efficiency of the proposed approach is confirmed by improving the success and error rates of AR for 10-20 % compared to that of the WL-L1-IF one, as well as making much better positioning accuracy.

  2. Super resolution microscopy of lipid bilayer phases and single molecule kinetic studies on merocyanine 540 bound lipid vesicles

    Science.gov (United States)

    Kuo, Chin-Kuei

    Recently, observing biological process and structural details in live cell became feasible after the introduction of super-resolution microscopy. Super-resolution microscopy by single molecule localization is the method that has commonly been used for such purpose. There are mainly three approaches to it: stochastic optical reconstruction microscopy (STORM), photoactivated localization microscopy (PALM), and point accumulation in nanoscale topology (PAINT). STORM and PALM rely on external laser control and use of photoactivable fluorescent protein or photoswitchable dyes and are technically challenging. The PAINT method relies on the control of thermal reaction rates to enable the switching between bright and dark states. Therefore, many conventional fluorescent probes can be applied in PAINT method and the images denote different information composed of interactions between the probe and its immediate environment by variations of probe parameters. The existence of lipid rafts has been under debates for decades due to the lack of a tool to directly visualize them in live cells. In the thesis, we combine PAINT with a phase sensitive dye, Merocyanine 540, to enable nanoscale observation of phase separation on supported lipid bilayers of mixed liquid/gel phases. The imaging results are presented in the chapter 3. Given that this is the first example of visualization of nanoscale phase separation of lipid bilayers using an optical microscope, we further looked into the kinetics of MC540 monomer dimer equilibrium in lipid bilayers using single molecule intensity time trajectory analysis and polarization dependent imaging. Our finding confirms that perpendicular monomeric MC540 (to the membrance surface) is the emitting speices in our system and it stays fluorescent for roughly 3 ms before it switches off to dark states. This part of analysis is presented in the chapter 4. All the materials, procedures to carry out experiments and data analysis, methods involved in our

  3. Coordinated Observations of X-ray and High-Resolution EUV Active Region Dynamics

    Science.gov (United States)

    Savage, Sabrina; Cirtain, Jonathan; Winebarger, Amy; Kobayashi, Ken; Golub, Leon; Korreck, Kelly

    2013-01-01

    The recently-launched High-resolution Coronal imager (Hi-C) sounding rocket provided the highest resolution images of coronal loops and other small-scale structures in the 193 Angstrom passband to date. With just 5 minutes of observations, the instrument recorded a variety of dynamic coronal events -- including even a small B-class flare. We will present our results comparing these extreme-ultraviolet (EUV) observations with X-ray imaging from Hinode/XRT as well as EUV AIA data to identify sources of hot plasma rooted in the photosphere and track their affect on the overall topology and dynamics of the active region.

  4. Dynamic nuclear renography kinetic analysis: Four-compartment model for assessing kidney function

    Energy Technology Data Exchange (ETDEWEB)

    Raswan, T. R., E-mail: tara.raissa@gmail.com; Haryanto, F., E-mail: tara.raissa@gmail.com [Department of Physics, Nuclear Physics and Biophysics Research Group, Institut Teknologi Bandung, Bandung (Indonesia)

    2014-09-30

    Dynamic nuclear renography method produces TACs of kidneys and bladder. Multiple TACs data can be further analyzed to obtain the overview of urinary system's condition. Tracer kinetic analysis was performed using four-compartment models. The system's model consist of four irreversible compartment with four transport constants (k1, k2, k3 and k4). The mathematical expressions of tracer's distributions is fitted to experimental data (TACs) resulting in model constants. This transport constants represent the urinary system behavior, and later can be used for analyzing system's condition. Different intervals of kinetics parameter are clearly shown by abnormal system with respect to the normal one. Furthermore, the system with delayed uptake has 82% lower uptake parameters (k1 and k2) than normal one. Meanwhile, the system with prolonged clearance time has its kinetics parameters k3 or k4 lower than the others. This model is promising for quantitatively describe urinary system's function especially if supplied with more data.

  5. 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.

  6. Catalytic Mechanism of Perosamine N-Acetyltransferase Revealed by High-Resolution X-ray Crystallographic Studies and Kinetic Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Thoden, James B.; Reinhardt, Laurie A.; Cook, Paul D.; Menden, Patrick; Cleland, W.W.; Holden, Hazel M. (UW); (Mount Union); (UW-MED)

    2012-09-17

    N-Acetylperosamine is an unusual dideoxysugar found in the O-antigens of some Gram-negative bacteria, including the pathogenic Escherichia coli strain O157:H7. The last step in its biosynthesis is catalyzed by PerB, an N-acetyltransferase belonging to the left-handed {beta}-helix superfamily of proteins. Here we describe a combined structural and functional investigation of PerB from Caulobacter crescentus. For this study, three structures were determined to 1.0 {angstrom} resolution or better: the enzyme in complex with CoA and GDP-perosamine, the protein with bound CoA and GDP-N-acetylperosamine, and the enzyme containing a tetrahedral transition state mimic bound in the active site. Each subunit of the trimeric enzyme folds into two distinct regions. The N-terminal domain is globular and dominated by a six-stranded mainly parallel {beta}-sheet. It provides most of the interactions between the protein and GDP-perosamine. The C-terminal domain consists of a left-handed {beta}-helix, which has nearly seven turns. This region provides the scaffold for CoA binding. On the basis of these high-resolution structures, site-directed mutant proteins were constructed to test the roles of His 141 and Asp 142 in the catalytic mechanism. Kinetic data and pH-rate profiles are indicative of His 141 serving as a general base. In addition, the backbone amide group of Gly 159 provides an oxyanion hole for stabilization of the tetrahedral transition state. The pH-rate profiles are also consistent with the GDP-linked amino sugar substrate entering the active site in its unprotonated form. Finally, for this investigation, we show that PerB can accept GDP-3-deoxyperosamine as an alternative substrate, thus representing the production of a novel trideoxysugar.

  7. Kinetic Monte Carlo and Cellular Particle Dynamics Simulations of Multicellular Systems

    CERN Document Server

    Flenner, Elijah; Barz, Bogdan; Neagu, Adrian; Forgacs, Gabor; Kosztin, Ioan

    2011-01-01

    Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Computer simulations based on Metropolis Monte Carlo (MMC) algorithms were successful in explaining and predicting the resulting stationary structures (corresponding to the lowest adhesion energy state). Here we introduce two alternatives to the MMC approach for modeling cellular motion and self-assembly: (1) a kinetic Monte Carlo (KMC), and (2) a cellular particle dynamics (CPD) method. Unlike MMC, both KMC and CPD methods are capable of simulating the dynamics of the cellular system in real time. In the KMC approach a transition rate is associated with possible rearrangements of the cellular system, and the corresponding time evolution is expressed in terms of these rates. In the CPD approach cells are modeled as interacting cellular ...

  8. Dynamic Kinetics of Methanol Synthesis over a Commercial Copper-Based Catalyst

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Adsorption, surface reaction and process dynamics on the surface of a commercial copper-based cata lyst for methanol synthesis from CO/CO2/H2 were systematically studied by means of temperature programmed desorption (TPD), tsmperature programmed surface reaction (TPSR), in-situ Fourier transform-inferred spec troscopy(FTIR) and stimulua-response techniques. As a part of results, an elementary step sequence was suggested and a group of ordinary differential equations (ODEs) for describing transient conversations relevant to all species on the catalyst surface and in the gas phase in a micro-fixed-bed reactor was derived. The values of the parameters referred to dynamic kinetics were estimated by fitting the solution of the ODEs with the transient response data obtained by the stimulus-response technique with a FTIR analyzer as an on-line detector.

  9. Charge to digital converter with constant resolution over the dynamic range

    Energy Technology Data Exchange (ETDEWEB)

    Nascetti, A. [Department of Aerospace and Astronautics Engineering, Sapienza University of Rome, via Eudossiana 16, 00184, Rome (Italy)

    2009-12-15

    A novel pixel-level charge to digital converter circuit suitable for multi-channel charge sensitive amplifiers or pixelated readout ICs for hybrid detectors is presented. The proposed circuit features large dynamic range operation with constant relative resolution over the whole dynamic range. These characteristics have been obtained by introducing the fractional charge packet counting concept. In particular, a solution has been proposed to obtain the analog-to-digital conversion with constant number of significant bits.

  10. Homogeneous states in driven granular mixtures: Enskog kinetic theory versus molecular dynamics simulations.

    Science.gov (United States)

    Khalil, Nagi; Garzó, Vicente

    2014-04-28

    The homogeneous state of a binary mixture of smooth inelastic hard disks or spheres is analyzed. The mixture is driven by a thermostat composed by two terms: a stochastic force and a drag force proportional to the particle velocity. The combined action of both forces attempts to model the interaction of the mixture with a bath or surrounding fluid. The problem is studied by means of two independent and complementary routes. First, the Enskog kinetic equation with a Fokker-Planck term describing interactions of particles with thermostat is derived. Then, a scaling solution to the Enskog kinetic equation is proposed where the dependence of the scaled distributions φi of each species on the granular temperature occurs not only through the dimensionless velocity c = v/v0 (v0 being the thermal velocity) but also through the dimensionless driving force parameters. Approximate forms for φi are constructed by considering the leading order in a Sonine polynomial expansion. The ratio of kinetic temperatures T1/T2 and the fourth-degree velocity moments λ1 and λ2 (which measure non-Gaussian properties of φ1 and φ2, respectively) are explicitly determined as a function of the mass ratio, size ratio, composition, density, and coefficients of restitution. Second, to assess the reliability of the theoretical results, molecular dynamics simulations of a binary granular mixture of spheres are performed for two values of the coefficient of restitution (α = 0.9 and 0.8) and three different solid volume fractions (ϕ = 0.00785, 0.1, and 0.2). Comparison between kinetic theory and computer simulations for the temperature ratio shows excellent agreement, even for moderate densities and strong dissipation. In the case of the cumulants λ1 and λ2, good agreement is found for the lower densities although significant discrepancies between theory and simulation are observed with increasing density.

  11. Differential kinetic dynamics and heating of ions in the turbulent solar wind

    Science.gov (United States)

    Valentini, F.; Perrone, D.; Stabile, S.; Pezzi, O.; Servidio, S.; De Marco, R.; Marcucci, F.; Bruno, R.; Lavraud, B.; De Keyser, J.; Consolini, G.; Brienza, D.; Sorriso-Valvo, L.; Retinò, A.; Vaivads, A.; Salatti, M.; Veltri, P.

    2016-12-01

    The solar wind plasma is a fully ionized and turbulent gas ejected by the outer layers of the solar corona at very high speed, mainly composed by protons and electrons, with a small percentage of helium nuclei and a significantly lower abundance of heavier ions. Since particle collisions are practically negligible, the solar wind is typically not in a state of thermodynamic equilibrium. Such a complex system must be described through self-consistent and fully nonlinear models, taking into account its multi-species composition and turbulence. We use a kinetic hybrid Vlasov-Maxwell numerical code to reproduce the turbulent energy cascade down to ion kinetic scales, in typical conditions of the uncontaminated solar wind plasma, with the aim of exploring the differential kinetic dynamics of the dominant ion species, namely protons and alpha particles. We show that the response of different species to the fluctuating electromagnetic fields is different. In particular, a significant differential heating of alphas with respect to protons is observed. Interestingly, the preferential heating process occurs in spatial regions nearby the peaks of ion vorticity and where strong deviations from thermodynamic equilibrium are recovered. Moreover, by feeding a simulator of a top-hat ion spectrometer with the output of the kinetic simulations, we show that measurements by such spectrometer planned on board the Turbulence Heating ObserveR (THOR mission), a candidate for the next M4 space mission of the European Space Agency, can provide detailed three-dimensional ion velocity distributions, highlighting important non-Maxwellian features. These results support the idea that future space missions will allow a deeper understanding of the physics of the interplanetary medium.

  12. Dynamic kinetic energy potential for orbital-free density functional theory.

    Science.gov (United States)

    Neuhauser, Daniel; Pistinner, Shlomo; Coomar, Arunima; Zhang, Xu; Lu, Gang

    2011-04-14

    A dynamic kinetic energy potential (DKEP) is developed for time-dependent orbital-free (TDOF) density function theory applications. This potential is constructed to affect only the dynamical (ω ≠ 0) response of an orbital-free electronic system. It aims at making the orbital-free simulation respond in the same way as that of a noninteracting homogenous electron gas (HEG), as required by a correct kinetic energy, therefore enabling extension of the success of orbital-free density functional theory in the static case (e.g., for embedding and description of processes in bulk materials) to dynamic processes. The potential is constructed by expansions of terms, each of which necessitates only simple time evolution (concurrent with the TDOF evolution) and a spatial convolution at each time-step. With 14 such terms a good fit is obtained to the response of the HEG at a large range of frequencies, wavevectors, and densities. The method is demonstrated for simple jellium spheres, approximating Na(9)(+) and Na(65)(+) clusters. It is applicable both to small and large (even ultralarge) excitations and the results converge (i.e., do not blow up) as a function of time. An extension to iterative frequency-resolved extraction is briefly outlined, as well as possibly numerically simpler expansions. The approach could also be extended to fit, instead of the HEG susceptibility, either an experimental susceptibility or a theoretically derived one for a non-HEG system. The DKEP potential should be a powerful tool for embedding a dynamical system described by a more accurate method (such as time-dependent density functional theory, TDDFT) in a large background described by TDOF with a DKEP potential. The type of expansions used and envisioned should be useful for other approaches, such as memory functionals in TDDFT. Finally, an appendix details the formal connection between TDOF and TDDFT.

  13. The kinetic Sunyaev-Zel'dovich Effect from Patchy Reionization: Simulated Full Sky Maps at Arcminute Resolution

    CERN Document Server

    Alvarez, Marcelo A

    2015-01-01

    The kinetic Sunyaev-Zel'dovich (kSZ) effect results from Thomson scattering by coherent flows the reionized intergalactic medium. The new results presented here follow from ray-tracing a 10 Gpc scale simulations at 2-3 Mpc scale resolution to create a full sky kSZ map that self-consistently includes the effects of reionization on scales corresponding to multipoles $10\\lesssim\\ell\\lesssim{5000}$. We separate the kSZ map into Doppler ($\\mathbf{v}$), Ostriker-Vishniac ($\\delta\\mathbf{v}$), patchy ($x\\mathbf{v}$), and third-order ($x\\delta\\mathbf{v}$) components, and compute explicitly all the auto and cross correlations (e.g., $\\langle\\mathbf{v}\\mathbf{v}\\rangle$, $\\langle\\delta\\mathbf{v}{x}\\mathbf{v}\\rangle$, etc.) that contribute to the total power. We find a complex and non-monotonic dependence on the duration of reionization at $\\ell\\sim{300}$ and evidence for a non-negligible (10-30 per cent) contribution from connected four point ionization-velocity correlations, $\\langle{x}\\mathbf{v}x\\mathbf{v}\\rangle_c$,...

  14. Charged particle dynamics and molecular kinetics in the hydrogen postdischarge plasma

    Science.gov (United States)

    Diomede, P.; Longo, S.; Capitelli, M.

    2006-11-01

    The afterglow of a parallel plate radio frequency discharge in hydrogen is studied by numerical modelling to compare ion dynamics and chemical effects on the behavior of negative ions. While the ion dynamics requires a kinetic description of space dependent plasma relaxation (at least 1D), chemical effects require a vibrational kinetics of hydrogen molecules. Since previous models did not include both features it has not been possible until now to realize both effects in a single simulation. We apply an updated version of the 1D Bari model which includes a 1.5D (1Dr2Dv) Particle in Cell/Monte Carlo (PIC/MC) multispecies module coupled to the space and time dependent master equation for H2(X1Σg+,v=0,…,14) vibrational level population. Negative ion fronts are described in hydrogen for the first time and their impact on the plasma limiting surfaces produces a negative ion current evolution compatible with experimental findings. In the same conditions, the attachment rate overshoot is found to contribute about 7% to the average ion density in the plasma.

  15. Dynamic Solvent Effect on Ultrafast Charge Recombination Kinetics in Excited Donor-Acceptor Complexes.

    Science.gov (United States)

    Mikhailova, Tatyana V; Mikhailova, Valentina A; Ivanov, Anatoly I

    2016-11-23

    Manifestation of the dynamic solvent effect (DSE) on the charge recombination (CR) kinetics of photoexcited donor-acceptor complexes in polar solvents has been investigated within the framework of the multichannel stochastic model. The model takes into account the reorganization of both the solvent and a number of intramolecular high-frequency vibration modes as well as their relaxation. The non-Markovian solvent dynamics is described in terms of two relaxation modes. The similarities and differences inherent to ultrafast charge transfer reactions occurring in the nonequilibrium and thermal regimes have been identified. The most important differences are as follows: (1) the DSE is strong in the area of weak exergonicity and is weak in the area of strong exergonicity for thermal reactions, whereas for the nonequilibrium reactions, the regions of strong and weak DSEs are reversed; (2) an increase in the electronic coupling value results in a decrease in the magnitude of DSE for nonequilibrium electron transfer and in its increase for the thermal reactions; and (3) the two-staged regime most clearly manifests if the reorganization energy of the relaxation modes noticeably exceeds the CR free-energy gap. With an increase in electronic coupling, the kinetics approaches the exponential regime because in the limit of strong electronic coupling, the reaction includes only single, nonequilibrium, stage.

  16. Clustering and heterogeneous dynamics in a kinetic Monte Carlo model of self-propelled hard disks.

    Science.gov (United States)

    Levis, Demian; Berthier, Ludovic

    2014-06-01

    We introduce a kinetic Monte Carlo model for self-propelled hard disks to capture with minimal ingredients the interplay between thermal fluctuations, excluded volume, and self-propulsion in large assemblies of active particles. We analyze in detail the resulting (density, self-propulsion) nonequilibrium phase diagram over a broad range of parameters. We find that purely repulsive hard disks spontaneously aggregate into fractal clusters as self-propulsion is increased and rationalize the evolution of the average cluster size by developing a kinetic model of reversible aggregation. As density is increased, the nonequilibrium clusters percolate to form a ramified structure reminiscent of a physical gel. We show that the addition of a finite amount of noise is needed to trigger a nonequilibrium phase separation, showing that demixing in active Brownian particles results from a delicate balance between noise, interparticle interactions, and self-propulsion. We show that self-propulsion has a profound influence on the dynamics of the active fluid. We find that the diffusion constant has a nonmonotonic behavior as self-propulsion is increased at finite density and that activity produces strong deviations from Fickian diffusion that persist over large time scales and length scales, suggesting that systems of active particles generically behave as dynamically heterogeneous systems.

  17. Nanometer resolution self-powered static and dynamic motion sensor based on micro-grated triboelectrification.

    Science.gov (United States)

    Zhou, Yu Sheng; Zhu, Guang; Niu, Simiao; Liu, Ying; Bai, Peng; Jing, Qingsheng; Wang, Zhong Lin

    2014-03-19

    A one-dimensional displacement and speed sensing technology that consists of a pair of micro-grating structures and utilizes the coupling between the triboelectric effect and electrostatic induction is demonstrated. Its distinct advantages, including being self-powered, high resolution, large dynamic range, and long detecting distance, show extensive potential applications in automation, manufacturing, process control, and portable devices.

  18. High spatial resolution three-dimensional mapping of vegetation spectral dynamics using computer vision

    Science.gov (United States)

    Jonathan P. Dandois; Erle C. Ellis

    2013-01-01

    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...

  19. Dynamics Analysis and Prediction of Genetic Regulation in Glycerol Metabolic Network via Structural Kinetic Modelling

    Directory of Open Access Journals (Sweden)

    Jianxiong Ye

    2015-01-01

    Full Text Available Glycerol can be biologically converted to 1,3-propanediol (1,3-PD by Klebsiella pneumoniae. In the synthesis pathway of 1,3-PD, the accumulation of an intermediary metabolite 3-hydroxypropionaldehyde (3-HPA would cause an irreversible cessation of the dynamic system. Genetic manipulation on the key enzymes which control the formation rate and consumption rate of 3-HPA would decrease the accumulation of 3-HPA, resulting in nonlinear regulation on the dynamic system. The interest of this work is to focus on analyzing the influence of 3-HPA inhibition on the stability of the dynamic system. Due to the lack of intracellular knowledge, structural kinetic modelling is applied. On the basis of statistical account of the dynamical capabilities of the system in the parameter space, we conclude that, under weak or no inhibition to the reaction of 3-HPA consumption, the system is much easier to obtain a stable state, whereas strong inhibition to its formation is in favor of stabilizing the system. In addition, the existence of Hopf bifurcation in this system is also verified. The obtained results are helpful for deeply understanding the metabolic and genetic regulations of glycerol fermentation by Klebsiella pneumoniae.

  20. Examining the limits of time reweighting and Kramers' rate theory to obtain correct kinetics from accelerated molecular dynamics.

    Science.gov (United States)

    Xin, Yao; Doshi, Urmi; Hamelberg, Donald

    2010-06-14

    Accelerated molecular dynamics simulations are routinely being used to recover the correct canonical probability distributions corresponding to the original potential energy landscape of biomolecular systems. However, the limits of time reweighting, based on transition state theory, in obtaining true kinetic rates from accelerated molecular dynamics for biomolecular systems are less obvious. Here, we investigate this issue by studying the kinetics of cis-trans isomerization of peptidic omega bond by accelerated molecular dynamics. We find that time reweighting is valid for obtaining true kinetics when the original potential is not altered at the transition state regions, as expected. When the original potential landscape is modified such that the applied boost potential alters the transition state regions, time reweighting fails to reproduce correct kinetics and the reweighted rate is much slower than the true rate. By adopting the overdamped limit of Kramers' rate theory, we are successful in recovering correct kinetics irrespective of whether or not the transition state regions are modified. Furthermore, we tested the validity of the acceleration weight factor from the path integral formalism for obtaining the correct kinetics of cis-trans isomerization. It was found that this formulation of the weight factor is not suitable for long time scale processes such as cis-trans isomerization with high energy barriers.

  1. Super-resolution imaging in digital holography by using dynamic grating with a spatial light modulator

    Science.gov (United States)

    Lin, Qiaowen; Wang, Dayong; Wang, Yunxin; Rong, Lu; Chang, Shifeng

    2015-03-01

    A super-resolution imaging method using dynamic grating based on liquid-crystal spatial light modulator (SLM) is developed to improve the resolution of a digital holographic system. The one-dimensional amplitude cosine grating is loaded on the SLM, which is placed between the object and hologram plane in order to collect more high-frequency components towards CCD plane. The point spread function of the system is given to confirm the separation condition of reconstructed images for multiple diffraction orders. The simulation and experiments are carried out for a standard resolution test target as a sample, which confirms that the imaging resolution is improved from 55.7 μm to 31.3 μm compared with traditional lensless Fourier transform digital holography. The unique advantage of the proposed method is that the period of the grating can be programmably adjusted according to the separation condition.

  2. 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.

  3. 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

  4. Tropical Pacific internal atmospheric dynamics and resolution in a coupled GCM

    Science.gov (United States)

    Lopez, Hosmay; Kirtman, Ben P.

    2015-01-01

    A noise reduction technique, namely the interactive ensemble (IE) approach is adopted to reduce noise at the air-sea interface due to internal atmospheric dynamics in a state-of-the-art coupled general circulation model (CGCM). The IE technique uses multiple realization of atmospheric general circulation models coupled to a single ocean general circulation model. The ensembles mean fluxes from the atmospheric simulations are communicated to the ocean component. Each atmospheric simulation receives the same SST coming from the ocean component. The only difference among the atmospheric simulations comes from perturbed initial conditions, thus the atmospheric states are, in principle synoptically independent. The IE technique can be used to better understand the importance of weather noise forcing of natural variability such as El Niño Southern Oscillation (ENSO). To study the impact of weather noise and resolution in the context of a CGCM, two IE experiments are performed at different resolutions. Atmospheric resolution is an important issue since the noise statistics will depend on the spatial scales resolved. A simple formulation to extract atmospheric internal variability is presented. The results are compared to their respective control cases where internal atmospheric variability is left unchanged. The noise reduction has a major impact on the coupled simulation and the magnitude of this effect strongly depends on the horizontal resolution of the atmospheric component model. Specifically, applying the noise reduction technique reduces the overall climate variability more effectively at higher resolution. This suggests that "weather noise" is more important in sustaining climate variability as resolution increases. ENSO statistics, dynamics, and phase asymmetry are all modified by the noise reduction, in particular ENSO becomes more regular with less phase asymmetry when noise is reduced. All these effects are more marked for the higher resolution case. In

  5. Real-time high-resolution heterodyne-based measurements of spectral dynamics in fibre lasers

    Science.gov (United States)

    Sugavanam, Srikanth; Fabbri, Simon; Le, Son Thai; Lobach, Ivan; Kablukov, Sergey; Khorev, Serge; Churkin, Dmitry

    2016-03-01

    Conventional tools for measurement of laser spectra (e.g. optical spectrum analysers) capture data averaged over a considerable time period. However, the generation spectrum of many laser types may involve spectral dynamics whose relatively fast time scale is determined by their cavity round trip period, calling for instrumentation featuring both high temporal and spectral resolution. Such real-time spectral characterisation becomes particularly challenging if the laser pulses are long, or they have continuous or quasi-continuous wave radiation components. Here we combine optical heterodyning with a technique of spatio-temporal intensity measurements that allows the characterisation of such complex sources. Fast, round-trip-resolved spectral dynamics of cavity-based systems in real-time are obtained, with temporal resolution of one cavity round trip and frequency resolution defined by its inverse (85 ns and 24 MHz respectively are demonstrated). We also show how under certain conditions for quasi-continuous wave sources, the spectral resolution could be further increased by a factor of 100 by direct extraction of phase information from the heterodyned dynamics or by using double time scales within the spectrogram approach.

  6. The Kinetic Sunyaev-Zel’dovich Effect from Reionization: Simulated Full-sky Maps at Arcminute Resolution

    Science.gov (United States)

    Alvarez, Marcelo A.

    2016-06-01

    The kinetic Sunyaev-Zel’dovich (kSZ) effect results from Thomson scattering by coherent flows in the reionized intergalactic medium. We present new results based on ray-tracing an 8 Gpc/h realization of reionization with resolution elements 2 Mpc/h (subtending ˜ 1‧ at z = 6) on a side to create a full-sky kSZ map. The realization includes, self-consistently, the effects of reionization on scales corresponding to multipoles 10≲ {\\ell }≲ 5000. We separate the kSZ map into Doppler ({\\boldsymbol{v}}), Ostriker-Vishniac (δ {\\boldsymbol{v}}), patchy (x{\\boldsymbol{v}}), and third-order (xδ {\\boldsymbol{v}}) components, and compute explicitly all the auto- and cross-correlations (e.g., , , etc.) that contribute to the total power. We find a complex and nonmonotonic dependence on the duration of reionization at {\\ell }˜ 300 and evidence for a non-negligible (10%-30%) contribution from connected four-point correlations, }c, usually neglected in analytical models. We also investigate the cross-correlation of linear matter and large-scale kSZ temperature fluctuations, focusing on (1) cross-power spectra with biased tracers of the matter density and (2) cold spots from infall onto large, rare H ii regions centered on peaks in the matter distribution at redshifts z\\gt 10 that are a generic non-Gaussian feature of patchy reionization. Finally, we show that the reionization history can be reconstructed at 5σ-10σ significance by correlating full-sky 21 cm maps stacked in bins with {{Δ }}ν = 10 {{MHz}} with existing cosmic microwave background (CMB) temperature maps at {\\ell }\\lt 500, raising the prospects for probing reionization by correlating CMB and LSS measurements. The resulting kSZ maps have been made publicly available at www.cita.utoronto.ca/~malvarez/research/ksz-data/.

  7. Microwave-Assisted Kinetic Resolution of Homochiral (Z-Cyclooct-5-ene-1,2-diol and (Z-2-Acetoxycyclooct-4-enyl Acetate Using Lipases

    Directory of Open Access Journals (Sweden)

    Hervé Rouillard

    2014-07-01

    Full Text Available Over the last decade, the use of biocatalysts has become an attractive alternative to conventional chemical methods, especially for organic synthesis, due to their unusual properties. Among these enzymes, lipases are the most widely used, because they are cheap, easily available, cofactor-free, and have broad substrate specificity. Combined to microwave heating in non-aqueous medium, recent results suggest that irradiation may influence the enzyme activity. This Communication reports the benefits of lipases and the microwave irradiation on the kinetic resolution of racemic homochiral (Z-cyclooct-5-ene-1,2-diol and (Z-2-acetoxycyclooct-4-enyl acetate. In order to best achieve the kinetic resolution, different parameters were studied including the type of lipase, the temperature, the impact of microwave power compared to conventional heating. Optimization of the reaction parameters lead to the obtainment of highly enriched or enantiopure diols and diesters in a clean, efficient and safe way.

  8. Analytical structure, dynamics, and coarse graining of a kinetic model of an active fluid

    Science.gov (United States)

    Gao, Tong; Betterton, Meredith D.; Jhang, An-Sheng; Shelley, Michael J.

    2017-09-01

    We analyze one of the simplest active suspensions with complex dynamics: a suspension of immotile "extensor" particles that exert active extensile dipolar stresses on the fluid in which they are immersed. This is relevant to several experimental systems, such as recently studied tripartite rods that create extensile flows by consuming a chemical fuel. We first describe the system through a Doi-Onsager kinetic theory based on microscopic modeling. This theory captures the active stresses produced by the particles that can drive hydrodynamic instabilities, as well as the steric interactions of rodlike particles that lead to nematic alignment. This active nematic system yields complex flows and disclination defect dynamics very similar to phenomenological Landau-deGennes Q -tensor theories for active nematic fluids, as well as by more complex Doi-Onsager theories for polar microtubule-motor-protein systems. We apply the quasiequilibrium Bingham closure, used to study suspensions of passive microscopic rods, to develop a nonstandard Q -tensor theory. We demonstrate through simulation that this B Q -tensor theory gives an excellent analytical and statistical accounting of the suspension's complex dynamics, at a far reduced computational cost. Finally, we apply the B Q -tensor model to study the dynamics of extensor suspensions in circular and biconcave domains. In circular domains, we reproduce previous results for systems with weak nematic alignment, but for strong alignment we find unusual dynamics with activity-controlled defect production and absorption at the boundaries of the domain. In biconcave domains, a Fredericks-like transition occurs as the width of the neck connecting the two disks is varied.

  9. Generating relevant kinetic Monte Carlo catalogs using temperature accelerated dynamics with control over the accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Chatterjee, Abhijit [Los Alamos National Laboratory; Voter, Arthur [Los Alamos National Laboratory

    2009-01-01

    We develop a variation of the temperature accelerated dynamics (TAD) method, called the p-TAD method, that efficiently generates an on-the-fly kinetic Monte Carlo (KMC) process catalog with control over the accuracy of the catalog. It is assumed that transition state theory is valid. The p-TAD method guarantees that processes relevant at the timescales of interest to the simulation are present in the catalog with a chosen confidence. A confidence measure associated with the process catalog is derived. The dynamics is then studied using the process catalog with the KMC method. Effective accuracy of a p-TAD calculation is derived when a KMC catalog is reused for conditions different from those the catalog was originally generated for. Different KMC catalog generation strategies that exploit the features of the p-TAD method and ensure higher accuracy and/or computational efficiency are presented. The accuracy and the computational requirements of the p-TAD method are assessed. Comparisons to the original TAD method are made. As an example, we study dynamics in sub-monolayer Ag/Cu(110) at the time scale of seconds using the p-TAD method. It is demonstrated that the p-TAD method overcomes several challenges plaguing the conventional KMC method.

  10. Effects of Collective Histone State Dynamics on Epigenetic Landscape and Kinetics of Cell Reprogramming

    Science.gov (United States)

    Ashwin, S. S.; Sasai, Masaki

    2015-11-01

    Cell reprogramming is a process of transitions from differentiated to pluripotent cell states via transient intermediate states. Within the epigenetic landscape framework, such a process is regarded as a sequence of transitions among basins on the landscape; therefore, theoretical construction of a model landscape which exhibits experimentally consistent dynamics can provide clues to understanding epigenetic mechanism of reprogramming. We propose a minimal gene-network model of the landscape, in which each gene is regulated by an integrated mechanism of transcription-factor binding/unbinding and the collective chemical modification of histones. We show that the slow collective variation of many histones around each gene locus alters topology of the landscape and significantly affects transition dynamics between basins. Differentiation and reprogramming follow different transition pathways on the calculated landscape, which should be verified experimentally via single-cell pursuit of the reprogramming process. Effects of modulation in collective histone state kinetics on transition dynamics and pathway are examined in search for an efficient protocol of reprogramming.

