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Sample records for enzyme-catalyzed dynamic kinetic

  1. 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.

  2. Enzyme catalyzed oxidative gelation of sugar beet pectin: Kinetics and rheology

    DEFF Research Database (Denmark)

    Abang Zaidel, Dayang Norulfairuz; Chronakis, Ioannis S.; Meyer, Anne S.

    2012-01-01

    Sugar beet pectin (SBP) is a marginally utilized co-processing product from sugar production from sugar beets. In this study, the kinetics of oxidative gelation of SBP, taking place via enzyme catalyzed cross-linking of ferulic acid moieties (FA), was studied using small angle oscillatory...

  3. Enzyme-catalyzed and binding reaction kinetics determined by titration calorimetry.

    Science.gov (United States)

    Hansen, Lee D; Transtrum, Mark K; Quinn, Colette; Demarse, Neil

    2016-05-01

    Isothermal calorimetry allows monitoring of reaction rates via direct measurement of the rate of heat produced by the reaction. Calorimetry is one of very few techniques that can be used to measure rates without taking a derivative of the primary data. Because heat is a universal indicator of chemical reactions, calorimetry can be used to measure kinetics in opaque solutions, suspensions, and multiple phase systems and does not require chemical labeling. The only significant limitation of calorimetry for kinetic measurements is that the time constant of the reaction must be greater than the time constant of the calorimeter which can range from a few seconds to a few minutes. Calorimetry has the unique ability to provide both kinetic and thermodynamic data. This article describes the calorimetric methodology for determining reaction kinetics and reviews examples from recent literature that demonstrate applications of titration calorimetry to determine kinetics of enzyme-catalyzed and ligand binding reactions. A complete model for the temperature dependence of enzyme activity is presented. A previous method commonly used for blank corrections in determinations of equilibrium constants and enthalpy changes for binding reactions is shown to be subject to significant systematic error. Methods for determination of the kinetics of enzyme-catalyzed reactions and for simultaneous determination of thermodynamics and kinetics of ligand binding reactions are reviewed. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Enzyme-catalyzed synthesis and kinetics of ultrasonic-assisted biodiesel production from waste tallow.

    Science.gov (United States)

    Adewale, Peter; Dumont, Marie-Josée; Ngadi, Michael

    2015-11-01

    The use of ultrasonic processing was evaluated for its ability to achieve adequate mixing while providing sufficient activation energy for the enzymatic transesterification of waste tallow. The effects of ultrasonic parameters (amplitude, cycle and pulse) and major reaction factors (molar ratio and enzyme concentration) on the reaction kinetics of biodiesel generation from waste tallow bio-catalyzed by immobilized lipase [Candida antarctica lipase B (CALB)] were investigated. Three sets of experiments namely A, B, and C were conducted. In experiment set A, two factors (ultrasonic amplitude and cycle) were investigated at three levels; in experiment set B, two factors (molar ratio and enzyme concentration) were examined at three levels; and in experiment set C, two factors (ultrasonic amplitude and reaction time) were investigated at five levels. A Ping Pong Bi Bi kinetic model approach was employed to study the effect of ultrasonic amplitude on the enzymatic transesterification. Kinetic constants of transesterification reaction were determined at different ultrasonic amplitudes (30%, 35%, 40%, 45%, and 50%) and enzyme concentrations (4, 6, and 8 wt.% of fat) at constant molar ratio (fat:methanol); 1:6, and ultrasonic cycle; 5 Hz. Optimal conditions for ultrasound-assisted biodiesel production from waste tallow were fat:methanol molar ratio, 1:4; catalyst level 6% (w/w of fat); reaction time, 20 min (30 times less than conventional batch processes); ultrasonic amplitude 40% at 5 Hz. The kinetic model results revealed interesting features of ultrasound assisted enzyme-catalyzed transesterification (as compared to conventional system): at ultrasonic amplitude 40%, the reaction activities within the system seemed to be steady after 20 min which means the reaction could proceed with or without ultrasonic mixing. Reversed phase high performance liquid chromatography indicated the biodiesel yield to be 85.6±0.08%. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Kinetics of enzyme-catalyzed cross-linking of feruloylated arabinan from sugar beet

    DEFF Research Database (Denmark)

    Abang Zaidel, Dayang Norulfairuz; Arnous, Anis; Holck, Jesper

    2011-01-01

    the kinetics of HRP catalyzed cross-linking of FA esterified to α-(1,5)-linked arabinans are affected by the length of the arabinan chains carrying the feruloyl substitutions. The kinetics of the HRP-catalyzed cross-linking of four sets of arabinan samples from sugar beet pulp, having different molecular...... weights and hence different degrees of polymerization, were monitored by the disappearance of FA absorbance at 316 nm. MALDI-TOF/TOF-MS analysis confirmed that the sugar beet arabinans were feruloyl-substituted, and HPLC analysis verified that the amounts of diFAs increased when FA levels decreased...

  6. Kinetics based reaction optimization of enzyme catalyzed reduction of formaldehyde to methanol with synchronous cofactor regeneration.

    Science.gov (United States)

    Marpani, Fauziah; Sárossy, Zsuzsa; Pinelo, Manuel; Meyer, Anne S

    2017-12-01

    Enzymatic reduction of carbon dioxide (CO 2 ) to methanol (CH 3 OH) can be accomplished using a designed set-up of three oxidoreductases utilizing reduced pyridine nucleotide (NADH) as cofactor for the reducing equivalents electron supply. For this enzyme system to function efficiently a balanced regeneration of the reducing equivalents during reaction is required. Herein, we report the optimization of the enzymatic conversion of formaldehyde (CHOH) to CH 3 OH by alcohol dehydrogenase, the final step of the enzymatic redox reaction of CO 2 to CH 3 OH, with kinetically synchronous enzymatic cofactor regeneration using either glucose dehydrogenase (System I) or xylose dehydrogenase (System II). A mathematical model of the enzyme kinetics was employed to identify the best reaction set-up for attaining optimal cofactor recycling rate and enzyme utilization efficiency. Targeted process optimization experiments were conducted to verify the kinetically modeled results. Repetitive reaction cycles were shown to enhance the yield of CH 3 OH, increase the total turnover number (TTN) and the biocatalytic productivity rate (BPR) value for both system I and II whilst minimizing the exposure of the enzymes to high concentrations of CHOH. System II was found to be superior to System I with a yield of 8 mM CH 3 OH, a TTN of 160 and BPR of 24 μmol CH 3 OH/U · h during 6 hr of reaction. The study demonstrates that an optimal reaction set-up could be designed from rational kinetics modeling to maximize the yield of CH 3 OH, whilst simultaneously optimizing cofactor recycling and enzyme utilization efficiency. © 2017 Wiley Periodicals, Inc.

  7. Representing Rate Equations for Enzyme-Catalyzed Reactions

    Science.gov (United States)

    Ault, Addison

    2011-01-01

    Rate equations for enzyme-catalyzed reactions are derived and presented in a way that makes it easier for the nonspecialist to see how the rate of an enzyme-catalyzed reaction depends upon kinetic constants and concentrations. This is done with distribution equations that show how the rate of the reaction depends upon the relative quantities of…

  8. Kinetic Studies on Enzyme-Catalyzed Reactions: Oxidation of Glucose, Decomposition of Hydrogen Peroxide and Their Combination

    Science.gov (United States)

    Tao, Zhimin; Raffel, Ryan A.; Souid, Abdul-Kader; Goodisman, Jerry

    2009-01-01

    The kinetics of the glucose oxidase-catalyzed reaction of glucose with O2, which produces gluconic acid and hydrogen peroxide, and the catalase-assisted breakdown of hydrogen peroxide to generate oxygen, have been measured via the rate of O2 depletion or production. The O2 concentrations in air-saturated phosphate-buffered salt solutions were monitored by measuring the decay of phosphorescence from a Pd phosphor in solution; the decay rate was obtained by fitting the tail of the phosphorescence intensity profile to an exponential. For glucose oxidation in the presence of glucose oxidase, the rate constant determined for the rate-limiting step was k = (3.0 ± 0.7) ×104 M−1s−1 at 37°C. For catalase-catalyzed H2O2 breakdown, the reaction order in [H2O2] was somewhat greater than unity at 37°C and well above unity at 25°C, suggesting different temperature dependences of the rate constants for various steps in the reaction. The two reactions were combined in a single experiment: addition of glucose oxidase to glucose-rich cell-free media caused a rapid drop in [O2], and subsequent addition of catalase caused [O2] to rise and then decrease to zero. The best fit of [O2] to a kinetic model is obtained with the rate constants for glucose oxidation and peroxide decomposition equal to 0.116 s−1 and 0.090 s−1 respectively. Cellular respiration in the presence of glucose was found to be three times as rapid as that in glucose-deprived cells. Added NaCN inhibited O2 consumption completely, confirming that oxidation occurred in the cellular mitochondrial respiratory chain. PMID:19348778

  9. Thermodynamics of Enzyme-Catalyzed Reactions Database

    Science.gov (United States)

    SRD 74 Thermodynamics of Enzyme-Catalyzed Reactions Database (Web, free access)   The Thermodynamics of Enzyme-Catalyzed Reactions Database contains thermodynamic data on enzyme-catalyzed reactions that have been recently published in the Journal of Physical and Chemical Reference Data (JPCRD). For each reaction the following information is provided: the reference for the data, the reaction studied, the name of the enzyme used and its Enzyme Commission number, the method of measurement, the data and an evaluation thereof.

  10. Mechanism and activation for allosteric adenosine 5'-monophosphate nucleosidase. Kinetic alpha-deuterium isotope effects for the enzyme-catalyzed hydrolysis of adenosine 5'-monophosphate and nicotinamide mononucleotide

    International Nuclear Information System (INIS)

    Skoog, M.T.

    1986-01-01

    The kinetic alpha-deuterium isotope effect on Vmax/Km for hydrolysis of NMN catalyzed by AMP nucleosidase at saturating concentrations of the allosteric activator MgATP2- is kH/kD = 1.155 +/- 0.012. This value is close to that reported previously for the nonenzymatic hydrolysis of nucleosides of related structure, suggesting that the full intrinsic isotope effect for enzymatic NMN hydrolysis is expressed under these conditions; that is, bond-changing reactions are largely or completely rate-determining and the transition state has marked oxocarbonium ion character. The kinetic alpha-deuterium isotope effect for this reaction is unchanged when deuterium oxide replaces water as solvent, corroborating this conclusion. Furthermore, this isotope effect is independent of pH over the range 6.95-9.25, for which values of Vmax/Km change by a factor of 90, suggesting that the isotope-sensitive and pH-sensitive steps for AMP-nucleosidase-catalyzed NMN hydrolysis are the same. Values of kH/kD for AMP nucleosidase-catalyzed hydrolysis of NMN decrease with decreasing saturation of enzyme with MgATP2- and reach unity when the enzyme is less than half-saturated with this activator. This requires that the rate-determining step changes from cleavage of the covalent C-N bond to one which is isotope-independent. In contrast to the case for NMN hydrolysis, AMP nucleosidase-catalyzed hydrolysis of AMP at saturating concentrations of MgATP2- shows a kinetic alpha-deuterium isotope effect of unity. Thus, covalent bond-changing reactions are largely or completely rate-determining for hydrolysis of a poor substrate, NMN, but make little or no contribution to rate-determining step for hydrolysis of a good substrate, AMP, by maximally activated enzyme. This behavior has several precedents

  11. Enzyme-Catalyzed Transetherification of Alkoxysilanes

    Directory of Open Access Journals (Sweden)

    Peter G. Taylor

    2013-01-01

    Full Text Available We report the first evidence of an enzyme-catalyzed transetherification of model alkoxysilanes. During an extensive enzymatic screening in the search for new biocatalysts for silicon-oxygen bond formation, we found that certain enzymes promoted the transetherification of alkoxysilanes when tert-butanol or 1-octanol were used as the reaction solvents.

  12. Stabilization of oil-in-water emulsions by enzyme catalyzed oxidative gelation of sugar beet pectin

    DEFF Research Database (Denmark)

    Abang Zaidel, Dayang Norulfairuz; Chronakis, Ioannis S.; Meyer, Anne S.