  11. Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle

    Science.gov (United States)

    Yu, Jin; Da, Lin-Tai; Huang, Xuhui

    2015-02-01

    The RNA polymerase II elongation is central in eukaryotic transcription. Although multiple intermediates of the elongation complex have been identified, the dynamical mechanisms remain elusive or controversial. Here we build a structure-based kinetic model of a full elongation cycle of polymerase II, taking into account transition rates and conformational changes characterized from both single molecule experimental studies and computational simulations at atomistic scale. Our model suggests a force-dependent slow transition detected in the single molecule experiments corresponds to an essential conformational change of a trigger loop (TL) opening prior to the polymerase translocation. The analyses on mutant study of E1103G and on potential sequence effects of the translocation substantiate this proposal. Our model also investigates another slow transition detected in the transcription elongation cycle which is independent of mechanical force. If this force-independent slow transition happens as the TL gradually closes upon NTP binding, the analyses indicate that the binding affinity of NTP to the polymerase has to be sufficiently high. Otherwise, one infers that the slow transition happens pre-catalytically but after the TL closing. Accordingly, accurate determination of intrinsic properties of NTP binding is demanded for an improved characterization of the polymerase elongation. Overall, the study provides a working model of the polymerase II elongation under a generic Brownian ratchet mechanism, with most essential structural transition and functional kinetics elucidated.

  12. Dynamic Recrystallization Kinetics and Microstructural Evolution for LZ50 Steel During Hot Deformation

    Science.gov (United States)

    Du, Shiwen; Chen, Shuangmei; Song, Jianjun

    2016-09-01

    The dynamic recrystallization (DRX) behavior of LZ50 steel was investigated using hot compression tests at a deformation temperature of 870-1170 °C and a strain rate of 0.05-3 s-1. The effects of deformation temperature, strain, strain rate, and initial austenite grain size on the microstructural evolution during DRX were studied in detail. The austenite grain size of DRX was refined with increasing strain rate and decreasing temperature, whereas the initial grain size had no influence on DRX grain size. A model based on the Avrami equation was proposed to estimate the kinetics of the DRX under different deformation conditions. A DRX map, which was derived from the DRX kinetics, the recrystallized microstructure, and the flow stress analysis, can be used to identify optimal deformation conditions. The initiation of DRX was lower than Z c (critical Zener-Hollomon parameter) and higher than ɛc (critical strain). The relationship between the DRX microstructure and the Z parameter was analyzed. Fine DRX grain sizes can be achieved with a moderate Z value, which can be used to identify suitable deformation parameters.

  13. Kinetic thin current sheets: their formation in relation to magnetotail mesoscale turbulent dynamics

    Directory of Open Access Journals (Sweden)

    A. P. Kropotkin

    2009-04-01

    Full Text Available Dynamics of the magnetotail plasma sheet (PS features nonlinear structures on two totally different scales. There are very thin current sheets (CS on kinetic scale of the ion gyroradius. And there are intense plasma flow and magnetic field variations on mesoscales (a few earth radii; those are interpreted as mostly 2-D MHD turbulence. On the other hand, the specific nature of slow large scale magnetotail evolution leads to large differences in the PS properties and those of the lobe plasma. As a result, while fast reconnection bursts in the tail provide quasi-stationary fast mesoscale reconfigurations in the lobes, they cannot however be accompanied by restructuring of CS on the same fast time scale. Violations of force balance in the PS are thus generated. Simulation using a hybrid code and starting with such imbalance, provides an evidence of very thin kinetic CS structures formation, embedded into the much thicker PS. The momentum balance gets locally restored by means of ion acceleration up to the Alfvénic velocity. The process provides an effective mechanism for transformation of magnetic energy accumulated in the magnetotail, into energy of plasma flows. The fast flows may drive turbulence on shorter spatial scales. In their turn, these motions may serve as an origin for new neutral line generation, and reconnection. Application to substorm phenomenology is discussed.

  14. Numerical investigation of kinetic energy dynamics during autoignition of n-heptane/air mixture

    Science.gov (United States)

    Lucena Kreppel Paes, Paulo; Brasseur, James; Xuan, Yuan

    2015-11-01

    Many engineering applications involve complex turbulent reacting flows, where nonlinear, multi-scale turbulence-combustion couplings are important. Direct representation of turbulent reacting flow dynamics is associated with prohibitive computational costs, which makes it necessary to employ turbulent combustion models to account for the effects of unresolved scales on resolved scales. Classical turbulence models are extensively employed in reacting flow simulations. However, they rely on assumptions about the energy cascade, which are valid for incompressible, isothermal homogeneous isotropic turbulence. A better understanding of the turbulence-combustion interactions is required for the development of more accurate, physics-based sub-grid-scale models for turbulent reacting flows. In order to investigate the effects of reaction-induced density, viscosity, and pressure variations on the turbulent kinetic energy, Direct Numerical Simulation (DNS) of autoignition of partially-premixed, lean n-heptane/air mixture in three-dimensional homogeneous isotropic turbulence has been performed. This configuration represents standard operating conditions of Homogeneous-Charge Compression-Ignition (HCCI) engines. The differences in the turbulent kinetic energy balance between the present turbulent reacting flow and incompressible, isothermal homogeneous isotropic turbulence are highlighted at different stages during the autoignition process.

  15. Binding kinetics of membrane-anchored receptors and ligands: Molecular dynamics simulations and theory.

    Science.gov (United States)

    Hu, Jinglei; Xu, Guang-Kui; Lipowsky, Reinhard; Weikl, Thomas R

    2015-12-28

    The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring of the proteins. In this article, we (i) present detailed data for the binding of membrane-anchored proteins from coarse-grained molecular dynamics simulations and (ii) provide a theory that describes how the binding kinetics depends on the average separation and thermal roughness of the adhering membranes and on the anchoring, lengths, and length variations of the proteins. An important element of our theory is the tilt of bound receptor-ligand complexes and transition-state complexes relative to the membrane normals. This tilt results from an interplay of the anchoring energy and rotational entropy of the complexes and facilitates the formation of receptor-ligand bonds at membrane separations smaller than the preferred separation for binding. In our simulations, we have considered both lipid-anchored and transmembrane receptor and ligand proteins. We find that the binding equilibrium constant and binding on-rate constant of lipid-anchored proteins are considerably smaller than the binding constant and on-rate constant of rigid transmembrane proteins with identical binding domains.

  16. 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

  17. Modeling vancomycin release kinetics from microporous calcium phosphate ceramics comparing static and dynamic immersion conditions.

    Science.gov (United States)

    Gbureck, Uwe; Vorndran, Elke; Barralet, Jake E

    2008-09-01

    The release kinetics of vancomycin from calcium phosphate dihydrate (brushite) matrices and polymer/brushite composites were compared using different fluid replacement regimes, a regular replacement (static conditions) and a continuous flow technique (dynamic conditions). The use of a constantly refreshed flowing resulted in a faster drug release due to a constantly high diffusion gradient between drug loaded matrix and the eluting medium. Drug release was modeled using the Weibull, Peppas and Higuchi equations. The results showed that drug liberation was diffusion controlled for the ceramics matrices, whereas ceramics/polymer composites led to a mixed diffusion and degradation controlled release mechanism. The continuous flow technique was for these materials responsible for a faster release due to an accelerated polymer degradation rate compared with the regular fluid replacement technique.

  18. Spin kinetic Monte Carlo method for nanoferromagnetism and magnetization dynamics of nanomagnets with large magnetic anisotropy

    Institute of Scientific and Technical Information of China (English)

    LIU Bang-gui; ZHANG Kai-cheng; LI Ying

    2007-01-01

    The Kinetic Monte Carlo (KMC) method based on the transition-state theory, powerful and famous for sim-ulating atomic epitaxial growth of thin films and nanostruc-tures, was used recently to simulate the nanoferromagnetism and magnetization dynamics of nanomagnets with giant mag-netic anisotropy. We present a brief introduction to the KMC method and show how to reformulate it for nanoscale spin systems. Large enough magnetic anisotropy, observed exper-imentally and shown theoretically in terms of first-principle calculation, is not only essential to stabilize spin orientation but also necessary in making the transition-state barriers dur-ing spin reversals for spin KMC simulation. We show two applications of the spin KMC method to monatomic spin chains and spin-polarized-current controlled composite nano-magnets with giant magnetic anisotropy. This spin KMC method can be applied to other anisotropic nanomagnets and composite nanomagnets as long as their magnetic anisotropy energies are large enough.

  19. 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.

  20. Bifurcation of resistive wall mode dynamics predicted by magnetohydrodynamic-kinetic hybrid theory

    Energy Technology Data Exchange (ETDEWEB)

    Yang, S. X.; Wang, Z. X., E-mail: zxwang@dlut.edu.cn [Key Laboratory of Materials Modification by Beams of the Ministry of Education, School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian 116024 (China); Wang, S.; Hao, G. Z., E-mail: haogz@swip.ac.cn; Song, X. M.; Wang, A. K. [Southwestern Institute of Physics, P.O.Box 432, Chengdu 610041 (China); Liu, Y. Q. [Culham Centre for Fusion Energy, Culham Science Centre, Abingdon OX14 3DB (United Kingdom); Southwestern Institute of Physics, P.O.Box 432, Chengdu 610041 (China)

    2015-09-15

    The magnetohydrodynamic-kinetic hybrid theory has been extensively and successfully applied for interpreting experimental observations of macroscopic, low frequency instabilities, such as the resistive wall mode, in fusion plasmas. In this work, it is discovered that an analytic version of the hybrid formulation predicts a bifurcation of the mode dynamics while varying certain physical parameters of the plasma, such as the thermal particle collisionality or the ratio of the thermal ion to electron temperatures. This bifurcation can robustly occur under reasonably large parameter spaces as well as with different assumptions, for instance, on the particle collision model. Qualitatively similar bifurcation features are also observed in full toroidal computations presented in this work, based on a non-perturbative hybrid formulation.

  1. 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

    2014-07-01

    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.

  2. Newtonian kinetic isotope effects. Observation, prediction, and origin of heavy-atom dynamic isotope effects.

    Science.gov (United States)

    Kelly, Kelmara K; Hirschi, Jennifer S; Singleton, Daniel A

    2009-06-24

    Intramolecular (13)C kinetic isotope effects were determined for the dimerization of cyclopentadiene. Substantial isotope effects were observed in three positions, despite the C(2) symmetry of the cycloaddition transition state and the absence of dynamical bottlenecks after this transition state. The observed isotope effects were predicted well from trajectory studies by extrapolating the outcomes of trajectories incorporating superheavy isotopes of carbon, ranging from (20)C to (140)C. Trajectory studies suggest that the isotope effects are unrelated to zero-point energy or the geometrical and momentum properties of the transition state. However, steepest-descent paths in mass-weighted coordinates correctly predict the direction of the isotope effects, supporting a novel origin in Newton's second law of motion.

  3. 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.

  4. 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.

  5. Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux.

    Science.gov (United States)

    Tan, Yikun; Rivera, Jimmy G Lafontaine; Contador, Carolina A; Asenjo, Juan A; Liao, James C

    2011-01-01

    Dynamic models of metabolism are instrumental for gaining insight and predicting possible outcomes of perturbations. Current approaches start from the selection of lumped enzyme kinetics and determine the parameters within a large parametric space. However, kinetic parameters are often unknown and obtaining these parameters requires detailed characterization of enzyme kinetics. In many cases, only steady-state fluxes are measured or estimated, but these data have not been utilized to construct dynamic models. Here, we extend the previously developed Ensemble Modeling methodology by allowing various kinetic rate expressions and employing a more efficient solution method for steady states. We show that anchoring the dynamic models to the same flux reduces the allowable parameter space significantly such that sampling of high dimensional kinetic parameters becomes meaningful. The methodology enables examination of the properties of the model's structure, including multiple steady states. Screening of models based on limited steady-state fluxes or metabolite profiles reduces the parameter space further and the remaining models become increasingly predictive. We use both succinate overproduction and central carbon metabolism in Escherichia coli as examples to demonstrate these results. Published by Elsevier Inc.

  6. Dynamic Kinetic Resolution of 2-Phenylpropanal Derivatives to Yield β-Chiral Primary Amines via Bioamination

    NARCIS (Netherlands)

    Fuchs, C.S.; Hollauf, M.; Meissner, M.; Simon, R.C.; Besset, T.; Reek, J.N.H.; Riethorst, W.; Zepeck, F.; Kroutil, W.

    2014-01-01

    The amination of racemic alpha-chiral aldehydes, 2-phenylpropanal derivatives, was investigated employing omega-transaminases. By medium and substrate engineering the optical purity of the resulting β-chiral chiral amine could be enhanced to reach optical purities up to 99% ee. Using enantiocompleme

  7. Dynamic nuclear magnetic resonance field sensing with part-per-trillion resolution

    Science.gov (United States)

    Gross, Simon; Barmet, Christoph; Dietrich, Benjamin E.; Brunner, David O.; Schmid, Thomas; Pruessmann, Klaas P.

    2016-12-01

    High-field magnets of up to tens of teslas in strength advance applications in physics, chemistry and the life sciences. However, progress in generating such high fields has not been matched by corresponding advances in magnetic field measurement. Based mostly on nuclear magnetic resonance, dynamic high-field magnetometry is currently limited to resolutions in the nanotesla range. Here we report a concerted approach involving tailored materials, magnetostatics and detection electronics to enhance the resolution of nuclear magnetic resonance sensing by three orders of magnitude. The relative sensitivity thus achieved amounts to 1 part per trillion (10-12). To exemplify this capability we demonstrate the direct detection and relaxometry of nuclear polarization and real-time recording of dynamic susceptibility effects related to human heart function. Enhanced high-field magnetometry will generally permit a fresh look at magnetic phenomena that scale with field strength. It also promises to facilitate the development and operation of high-field magnets.

  8. DUSTER: dynamic contrast enhance up-sampled temporal resolution analysis method.

    Science.gov (United States)

    Liberman, Gilad; Louzoun, Yoram; Artzi, Moran; Nadav, Guy; Ewing, James R; Ben Bashat, Dafna

    2016-05-01

    Dynamic contrast enhanced (DCE) MRI using Tofts' model for estimating vascular permeability is widely accepted, yet inter-tissue differences in bolus arrival time (BAT) are generally ignored. In this work we propose a method, incorporating the BAT in the analysis, demonstrating its applicability and advantages in healthy subjects and patients. A method for DCE Up Sampled TEmporal Resolution (DUSTER) analysis is proposed which includes: baseline T1 map using DESPOT1 analyzed with flip angle (FA) correction; preprocessing; raw-signal-to-T1-to-concentration time curves (CTC) conversion; automatic arterial input function (AIF) extraction at temporal super-resolution; model fitting with model selection while incorporating BAT in the pharmacokinetic (PK) model, and fits contrast agent CTC while using exhaustive search in the BAT dimension in super-resolution. The method was applied to simulated data and to human data from 17 healthy subjects, six patients with glioblastoma, and two patients following stroke. BAT values were compared to time-to-peak (TTP) values extracted from dynamic susceptibility contrast imaging. Results show that the method improved the AIF estimation and allowed extraction of the BAT with a resolution of 0.8 s. In simulations, lower mean relative errors were detected for all PK parameters extracted using DUSTER compared to analysis without BAT correction (vp:5% vs. 20%, Ktrans: 9% vs. 24% and Kep: 8% vs. 17%, respectively), and BAT estimates demonstrated high correlations (r = 0.94, p resolution (2 s) and sub-sampled standard resolution data (6 s) (mean r = 0.85,p < 1e− 10). BAT and TTP values were significantly correlated in the different brain regions in healthy subjects (mean r = 0.72,p = < 1e− 3), as were voxel-wise comparisons in patients (mean r = 0.89, p < 1e− 10). In conclusion, incorporating BAT in DCE analysis improves estimation accuracy for the AIF and the PK parameters while providing an additional clinically important parameter.

  9. Towards a resolution of certain dilemmas in preon dynamics through local supersymmetry

    Science.gov (United States)

    Pati, Jogesh C.; Cveti, Mirjam; Sharatchandra, H. S.

    1987-03-01

    A resolution of one of the major dilemmas of preon dynamics, i.e., why (mq,ml)<<(1/r0)≡Λ0, is provided. In a class of models, supersymmetry (SUSY) in its local rather than global form permits a breaking of SUSY and also a generation of composite-fermion masses, but both with a severe damping by powers of (Λ0/MPlanck).

  10. High resolution ultrasonic monitoring of muscle dynamics and novel approach to modelling

    OpenAIRE

    Muhammad, Zakir Hossain

    2013-01-01

    The presented work is concerned with the development and application of an ultrasonic detection scheme suitable for the monitoring of muscle dynamics with high temporal - down to 5 µs - and spatial resolution - down to 0.78 µm. A differential detection scheme has been developed to monitor the variations of the velocity of longitudinal polarized ultrasound waves travelling in contracting and relaxing muscle, compensating for variations of the path length by referencing to a frame. The observed...

  11. Temporal Dynamics of Motivation-Cognitive Control Interactions Revealed by High-Resolution Pupillometry

    OpenAIRE

    Chiew, Kimberly S.; Braver, Todd S.

    2013-01-01

    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 cue...

  12. Dynamic kinetic analysis of growth of Listeria monocytogenes in a simulated comminuted, non-cured cooked pork product

    Science.gov (United States)

    The objective of this study was to directly construct a tertiary growth model for Listeria monocytogenes in cooked pork and simultaneously determine the kinetic parameters using a combination of dynamic and isothermal growth curves. Growth studies were conducted using a cocktail of 5 strains of L. ...

  13. 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...

  14. Confined martensitic phase transformation kinetics and lattice dynamics in Ni–Co–Fe–Ga shape memory alloys

    Energy Technology Data Exchange (ETDEWEB)

    Cong, Daoyong; Rule, Kirrily Clair; Li, Wen-Hsien; Lee, Chi-Hung; Zhang, Qinghua; Wang, Haoliang; Hao, Yulin; Wang, Yandong; Huang, E-Wen (UST - China); (NCU-Taiwan); (Beijing Inst. Tech.); (Chinese Aca. Sci.); (ANSTO); (NCTU)

    2016-09-02

    Here we describe insights into the phase transformation kinetics and lattice dynamics associated with the newly discovered confined martensitic transformation, which are of great significance to the in-depth understanding of the phase transformation behavior responsible for the rich new physical phenomena in shape memory alloys and could shed light on the design of novel multifunctional properties through tuning the confined martensitic transformation.

  15. Dynamic Proteomics: In Vivo Proteome-Wide Measurement of Protein Kinetics Using Metabolic Labeling.

    Science.gov (United States)

    Holmes, W E; Angel, T E; Li, K W; Hellerstein, M K

    2015-01-01

    Control of biosynthetic and catabolic rates of polymers, including proteins, stands at the center of phenotype, physiologic adaptation, and disease pathogenesis. Advances in stable isotope-labeling concepts and mass spectrometric instrumentation now allow accurate in vivo measurement of protein synthesis and turnover rates, both for targeted proteins and for unbiased screening across the proteome. We describe here the underlying principles and operational protocols for measuring protein dynamics, focusing on metabolic labeling with (2)H2O (heavy water) combined with tandem mass spectrometric analysis of mass isotopomer abundances in trypsin-generated peptides. The core principles of combinatorial analysis (mass isotopomer distribution analysis or MIDA) are reviewed in detail, including practical advantages, limitations, and technical procedures to ensure optimal kinetic results. Technical factors include heavy water labeling protocols, optimal duration of labeling, clean up and simplification of sample matrices, accurate quantitation of mass isotopomer abundances in peptides, criteria for adequacy of mass spectrometric abundance measurements, and calculation algorithms. Some applications are described, including the noninvasive "virtual biopsy" strategy for measuring molecular flux rates in tissues through measurements in body fluids. In addition, application of heavy water labeling to measure flux lipidomics is noted. In summary, the combination of stable isotope labeling, particularly from (2)H2O, with tandem mass spectrometric analysis of mass isotopomer abundances in peptides, provides a powerful approach for characterizing the dynamics of proteins across the global proteome. Many applications in research and clinical medicine have been achieved and many others can be envisioned.

  16. 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.

  17. Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories.

    Science.gov (United States)

    Zhang, Jun; Yang, Y Isaac; Yang, Lijiang; Gao, Yi Qin

    2015-11-12

    High potential energy barriers and engagement of solvent coordinates set challenges for in silico studies of chemical reactions, and one is quite commonly limited to study reactions along predefined reaction coordinate(s). A systematic protocol, QM/MM MD simulations using enhanced sampling of reactive trajectories (ESoRT), is established to quantitatively study chemical transitions in complex systems. A number of trajectories for Claisen rearrangement in water and toluene were collected and analyzed, respectively. Evidence was found that the bond making and breaking during this reaction are concerted processes in solutions, preferentially through a chairlike configuration. Water plays an important dynamic role that helps stabilize the transition sate, and the dipole-dipole interaction between water and the solute also lowers the transition barrier. The calculated rate coefficient is consistent with the experimental measurement. Compared with water, the reaction pathway in toluene is "narrower" and the reaction rate is slower by almost three orders of magnitude due to the absence of proper interactions to stabilize the transition state. This study suggests that the "in-water" nature of the Claisen rearrangement in aqueous solution influences its thermodynamics, kinetics, as well as dynamics.

  18. Modeling of an aerobic biofilm reactor with double-limiting substrate kinetics: bifurcational and dynamical analysis.

    Science.gov (United States)

    Olivieri, Giuseppe; Russo, Maria Elena; Marzocchella, Antonio; Salatino, Piero

    2011-01-01

    A mathematical model of an aerobic biofilm reactor is presented to investigate the bifurcational patterns and the dynamical behavior of the reactor as a function of different key operating parameters. Suspended cells and biofilm are assumed to grow according to double limiting kinetics with phenol inhibition (carbon source) and oxygen limitation. The model presented by Russo et al. is extended to embody key features of the phenomenology of the granular-supported biofilm: biofilm growth and detachment, gas-liquid oxygen transport, phenol, and oxygen uptake by both suspended and immobilized cells, and substrate diffusion into the biofilm. Steady-state conditions and stability, and local dynamic behavior have been characterized. The multiplicity of steady states and their stability depend on key operating parameter values (dilution rate, gas-liquid mass transfer coefficient, biofilm detachment rate, and inlet substrate concentration). Small changes in the operating conditions may be coupled with a drastic change of the steady-state scenario with transcritical and saddle-node bifurcations. The relevance of concentration profiles establishing within the biofilm is also addressed. When the oxygen level in the liquid phase is <10% of the saturation level, the biofilm undergoes oxygen starvation and the active biofilm fraction becomes independent of the dilution rate. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011.

  19. 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.

  20. High-resolution dynamic atomic force microscopy in liquids with different feedback architectures

    Directory of Open Access Journals (Sweden)

    John Melcher

    2013-02-01

    Full Text Available The recent achievement of atomic resolution with dynamic atomic force microscopy (dAFM [Fukuma et al., Appl. Phys. Lett. 2005, 87, 034101], where quality factors of the oscillating probe are inherently low, challenges some accepted beliefs concerning sensitivity and resolution in dAFM imaging modes. Through analysis and experiment we study the performance metrics for high-resolution imaging with dAFM in liquid media with amplitude modulation (AM, frequency modulation (FM and drive-amplitude modulation (DAM imaging modes. We find that while the quality factors of dAFM probes may deviate by several orders of magnitude between vacuum and liquid media, their sensitivity to tip–sample forces can be remarkable similar. Furthermore, the reduction in noncontact forces and quality factors in liquids diminishes the role of feedback control in achieving high-resolution images. The theoretical findings are supported by atomic-resolution images of mica in water acquired with AM, FM and DAM under similar operating conditions.

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

    Science.gov (United States)

    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 200l stirred stainless steel vessel at a pH of 7.2 and a temperature of 38 degrees 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 2-50mm). 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.

  2. 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.

  3. Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application

    CERN Document Server

    Agarwal, Animesh

    2016-01-01

    We have implemented the Centroid Molecular Dynamics scheme (CMD) into the Grand Canonical-like version of the Adaptive Resolution Simulation Molecular Dynamics (GC-AdResS) method. We have tested the implementation on two different systems, liquid parahydrogen at extreme thermodynamic conditions and liquid water at ambient conditions; the reproduction of structural as well as dynamical results of reference systems are highly satisfactory. The capability of performing GC-AdResS CMD simulations allows for the treatment of a system characterized by some quantum features and open boundaries. This latter characteristic not only is of computational convenience, allowing for equivalent results of much larger and computationally more expensive systems, but also suggests a tool of analysis so far not explored, that is the unambiguous identification of the essential (quantum) degrees of freedom required for a given property.

  4. Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and application

    Science.gov (United States)

    Agarwal, Animesh; Delle Site, Luigi

    2016-09-01

    We have implemented the Centroid Molecular Dynamics scheme (CMD) into the Grand Canonical-like version of the Adaptive Resolution Simulation Molecular Dynamics (GC-AdResS) method. We have tested the implementation on two different systems, liquid parahydrogen at extreme thermodynamic conditions and liquid water at ambient conditions; the reproduction of structural as well as dynamical results of reference systems are highly satisfactory. The capability of performing GC-AdResS CMD simulations allows for the treatment of a system characterized by some quantum features and open boundaries. This latter characteristic not only is of computational convenience, allowing for equivalent results of much larger and computationally more expensive systems, but also suggests a tool of analysis so far not explored, that is the unambiguous identification of the essential degrees of freedom required for a given property.

  5. Dynamic imaging with high resolution time-of-flight pet camera - TOFPET I

    Energy Technology Data Exchange (ETDEWEB)

    Mullani, N.A.; Bristow, D.; Gaeta, J.; Gould, K.L.; Hartz, R.K.; Philipe, E.A.; Wong, W.H.; Yerian, K.

    1984-02-01

    One of the major design goals of the TOFPET I positron camera was to produce a high resolution whole body positron camera capable of dynamically imaging an organ such as the heart. TOFPET I is now nearing completion and preliminary images have been obtained to assess its dynamic and three dimensional imaging capabilities. Multiple gated images of the uptake of Rubidium in the dog heart and three dimensional surface displays of the distribution of the Rubidium-82 in the myocardium have been generated to demonstrate the three dimensional imaging properties. Fast dynamic images of the first pass of a bolus of radio-tracer through the heart have been collected with 4 second integration time and 50% gating (2 second equivalent integration time) with 18 mCi of Rb-82.

  6. Wetting dynamics of drop spreading. New evidence for the microscopic validity of the molecular-kinetic theory.

    Science.gov (United States)

    Seveno, D; Dinter, N; De Coninck, J

    2010-09-21

    We study the spontaneous wetting of liquid drops on FCC solid substrates using large-scale molecular dynamics simulations. By varying the solid lattice parameter, five different drop/solid dynamic systems are investigated. It is shown that the results are in agreement with the molecular-kinetic theory (MKT) describing the dynamics of wetting. Moreover, it is established that the microscopic parameters resulting from fits using the MKT, the so-called molecular jump frequency at equilibrium and the jump length, correspond to the values that can be estimated directly from the simulations. This agreement strongly supports the validity of the MKT at the microscopic scale.

  7. 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

  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. Comparison of dynamic 2D and 3D brain PET for kinetic analysis of C-11 win 35,428 binding to dopamine transporters

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sang Eun; Choi, Joon Young; Choi, Yong; Kim, Joon Young; Choe, Yearn Seong; Oh, Seung Jun; Kim, Byung Tae [College of Medicine, Sungkyunkwan Univ., Seoul (Korea, Republic of)

    1998-07-01

    3D PET data acquisition is now being used for clinical FDG-PET brain studies. However, its validity for studying kinetics of receptor-ligand interaction has not been fully evaluated. To examine the feasibility and quantitative accuracy of dynamic 3D brain PET for kinetic analysis of radioligand binding, 4 healthy volunteers and 1 Parkinson's disease patient were studied. Each subject received two 555 MBq C-11 WIN 35,428 injections and a dynamic sequence of 31 scans were acquired until 90 min p.i. in 2D and 3D mode using a GE Advance PET scanner. Both 2D and 3D image sets were reconstructed employing a Hanning filter 4.5 mm and resulting axial resolution was about 7 mm for both 2D and 3D images. The 3D data were corrected for scatter employing a method using 2D fitted Gaussian functions. Attenuation correction was performed using a 20 min transmission scan. Tissue time-activity curves were generated in the striatum and cerebellum. The forward (k3) and dissociation (k4) rate constants were calculated in the striatum using a two-compartment model, which consists of free plus nonspecifically bound (cerebellar) and specifically bound (striatal-cerebellar) compartments. The 3D kinetic results were comparable to the 2D results and within the expected range. The 3D %SE was less than 2D %SE. Striatal-to-cerebellar ratios from 2D and 3D images showed excellent correlation and agreement (r=0.994, p<0.0001, slope=0.952). The plot of striatal-to-cerebellar ratios versus time showed a linearly increasing pattern, with significantly lower RMSE in 3D than in 2D studies in linear regression analysis (0.119{+-}0.025 vs. 0.276{+-}0.087, p=0.028). These preliminary data suggest that 3D PET provides more reliable tissue kinetic data for the analysis of C-11 WIN 35,428 kinetics. Improved sensitivity in 3D may allow more accurate receptor characterization, especially in small brain structures or in low specific binding areas.

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

    Science.gov (United States)

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

    2015-05-01

    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. Super-resolution infrared time measurement method based on target dynamic characteristics

    Science.gov (United States)

    Li, Bin; Hu, Qiuping; Tang, Zili; Zhang, Sanxi; Zhang, Hua; Yue, Peng; Liu, Biao

    2016-10-01

    High precision time control in the use of weapons and equipment is an important part of product design and development. In order to satisfy the data acquisition requirement of high accuracy and reliability in the rapid flight process, the super-resolution time measurement method based on target dynamic characteristics was put forward and proved by the cabin opening time measurement experiment. First, the changes of explosion pressure wave and image in the cabin opening process were analyzed in detail. The change regulation of explosion flame shape was analyzed by the characteristics of typical pressure wave, and then the high frequency images of the explosion process were shot by high speed camera. The change regulation of the infrared image was obtained through the comparison of visible and infrared image mechanism. Then, combined with the target motion features, and the observed station parameters, the observation model of movement process was built. On the basis of the above research, the infrared characteristic and the movement characteristic were transformed, and the super resolution model was established. For test method, combined with the actual class time measuring process in experimental design, to obtain the special radar for measuring high precision open class time as the true value of the precision appraisal. Experimental results show that the infrared feature and motion feature can realize open class time super resolution measurement, can effectively improve the accuracy and reliability of the data, to achieve specific action of high accuracy measurement that plays an important role by making use of the target dynamic characteristics.

  13. 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 orde

  14. Dynamic voxel modeling resolution based on quality assessments from LIDAR path tracing

    Science.gov (United States)

    Hagstrom, Shea; Broadwater, Joshua

    2015-05-01

    Airborne LIDAR instruments are capable of delivering high density point clouds, but sampling is inherently uneven in both 2D and 3D space due to collection patterns as well as effects like occlusion. Taking full advantage of the detail available when creating 3D models therefore requires that resolution be adaptable to the amount of localized data. Voxel-based modeling of LIDAR has proven advantageous in many situations, but the traditional use of a fixed grid size prevents full realization of the potential resolution. Allowing voxel sizes to vary across the model using spatial subdivision techniques overcomes this limitation. An important part of this process is defining an appropriate limit of resolution for different sections of a model, and we incorporate information gained through tracing of LIDAR pulses to guide this decision process. Real-world data are used to demonstrate our results, and we show how dynamic resolution voxelization of LIDAR allows for both reduced storage requirements as well as improved modeling flexibility.

  15. 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

    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...... in the accumulation kinetics of αvβ3-integrin targeted nanoparticles and hypothesize that this periodicity is caused by receptor binding, internalization and recycling dynamics. Taken together, this demonstrates that our experimental approach provides new insights in in vivo nanoparticle targeting, which may proof...

  16. 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

  17. Dynamic high-resolution ultrasound of the shoulder: how we do it.

    Science.gov (United States)

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

    2015-02-01

    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.

  18. 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.

  19. Kinetic Monte Carlo and cellular particle dynamics simulations of multicellular systems

    Science.gov (United States)

    Flenner, Elijah; Janosi, Lorant; Barz, Bogdan; Neagu, Adrian; Forgacs, Gabor; Kosztin, Ioan

    2012-03-01

    Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Here we formulate two computer simulation methods: (1) a kinetic Monte Carlo (KMC) and (2) a cellular particle dynamics (CPD) method, which are capable of describing and predicting the shape evolution in time of three-dimensional multicellular systems during their biomechanical relaxation. Our work is motivated by the need of developing quantitative methods for optimizing postprinting structure formation in bioprinting-assisted tissue engineering. The KMC and CPD model parameters are determined and calibrated by using an original computational-theoretical-experimental framework applied to the fusion of two spherical cell aggregates. The two methods are used to predict the (1) formation of a toroidal structure through fusion of spherical aggregates and (2) cell sorting within an aggregate formed by two types of cells with different adhesivities.

  20. Isolation of kinetic and spatial properties of uni-axial dynamic tensile loading of OFHC copper

    Directory of Open Access Journals (Sweden)

    Mourad H.