    2013-01-01

    Enzyme catalyzed oxidative cross-linking of feruloyl groups can promote gelation of sugar beet pectin (SBP). It is uncertain how the enzyme kinetics of this cross-linking reaction are affected in emulsion systems and whether the gelation affects emulsion stability. In this study, SBP (2.5% w...... larger average particle sizes than the emulsions in which the SBP was homogenized into the emulsion system during emulsion preparation (referred as Mix B). Mix B type emulsions were stable. Enzyme catalyzed oxidative gelation of SBP helped stabilize the emulsions in Mix A. The kinetics of the enzyme...... catalyzed oxidative gelation of SBP was evaluated by small angle oscillatory measurements for horseradish peroxidase (HRP) (EC 1.11.1.7) and laccase (EC 1.10.3.2) catalysis, respectively. HRP catalyzed gelation rates, determined from the slopes of the increase of elastic modulus (G0) with time, were higher...

  13. Stochastic simulation of enzyme-catalyzed reactions with disparate timescales.

    Science.gov (United States)

    Barik, Debashis; Paul, Mark R; Baumann, William T; Cao, Yang; Tyson, John J

    2008-10-01

    Many physiological characteristics of living cells are regulated by protein interaction networks. Because the total numbers of these protein species can be small, molecular noise can have significant effects on the dynamical properties of a regulatory network. Computing these stochastic effects is made difficult by the large timescale separations typical of protein interactions (e.g., complex formation may occur in fractions of a second, whereas catalytic conversions may take minutes). Exact stochastic simulation may be very inefficient under these circumstances, and methods for speeding up the simulation without sacrificing accuracy have been widely studied. We show that the "total quasi-steady-state approximation" for enzyme-catalyzed reactions provides a useful framework for efficient and accurate stochastic simulations. The method is applied to three examples: a simple enzyme-catalyzed reaction where enzyme and substrate have comparable abundances, a Goldbeter-Koshland switch, where a kinase and phosphatase regulate the phosphorylation state of a common substrate, and coupled Goldbeter-Koshland switches that exhibit bistability. Simulations based on the total quasi-steady-state approximation accurately capture the steady-state probability distributions of all components of these reaction networks. In many respects, the approximation also faithfully reproduces time-dependent aspects of the fluctuations. The method is accurate even under conditions of poor timescale separation.

  14. Enzyme catalyzed oxidative cross-linking of feruloylated pectic polysaccharides from sugar beet

    DEFF Research Database (Denmark)

    Abang Zaidel, Dayang Norulfairuz

    beet pulp as a potential starting material for production of pectin derived products which could help maintain the competitiveness of the sugar beet based industry. The overall objective of this study has been focusing on understanding the kinetics of enzyme catalyzed oxidative crosslinking......-linked by HRP catalysis in the presence of hydrogen peroxide (H2O2) to form ferulic acid dehydrodimers (diFAs). The composition of the substrate was analyzed by HPAEC, HPLC and MALDI-TOF, confirming the structural make up of the arabinan-oligosaccharide (Arabinose: 2.9- 3.4 mmol?g-1 DM; FA: 2.5-7.0 mg?g-1 DM......, identically composed, oil-in-water emulsion systems to study the effect of different methods of emulsion preparation on the emulsion stability in the presence of SBP and the kinetics of enzyme catalyzed oxidative gelation of SBP. The result shows that the different methods of emulsion preparation affect...

  15. Stereochemical course of enzyme-catalyzed aminopropyl transfer: spermidine synthase

    International Nuclear Information System (INIS)

    Kullberg, D.W.; Orr, G.R.; Coward, J.K.

    1986-01-01

    The R and S enantionmers of S-adenosyl-3-[ 2 H]3-(methylthio)-1-propylamine (decarboxylated S-adenosylmethionine), previously synthesized in this laboratory, were incubated with [1,4- 2 H 4 ]-putrescine in the presence of spermidine synthase from E. coli. The resulting chiral [ 2 H 5 ]spermidines were isolated and converted to their N 1 ,N 7 -dibocspermidine-N 4 -(1S,4R)-camphanamides. The derivatives were analyzed by 500 MHz 1 H-NMR and the configuration of the chiral center assigned by correlation with the spectra of synthetic chiral [ 2 H 3 ]dibocspermidine camphanamide standards. The enzyme-catalyzed aminopropyl transfer was shown to occur with net retention of configuration, indicative of a double-displacement mechanism. This result concurs with that of a previous steady-state kinetics study of spermidine synthase isolated from E. coli, but contradicts the single-displacement mechanism suggested by a stereochemical analysis of chiral spermidines biosynthesized in E. coli treated with chirally deuterated methionines. It also indicates that this aminopropyltransferase is mechanistically distinct from the methyltransferases, which have been shown to act via a single-displacement mechanism (net inversion at -CH 3 ) in all cases studied to date

  16. Biodiesel production by enzyme-catalyzed transesterification

    Directory of Open Access Journals (Sweden)

    Stamenković Olivera S.

    2005-01-01

    Full Text Available The principles and kinetics of biodiesel production from vegetable oils using lipase-catalyzed transesterification are reviewed. The most important operating factors affecting the reaction and the yield of alkyl esters, such as: the type and form of lipase, the type of alcohol, the presence of organic solvents, the content of water in the oil, temperature and the presence of glycerol are discussed. In order to estimate the prospects of lipase-catalyzed transesterification for industrial application, the factors which influence the kinetics of chemically-catalysed transesterification are also considered. The advantages of lipase-catalyzed transesterification compared to the chemically-catalysed reaction, are pointed out. The cost of down-processing and ecological problems are significantly reduced by applying lipases. It was also emphasized that lipase-catalysed transesterification should be greatly improved in order to make it commercially applicable. The further optimization of lipase-catalyzed transesterification should include studies on the development of new reactor systems with immobilized biocatalysts and the addition of alcohol in several portions, and the use of extra cellular lipases tolerant to organic solvents, intracellular lipases (i.e. whole microbial cells and genetically-modified microorganisms ("intelligent" yeasts.

  17. On the Temperature Dependence of Enzyme-Catalyzed Rates.

    Science.gov (United States)

    Arcus, Vickery L; Prentice, Erica J; Hobbs, Joanne K; Mulholland, Adrian J; Van der Kamp, Marc W; Pudney, Christopher R; Parker, Emily J; Schipper, Louis A

    2016-03-29

    One of the critical variables that determine the rate of any reaction is temperature. For biological systems, the effects of temperature are convoluted with myriad (and often opposing) contributions from enzyme catalysis, protein stability, and temperature-dependent regulation, for example. We have coined the phrase "macromolecular rate theory (MMRT)" to describe the temperature dependence of enzyme-catalyzed rates independent of stability or regulatory processes. Central to MMRT is the observation that enzyme-catalyzed reactions occur with significant values of ΔCp(‡) that are in general negative. That is, the heat capacity (Cp) for the enzyme-substrate complex is generally larger than the Cp for the enzyme-transition state complex. Consistent with a classical description of enzyme catalysis, a negative value for ΔCp(‡) is the result of the enzyme binding relatively weakly to the substrate and very tightly to the transition state. This observation of negative ΔCp(‡) has important implications for the temperature dependence of enzyme-catalyzed rates. Here, we lay out the fundamentals of MMRT. We present a number of hypotheses that arise directly from MMRT including a theoretical justification for the large size of enzymes and the basis for their optimum temperatures. We rationalize the behavior of psychrophilic enzymes and describe a "psychrophilic trap" which places limits on the evolution of enzymes in low temperature environments. One of the defining characteristics of biology is catalysis of chemical reactions by enzymes, and enzymes drive much of metabolism. Therefore, we also expect to see characteristics of MMRT at the level of cells, whole organisms, and even ecosystems.

  18. Possibilities and scope of the double isotope effect method in the elucidation of mechanisms of enzyme catalyzed reactions

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, H L; Medina, R [Technische Univ. Muenchen, Freising (Germany, F.R.). Lehrstuhl fuer Allgemeine Chemie und Biochemie

    1991-01-01

    Kinetic isotope effects on enzyme catalyzed reactions are indicative for the first irreversible in a sequence of individual steps. Hints on the relative velocities of other steps can only be obtained from the partitioning factor R and its dependence on external reaction conditions. In general, the experimental data needed are obtained from isotope abundance measurements in a defined position of the substrate or product as a function of turnover. This method does not reveal events dealing with neighbour atoms or preceding the main isotope sensitive step. In the method presented here, the analytical measurement is extended to the second atom involved in a bond fission of formation (Double Isotope Effect Method). It is shown that the additional results obtained support the identification of the main isotopically sensitive step and its relative contribution to the overall reaction rate, the identification of other kinetically significant steps and the differentiation between stepwise and concerted reaction mechanisms. The method and its advantages are demonstrated on reactions comprising C-N-bond splitting (urease and arginase reaction), C-C-bound fission (reactions catalyzed by pyruvate-dehydrogenase, pyruvate-formiate-lyase and lactate-oxidase), C-O-bound formation (ribulose-bisphosphate-oxygenase reaction), and N-O-bond fission (nitrate- and nitrite-reductase reactions). (orig.).

  19. Enzyme-Catalyzed Modifications of Polysaccharides and Poly(ethylene glycol

    Directory of Open Access Journals (Sweden)

    H. N. Cheng

    2012-06-01

    Full Text Available Polysaccharides are used extensively in various industrial applications, such as food, adhesives, coatings, construction, paper, pharmaceuticals, and personal care. Many polysaccharide structures need to be modified in order to improve their end-use properties; this is mostly done through chemical reactions. In the past 20 years many enzyme-catalyzed modifications have been developed to supplement chemical derivatization methods. Typical reactions include enzymatic oxidation, ester formation, amidation, glycosylation, and molecular weight reduction. These reactions are reviewed in this paper, with emphasis placed on the work done by the authors. The polymers covered in this review include cellulosic derivatives, starch, guar, pectin, and poly(ethylene glycol.

  20. Kinetics from Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Stelzl, Lukas S; Hummer, Gerhard

    2017-08-08

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

  1. 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

  2. Stereo-specificity for pro-(R) hydrogen of NAD(P)H during enzyme-catalyzed hydride transfer to CL-20

    International Nuclear Information System (INIS)

    Bhushan, Bharat; Halasz, Annamaria; Hawari, Jalal

    2005-01-01

    A dehydrogenase from Clostridium sp. EDB2 and a diaphorase from Clostridium kluyveri were reacted with CL-20 to gain insights into the enzyme-catalyzed hydride transfer to CL-20, and the enzyme's stereo-specificity for either pro-R or pro-S hydrogens of NAD(P)H. Both enzymes biotransformed CL-20 at rates of 18.5 and 24 nmol/h/mg protein, using NADH and NADPH as hydride-source, respectively, to produce a N-denitrohydrogenated product with a molecular weight of 393 Da. In enzyme kinetics studies using reduced deuterated pyridine nucleotides, we found a kinetic deuterium isotopic effect of 2-fold on CL-20 biotransformation rate using dehydrogenase enzyme against (R)NADD as a hydride-source compared to either (S)NADD or NADH. Whereas, in case of diaphorase, the kinetic deuterium isotopic effect of about 1.5-fold was observed on CL-20 biotransformation rate using (R)NADPD as hydride-source. In a comparative study with LC-MS, using deuterated and non-deuterated NAD(P)H, we found a positive mass-shift of 1 Da in the N-denitrohydrogenated product suggesting the involvement of a deuteride (D - ) transfer from NAD(P)D. The present study thus revealed that both dehydrogenase and diaphorase enzymes from the two Clostridium species catalyzed a hydride transfer to CL-20 and showed stereo-specificity for pro-R hydrogen of NAD(P)H

  3. An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation.

    Directory of Open Access Journals (Sweden)

    Ke Shi

    Full Text Available Hairpin telomeres of bacterial linear chromosomes are generated by a DNA cutting-rejoining enzyme protelomerase. Protelomerase resolves a concatenated dimer of chromosomes as the last step of chromosome replication, converting a palindromic DNA sequence at the junctions between chromosomes into covalently closed hairpins. The mechanism by which protelomerase transforms a duplex DNA substrate into the hairpin telomeres remains largely unknown. We report here a series of crystal structures of the protelomerase TelA bound to DNA that represent distinct stages along the reaction pathway. The structures suggest that TelA converts a linear duplex substrate into hairpin turns via a transient strand-refolding intermediate that involves DNA-base flipping and wobble base-pairs. The extremely compact di-nucleotide hairpin structure of the product is fully stabilized by TelA prior to strand ligation, which drives the reaction to completion. The enzyme-catalyzed, multistep strand refolding is a novel mechanism in DNA rearrangement reactions.