    2012-08-01

    Full Text Available Materials performance is recognized as being central to many emergent technologies. Future technologies will place increasing demands on materials performance with respect to extremes in stress, strain, temperature, and pressure. In this study, the dynamic ductile damage evolution of OFHC Cu is explored as a test bed to understand the role of spatial effects due to loading profile and defect density as well as the role of the kinetics of tensile pulse evolution. Well-characterized OFHC Cu samples of 30 μm, 60 μm, 100 μm, and 200 μm grain sizes were subjected to plate impact uniaxial strain loading in spall geometry to produce early stage (incipient damage. Using 2D metallographic techniques, soft recovered samples were studied to statistically link mesoscale processes to continuum level observations of free surface particle velocity measured with VISAR. Based on these findings, mechanisms for the void nucleation/growth and coalescence are proposed.

  1. Molecular kinetic theory of boundary slip on textured surfaces by molecular dynamics simulations

    Science.gov (United States)

    Wang, LiYa; Wang, FengChao; Yang, FuQian; Wu, HengAn

    2014-11-01

    A theoretical model extended from the Frenkel-Eyring molecular kinetic theory (MKT) was applied to describe the boundary slip on textured surfaces. The concept of the equivalent depth of potential well was adopted to characterize the solid-liquid interactions on the textured surfaces. The slip behaviors on both chemically and topographically textured surfaces were investigated using molecular dynamics (MD) simulations. The extended MKT slip model is validated by our MD simulations under various situations, by constructing different complex surfaces and varying the surface wettability as well as the shear stress exerted on the liquid. This slip model can provide more comprehensive understanding of the liquid flow on atomic scale by considering the influence of the solid-liquid interactions and the applied shear stress on the nano-flow. Moreover, the slip velocity shear-rate dependence can be predicted using this slip model, since the nonlinear increase of the slip velocity under high shear stress can be approximated by a hyperbolic sine function.

  2. Dynamic evolution of a flow to localized, kinetics-driven ablation or coagulation

    Science.gov (United States)

    Hagan, Daniel; Crocker, Ryan; Dubief, Yves

    2012-11-01

    This research focuses on the numerical simulation of the ablative creation of a cavity or a coagulative formation at a wall in a flow. The fluid-solid interface is defined by a level set (LS) variable, whose transport equation is driven by the mass-loss or growth process. The boundary conditions at the fluid-solid interface are enforced by a mass and energy-conserving immersed boundary method (IBM) using the ghost-fluid node approach for the latter and for the transport of chemical species. The first application of the LS/IBM algorithm is a channel flow in which both walls are cavity-free, but one wall contains a section made of ablatable material, which could correspond to a hole or gap in a spacecraft thermal protection shield. The second application is a pipe flow in which the wall is capable of accumulating material, which could describe the coagulation of blood at a vessel wall. The solid mass loss or growth is driven by one step kinetics. For both flows, the dynamical interplay between the ablative or coagulative patch is investigated through statistics and flow topology. We gratefully acknowledge the financial support of NASA, grant No. NNX11AM07A, and NIH, grant No. P01HL46703, and the computational support of the Vermont Advanced Computing Core.

  3. Molecular kinetic theory of boundary slip on textured surfaces by molecular dynamics simulations

    Institute of Scientific and Technical Information of China (English)

    WANG LiYa; WANG FengChao; YANG FuQian; WU HengAn

    2014-01-01

    A theoretical model extended from the Frenkel-Eyring molecular kinetic theory (MKT) was applied to describe the boundary slip on textured surfaces.The concept of the equivalent depth of potential well was adopted to characterize the solid-liquid interactions on the textured surfaces.The slip behaviors on both chemically and topographically textured surfaces were investigated using molecular dynamics (MD) simulations.The extended MKT slip model is validated by our MD simulations under various situations,by constructing different complex surfaces and varying the surface wettability as well as the shear stress exerted on the liquid.This slip model can provide more comprehensive understanding of the liquid flow on atomic scale by considering the influence of the solid-liquid interactions and the applied shear stress on the nano-flow.Moreover,the slip velocity shear-rate dependence can be predicted using this slip model,since the nonlinear increase of the slip velocity under high shear stress can be approximated by a hyperbolic sine function.

  4. Enantioselective synthesis of angularly substituted 1-azabicylic rings: coupled dynamic kinetic epimerization and chirality transfer.

    Science.gov (United States)

    Aron, Zachary D; Ito, Tatsuya; May, Tricia L; Overman, Larry E; Wang, Jocelyn

    2013-10-01

    A new strategy for enantioselective synthesis of azacyclic molecules in which dynamic kinetic equilibration of diastereomeric iminium ions precedes a stereochemistry-determining sigmatropic rearrangement is reported. The method is illustrated by the synthesis, in high enantiomeric purity (generally 95-99% ee), of a variety of 1-azabicyclic molecules containing angular allyl or 3-substituted 2-propenyl side chains adjacent to nitrogen and up to three stereogenic centers. In these products, the size of the carbocyclic ring is varied widely (5-12 membered); however, useful yields are obtained in forming 1-azabicyclic products containing only fused pyrrolidine and piperidine rings. Chirality transfer from substituents at carbons 1 and 2 of the 3-butenylamine fragment of the starting material is investigated, with methyl and phenyl substituents at the allylic position shown to provide exquisite stereocontrol (generally 98-99% chirality transfer). An attractive feature of the method is the ability to carry out the key transformation in the absence of solvent. Illustrated also is the high yielding conversion of four such products to a new family of bicyclic β-amino acids of high enantiomeric purity.

  5. 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.

  6. Exploring the dynamic range of the kinetic exclusion assay in characterizing antigen-antibody interactions.

    Directory of Open Access Journals (Sweden)

    Christine Bee

    Full Text Available Therapeutic antibodies are often engineered or selected to have high on-target binding affinities that can be challenging to determine precisely by most biophysical methods. Here, we explore the dynamic range of the kinetic exclusion assay (KinExA by exploiting the interactions of an anti-DKK antibody with a panel of DKK antigens as a model system. By tailoring the KinExA to each studied antigen, we obtained apparent equilibrium dissociation constants (K(D values spanning six orders of magnitude, from approximately 100 fM to 100 nM. Using a previously calibrated antibody concentration and working in a suitable concentration range, we show that a single experiment can yield accurate and precise values for both the apparent K(D and the apparent active concentration of the antigen, thereby increasing the information content of an assay and decreasing sample consumption. Orthogonal measurements obtained on Biacore and Octet label-free biosensor platforms further validated our KinExA-derived affinity and active concentration determinations. We obtained excellent agreement in the apparent affinities obtained across platforms and within the KinExA method irrespective of the assay orientation employed or the purity of the recombinant or native antigens.

  7. Dynamic Scaling and Island Growth Kinetics in Pulsed Laser Deposition of SrTiO3

    Science.gov (United States)

    Eres, Gyula; Tischler, J. Z.; Rouleau, C. M.; Lee, Ho Nyung; Christen, H. M.; Zschack, P.; Larson, B. C.

    2016-11-01

    We use real-time diffuse surface x-ray diffraction to probe the evolution of island size distributions and its effects on surface smoothing in pulsed laser deposition (PLD) of SrTiO3 . We show that the island size evolution obeys dynamic scaling and two distinct regimes of island growth kinetics. Our data show that PLD film growth can persist without roughening despite thermally driven Ostwald ripening, the main mechanism for surface smoothing, being shut down. The absence of roughening is concomitant with decreasing island density, contradicting the prevailing view that increasing island density is the key to surface smoothing in PLD. We also report a previously unobserved crossover from diffusion-limited to attachment-limited island growth that reveals the influence of nonequilibrium atomic level surface transport processes on the growth modes in PLD. We show by direct measurements that attachment-limited island growth is the dominant process in PLD that creates step flowlike behavior or quasistep flow as PLD "self-organizes" local step flow on a length scale consistent with the substrate temperature and PLD parameters.

  8. Nonlinear Dynamics of Kinetic Alfvén and Whistler Waves in the Solar Wind

    Science.gov (United States)

    Rai, Rajesh Kumar; Sharma, Swati; Sharma, R. P.

    2017-03-01

    In this article we investigate the nonlinear dynamics of 3D kinetic Alfvén waves (KAWs) and quasi-transverse weak whistler waves in a magnetized plasma. We have studied the problem numerically to examine the transient evolution of localized structures of 3D KAWs and whistler waves. The nonlinearity arises as a result of ponderomotive effects associated with 3D KAWs; consequently, the background density modifies. The weak whistler waves propagating in this modified density are localized and amplified. To improve our insight into the basic physics behind the formation of these localized structures, we have also solved the system semi-analytically. The power spectra show a Kolmogorov scaling (with a power of -5/3) in the inertial range that lies above the ion gyroradius. Below this scale, dispersive effects start to appear, and the power spectrum follows a steeper scaling (-2 to -4). Our results show the important role that KAWs and whistler waves play in the energy cascading from larger to smaller scales. The results are consistent with the solar wind observations by the Cluster spacecraft.

  9. 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

  10. 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.

  11. High resolution dynamic ocean topography in the Southern Ocean from GOCE

    Science.gov (United States)

    Albertella, A.; Savcenko, R.; Janjić, T.; Rummel, R.; Bosch, W.; Schröter, J.

    2012-08-01

    A mean dynamic ocean topography (MDT) has been computed using a high resolution GOCE (Gravity field and steady-state Ocean Circulation Explorer) gravity model and a new mean sea surface obtained from a combination of satellite altimetry covering the period 1992 October till 2010 April. The considered gravity model is GO-CONS-GCF-2-TIM-R3, which computes geoid using 12 months of GOCE gravity field data. The GOCE gravity data allow for more detailed and accurate estimates of MDT. This is illustrated in the Southern Ocean where the commission error is reduced from 20 to 5 cm compared to the MDT computed using the GRACE gravity field model ITG-Grace2010. As a result of the more detailed and accurate MDT, the calculation of geostrophic velocities from the MDT is now possible with higher accuracy and spatial resolution, and the error estimate is about 7 cm s-1 for the Southern Ocean.

  12. Validation of the Aura High Resolution Dynamics Limb Sounder geopotential heights

    Directory of Open Access Journals (Sweden)

    L. L. Smith

    2014-02-01

    Full Text Available Global satellite observations from the EOS Aura spacecraft's High Resolution Dynamics Limb Sounder (HIRDLS of temperature and geopotential height (GPH are discussed. The accuracy, resolution and precision of the HIRDLS version 7 algorithms are assessed and data screening recommendations are made. Comparisons with GPH from observations, reanalyses and models including European Center for Medium-Range Weather Forecasts Interim Reanalysis (ERA-Interim, National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR Reanalysis, Goddard Earth Observing System Model (GEOS version 5, and EOS Aura Microwave Limb Sounder (MLS illustrate the HIRDLS GPH have a precision ranging from 2 m to 30 m and an accuracy of ±100 m. Comparisons indicate HIRDLS GPH may have a slight low bias in the tropics and a slight high bias at high latitudes. Geostrophic winds computed with HIRDLS GPH qualitatively agree with winds from other data sources including ERA-Interim, NCEP and GEOS-5.

  13. Nonequilibrium dynamic transition in a kinetic Ising model driven by both deterministic modulation and correlated stochastic noises

    Institute of Scientific and Technical Information of China (English)

    SHAO Yuanzhi; ZHONG Weirong; HE Zhenhui

    2005-01-01

    We report the nonequilibrium dynamical phase transition (NDPT) appearing in a kinetic Ising spin system (ISS) subject to the joint application of a deterministic external field and the stochastic mutually correlated noises simultaneously. A time-dependent Ginzburg-Landau stochastic differential equation, including an oscillating modulation and the correlated multiplicative and additive white noises, was addressed and the numerical solution to the relevant Fokker-Planck equation was presented on the basis of an average-period approach of driven field. The correlated white noises and the deterministic modulation induce a kind of dynamic symmetry-breaking order, analogous to the stochastic resonance in trend, in the kinetic ISS, and the reentrant transition has been observed between the dynamic disorder and order phases when the intensities of multiplicative and additive noises were changing. The dependencies of a dynamic order parameter Q upon the intensities of additive noise A and multiplicative noise M, the correlation λ between two noises, and the amplitude of applied external field h were investigated quantitatively and visualized vividly. Here a brief discussion is given to outline the underlying mechanism of the NDPT in a kinetic ISS driven by an external force and correlated noises.

  14. High resolution photoelectron spectroscopy and femtosecond intramolecular dynamics using supersonic molecular beams

    Energy Technology Data Exchange (ETDEWEB)

    Niu, B.

    1992-09-01

    High resolution He I[alpha] photoelectron spectroscopy of formaldehyde and ketene and their deuterated compounds, are reported. The combination of a (H2CO) double-pass high-resolution electron-energy analyzer and effective rotational cooling of the sample by supersonic expansion enable the spectroscopy of these molecular cations. The vibrational autocorrelation functions are calculated from the high-resolution photoelectron spectra, shedding light on the ultrafast intramolecular dynamics of the molecular cations. This study reveals much more vibrational structural detail in the first electronic excited state of H2CO cations. The first electronic excited state of H2CO cations may have nonplanar equilibrium geometry. Strong isotope effects on vibronic (vibrational) coupling are observed in the second electronic excited state of H2CO. Vibrational autocorrelation functions are calculated for all four observed electronic states of H2CO. The correlation function of the first electronic excited state of H2CO shows a slow decay rate on the femtosecond time scale. The ultrafast decay of the H2CO cations in the third electronic excited state implies that dissociation and intramolecular processes are the main decay pathways. The present spectra of the ground states of ketene cations have more fine structure than before. The AIEs of the first and fifth excited states are determined unambiguously more accurately. The doublet-like fine structures present in the lint excited state of ketene implies the excitation of a soft'' mode not observed before. The vibrational autocorrelation functions are calculated for 4 of the 6 observed electronic states. The dynamics of the ground states of the cations are characterized by a wave packet oscillating with small amplitude around the minimum on the upper PES. The decay dynamics of the first and the fifth excited states of ketene are characterized by ultra-fast intramolecular processes like predissociation.

  15. High resolution photoelectron spectroscopy and femtosecond intramolecular dynamics using supersonic molecular beams

    Energy Technology Data Exchange (ETDEWEB)

    Niu, B.

    1992-09-01

    High resolution He I{alpha} photoelectron spectroscopy of formaldehyde and ketene and their deuterated compounds, are reported. The combination of a (H2CO) double-pass high-resolution electron-energy analyzer and effective rotational cooling of the sample by supersonic expansion enable the spectroscopy of these molecular cations. The vibrational autocorrelation functions are calculated from the high-resolution photoelectron spectra, shedding light on the ultrafast intramolecular dynamics of the molecular cations. This study reveals much more vibrational structural detail in the first electronic excited state of H2CO cations. The first electronic excited state of H2CO cations may have nonplanar equilibrium geometry. Strong isotope effects on vibronic (vibrational) coupling are observed in the second electronic excited state of H2CO. Vibrational autocorrelation functions are calculated for all four observed electronic states of H2CO. The correlation function of the first electronic excited state of H2CO shows a slow decay rate on the femtosecond time scale. The ultrafast decay of the H2CO cations in the third electronic excited state implies that dissociation and intramolecular processes are the main decay pathways. The present spectra of the ground states of ketene cations have more fine structure than before. The AIEs of the first and fifth excited states are determined unambiguously more accurately. The doublet-like fine structures present in the lint excited state of ketene implies the excitation of a ``soft`` mode not observed before. The vibrational autocorrelation functions are calculated for 4 of the 6 observed electronic states. The dynamics of the ground states of the cations are characterized by a wave packet oscillating with small amplitude around the minimum on the upper PES. The decay dynamics of the first and the fifth excited states of ketene are characterized by ultra-fast intramolecular processes like predissociation.

  16. 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

  17. 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.)

  18. Studying Vortex Dynamics of Rotating Convection with High-resolution PIV Measurement

    Science.gov (United States)

    Fu, Hao; Sun, Shiwei; Wang, Yu; Zhou, Bowen; Wang, Yuan

    2016-11-01

    A novel experimental setup for studying vortex dynamics in rotating Rayleigh-Benard convection has been made in School of Atmospheric Sciences, Nanjing University. With water as the working fluid, three lasers with different frequencies and the corresponding three CCDs have been placed to complete 2D2C (two dimensions, two components) PIV measurement. The lasers are fixed on two crossing guiding ways and can move up and down to scan the flow field. An algorithm has been made to reconstruct 3D velocity field based on multiple 2D2C PIV data. This time, we are going to present the details of this new machine and algorithm, as well as some scientific understanding of vortex dynamics owing to this high-resolution velocity measurement system. This work was supported by "LMSWE Lab Funding No. 14380001".

  19. Correlating structure and fluorescence dynamics of quantum dot clusters using super-resolution imaging

    Science.gov (United States)

    Ryan, Duncan P.; Goodwin, Peter M.; Sheehan, Chris J.; Whitcomb, Kevin J.; Gelfand, Martin P.; Van Orden, Alan

    2016-02-01

    Clusters of quantum dots exhibit fluorescent behavior that differs from that of individual particles. Bulk measurements involving a large number of particles obscure these dynamics. Synthesizing clusters with 5-10 particles enables the study of collective behavior where single-molecule fluorescence techniques can be applied. Super-resolution microscopy of these clusters correlated with SEM imaging reveals the influence of geometry and structure on emission dynamics. Signatures of energy transfer can be seen in the form of enhanced blinking. Motion of the emission center of the cluster is tracked, made possible by the independent blinking events of the individual particles. Discrete steps in the localization are observed as random switching between various on/off configurations moves the location of the emission center.

  20. 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.

  1. Nonlinear interactions between the pumping kinetics, fluid dynamics and optical resonator of cw fluid flow lasers. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    Sentman, L.H.; Nayfeh, M.H.

    1983-12-01

    This research is an integrated theoretical and experimental investigation of the nonlinear interactions which may occur between the chemical kinetics, the fluid dynamics and the unstable resonator of a continuous wave fluid flow laser. The objectives of this grant were to measure the frequency and amplitude of the time dependent pulsations in the power spectral output which have been predicted to occur in cw chemical lasers employing unstable resonators to extract power.

  2. Dynamic Kinetic Asymmetric Amination of Alcohols: From A Mixture of Four Isomers to Diastereo- and Enantiopure α-Branched Amines.

    Science.gov (United States)

    Rong, Zi-Qiang; Zhang, Yao; Chua, Raymond Hong Bing; Pan, Hui-Jie; Zhao, Yu

    2015-04-22

    The first dynamic kinetic asymmetric amination of alcohols via borrowing hydrogen methodology is presented. Under the cooperative catalysis by an iridium complex and a chiral phosphoric acid, α-branched alcohols that exist as a mixture of four isomers undergo racemization by two orthogonal mechanisms and are converted to diastereo- and enantiopure amines bearing adjacent stereocenters. The preparation of diastereo- and enantiopure 1,2-amino alcohols is also realized using this catalytic system.

  3. Bending Dynamics of Fluctuating Biopolymers Probed by Automated High-Resolution Filament Tracking

    Science.gov (United States)

    Brangwynne, Clifford P.; Koenderink, Gijsje H.; Barry, Ed; Dogic, Zvonimir; MacKintosh, Frederick C.; Weitz, David A.

    2007-01-01

    Microscope images of fluctuating biopolymers contain a wealth of information about their underlying mechanics and dynamics. However, successful extraction of this information requires precise localization of filament position and shape from thousands of noisy images. Here, we present careful measurements of the bending dynamics of filamentous (F-)actin and microtubules at thermal equilibrium with high spatial and temporal resolution using a new, simple but robust, automated image analysis algorithm with subpixel accuracy. We find that slender actin filaments have a persistence length of ∼17 μm, and display a q−4-dependent relaxation spectrum, as expected from viscous drag. Microtubules have a persistence length of several millimeters; interestingly, there is a small correlation between total microtubule length and rigidity, with shorter filaments appearing softer. However, we show that this correlation can arise, in principle, from intrinsic measurement noise that must be carefully considered. The dynamic behavior of the bending of microtubules also appears more complex than that of F-actin, reflecting their higher-order structure. These results emphasize both the power and limitations of light microscopy techniques for studying the mechanics and dynamics of biopolymers. PMID:17416612

  4. Progress in BazookaSPECT: High-Resolution, Dynamic Scintigraphy with Large-Area Imagers.

    Science.gov (United States)

    Miller, Brian W; Barber, H Bradford; Barrett, Harrison H; Liu, Zhonglin; Nagarkar, Vivek V; Furenlid, Lars R

    2012-08-12

    We present recent progress in BazookaSPECT, a high-resolution, photon-counting gamma-ray detector. It is a new class of scintillation detector that combines columnar scintillators, image intensifiers, and CCD (charge-coupled device) or CMOS (complementary metal-oxide semiconductors) sensors for high-resolution imaging. A key feature of the BazookaSPECT paradigm is the capability to easily design custom detectors in terms of the desired intrinsic detector resolution and event detection rate. This capability is possible because scintillation light is optically amplified by the image intensifier prior to being imaging onto the CCD/CMOS sensor, thereby allowing practically any consumer-grade CCD/CMOS sensor to be used for gamma-ray imaging. Recent efforts have been made to increase the detector area by incorporating fiber-optic tapers between the scintillator and image intensifier, resulting in a 16× increase in detector area. These large-area BazookaSPECT detectors can be used for full-body imaging and we present preliminary results of their use as dynamic scintigraphy imagers for mice and rats. Also, we discuss ongoing and future developments in BazookaSPECT and the improved event-detection rate capability that is achieved using Graphics Processing Units (GPUs), multi-core processors, and new high-speed, USB 3.0 CMOS cameras.

  5. 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.

  6. 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.

  7. High resolution photoelectron spectroscopy and femtosecond intramolecular dynamics of H2CCO + and D2CCO +

    Science.gov (United States)

    Niu, Baohua; Bai, Ying; Shirley, David A.

    1993-08-01

    High resolution helium Iα (584 Å) photoelectron spectra of H2CCO and D2CCO are reported. The present spectra of the ground states of ketene cations show more vibrational fine structure than previously reported. The adiabatic ionization energies (AIEs) of the cations' first, second, and fifth excited states are determined unambiguously. The doubletlike fine structures present in the first excited states of ketene cations imply the excitation of a ``soft'' mode that was not observed before. It was assigned to the ν5 mode, which is characterized by the CH2 (CD2) group out-of-plane wagging motion. The complexity of the photoelectron spectra obtained for the ionic first excited states is attributed to the possible dissociation and predissociation of this state. Strong isotope effects are observed in the vibronic (vibrational) couplings in most of the ionic states. Vibrational autocorrelation functions are calculated from the high-resolution photoelectron spectra for four of the six ionic states observed. The dynamics of the ground states of the cations are characterized by a wave packet oscillating with small amplitude around the minimum of the upper potential energy surfaces (PES). The decay dynamics of the ionic first and fifth excited states of ketene are characterized by ultrafast intramolecular processes such as dissociation and predissociation.

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

    Science.gov (United States)

    Chiew, Kimberly S; Braver, Todd S

    2013-01-01

    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.

  9. Super-resolution restoration applied to the characterisation of dynamic surface changes on the Martian surface

    Science.gov (United States)

    Tao, Yu; Muller, Jan-Peter

    2016-10-01

    Higher spatial resolution imaging data is always desirable to the international community of planetary scientists interested in improving understanding of surface formation processes. We have previously developed a novel Super-resolution restoration (SRR) technique using Gotcha sub-pixel matching [Shin & Muller, PR, 2012], orthorectification, segmentation, and 4th order PDE-TV, called GPT SRR [Tao & Muller, PSS, 2016]. This technique is able to restore 5cm-12.5cm near rover scale images (Navcam at a range of ≥5m) from multi-angle repeat-pass 25cm resolution MRO HiRISE images [Tao & Muller, ISPRS, 2016].We have successfully applied the GPT-SRR to the MER and MSL missions (http://www.progisweb.eu), as well as the alleged site of the Beagle-2 spacecraft (https://www.flickr.com/photos/uclnews/albums/72157667609698345). In this work, we further apply GPT-SRR on areas with known dynamic changes, including Recurring Slope Lineae (RSL), Gullies, and Polar Dune Flows. We restore static surface and meanwhile track the dynamic features to characterise the "change", including directions and speed of the changes. We also demonstrate that such repeat images can be used to image the MER-A rover stuck in the sands.AcknowledgementsThe research leading to these results has received funding from the European Union's Seventh Framework Programme (FP7/2007-2013) under iMars grant agreement no. 607379 as well as partial funding from the STFC "MSSL Consolidated Grant" ST/K000977/1.

  10. Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments.

    Science.gov (United States)

    Ollila, O H Samuli; Pabst, Georg

    2016-10-01

    Accurate details on the sampled atomistic resolution structures of lipid bilayers can be experimentally obtained by measuring C-H bond order parameters, spin relaxation rates and scattering form factors. These parameters can be also directly calculated from the classical atomistic resolution molecular dynamics simulations (MD) and compared to the experimentally achieved results. This comparison measures the simulation model quality with respect to 'reality'. If agreement is sufficient, the simulation model gives an atomistic structural interpretation of the acquired experimental data. Significant advance of MD models is made by jointly interpreting different experiments using the same structural model. Here we focus on phosphatidylcholine lipid bilayers, which out of all model membranes have been studied mostly by experiments and simulations, leading to the largest available dataset. From the applied comparisons we conclude that the acyl chain region structure and rotational dynamics are generally well described in simulation models. Also changes with temperature, dehydration and cholesterol concentration are qualitatively correctly reproduced. However, the quality of the underlying atomistic resolution structural changes is uncertain. Even worse, when focusing on the lipid bilayer properties at the interfacial region, e.g. glycerol backbone and choline structures, and cation binding, many simulation models produce an inaccurate description of experimental data. Thus extreme care must be applied when simulations are applied to understand phenomena where the interfacial region plays a significant role. This work is done by the NMRlipids Open Collaboration project running at https://nmrlipids.blogspot.fi and https://github.com/NMRLipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

  11. On the dynamics of immobilized enzyme kinetics in a microreactor: A study of AP-catalyzed reactions

    Directory of Open Access Journals (Sweden)

    Pratap R Patnaik

    2011-11-01

    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin-top:0in; mso-para-margin-right:0in; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0in; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} The kinetics of immobilized enzyme-catalyzed reactions in microreactors differ from those in macro-scale reactors. Recognizing this, a recent study (Patnaik 2011 based on a new interpretation of the kinetics of AP-catalyzed reactions showed that dynamic behavior is feasible only certain loci relating key kinetic parameters. That work has been extended here, and the kinetic parameters have now been related to bulk phase concentrations, thereby providing a link with the reaction system per se. It has also been shown that under certain conditions the reaction may become self-quenching but either monotonically or as damped oscillations. These two studies thus establish the importance of understanding kinetic dynamics in microreactors and in selecting feasible operating conditions.

  12. Kinetic adsorption profile and conformation evolution at the DNA-gold nanoparticle interface probed by dynamic light scattering.

    Science.gov (United States)

    Wang, Wenjie; Ding, XiaoFan; He, Miao; Wang, Jing; Lou, Xinhui

    2014-10-21

    The kinetic adsorption profile at the DNA-gold nanoparticle (AuNP) interface is probed by following the binding and organization of thiolated linear DNA and aptamers of varying chain lengths (15, 30, 44, and 51 mer) to the surface of AuNPs (13.0 ± 1.0 nm diameter). A systematic investigation utilizing dynamic light scattering has been performed to directly measure the changes in particle size during the course of a typical aging-salting thiolated DNA/AuNP preparation procedure. We discuss the effect of DNA chain length, composition, salt concentration, and secondary structure on the kinetics and conformation at the DNA-AuNP interface. The adsorption kinetics are chain-length dependent, composition independent, and not diffusion rate limited for the conditions we report here. The kinetic data support a mechanism of stepwise adsorption of thiols to the surface of AuNPs and reorganization of the thiols at the interface. Very interestingly, the kinetic increases of the particle sizes are modeled accurately by the pseudo-second-order rate model, suggesting that DNA could possess the statistically well-defined conformational evolution. Together with other experimental evidence, we propose a dynamic inner-layer and outer-tail (DILOT) model to describe the evolution of the DNA conformation after the initial adsorption of a single oligonucleotide layer. According to this model, the length of the tails that extend from the surface of AuNPs, capable for hybridization or molecular recognition, can be conveniently calculated. Considering the wide applications of DNA/AuNPs, the results should have important implications in sensing and DNA-directed nanoparticle assembly.

  13. The Application of Transient-State Kinetic Isotope Effects to the Resolution of Mechanisms of Enzyme-Catalyzed Reactions

    Directory of Open Access Journals (Sweden)

    Harvey F. Fisher

    2013-07-01

    Full Text Available Much of our understanding of the mechanisms of enzyme-catalyzed reactions is based on steady-state kinetic studies. Experimentally, this approach depends solely on the measurement of rates of free product appearance (d[P]/dt, a mechanistically and mathematically complex entity. Despite the ambiguity of this observed parameter, the method’s success is due in part to the elaborate rigorously derived algebraic theory on which it is based. Transient-state kinetics, on the other hand, despite its ability to observe the formation of intermediate steps in real time, has contributed relatively little to the subject due in, some measure, to the lack of such a solid mathematical basis. Here we discuss the current state of existing transient-state theory and the difficulties in its realistic application to experimental data. We describe a basic analytic theory of transient-state kinetic isotope effects in the form of three novel fundamental rules. These rules are adequate to define an extended mechanism, locating the isotope-sensitive step and identifying missing steps from experimental data. We demonstrate the application of these rules to resolved component time courses of the phenylalanine dehydrogenase reaction, extending the previously known reaction by one new prehydride transfer step and two new post hydride transfer steps. We conclude with an assessment of future directions in this area.

  14. Evaluation of the variable depth resolution of active dynamic thermography on human skin

    Science.gov (United States)

    Prindeze, Nicholas J.; Hoffman, Hilary A.; Carney, Bonnie C.; Moffatt, Lauren T.; Loew, Murray H.; Shupp, Jeffrey W.

    2015-06-01

    Active dynamic thermography (ADT) is an imaging technique capable of characterizing the non-homogenous thermal conductance of damaged tissues. The purpose of this study was to determine optimal stimulation parameters and quantify the optical resolution of ADT through various depths of human skin. Excised tissue from plastic surgery operations was collected immediately following excision. A total of 12 thin to thick split-thickness grafts were harvested from 3 patients. Grafts were placed on top of a 3D printed resolution chart and thermal stimulation was applied from a 300W halogen lamp array for between 0.5-10 seconds to determine optimal parameters. Video was captured with a thermal camera, and analysis was performed by reconstructing an image from thermal gradients. In this study ADT resolved 0.445+/-0 lp/mm at a depth of 0.010", 0.356+/-0.048 lp/mm at a depth of 0.015", 0.334+/-0.027 lp/mm at a depth of 0.020" and 0.265+/-0.022 lp/mm at a depth of 0.025". The stimulus energy required for maximum resolution at each depth was 3- 4s, 8s, 12s and 12s respectively. ADT is a sensitive technique for imaging dermal structure, capable of resolving detail as fine as 1124 μm, 1427 μm, 1502 μm and 1893 μm in thin to thick split-thickness skin grafts respectively. This study has characterized a correlation between stimulus input and maximal resolution at differing depths of skin. It has also defined the functional imaging depth of ADT to below the sub-cutis, well below conventional spectrophotometric techniques.

  15. Daniel K. Inouye Solar Telescope: High-resolution observing of the dynamic Sun

    Science.gov (United States)

    Tritschler, A.; Rimmele, T. R.; Berukoff, S.; Casini, R.; Kuhn, J. R.; Lin, H.; Rast, M. P.; McMullin, J. P.; Schmidt, W.; Wöger, F.; DKIST Team

    2016-11-01

    The 4-m aperture Daniel K. Inouye Solar Telescope (DKIST) formerly known as the Advanced Technology Solar Telescope (ATST) is currently under construction on Haleakalā (Maui, Hawai'i) projected to start operations in 2019. At the time of completion, DKIST will be the largest ground-based solar telescope providing unprecedented resolution and photon collecting power. The DKIST will be equipped with a set of first-light facility-class instruments offering unique imaging, spectroscopic and spectropolarimetric observing opportunities covering the visible to infrared wavelength range. This first-light instrumentation suite will include: a Visible Broadband Imager (VBI) for high-spatial and -temporal resolution imaging of the solar atmosphere; a Visible Spectro-Polarimeter (ViSP) for sensitive and accurate multi-line spectropolarimetry; a Fabry-Pérot based Visible Tunable Filter (VTF) for high-spatial resolution spectropolarimetry; a fiber-fed Diffraction-Limited Near Infra-Red Spectro-Polarimeter (DL-NIRSP) for two-dimensional high-spatial resolution spectropolarimetry (simultaneous spatial and spectral information); and a Cryogenic Near Infra-Red Spectro-Polarimeter (Cryo-NIRSP) for coronal magnetic field measurements and on-disk observations of, e.g., the CO lines at 4.7 μm. We will provide an overview of the DKIST's unique capabilities with strong focus on the first-light instrumentation suite, highlight some of the additional properties supporting observations of transient and dynamic solar phenomena, and touch on some operational strategies and the DKIST critical science plan.