  4. Degradation of Perfluorooctanoic Acid and Perfluoroctane Sulfonate by Enzyme Catalyzed Oxidative Humification Reactions

    Science.gov (United States)

    Huang, Q.

    2016-12-01

    Poly- and perfluoroalkyl substances (PFASs) are alkyl based chemicals having multiple or all hydrogens replaced by fluorine atoms, and thus exhibit high thermal and chemical stability and other unusual characteristics. PFASs have been widely used in a wide variety of industrial and consumer products, and tend to be environmentally persistent. Perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) are two representative PFASs that have drawn particular attention because of their ubiquitous presence in the environment, resistance to degradation and toxicity to animals. This study examined the decomposition of PFOA and PFOS in enzyme catalyzed oxidative humification reactions (ECOHR), a class of reactions that are ubiquitous in the environment involved in natural organic humification. Reaction rates and influential factors were examined, and high-resolution mass spectrometry was used to identify possible products. Fluorides and partially fluorinated compounds were identified as likely products from PFOA and PFOS degradation, which were possibly formed via a combination of free radical decomposition, rearrangements and coupling processes. The findings suggest that PFOA and PFOS may be transformed during humification, and ECOHR can potentially be used for the remediation of these chemicals.

  5. Size exclusion chromatography for the quantitative profiling of the enzyme-catalyzed hydrolysis of xylo-oligosaccharides

    DEFF Research Database (Denmark)

    Rasmussen, Louise Enggaard; Meyer, Anne S.

    2010-01-01

    High-performance size exclusion chromatography (HPSEC) is a widely used method for the qualitative profiling of oligosaccharide mixtures, including, for example, enzymatic hydrolysates of plant biomass materials. A novel method employing HPSEC for the quantitative analytical profiling......, the method was designed using 0.1 M CH3COONa both in the mobile phase and as the sample solution matrix, after systematic evaluation of the influence of the mobile phase, including the type, ionic strength, and pH, on the refractive index detector response. A time study of the enzyme-catalyzed hydrolysis...

  6. Dynamics of asymmetric kinetic Ising systems revisited

    International Nuclear Information System (INIS)

    Huang, Haiping; Kabashima, Yoshiyuki

    2014-01-01

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

  7. 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.

  8. Red Seaweed Enzyme-Catalyzed Bromination of Bromophenol Red: An Inquiry-Based Kinetics Laboratory Experiment for Undergraduates

    Science.gov (United States)

    Jittam, Piyachat; Boonsiri, Patcharee; Promptmas, Chamras; Sriwattanarothai, Namkang; Archavarungson, Nattinee; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2009-01-01

    Haloperoxidase enzymes are of interest for basic and applied bioscientists because of their increasing importance in pharmaceutical industry and environmental cleanups. In a guided inquiry-based laboratory experiment for life-science, agricultural science, and health science undergraduates, the bromoperoxidase from a red seaweed was used to…

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

    DEFF Research Database (Denmark)

    Toxvaerd, Søren

    2001-01-01

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

  10. Rubber muscle actuation with pressurized CO2 from enzyme-catalyzed urea hydrolysis

    Science.gov (United States)

    Sutter, Thomas M.; Dickerson, Matthew B.; Creasy, Terry S.; Justice, Ryan S.

    2013-09-01

    A biologically inspired pneumatic pressure source was designed and sized to supply high pressure CO2(g) to power a rubber muscle actuator. The enzyme urease served to catalyze the hydrolysis of urea, producing CO2(g) that flowed into the actuator. The actuator’s power envelope was quantified by testing actuator response on a custom-built linear-motion rig. Reaction kinetics and available work density were determined by replacing the actuator with a double-action piston and measuring volumetric gas generation against a fixed pressure on the opposing piston. Under the conditions investigated, urease catalyzed the generation of up to 0.81 MPa (117 psi) of CO2(g) in the reactor headspace within 18 min, and the evolved gas produced a maximum work density of 0.65 J ml-1.

  11. Rubber muscle actuation with pressurized CO2 from enzyme-catalyzed urea hydrolysis

    International Nuclear Information System (INIS)

    Sutter, Thomas M; Dickerson, Matthew B; Creasy, Terry S; Justice, Ryan S

    2013-01-01

    A biologically inspired pneumatic pressure source was designed and sized to supply high pressure CO 2(g) to power a rubber muscle actuator. The enzyme urease served to catalyze the hydrolysis of urea, producing CO 2(g) that flowed into the actuator. The actuator’s power envelope was quantified by testing actuator response on a custom-built linear-motion rig. Reaction kinetics and available work density were determined by replacing the actuator with a double-action piston and measuring volumetric gas generation against a fixed pressure on the opposing piston. Under the conditions investigated, urease catalyzed the generation of up to 0.81 MPa (117 psi) of CO 2(g) in the reactor headspace within 18 min, and the evolved gas produced a maximum work density of 0.65 J ml −1 . (paper)

  12. Key factors of combustion from kinetics to gas dynamics

    CERN Document Server

    Rubtsov, Nikolai M

    2017-01-01

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

  13. Critical role of DNA intercalation in enzyme-catalyzed nucleotide flipping

    Science.gov (United States)

    Hendershot, Jenna M.; O'Brien, Patrick J.

    2014-01-01

    Nucleotide flipping is a common feature of DNA-modifying enzymes that allows access to target sites within duplex DNA. Structural studies have identified many intercalating amino acid side chains in a wide variety of enzymes, but the functional contribution of these intercalating residues is poorly understood. We used site-directed mutagenesis and transient kinetic approaches to dissect the energetic contribution of intercalation for human alkyladenine DNA glycosylase, an enzyme that initiates repair of alkylation damage. When AAG flips out a damaged nucleotide, the void in the duplex is filled by a conserved tyrosine (Y162). We find that tyrosine intercalation confers 140-fold stabilization of the extrahelical specific recognition complex, and that Y162 functions as a plug to slow the rate of unflipping by 6000-fold relative to the Y162A mutant. Surprisingly, mutation to the smaller alanine side chain increases the rate of nucleotide flipping by 50-fold relative to the wild-type enzyme. This provides evidence against the popular model that DNA intercalation accelerates nucleotide flipping. In the case of AAG, DNA intercalation contributes to the specific binding of a damaged nucleotide, but this enhanced specificity comes at the cost of reduced speed of nucleotide flipping. PMID:25324304

  14. Long-term effect of medium-chain triglyceride on hepatic enzymes catalyzing lipogenesis and cholesterogenesis in rats

    International Nuclear Information System (INIS)

    Takase, Sachiko; Morimoto, Ayami; Nakanishi, Mayumi; Muto, Yasutoshi.

    1977-01-01

    This study was conducted to investigate the long-term effect of dietary medium-chain triglyceride (MCT) as compared with that of corn oil feeding on lipid metabolism in rats. Both serum cholesterol and triglyceride levels in MCT-fed rats showed significant decrease during the experimental period of eight weeks, although liver cholesterol and triglyceride contents were not distinguishable between the two groups. Significant elevation of the activity of lipogenic enzymes, such as fatty acid synthetase (FAS) and malic enzyme (ME) of the liver, was observed in MCT-fed rats without any fat accumulation of the liver (fatty liver). The increase of lipogenic enzyme activity was accompanied by a significant reduction of essential fatty acids (EFA) such as 18:2 (ωsigma) and 20:4 (ωsigma) in total liver lipid. In contrast, hepatic β-hydroxy-β-methylglutaryl CoA(HMG-CoA) reductase activity was significantly decreased in MCT-fed rats, that would play an important role in achieving hypocholesterolemia. From these results obtained in a long-term experiment, it is concluded that exogenous MCT depresses the key enzyme catalyzing cholesterol synthesis with a concomitant elevation of lipogenic enzyme activity in the rat liver. (auth.)

  15. Advanced Low Energy Enzyme Catalyzed Solvent for CO2 Capture

    Energy Technology Data Exchange (ETDEWEB)

    Zaks, Alex [Akermin Inc., St. Louis, MO (United States); Reardon, John [Akermin Inc., St. Louis, MO (United States)

    2013-09-30

    A proof-of-concept biocatalyst enhanced solvent process was developed and demonstrated in an integrated bench-scale system using coal post combustion flue gas. The biocatalyst was deployed as a coating on M500X structured packing. Rate enhancement was evaluated using a non-volatile and non-toxic 20 wt% potassium carbonate solution. Greater than 500-fold volumetric scale-up from laboratory to bench scale was demonstrated in this project. Key technical achievements included: 10-fold mass transfer enhancement demonstrated in laboratory testing relative to blank potassium carbonate at 45°C; ~ 7-fold enhancement over blank in bench-scale field testing at National Carbon Capture Center; aerosol emissions were below detection limits (< 0.8 ppm); 90% capture was demonstrated at ~19.5 Nm3/hr (dry basis); and ~ 80% CO2 capture was demonstrated at ~ 30 Nm3/hr (dry basis) for more than 2800-hrs on flue gas with minimal detectible decline in activity. The regeneration energy requirement was 3.5 GJ/t CO2 for this solvent, which was below the target of <2.1 GJ/t CO2. Bench unit testing revealed kinetic limitations in the un-catalyzed stripper at around 85°C, but process modeling based on bench unit data showed that equivalent work of less than 300 kWh/t CO2 including all CO2 compression can be achieved at lower temperature stripping conditions. Cost analysis showed that 20% potassium carbonate in a basic solvent flow sheet with biocatalyst coated packing has economic performance comparable to the reference NETL Case-12, 30% MEA. A detailed techno-economic analysis indicated that addition of catalyst in the stripper could reduce the cost of capture by ~6% and cost of avoided CO2 by ~10% below reference NETL Case-12. Based on these results, a directional plan was identified to reduce the cost of CO2 capture in future work.

  16. 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.

  17. Kinetic analysis of dynamic PET data

    International Nuclear Information System (INIS)

    Knittel, B.

    1983-12-01

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

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

    African Journals Online (AJOL)

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

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

    Science.gov (United States)

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

    2018-05-02

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

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

    DEFF Research Database (Denmark)

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

    2001-01-01

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

  1. Fractional neutron point kinetics equations for nuclear reactor dynamics

    International Nuclear Information System (INIS)

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

    2011-01-01

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

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

    DEFF Research Database (Denmark)

    Lin, Fengxiang; Zhang, Yubin; Pantleon, Wolfgang

    2012-01-01

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

  3. Inflationary dynamics of kinetically-coupled gauge fields

    DEFF Research Database (Denmark)

    Ferreira, Ricardo J. Z.; Ganc, Jonathan

    2015-01-01

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

  4. 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.

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

    International Nuclear Information System (INIS)

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

    1999-01-01

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

  6. 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.

  7. Mesoscopic dynamics of diffusion-influenced enzyme kinetics.

    Science.gov (United States)

    Chen, Jiang-Xing; Kapral, Raymond

    2011-01-28

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

  8. Mesoscopic dynamics of diffusion-influenced enzyme kinetics

    Science.gov (United States)

    Chen, Jiang-Xing; Kapral, Raymond

    2011-01-01

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

  9. Enzyme-catalyzed degradation of biodegradable polymers derived from trimethylene carbonate and glycolide by lipases from Candida antarctica and Hog pancreas.

    Science.gov (United States)

    Liu, Feng; Yang, Jian; Fan, Zhongyong; Li, Suming; Kasperczyk, Janusz; Dobrzynski, Piotr

    2012-01-01

    Enzyme-catalyzed degradation of poly(trimethylene carbonate) homo-polymer (PTMC) and poly(trimethylene carbonate-co-glycolide) co-polymer (PTGA) was investigated in the presence of lipases from Candida antarctica and Hog pancreas. Degradation was monitored by gravimetry, size-exclusion chromatography (SEC), nuclear magnetic resonance (NMR), tensiometry and environmental scanning electron microscopy (ESEM). PTMC can be rapidly degraded by Candida antarctica lipase with 98% mass loss after 9 days, while degradation by Hog pancreas lipase leads to 27% mass loss. Introduction of 16% glycolide units in PTMC chains strongly affects the enzymatic degradation. Hog pancreas lipase becomes more effective to PTGA co-polymer with a mass loss of 58% after 9 days, while Candida antarctica lipase seems not able to degrade PTGA. Bimodal molecular weight distributions are observed during enzymatic degradation of both PTMC and PTGA, which can be assigned to the fact that the surface is largely degraded while the internal part remains intact. The composition of the PTGA co-polymer remains constant, and ESEM shows that the polymers are homogeneously eroded during enzymatic degradation. Contact angle measurements confirm the enzymatic degradation mechanism, i.e., enzyme adsorption on the polymer surface followed by enzyme-catalyzed chain cleavage.

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

    International Nuclear Information System (INIS)

    Pazsit, Imre

    2013-01-01

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

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  12. Fouling Kinetics and Associated Dynamics of Structural Modifications

    DEFF Research Database (Denmark)

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

    1998-01-01

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

  13. Relativistic nuclear fluid dynamics and VUU kinetic theory

    International Nuclear Information System (INIS)

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

    1987-01-01

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

  14. pH-sensitive pHluorins as a molecular sensor for in situ monitoring of enzyme-catalyzed prodrug activation.

    Science.gov (United States)

    Liu, Hui; Cao, Xiaodan; Wang, Ping; Ma, Xingyuan

    2017-07-01

    This work examines the feasibility of using a pH-sensitive fluorescent protein as a molecular reporter for enzyme-catalyzed prodrug activation reaction. Specifically, a ratiometric pHluorins was examined for detection of the activity of horseradish peroxidase (HRP) for the activation of indole-3-acetic acid. The pHluorins and HRP were conjugated chemically, forming a biocatalyst with a self-reporting function. Results showed that the characteristic fluorescence intensity ratio of the conjugate shifted from 1.47 to 1.40 corresponding to the progress of the prodrug activation reaction. The effectiveness of applying the conjugate for inhibition of the growth of Bcap-37 cells was also demonstrated simultaneously with reaction monitoring. The results reveal a very promising approach to realizing in situ monitoring of enzyme activities based on pH shifting for enzyme-based prodrug therapy applications. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

  15. Spectroscopic Analyses of the Biofuels-Critical Phytochemical Coniferyl Alcohol and Its Enzyme-Catalyzed Oxidation Products

    Energy Technology Data Exchange (ETDEWEB)

    Achyuthan, Komandoor; Adams, Paul; Simmons, Blake; Singh, Anup

    2011-07-13

    Lignin composition (monolignol types of coniferyl, sinapyl or p-coumaryl alcohol) is causally related to biomass recalcitrance. We describe multiwavelength (220, 228, 240, 250, 260, 290, 295, 300, 310 or 320 nm) absorption spectroscopy of coniferyl alcohol and its laccase- or peroxidase-catalyzed products during real time kinetic, pseudo-kinetic and endpoint analyses, in optical turn on or turn off modes, under acidic or basic conditions. Reactions in microwell plates and 100 mu L volumes demonstrated assay miniaturization and high throughput screening capabilities. Bathochromic and hypsochromic shifts along with hyperchromicity or hypochromicity accompanied enzymatic oxidations by laccase or peroxidase. The limits of detection and quantitation of coniferyl alcohol averaged 2.4 and 7.1 mu M respectively, with linear trend lines over 3 to 4 orders of magnitude. Coniferyl alcohol oxidation was evident within 10 minutes or with 0.01 mu g/mL laccase and 2 minutes or 0.001 mu g/mL peroxidase. Detection limit improved to 1.0 mu M coniferyl alcohol with Km of 978.7 +/- 150.7 mu M when examined at 260 nm following 30 minutes oxidation with 1.0 mu g/mL laccase. Our assays utilized the intrinsic spectroscopic properties of coniferyl alcohol or its oxidation products for enabling detection, without requiring chemical synthesis or modification of the substrate or product(s). These studies facilitate lignin compositional analyses and augment pretreatment strategies for reducing biomass recalcitrance.

  16. Thermodynamic Activity-Based Progress Curve Analysis in Enzyme Kinetics.

    Science.gov (United States)

    Pleiss, Jürgen

    2018-03-01

    Macrokinetic Michaelis-Menten models based on thermodynamic activity provide insights into enzyme kinetics because they separate substrate-enzyme from substrate-solvent interactions. Kinetic parameters are estimated from experimental progress curves of enzyme-catalyzed reactions. Three pitfalls are discussed: deviations between thermodynamic and concentration-based models, product effects on the substrate activity coefficient, and product inhibition. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Kinetic studies of ICF target dynamics with ePLAS

    Science.gov (United States)

    Mason, R. J.

    2016-10-01

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

  18. Kinetic and dynamic Delaunay tetrahedralizations in three dimensions

    Science.gov (United States)

    Schaller, Gernot; Meyer-Hermann, Michael

    2004-09-01

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

  19. Kinetic properties and inhibition of Trypanosoma cruzi 3-hydroxy-3-methylglutaryl CoA reductase

    DEFF Research Database (Denmark)

    Hurtado-Guerrrero, Ramón; Pena Diaz, Javier; Montalvetti, Andrea

    2002-01-01

    A detailed kinetic analysis of the recombinant soluble enzyme 3-hydroxy-3-methylglutaryl CoA reductase (HMGR) from Trypanosoma cruzi has been performed. The enzyme catalyzes the normal anabolic reaction and the reductant is NADPH. It also catalyzes the oxidation of mevalonate but at a lower propo...

  20. Bisubstrate Kinetics of Glutathione S-Transferase: A Colorimetric Experiment for the Introductory Biochemistry Laboratory

    Science.gov (United States)

    Stefanidis, Lazaros; Scinto, Krystal V.; Strada, Monica I.; Alper, Benjamin J.

    2018-01-01

    Most biochemical transformations involve more than one substrate. Bisubstrate enzymes catalyze multiple chemical reactions in living systems and include members of the transferase, oxidoreductase, and ligase enzyme classes. Working knowledge of bisubstrate enzyme kinetic models is thus of clear importance to the practicing biochemist. However,…

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

    NARCIS (Netherlands)

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

    2001-01-01

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

  2. Controlled enzyme catalyzed heteropolysaccharide degradation

    DEFF Research Database (Denmark)

    Rasmussen, Louise Enggaard

    for using high-performance size exclusion chromatography (HPSEC) as a quantitative method to assess xylo-oligosaccharide profiles was examined. HPSEC is a widely used method for the qualitative profiling of oligosaccharide mixtures. A novel method employing HPSEC for the quantitative analytical profiling......-performance size exclusion chromatography profiles, the method was designed using 0.1 M CH3COONa in both the mobile phase and as the sample solution. This was based on the systematic evaluation of the influence of the mobile phase, including the type, ionic strength and pH, on the refractive index detector...... larger amount of RGI was present in the obtained samples together with phosphate. Therefore, further purification has to be made in order to obtain GXOS....

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

    Directory of Open Access Journals (Sweden)

    Bin Du

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

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

    Science.gov (United States)

    Easter, Quinn T; Blum, Suzanne A

    2018-02-05

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

  5. 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.

  6. Dynamic range broadening for photomultipliers in kinetic spectrophotometry

    International Nuclear Information System (INIS)

    Rumas, V.K.

    1983-01-01

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

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

    DEFF Research Database (Denmark)

    Flyvbjerg, H.; Jobs, E.

    1997-01-01

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

  8. 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.

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

    Science.gov (United States)

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

    2011-06-01

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

  10. Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent

    Czech Academy of Sciences Publication Activity Database

    Duboué-Dijon, Elise; Pluhařová, E.; Domin, D.; Sen, K.; Fogarty, A. C.; Chéron, N.; Laage, D.

    2017-01-01

    Roč. 121, č. 29 (2017), s. 7027-7041 ISSN 1520-6106 Institutional support: RVO:61388963 Keywords : free energy calculations * purine nucleoside phosphorylase * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 3.177, year: 2016

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-08-28

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

  13. 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.

  14. Kinetic theory for electron dynamics near a positive ion

    International Nuclear Information System (INIS)

    Wrighton, Jeffrey M; Dufty, James W

    2008-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Pan Li

    2016-10-01

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

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

    Science.gov (United States)

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

    2018-06-13

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

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

    International Nuclear Information System (INIS)

    Shadbahr, Jalil; Khan, Faisal; Zhang, Yan

    2017-01-01

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

  18. 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.

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

    Science.gov (United States)

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

    2015-01-01

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

  20. 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.

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

    NARCIS (Netherlands)

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

    2008-01-01

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

  2. 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.

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

    International Nuclear Information System (INIS)

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

    1995-01-01

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

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

    NARCIS (Netherlands)

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

    2017-01-01

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

  5. Mathematical treatment of isotopologue and isotopomer speciation and fractionation in biochemical kinetics

    Science.gov (United States)

    Maggi, Federico; Riley, William J.

    2010-03-01

    We present a mathematical treatment of the kinetic equations that describe isotopologue and isotopomer speciation and fractionation during enzyme-catalyzed biochemical reactions. These equations, presented here with the name GEBIK (general equations for biochemical isotope kinetics) and GEBIF (general equations for biochemical isotope fractionation), take into account microbial biomass and enzyme dynamics, reaction stoichiometry, isotope substitution number, and isotope location within each isotopologue and isotopomer. In addition to solving the complete GEBIK and GEBIF, we also present and discuss two approximations to the full solutions under the assumption of biomass-free and enzyme steady-state, and under the quasi-steady-state assumption as applied to the complexation rate. The complete and approximate approaches are applied to observations of biological denitrification in soils. Our analysis highlights that the full GEBIK and GEBIF provide a more accurate description of concentrations and isotopic compositions of substrates and products throughout the reaction than do the approximate forms. We demonstrate that the isotopic effects of a biochemical reaction depend, in the most general case, on substrate and complex concentrations and, therefore, the fractionation factor is a function of time. We also demonstrate that inverse isotopic effects can occur for values of the fractionation factor smaller than 1, and that reactions that do not discriminate isotopes do not necessarily imply a fractionation factor equal to 1.

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

    Science.gov (United States)

    Carlsson, Philip T. M.; Zeuch, Thomas

    2018-03-01

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

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

    Science.gov (United States)

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

    2013-03-15

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

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

    International Nuclear Information System (INIS)

    Arimitsu, Toshihico

    1988-01-01

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

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

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

    International Nuclear Information System (INIS)

    Lagana, A.

    1989-01-01

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

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

    International Nuclear Information System (INIS)

    Kolobov, Vladimir; Arslanbekov, Robert; Frolova, Anna

    2014-01-01

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

  12. 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.

  13. Mushroom Tyrosinase: A Model System to Combine Experimental Investigation of Enzyme-Catalyzed Reactions, Data Handling Using R, and Enzyme-Inhibitor Structural Studies

    Science.gov (United States)

    Nairn, Robert; Cresswell, Will; Nairn, Jacqueline

    2015-01-01

    The activity of mushroom tyrosinase can be measured by monitoring the conversion of phenolic compounds into quinone derivatives using spectrophotometry. This article describes a series of experiments which characterize the functional properties of tyrosinase, the analysis of the resulting data using R to determine the kinetic parameters, and the…

  14. 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.

  15. 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

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

    Directory of Open Access Journals (Sweden)

    Joseph A. Wayman

    2015-03-01

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

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

    Science.gov (United States)

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

    2014-01-15

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

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

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

    Science.gov (United States)

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

    2017-03-07

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-12-15

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    International Nuclear Information System (INIS)

    Saha Ray, S.

    2012-01-01

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

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

    International Nuclear Information System (INIS)

    Costa Oliveira, Jaime M.

    1969-03-01

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

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

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

    International Nuclear Information System (INIS)

    Morita, Akihiro; Garrett, Bruce C

    2008-01-01

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

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

    Science.gov (United States)

    Minier, Jean-Pierre; Profeta, Christophe

    2015-11-01

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

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

    Science.gov (United States)

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

    2018-03-01

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

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

    Science.gov (United States)

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

    2018-06-01

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

  9. 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.

  10. 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.

  11. 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.

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

    International Nuclear Information System (INIS)

    Kelton, K F

    2017-01-01

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

  13. 3.5D dynamic PET image reconstruction incorporating kinetics-based clusters

    International Nuclear Information System (INIS)

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

    2012-01-01

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2014-08-07

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2009-08-01

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

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

    Science.gov (United States)

    Bianca, Carlo; Mogno, Caterina

    2018-06-01

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  1. 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.

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

    Science.gov (United States)

    Zong, Diyuan; Yang, Zhen; Duan, Yuanyuan

    2017-10-01

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

  3. Atypical profiles and modulations of heme-enzymes catalyzed outcomes by low amounts of diverse additives suggest diffusible radicals' obligatory involvement in such redox reactions.