  16. 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.

  17. Charge recombination kinetics and protein dynamics in wild type and carotenoid-less bacterial reaction centers: studies in trehalose glasses.

    Science.gov (United States)

    Francia, Francesco; Malferrari, Marco; Sacquin-Mora, Sophie; Venturoli, Giovanni

    2009-07-30

    The coupling between electron transfer and protein dynamics has been investigated in reaction centers (RCs) from the wild type (wt) and the carotenoid-less strain R26 of the photosynthetic bacterium Rhodobacter sphaeroides. Recombination kinetics between the primary photoreduced quinone acceptor (QA-) and photoxidized donor (P+) have been analyzed at room temperature in RCs incorporated into glassy trehalose matrices of different water/sugar ratios. As previously found in R26 RCs, also in the wt RC, upon matrix dehydration, P+QA- recombination accelerates and becomes broadly distributed, reflecting the inhibition of protein relaxation from the dark-adapted to the light-adapted conformation and the hindrance of interconversion between conformational substates. While in wet trehalose matrices (down to approximately one water per trehalose molecule) P+QA- recombination kinetics are essentially coincident in wt and R26 RCs, more extensive dehydration leads to two-times faster and more distributed kinetics in the carotenoid-containing RC, indicating a stronger inhibition of the internal protein dynamics in the wt RC. Coarse-grained Brownian dynamics simulations performed on the two RC structures reveal a markedly larger flexibility of the R26 RC, showing that a rigid core of residues, close to the quinone acceptors, is specifically softened in the absence of the carotenoid. These experimental and computational results concur to indicate that removal of the carotenoid molecule has long-range effects on protein dynamics and that the structural/dynamical coupling between the protein and the glassy matrix depends strongly upon the local mechanical properties of the protein interior. The data also suggest that the conformational change stabilizing P+QA- is localized around the QA binding pocket.

  18. Intravital correlated microscopy reveals differential macrophage and microglial dynamics during resolution of neuroinflammation

    Directory of Open Access Journals (Sweden)

    Tjakko J. van Ham

    2014-07-01

    Full Text Available Many brain diseases involve activation of resident and peripheral immune cells to clear damaged and dying neurons. Which immune cells respond in what way to cues related to brain disease, however, remains poorly understood. To elucidate these in vivo immunological events in response to brain cell death we used genetically targeted cell ablation in zebrafish. Using intravital microscopy and large-scale electron microscopy, we defined the kinetics and nature of immune responses immediately following injury. Initially, clearance of dead cells occurs by mononuclear phagocytes, including resident microglia and macrophages of peripheral origin, whereas amoeboid microglia are exclusively involved at a later stage. Granulocytes, on the other hand, do not migrate towards the injury. Remarkably, following clearance, phagocyte numbers decrease, partly by phagocyte cell death and subsequent engulfment of phagocyte corpses by microglia. Here, we identify differential temporal involvement of microglia and peripheral macrophages in clearance of dead cells in the brain, revealing the chronological sequence of events in neuroinflammatory resolution. Remarkably, recruited phagocytes undergo cell death and are engulfed by microglia. Because adult zebrafish treated at the larval stage lack signs of pathology, it is likely that this mode of resolving immune responses in brain contributes to full tissue recovery. Therefore, these findings suggest that control of such immune cell behavior could benefit recovery from neuronal damage.

  19. Dynamic high-resolution US of ankle and midfoot ligaments: normal anatomic structure and imaging technique.

    Science.gov (United States)

    Sconfienza, Luca Maria; Orlandi, Davide; Lacelli, Francesca; Serafini, Giovanni; Silvestri, Enzo

    2015-01-01

    The ankle is the most frequently injured major joint in the body, and ankle sprains are frequently encountered in individuals playing football, basketball, and other team sports, in addition to occurring in the general population. Imaging plays a crucial role in the evaluation of ankle ligaments. Magnetic resonance imaging has been proven to provide excellent evaluation of ligaments around the ankle, with the ability to show associated intraarticular abnormalities, joint effusion, and bone marrow edema. Ultrasonography (US) performed with high-resolution broadband linear-array probes has become increasingly important in the assessment of ligaments around the ankle because it is low cost, fast, readily available, and free of ionizing radiation. US can provide a detailed depiction of normal anatomic structures and is effective for evaluating ligament integrity. In addition, US allows the performance of dynamic maneuvers, which may contribute to increased visibility of normal ligaments and improved detection of tears. In this article, the authors describe the US techniques for evaluation of the ankle and midfoot ligaments and include a brief review of the literature related to their basic anatomic structures and US of these structures. Short video clips showing dynamic maneuvers and dynamic real-time US of ankle and midfoot structures and their principal pathologic patterns are included as supplemental material. Use of a standardized imaging technique may help reduce the intrinsic operator dependence of US. Online supplemental material is available for this article.

  20. Learning and dynamics in social systems. Comment on "Collective learning modeling based on the kinetic theory of active particles" by D. Burini et al.

    Science.gov (United States)

    Dolfin, Marina

    2016-03-01

    The interesting novelty of the paper by Burini et al. [1] is that the authors present a survey and a new approach of collective learning based on suitable development of methods of the kinetic theory [2] and theoretical tools of evolutionary game theory [3]. Methods of statistical dynamics and kinetic theory lead naturally to stochastic and collective dynamics. Indeed, the authors propose the use of games where the state of the interacting entities is delivered by probability distributions.

  1. Nonlinear Stochastic Dynamics of Complex Systems, III: Noneqilibrium Thermodynamics of Self-Replication Kinetics

    CERN Document Server

    Saakian, David B

    2016-01-01

    We briefly review the recently developed, Markov process based isothermal chemical thermodynamics for nonlinear, driven mesoscopic kinetic systems. Both the instantaneous Shannon entropy {\\boldmath $S[p_{\\alpha}(t)]$} and relative entropy {\\boldmath $F[p_{\\alpha}(t)]$}, defined based on probability distribution {\\boldmath $\\{p_{\\alpha}(t)\\}$}, play prominent roles. The theory is general; and as a special case when a chemical reaction system is situated in an equilibrium environment, it agrees perfectly with Gibbsian chemical thermodynamics: {\\boldmath $k_BS$} and {\\boldmath $k_BTF$} become thermodynamic entropy and free energy, respectively. We apply this theory to a fully reversible autocatalytic reaction kinetics, represented by a Delbr\\"{u}ck-Gillespie process, in a chemostatic nonequilibrium environment. The open, driven chemical system serves as an archetype for biochemical self-replication. The significance of {\\em thermodynamically consistent} kinetic coarse-graining is emphasized. In a kinetic system ...

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

    Science.gov (United States)

    Costa, Rafael S; Machado, Daniel; Rocha, Isabel; Ferreira, Eugénio C

    2010-05-01

    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, 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, convenience kinetics, lin-log and power-law). Using the mechanistic model for Escherichia coli central carbon metabolism as a benchmark, we investigate the alternative modeling approaches through comparative simulations analyses. The good dynamic behavior and the powerful predictive capabilities obtained using the hybrid model composed of Michaelis-Menten and the approximate lin-log kinetics indicate that this is a possible suitable approach to model complex large-scale networks where the exact rate laws are unknown. 2010 Elsevier Ireland Ltd. All rights reserved.

  3. 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.

  4. DYNAMIC MATHEMATICAL MODELLING OF REACTION KINETICS FOR CYCLODEXTRINS PRODUCTION FROM DIFFERENT STARCH SOURCES USING BACILLUS MACERANS CYCLODEXTRIN GLUCANOTRANSFERASE

    Directory of Open Access Journals (Sweden)

    Syahinaz Shahrazi

    2013-01-01

    Full Text Available This study relates to the mathematical modelling of enzymatic production of Cyclodextrins (CDs by Cyclodextrin Glucanotransferase (CGTase from Bacillus macerans. The experiments were carried out in batch mode using different starch sources and the results were used to estimate unknown parameters using linearization and dynamic simulation methods. α- and β-CD produced from tapioca were found to give the highest Michaelis-Menten constant, KM,i of 58.23 and 54.07 g L-1, respectively and maximum velocity, Vmax,i of 3.45 and 2.76 g L-1.min, respectively, while sago resulted in the highest KM,i and Vmax,i values of 342.35 g L-1 and 5.97 g L-1.min, respectively, for γ-CD obtained by the linearization method. Value of product inhibition, K1,i and CD degradation coefficient rate, δCD,i, were estimated using dynamic simulation, indicating that exponential reaction kinetics could be fitted better with the experimental data. Sensitivity analysis revealed that the product inhibition parameter in the exponential reaction kinetic equation is more significant in the process. For validation, the production of CDs by fed batch method was undertaken and starch and enzyme were added into the reaction medium. Then, the predicted profiles generated by simulation were compared with the experimental values. The proposed exponential reaction kinetics shows good fitting with the experimental data.

  5. Effect of heliox on heart rate kinetics and dynamic hyperinflation during high-intensity exercise in COPD.

    Science.gov (United States)

    Laveneziana, Pierantonio; Valli, Gabriele; Onorati, Paolo; Paoletti, Patrizia; Ferrazza, Alessandro Maria; Palange, Paolo

    2011-02-01

    Respiratory mechanical abnormalities in patients with chronic obstructive pulmonary disease (COPD) may impair cardiodynamic responses and slow down heart rate (HR) kinetics compared with normal resulting in reduced convective oxygen delivery during exercise. We reasoned that heliox breathing (79% helium-21% oxygen) and the attendant reduction of operating lung volumes should accelerate HR kinetics in the transition from rest to high-intensity exercise. Eleven male ambulatory patients with clinically stable COPD undertook constant work-rate cycle testing at 80% of each individuals' maximum work capacity while breathing room air (RA) or heliox (HX), randomly. Mean response time (MRT) for HR and dynamic end-expiratory lung volume (EELV) were measured. Resting EELV was not affected by HX breathing, while exercise EELV decreased significantly by 0.23 L at isotime during HX breathing compared with RA. During HX breathing, MRT for HR significantly accelerated (p = 0.002) by an average of 20 s (i.e., 17%). Speeded MRT for HR correlated with indices of reduced lung hyperinflation, such as EELV at isotime (r = 0.88, p = 0.03), and with improved exercise endurance time (r = -0.64, p = 0.03). The results confirm that HX-induced reduction of dynamic lung hyperinflation is associated with consistent improvement in indices of cardio-circulatory function such as HR kinetics in the rest-to-exercise transition in COPD patients.

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

    Energy Technology Data Exchange (ETDEWEB)

    Roee, Kathrine; Aleksandersen, Thomas B.; Nilsen, Line B.; Hong Qu; Ree, Anne H.; Malinen, Eirik (Univ. of Oslo, Oslo (Norway)), E-mail: Kathrine.Roe@rr-research.no; Kristian, Alexandr (Dept. of Tumor Biology, Inst. for Cancer Research, The Norwegian Radium Hospital, Oslo Univ. Hospital, Oslo (Norway)); Seierstad, Therese (Dept. of Radiation Biology, Inst. for Cancer Research, The Norwegian Radium Hospital, Oslo Univ. Hospital, Oslo (Norway)); Olsen, Dag R. (Univ. of Bergen, Bergen (Norway))

    2010-10-15

    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 18F-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 18F-FDG uptake by analytic two-tissue compartment modeling, extracting kinetic tumor parameters from dynamic 18F-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 18F-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 18F-FDG uptake was fitted voxel-by-voxel to a compartment model, producing kinetic parameter maps. Results. The kinetic model separated the 18F-FDG uptake into free and bound tracer and quantified three parameters; forward tracer diffusion (k1), backward tracer diffusion (k2), and rate of 18F-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 18F-FDG PET. Conclusions. This study demonstrates the feasibility of a two-tissue compartment kinetic analysis of dynamic 18F-FDG PET images. If validated, extracted parametrical

  7. Theoretical and experimental studies of chemically induced dynamic nuclear polarization kinetics in recombination of radical pairs by the method of switched external magnetic field. II. 13C CIDNP of micellized radical pairs

    Science.gov (United States)

    Fedin, M. V.; Bagryanskaya, E. G.; Purtov, P. A.

    1999-09-01

    The method of 13C chemically induced dynamic nuclear polarization in a switched external magnetic field (SEMF CIDNP) has been applied for the first time in an experimental investigation of micellized radical pairs (RP). Using the examples of three photochemical reactions it has been shown, that SEMF CIDNP allows the investigation of the kinetics of short-lived micellized RPs with high time-resolution in low and intermediate magnetic fields. The experimental kinetics have been analyzed and simulated on the basis of a previously developed theory [Parnachev et al., J. Chem. Phys. 107, 9942 (1997)]. It has been demonstrated that such an analysis provides information on the rates of radical escape from the micelle, on electron relaxation and on the rate of S-T- transitions. The analysis of the estimated rates of S-T- transitions showed that the exchange interaction is essentially anisotropic in the RPs studied.

  8. Dynamics of genomic clones in breast cancer patient xenografts at single cell resolution

    Science.gov (United States)

    Eirew, Peter; Steif, Adi; Khattra, Jaswinder; Ha, Gavin; Yap, Damian; Farahani, Hossein; Gelmon, Karen; Chia, Stephen; Mar, Colin; Wan, Adrian; Laks, Emma; Biele, Justina; Shumansky, Karey; Rosner, Jamie; McPherson, Andrew; Nielsen, Cydney; Roth, Andrew J. L.; Lefebvre, Calvin; Bashashati, Ali; de Souza, Camila; Siu, Celia; Aniba, Radhouane; Brimhall, Jazmine; Oloumi, Arusha; Osako, Tomo; Bruna, Alejandra; Sandoval, Jose; Algara, Teresa; Greenwood, Wendy; Leung, Kaston; Cheng, Hongwei; Xue, Hui; Wang, Yuzhuo; Lin, Dong; Mungall, Andrew J.; Moore, Richard; Zhao, Yongjun; Lorette, Julie; Nguyen, Long; Huntsman, David; Eaves, Connie J.; Hansen, Carl; Marra, Marco A.; Caldas, Carlos; Shah, Sohrab P.; Aparicio, Samuel

    2016-01-01

    Human cancers, including breast cancers, are comprised of clones differing in mutation content. Clones evolve dynamically in space and time following principles of Darwinian evolution1,2, underpinning important emergent features such as drug resistance and metastasis3–7. Human breast cancer xenoengraftment is used as a means of capturing and studying tumour biology, and breast tumour xenografts are generally assumed to be reasonable models of the originating tumours8–10. However the consequences and reproducibility of engraftment and propagation on the genomic clonal architecture of tumours has not been systematically examined at single cell resolution. Here we show by both deep genome and single cell sequencing methods, the clonal dynamics of initial engraftment and subsequent serial propagation of primary and metastatic human breast cancers in immunodeficient mice. In all 15 cases examined, clonal selection on engraftment was observed in both primary and metastatic breast tumours, varying in degree from extreme selective engraftment of minor (<5% of starting population) clones to moderate, polyclonal engraftment. Furthermore, ongoing clonal dynamics during serial passaging is a feature of tumours experiencing modest initial selection. Through single cell sequencing, we show that major mutation clusters estimated from tumour population sequencing relate predictably to the most abundant clonal genotypes, even in clonally complex and rapidly evolving cases. Finally, we show that similar clonal expansion patterns can emerge in independent grafts of the same starting tumour population, indicating that genomic aberrations can be reproducible determinants of evolutionary trajectories. Our results show that measurement of genomically defined clonal population dynamics will be highly informative for functional studies utilizing patient-derived breast cancer xenoengraftment. PMID:25470049

  9. Glycation promoted by dynamic high pressure microfluidisation pretreatment revealed by high resolution mass spectrometry.

    Science.gov (United States)

    Huang, Xiaoqin; Tu, Zongcai; Wang, Hui; Zhang, Qiuting; Hu, Yueming; Zhang, Lan; Niu, Peipei; Shi, Yan; Xiao, Hui

    2013-12-01

    The effect of dynamic high pressure microfluidisation (DHPM) pretreatment on the glycation of bovine serum albumin (BSA) was investigated. A detailed glycation map was obtained from high resolution mass spectrometry. Without DHPM pretreatment, only 7 glycation sites were identified, whereas the numbers were increased to 10, 11 and 11 when BSA-glucose was pretreated with DHPM at 50, 100 and 200 MPa, respectively, suggesting that DHPM pretreatment can significantly promote the Maillard reaction. Average degree of substitution per peptide molecule BSA (DSP) was used to further evaluate the glycation level under various DHPM conditions. All the DHPM pretreated samples exhibited elevated glycation level compared to the un-pretreated sample. With 100 MPa DHPM pretreatment, the protein showed the most significantly enhanced glycation extent. In addition, our results suggest that Maillard-type glycation followed by mass spectrometry analysis can be used to study the conformational changes when proteins are disturbed by external forces.

  10. 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*.

  11. An unstructured-mesh atmospheric model for nonhydrostatic dynamics: Towards optimal mesh resolution

    Science.gov (United States)

    Szmelter, Joanna; Zhang, Zhao; Smolarkiewicz, Piotr K.

    2015-08-01

    The paper advances the limited-area anelastic model (Smolarkiewicz et al. (2013) [45]) for investigation of nonhydrostatic dynamics in mesoscale atmospheric flows. New developments include the extension to a tetrahedral-based median-dual option for unstructured meshes and a static mesh adaptivity technique using an error indicator based on inherent properties of the Multidimensional Positive Definite Advection Transport Algorithm (MPDATA). The model employs semi-implicit nonoscillatory forward-in-time integrators for soundproof PDEs, built on MPDATA and a robust non-symmetric Krylov-subspace elliptic solver. Finite-volume spatial discretisation adopts an edge-based data structure. Simulations of stratified orographic flows and the associated gravity-wave phenomena in media with uniform and variable dispersive properties verify the advancement and demonstrate the potential of heterogeneous anisotropic discretisation with large variation in spatial resolution for study of complex stratified flows that can be computationally unattainable with regular grids.

  12. In vitro high-resolution structural dynamics of single germinating bacterial spores

    Energy Technology Data Exchange (ETDEWEB)

    Plomp, M; Leighton, T; Wheeler, K; Malkin, A

    2006-11-14

    Although significant progress has been achieved in understanding the genetic and biochemical bases of the spore germination process, the structural basis for breaking the dormant spore state remains poorly understood. We have used atomic force microscopy (AFM) to probe the high-resolution structural dynamics of single Bacillus atrophaeus spores germinating under native conditions. Here we show that AFM can reveal previously unrecognized germination-induced alterations in spore coat architecture and topology as well as the disassembly of outer spore coat rodlet structures. These results and previous studies in other microorganisms suggest that the spore coat rodlets are structurally similar to amyloid fibrils. AFM analysis of the nascent surface of the emerging germ cell revealed a porous network of peptidoglycan fibers. The results are consistent with a honeycomb model structure for synthetic peptidoglycan oligomers determined by nuclear magnetic resonance. AFM is a promising experimental tool for investigating the morphogenesis of spore germination and cell wall peptidoglycan structure.

  13. In vitro high-resolution structural dynamics of single germinating bacterial spores

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence Livermore National Laboratory

    2006-12-11

    Although significant progress has been achieved in understanding the genetic and biochemical bases of the spore germination process, the structural basis for breaking the dormant spore state remains poorly understood. We have used atomic force microscopy (AFM) to probe the high-resolution structural dynamics of single Bacillus atrophaeus spores germinating under native conditions. Here we show that AFM can reveal previously unrecognized germination-induced alterations in spore coat architecture and topology as well as the disassembly of outer spore coat rodlet structures. These results and previous studies in other microorganisms suggest that the spore coat rodlets are structurally similar to amyloid fibrils. AFM analysis of the nascent surface of the emerging germ cell revealed a porous network of peptidoglycan fibers. The results are consistent with a honeycomb model structure for synthetic peptidoglycan oligomers determined by nuclear magnetic resonance. AFM is a promising experimental tool for investigating the morphogenesis of spore germination and cell wall peptidoglycan structure.

  14. Kinetic modeling of a high power fast-axial-flow CO2 laser with computational fluid dynamics method

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A new computational fluid dynamics (CFD) method for the simulation of fast-axial-flow CO2 laser is developed.The model which is solved by CFD software uses a set of dynamic differential equations to describe the dynamic process in one discharge tube.The velocity,temperature,pressure and turbulence energy distributions in discharge passage are presented.There is a good agreement between the theoretical prediction and the experimental results.This result indicates that the parameters of the laser have significant effect on the flow distribution in the discharge passage.It is helpful to optimize the output of high power CO2 laser by mastering its kinetic characteristics.

  15. Kinetics of Hexagonal Cylinders to Face-centered Cubic Spheres Transition of Triblock Copolymer in Selective Solvent: Brownian Dynamics Simulation

    CERN Document Server

    Li, Minghai; Bansil, Rama

    2010-01-01

    The kinetics of the transformation from the hexagonal packed cylinder (HEX) phase to the face-centered-cubic (FCC) phase was simulated using Brownian Dynamics for an ABA triblock copolymer in a selective solvent for the A block. The kinetics was obtained by instantaneously changing either the temperature of the system or the well-depth of the Lennard-Jones potential. Detailed analysis showed that the transformation occurred via a rippling mechanism. The simulation results indicated that the order-order transformation (OOT) was a nucleation and growth process when the temperature of the system instantly jumped from 0.8 to 0.5. The time evolution of the structure factor obtained by Fourier Transformation showed that the peak intensities of the HEX and FCC phases could be fit well by an Avrami equation.

  16. Super-resolution chemical imaging with dynamic placement of plasmonic hotspots

    Science.gov (United States)

    Olson, Aeli P.; Ertsgaard, Christopher T.; McKoskey, Rachel M.; Rich, Isabel S.; Lindquist, Nathan C.

    2015-08-01

    We demonstrate dynamic placement of plasmonic "hotspots" for super-resolution chemical imaging via Surface Enhanced Raman Spectroscopy (SERS). A silver nanohole array surface was coated with biological samples and illuminated with a laser. Due to the large plasmonic field enhancements, blinking behavior of the SERS hotspots was observed and processed using a Stochastic Optical Reconstruction Microscopy (STORM) algorithm enabling localization to within 10 nm. However, illumination of the sample with a single static laser beam (i.e., a slightly defocused Gaussian beam) only produced SERS hotspots in fixed locations on the surface, leaving noticeable gaps in any final image. But, by using a spatial light modulator (SLM), the illumination profile of the beam could be altered, shifting any hotspots across the nanohole array surface in sub-wavelength steps. Therefore, by properly structuring an illuminating light field with the SLM, we show the possibility of positioning plasmonic hotspots over a metallic nanohole surface on-the-fly. Using this and our SERS-STORM imaging technique, we show potential for high-resolution chemical imaging without the noticeable gaps that were present with static laser illumination. Interestingly, even illuminating the surface with randomly shifting SLM phase profiles was sufficient to completely fill in a wide field of view for super-resolution SERS imaging of a single strand of 100-nm thick collagen protein fibrils. Images were then compared to those obtained with a scanning electron microscope (SEM). Additionally, we explored alternative methods of phase shifting other than holographic illumination through the SLM to create localization of hotspots necessary for SERS-STORM imaging.

  17. Carbon budget estimation of a subarctic catchment using a dynamic ecosystem model at high spatial resolution

    Science.gov (United States)

    Tang, J.; Miller, P. A.; Persson, A.; Olefeldt, D.; Pilesjo, P.; Heliasz, M.; Jackowicz-Korczynski, M.; Yang, Z.; Smith, B.; Callaghan, T. V.; Christensen, T. R.

    2015-05-01

    A large amount of organic carbon is stored in high-latitude soils. A substantial proportion of this carbon stock is vulnerable and may decompose rapidly due to temperature increases that are already greater than the global average. It is therefore crucial to quantify and understand carbon exchange between the atmosphere and subarctic/arctic ecosystems. In this paper, we combine an Arctic-enabled version of the process-based dynamic ecosystem model, LPJ-GUESS (version LPJG-WHyMe-TFM) with comprehensive observations of terrestrial and aquatic carbon fluxes to simulate long-term carbon exchange in a subarctic catchment at 50 m resolution. Integrating the observed carbon fluxes from aquatic systems with the modeled terrestrial carbon fluxes across the whole catchment, we estimate that the area is a carbon sink at present and will become an even stronger carbon sink by 2080, which is mainly a result of a projected densification of birch forest and its encroachment into tundra heath. However, the magnitudes of the modeled sinks are very dependent on future atmospheric CO2 concentrations. Furthermore, comparisons of global warming potentials between two simulations with and without CO2 increase since 1960 reveal that the increased methane emission from the peatland could double the warming effects of the whole catchment by 2080 in the absence of CO2 fertilization of the vegetation. This is the first process-based model study of the temporal evolution of a catchment-level carbon budget at high spatial resolution, including both terrestrial and aquatic carbon. Though this study also highlights some limitations in modeling subarctic ecosystem responses to climate change, such as aquatic system flux dynamics, nutrient limitation, herbivory and other disturbances, and peatland expansion, our study provides one process-based approach to resolve the complexity of carbon cycling in subarctic ecosystems while simultaneously pointing out the key model developments for capturing

  18. Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping

    Directory of Open Access Journals (Sweden)

    Jessica L. Mark Welch

    2014-11-01

    Full Text Available The human mouth is an excellent system to study the dynamics of microbial communities and their interactions with their host. We employed oligotyping to analyze, with single-nucleotide resolution, oral microbial 16S ribosomal RNA (rRNA gene sequence data from a time course sampled from the tongue of two individuals, and we interpret our results in the context of oligotypes that we previously identified in the oral data from the Human Microbiome Project. Our previous work established that many of these oligotypes had dramatically different distributions between individuals and across oral habitats, suggesting that they represented functionally different organisms. Here we demonstrate the presence of a consistent tongue microbiome but with rapidly fluctuating proportions of the characteristic taxa. In some cases closely related oligotypes representing strains or variants within a single species displayed fluctuating relative abundances over time, while in other cases an initially dominant oligotype was replaced by another oligotype of the same species. We use this high temporal and taxonomic level of resolution to detect correlated changes in oligotype abundance that could indicate which taxa likely interact synergistically or occupy similar habitats, and which likely interact antagonistically or prefer distinct habitats. For example, we found a strong correlation in abundance over time between two oligotypes from different families of Gamma Proteobacteria, suggesting a close functional or ecological relationship between them. In summary, the tongue is colonized by a microbial community of moderate complexity whose proportional abundance fluctuates widely on time scales of days. The drivers and functional consequences of these community dynamics are not known, but we expect they will prove tractable to future, targeted studies employing taxonomically resolved analysis of high-throughput sequencing data sampled at appropriate temporal intervals and

  19. 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

  20. 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

  1. Origin of stereocontrol in guanidine-bisurea bifunctional organocatalyst that promotes α-hydroxylation of tetralone-derived β-ketoesters: asymmetric synthesis of β- and γ-substituted tetralone derivatives via organocatalytic oxidative kinetic resolution.

    Science.gov (United States)

    Odagi, Minami; Furukori, Kota; Yamamoto, Yoshiharu; Sato, Makoto; Iida, Keisuke; Yamanaka, Masahiro; Nagasawa, Kazuo

    2015-02-11

    The mechanism of asymmetric α-hydroxylation of tetralone-derived β-ketoesters with guanidine-bisurea bifunctional organocatalyst in the presence of cumene hydroperoxide (CHP) was examined by means of DFT calculations to understand the origin of the stereocontrol in the reaction. The identified transition-state model was utilized to design an enantioselective synthesis of β- or γ-substituted tetralones by catalytic oxidative kinetic resolution reaction of tetralone-derived β-ketoesters. This kinetic resolution reaction proceeded with high selectivity, and selectivity factors (s value) of up to 99 were obtained. The potential utility of this oxidative kinetic resolution method for synthesis of natural products was confirmed by applying it to achieve an enantioselective synthesis of (+)-linoxepin (13) from β-substituted tetralone rac-7 in only six steps.

  2. Energy dynamics and current sheet structure in fluid and kinetic simulations of decaying magnetohydrodynamic turbulence

    CERN Document Server

    Makwana, K D; Li, H; Daughton, W; Cattaneo, F

    2014-01-01

    Simulations of decaying magnetohydrodynamic (MHD) turbulence are performed with a fluid and a kinetic code. The initial condition is an ensemble of long-wavelength, counter-propagating, shear-Alfv\\'{e}n waves, which interfere and rapidly generate strong MHD turbulence. The total energy is conserved and the rate of turbulent energy decay is very similar in both codes, although the fluid code has numerical dissipation whereas the kinetic code has kinetic dissipation. The inertial range power spectrum index is similar in both the codes. The fluid code shows a perpendicular wavenumber spectral slope of $k_{\\perp}^{-1.3}$. The kinetic code shows a spectral slope of $k_{\\perp}^{-1.5}$ for smaller simulation domain, and $k_{\\perp}^{-1.3}$ for larger domain. We estimate that collisionless damping mechanisms in the kinetic code can account for the dissipation of the observed nonlinear energy cascade. Current sheets are geometrically characterized. Their lengths and widths are in good agreement between the two codes. T...

  3. From meso-Lactide to Isotactic Polylactide: Epimerization by B/N Lewis Pairs and Kinetic Resolution by Organic Catalysts.

    Science.gov (United States)

    Zhu, Jian-Bo; Chen, Eugene Y-X

    2015-10-07

    B/N Lewis pairs have been discovered to catalyze rapid epimerization of meso-lactide (LA) or LA diastereomers quantitatively into rac-LA. The obtained rac-LA is kinetically polymerized into poly(L-lactide) and optically resolved D-LA, with a high stereoselectivity k(L)/k(D) of 53 and an ee of 91% at 50.6% monomer conversion, by newly designed bifunctional chiral catalyst 4 that incorporates three key elements (β-isocupreidine core, thiourea functionality, and chiral BINAM) into a single organic molecule. The epimerization and enantioselective polymerization can be coupled into a one-pot process for transforming meso-LA directly into poly(L-lactide) and D-LA.

  4. ARTICLES: A Surface Femtosecond Two-Photon Photoemission Spectrometer for Excited Electron Dynamics and Time-Dependent Photochemical Kinetics

    Science.gov (United States)

    Ren, Ze-feng; Zhou, Chuan-yao; Ma, Zhi-bo; Xiao, Chun-lei; Mao, Xin-chun; Dai, Dong-xu; LaRue, Jerry; Cooper, Russell; Wodtke, Alec M.; Yang, Xue-ming

    2010-06-01

    A surface femtosecond two-photon photoemission (2PPE) spectrometer devoted to the study of ultrafast excited electron dynamics and photochemical kinetics on metal and metal oxide surfaces has been constructed. Low energy photoelectrons are measured using a hemispherical electron energy analyzer with an imaging detector that allows us to detect the energy and the angular distributions of the photoelectrons simultaneously. A Mach-Zehnder interferometer was built for the time-resolved 2PPE (TR-2PPE) measurement to study ultrafast surface excited electron dynamics, which was demonstrated on the Cu(111) surface. A scheme for measuring time-dependent 2PPE (TD-2PPE) spectra has also been developed for studies of surface photochemistry. This technique has been applied to a preliminary study on the photochemical kinetics on ethanol/TiO2(110). We have also shown that the ultrafast dynamics of photoinduced surface excited resonances can be investigated in a reliable way by combining the TR-2PPE and TD-2PPE techniques.

  5. Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study

    Science.gov (United States)

    de Oliveira, César Augusto F.; Hamelberg, Donald; McCammon, J. Andrew

    2007-11-01

    Molecular dynamics (MD) simulation is the standard computational technique used to obtain information on the time evolution of the conformations of proteins and many other molecular systems. However, for most biological systems of interest, the time scale for slow conformational transitions is still inaccessible to standard MD simulations. Several sampling methods have been proposed to address this issue, including the accelerated molecular dynamics method. In this work, we study the extent of sampling of the phi/psi space of alanine dipeptide in explicit water using accelerated molecular dynamics and present a framework to recover the correct kinetic rate constant for the helix to beta-strand transition. We show that the accelerated MD can drastically enhance the sampling of the phi/psi conformational phase space when compared to normal MD. In addition, the free energy density plots of the phi/psi space show that all minima regions are accurately sampled and the canonical distribution is recovered. Moreover, the kinetic rate constant for the helix to beta-strand transition is accurately estimated from these simulations by relating the diffusion coefficient to the local energetic roughness of the energy landscape. Surprisingly, even for such a low barrier transition, it is difficult to obtain enough transitions to accurately estimate the rate constant when one uses normal MD.

  6. Sarcomere dynamics in single myocardial cells as revealed by high-resolution light diffractometry.

    Science.gov (United States)

    Leung, A F

    1983-08-01

    A specially designed diffractometer with a high spatial and temporal resolution recorded the diffraction of a laser beam by single enzymatically isolated myocardial cells. The fine structures within the first-order diffraction were resolved and each structure was interpreted as the diffraction from a group of sarcomeres of nearly equal length. During activation of the cell dynamics of each discrete group of sarcomeres was uniform and independent of the other groups. However, a small nonuniform component in the sarcomere dynamics was observed and attributed to the coupling between the shortening tension and the radial stress resulting from the expansion of the myofibrillar cross-section. The time-course of the diffraction fine structures during contractile activity revealed (1) the period of the contraction-relaxation cycle, (2) the latent period, (3) the shortening and relengthening speeds and (4) the variation in the line width and intensity of the fine structure. Measurements showed that the latent period was dependent on the free Ca2+ of the cell's bathing solution while the initial shortening speed was not. The diffraction line width and intensity of the shortening cell were explained by the grating model.

  7. Hybrid Young interferometer for high resolution measurement of dynamic speckle using high birefringence liquid crystal

    Science.gov (United States)

    Bennis, N.; Holdynski, Z.; Merta, I.; Marc, P.; Kula, P.; Mazur, R.; Piecek, W.; Jaroszewicz, L. R.

    2015-08-01

    It is well known that the Young interference experiment is the fundamental setup to combine two beams and to construct the phase modulated light. Moreover, homodyne phase demodulator is based on signal decoding in back Fourier focal plane using bicell photodetector (B-PD). On the above base, we propose a novel experimental approach to the signals demodulation by using the optical interferometer which operates in homodyne mode, combined with liquid crystal spatial light modulators operating both phase as speckle modulator. Dynamic phase changes between the two beams can be controlled by monopixel liquid crystals cell placed in one branch of the interferometer. A phase modulation effect in a signal arm of interferometer is observed as a dynamic shift of the speckle pattern. Simple arithmetic combination of signals from B-PD placed in speckle pattern plane is only one necessary numerical manipulation to obtain exactly phase difference. Concept of signals demodulation in the Fourier focal plane can be only used for exactly defined geometrical (B-PD as well as Young interferometer) and physical parameters (polarization, wavelength). We optimize the setup geometry to obtain extremely high measurement resolution. In this paper we focus on the principles of operation of each part of the system as well as discussion their requirement in order to increase the signal to noise ratio.

  8. A solar radio dynamic spectrograph with flexible temporal-spectral resolution

    Science.gov (United States)

    Du, Qing-Fu; Chen, Lei; Zhao, Yue-Chang; Li, Xin; Zhou, Yan; Zhang, Jun-Rui; Yan, Fa-Bao; Feng, Shi-Wei; Li, Chuan-Yang; Chen, Yao

    2017-09-01

    Observation and research on solar radio emission have unique scientific values in solar and space physics and related space weather forecasting applications, since the observed spectral structures may carry important information about energetic electrons and underlying physical mechanisms. In this study, we present the design of a novel dynamic spectrograph that has been installed at the Chashan Solar Radio Observatory operated by the Laboratory for Radio Technologies, Institute of Space Sciences at Shandong University. The spectrograph is characterized by real-time storage of digitized radio intensity data in the time domain and its capability to perform off-line spectral analysis of the radio spectra. The analog signals received via antennas and amplified with a low-noise amplifier are converted into digital data at a speed reaching up to 32 k data points per millisecond. The digital data are then saved into a high-speed electronic disk for further off-line spectral analysis. Using different word lengths (1–32 k) and time cadences (5 ms–10 s) for off-line fast Fourier transform analysis, we can obtain the dynamic spectrum of a radio burst with different (user-defined) temporal (5 ms–10 s) and spectral (3 kHz∼320 kHz) resolutions. This enables great flexibility and convenience in data analysis of solar radio bursts, especially when some specific fine spectral structures are under study.

  9. Realistic initiation and dynamics of the Madden-Julian Oscillation in a coarse resolution aquaplanet GCM

    Science.gov (United States)

    Ajayamohan, R. S.; Khouider, Boualem; Majda, Andrew J.

    2013-12-01

    The main mechanisms for the initiation and propagation of the Madden-Julian Oscillation (MJO) are still widely debated. The capacity of operational global climate models (GCMs) to correctly simulate the MJO is hindered by the inadequacy of the underlying cumulus parameterizations. Here we show that a coarse resolution GCM, coupled to a simple multicloud model parameterization mimicking the observed dynamics and physical structure of organized tropical convection, simulates the MJO in an idealized setting of an aquaplanet without ocean dynamics. We impose a fixed nonhomogeneous sea-surface temperature replicating the Indian Ocean/Western Pacific warm pool. This results in a succession of MJOs with realistic phase speed, amplitude, and physical structure. Each MJO event is initiated at a somewhat random location over the warm pool and dies sometimes near the eastern boundary of the warm pool and sometimes at a random location way beyond the warm pool. Also occasionally the MJO events stall at the center of maximum heating. This is reminiscent of the fact that in nature some MJOs stall over the maritime continent while others reach the central Pacific Ocean and beyond. The initiation mechanism in the model is believed to be a combination of persistent intermittent convective events interacting with observed large-scale flow patterns and internal tropical dynamics. The large-scale flow patterns are associated with planetary-scale dry Kelvin waves that are triggered by preceding MJO events and circle the globe, while congestus cloud decks on the flanks of the warm pool are believed to force Rossby gyres which then funnel moisture toward the equatorial region.

  10. Combination Of Static And Dynami,C Stereophotogrammetry For The Kinetic Analysis Of Human Locomotion: Preliminary Results

    Science.gov (United States)

    Schaer, Alex R.; Sheffer, Daniel B.; Jones, D.; Meier, G.; Baumann, Juerg U.

    1989-04-01

    For a deeper understanding of the complexity of human walking movement not only a kinematic analysis , but also a comprehensive three-dimensional biomechanical model of the human body is required to detail the kinetic activities. This research combined static stereophotogrammetric determination of body segment mass parameters with three-dimensional gait analysis by cinephotography, direct linear transformation and two force plates. A method of combining the two independent analyses by defining the anatomical axes of each segment is shown. Practical problems arising in dynamic and stereometric analysis are demonstrated. Power spectra of a normal and a matched subject with spastic diplegia were calculated for a proper design of the kinematic analysis.

  11. 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

    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...... 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...

  12. 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 ...... than direct fitting of rate constants using the parametrized transients of the compartment model...

  13. Ion kinetic dynamics in strongly-shocked plasmas relevant to ICF

    Science.gov (United States)

    Rinderknecht, H. G.; Amendt, P. A.; Rosenberg, M. J.; Li, C. K.; Frenje, J. A.; Gatu Johnson, M.; Sio, H.; Séguin, F. H.; Petrasso, R. D.; Zylstra, A. B.; Kagan, G.; Hoffman, N. M.; Svyatsky, D.; Wilks, S. C.; Glebov, V. Yu.; Stoeckl, C.; Sangster, T. C.

    2017-06-01

    Implosions of thin-shell capsules produce strongly-shocked (M  >  10), low-density (ρ ˜ 1 mg cc-1), high-temperature ({{T}\\text{i}}˜ keV) plasmas, comparable to those produced in the strongly-shocked DT-vapor in inertial confinement fusion (ICF) experiments. A series of thin-glass targets filled with mixtures of deuterium and Helium-3 gas ranging from 7% to 100% deuterium was imploded to investigate the impact of multi-species ion kinetic mechanisms in ICF-relevant plasmas over a wide range of Knudsen numbers ({{N}\\text{K}}\\equiv {λ\\text{ii}}/R ). Slightly kinetic implosions ({{N}\\text{K}}˜ 0.01 -0.05) follow the expected yield trend with experimentally-inferred N K, suggesting effects associated with long mean-free-paths (such as energetic tail-ion loss) provide the dominant yield reduction mechanisms. In contrast, highly kinetic implosions (Rinderknecht et al 2015 Phys. Rev. Lett. 114 025001) with inferred {{N}\\text{K}}>0.5 produce the opposite yield trend from the Knudsen-number prediction, confirming the dominance of multi-species physics in these experiments. The impact of the observed kinetic physics mechanisms on the formation of the hotspot in ICF experiments is discussed.

  14. Dynamic identification of growth and survival kinetic parameters of microorganisms in foods

    Science.gov (United States)

    Inverse analysis is a mathematical method used in predictive microbiology to determine the kinetic parameters of microbial growth and survival in foods. The traditional approach in inverse analysis relies on isothermal experiments that are time-consuming and labor-intensive, and errors are accumula...

  15. CANCELLED Molecular dynamics simulations of noble gases in liquidwater: Solvati on structure, self-diffusion, and kinetic isotopeeffect

    Energy Technology Data Exchange (ETDEWEB)

    Bourg, I.C.; Sposito, G.

    2007-05-25

    Despite their great importance in low-temperaturegeochemistry, self-diffusion coefficients of noble gas isotopes in liquidwater (D) have been measured only for the major isotopes of helium, neon,krypton and xenon. Data on the self-diffusion coefficients of minor noblegas isotopes are essentially non-existent and so typically are estimatedby a kinetic theory model in which D varies as the inverse square root ofthe isotopic mass (m): D proportional to m-0.5. To examine the validityof the kinetic theory model, we performed molecular dynamics (MD)simulations of the diffusion of noble gases in ambient liquid water withan accurate set of noble gas-water interaction potentials. Our simulationresults agree with available experimental data on the solvation structureand self-diffusion coefficients of the major noble gas isotopes in liquidwater and reveal for the first time that the isotopic mass-dependence ofall noble gas self-diffusion coefficients has the power-law form Dproportional to m-beta with 0kinetic fractionation of noble gasisotopes caused by diffusion in ambient liquid water.

  16. 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.

  17. 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

  18. 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.

  19. High resolution simulations of energy absorption in dynamically loaded cellular structures

    Science.gov (United States)

    Winter, R. E.; Cotton, M.; Harris, E. J.; Eakins, D. E.; McShane, G.

    2017-03-01

    Cellular materials have potential application as absorbers of energy generated by high velocity impact. CTH, a Sandia National Laboratories Code which allows very severe strains to be simulated, has been used to perform very high resolution simulations showing the dynamic crushing of a series of two-dimensional, stainless steel metal structures with varying architectures. The structures are positioned to provide a cushion between a solid stainless steel flyer plate with velocities ranging from 300 to 900 m/s, and an initially stationary stainless steel target. Each of the alternative architectures under consideration was formed by an array of identical cells each of which had a constant volume and a constant density. The resolution of the simulations was maximised by choosing a configuration in which one-dimensional conditions persisted for the full period over which the specimen densified, a condition which is most readily met by impacting high density specimens at high velocity. It was found that the total plastic flow and, therefore, the irreversible energy dissipated in the fully densified energy absorbing cell, increase (a) as the structure becomes more rodlike and less platelike and (b) as the impact velocity increases. Sequential CTH images of the deformation processes show that the flow of the cell material may be broadly divided into macroscopic flow perpendicular to the compression direction and jetting-type processes (microkinetic flow) which tend to predominate in rod and rodlike configurations and also tend to play an increasing role at increased strain rates. A very simple analysis of a configuration in which a solid flyer impacts a solid target provides a baseline against which to compare and explain features seen in the simulations. The work provides a basis for the development of energy absorbing structures for application in the 200-1000 m/s impact regime.

  20. Variational perturbation and extended Plefka approaches to dynamics on random networks: the case of the kinetic Ising model

    CERN Document Server

    Bachschmid-Romano, Ludovica; Opper, Manfred; Roudi, Yasser

    2016-01-01

    We describe and analyze some novel approaches for studying the dynamics of Ising spin glass models. We first briefly consider the variational approach based on minimizing the Kullback-Leibler divergence between independent trajectories and the real ones and note that this approach only coincides with the mean field equations from the saddle point approximation to the generating functional when the dynamics is defined through a logistic link function, which is the case for the kinetic Ising model with parallel update. We then spend the rest of the paper developing two ways of going beyond the saddle point approximation to the generating functional. In the first one, we develop a variational perturbative approximation to the generating functional by expanding the action around a quadratic function of the local fields and conjugate local fields whose parameters are optimized. We derive analytical expressions for the optimal parameters and show that when the optimization is suitably restricted, we recover the mea...

  1. High order magnetic optics for high dynamic range proton radiography at a kinetic energy of 800 MeV

    Energy Technology Data Exchange (ETDEWEB)

    Sjue, S. K. L., E-mail: sjue@lanl.gov; Mariam, F. G.; Merrill, F. E.; Morris, C. L.; Saunders, A. [Physics Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

    2016-01-15

    Flash radiography with 800 MeV kinetic energy protons at Los Alamos National Laboratory is an important experimental tool for investigations of dynamic material behavior driven by high explosives or pulsed power. The extraction of quantitative information about density fields in a dynamic experiment from proton generated images requires a high fidelity model of the proton imaging process. It is shown that accurate calculations of the transmission through the magnetic lens system require terms beyond second order for protons far from the tune energy. The approach used integrates the correlated multiple Coulomb scattering distribution simultaneously over the collimator and the image plane. Comparison with a series of static calibration images demonstrates the model’s accurate reproduction of both the transmission and blur over a wide range of tune energies in an inverse identity lens that consists of four quadrupole electromagnets.

  2. Magnetic dynamics studied by high-resolution electron spectroscopy and time-resolved electron microscopy

    Science.gov (United States)

    Jayaraman, Rajeswari

    Future information technology requires an increased magnetically encoded data density and novel electromagnetic modes of data transfer. While to date magnetic properties are observed and characterized mostly statically, the need emerges to monitor and capture their fast dynamics. In this talk, I will focus on the spin dynamics i.e. spin wave excitations and the dynamics of a new topological distribution of spins termed ``skyrmions''. Wave packets of spin waves offer the unique capability to transport a quantum bit, the spin, without the transport of charge or mass. Here, large wave-vector spin waves are of particular interest as they admit spin localization within a few nanometers. By using our recently developed electron energy loss spectrometer, we could study such spin waves in ultrathin films with an unprecedented energy resolution of 4 meV. By virtue of the finite penetration depth of low energy electrons, spin waves localized at interfaces between a substrate and a thin capping layer can be been studied yielding information about the exchange coupling between atoms at the interface. The quantization of spin waves with wave vectors perpendicular to the film gives rise to standing modes to which EELS has likewise access. Such studies when carried out as function of the film thickness again yield information on the layer dependence of the exchange coupling. Magnetic skyrmions are promising candidates as information carriers in logic or storage devices. Currently, little is known about the influence of disorder, defects, or external stimuli on the spatial distribution and temporal evolution of the skyrmion lattice. In this talk, I will describe the dynamical role of disorder in a large and flat thin film of Cu2OSeO3, exhibiting a skyrmion phase in an insulating material. We image up to 70,000 skyrmions by means of cryo-Lorentz Transmission Electron Microscopy as a function of the applied magnetic field. In the skyrmion phase, dislocations are shown to cause the

  3. The impact of resolution on the dynamics of the martian global atmosphere: Varying resolution studies with the MarsWRF GCM

    Science.gov (United States)

    Toigo, Anthony D.; Lee, Christopher; Newman, Claire E.; Richardson, Mark I.

    2012-09-01

    latitudes at equinox, even the lowest model resolution considered here appears to do a good job for the southern winter and southern equinoctial pole (although in detail some discrepancies remain). These results suggest that studies of the northern winter jet (e.g., transient waves and cyclogenesis) will be more sensitive to global model resolution that those of the south (e.g., the confining dynamics of the southern polar vortex relevant to studies of argon transport). For surface winds, the major effect of increased horizontal resolution is in the superposition of circulations forced by local-scale topography upon the large-scale surface wind patterns. While passive predictions of dust lifting are generally insensitive to model horizontal resolution when no lifting threshold is considered, increasing the stress threshold produces significantly more lifting in higher resolution simulations with the generation of finer-scale, higher-stress winds due primarily to better-resolved topography. Considering the positive feedbacks expected for radiatively active dust lifting, we expect this bias to increase when such feedbacks are permitted.

  4. Using very high resolution satellite images to identify coastal zone dynamics at North Western Black Sea

    Science.gov (United States)

    Florin Zoran, Liviu; Ionescu Golovanov, Carmen; Zoran, Maria

    2010-05-01

    The availability of updated information about the extension and characteristics of land cover is a crucial issue in the perspective of a correct landscape planning and management of marine coastal zones. Satellite remote sensing data can provide accurate information about land coverage at different scales and the recent availability of very high resolution images definitely improved the precision of coastal zone spatio-temporal changes. The Romanian North Western coastal and shelf zones of the Black Sea and Danube delta are a mosaic of complex, interacting ecosystems, rich natural resources and socio-economic activity. Dramatic changes in the Black Sea's ecosystem and resources are due to natural and anthropogenic causes (increase in the nutrient and pollutant load of rivers input, industrial and municipal wastewater pollution along the coast, and dumping on the open sea). A scientific management system for protection, conservation and restoration must be based on reliable information on bio-geophysical and geomorphologic processes, coastal erosion, sedimentation dynamics, mapping of macrophyte fields, water quality, and climatic change effects. Use of satellite images is of great help for coastal zone monitoring and environmental impact assessment. Synergetic use of in situ measurements with multisensors satellite data could provide a complex assessment of spatio-temporal changes. In this study was developed a method for extracting coastal zone features information as well as landcover dynamics from IKONOS, very high resolution images for North-Western Black Sea marine coastal zone. The main objective was obtaining reliable data about the spatio-temporal coastal zone changes in two study areas located in Constanta urban area and Danube Delta area. We used an object-oriented approach based on preliminary segmentation and classification of the resulting object. First of all, segmentation parameters were tested and selected comparing segmented polygons with

  5. Recent Research Development in Resolution Kinetics of Racemic Menthol by Lipase%脂肪酶动力学拆分薄荷醇的研究进展

    Institute of Scientific and Technical Information of China (English)

    念保义; 黄志华; 罗菊香; 牛玉

    2011-01-01

    从脂肪酶拆分薄荷醇的转酯化、水解反应的工艺和影响因素等方面,分析了脂肪酶动力学拆分过程的转酯化和水解反应的催化路径与特点,指出了脂肪酶拆分薄荷醇的最佳路径和工艺选择.综述了近10年来脂肪酶拆分制备工业重要的手性香料l-薄荷醇的研究进展,特别综述了具有工业化前景的脂肪酶催化拆分和单元操作工艺的研究进展.同时展望了未来脂肪酶拆分薄荷醇的研究方向.%A condensed review of the potential offered by lipase for resolution of racemic menthols for the past 10 years is presented.Especially, recent applications of the lipase catalytic approach and industrialization of unit operation to the preparation of the most important flavor, l-menthol, are comprehensively covered by analyzing their processes of transesterification, hydrolysis reaction and influential factors. The potential industrial processes based on lipase-catalytie methods are discussed in the terms of their advantages over classical ones. The optimal pathway of resolution is achieved by analyzing resolving routes of menthol and alternative of acyl agent for transesterification of menthol. And a vista of the future investigations is opened up for new realms from macro-kinetics of menthol resolution for the industrial processes.

  6. Fat suppression techniques for obtaining high resolution dynamic contrast enhanced bilateral breast MR images at 7 tesla

    DEFF Research Database (Denmark)

    van der Velden, Tijl A; Schmitz, Alexander M Th; Gilhuijs, Kenneth G A

    2016-01-01

    OBJECTIVES: To compare water selective excitation (WSE) and Dixon fat suppression in the context of high-resolution dynamic contrast enhanced MRI of the breast at 7 tesla. METHODS: Ten healthy volunteers and one patient with a malignant breast lesion were scanned at 7 tesla. The MRI protocol...

  7. Refinement of horizontal resolution in dynamical downscaling of climate information using WRF: Costs, benefits, and lessons learned

    Science.gov (United States)

    Dynamical downscaling techniques have previously been developed by the U.S. Environmental Protection Agency (EPA) using a nested WRF at 108- and 36-km. Subsequent work extended one-way nesting down to 12-km resolution. Recently, the EPA Office of Research and Development used com...

  8. Interaction networks in protein folding via atomic-resolution experiments and long-time-scale molecular dynamics simulations

    DEFF Research Database (Denmark)

    Sborgi, Lorenzo; Verma, Abhinav; Piana, Stefano;

    2015-01-01

    The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulation...

  9. Ejecta Cloud from a Kinetic Impact on the Secondary of a Binary Asteroid: I. Mechanical Environment and Dynamic Model

    CERN Document Server

    Yu, Yang; Schwartz, Stephen R; Naidu, Shantanu P; Benner, Lance A M

    2016-01-01

    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 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 composition of fragments is modeled with a power law fitted from obs...

  10. 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.

  11. 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.

  12. Motor cortical prediction of EMG: evidence that a kinetic brain-machine interface may be robust across altered movement dynamics.

    Science.gov (United States)

    Cherian, A; Krucoff, M O; Miller, L E

    2011-08-01

    During typical movements, signals related to both the kinematics and kinetics of movement are mutually correlated, and each is correlated to some extent with the discharge of neurons in the primary motor cortex (M1). However, it is well known, if not always appreciated, that causality cannot be inferred from correlations. Although these mutual correlations persist, their nature changes with changing postural or dynamical conditions. Under changing conditions, only signals directly controlled by M1 can be expected to maintain a stable relationship with its discharge. If one were to rely on noncausal correlations for a brain-machine interface, its generalization across conditions would likely suffer. We examined this effect, using multielectrode recordings in M1 as input to linear decoders of both end point kinematics (position and velocity) and proximal limb myoelectric signals (EMG) during reaching. We tested these decoders across tasks that altered either the posture of the limb or the end point forces encountered during movement. Within any given task, the accuracy of the kinematic predictions tended to be somewhat better than the EMG predictions. However, when we used the decoders developed under one task condition to predict the signals recorded under different postural or dynamical conditions, only the EMG decoders consistently generalized well. Our results support the view that M1 discharge is more closely related to kinetic variables like EMG than it is to limb kinematics. These results suggest that brain-machine interface applications using M1 to control kinetic variables may prove to be more successful than the more standard kinematic approach.

  13. High-Resolution Modeling Disturbance-Induced Forest Carbon Dynamics with Lidar and Landsat Observations

    Science.gov (United States)

    Zhao, M.; Huang, C.; Hurtt, G. C.; Dubayah, R.; Fisk, J.; Sahajpal, R.; Flanagan, S.; Swatantran, A.; Huang, W.; Tang, H.; ONeil-Dunne, J.; Johnson, K. D.

    2015-12-01

    Forest stands are dynamic in a status from severely, partially disturbed, or undisturbed to different stages of recovery towards maturity and equilibrium. Forest ecosystem models generally use potential biomass (an assumption of equilibrium status) as initial biomass, which is unrealistic and could result in unreliable estimates of disturbance-induced carbon changes. To accurately estimate spatiotemporal changes of forest carbon stock and fluxes, it requires accurate information on initial biomass, the extent and severity of disturbance, and following land use. We demonstrate a prototype system to achieve this goal by integrating 1-m small footprint Lidar acquired in year 2004, 30-m Landsat disturbances from 1984 to 2011, and an individual-based structure height Ecosystem Demography (ED) model. Lidar provides critical information on forest canopy height, improving the accuracy of initial forest biomass estimates; impervious surfaces data and yearly disturbance data from Landsat provide information on wall-to-wall yearly natural and anthropogenic disturbances and their severity (on average 0.32% for the natural and 0.19% for the anthropogenic for below test area); ED model plays a central role by linking both Lidar canopy height and Landsat disturbances with ecosystem processes. We tested the system at 90-m spatial resolution in Charles County, Maryland, by running ED model for six experiments, the combinations of three initial biomass (potential, moderate and low initial biomass constrained by Lidar canopy height) with two disturbance scenarios (with and without anthropogenic disturbances). Our experiments show that estimated changes of carbon stock and flux are sensitive to initial biomass status and human-induced land cover change. Our prototype system can assess regional carbon dynamics at local scale under changing climate and disturbance regimes, and provide useful information for forest management and land use policies.

  14. Computational fluid dynamics modelling of biomass fast pyrolysis in fluidised bed reactors, focusing different kinetic schemes.

    Science.gov (United States)

    Ranganathan, Panneerselvam; Gu, Sai

    2016-08-01

    The present work concerns with CFD modelling of biomass fast pyrolysis in a fluidised bed reactor. Initially, a study was conducted to understand the hydrodynamics of the fluidised bed reactor by investigating the particle density and size, and gas velocity effect. With the basic understanding of hydrodynamics, the study was further extended to investigate the different kinetic schemes for biomass fast pyrolysis process. The Eulerian-Eulerian approach was used to model the complex multiphase flows in the reactor. The yield of the products from the simulation was compared with the experimental data. A good comparison was obtained between the literature results and CFD simulation. It is also found that CFD prediction with the advanced kinetic scheme is better when compared to other schemes. With the confidence obtained from the CFD models, a parametric study was carried out to study the effect of biomass particle type and size and temperature on the yield of the products.

  15. Efficient 3D Kinetic Monte Carlo Method for Modeling of Molecular Structure and Dynamics

    DEFF Research Database (Denmark)

    Panshenskov, Mikhail; Solov'yov, Ilia; Solov'yov, Andrey V.

    2014-01-01

    Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures with...... the kinetic Monte Carlo approach in a three-dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system....

  16. Solvent Effects upon Electrochemical Kinetics: Influences of Interfacial Solvation and Solvent Relaxation Dynamics.

    Science.gov (United States)

    1984-09-01

    by block number) incganic and organometallic complexes ; inner-shell barrier; electrochemical kinetics Z-. ASS-ACT (Continue on reverse aid* If...valuable class of model systems is provided by one- electron couples involving substitutionally inert inorganic and organometallic complexes . Important...specific ligand- solventOs interactions, perhaps with accompanying decreases in Kel (6). This explanation is consisterwith the observation that ksb decreases

  17. Chemical gas-dynamics beyond Wang Chang-Uhlenbeck's kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Kolesnichenko, Evgeniy G. [Gas Kinetics Lab, Moscow State University, Institute for Mechanics, Moscow, 117192 (Russian Federation); Gorbachev, Yuriy E. [Research Department, Coddan Technologies LLC, St. Petersburg, 197342 (Russian Federation)

    2014-12-09

    Wang Chang-Uhlenbeck equation does not give possibility to take into account intermolecular processes such as redistribution of the energy among different degrees of freedom. The modification of the generalized Wang Chang-Uhlenbeck equation including such processes is proposed. It allows to study for instance the kinetics of non-radiative transitions. Limitations of this approach are connected with the requirements of absence of polarization of rotational momentum and phases of intermolecular vibrations.

  18. Wide-dynamic-range kinetic investigations of deep proton tunnelling in proteins

    Science.gov (United States)

    Salna, Bridget; Benabbas, Abdelkrim; Sage, J. Timothy; van Thor, Jasper; Champion, Paul M.

    2016-09-01

    Directional proton transport along ‘wires’ that feed biochemical reactions in proteins is poorly understood. Amino-acid residues with high pKa are seldom considered as active transport elements in such wires because of their large classical barrier for proton dissociation. Here, we use the light-triggered proton wire of the green fluorescent protein to study its ground-electronic-state proton-transport kinetics, revealing a large temperature-dependent kinetic isotope effect. We show that ‘deep’ proton tunnelling between hydrogen-bonded oxygen atoms with a typical donor-acceptor distance of 2.7-2.8 Å fully accounts for the rates at all temperatures, including the unexpectedly large value (2.5 × 109 s-1) found at room temperature. The rate-limiting step in green fluorescent protein is assigned to tunnelling of the ionization-resistant serine hydroxyl proton. This suggests how high-pKa residues within a proton wire can act as a ‘tunnel diode’ to kinetically trap protons and control the direction of proton flow.

  19. Dynamical decimation renormalization-group technique: kinetic gaussian model on nonbranching, branching, and multibranching koch curves

    Science.gov (United States)

    Zhu; Yang

    2000-06-01

    A generalizing formulation of dynamical real-space renormalization that is appropriate for arbitrary spin systems is suggested. The alternative version replaces single-spin flipping Glauber dynamics with single-spin transition dynamics. As an application, in this paper we mainly investigate the critical slowing down of the Gaussian spin model on three fractal lattices, including nonbranching, branching, and multibranching Koch curves. The dynamical critical exponent z is calculated for these lattices using an exact decimation renormalization transformation in the assumption of the magneticlike perturbation, and a universal result z=1/nu is found.

  20. Simulations of Kinetic Electrostatic Electron Nonlinear (KEEN) Waves with Variable Velocity Resolution Grids and High-Order Time-Splitting

    CERN Document Server

    Afeyan, Bedros; Crouseilles, Nicolas; Dodhy, Adila; Faou, Erwan; Mehrenberger, Michel; Sonnendrücker, Eric

    2014-01-01

    KEEN waves are nonlinear, non-stationary, self-organized asymptotic states in Vlasov plasmas outside the scope or purview of linear theory constructs such as electron plasma waves or ion acoustic waves. Nonlinear stationary mode theories such as those leading to BGK modes also do not apply. The range in velocity that is strongly perturbed by KEEN waves depends on the amplitude and duration of the ponderomotive force used to drive them. Smaller amplitude drives create highly localized structures attempting to coalesce into KEEN waves. These cases have much more chaotic and intricate time histories than strongly driven ones. The narrow range in which one must maintain adequate velocity resolution in the weakly driven cases challenges xed grid numerical schemes. What is missing there is the capability of resolving locally in velocity while maintaining a coarse grid outside the highly perturbed region of phase space. We here report on a new Semi-Lagrangian Vlasov-Poisson solver based on conservative non-uniform c...

  1. 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.

  2. High-resolution isotope measurements resolve rapid ecohydrological dynamics at the soil-plant interface.

    Science.gov (United States)

    Volkmann, Till H M; Haberer, Kristine; Gessler, Arthur; Weiler, Markus

    2016-05-01

    Plants rely primarily on rainfall infiltrating their root zones - a supply that is inherently variable, and fluctuations are predicted to increase on most of the Earth's surface. Yet, interrelationships between water availability and plant use on short timescales are difficult to quantify and remain poorly understood. To overcome previous methodological limitations, we coupled high-resolution in situ observations of stable isotopes in soil and transpiration water. We applied the approach along with Bayesian mixing modeling to track the fate of (2) H-labeled rain pulses following drought through soil and plants of deciduous tree ecosystems. We resolve how rainwater infiltrates the root zones in a nonequilibrium process and show that tree species differ in their ability to quickly acquire the newly available source. Sessile oak (Quercus petraea) adjusted root uptake to vertical water availability patterns under drought, but readjustment toward the rewetted topsoil was delayed. By contrast, European beech (Fagus sylvatica) readily utilized water from all soil depths independent of water depletion, enabling faster uptake of rainwater. Our results demonstrate that species-specific plasticity and responses to water supply fluctuations on short timescales can now be identified and must be considered to predict vegetation functional dynamics and water cycling under current and future climatic conditions.

  3. Carbon budget estimation of a subarctic catchment using a dynamic ecosystem model at high spatial resolution

    Directory of Open Access Journals (Sweden)

    J. Tang

    2015-01-01

    Eriophorum, Sphagnum and then tundra heath during the observation periods. The catchment-level carbon fluxes from aquatic systems are dominated by CO2 emissions from streams. Integrated across the whole catchment, we estimate that the area is a carbon sink at present, and will become an even stronger carbon sink by 2080, which is mainly a result of a projected densification of birch forest and its encroachment into tundra heath. However, the magnitudes of the modelled sinks are very dependent on future atmospheric CO2 concentrations. Furthermore, comparisons of global warming potentials between two simulations with and without CO2 increase since 1960 reveal that the increased methane emission from the peatland could double the warming effects of the whole catchment by 2080 in the absence of CO2 fertilization of the vegetation. This is the first process-based model study of the temporal evolution of a catchment-level carbon budget at high spatial resolution, integrating comprehensive and diverse fluxes including both terrestrial and aquatic carbon. Though this study also highlights some limitations in modelling subarctic ecosystem responses to climate change including aquatic system flux dynamics, nutrient limitation, herbivory and other disturbances and peatland expansion, our application provides a mechanism to resolve the complexity of carbon cycling in subarctic ecosystems while simultaneously pointing out the key model developments for capturing complex subarctic processes.

  4. Expanding the linear dynamic range for quantitative liquid chromatography-high resolution mass spectrometry utilizing natural isotopologue signals

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Hanghui, E-mail: Hanghui.Liu@senomyx.com [Senomyx Inc. 4767 Nexus Centre Dr., San Diego, CA 92121 (United States); Lam, Lily; Yan, Lin; Chi, Bert [Senomyx Inc. 4767 Nexus Centre Dr., San Diego, CA 92121 (United States); Dasgupta, Purnendu K., E-mail: Dasgupta@uta.edu [Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019-0065 (United States)

    2014-11-19

    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.

  5. Dynamic phase transition in the two-dimensional kinetic Ising model in an oscillating field: universality with respect to the stochastic dynamics.