    Science.gov (United States)

    Manoj, Kelath Murali; Parashar, Abhinav; Venkatachalam, Avanthika; Goyal, Sahil; Satyalipsu; Singh, Preeti Gunjan; Gade, Sudeep K; Periyasami, Kalaiselvi; Jacob, Reeba Susan; Sardar, Debosmita; Singh, Shanikant; Kumar, Rajan; Gideon, Daniel A

    2016-06-01

    Peroxidations mediated by heme-enzymes have been traditionally studied under a single-site (heme distal pocket), non-sequential (ping-pong), two-substrates binding scheme of Michaelis-Menten paradigm. We had reported unusual modulations of peroxidase and P450 reaction outcomes and explained it invoking diffusible reactive species [Manoj, 2006; Manoj et al., 2010; Andrew et al., 2011, Parashar et al., 2014 & Venkatachalam et al., 2016]. A systematic investigation of specific product formation rates was undertaken to probe the hypothesis that involvement of diffusible reactive species could explain undefined substrate specificities and maverick modulations (sponsored by additives) of heme-enzymes. When the rate of specific product formation was studied as a function of reactants' concentration or environmental conditions, we noted marked deviations from normal profiles. We report that heme-enzyme mediated peroxidations of various substrates are inhibited (or activated) by sub-equivalent concentrations of diverse redox-active additives and this is owing to multiple redox equilibriums in the milieu. At low enzyme and peroxide concentrations, the enzyme is seen to recycle via a one-electron (oxidase) cycle, which does not require the substrate to access the heme centre. Schemes are provided that explain the complex mechanistic cycle, kinetics & stoichiometry. It is not obligatory for an inhibitor or substrate to interact with the heme centre for influencing overall catalysis. Roles of diffusible reactive species explain catalytic outcomes at low enzyme and reactant concentrations. The current work highlights the scope/importance of redox enzyme reactions that could occur "out of the active site" in biological or in situ systems. Copyright © 2016 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

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

    Science.gov (United States)

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

    2018-04-01

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

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

    International Nuclear Information System (INIS)

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

    2003-01-01

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

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

    Science.gov (United States)

    Cai, Kaimin; Ying, Hanze; Cheng, Jianjun

    2018-04-06

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

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

    International Nuclear Information System (INIS)

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

    1997-01-01

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

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

    International Nuclear Information System (INIS)

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

    1979-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Aaron M Streets

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

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Fabrizio Marinelli

    2009-08-01

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

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

    Science.gov (United States)

    Zhao, Lei; Cheng, Jiangtao

    2017-09-07

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

  14. 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

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

    Directory of Open Access Journals (Sweden)

    K. Kim

    2014-07-01

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

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

    Science.gov (United States)

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

    2014-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-08-15

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

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

    Science.gov (United States)

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

    2016-10-14

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Yu Lin; Xueyi Wang; Liu Chen; Zhihong Lin

    2009-08-11

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

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

    International Nuclear Information System (INIS)

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

    2009-01-01

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

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

    International Nuclear Information System (INIS)

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

    1989-01-01

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

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

    Science.gov (United States)

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

    2018-03-01

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

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

    Science.gov (United States)

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

    2018-07-01

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

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

    Science.gov (United States)

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

    2007-11-01

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

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

    Science.gov (United States)

    Wang, Meng; Yuan, Wenqiao

    2016-01-01

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

  6. 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.

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

    Science.gov (United States)

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

    2014-07-04

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

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  9. 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.

  10. 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.

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

    Science.gov (United States)

    Thalén, Lisa K; Bäckvall, Jan-E

    2010-09-13

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

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

    Science.gov (United States)

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

    2014-05-02

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

  13. 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

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

    Science.gov (United States)

    Vavilin, V A; Rytov, S V

    2015-09-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  16. Method for predicting enzyme-catalyzed reactions

    Science.gov (United States)

    Hlavacek, William S.; Unkefer, Clifford J.; Mu, Fangping; Unkefer, Pat J.

    2013-03-19

    The reactivity of given metabolites is assessed using selected empirical atomic properties in the potential reaction center. Metabolic reactions are represented as biotransformation rules. These rules are generalized from the patterns in reactions. These patterns are not unique to reactants but are widely distributed among metabolites. Using a metabolite database, potential substructures are identified in the metabolites for a given biotransformation. These substructures are divided into reactants or non-reactants, depending on whether they participate in the biotransformation or not. Each potential substructure is then modeled using descriptors of the topological and electronic properties of atoms in the potential reaction center; molecular properties can also be used. A Support Vector Machine (SVM) or classifier is trained to classify a potential reactant as a true or false reactant using these properties.

  17. ENZYME-CATALYZED MUTATION IN BREAST CANCER

    Science.gov (United States)

    2015-10-01

    cells overexpressing A3B or A3B-E255Q in the ab- sence or presence of tamoxifen treatment. The graph reports tumor volumes measured weekly (mean + SEM...advances.sciencem ag.org/ D ow nloaded from on the pLenti4TO backbone (Life Technologies). Overlapping PCR was used to place a sense-encoded intron between

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

    Science.gov (United States)

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

    2013-08-01

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

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

    Science.gov (United States)

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

    2018-05-30

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

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

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

    International Nuclear Information System (INIS)

    Karwan, Khamphee

    2011-01-01

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

  3. 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.

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

    Science.gov (United States)

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

    1984-01-01

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

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

    Science.gov (United States)

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

    2017-08-01

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

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

  7. 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.

  8. 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

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

    Science.gov (United States)

    Twellmann, Thorsten; ter Haar Romeny, Bart

    2008-03-01

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

  10. 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.

  11. 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

  12. 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

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

    Science.gov (United States)

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

    2018-03-01

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

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

    International Nuclear Information System (INIS)

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

    2017-01-01

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

  15. 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

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

    Directory of Open Access Journals (Sweden)

    A. C. Mathpati

    2018-03-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

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

    International Nuclear Information System (INIS)

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

    2005-01-01

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

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

    Science.gov (United States)

    2015-01-01

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

  20. 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.

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

    Science.gov (United States)

    Riabkov, Dmitri

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

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

    OpenAIRE

    Ishiyama, Tatsuya; Yano, Takeru; Fujikawa, Shigeo

    2004-01-01

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

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

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

    NARCIS (Netherlands)

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

    2015-01-01

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

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

    Science.gov (United States)

    Yen, Chi-Fu; Sivasankar, Sanjeevi

    2018-03-01

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

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

    KAUST Repository

    Tingas, Alexandros

    2017-10-13

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

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

    International Nuclear Information System (INIS)

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

    1995-01-01

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

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

    International Nuclear Information System (INIS)

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

    2017-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-07-01

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

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

    DEFF Research Database (Denmark)

    Lin, Fengxiang; Zhang, Yubin; Tao, Nairong

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Jacob U. Fluckiger

    2013-01-01

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

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

    Science.gov (United States)

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

    2011-06-09

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

  13. 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.

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-07-26

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

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

    International Nuclear Information System (INIS)

    Canko, Osman; Deviren, Bayram; Keskin, Mustafa

    2006-01-01

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

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-06-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-06-15

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

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

    International Nuclear Information System (INIS)

    Ertas, Mehmet; Canko, Osman; Keskin, Mustafa

    2008-01-01

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

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

    Science.gov (United States)

    Ertaş, Mehmet; Canko, Osman; Keskin, Mustafa

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

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

    DEFF Research Database (Denmark)

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

    1999-01-01

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

  3. 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

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

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

    KAUST Repository

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

    2016-01-01

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

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

    International Nuclear Information System (INIS)

    Zhao, Qingze; Purohit, Prashant K

    2014-01-01

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

  7. 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 ...

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

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

    Science.gov (United States)

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

    2016-07-01

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

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

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

    International Nuclear Information System (INIS)

    Schikorr, W.M.

    2001-01-01

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

  12. 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.

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

    DEFF Research Database (Denmark)

    Mouritsen, Ole G.; Praestgaard, Eigil

    1988-01-01

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

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

    Science.gov (United States)

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

    2017-05-01

    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.

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

    International Nuclear Information System (INIS)

    Ertaş, Mehmet; Keskin, Mustafa; Deviren, Bayram

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-04-15

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

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

    International Nuclear Information System (INIS)

    Ignaszewski, A.; Vaillant, D.; Sabatier, J.P.; Fernandez, Y.

    1975-01-01

    In heart cavity studies the simplicity and harmlessness nuclear imagery are great advantages, but it is necessary to improve on the data obtainable by this technique. The usual image is faulty, owing to the presence of a kinetic softness, and deficient because it fails to account for the mobility of the walls. An attempt was made to correct the kinetic softness on an image and to reconstitute the film of a heart cycle, an aim achieved by combining a computer with the camera. The examination conditions generally adopted include storage of all data and a reconstitution of the entire cycle is programmed taking a multiple time unit of 20ms; this supplies a sequence of images which when observed in succession resembles the heat contractility film [fr

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

    Science.gov (United States)

    2015-03-03

    based whole-cell models of E. coli [6]. Conversely , highly abstracted kinetic frameworks, such as the cybernetic framework, represented a paradigm shift...metabolic objective function has been the optimization of biomass formation [18], although other metabolic objectives have also been estimated [19...experimental data. Toward these questions, we explored five hypothetical cell-free networks. Each network shared the same enzymatic connectivity, but

  19. The onset of fluid-dynamical behavior in relativistic kinetic theory

    Science.gov (United States)

    Noronha, Jorge; Denicol, Gabriel S.

    2017-11-01

    In this proceedings we discuss recent findings regarding the large order behavior of the Chapman-Enskog expansion in relativistic kinetic theory. It is shown that this series in powers of the Knudsen number has zero radius of convergence in the case of a Bjorken expanding fluid described by the Boltzmann equation in the relaxation time approximation. This divergence stems from the presence of non-hydrodynamic modes, which give non-perturbative contributions to the Knudsen series.

  20. Opinion dynamics: kinetic modelling with mass media, application to the Scottish independence referendum

    OpenAIRE

    Boudin , Laurent; Salvarani , Francesco

    2016-01-01

    International audience; We consider a kinetic model describing some mechanisms of opinion formation in the framework of referendums, by allowing that the individuals, who can interact between themselves and modify their opinion by means of spontaneous self-thinking, are moreover under the influence of mass media. After proving the main properties of the model, such as existence of solutions and conservation properties, we study, at the numerical level, both the transient and the asymptotic re...

  1. Recent Insight into the Kinetic Mechanisms and Conformational Dynamics of Y-Family DNA Polymerases

    OpenAIRE

    Maxwell, Brian A.; Suo, Zucai

    2014-01-01

    The kinetic mechanisms by which DNA polymerases catalyze DNA replication and repair have long been areas of active research. Recently discovered Y-family DNA polymerases catalyze the bypass of damaged DNA bases that would otherwise block replicative DNA polymerases and stall replication forks. Unlike DNA polymerases from the five other families, the Y-family DNA polymerases have flexible, solvent-accessible active sites that are able to tolerate various types of damaged template bases and all...

  2. Dynamic hysteresis behaviors in the kinetic Ising system on triangular lattice

    Science.gov (United States)

    Kantar, Ersin; Ertaş, Mehmet

    2018-04-01

    We studied dynamic hysteresis behaviors of the spin-1 Blume-Capel (BC) model in a triangular lattice by means of the effective-field theory (EFT) with correlations and using Glauber-type stochastic dynamics. The effects of the exchange interaction (J), crystal field (D), temperature (T) and oscillating frequency (w) on the hysteresis behaviors of the BC model in a triangular lattice are investigated in detail. Results are compared with some other dynamic studies and quantitatively good agreement is found.

  3. Dosimetric and qualitative analysis of kinetic properties of millennium 80 multileaf collimator system for dynamic intensity modulated radiotherapy treatments

    Directory of Open Access Journals (Sweden)

    Bhardwaj Anup

    2007-01-01

    Full Text Available The aim of this paper is to analyze the positional accuracy, kinetic properties of the dynamic multileaf collimator (MLC and dosimetric evaluation of fractional dose delivery for the intensity modulated radiotherapy (IMRT for step and shoot and sliding window (dynamic techniques of Varian multileaf collimator millennium 80. Various quality assurance tests such as accuracy in leaf positioning and speed, stability of dynamic MLC output, inter and intra leaf transmission, dosimetric leaf separation and multiple carriage field verification were performed. Evaluation of standard field patterns as pyramid, peaks, wedge, chair, garden fence test, picket fence test and sweeping gap output was done. Patient dose quality assurance procedure consists of an absolute dose measurement for all fields at 5 cm depth on solid water phantom using 0.6cc water proof ion chamber and relative dose verification using Kodak EDR-2 films for all treatment fields along transverse and coronal direction using IMRT phantom. The relative dose verification was performed using Omni Pro IMRT film verification software. The tests performed showed acceptable results for commissioning the millennium 80 MLC and Clinac DHX for dynamic and step and shoot IMRT treatments.