    Science.gov (United States)

    Buendía, G M; Rikvold, P A

    2008-11-01

    We study the dynamical response of a two-dimensional Ising model subject to a square-wave oscillating external field. In contrast to earlier studies, the system evolves under a so-called soft Glauber dynamic [Rikvold and Kolesik, J. Phys. A 35, L117 (2002)], for which both nucleation and interface propagation are slower and the interfaces smoother than for the standard Glauber dynamic. We choose the temperature and magnitude of the external field such that the metastable decay of the system following field reversal occurs through nucleation and growth of many droplets of the stable phase, i.e., the multidroplet regime. Using kinetic Monte Carlo simulations, we find that the system undergoes a nonequilibrium phase transition, in which the symmetry-broken dynamic phase corresponds to an asymmetric stationary limit cycle for the time-dependent magnetization. The critical point is located where the half period of the external field is approximately equal to the metastable lifetime of the system. We employ finite-size scaling analysis to investigate the characteristics of this dynamical phase transition. The critical exponents and the fixed-point value of the fourth-order cumulant are found to be consistent with the universality class of the two-dimensional equilibrium Ising model. This universality class has previously been established for the same nonequilibrium model evolving under the standard Glauber dynamic, as well as in a different nonequilibrium model of CO oxidation. The results reported in the present paper support the hypothesis that this far-from-equilibrium phase transition is universal with respect to the choice of the stochastic dynamics.

  6. Dynamic order reduction of thin-film deposition kinetics models: A reaction factorization approach

    Energy Technology Data Exchange (ETDEWEB)

    Adomaitis, Raymond A., E-mail: adomaiti@umd.edu [Department of Chemical and Biomolecular Engineering, Institute for Systems Research, University of Maryland, College Park, Maryland 20742 (United States)

    2016-01-15

    A set of numerical tools for the analysis and dynamic dimension reduction of chemical vapor and atomic layer deposition (ALD) surface reaction models is developed in this work. The approach is based on a two-step process where in the first, the chemical species surface balance dynamic equations are factored to effectively decouple the (nonlinear) reaction rates, a process that eliminates redundant dynamic modes and that identifies conserved quantities. If successful, the second phase is implemented to factor out redundant dynamic modes when species relatively minor in concentration are omitted; if unsuccessful, the technique points to potential model structural problems. An alumina ALD process is used for an example consisting of 19 reactions and 23 surface and gas-phase species. Using the approach developed, the model is reduced by nineteen modes to a four-dimensional dynamic system without any knowledge of the reaction rate values. Results are interpreted in the context of potential model validation studies.

  7. The mesoscale forcing of a midlatitude upper-tropospheric jet streak by a simulated convective system. 2: Kinetic energy and resolution analysis

    Science.gov (United States)

    Wolf, Bart J.; Johnson, D. R.

    1995-01-01

    A kinetic energy (KE) analysis of the forcing of a mesoscale upper-tropospheric jet streak by organized diabatic processes within the simulated convective system (SCS) that was discussed in Part 1 is presented in this study. The relative contributions of the ageostrophic components of motion to the generation of KE of the convectively generated jet streak are compared, along with the KE generation by the rotational (nondivergent) and irrotational (divergent) mass transport. The sensitivity of the numerical simulations of SCS development to resolution is also briefly examined. Analysis within isentropic coordinates provides for an explicit determination of the influence of the diabatic processes on the generation of KE. The upper-level production of specific KE is due predominatly to the inertial advective ageostrophic component (IAD), and as such represents the primary process through which the KE of the convectively generated jet streak is realized. A secondary contribution by the inertial diabatic (IDI) term is observed. Partitioning the KE generation into its rotational and irrotational components reveals that the latter, which is directly linked to the diabatic heating within the SCS through isentropic continuity requirements, is the ultimate source of KE generation as the global area integral of generation by the rotational component vanishes. Comparison with an identical dry simulation reveals that the net generation of KE must be attributed to latent heating. Both the IAD and IDI ageostrophic components play important roles in this regard. Examination of results from simulations conducted at several resolutions supports the previous findings in that the effects of diabatic processes and ageostrophic motion on KE generation remain consistent. Resolution does impact the location and timing of SCS development, a result that has important implications in forecasting the onset of convection that develops from evolution of the large-scale flow and moisture

  8. Opinion dynamics: Kinetic modelling with mass media, application to the Scottish independence referendum

    Science.gov (United States)

    Boudin, Laurent; Salvarani, Francesco

    2016-02-01

    We consider a kinetic model describing some mechanisms of opinion formation in the framework of referendums, where 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. We study, at the numerical level, both the transient and the asymptotic regimes. In particular, we point out that a plurality of media, with different orientations, is a key ingredient to allow pluralism and prevent consensus. The forecasts of the model are compared to some surveys related to the Scottish independence referendum of 2014.

  9. Nonlinear excitation kinetics of biased quantum wells. Coherent dynamical screening effect

    DEFF Research Database (Denmark)

    Turchinovich, Dmitry; Jepsen, Peter Uhd

    2006-01-01

    In this paper we describe a strongly nonlinear process of ultrafast photoexcitation of a biased quantum well. This process is governed by coherent dynamical screening, where the instantaneously polarized photoexcited carriers screen initial bias field. This results in a dynamic modification...... of the bandstructure of the quantum well, which is totally coherent with the temporal intensity distribution of the excitation laser pulse. We developed a time-resolved theoretical model of coherent dynamical screening, which predicts interesting fundamental consequences, such as nonlinear absorption and ultra......-broadband THz emission. The results of our THz and optical experiments are in good agreement with the theoretical model....

  10. 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.)

  11. Glassy dynamics, spinodal fluctuations, and the kinetic limit of nucleation in suspensions of colloidal hard rods

    NARCIS (Netherlands)

    Ni, R.; Belli, S; Van Roij, R.; Dijkstra, M.

    2010-01-01

    Using simulations we identify three dynamic regimes in supersaturated isotropic fluid states of short hard rods: (i) for moderate supersaturations, we observe nucleation of multilayered crystalline clusters; (ii) at higher supersaturation, we find nucleation of small crystallites which arrange into

  12. 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.

  13. Lipid-assisted protein transport: A diffusion-reaction model supported by kinetic experiments and molecular dynamics simulations

    Science.gov (United States)

    La Rosa, Carmelo; Scalisi, Silvia; Lolicato, Fabio; Pannuzzo, Martina; Raudino, Antonio

    2016-05-01

    The protein transport inside a cell is a complex phenomenon that goes through several difficult steps. The facilitated transport requires sophisticated machineries involving protein assemblies. In this work, we developed a diffusion-reaction model to simulate co-transport kinetics of proteins and lipids. We assume the following: (a) there is always a small lipid concentration of order of the Critical Micellar Concentration (CMC) in equilibrium with the membrane; (b) the binding of lipids to proteins modulates the hydrophobicity of the complexes and, therefore, their ability to interact and merge with the bilayer; and (c) some lipids leave the bilayer to replenish those bound to proteins. The model leads to a pair of integral equations for the time-evolution of the adsorbed proteins in the lipid bilayer. Relationships between transport kinetics, CMC, and lipid-protein binding constants were found. Under particular conditions, a perturbation analysis suggests the onset of kinks in the protein adsorption kinetics. To validate our model, we performed leakage measurements of vesicles composed by either high or low CMC lipids interacting with Islet Amyloid PolyPeptide (IAPP) and Aβ (1-40) used as sample proteins. Since the lipid-protein complex stoichiometry is not easily accessible, molecular dynamics simulations were performed using monomeric IAPP interacting with an increasing number of phospholipids. Main results are the following: (a) 1:1 lipid-protein complexes generally show a faster insertion rate proportional to the complex hydrophobicity and inversely related to lipid CMC; (b) on increasing the number of bound lipids, the protein insertion rate decreases; and (c) at slow lipids desorption rate, the lipid-assisted proteins transport might exhibit a discontinuous behavior and does non-linearly depend on protein concentration.

  14. 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.

  15. A novel xenograft model in zebrafish for high-resolution investigating dynamics of neovascularization in tumors.

    Directory of Open Access Journals (Sweden)

    Chengjian Zhao

    Full Text Available Tumor neovascularization is a highly complex process including multiple steps. Understanding this process, especially the initial stage, has been limited by the difficulties of real-time visualizing the neovascularization embedded in tumor tissues in living animal models. In the present study, we have established a xenograft model in zebrafish by implanting mammalian tumor cells into the perivitelline space of 48 hours old Tg(Flk1:EGFP transgenic zebrafish embryos. With this model, we dynamically visualized the process of tumor neovascularization, with unprecedented high-resolution, including new sprouts from the host vessels and the origination from VEGFR2(+ individual endothelial cells. Moreover, we quantified their contributions during the formation of vascular network in tumor. Real-time observations revealed that angiogenic sprouts in tumors preferred to connect each other to form endothelial loops, and more and more endothelial loops accumulated into the irregular and chaotic vascular network. The over-expression of VEGF165 in tumor cells significantly affected the vascularization in xenografts, not only the number and size of neo-vessels but the abnormalities of tumor vascular architecture. The specific inhibitor of VEGFR2, SU5416, significantly inhibited the vascularization and the growth of melanoma xenografts, but had little affects to normal vessels in zebrafish. Thus, this zebrafish/tumor xenograft model not only provides a unique window to investigate the earliest events of tumoral neoangiogenesis, but is sensitive to be used as an experimental platform to rapidly and visually evaluate functions of angiogenic-related genes. Finally, it also offers an efficient and cost-effective means for the rapid evaluation of anti-angiogenic chemicals.

  16. 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.

  17. Dynamics of the MAP IOP 15 severe Mistral event: Observations and high-resolution numerical simulations

    Science.gov (United States)

    Guénard, V.; Drobinski, P.; Caccia, J. L.; Tedeschi, G.; Currier, P.

    2006-04-01

    This paper investigates the fundamental processes involved in a severe Mistral event that occurred during the Mesoscale Alpine Program (from 6 to 9 November 1999). The Mistral refers to a violent north/north-westerly wind blowing in south-eastern France from the Rhône valley to the French Riviera. The study is based on measurements from radiosoundings launched from Lyon and Nîmes and from two UHF wind profilers located near Marseille and Toulon allowing a good description of the flow in the complex terrain formed by the south-western Alps. Observational results are compared with RAMS non-hydrostatic numerical simulations performed with 27 km, 9 km and 3 km nested grids. The numerical simulations capture the flow complexity both upstream of the Alps and in the coastal area affected by the Mistral. They correctly reproduce horizontal wind speeds and directions, vertical velocities, virtual potential temperature and relative humidity documented by the observational network. The simulations are used to point out the main dynamical processes generating the Mistral. It is found that flow splitting around the Alps and around the isolated peaks bordering the south-eastern part of the Rhône valley (Mont Ventoux 1909 m, Massif du Lubéron 1425 m) induces the low-level jet observed near Marseille that lasts for 36 hours. The high-resolution simulation indicates that the transient low-level jet lasting for only 9 hours observed at Toulon is due to a gravity wave breaking over local topography (the Sainte Baume 1147 m) where hydraulic jumps are involved. A mountain wake with two opposite-sign potential-vorticity banners is generated. The mesoscale wake explains the westward progression of the large-scale Alpine wake.

  18. Kinetics of liquid-mediated crystallization of amorphous Ge from multi-frame dynamic transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Santala, M. K., E-mail: melissa.santala@oregonstate.edu; Campbell, G. H. [Materials Science Division, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, California 94551 (United States); Raoux, S. [Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, D-14109 Berlin (Germany)

    2015-12-21

    The kinetics of laser-induced, liquid-mediated crystallization of amorphous Ge thin films were studied using multi-frame dynamic transmission electron microscopy (DTEM), a nanosecond-scale photo-emission transmission electron microscopy technique. In these experiments, high temperature gradients are established in thin amorphous Ge films with a 12-ns laser pulse with a Gaussian spatial profile. The hottest region at the center of the laser spot crystallizes in ∼100 ns and becomes nano-crystalline. Over the next several hundred nanoseconds crystallization continues radially outward from the nano-crystalline region forming elongated grains, some many microns long. The growth rate during the formation of these radial grains is measured with time-resolved imaging experiments. Crystal growth rates exceed 10 m/s, which are consistent with crystallization mediated by a very thin, undercooled transient liquid layer, rather than a purely solid-state transformation mechanism. The kinetics of this growth mode have been studied in detail under steady-state conditions, but here we provide a detailed study of liquid-mediated growth in high temperature gradients. Unexpectedly, the propagation rate of the crystallization front was observed to remain constant during this growth mode even when passing through large local temperature gradients, in stark contrast to other similar studies that suggested the growth rate changed dramatically. The high throughput of multi-frame DTEM provides gives a more complete picture of the role of temperature and temperature gradient on laser crystallization than previous DTEM experiments.

  19. Integration of Inhibition Kinetics and Molecular Dynamics Simulations: A Urea-Mediated Folding Study on Acetaldehyde Dehydrogenase 1.

    Science.gov (United States)

    Xu, Yingying; Lee, Jinhyuk; Lü, Zhi-Rong; Mu, Hang; Zhang, Qian; Park, Yong-Doo

    2016-07-01

    Understanding the mechanism of acetaldehyde dehydrogenase 1 (ALDH1) folding is important because this enzyme is directly involved in several types of cancers and other diseases. We investigated the urea-mediated unfolding of ALDH1 by integrating kinetic inhibition studies with computational molecular dynamics (MD) simulations. Conformational changes in the enzyme structure were also analyzed using intrinsic and 1-anilinonaphthalene-8-sulfonate (ANS)-binding fluorescence measurements. Kinetic studies revealed that the direct binding of urea to ALDH1 induces inactivation of ALDH1 in a manner of mixed-type inhibition. Tertiary structural changes associated with regional hydrophobic exposure of the active site were observed. The urea binding regions on ALDH1 were predicted by docking simulations and were partly shared with active site residues of ALDH1 and with interface residues of the oligomerization domain for tetramer formation. The docking results suggest that urea prevents formation of the ALDH1 normal shape for the tetramer state as well as entrance of the substrate into the active site. Our study provides insight into the structural changes that accompany urea-mediated unfolding of ALDH1 and the catalytic role associated with conformational changes.

  20. In Situ Atomic Scale Visualization Of Surface Kinetics Driven Dynamics Of Oxide Growth On A Ni–Cr Surface

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Langli; Zou, Lianfeng; Schreiber, Daniel K.; Olszta, Matthew J.; Baer, Donald R.; Bruemmer, Stephen M.; Zhou, Guangwen; Wang, Chong M.

    2016-01-20

    We report in situ atomic-scale visualization of the dynamical three-dimensional (3D) growth of NiO during initial oxidation of Ni-10at%Cr using environmental transmission electron microscopy (ETEM). Despite the thermodynamic preference for Cr2O3 formation, cubic NiO oxides nucleated and grew epitaxially as the dominating oxide phase on the Ni-Cr (100) surface during initial oxidation. The growth of NiO islands proceeds through step-by-step adatom mechanism in 3D, which is sustained by surface diffusion of Ni and O atoms. Although the shapes of oxide islands are controlled by strain energy between oxide and alloy substrate, local surface kinetic variations can lead to the change of surface planes of oxide islands. These results demonstrate that surface diffusion dominates initial oxidation of Ni-Cr in these test conditions.

  1. Enhanced reaction kinetics and reactive mixing scale dynamics in mixing fronts under shear flow for arbitrary Damk\\"ohler numbers

    CERN Document Server

    Bandopadhyay, Aditya; Méheust, Yves; Dentz, Marco

    2016-01-01

    Mixing fronts, where fluids of different chemical compositions mix with each other, are typically subjected to velocity gradients, ranging from the pore scale to the catchment scale due to permeability variations and flow line geometries. A common trait of these processes is that the mixing interface is strained by shear. Depending on the P\\'eclet number $Pe$, which represents the ratio of the characteristic diffusion time to the characteristic advection time, and the Damk\\"ohler number $Da$, which represents the ratio of the characteristic diffusion time to the characteristic reaction time, the local reaction rates can be strongly impacted by the dynamics of the mixing interface. This impact has been characterized mostly either in kinetics-limited or in mixing-limited conditions, that is, for either very low or very high $Da$. Here the coupling of shear flow and chemical reactivity is investigated for arbitrary Damk\\"ohler numbers, for a bimolecular reaction and an initial interface with separated reactants....

  2. Delaunay-Object-Dynamics: cell mechanics with a 3D kinetic and dynamic weighted Delaunay-triangulation.

    Science.gov (United States)

    Meyer-Hermann, Michael

    2008-01-01

    Mathematical methods in Biology are of increasing relevance for understanding the control and the dynamics of biological systems with medical relevance. In particular, agent-based methods turn more and more important because of fast increasing computational power which makes even large systems accessible. An overview of different mathematical methods used in Theoretical Biology is provided and a novel agent-based method for cell mechanics based on Delaunay-triangulations and Voronoi-tessellations is explained in more detail: The Delaunay-Object-Dynamics method. It is claimed that the model combines physically realistic cell mechanics with a reasonable computational load. The power of the approach is illustrated with two examples, avascular tumor growth and genesis of lymphoid tissue in a cell-flow equilibrium.

  3. Chronic impact of sulfamethoxazole on acetate utilization kinetics and population dynamics of fast growing microbial culture.

    Science.gov (United States)

    Kor-Bicakci, G; Pala-Ozkok, I; Rehman, A; Jonas, D; Ubay-Cokgor, E; Orhon, D

    2014-08-01

    The study evaluated the chronic impact of sulfamethoxazole on metabolic activities of fast growing microbial culture. It focused on changes induced on utilization kinetics of acetate and composition of the microbial community. The experiments involved a fill and draw reactor, fed with acetate and continuous sulfamethoxazole dosing of 50 mg/L. The evaluation relied on model evaluation of the oxygen uptake rate profiles, with parallel assessment of microbial community structure by 454-pyrosequencing. Continuous sulfamethoxazole dosing inflicted a retardation effect on acetate utilization in a way commonly interpreted as competitive inhibition, blocked substrate storage and accelerated endogenous respiration. A fraction of acetate was utilized at a much lower rate with partial biodegradation of sulfamethoxazole. Results of pyrosequencing with a replacement mechanism within a richer more diversified microbial culture, through inactivation of vulnerable fractions in favor of species resistant to antibiotic, which made them capable of surviving and competing even with a slower metabolic response. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. 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.

  5. Features of the Jovian DAM radiation dynamic spectra as observed by modern receivers with high frequency-temporal resolution

    Science.gov (United States)

    Litvinenko, G.; Konovalenko, A.; Zakharenko, V.; Vinogradov, V.; Shaposhnikov, V.; Zarka, Ph.

    2012-09-01

    One of the promising approaches to investigating features of the Jovian decameter radio emission (DAM) is application of novel experimental techniques with a further detailed analysis of the obtained data using both well-known and modern mathematical methods. Several observational campaigns were performed in November 2009 with the use of the UTR-2 radio telescope (Kharkov, Ukraine) and efficient registration systems with high frequency and temporal resolutions (the antenna effective area is about 105 m2, the frequency resolution is 4 kHz, the temporal resolution is 0.25 ms, and the dynamic range is 70 dB) [1]. The main goal of these campaigns was to experimentally investigate new properties of the Jovian DAM emission which could be detected using the above mentioned equipment. Also an original software package was developed for control the digital receiver and for off-line data analysis at the postprocessing stage.

  6. High Spatio-Temporal-Resolution Detection of Chlorophyll Fluorescence Dynamics from a Single Chloroplast with Confocal Imaging Fluorometer

    CERN Document Server

    Tseng, Yi-Chin

    2016-01-01

    Chlorophyll fluorescence (CF) is a key indicator to study plant physiology or photosynthesis efficiency. Conventionally, CF is characterized by fluorometers, which only allows ensemble measurement through wide-field detection. For imaging fluorometers, the typical spatial and temporal resolutions are on the order of millimeter and second, far from enough to study cellular/sub-cellular CF dynamics. In addition, due to the lack of optical sectioning capability, conventional imaging fluorometers cannot identify CF from a single cell or even a single chloroplast. Here we demonstrated a novel fluorometer based on confocal imaging, that not only provides high contrast images, but also allows CF measurement with spatiotemporal resolution as high as micrometer and millisecond. CF transient (the Kautsky curve) from a single chloroplast is successfully obtained, with both the temporal dynamics and the intensity dependences corresponding well to the ensemble measurement from conventional studies. The significance of con...

  7. 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

  8. Dynamic high-resolution sonography compared to magnetic resonance imaging for diagnosis of temporomandibular joint disk displacement.

    Science.gov (United States)

    Habashi, Hadeel; Eran, Ayelet; Blumenfeld, Israel; Gaitini, Diana

    2015-01-01

    The purpose of this study was to determine the value of dynamic high-resolution sonography for evaluation of temporomandibular joint (TMJ) disk displacement compared to magnetic resonance imaging (MRI) with the mouth closed and during the maximal mandibular range of motion. Dynamic high-resolution sonography with the mouth closed and during the maximal mandibular range of motion was performed on 39 consecutive patients (78 joints; 13 male and 26 female; age range, 18-77 years; mean age ± SD, 37.23 ± 16.26 years) with TMJ disorders. A TMJ MRI study was performed 1 to 7 days after sonography. We searched for signs of disk displacement and findings compatible with degenerative joint disease. Both studies were performed and interpreted independently by blinded operators. Magnetic resonance imaging depicted 22 normal joints (28.2%), 21 (26.9%) with anterior disk displacement with reduction, 15 (19.2%) with anterior disk displacement without reduction, and 20 (25.6%) with degenerative disease. Sonography depicted 30 normal joints (38.5%), 22 (28.2%) with anterior disk displacement with reduction, 12 (15.4%) with anterior disk displacement without reduction, and 14 (17.9%) with degenerative disease. The overall sensitivity, specificity, and accuracy of sonography for diagnosis of disk displacement were 74.3%, 84.2%, and 77.7%, respectively. The sensitivity, specificity, and accuracy for diagnosis of disk displacement with reduction were 78.6%, 66.7%, and 73.0%, and the values for diagnosis of disk displacement without reduction were 66.7%, 78.6%, and 73.0%. Dynamic high-resolution sonography is a potential imaging method for diagnosis of TMJ disk displacement and degenerative diseases. Further studies are needed to make dynamic high-resolution sonography the first-line test for diagnosis of TMJ disk displacement. © 2015 by the American Institute of Ultrasound in Medicine.

  9. Applying High Resolution Imagery to Understand the Role of Dynamics in the Diminishing Arctic Sea Ice Cover

    Science.gov (United States)

    2015-09-30

    Role of Dynamics in the Diminishing Arctic Sea Ice Cover ” Dr. Sinead L. Farrell University of Maryland, ESSIC, 5825 University Research Court...day Arctic ice cover , enabling the improvement of models used to forecast ice drift. APPROACH Our research is centered on the application of...resolution visible band imagery for deriving geophysical information on the sea ice pack of the Arctic Ocean , and improve understanding of key

  10. Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models.

    Science.gov (United States)

    Liao, Chenyi; Zhao, Xiaochuan; Liu, Jiyuan; Schneebeli, Severin T; Shelley, John C; Li, Jianing

    2017-03-20

    The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop. For the models at different resolutions, we observed consistent structural stability but various levels of speed-ups in protein dynamics. The mixed-resolution and coarse-grained models show two and four times faster protein diffusion than the all-atom models, in addition to a 4- and 400-fold speed-up in the simulation performance. Furthermore, by elucidating the strengths and challenges of combining all-atom models with reduced resolution models, this study can serve as a guide to simulating other complex systems in heterogeneous environments efficiently.

  11. 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…

  12. Diagnosis and identification of respirometer dynamics and sludge kinetics in continuous-flow respirometers

    NARCIS (Netherlands)

    Lukasse, L.J.S.; Keesman, K.J.; Spanjers, H.; Bloemen, M.

    2000-01-01

    This paper deals with excitation of respiration chamber dynamics in a continuous-flow respirometer with the objective of extracting additional information from its dissolved oxygen (DO) sensor readings. A measurement strategy is proposed from which it is theoretically possible to identify

  13. 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…

  14. Variational perturbation and extended Plefka approaches to dynamics on random networks: the case of the kinetic Ising model

    Science.gov (United States)

    Bachschmid-Romano, L.; Battistin, C.; Opper, M.; Roudi, Y.

    2016-10-01

    We describe and analyze some novel approaches for studying the dynamics of Ising spin glass models. We first briefly consider the variational approach based on minimizing the Kullback-Leibler divergence between independent trajectories and the real ones and note that this approach only coincides with the mean field equations from the saddle point approximation to the generating functional when the dynamics is defined through a logistic link function, which is the case for the kinetic Ising model with parallel update. We then spend the rest of the paper developing two ways of going beyond the saddle point approximation to the generating functional. In the first one, we develop a variational perturbative approximation to the generating functional by expanding the action around a quadratic function of the local fields and conjugate local fields whose parameters are optimized. We derive analytical expressions for the optimal parameters and show that when the optimization is suitably restricted, we recover the mean field equations that are exact for the fully asymmetric random couplings (Mézard and Sakellariou 2011 J. Stat. Mech. 2011 L07001). However, without this restriction the results are different. We also describe an extended Plefka expansion in which in addition to the magnetization, we also fix the correlation and response functions. Finally, we numerically study the performance of these approximations for Sherrington-Kirkpatrick type couplings for various coupling strengths and the degrees of coupling symmetry, for both temporally constant but random, as well as time varying external fields. We show that the dynamical equations derived from the extended Plefka expansion outperform the others in all regimes, although it is computationally more demanding. The unconstrained variational approach does not perform well in the small coupling regime, while it approaches dynamical TAP equations of (Roudi and Hertz 2011 J. Stat. Mech. 2011 P03031) for strong couplings.

  15. Modeling Carbon Dynamics in Paddy Soils in Jiangsu Province of China with Soil Databases Differing in Spatial Resolution

    Institute of Scientific and Technical Information of China (English)

    XU Sheng-Xiang; SHI Xue-Zheng; ZHAO Yong-Cun; YU Dong-Sheng; WANG Shi-Hang; ZHANG Li-Ming; C. S. LI; TAN Man-Zhi

    2011-01-01

    A number of process-based models have been developed for quantifying carbon (C) sequestration in ago-ecosystems.The DeNitrification-DeComposition (DNDC) model was used to simulate and quantify long-term (1980-2008) soil organic carbon (SOC) dynamics in the important rice-producing province,Jiangsu,China.Changes in SOC storages were estimated from two soil databases differing in spatial resolution:a county database consisting of 68 polygons and a soil patch-based database of 701 polygons for all 3.7 Mha of rice fields in Jiangsu.The simulated SOC storage with the coarse resolution county database ranged between 131.0-320.6 Tg C in 1980 and 170.3-305.1 Tg C in 2008,respectively,while that estimated with the fine resolution database was 201.6 and 216.2 Tg C in 1980 and 2008,respectively.The results modeled with the soil databases differing in spatial resolution indicated that using the soil input data with higher resolution substantially increased the accuracy of the modeled results; and when lacking detailed soil datasets,the DNDC model,parameterized with the most sensitive factor (MSF) method to cope with attribute uncertainty,could still produce acceptable results although with deviations of up to 60% for the case study reported in this paper.

  16. Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site

    Energy Technology Data Exchange (ETDEWEB)

    Grossman, Moran; Born, Benjamin; Heyden, Matthias; Tworowski, Dmitry; Fields, Gregg B.; Sagi, Irit; Havenith, Martina

    2011-09-18

    Solvent dynamics can play a major role in enzyme activity, but obtaining an accurate, quantitative picture of solvent activity during catalysis is quite challenging. Here, we combine terahertz spectroscopy and X-ray absorption analyses to measure changes in the coupled water-protein motions during peptide hydrolysis by a zinc-dependent human metalloprotease. These changes were tightly correlated with rearrangements at the active site during the formation of productive enzyme-substrate intermediates and were different from those in an enzyme–inhibitor complex. Molecular dynamics simulations showed a steep gradient of fast-to-slow coupled protein-water motions around the protein, active site and substrate. Our results show that water retardation occurs before formation of the functional Michaelis complex. We propose that the observed gradient of coupled protein-water motions may assist enzyme-substrate interactions through water-polarizing mechanisms that are remotely mediated by the catalytic metal ion and the enzyme active site.

  17. Kinetic modeling of the composition and dynamics of volatile's distribution in Europa's exosphere

    Science.gov (United States)

    Tenishev, V.; Borovikov, D.; Tucker, O. J.; Combi, M. R.; Rubin, M.; Jia, X.; Gombosi, T. I.

    2014-12-01

    The surface-bound Europa's exosphere is tightly connected to both the Jovian magnetosphere as well as to Europa's icy surface. The neutral species in the exosphere are mostly produced by the Jovian magnetospheric ion sputtering of the water ice surface and direct ejection from Europa's plume. Here, we present results of our model study of the distribution of the neutral species in Europa's exosphere, their escape and migration over the moon's surface. The work is a part of a more global effort aimed at fully coupled understanding of the interaction between Europa's exosphere and Jovian magnetosphere. The modeled neutral species are produced via sputtering (O2 and H2O), directly ejected into the plume (H2O), or produced via photolytic or electron impact reactions (OH, O2, O, H). The computational domain extends to altitudes up to ~10 RE, which exceeds the radius of Europa's Hill sphere (~8.5 RE, Miljkovic et al., 2012). Jupiter's and Europa's gravity are taken into consideration. The modeling is performed using our kinetic Adaptive Mesh Particle Simulator (Tenishev et al., 2013), where the exospheric species are represented by a large set of the model particles governed by the same physical laws as those of the real exosphere. The calculated HI and OI brightness synthetic images are compared with those obtained with Hubble Space Telescope (Roth et al., 2014).

  18. Daphnicle dynamics based on kinetic theory: an analogue-modelling of swarming and behaviour of daphnia.

    Science.gov (United States)

    Øien, Alf H

    2004-01-01

    Attempts are presented of an analogue modelling of Daphnia responses to various influences and stimuli, as distribution of food and of predators. An aim of the study is to examine to what extent a statistical-mechanical approach may be useful as a tool in modelling of Daphnia swarms behaviour. In the modelling we follow a line close to test particle studies in physical sciences. A generalized kinetic equation of what we shall call daphnicles is derived. The modelling incorporates individual characteristics of daphnicles, as position, velocity, degree of food saturation and responses daphnicles have to outside influences. Each daphnicle we assume responds to some stimuli in ordered ways and to others in stochastic ways, and the degree or strength of reactions depends on the density of all daphnicles, the density of food available, the saturation level of daphnicles and the threat level in the environment, or background, the daphnicles are living on. Some fluid equations of daphnicle swarms are subsequently derived from the basic equation, and solutions are given of the model-equations, including a food distribution equation, in some particular cases that show peculiarities in reactions of daphnicles to food, degree of saturation and to threat, when these are acting alone, and in combination. The modelling results may be compared to results of laboratory experiments of Daphnia behaviour that soon will be performed.

  19. 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.

  20. Kinetics of linear rouleaux formation studied by visual monitoring of red cell dynamic organization.

    Science.gov (United States)

    Barshtein, G; Wajnblum, D; Yedgar, S

    2000-05-01

    Red blood cells (RBCs) in the presence of plasma proteins or other macromolecules may form aggregates, normally in rouleaux formations, which are dispersed with increasing blood flow. Experimental observations have suggested that the spontaneous aggregation process involves the formation of linear rouleaux (FLR) followed by formation of branched rouleaux networks. Theoretical models for the spontaneous rouleaux formation were formulated, taking into consideration that FLR may involve both "polymerization," i.e., interaction between two single RBCs (e + e) and the addition of a single RBC to the end of an existing rouleau (e + r), as well as "condensation" between two rouleaux by end-to-end addition (r + r). The present study was undertaken to experimentally examine the theoretical models and their assumptions, by visual monitoring of the spontaneous FLR (from singly dispersed RBC) in plasma, in a narrow gap flow chamber. The results validate the theoretical model, showing that FLR involves both polymerization and condensation, and that the kinetic constants for the above three types of intercellular interactions are the same, i.e., k(ee) = k(er) = k(rr) = k, and for all tested hematocrits (0.625-6%) k < 0.13 +/- 0.03 s(-1).

  1. Temperature Dependence of the Kinetic Energy of the Correlated Electron Plasma by Restricted Path-Integral Molecular Dynamics

    Science.gov (United States)

    Runge, Keith; Deymier, Pierre

    2013-03-01

    Recent progress in orbital-free Density Functional Theory (OF-DFT), particularly with regard to temperature dependent functionals, has promise for the simulation of warm dense matter (WDM) systems. WDM includes systems with densities of an order of magnitude beyond ambient or more and temperatures measured in kilokelvin. A challenge for the development of temperature dependent OF-DFT functionals is the lack of benchmark information with temperature and pressure dependence on simple models under WDM conditions. We present an approach to fill this critical gap using the restricted path-integral molecular dynamics (rPIMD) method. Electrons are described as harmonic necklaces within the discrete path integral representation while quantum exchange takes the form of cross linking between electron necklaces. A molecular dynamics algorithm is used to sample phase space and the fermion sign problem is addressed by restricting the density matrix to positive values. The temperature dependence of kinetic energies for the strongly coupled electron plasma is presented for a number of Wigner-Seitz radii in terms of a fourth order Sommerfeld expansion. Supported by US DoE Grant DE-SC0002139

  2. Adaptive Resolution Simulation as a Grand Canonical Molecular Dynamics Scheme: Principles, Applications and Perspectives

    CERN Document Server

    Site, Luigi Delle; Junghans, Christoph; Wang, Han

    2014-01-01

    We describe the adaptive resolution multiscale method AdResS. The conceptual evolution as well as the improvements of its technical efficiency are described step by step, with an explicit reference to current limitations and open problems.

  3. A flexible fiber displacement sensor with tunable resolution and dynamic range based on a few-mode fiber loop

    Science.gov (United States)

    Fu, Xin; Lu, Ping; Liu, Deming; Zhang, Jiangshan; Jiang, Shibin

    2017-02-01

    In this article, we propose a fiber displacement sensor based on a few mode fiber loop sandwiched between two single mode fibers (SMF). The proposed sensor is flexible due to the tunable resolution and dynamic range. The FMF is coiled to a fiber loop by making a knot. The in-line MZI sensing structure is fixed on a two dimensional (2D) translation stages. By moving one stage while another stage is fixed, the displacement is applied on the sensing structure. The resolution of the translation stage is 10μm. The few mode fiber loop acts as the transducer for the displacement sensing. The displacement will change the radius of the few mode fiber loop, which leads to a wavelength shift of the interference pattern. When the fiber loop has different initial radius, the same displacement will cause a different curvature variation. So the sensitivity of the wavelength shift to the displacement is dependent on the initial radius. A smaller initial radius of the loop will lead to a larger sensitivity, higher resolution but smaller dynamic range, so it is proper for micro displacement sensing. On the contrary is the lager initial radius that is proper for sensing in a large dynamic range. By simply adjusting the initial radius of the transducer loop, different sensitivity and resolution can be reached. Experimental results show the sensitivities of 0.267nm/mm, 0.384nm/mm, 0.749nm/mm and 1.06nm/mm for initial loop radius of 1.9cm, 1.5cm, 1cm and 0.75cm, respectively.

  4. Two-color, laser excitation improves temporal resolution for detecting the dynamic, plasmonic coupling between metallic nanoparticles.

    Science.gov (United States)

    Wiener, Diane M; Lionberger, Troy A

    2013-05-21

    The ability of two, scattering gold nanoparticles (GNPs) to plasmonically couple in a manner that is dependent on the interparticle separation has been exploited to measure nanometer-level displacements. However, despite broad applicability to monitoring biophysical dynamics, the long time scales (dynamic molecular processes, generally occurring over several milliseconds. Here, we introduce a new technique intended to overcome this technical limitation: ratiometric analysis using monochromatic, evanescent darkfield illumination (RAMEDI). As a proof-of-principle, we monitored dynamic, plasmonic coupling arising from the binding of single biotin- and neutravidin-GNPs with a temporal resolution of 38 ms. We also show that the observable bandwidth is extendable to faster time scales by demonstrating that RAMEDI is capable of achieving a signal-to-noise ratio greater than 20 from individual GNPs observed with 200 Hz bandwidth.

  5. A novel approach to contrast-enhanced breast magnetic resonance imaging for screening: high-resolution ultrafast dynamic imaging.

    Science.gov (United States)

    Mann, Ritse M; Mus, Roel D; van Zelst, Jan; Geppert, Christian; Karssemeijer, Nico; Platel, Bram

    2014-09-01

    The use of breast magnetic resonance imaging (MRI) as screening tool has been stalled by high examination costs. Scan protocols have lengthened to optimize specificity. Modern view-sharing sequences now enable ultrafast dynamic whole-breast MRI, allowing much shorter and more cost-effective procedures. This study evaluates whether dynamic information from ultrafast breast MRI can be used to replace standard dynamic information to preserve accuracy. We interleaved 20 ultrafast time-resolved angiography with stochastic trajectory (TWIST) acquisitions (0.9 × 1 × 2.5 mm, temporal resolution, 4.3 seconds) during contrast inflow in a regular high-resolution dynamic MRI protocol. A total of 160 consecutive patients with 199 enhancing abnormalities (95 benign and 104 malignant) were included. The maximum slope of the relative enhancement versus time curve (MS) obtained from the TWIST and curve type obtained from the regular dynamic sequence as defined in the breast imaging reporting and data system (BIRADS) lexicon were recorded. Diagnostic performance was compared using receiver operating characteristic analysis. All lesions were visible on both the TWIST and standard series. Maximum slope allows discrimination between benign and malignant disease with high accuracy (area under the curve, 0.829). Types of MS were defined in analogy to BIRADS curve types: MS type 3 implies a high risk of malignancy (MS >13.3%/s; specificity, 85%), MS type 2 yields intermediate risk (MS 6.4%/s), and MS type 1 implies a low risk (MS BIRADS curve type analysis does (area under the curve, 0.812 vs 0.692; P = 0.0061). Ultrafast dynamic breast MRI allows detection of breast lesions and classification with high accuracy using MS. This allows substantial shortening of scan protocols and hence reduces imaging costs, which is beneficial especially for screening.

  6. Dynamic dual-energy chest radiography: a potential tool for lung tissue motion monitoring and kinetic study.

    Science.gov (United States)

    Xu, Tong; Ducote, Justin L; Wong, Jerry T; Molloi, Sabee

    2011-02-21

    Dual-energy chest radiography has the potential to provide better diagnosis of lung disease by removing the bone signal from the image. Dynamic dual-energy radiography is now possible with the introduction of digital flat-panel detectors. The purpose of this study is to evaluate the feasibility of using dynamic dual-energy chest radiography for functional lung imaging and tumor motion assessment. The dual-energy system used in this study can acquire up to 15 frames of dual-energy images per second. A swine animal model was mechanically ventilated and imaged using the dual-energy system. Sequences of soft-tissue images were obtained using dual-energy subtraction. Time subtracted soft-tissue images were shown to be able to provide information on regional ventilation. Motion tracking of a lung anatomic feature (a branch of pulmonary artery) was performed based on an image cross-correlation algorithm. The tracking precision was found to be better than 1 mm. An adaptive correlation model was established between the above tracked motion and an external surrogate signal (temperature within the tracheal tube). This model is used to predict lung feature motion using the continuous surrogate signal and low frame rate dual-energy images (0.1-3.0 frames per second). The average RMS error of the prediction was (1.1 ± 0.3) mm. The dynamic dual energy was shown to be potentially useful for lung functional imaging such as regional ventilation and kinetic studies. It can also be used for lung tumor motion assessment and prediction during radiation therapy.

  7. Contrast-enhanced dynamic MRI protocol with improved spatial and time resolution for in vivo microimaging of the mouse with a 1.5-T body scanner and a superconducting surface coil.

    Science.gov (United States)

    Ginefri, Jean-Christophe; Poirier-Quinot, Marie; Robert, Philippe; Darrasse, Luc

    2005-02-01

    Magnetic resonance imaging (MRI) is well suited for small animal model investigations to study various human pathologies. However, the assessment of microscopic information requires a high-spatial resolution (HSR) leading to a critical problem of signal-to-noise ratio limitations in standard whole-body imager. As contrast mechanisms are field dependent, working at high field do not allow to derive MRI criteria that may apply to clinical settings done in standard whole-body systems. In this work, a contrast-enhanced dynamic MRI protocol with improved spatial and time resolution was used to perform in vivo tumor model imaging on the mouse at 1.5 T. The needed sensitivity is provided by the use of a 12-mm superconducting surface coil operating at 77 K. High quality in vivo images were obtained and revealed well-defined internal structures of the tumor. A 3-D HSR sequence with voxels of 59x59x300 microm3 encoded within 6.9 min and a 2-D sequence with subsecond acquisition time and isotropic in-plane resolution of 234 microm were used to analyze the contrast enhancement kinetics in tumoral structures at long and short time scales. This work is a first step to better characterize and differentiate the dynamic behavior of tumoral heterogeneities.

  8. Nanofluids droplets evaporation kinetics and wetting dynamics on rough heated substrates.

    Science.gov (United States)

    Sefiane, K; Bennacer, R

    2009-01-01

    The influence of aluminium nanoparticles on the evaporation and wetting dynamics of ethanol sessile droplets on a heated PTFE surface is investigated experimentally. The experimental technique uses a goniometer to measure the evolution in time of the shape of the droplets (contact angle, base diameter and volume). The evaporation rate is deduced from the measurements of the evolution of volume in time. During the "pinning" phase and contrary to what is expected, the presence of nanoparticles leads to a reduction of the evaporation rate compared to the base fluid. It is found that the deposition of nanoparticles into the triple contact line wedge during the evaporation of the droplet causes a greater pinning time for nanofluid droplets. The overall evaporation time for base fluid droplets is found to be longer than for nanofluid ones. The wetting dynamics of the droplets throughout the evaporation process shows major influence of nanoparticles. Depinning contact angles tend to be larger for nanofluid droplets than for base liquid ones. Over a range of imposed substrate temperatures, no effect on the nanofluids depinning contact angle is observed. The alteration of contact line behavior as well as wettability can have important implications in a wide range of applications, e.g. two phase boiling heat transfer [Kim, S. J. et al., Appl. Phys. Lett., 2006, 89, 153107].

  9. 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)

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Dynamic path bifurcation in the Beckmann reaction: support from kinetic analyses.

    Science.gov (United States)

    Yamamoto, Yutaro; Hasegawa, Hiroto; Yamataka, Hiroshi

    2011-06-03

    The reactions of oximes to amides, known as the Beckmann rearrangement, may undergo fragmentation to form carbocations + nitriles when the migrating groups have reasonable stability as cations. The reactions of oxime sulfonates of 1-substituted-phenyl-2-propanone derivatives (7-X) and related substrates (8-X, 9a-X) in aqueous CH(3)CN gave both rearrangement products (amides) and fragmentation products (alcohols), the ratio of which depends on the system; the reactions of 7-X gave amides predominantly, whereas 9a-X yielded alcohols as the major product. The logk-logk plots between the systems gave excellent linear correlations with slopes of near unity. The results support the occurrence of path bifurcation after the rate-determining TS of the Beckmann rearrangement/fragmentation reaction, which has previously been proposed on the basis of molecular dynamics simulations. It was concluded that path-bifurcation phenomenon could be more common than thought and that a reactivity-selectivity argument based on the traditional TS theory may not always be applicable even to a well-known textbook organic reaction.

  15. Dynamics of atomic kinetics in a pulsed positive-column discharge at 100 Pa

    Science.gov (United States)

    Franek, J. B.; Nogami, S. H.; Koepke, M. E.; Demidov, V. I.; Barnat, E. V.

    2017-01-01

    Temporal measurements of the electron density, metastable-atom density, and reduced electric field demonstrate that four orders of magnitude variation in the dynamic range of the electron-atom collision-induced excitation rates takes place during the 2.0 kV height, 40 µs duration repeating pulse applied to a 100 Pa (1 Torr), argon positive column in a hollow-cathode discharge. Correlation between metastable-atom density and emission-line ratio is demonstrated to be sufficiently reliable to infer one quantity based on the measurement of the other quantity during the Initiation, Transient, and Post-Transient spectroscopic stages of the pulse. Observed emission-line ratio and the predicted emission-line ratio are in quantitative agreement with each other in the Transient and Post-Transient stages of the discharge and are in qualitative agreement with each other in the Initiation stage of the discharge. Reasonable assumptions regarding the interpretation of the electron energy probability function (EEPF), as it starts off being Druyvesteyn and becomes more Maxwellian later with the increasing electron density, is key to interpreting the correlation and explaining the temporal behavior of the emission-line ratio in all stages of the discharge.

  16. 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.

  17. A dynamic aerodynamic resistance approach to calculate high resolution sensible heat fluxes in urban areas

    Science.gov (United States)

    Crawford, Ben; Grimmond, Sue; Kent, Christoph; Gabey, Andrew; Ward, Helen; Sun, Ting; Morrison, William

    2017-04-01

    Remotely sensed data from satellites have potential to enable high-resolution, automated calculation of urban surface energy balance terms and inform decisions about urban adaptations to environmental change. However, aerodynamic resistance methods to estimate sensible heat flux (QH) in cities using satellite-derived observations of surface temperature are difficult in part due to spatial and temporal variability of the thermal aerodynamic resistance term (rah). In this work, we extend an empirical function to estimate rah using observational data from several cities with a broad range of surface vegetation land cover properties. We then use this function to calculate spatially and temporally variable rah in London based on high-resolution (100 m) land cover datasets and in situ meteorological observations. In order to calculate high-resolution QH based on satellite-observed land surface temperatures, we also develop and employ novel methods to i) apply source area-weighted averaging of surface and meteorological variables across the study spatial domain, ii) calculate spatially variable, high-resolution meteorological variables (wind speed, friction velocity, and Obukhov length), iii) incorporate spatially interpolated urban air temperatures from a distributed sensor network, and iv) apply a modified Monte Carlo approach to assess uncertainties with our results, methods, and input variables. Modeled QH using the aerodynamic resistance method is then compared to in situ observations in central London from a unique network of scintillometers and eddy-covariance measurements.

  18. High-resolution modeling of atmospheric dynamics in the Nepalese Himalaya

    NARCIS (Netherlands)

    Collier, Emily; Immerzeel, Walter W.

    2015-01-01

    High-altitude meteorological processes in the Himalaya are influenced by complex interactions between the topography and the monsoon and westerly circulation systems. In this study, we use the Weather Research and Forecasting model configured with high spatial resolution to understand seasonal patte

  19. Double domain wavelength multiplexed Fizeau interferometer with high resolution dynamic sensing and absolute length detection

    Science.gov (United States)

    Antonacci, Julián; Arenas, Gustavo F.; Duchowicz, Ricardo

    2017-04-01

    In this work, we present a simple photonic instrument that has the ability of measuring positions, distances and vibrations with very high resolution by means of two Fizeau interferometers (FI), both using the same optical fiber end as a probe tip itself. On the one hand we have a time domain FI powered with a 1310 nm laser and monitored by an InGaAs detector providing displacement information with resolution around a tenth of nm but regardless of the absolute position of object and of the displacement sense. On the other, a spectral domain FI version based on a super luminescent source (SLED) centred at 800 nm with bandwidth of nearly 40 nm is analysed in real time by means of a digital spectrometer. Each spectrum is acquired in a very small time interval and provides information of both length of the cavity as well as its correct sense of evolution. Resolution of this system is lower than its complementary temporal case, but distance and sense measurements are absolute and can be determined successfully by adequate processing of spectral signal.Both interferometers are optically coupled to a single fiber optic probe and are wavelength modulated.Therefore, combination of both sensors results in a new one which allows the correct knowledge of an object or surfaces under test, i.e. a high resolution of displacement data plus its absolute position and true sense of movement.

  20. Adherence and kinetics of biofilm formation of Staphylococcus epidermidis to different types of intraocular lenses under dynamic flow conditions.

    Science.gov (United States)

    Baillif, Stéphanie; Ecochard, René; Casoli, Emmanuelle; Freney, Jean; Burillon, Carole; Kodjikian, Laurent

    2008-01-01

    To compare the adherence and biofilm formation of Staphylococcus epidermidis under in vitro flow conditions on intraocular lenses (IOLs) made of 4 biomaterials: poly(methyl methacrylate) (PMMA), silicone, hydrophilic acrylic, and hydrophobic acrylic. Department of Ophthalmology, Croix-Rousse University Hospital and University Research Laboratory, Lyon, France. Intraocular lenses were placed in a bioreactor designed to replicate intraocular conditions. The model consisted of Tygon tubing connected to a vial. Three septa allowed the entry and elimination of the artificial aqueous humor and inoculation of the bacterial suspension. The first of 2 pumps moved the aqueous humor along the circuit; the second pump regulated the flow at which the nutritive environment was regenerated. At various times (12, 16, 24, 40, 48, 60, and 72 hours), IOLs were taken from this environment and the bound bacteria were removed and counted. The distribution of bacterial adhesion on the IOLs was modeled using polynomial Poisson regression. To test the effect of the IOL biomaterial on bacterial adhesion, likelihood ratio tests were performed. The model provided the kinetics of S epidermidis biofilm growth on IOLs. The biofilm growth on each of the 4 biomaterials occurred in 3 phases: latent, dynamic or accelerated growth, and linear growth. The extent of bacterial binding to IOLs increased from hydrophilic acrylic polymer to PMMA, hydrophobic acrylic, and silicone. The differences were statistically significant. Bacterial adhesion to and biofilm development on the IOL surface depended on the characteristics of the biomaterial.

  1. A combined molecular dynamics and kinetic Monte Carlo calculation to study sputter erosion and beam assisted deposition

    CERN Document Server

    Betz, G

    2002-01-01

    To extend the time scale in molecular dynamics (MD) calculations of sputtering and ion assisted deposition we have coupled our MD calculations to a kinetic Monte Carlo (KMC) calculation. In this way we have studied surface erosion of Cu(1 0 0) under 200-600 eV Cu ion bombardment and growth of Cu on Cu(1 0 0) for deposition at thermal energies up to energies of 100 eV per atom. Target temperatures were varied from 100 to 400 K. The coupling of the MD calculation to a KMC calculation allows us to extend our calculations from a few ps, a time scale typical for MD, to times of up to seconds until the next Cu particle will impinge/be deposited on the crystal surface of about 100 nm sup 2 in size. The latter value of 1 s is quite realistic for a typical experimental sputter erosion or deposition experiment. In such a calculation thermal diffusion processes at the surface and annealing of the surface after energetic ion bombardment can be taken into account. To achieve homo-epitaxial growth of a film the results cle...

  2. Hot deformation behavior and dynamic recrystallization kinetics of AZ61 and AZ61 + Sr magnesium alloys

    Directory of Open Access Journals (Sweden)

    S. Aliakbari Sani

    2016-06-01

    Full Text Available In this study, the effect of strontium addition on hot deformation of AZ61 alloy was investigated by hot compression tests. A reference alloy (AZ61 and an Sr-containing alloy (AZ61 + Sr was cast while their average initial grain size were supposed to be about 140 and 40 µm, respectively. In AZ61 + Sr alloy, the Sr-containing precipitations were stable at homogenization temperature. Analysing the hot compression curves, it was revealed that dynamic recrystallization phenomenon had occurred and controlled the thermomechanical behaviour of the alloys. The derived constitutive equations showed that the hot deformation parameters (n and Q in AZ61 + Sr alloy is smaller than those of AZ61 alloy; this can be related to the small initial grain size and the lower amounts of solute aluminium atoms. The analysis of DRX kinetics along with the micrographs of the deformed microstructures showed that at the same condition the development of DRXed microstructure in AZ61 + Sr alloy was faster than AZ61 alloy. The increased recrystallized microstructure was interpretated to be attributed to (1 the more grain boundaries present and (2 the existance of the Al-Mg-Sr precipitations assisted the PSN mechanism. Also, the attenuated intensity of the basal texture of AZ61 + Sr was related to the DRX fraction of microstructure.

  3. Highly Dynamic Interactions Maintain Kinetic Stability of the ClpXP Protease During the ATP-Fueled Mechanical Cycle.

    Science.gov (United States)

    Amor, Alvaro J; Schmitz, Karl R; Sello, Jason K; Baker, Tania A; Sauer, Robert T

    2016-06-17

    The ClpXP protease assembles in a reaction in which an ATP-bound ring hexamer of ClpX binds to one or both heptameric rings of the ClpP peptidase. Contacts between ClpX IGF-loops and clefts on a ClpP ring stabilize the complex. How ClpXP stability is maintained during the ATP-hydrolysis cycle that powers mechanical unfolding and translocation of protein substrates is poorly understood. Here, we use a real-time kinetic assay to monitor the effects of nucleotides on the assembly and disassembly of ClpXP. When ATP is present, complexes containing single-chain ClpX assemble via an intermediate and remain intact until transferred into buffers containing ADP or no nucleotides. ATP binding to high-affinity subunits of the ClpX hexamer prevents rapid dissociation, but additional subunits must be occupied to promote assembly. Small-molecule acyldepsipeptides, which compete with the IGF loops of ClpX for ClpP-cleft binding, cause exceptionally rapid dissociation of otherwise stable ClpXP complexes, suggesting that the IGF-loop interactions with ClpP must be highly dynamic. Our results indicate that the ClpX hexamer spends almost no time in an ATP-free state during the ATPase cycle, allowing highly processive degradation of protein substrates.

  4. 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.

  5. 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.

  6. Chemical Dynamic Thermodynamic Resolution and S/R Interconversion of Unprotected Unnatural Tailor-made α-Amino Acids.

    Science.gov (United States)

    Wang, Shuni; Zhou, Shengbin; Wang, Jiang; Nian, Yong; Kawashima, Aki; Moriwaki, Hiroki; Aceña, José L; Soloshonok, Vadim A; Liu, Hong

    2015-10-16

    Described here is an advanced, general method for purely chemical dynamic thermodynamic resolution and S/R interconversion of unprotected tailor-made α-amino acids (α-AAs) through intermediate formation of the corresponding nickel(II)-chelated Schiff bases. The method features virtually complete stereochemical outcome, broad substrate generality (35 examples), and operationally convenient conditions allowing for large-scale preparation of the target α-AAs in enantiomerically pure form. Furthermore, the new type of nonracemizable axially chiral ligands can be quantitatively recycled and reused, rendering the whole process economically and synthetically attractive.

  7. Measuring the dynamics of second-order photon correlation functions inside a pulse with picosecond time resolution

    DEFF Research Database (Denmark)

    Assmann, Marc; Veit, Franziska; Tempel, Jean-Sebastian;

    2010-01-01

    We present a detailed discussion of a recently demonstrated experimental technique capable of measuring the orrelation function of a pulsed light source with picosecond time resolution. The measurement involves a streak camera in single photon counting mode, which is modified such that a signal...... at a fixed repetition rate, and well defined energy, can be monitored after each pulsed laser excitation. The technique provides further insight into the quantum optical properties of pulsed light emission from semiconductor nanostructures, and the dynamics inside a pulse, on the subnanosecond time scale....

  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. Self-consistent system of equations for a kinetic description of the low-pressure discharges accounting for the nonlocal and collisionless electron dynamics.

    Science.gov (United States)

    Kaganovich, Igor D; Polomarov, Oleg

    2003-08-01

    In low-pressure discharges, where the electron mean free path is larger or comparable with the discharge length, the electron dynamics is essentially nonlocal. 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 nonlocal 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, nonuniform, 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 nonuniform plasma density profile on both the current density profile and the EEDF is demonstrated.

  10. Computational Plasma Physics at the Bleeding Edge: Simulating Kinetic Turbulence Dynamics in Fusion Energy Sciences

    Science.gov (United States)

    Tang, William

    2013-04-01

    Advanced computing is generally recognized to be an increasingly vital tool for accelerating progress in scientific research in the 21st Century. The imperative is to translate the combination of the rapid advances in super-computing power together with the emergence of effective new algorithms and computational methodologies to help enable corresponding increases in the physics fidelity and the performance of the scientific codes used to model complex physical systems. If properly validated against experimental measurements and verified with mathematical tests and computational benchmarks, these codes can provide more reliable predictive capability for the behavior of complex systems, including fusion energy relevant high temperature plasmas. The magnetic fusion energy research community has made excellent progress in developing advanced codes for which computer run-time and problem size scale very well with the number of processors on massively parallel supercomputers. A good example is the effective usage of the full power of modern leadership class computational platforms from the terascale to the petascale and beyond to produce nonlinear particle-in-cell simulations which have accelerated progress in understanding the nature of plasma turbulence in magnetically-confined high temperature plasmas. Illustrative results provide great encouragement for being able to include increasingly realistic dynamics in extreme-scale computing campaigns to enable predictive simulations with unprecedented physics fidelity. Some illustrative examples will be presented of the algorithmic progress from the magnetic fusion energy sciences area in dealing with low memory per core extreme scale computing challenges for the current top 3 supercomputers worldwide. These include advanced CPU systems (such as the IBM-Blue-Gene-Q system and the Fujitsu K Machine) as well as the GPU-CPU hybrid system (Titan).

  11. An efficient non hydrostatic dynamical care far high-resolution simulations down to the urban scale

    Energy Technology Data Exchange (ETDEWEB)

    Bonaventura, L. [MOX-Politecnico, Milano (Italy); Cesari, D. [ARPA, Bologna (Italy). Servizio Idro Meteo

    2005-03-15

    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.

  12. Enzymes involved in the glycidaldehyde (2,3-epoxy-propanal) oxidation step in the kinetic resolution of racemic glycidol (2,3-epoxy-1-propanol) by Acetobacter pasteurianus.

    Science.gov (United States)

    Wandel, U; Machado, S S.; Jongejan, J A.; Duine, J A.

    2001-02-01

    It is already known that kinetic resolution of racemic glycidol (2,3-epoxy-1-propanol) takes place when Acetobacter pasteurianus oxidizes the compound to glycidic acid (2,3-epoxy-propionic acid) with glycidaldehyde (2,3-epoxy-propanal) proposed to be the transient seen in this conversion. Since inhibition affects the feasibility of a process based on this conversion in a negative sense, and the chemical reactivity of glycidaldehyde predicts that it could be the cause for the phenomena observed, it is important to know which enzyme(s) oxidise(s) this compound. To study this, rac.- as well as (R)-glycidaldehyde were prepared by chemical synthesis and analytical methods developed for their determination. It appears that purified quinohemoprotein alcohol dehydrogenase (QH-ADH type II), the enzyme responsible for the kinetic resolution of rac.-glycidol, also catalyses the oxidation of glycidaldehyde. In addition, a preparation exhibiting dye-linked aldehyde dehydrogenase activity for acetaldehyde, most probably originating from molybdohemoprotein aldehyde dehydrogenase (ALDH), which has been described for other Acetic acid bacteria, oxidised glycidaldehyde as well with a preference for the (R)-enantiomer, the selectivity quantified by an enantiomeric ratio (E) value of 7. From a comparison of the apparent kinetic parameter values of QH-ADH and ALDH, it is concluded that ALDH is mainly responsible for the removal of glycidaldehyde in conversions of glycidol catalysed by A. pasteurianus cells. It is shown that the transient observed in rac.-glycidol conversion by whole cells, is indeed (R)-glycidaldehyde. Since both QH-ADH and ALDH are responsible for vinegar production from ethanol by Acetobacters, growth and induction conditions optimal for this process seem also suited to yield cells with high catalytic performance with respect to kinetic resolution of glycidol and prevention of formation of inhibitory concentrations glycidaldehyde.

  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. Stereodirectional Origin of anti-Arrhenius Kinetics for a Tetraatomic Hydrogen Exchange Reaction: Born-Oppenheimer Molecular Dynamics for OH + HBr.

    Science.gov (United States)

    Coutinho, Nayara D; Aquilanti, Vincenzo; Silva, Valter H C; Camargo, Ademir J; Mundim, Kleber C; de Oliveira, Heibbe C B

    2016-07-14

    Among four-atom processes, the reaction OH + HBr → H2O + Br is one of the most studied experimentally: its kinetics has manifested an unusual anti-Arrhenius behavior, namely, a marked decrease of the rate constant as the temperature increases, which has intrigued theoreticians for a long time. Recently, salient features of the potential energy surface have been characterized and most kinetic aspects can be considered as satisfactorily reproduced by classical trajectory simulations. Motivation of the work reported in this paper is the investigation of the stereodirectional dynamics of this reaction as the prominent reason for the peculiar kinetics: we started in a previous Letter ( J. Phys. Chem. Lett. 2015 , 6 , 1553 - 1558 ) a first-principles Born-Oppenheimer "canonical" molecular dynamics approach. Trajectories are step-by-step generated on a potential energy surface quantum mechanically calculated on-the-fly and are thermostatically equilibrated to correspond to a specific temperature. Here, refinements of the method permitted a major increase of the number of trajectories and the consideration of four temperatures -50, +200, +350, and +500 K, for which the sampling of initial conditions allowed us to characterize the stereodynamical effect. The role is documented of the adjustment of the reactants' mutual orientation to encounter the entrance into the "cone of acceptance" for reactivity. The aperture angle of this cone is dictated by a range of directions of approach compatible with the formation of the specific HOH angle of the product water molecule; and consistently the adjustment is progressively less effective the higher the kinetic energy. Qualitatively, this emerging picture corroborates experiments on this reaction, involving collisions of aligned and oriented molecular beams, and covering a range of energies higher than the thermal ones. The extraction of thermal rate constants from this molecular dynamics approach is discussed and the systematic

  15. Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics.

    Science.gov (United States)

    Chatterjee, Abhijit; Bhattacharya, Swati

    2015-09-21

    Several studies in the past have generated Markov State Models (MSMs), i.e., kinetic models, of biomolecular systems by post-analyzing long standard molecular dynamics (MD) calculations at the temperature of interest and focusing on the maximally ergodic subset of states. Questions related to goodness of these models, namely, importance of the missing states and kinetic pathways, and the time for which the kinetic model is valid, are generally left unanswered. We show that similar questions arise when we generate a room-temperature MSM (denoted MSM-A) for solvated alanine dipeptide using state-constrained MD calculations at higher temperatures and Arrhenius relation — the main advantage of such a procedure being a speed-up of several thousand times over standard MD-based MSM building procedures. Bounds for rate constants calculated using probability theory from state-constrained MD at room temperature help validate MSM-A. However, bounds for pathways possibly missing in MSM-A show that alternate kinetic models exist that produce the same dynamical behaviour at short time scales as MSM-A but diverge later. Even in the worst case scenario, MSM-A is found to be valid longer than the time required to generate it. Concepts introduced here can be straightforwardly extended to other MSM building techniques.

  16. Growth from Solutions: Kink dynamics, Stoichiometry, Face Kinetics and stability in turbulent flow

    Science.gov (United States)

    Chernov, A. A.; DeYoreo, J. J.; Rashkovich, L. N.; Vekilov, P. G.

    2005-01-01

    1. Kink dynamics. The first segment of a polygomized dislocation spiral step measured by AFM demonstrates up to 60% scattering in the critical length l*- the length when the segment starts to propagate. On orthorhombic lysozyme, this length is shorter than that the observed interkink distance. Step energy from the critical segment length based on the Gibbs-Thomson law (GTL), l* = 20(omega)alpha/(Delta)mu is several times larger than the energy from 2D nucleation rate. Here o is tine building block specific voiume, a is the step riser specific free energy, Delta(mu) is the crystallization driving force. These new data support our earlier assumption that the classical Frenkel, Burton -Cabrera-Frank concept of the abundant kink supply by fluctuations is not applicable for strongly polygonized steps. Step rate measurements on brushite confirms that statement. This is the1D nucleation of kinks that control step propagation. The GTL is valid only if l*

  17. Monodomain dynamics for rigid rod and platelet suspensions in strongly coupled coplanar linear flow and magnetic fields. II. Kinetic theory

    Science.gov (United States)

    Forest, M. Gregory; Sircar, Sarthok; Wang, Qi; Zhou, Ruhai

    2006-10-01

    We establish reciprocity relations of the Doi-Hess kinetic theory for rigid rod macromolecular suspensions governed by the strong coupling among an excluded volume potential, linear flow, and a magnetic field. The relation provides a reduction of the flow and field driven Smoluchowski equation: from five parameters for coplanar linear flows and magnetic field, to two field parameters. The reduced model distinguishes flows with a rotational component, which map to simple shear (with rate parameter) subject to a transverse magnetic field (with strength parameter), and irrotational flows, for which the reduced model consists of a triaxial extensional flow (with two extensional rate parameters). We solve the Smoluchowski equation of the reduced model to explore: (i) the effect of introducing a coplanar magnetic field on each sheared monodomain attractor of the Doi-Hess kinetic theory and (ii) the coupling of coplanar extensional flow and magnetic fields. For (i), we show each sheared attractor (steady and unsteady, with peak axis in and out of the shearing plane, periodic and chaotic orbits) undergoes its own transition sequence versus magnetic field strength. Nonetheless, robust predictions emerge: out-of-plane degrees of freedom are arrested with increasing field strength, and a unique flow-aligning or tumbling/wagging limit cycle emerges above a threshold magnetic field strength or modified geometry parameter value. For (ii), irrotational flows coupled with a coplanar magnetic field yield only steady states. We characterize all (generically biaxial) equilibria in terms of an explicit Boltzmann distribution, providing a natural generalization of analytical results on pure nematic equilibria [P. Constantin, I. Kevrekidis, and E. S. Titi, Arch. Rat. Mech. Anal. 174, 365 (2004); P. Constantin, I. Kevrekidis, and E. S. Titi, Discrete and Continuous Dynamical Systems 11, 101 (2004); P. Constantin and J. Vukadinovic, Nonlinearity 18, 441 (2005); H. Liu, H. Zhang, and P

  18. 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

    2016-01-01

    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. PMID:27160346

  19. Varying the resolution of the Rouse model on temporal and spatial scales: application to multiscale modelling of DNA dynamics

    CERN Document Server

    Rolls, Edward; Erban, Radek

    2016-01-01

    A multi-resolution bead-spring model for polymer dynamics is developed as a generalization of the Rouse model. A polymer chain is described using beads of variable sizes connected by springs with variable spring constants. A numerical scheme which can use different timesteps to advance the positions of different beads is presented and analyzed. The position of a particular bead is only updated at integer multiples of the timesteps associated with its connecting springs. This approach extends the Rouse model to a multiscale model on both spatial and temporal scales, allowing simulations of localized regions of a polymer chain with high spatial and temporal resolution, while using a coarser modelling approach to describe the rest of the polymer chain. A method for changing the model resolution on-the-fly is developed using the Metropolis-Hastings algorithm. It is shown that this approach maintains key statistics of the end-to-end distance and diffusion of the polymer filament and makes computational savings whe...