  4. Brownian dynamics of aggregation kinetics of hard spheres with flexibele bounds

    NARCIS (Netherlands)

    Rzepiela, A.A.; Opheusden, van J.; Vliet, van T.

    2001-01-01

    Brownian dynamics (BD) simulations have been performed on the aggregation dynamics of colloidal particles within the context of a ball-and-string model. Particles are treated as hard spheres that can bind irreversibly through a string attached to their surface. The model is set up to mimic some

  5. Contrast kinetics of the malignant breast tumour - border versus centre enhancement on dynamic midfield MRI

    DEFF Research Database (Denmark)

    Marklund, M.; Torp-Pedersen, S.; Bentzon, N.

    2008-01-01

    receptor negative tumours. CONCLUSION: The border/centre enhancement difference in malignant breast tumours is easily visualized on midfield dynamic magnetic resonance mammography. The dynamic behaviour is significantly correlated to histological features and receptor status of the tumours Udgivelsesdato......PURPOSE: To quantify the border versus centre enhancement of malignant breast tumours on dynamic magnetic resonance mammography. MATERIALS AND METHODS: Fifty-two women diagnosed with primary breast cancer underwent dynamic magnetic resonance mammography (Omniscan 0.2 mmol/kg bodyweight......) on a midfield scanner (0.6 T), prior to surgery. The following five variables were recorded from the border and centre regions of the tumours: Early Enhancement, Time to Peak, Wash-in rate, Wash-out rate and Area under Curve. Information on histology type, oestrogen and progesterone receptor status...

  6. Photodissociation dynamics of formyl fluoride (HFCO) at 193 nm: Branching ratios and distributions of kinetic energy

    International Nuclear Information System (INIS)

    Lee, H.; Wu, C.-Y.; Yang, S.K.; Lee, Y.-P.

    2005-01-01

    Following photodissociation of formyl fluoride (HFCO) at 193 nm, we detected products with fragmentation translational spectroscopy utilizing a tunable vacuum ultraviolet beam from a synchrotron for ionization. Among three primary dissociation channels observed in this work, the F-elimination channel HFCO→HCO+F dominates, with a branching ratio ∼0.66 and an average release of kinetic energy ∼55 kJ mol -1 ; about 17% of HCO further decomposes to H+CO. The H-elimination channel HFCO→FCO+H has a branching ratio ∼0.28 and an average release of kinetic energy ∼99 kJ mol -1 ; about 21% of FCO further decomposes to F+CO. The F-elimination channel likely proceeds via the S 1 surface whereas the H-elimination channel proceeds via the T 1 surface; both channels exhibit moderate barriers for dissociation. The molecular HF-elimination channel HFCO→HF+CO, correlating with the ground electronic surface, has a branching ratio of only ∼0.06; the average translational release of 93 kJ mol -1 , ∼15% of available energy, implies that the fragments are highly internally excited. Detailed mechanisms of photodissociation are discussed

  7. Quantification of in vivo metabolic kinetics of hyperpolarized pyruvate in rat kidneys using dynamic 13C MRSI.

    Science.gov (United States)

    Xu, Tao; Mayer, Dirk; Gu, Meng; Yen, Yi-Fen; Josan, Sonal; Tropp, James; Pfefferbaum, Adolf; Hurd, Ralph; Spielman, Daniel

    2011-10-01

    With signal-to-noise ratio enhancements on the order of 10,000-fold, hyperpolarized MRSI of metabolically active substrates allows the study of both the injected substrate and downstream metabolic products in vivo. Although hyperpolarized [1-(13)C]pyruvate, in particular, has been used to demonstrate metabolic activities in various animal models, robust quantification and metabolic modeling remain important areas of investigation. Enzyme saturation effects are routinely seen with commonly used doses of hyperpolarized [1-(13)C]pyruvate; however, most metrics proposed to date, including metabolite ratios, time-to-peak of metabolic products and single exchange rate constants, fail to capture these saturation effects. In addition, the widely used small-flip-angle excitation approach does not correctly model the inflow of fresh downstream metabolites generated proximal to the target slice, which is often a significant factor in vivo. In this work, we developed an efficient quantification framework employing a spiral-based dynamic spectroscopic imaging approach. The approach overcomes the aforementioned limitations and demonstrates that the in vivo (13)C labeling of lactate and alanine after a bolus injection of [1-(13)C]pyruvate is well approximated by saturatable kinetics, which can be mathematically modeled using a Michaelis-Menten-like formulation, with the resulting estimated apparent maximal reaction velocity V(max) and apparent Michaelis constant K(M) being unbiased with respect to critical experimental parameters, including the substrate dose, bolus shape and duration. Although the proposed saturatable model has a similar mathematical formulation to the original Michaelis-Menten kinetics, it is conceptually different. In this study, we focus on the (13)C labeling of lactate and alanine and do not differentiate the labeling mechanism (net flux or isotopic exchange) or the respective contribution of various factors (organ perfusion rate, substrate transport

  8. Adsorption kinetics and dynamics of small organic molecules on a silica wafer: Butane, pentane, nonane, thiophene, and methanol adsorption on SiO2/Si(1 1 1)

    International Nuclear Information System (INIS)

    Funk, S.; Goering, J.; Burghaus, U.

    2008-01-01

    The adsorption kinetics (by thermal desorption spectroscopy) and adsorption dynamics (by molecular beam scattering) have been determined for a number of alkanes, methanol, thiophene, and water on a silica wafer-SiO 2 /Si(1 1 1). No indications for bond activation were present, i.e., all probe molecules adsorb molecularly obeying 1st order kinetics. The coverage-dependent heat of adsorption has been determined accordingly. The adsorption dynamics are precursor-mediated with Kisliuk-like shapes of the adsorption probabilities at low impact energies and adsorbate-assisted adsorption at large impact energies

  9. 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.

  10. Comparison of quasi-static and dynamic squats: a three-dimensional kinematic, kinetic and electromyographic study of the lower limbs.

    Science.gov (United States)

    Clément, Julien; Hagemeister, Nicola; Aissaoui, Rachid; de Guise, Jacques A

    2014-01-01

    Numerous studies have described 3D kinematics, 3D kinetics and electromyography (EMG) of the lower limbs during quasi-static or dynamic squatting activities. One study compared these two squatting conditions but only at low speed on healthy subjects, and provided no information on kinetics and EMG of the lower limbs. The purpose of the present study was to contrast simultaneous recordings of 3D kinematics, 3D kinetics and EMG of the lower limbs during quasi-stat ic and fast-dynamic squats in healthy and pathological subjects. Ten subjects were recruited: five healthy and five osteoarthritis subjects. A motion-capture system, force plate, and surface electrodes respectively recorded 3D kinematics, 3D kinetics and EMG of the lower limbs. Each subject performed a quasi-static squat and several fast-dynamic squats from 0° to 70° of knee flexion. The two squatting conditions were compared for positions where quasi-static and fast-dynamic knee flexion-extension angles were similar. Mean differences between quasi-static and fast-dynamic squats were 1.5° for rotations, 1.9 mm for translations, 2.1% of subjects' body weight for ground reaction forces, 6.6 Nm for torques, 11.2 mm for center of pressure, and 6.3% of maximum fast-dynamic electromyographic activities for EMG. Some significant differences (psquats were small. 69.5% of compared data were equivalent. In conclusion, this study showed that quasi-static and fast-dynamic squatting activities are comparable in terms of 3D kinematics, 3D kinetics and EMG, although some reservations still remain. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Deduction of kinetic mechanism in multisubstrate enzyme reactions from tritium isotope effects. Application to dopamine beta-hydroxylase

    International Nuclear Information System (INIS)

    Klinman, J.P.; Humphries, H.; Voet, J.G.

    1980-01-01

    Primary tritium isotope effects have been measured for the hydroxylation of [2-3H] dopamine catalyzed by dopamine beta-hydroxylase. Experimental values vary from 8.8 +/- 1.4 at 0.02 mM oxygen to 4.1 +/- 0.6 at 1.0 mM oxygen. It is shown that the observed dependence of the isotope effect on oxygen concentration provides unequivocal evidence for a kinetically significant dissociation of both dopamine and oxygen from enzyme, ternary complex. This approach, which is applicable to any multisubstrate enzyme characterized by detectable kinetic isotope effects, provides an alternate to classical methods for the elucidation of kinetic order in enzyme-catalyzed reactions

  12. Experimental kinetic parameters in the thermo-fluid-dynamic modelling of coal combustion

    International Nuclear Information System (INIS)

    Migliavacca, G.; Perini, M.; Parodi, E.

    2001-01-01

    The designing and the optimisation of modern and efficient combustion systems are nowadays frequently based on calculation tools for mathematical modelling, which are able to predict the evolution of the process starting from the first principles of physics. Otherwise, in many cases, specific experimental parameters are needed to describe the specific nature of the materials considered in the calculations. It is especially true in the modelling of coal combustion, which is a complex process strongly dependent on the chemical and physical features of the fuel. This paper describes some experimental techniques used to estimate the fundamental kinetic parameters of coal combustion and shows how this data may be introduced in a model calculation to predict the pollutant emissions from a real scale combustion plant [it

  13. Wastewater treatment using photo-impinging streams cyclone reactor: Computational fluid dynamics and kinetics modeling

    Energy Technology Data Exchange (ETDEWEB)

    Royaee, Sayed Javid; Shafeghat, Amin [Research Institute of Petroleum Industry, Tehran (Iran, Islamic Republic of); Sohrabi, Morteza [Amirkabir University of Technology, Tehran (Iran, Islamic Republic of)

    2014-02-15

    A photo impinging streams cyclone reactor has been used as a novel apparatus in photocatalytic degradation of organic compounds using titanium dioxide nanoparticles in wastewater. The operating parameters, including catalyst loading, pH, initial phenol concentration and light intensity have been optimized to increase the efficiency of the photocatalytic degradation process within this photoreactor. The results have demonstrated a higher efficiency and an increased performance capability of the present reactor in comparison with the conventional processes. In the next step, residence time distribution (RTD) of the slurry phase within the reactor was measured using the impulse tracer method. A CFD-based model for predicting the RTD was also developed which compared well with the experimental results. The RTD data was finally applied in conjunction with the phenol degradation kinetic model to predict the apparent rate coefficient for such a reaction.

  14. Structural and dynamical properties of solvated electrons; a study of kinetic spectroscopy using pulse radiolysis

    International Nuclear Information System (INIS)

    Huis, C. van

    1977-01-01

    In this thesis the pulse radiolysis experiments of hexamethyl-phosphortriamide (HMPA), propanol-1, 3-methylpentane and mixtures of propanol-1 and 3-methylpentane are reported. In the pulse radiolysis of HMPA, carried out at room temperature, the high yield of esub(s) - (G=2) and the very high wavelength of the maximum absorption (max= 2200 nm) in the esub(s) - absorption spectrum are explained by considering the aprotic nature and the molecular structure of this compound. In the experiment with propanol-1 (temperature range 93deg-123degK) a temporal shift to lower wavelengths in the time range of 10 s-10 ms is observed. In further experiments biphenyl was used as electron scavenger. It was concluded that after the electron pulse the following sequence of events takes place: 1) electron redistribution in times shorter than 1 s; 2) dipole reorientation during 10 s-10 ms; 3) recombination of a part of the solvated electrons; 4) a reaction of the solvated electrons with the neighbouring propanol-1 molecules. In the experiments with 3-methylpentane at 103deg-113degK an esub(s) - absorption band with third order decay kinetics was observed. This is attributed to geminate recombination. The activation energy of the recombination process was 0.4 eV. The experiments with mixtures of propanol-1 and 3-methylpentane were carried out at 103degK. At low propanol-1 concentrations the build-up at 500 nm obeys first order kinetics, whereas at high concentrations this build-up can be split up into three first order components, as was measured in pure propanol-1. The half-lives of the three components were in the ratio of 1:10:100. In the last chapter theoretical models for the electron redistribution and the matric relaxation are discussed and compared with the experiments

  15. 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.