  20. 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.

  1. Unraveling the Architecture and Structural Dynamics of Pathogens by High-Resolution in vitro Atomic Force Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Malkin, A J; Plomp, M; Leighton, T J; McPherson, A; Wheeler, K E

    2005-04-12

    Progress in structural biology very much depends upon the development of new high-resolution techniques and tools. Despite decades of study of viruses, bacteria and bacterial spores and their pressing importance in human medicine and biodefense, many of their structural properties are poorly understood. Thus, characterization and understanding of the architecture of protein surface and internal structures of pathogens is critical to elucidating mechanisms of disease, immune response, physicochemical properties, environmental resistance and development of countermeasures against bioterrorist agents. Furthermore, even though complete genome sequences are available for various pathogens, the structure-function relationships are not understood. Because of their lack of symmetry and heterogeneity, large human pathogens are often refractory to X-ray crystallographic analysis or reconstruction by cryo-electron microscopy (cryo-EM). An alternative high-resolution method to examine native structure of pathogens is atomic force microscopy (AFM), which allows direct visualization of macromolecular assemblies at near-molecular resolution. The capability to image single pathogen surfaces at nanometer scale in vitro would profoundly impact mechanistic and structural studies of pathogenesis, immunobiology, specific cellular processes, environmental dynamics and biotransformation.

  2. 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 (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 multispectral 3D scanning of vegetation at landscape scales (< 1 km2) heralds a new era of participatory remote sensing by field ecologists, community foresters and the interested public.

  3. Ultrahigh-performance liquid chromatography-ultraviolet absorbance detection-high-resolution-mass spectrometry combined with automated data processing for studying the kinetics of oxidative thermal degradation of thyroxine in the solid state.

    Science.gov (United States)

    Neu, Volker; Bielow, Chris; Reinert, Knut; Huber, Christian G

    2014-12-01

    Levothyroxine as active pharmaceutical ingredient of formulations used for the treatment of hypothyroidism is distributed worldwide and taken by millions of people. An important issue in terms of compound stability is its capability to react with ambient oxygen, especially in case of long term compound storage at elevated temperature. In this study we demonstrate that ultrahigh-performance liquid chromatography coupled to UV spectrometry and high-resolution mass spectrometry (UHPLC-UV-HRMS) represent very useful approaches to investigate the influence of ambient oxygen on the degradation kinetics of levothyroxine in the solid state at enhanced degradation conditions. Moreover, the impurity pattern of oxidative degradation of levothyroxine is elucidated and classified with respect to degradation kinetics at different oxygen levels. Kinetic analysis of thyroxine bulk material at 100 °C reveals bi-phasic degradation kinetics with a distinct change in degradation phases dependent on the availability of oxygen. The results clearly show that contact of the bulk material to ambient oxygen is a key factor for fast compound degradation. Furthermore, the combination of time-resolved HRMS data and automated data processing is shown to allow insights into the kinetics and mechanism of impurity formation on individual compound basis. By comparing degradation profiles, four main classes of profiles linked to reaction pathways of thyroxine degradation were identifiable. Finally, we show the capability of automated data processing for the matching of different stressing conditions, in order to extract information about mechanistic similarities. As a result, degradation kinetics is influenced by factors like availability of oxygen, stressing time, or stressing temperature, while the degradation mechanisms appear to be conserved.

  4. 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...

  5. Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique

    Science.gov (United States)

    Peters, J. H.; Klein, R.; Delle Site, L.

    2016-08-01

    We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle the change of representation of large molecules. The robustness of the approach is shown by calculating several relevant structural properties and comparing them with the results of full atomistic simulations. The extended scheme represents a robust prototype for the simulation of macromolecular systems of interest in several fields, from material science to biophysics.

  6. 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.

  7. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    Science.gov (United States)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work

  8. Study on a hidden protein-DNA binding in salmon sperm DNA sample by dynamic kinetic capillary isoelectric focusing

    Energy Technology Data Exchange (ETDEWEB)

    Liang Liang; Dou Peng; Dong Mingming; Ke Xiaokang; Bian Ningsheng [School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093 (China); Liu Zhen, E-mail: zhenliu@nju.edu.cn [School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093 (China)

    2009-09-14

    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{sup -3} s{sup -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.

  9. Bogoliubov-Born-Green-Kirkwood-Yvon chain and kinetic equations for the level dynamics in an externally perturbed quantum system

    Science.gov (United States)

    Qureshi, Mumnuna A.; Zhong, Johnny; Betouras, Joseph J.; Zagoskin, Alexandre M.

    2017-03-01

    Theoretical description and simulation of large quantum coherent systems out of equilibrium remains a daunting task. Here we are developing an approach to it based on the Pechukas-Yukawa formalism, which is especially convenient in the case of an adiabatically slow external perturbation, though it is not restricted to adiabatic systems. In this formalism the dynamics of energy levels in an externally perturbed quantum system as a function of the perturbation parameter is mapped on that of a fictitious one-dimensional classical gas of particles with cubic repulsion. Equilibrium statistical mechanics of this Pechukas gas allows us to reproduce the random matrix theory of energy levels. In the present work, we develop the nonequilibrium statistical mechanics of the Pechukas gas, starting with the derivation of the Bogoliubov-Born-Green-Kirkwood-Yvon (BBGKY) chain of equations for the appropriate generalized distribution functions. Sets of approximate kinetic equations can be consistently obtained by breaking this chain at a particular point (i.e., approximating all higher-order distribution functions by the products of the lower-order ones). When complemented by the equations for the level occupation numbers and interlevel transition amplitudes, they allow us to describe the nonequilibrium evolution of the quantum state of the system, which can describe better a large quantum coherent system than the currently used approaches. In particular, we find that corrections to the factorized approximation of the distribution function scale as 1 /N , where N is the number of the "Pechukas gas particles" (i.e., energy levels in the system).

  10. Understanding High-Resolution Spatiotemporal Dynamics of Groundwater Recharge Using Process Based Hydrologic Modeling

    Science.gov (United States)

    Kang, G.; Qiu, H.; Li, S. G.; Lusch, D.; Phanikumar, M. S.

    2016-12-01

    Quantifying the natural rates of groundwater recharge and identifying the location and timing of major recharge events are essential for maintaining sustainable water yields and for understanding contaminant transport mechanisms in groundwater systems. Using Ottawa County, Michigan as a case study in sustainable water resources management, this research is part of a larger project that examines the issues of declining water tables and increasing chloride concentrations within the county. A process-based hydrologic model (PAWS) is used to mechanistically evaluate the integrated hydrologic response of both the surface and subsurface systems to further compute daily fluxes due to evapotranspiration, surface runoff, recharge and groundwater-stream interactions. Both rain gauge (NCDC) and NEXRAD precipitation data are used as input for the model. The model is built based on three major watersheds at 300m spatial resolution and daily temporal resolution, covering all of Ottawa County and is calibrated using streamflow data from USGS gauging stations. In addition, synoptic and time-series baseflow data collected using Acoustic Doppler Current Profilers and electromagnetic flow meters during the summer of 2015 are used to test the ability of the model to simulate baseflows and to quantify the uncertainty. The MODIS evapotranspiration product is used to evaluate model performance in simulating ET. The primary objectives of this study are to (1) understand the periods of high and low groundwater recharge in the county between the years 2009 and 2015; and (2) analyze the impacts of different types of land use, soil, elevation, and slope on groundwater recharge.

  11. A multicrystal diffraction data-collection approach for studying structural dynamics with millisecond temporal resolution

    Directory of Open Access Journals (Sweden)

    Robin Schubert

    2016-11-01

    Full Text Available Many biochemical processes take place on timescales ranging from femtoseconds to seconds. Accordingly, any time-resolved experiment must be matched to the speed of the structural changes of interest. Therefore, the timescale of interest defines the requirements of the X-ray source, instrumentation and data-collection strategy. In this study, a minimalistic approach for in situ crystallization is presented that requires only a few microlitres of sample solution containing a few hundred crystals. It is demonstrated that complete diffraction data sets, merged from multiple crystals, can be recorded within only a few minutes of beamtime and allow high-resolution structural information of high quality to be obtained with a temporal resolution of 40 ms. Global and site-specific radiation damage can be avoided by limiting the maximal dose per crystal to 400 kGy. Moreover, analysis of the data collected at higher doses allows the time-resolved observation of site-specific radiation damage. Therefore, our approach is well suited to observe structural changes and possibly enzymatic reactions in the low-millisecond regime.

  12. Temperature dependence of the OH(-) + CH3I reaction kinetics. experimental and simulation studies and atomic-level dynamics.

    Science.gov (United States)

    Xie, Jing; Kohale, Swapnil C; Hase, William L; Ard, Shaun G; Melko, Joshua J; Shuman, Nicholas S; Viggiano, Albert A

    2013-12-27

    Direct dynamics simulations and selected ion flow tube (SIFT) experiments were performed to study the kinetics and dynamics of the OH(-) + CH3I reaction versus temperature. This work complements previous direct dynamics simulation and molecular beam ion imaging experiments of this reaction versus reaction collision energy (Xie et al. J. Phys. Chem. A 2013, 117, 7162). The simulations and experiments are in quite good agreement. Both identify the SN2, OH(-) + CH3I → CH3OH + I(-), and proton transfer, OH(-) + CH3I → CH2I(-) + H2O, reactions as having nearly equal importance. In the experiments, the SN2 pathway constitutes 0.64 ± 0.05, 0.56 ± 0.05, 0.51 ± 0.05, and 0.46 ± 0.05 of the total reaction at 210, 300, 400, and 500 K, respectively. For the simulations this fraction is 0.56 ± 0.06, 0.55 ± 0.04, and 0.50 ± 0.05 at 300, 400, and 500 K, respectively. The experimental total reaction rate constant is (2.3 ± 0.6) × 10(-9), (1.7 ± 0.4) × 10(-9), (1.9 ± 0.5) × 10(-9), and (1.8 ± 0.5) × 10(-9) cm(3) s(-1) at 210, 300, 400, and 500 K, respectively, which is approximately 25% smaller than the collision capture value. The simulation values for this rate constant are (1.7 ± 0.2) × 10(-9), (1.8 ± 0.1) × 10(-9), and (1.6 ± 0.1) × 10(-9) cm(3)s(-1) at 300, 400, and 500 K. From the simulations, direct rebound and stripping mechanisms as well as multiple indirect mechanisms are identified as the atomic-level reaction mechanisms for both the SN2 and proton-transfer pathways. For the SN2 reaction the direct and indirect mechanisms have nearly equal probabilities; the direct mechanisms are slightly more probable, and direct rebound is more important than direct stripping. For the proton-transfer pathway the indirect mechanisms are more important than the direct mechanisms, and stripping is significantly more important than rebound for the latter. Calculations were performed with the OH(-) quantum number J equal to 0, 3, and 6 to investigate the effect of

  13. Gelation-driven Dynamic Systemic Resolution: in situ Generation and Self-Selection of an Organogelator

    Science.gov (United States)

    Hu, Lei; Zhang, Yang; Ramström, Olof

    2015-06-01

    An organogelator was produced and identified from a dynamic imine system, resolved and amplified by selective gelation. The formation of the organogel was monitored in situ by 1H NMR, showing the existence of multiple reversible reactions operating simultaneously, and the redistribution of the involved species during gelation. The formed organogelator proved effective with a range of organic solvents, including DMSO, toluene, and longer, linear alcohols.

  14. 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.

  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

    2017-01-01

    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. PMID:28881772

  16. 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

    could distinguish three insect clusters based on morphology and found that two contained insects predominantly recorded above the field in the evening, whereas the third was formed by insects near the forest at around 21:30. Together our results demonstrate the capability of lidar for distinguishing......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...... summer night in Sweden. We compare lidar recordings with data from a light trap deployed alongside the lidar. A total of 22808 insect were recorded, and the relative temporal quantities measured matched the quantities recorded with the light trap within a radius of 5 m. Lidar records showed that small...

  17. 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.

  18. Diastereo- and enantioselective synthesis of (E)-2-Methyl-1,2-syn- and (E)-2-Methyl-1,2-anti-3-pentenediols via allenylboronate kinetic resolution with ((d)Ipc)2BH and aldehyde allylboration.

    Science.gov (United States)

    Han, Jeng-Liang; Chen, Ming; Roush, William R

    2012-06-15

    Enantioselective hydroboration of racemic allenylboronate (±)-1 with 0.48 equiv of ((d)Ipc)(2)BH at -25 °C proceeds with efficient kinetic resolution and provides allylborane (R)-Z-4. When heated to 95 °C, allylborane (R)-Z-4 isomerizes to the thermodynamically more stable allylborane isomer (S)-E-7. Subsequent allylboration of aldehydes with (R)-Z-4 or (S)-E-7 at -78 °C followed by oxidative workup provides 1,2-syn- or 1,2-anti-diols, 2 or 3, respectively, in 87-94% ee.

  19. Kinetic Biochemistry

    Directory of Open Access Journals (Sweden)

    Lorentz JÄNTSCHI

    2003-03-01

    Full Text Available Mathematics and computer programming have a major contribution to chemistry. Two directions can be identified: one that searches and tries (rich to explain the structural binding and shape of the chemical compounds [1] with major applications in QSPR/QSAR studies [2], and applied sciences such as engineering of materials or agriculture [3]; the second direction is to models the kinetic processes that are involved in chemical reactions [4]. Many such models are available here. The present paper describes three variants of well the known kinetic models and presents the mathematical equations associated with them. The differential equations are numerically solved and fitted with MathCad program. [1] Diudea M., Gutman I., Jäntschi L., Molecular Topology, Nova Science, Huntington, New York, 332 p., 2001, 2002. [2] Diudea M. V., Ed., QSPR / QSAR Studies by Molecular Descriptors, Nova Science, Huntington, New York, 438 p., 2001. [3] Jäntschi L., Microbiology and Toxicology. Phytochemistry Studies (in Romanian, Amici, Cluj-Napoca, 184 p., 2003. [4] Jäntschi L., Unguresan M., Physical Chemistry. Molecular Kinetic and Dynamic (in Romanian, Mediamira, Cluj-Napoca, 159 p., 2001.

  20. Resolution of discordant HIV-1 protease resistance rankings using molecular dynamics simulations.

    Science.gov (United States)

    Wright, David W; Coveney, Peter V

    2011-10-24

    The emergence of drug resistance is a major challenge for the effective treatment of HIV. In this article, we explore the application of atomistic molecular dynamics simulations to quantify the level of resistance of a patient-derived HIV-1 protease sequence to the inhibitor lopinavir. A comparative drug ranking methodology was developed to compare drug resistance rankings produced by the Stanford HIVdb, ANRS, and RegaDB clinical decision support systems. The methodology was used to identify a patient sequence for which the three rival online tools produced differing resistance rankings. Mutations at only three positions ( L10I , A71IV, and L90M ) influenced the resistance level assigned to the sequence. We use ensemble molecular dynamics simulations to elucidate the origin of these discrepancies and the mechanism of resistance. By simulating not only the full patient sequences but also systems containing the constituent mutations, we gain insight into why resistance estimates vary and the interactions between the various mutations. In the same way, we also gain valuable knowledge of the mechanistic causes of resistance. In particular, we identify changes in the relative conformation of the two beta sheets that form the protease dimer interface which suggest an explanation of the relative frequency of different amino acids observed in patients at residue 71.

  1. Analog filtering of large solvent signals for improved dynamic range in high-resolution NMR.

    Science.gov (United States)

    Redfield, A G; Kunz, S D

    1998-01-01

    The large solvent signal from samples in H2O solvent still challenges the dynamic range capability of any spectrometer. The solvent signal can be largely removed with a pair of simple resistor-capacitor (RC) high-pass filters when the solvent frequency is set at center band (zero frequency) using quadrature detection, with RC approximately 0.5 ms. However, an approximately 0.5-ms transient remains at initial time, which we reduce fourfold for a short time only, just before the A/D converter, by means of a variable-gain amplifier, and later restore with software. This modification can result in a nearly fourfold increase in dynamic range. When we converted to a frequency-shifted mode (A. G. Redfield and S. D. Kunz, 1994, J. Magn. Reson. A 108, 234-237) we replaced the RC high-pass filter with a quadrature feedback notch filter tuned to the solvent frequency (5.06 kHz). This filter is an example of a class of two-input/two-output filters which maintain the spectral integrity (image-free character) of quadrature signals. Digital filters of the same type are also considered briefly. We discuss the implications of these ideas for spectrometer input design, including schemes for elimination of radiation damping, and effects of probe bandwidth on extreme oversampling.

  2. Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Quantum-Classical Simulation of Liquid Water

    CERN Document Server

    Agarwal, Animesh

    2015-01-01

    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 abovementioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One possible solution 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 ...

  3. 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.

  4. High resolution polarimeter-interferometer system for fast equilibrium dynamics and MHD instability studies on Joint-TEXT tokamak (invited).

    Science.gov (United States)

    Chen, J; Zhuang, G; Li, Q; Liu, Y; Gao, L; Zhou, Y N; Jian, X; Xiong, C Y; Wang, Z J; Brower, D L; Ding, W X

    2014-11-01

    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 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.

  5. 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.

  6. Fluid dynamics and convective heat transfer in impinging jets through implementation of a high resolution liquid crystal technique

    Science.gov (United States)

    Kim, K.; Wiedner, B.; Camci, C.

    1993-01-01

    A combined convective heat transfer and fluid dynamics investigation in a turbulent round jet impinging on a flat surface is presented. The experimental study uses a high resolution liquid crystal technique for the determination of the convective heat transfer coefficients on the impingement plate. The heat transfer experiments are performed using a transient heat transfer method. The mean flow and the character of turbulent flow in the free jet is presented through five hole probe and hot wire measurements, respectively. The flow field character of the region near the impingement plate plays an important role in the amount of convective heat transfer. Detailed surveys obtained from five hole probe and hot wire measurements are provided. An extensive validation of the liquid crystal based heat transfer method against a conventional technique is also presented. After a complete documentation of the mean and turbulent flow field, the convective heat transfer coefficient distributions on the impingement plate are presented. The near wall of the impingement plate and the free jet region is treated separately. The current heat transfer distributions are compared to other studies available from the literature. The present paper contains complete sets of information on the three dimensional mean flow, turbulent velocity fluctuations, and convective heat transfer to the plate. The experiments also prove that the present nonintrusive heat transfer method is highly effective in obtaining high resolution heat transfer maps with a heat transfer coefficient uncertainty of 5.7 percent.

  7. The high-resolution architecture and structural dynamics of Bacillus spores

    Energy Technology Data Exchange (ETDEWEB)

    Plomp, M; Leighton, T J; Wheeler, K E; Malkin, A J

    2004-05-06

    The capability to image single microbial cell surfaces at nanometer scale under native conditions would profoundly impact mechanistic and structural studies of pathogenesis, immunobiology, environmental resistance and biotransformation. We report here that advances in atomic force microscopy (AFM) have allowed us to directly visualize high-resolution native structures of bacterial endospores, including the exosporium and spore coats of four Bacillus species in air and water environments. The dimensions of individual Bacillus atrophaeus spores were found to decrease reversibly by 12% in response to a change in the environment from aqueous to aerial phase. Intraspecies spore size distribution analyses revealed that spore length could vary by a factor of 2 while the absolute deviation is 7 - 13% in length and 4 - 6 % in width. AFM analysis also demonstrated that the mechanisms of spore coat self-assembly are similar to those described for inorganic and macromolecular crystallization. These results establish AFM as a powerful new tool for the analysis of molecular architecture and variability as a function of spatial, temporal and developmental organizational scales.

  8. Observations of movement dynamics of flying insects using high resolution lidar.

    Science.gov (United States)

    Kirkeby, Carsten; Wellenreuther, Maren; Brydegaard, Mikkel

    2016-07-04

    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 summer night in Sweden. We compare lidar recordings with data from a light trap deployed alongside the lidar. A total of 22808 insect were recorded, and the relative temporal quantities measured matched the quantities recorded with the light trap within a radius of 5 m. Lidar records showed that small insects (wing size 2.5 mm(2) 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 could distinguish three insect clusters based on morphology and found that two contained insects predominantly recorded above the field in the evening, whereas the third was formed by insects near the forest at around 21:30. Together our results demonstrate the capability of lidar for distinguishing different types of insect during flight and quantifying their movements.

  9. Observations of movement dynamics of flying insects using high resolution lidar

    Science.gov (United States)

    Kirkeby, Carsten; Wellenreuther, Maren; Brydegaard, Mikkel

    2016-07-01

    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 summer night in Sweden. We compare lidar recordings with data from a light trap deployed alongside the lidar. A total of 22808 insect were recorded, and the relative temporal quantities measured matched the quantities recorded with the light trap within a radius of 5 m. Lidar records showed that small insects (wing size 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 could distinguish three insect clusters based on morphology and found that two contained insects predominantly recorded above the field in the evening, whereas the third was formed by insects near the forest at around 21:30. Together our results demonstrate the capability of lidar for distinguishing different types of insect during flight and quantifying their movements.

  10. Dynamic fault trees resolution: A conscious trade-off between analytical and simulative approaches

    Energy Technology Data Exchange (ETDEWEB)

    Chiacchio, F., E-mail: chiacchio@dmi.unict.it [Dipartimento di Matematica e Informatica-DMI, Universita degli Studi di Catania (Italy); Compagno, L., E-mail: lco@diim.unict.it [Dipartimento di Ingegneria Industriale e Meccanica-DIIM, Universita degli Studi di Catania (Italy); D' Urso, D., E-mail: ddurso@diim.unict.it [Dipartimento di Ingegneria Industriale e Meccanica-DIIM, Universita degli Studi di Catania (Italy); Manno, G., E-mail: gmanno@dmi.unict.it [Dipartimento di Matematica e Informatica-DMI, Universita degli Studi di Catania (Italy); Trapani, N., E-mail: ntrapani@diim.unict.it [Dipartimento di Ingegneria Industriale e Meccanica-DIIM, Universita degli Studi di Catania (Italy)

    2011-11-15

    Safety assessment in industrial plants with 'major hazards' requires a rigorous combination of both qualitative and quantitative techniques of RAMS. Quantitative assessment can be executed by static or dynamic tools of dependability but, while the former are not sufficient to model exhaustively time-dependent activities, the latter are still too complex to be used with success by the operators of the industrial field. In this paper we present a review of the procedures that can be used to solve quite general dynamic fault trees (DFT) that present a combination of the following characteristics: time dependencies, repeated events and generalized probability failure. Theoretical foundations of the DFT theory are discussed and the limits of the most known DFT tools are presented. Introducing the concept of weak and strong hierarchy, the well-known modular approach is adapted to study a more generic class of DFT. In order to quantify the approximations introduced, an ad-hoc simulative environment is used as benchmark. In the end, a DFT of an accidental scenario is analyzed with both analytical and simulative approaches. Final results are in good agreement and prove how it is possible to implement a suitable Monte Carlo simulation with the features of a spreadsheet environment, able to overcome the limits of the analytical tools, thus encouraging further researches along this direction. - Highlights: > Theoretical foundations of the DFT are reviewed and the limits of the analytical techniques are assessed. > Hierarchical technique is discussed, introducing the concepts of weak and strong equivalence. > Simulative environment developed with a spreadsheet electronic document is tested. > Comparison between the simulative and the analytical results is performed. > Classification of which technique is more suitable is provided, depending on the complexity of the DFT.

  11. Measuring hepatic functional reserve using low temporal resolution Gd-EOB-DTPA dynamic contrast-enhanced MRI: a preliminary study comparing galactosyl human serum albumin scintigraphy with indocyanine green retention

    Energy Technology Data Exchange (ETDEWEB)

    Saito, Kazuhiro; Hashimoto, Tsuyoshi; Araki, Yoichi; Akata, Soichi; Tokuuye, Koichi [Tokyo Medical University, Department of Radiology, Tokyo (Japan); Ledsam, Joseph; Sourbron, Steven [University of Leeds, Division of Medical Physics, Leeds (United Kingdom)

    2014-01-15

    To investigate if tracer kinetic modelling of low temporal resolution dynamic contrast-enhanced (DCE) MRI with Gd-EOB-DTPA could replace technetium-99 m galactosyl human serum albumin (GSA) single positron emission computed tomography (SPECT) and indocyanine green (ICG) retention for the measurement of liver functional reserve. Twenty eight patients awaiting liver resection for various cancers were included in this retrospective study that was approved by the institutional review board. The Gd-EOB-DTPA MRI sequence acquired five images: unenhanced, double arterial phase, portal phase, and 4 min after injection. Intracellular contrast uptake rate (UR) and extracellular volume (Ve) were calculated from DCE-MRI, along with the ratio of GSA radioactivity of liver to heart-plus-liver and per cent of cumulative uptake from 15-16 min (LHL15 and LU15, respectively) from GSA-scintigraphy. ICG retention at 15 min, Child-Pugh cirrhosis score (CPS) and postoperative Inuyama fibrosis criteria were also recorded. Statistical analysis was with Spearman rank correlation analysis. Comparing MRI parameters with the reference methods, significant correlations were obtained for UR and LHL15, LU15, ICG15 (all 0.4-0.6, P < 0.05); UR and CPS (-0.64, P < 0.001); Ve and Inuyama (0.44, P < 0.05). Measures of liver function obtained by routine Gd-EOB-DTPA DCE-MRI with tracer kinetic modelling may provide a suitable method for the evaluation of liver functional reserve. (orig.)

  12. Numerical modeling of permafrost dynamics in Alaska using a high spatial resolution dataset

    Directory of Open Access Journals (Sweden)

    E. E. Jafarov

    2012-01-01

    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. Input parameters to the model are spatial datasets of mean monthly air temperature and precipitation, prescribed thermal properties of the multilayered soil column, and water content which 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 preliminary modeling results based on input of 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 CALM active layer monitoring stations. Calibrated model was used to address possible ground temperature changes for the 21st century. The model simulation results show the widespread permafrost degradation in Alaska could begin in 2040–2099 time frame within the vast area southward from the Brooks Range except for the high altitudes of the Alaska Range and Wrangell Mountains.

  13. 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.

  14. 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

  15. High-resolution ocean pH dynamics in four subtropical Atlantic benthic habitats

    Science.gov (United States)

    Hernández, C. A.; Clemente, S.; Sangil, C.; Hernández, J. C.

    2015-12-01

    Oscillations of ocean pH are largely unknown in coastal environments and ocean acidification studies often do not account for natural variability yet most of what is known about marine species and populations is found out via studies conducted in near shore environments. Most experiments designed to make predictions about future climate change scenarios are carried out in coastal environments with no research that takes into account the natural pH variability. In order to fill this knowledge gap and to provide reliable measures of pH oscillation, seawater pH was measured over time using moored pH sensors in four contrasting phytocenoses typical of the north Atlantic subtropical region. Each phytocenosis was characterized by its predominant engineer species: (1) Cystoseira abies-marina, (2) a mix of gelidiales and geniculate corallines, (3) Lobophora variegata, and (4) encrusting corallines. The autonomous pH measuring systems consisted of a pH sensor; a data logger and a battery encased in a waterproof container and allowed the acquisition of high-resolution continuous pH data at each of the study sites. The pH variation observed ranged by between 0.09 and 0.24 pHNBS units. A clear daily variation in seawater pH was detected at all the studied sites (0.04-0.12 pHNBS units). Significant differences in daily pH oscillations were also observed between phytocenoses, which shows that macroalgal communities influence the seawater pH in benthic habitats. Natural oscillations in pH must be taken into account in future ocean acidification studies to put findings in perspective and for any ecological recommendations to be realistic.

  16. 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.

  17. Towards a microchannel-based X-ray detector with two-dimensional spatial and time resolution and high dynamic range.

    Science.gov (United States)

    Adams, Bernhard W; Mane, Anil U; Elam, Jeffrey W; Obaid, Razib; Wetstein, Matthew; Chollet, Matthieu

    2015-09-01

    X-ray detectors that combine two-dimensional spatial resolution with a high time resolution are needed in numerous applications of synchrotron radiation. Most detectors with this combination of capabilities are based on semiconductor technology and are therefore limited in size. Furthermore, the time resolution is often realised through rapid time-gating of the acquisition, followed by a slower readout. Here, a detector technology is realised based on relatively inexpensive microchannel plates that uses GHz waveform sampling for a millimeter-scale spatial resolution and better than 100 ps time resolution. The technology is capable of continuous streaming of time- and location-tagged events at rates greater than 10(7) events per cm(2). Time-gating can be used for improved dynamic range.

  18. Towards a microchannel-based X-ray detector with two-dimensional spatial and time resolution and high dynamic range

    Energy Technology Data Exchange (ETDEWEB)

    Adams, Bernhard W.; Mane, Anil; Elam, Jeffrey; Obaid, Razib; Wetstein, Matthew J.

    2015-09-01

    X-ray detectors that combine two-dimensional spatial resolution with a high time resolution are needed in numerous applications of synchrotron radiation. Most detectors with this combination of capabilities are based on semiconductor technology and are therefore limited in size. Furthermore, the time resolution is often realised through rapid time-gating of the acquisition, followed by a slower readout. Here, a detector technology is realised based on relatively inexpensive microchannel plates that uses GHz waveform sampling for a millimeter-scale spatial resolution and better than 100 ps time resolution. The technology is capable of continuous streaming of time- and location-tagged events at rates greater than 10(7) events per cm(2). Time-gating can be used for improved dynamic range.

  19. Periodicity in tumor vasculature targeting kinetics of ligand-functionalized nanoparticles studied by dynamic contrast enhanced magnetic resonance imaging and intravital microscopy.

    Science.gov (United States)

    Hak, Sjoerd; Cebulla, Jana; Huuse, Else Marie; Davies, Catharina de L; Mulder, Willem J M; Larsson, Henrik B W; Haraldseth, Olav

    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 on tumor images acquired before and at set time points after administration. Although several exciting proof-of-concept studies demonstrated qualitative assessment of relative target concentration and distribution, these studies did not provide quantitative information on the nanoparticle targeting 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, and using compartment modeling we were able to quantify nanoparticle targeting rates. As such, this approach can facilitate optimization of targeted nanoparticle design and it holds promise for providing more quantitative information on in vivo receptor levels. Interestingly, we also observed a periodicity in the accumulation kinetics of αvβ3-integrin targeted nanoparticles and hypothesize that this periodicity is caused by receptor binding, internalization and recycling dynamics. Taken together, this demonstrates that our experimental approach provides new insights in in vivo nanoparticle targeting, which may proof useful for vascular targeting in general.

  20. Advancing Access to New Technology for Sustained High Resolution Observations of Plankton: From Bloom Dynamics to Climate Change

    Science.gov (United States)

    Sosik, H. M.; Olson, R. J.

    2012-12-01

    The combination of ocean observatory infrastructure and automated submersible flow cytometry can provide unprecedented capability for sustained high resolution time series of plankton, including taxa that are harmful or early indicators of ecosystem response to environmental change. Over the past decade, we have developed the FlowCytobot series of instruments that exemplify this capability. FlowCytobot and Imaging FlowCytobot use a combination of laser-based scattering and fluorescence measurements and video imaging of individual particles to enumerate and characterize cells ranging from picocyanobacteria to large chaining-forming diatoms. The process of developing these complex instruments was streamlined by access to the Martha's Vineyard Coastal Observatory (MVCO), a cabled facility on the New England Shelf, where real time two-way communications and access to shore power expedited cycles of instrument evaluation and design refinement. Repeated deployments at MVCO, typically 6 months in duration, have produced multi-year high resolution (hourly to daily) time series that are providing new insights into dynamics of community structure such as blooms, seasonality, and possibly even trends linked to regional climate change. The high temporal resolution observations of single cell properties make it possible not only to characterize taxonomic composition and size structure, but also to quantify taxon-specific growth rates. To meet the challenge of broadening access to this enabling technology, we have taken a two-step approach. First, we are partnering with a few scientific collaborators interested in using the instruments in different environments and to address different applications, notably the detection and characterization of harmful algal bloom events. Collaboration at this stage ensured that these first users outside the developers' lab had access to technical know-how required for successful outcomes; it also provided additional feedback that could be