  16. Superfluid kinetic equation approach to the dynamics of the 3He A-B phase boundary

    International Nuclear Information System (INIS)

    Palmeri, J.

    1990-01-01

    The dynamics of the A-B phase boundary is studied using a nonequilibrium theory inspired by the microscopic approach to flux flow in type-II superconductors, namely a generalized two-fluid model consisting of coupled dynamical equations for the superfluid order parameter and the quasiparticle fluid. The interface mobility is obtained to lowest order in the front velocity in three different dynamical regimes: the gapless, hydrodynamic, and ballistic. Experiments have so far only been performed in the ballistic regime, and in this regime we find that, if only Andreev scattering processes are accounted for in the interface mobility, then the theoretical predictions for the terminal velocity of the planar interface are too big by a factor ∼2. From this we conclude that there may be other important contributions to the interface mobility in the ballistic regime, and we discuss a few possibilities

  17. 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…

  18. Dynamic PET simulator via tomographic emission projection for kinetic modeling and parametric image studies.

    Science.gov (United States)

    Häggström, Ida; Beattie, Bradley J; Schmidtlein, C Ross

    2016-06-01

    To develop and evaluate a fast and simple tool called dpetstep (Dynamic PET Simulator of Tracers via Emission Projection), for dynamic PET simulations as an alternative to Monte Carlo (MC), useful for educational purposes and evaluation of the effects of the clinical environment, postprocessing choices, etc., on dynamic and parametric images. The tool was developed in matlab using both new and previously reported modules of petstep (PET Simulator of Tracers via Emission Projection). Time activity curves are generated for each voxel of the input parametric image, whereby effects of imaging system blurring, counting noise, scatters, randoms, and attenuation are simulated for each frame. Each frame is then reconstructed into images according to the user specified method, settings, and corrections. Reconstructed images were compared to MC data, and simple Gaussian noised time activity curves (GAUSS). dpetstep was 8000 times faster than MC. Dynamic images from dpetstep had a root mean square error that was within 4% on average of that of MC images, whereas the GAUSS images were within 11%. The average bias in dpetstep and MC images was the same, while GAUSS differed by 3% points. Noise profiles in dpetstep images conformed well to MC images, confirmed visually by scatter plot histograms, and statistically by tumor region of interest histogram comparisons that showed no significant differences (p dynamic PET and parametric images, and demonstrated that it generates both images and subsequent parametric images with very similar noise properties to those of MC images, in a fraction of the time. They believe dpetstep to be very useful for generating fast, simple, and realistic results, however since it uses simple scatter and random models it may not be suitable for studies investigating these phenomena. dpetstep can be downloaded free of cost from https://github.com/CRossSchmidtlein/dPETSTEP.

  19. Probing the hydrogen equilibrium and kinetics in zeolite imidazolate frameworks via molecular dynamics and quasi-elastic neutron scattering experiments.

    Science.gov (United States)

    Pantatosaki, Evangelia; Jobic, Hervé; Kolokolov, Daniil I; Karmakar, Shilpi; Biniwale, Rajesh; Papadopoulos, George K

    2013-01-21

    The problem of simulating processes involving equilibria and dynamics of guest sorbates within zeolitic imidazolate frameworks (ZIF) by means of molecular dynamics (MD) computer experiments is of growing importance because of the promising role of ZIFs as molecular "traps" for clean energy applications. A key issue for validating such an atomistic modeling attempt is the possibility of comparing the MD results, with real experiments being able to capture analogous space and time scales to the ones pertained to the computer experiments. In the present study, this prerequisite is fulfilled through the quasi-elastic neutron scattering technique (QENS) for measuring self-diffusivity, by elaborating the incoherent scattering signal of hydrogen nuclei. QENS and MD experiments were performed in parallel to probe the hydrogen motion, for the first time in ZIF members. The predicted and measured dynamics behaviors show considerable concentration variation of the hydrogen self-diffusion coefficient in the two topologically different ZIF pore networks of this study, the ZIF-3 and ZIF-8. Modeling options such as the flexibility of the entire matrix versus a rigid framework version, the mobility of the imidazolate ligand, and the inclusion of quantum mechanical effects in the potential functions were examined in detail for the sorption thermodynamics and kinetics of hydrogen and also of deuterium, by employing MD combined with Widom averaging towards studying phase equilibria. The latter methodology ensures a rigorous and efficient way for post-processing the dynamics trajectory, thereby avoiding stochastic moves via Monte Carlo simulation, over the large number of configurational degrees of freedom a nonrigid framework encompasses.

  20. Random Forests Are Able to Identify Differences in Clotting Dynamics from Kinetic Models of Thrombin Generation.

    Science.gov (United States)

    Arumugam, Jayavel; Bukkapatnam, Satish T S; Narayanan, Krishna R; Srinivasa, Arun R

    2016-01-01

    Current methods for distinguishing acute coronary syndromes such as heart attack from stable coronary artery disease, based on the kinetics of thrombin formation, have been limited to evaluating sensitivity of well-established chemical species (e.g., thrombin) using simple quantifiers of their concentration profiles (e.g., maximum level of thrombin concentration, area under the thrombin concentration versus time curve). In order to get an improved classifier, we use a 34-protein factor clotting cascade model and convert the simulation data into a high-dimensional representation (about 19000 features) using a piecewise cubic polynomial fit. Then, we systematically find plausible assays to effectively gauge changes in acute coronary syndrome/coronary artery disease populations by introducing a statistical learning technique called Random Forests. We find that differences associated with acute coronary syndromes emerge in combinations of a handful of features. For instance, concentrations of 3 chemical species, namely, active alpha-thrombin, tissue factor-factor VIIa-factor Xa ternary complex, and intrinsic tenase complex with factor X, at specific time windows, could be used to classify acute coronary syndromes to an accuracy of about 87.2%. Such a combination could be used to efficiently assay the coagulation system.

  1. Coarse-grained molecular dynamics modeling of the kinetics of lamellar block copolymer defect annealing

    Science.gov (United States)

    Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.

    2016-01-01

    State-of-the-art block copolymer (BCP)-directed self-assembly (DSA) methods still yield defect densities orders of magnitude higher than is necessary in semiconductor fabrication despite free-energy calculations that suggest equilibrium defect densities are much lower than is necessary for economic fabrication. This disparity suggests that the main problem may lie in the kinetics of defect removal. This work uses a coarse-grained model to study the rates, pathways, and dependencies of healing a common defect to give insight into the fundamental processes that control defect healing and give guidance on optimal process conditions for BCP-DSA. It is found that bulk simulations yield an exponential drop in defect heal rate above χN˜30. Thin films show no change in rate associated with the energy barrier below χN˜50, significantly higher than the χN values found previously for self-consistent field theory studies that neglect fluctuations. Above χN˜50, the simulations show an increase in energy barrier scaling with 1/2 to 1/3 of the bulk systems. This is because thin films always begin healing at the free interface or the BCP-underlayer interface, where the increased A-B contact area associated with the transition state is minimized, while the infinitely thick films cannot begin healing at an interface.

  2. 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.

  3. Kinetics and dynamics of near-resonant vibrational energy transfer in gas ensembles of atmospheric interest

    Science.gov (United States)

    McCaffery, Anthony J.

    2018-03-01

    This study of near-resonant, vibration-vibration (V-V) gas-phase energy transfer in diatomic molecules uses the theoretical/computational method, of Marsh & McCaffery (Marsh & McCaffery 2002 J. Chem. Phys. 117, 503 (doi:10.1063/1.1489998)) The method uses the angular momentum (AM) theoretical formalism to compute quantum-state populations within the component molecules of large, non-equilibrium, gas mixtures as the component species proceed to equilibration. Computed quantum-state populations are displayed in a number of formats that reveal the detailed mechanism of the near-resonant V-V process. Further, the evolution of quantum-state populations, for each species present, may be followed as the number of collision cycles increases, displaying the kinetics of evolution for each quantum state of the ensemble's molecules. These features are illustrated for ensembles containing vibrationally excited N2 in H2, O2 and N2 initially in their ground states. This article is part of the theme issue `Modern theoretical chemistry'.

  4. Kinetic and dynamic aspects of soil-plant-snail transfer of cadmium in the field

    International Nuclear Information System (INIS)

    Gimbert, Frederic; Mench, Michel; Coeurdassier, Michael; Badot, Pierre-Marie; Vaufleury, Annette de

    2008-01-01

    The proper use of bioaccumulation in the assessment of environmental quality involves accounting for chemical fluxes in organisms. Cadmium (Cd) accumulation kinetics in a soil-plant-snail food chain were therefore investigated in the field under different soil contamination (from 0 to 40 mg kg -1 ), soil pH (6 and 7) and season. Allowing for an accurate and sensitive assessment of Cd transfer to snails, toxicokinetics appears an interesting tool in the improvement of risk assessment procedures and a way to quantify metal bioavailability for a defined target. On the basis of uptake fluxes, snails proved to be sensitive enough to distinguish moderate soil contaminations. The soil pH did not appear, in the range studied, as a modulating parameter of the Cd transfer from soil to snail whereas the season, by influencing the snail mass, may modify the internal concentrations. The present data specifying a time integrated assessment of environmental factors on metal bioavailability and transfer to terrestrial snails should ensure their rational use in environmental biomonitoring. - Toxicokinetics and uptake fluxes can be used to describe the environment contamination by Cd, its bioavailability and transfer to Helix aspersa snails in the field

  5. A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics

    Science.gov (United States)

    Byun, Hye Suk; El-Naggar, Mohamed Y.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2017-10-01

    Kinetic Monte Carlo (KMC) simulations are used to study long-time dynamics of a wide variety of systems. Unfortunately, the conventional KMC algorithm is not scalable to larger systems, since its time scale is inversely proportional to the simulated system size. A promising approach to resolving this issue is the synchronous parallel KMC (SPKMC) algorithm, which makes the time scale size-independent. This paper introduces a formal derivation of the SPKMC algorithm based on local transition-state and time-dependent Hartree approximations, as well as its scalable parallel implementation based on a dual linked-list cell method. The resulting algorithm has achieved a weak-scaling parallel efficiency of 0.935 on 1024 Intel Xeon processors for simulating biological electron transfer dynamics in a 4.2 billion-heme system, as well as decent strong-scaling parallel efficiency. The parallel code has been used to simulate a lattice of cytochrome complexes on a bacterial-membrane nanowire, and it is broadly applicable to other problems such as computational synthesis of new materials.

  6. Dynamic PET simulator via tomographic emission projection for kinetic modeling and parametric image studies

    Energy Technology Data Exchange (ETDEWEB)

    Häggström, Ida, E-mail: haeggsti@mskcc.org [Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York 10065 and Department of Radiation Sciences, Umeå University, Umeå 90187 (Sweden); Beattie, Bradley J.; Schmidtlein, C. Ross [Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, New York 10065 (United States)

    2016-06-15

    Purpose: To develop and evaluate a fast and simple tool called dPETSTEP (Dynamic PET Simulator of Tracers via Emission Projection), for dynamic PET simulations as an alternative to Monte Carlo (MC), useful for educational purposes and evaluation of the effects of the clinical environment, postprocessing choices, etc., on dynamic and parametric images. Methods: The tool was developed in MATLAB using both new and previously reported modules of PETSTEP (PET Simulator of Tracers via Emission Projection). Time activity curves are generated for each voxel of the input parametric image, whereby effects of imaging system blurring, counting noise, scatters, randoms, and attenuation are simulated for each frame. Each frame is then reconstructed into images according to the user specified method, settings, and corrections. Reconstructed images were compared to MC data, and simple Gaussian noised time activity curves (GAUSS). Results: dPETSTEP was 8000 times faster than MC. Dynamic images from dPETSTEP had a root mean square error that was within 4% on average of that of MC images, whereas the GAUSS images were within 11%. The average bias in dPETSTEP and MC images was the same, while GAUSS differed by 3% points. Noise profiles in dPETSTEP images conformed well to MC images, confirmed visually by scatter plot histograms, and statistically by tumor region of interest histogram comparisons that showed no significant differences (p < 0.01). Compared to GAUSS, dPETSTEP images and noise properties agreed better with MC. Conclusions: The authors have developed a fast and easy one-stop solution for simulations of dynamic PET and parametric images, and demonstrated that it generates both images and subsequent parametric images with very similar noise properties to those of MC images, in a fraction of the time. They believe dPETSTEP to be very useful for generating fast, simple, and realistic results, however since it uses simple scatter and random models it may not be suitable for

  7. Dynamic PET simulator via tomographic emission projection for kinetic modeling and parametric image studies

    International Nuclear Information System (INIS)

    Häggström, Ida; Beattie, Bradley J.; Schmidtlein, C. Ross

    2016-01-01

    Purpose: To develop and evaluate a fast and simple tool called dPETSTEP (Dynamic PET Simulator of Tracers via Emission Projection), for dynamic PET simulations as an alternative to Monte Carlo (MC), useful for educational purposes and evaluation of the effects of the clinical environment, postprocessing choices, etc., on dynamic and parametric images. Methods: The tool was developed in MATLAB using both new and previously reported modules of PETSTEP (PET Simulator of Tracers via Emission Projection). Time activity curves are generated for each voxel of the input parametric image, whereby effects of imaging system blurring, counting noise, scatters, randoms, and attenuation are simulated for each frame. Each frame is then reconstructed into images according to the user specified method, settings, and corrections. Reconstructed images were compared to MC data, and simple Gaussian noised time activity curves (GAUSS). Results: dPETSTEP was 8000 times faster than MC. Dynamic images from dPETSTEP had a root mean square error that was within 4% on average of that of MC images, whereas the GAUSS images were within 11%. The average bias in dPETSTEP and MC images was the same, while GAUSS differed by 3% points. Noise profiles in dPETSTEP images conformed well to MC images, confirmed visually by scatter plot histograms, and statistically by tumor region of interest histogram comparisons that showed no significant differences (p < 0.01). Compared to GAUSS, dPETSTEP images and noise properties agreed better with MC. Conclusions: The authors have developed a fast and easy one-stop solution for simulations of dynamic PET and parametric images, and demonstrated that it generates both images and subsequent parametric images with very similar noise properties to those of MC images, in a fraction of the time. They believe dPETSTEP to be very useful for generating fast, simple, and realistic results, however since it uses simple scatter and random models it may not be suitable for

  8. Coarse-grained molecular dynamics modeling of the kinetics of lamellar BCP defect annealing

    Science.gov (United States)

    Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.

    2015-03-01

    Directed self-assembly of block copolymers (BCPs) is a process that has received great interest in the field of nanomanufacturing in the past decade, and great strides towards forming high quality aligned patterns have been made. But state of the art methods still yield defectivities orders of magnitude higher than is necessary in semi-conductor fabrication even though free energy calculations suggest that equilibrium defectivities are much lower than is necessary for economic semi-conductor fabrication. This disparity suggests that the main problem may lie in the kinetics of defect removal. This work uses a coarse-grained model to study the rates, pathways, and dependencies of healing a common defect to give insight into the fundamental processes that control defect healing and give guidance on optimal process conditions for BCP-DSA. It is found that infinitely thick films yield an exponential drop in defect heal rate above χN ~ 30. Below χN ~ 30, the rate of transport was similar to the rate at which the transition state was reached so that the overall rate changed only slightly. The energy barrier in periodic simulations increased with 0.31 χN on average. Thin film simulations show no change in rate associated with the energy barrier below χN ~ 50, and then show an increase in energy barrier scaling with 0.16χN. Thin film simulations always begin to heal at either the free interface or the BCP-underlayer interface where the increased A-B contact area associated with the transition state will be minimized, while the infinitely thick films must start healing in the bulk where the A-B contact area is increased. It is also found that cooperative chain movement is required for the defect to start healing.

  9. Absolute quantitation of myocardial blood flow with 201Tl and dynamic SPECT in canine: optimisation and validation of kinetic modelling

    International Nuclear Information System (INIS)

    Iida, Hidehiro; Kim, Kyeong-Min; Nakazawa, Mayumi; Sohlberg, Antti; Zeniya, Tsutomu; Hayashi, Takuya; Watabe, Hiroshi; Eberl, Stefan; Tamura, Yoshikazu; Ono, Yukihiko

    2008-01-01

    201 Tl has been extensively used for myocardial perfusion and viability assessment. Unlike 99m Tc-labelled agents, such as 99m Tc-sestamibi and 99m Tc-tetrofosmine, the regional concentration of 201 Tl varies with time. This study is intended to validate a kinetic modelling approach for in vivo quantitative estimation of regional myocardial blood flow (MBF) and volume of distribution of 201 Tl using dynamic SPECT. Dynamic SPECT was carried out on 20 normal canines after the intravenous administration of 201 Tl using a commercial SPECT system. Seven animals were studied at rest, nine during adenosine infusion, and four after beta-blocker administration. Quantitative images were reconstructed with a previously validated technique, employing OS-EM with attenuation-correction, and transmission-dependent convolution subtraction scatter correction. Measured regional time-activity curves in myocardial segments were fitted to two- and three-compartment models. Regional MBF was defined as the influx rate constant (K 1 ) with corrections for the partial volume effect, haematocrit and limited first-pass extraction fraction, and was compared with that determined from radio-labelled microspheres experiments. Regional time-activity curves responded well to pharmacological stress. Quantitative MBF values were higher with adenosine and decreased after beta-blocker compared to a resting condition. MBFs obtained with SPECT (MBF SPECT ) correlated well with the MBF values obtained by the radio-labelled microspheres (MBF MS ) (MBF SPECT = -0.067 + 1.042 x MBF MS , p 201 Tl and dynamic SPECT. (orig.)

  10. Diagnostic value of kinetic analysis using dynamic FDG PET in immunocompetent patients with primary CNS lymphoma

    International Nuclear Information System (INIS)

    Nishiyama, Yoshihiro; Yamamoto, Yuka; Monden, Toshihide; Sasakawa, Yasuhiro; Satoh, Katashi; Ohkawa, Motoomi; Kawai, Nobuyuki

    2007-01-01

    The purpose of this study was to investigate the accumulation of FDG in immunocompetent patients with primary central nervous system (CNS) lymphoma using qualitative and quantitative PET images and to compare baseline with follow-up PET after therapy. Twelve immunocompetent patients with CNS lymphoma were examined. Dynamic emission data were acquired for 60 min immediately following injection of FDG. In seven patients, repeated PET studies were performed after treatment. Applying a three-compartment five-parameter model, K 1 , k 2 , k 3 , k 4 , vascular fraction (V B ) and cerebral metabolic rate of glucose (CMR Glc ) were obtained. We evaluated the FDG uptake visually using qualitative and parametric images and quantitatively using parametric images. A total of 12 lesions were identified in ten patients with newly diagnosed CNS lymphoma. On visual analysis, ten lesions showed an increase on qualitative images, eight showed an increase on K 1 images, 12 showed an increase on k 3 images and ten showed an increase on CMR Glc images. On quantitative analysis, k 2 , k 3 and CMR Glc values of the lesion were significantly different from those of the normal grey matter (p 3 and CMR Glc images. The K 1 , k 2 , k 3 and CMR Glc values after treatment were significantly different from those obtained before treatment (p 3 , using dynamic FDG PET might be helpful for diagnosis of CNS lymphoma and for monitoring therapeutic assessment. (orig.)

  11. Dynamic phase transition in the kinetic spin-32 Blume-Capel model: Phase diagrams in the temperature and crystal-field interaction plane

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-06-15

    We analyze, within a mean-field approach, the stationary states of the kinetic spin-32 Blume-Capel (BC) model by the Glauber-type stochastic dynamics and subject to a time-dependent oscillating external magnetic field. The dynamic phase transition (DPT) points are obtained by investigating the behavior of the dynamic magnetization as a function of temperature and as well as calculating the Liapunov exponent. Phase diagrams are constructed in the temperature and crystal-field interaction plane. We find five fundamental types of phase diagrams for the different values of the reduced magnetic field amplitude parameter (h) in which they present a disordered, two ordered phases and the coexistences phase regions. The phase diagrams also exhibit a dynamic double-critical end point for 0dynamic tricritical point for 1.44dynamic tricritical points for h>5.06.

  12. Coupling of the computational fluid dynamics code ANSYS CFX with the 3D neutron kinetic core model DYN3D

    International Nuclear Information System (INIS)

    Kliem, S.; Grahn, A.; Rohde, U.; Schuetze, J.; Frank, Th.

    2010-01-01

    The computational fluid dynamics code ANSYS CFX has been coupled with the neutron-kinetic core model DYN3D. ANSYS CFX calculates the fluid dynamics and related transport phenomena in the reactors coolant and provides the corresponding data to DYN3D. In the fluid flow simulation of the coolant, the core itself is modeled within the porous body approach. DYN3D calculates the neutron kinetics and the fuel behavior including the heat transfer to the coolant. The physical data interface between the codes is the volumetric heat release rate into the coolant. In the prototype that is currently available, the coupling is restricted to single-phase flow problems. In the time domain an explicit coupling of the codes has been implemented so far. Steady-state and transient verification calculations for two small-size test problems confirm the correctness of the implementation of the prototype coupling. The first test problem was a mini-core consisting of nine real-size fuel assemblies with quadratic cross section. Comparison was performed with the DYN3D stand-alone code. In the steady state, the effective multiplication factor obtained by the DYN3D/ANSYS CFX codes hows a deviation of 9.8 pcm from the DYN3D stand-alone solution. This difference can be attributed to the use of different water property packages in the two codes. The transient test case simulated the withdrawal of the control rod from the central fuel assembly at hot zero power in the same mini-core. Power increase during the introduction of positive reactivity and power reduction due to fuel temperature increase are calculated in the same manner by the coupled and the stand-alone codes. The maximum values reached during the power rise differ by about 1 MW at a power level of 50 MW. Beside the different water property packages, these differences are caused by the use of different flow solvers. The same calculations were carried for a mini-core with seven real-size fuel assemblies with hexagonal cross section in

  13. 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)

  14. Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling.

    Science.gov (United States)

    Huang, Yu-Ming M; Huber, Gary A; Wang, Nuo; Minteer, Shelley D; McCammon, J Andrew

    2018-02-01

    Malate dehydrogenase (MDH) and citrate synthase (CS) are two pacemaking enzymes involved in the tricarboxylic acid (TCA) cycle. Oxaloacetate (OAA) molecules are the intermediate substrates that are transferred from the MDH to CS to carry out sequential catalysis. It is known that, to achieve a high flux of intermediate transport and reduce the probability of substrate leaking, a MDH-CS metabolon forms to enhance the OAA substrate channeling. In this study, we aim to understand the OAA channeling within possible MDH-CS metabolons that have different structural orientations in their complexes. Three MDH-CS metabolons from native bovine, wild-type porcine, and recombinant sources, published in recent work, were selected to calculate OAA transfer efficiency by Brownian dynamics (BD) simulations and to study, through electrostatic potential calculations, a possible role of charges that drive the substrate channeling. Our results show that an electrostatic channel is formed in the metabolons of native bovine and recombinant porcine enzymes, which guides the oppositely charged OAA molecules passing through the channel and enhances the transfer efficiency. However, the channeling probability in a suggested wild-type porcine metabolon conformation is reduced due to an extended diffusion length between the MDH and CS active sites, implying that the corresponding arrangements of MDH and CS result in the decrease of electrostatic steering between substrates and protein surface and then reduce the substrate transfer efficiency from one active site to another. © 2017 The Protein Society.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  16. Kinetics of Quality Changes of Pangasius Fillets at Stable and Dynamic Temperatures, Simulating Downstream Cold Chain Conditions

    Directory of Open Access Journals (Sweden)

    Nga Mai

    2017-01-01

    Full Text Available This study was about the quality changes of Pangasius fillets during storage under simulated temperature conditions of downstream cold chain. Sensory, chemical, and microbiological analyses were conducted over storage time and bacterial growth was modelled. Sensory quality index (QI, at five stable (1, 4, 9, 15, and 19 ± 1°C and three dynamic temperatures, progressed faster at higher temperatures, especially with sooner temperature abuses. Total volatile basic nitrogen remained under the acceptable limit throughout all the storage conditions. Total viable psychrotrophic counts (TVC were around 5.68 ± 0.24 log CFU g−1 at the beginning and exceeded the limit of 6 log CFU g−1 after 216, 96, 36, 16, and 7 h at 1, 4, 9, 15, and 19 ± 1°C, respectively. Meanwhile, Pseudomonas counts started at 3.81 ± 0.53 log CFU g−1 and reached 4.60–6.36 log CFU g−1 by the time of TVC rejection. Since lower shelf lives were given by TVC rather than QI, it should be appropriate to base the product shelf life on the TVC acceptable limit. Kinetics models based on the Baranyi and Roberts and square root models, developed for TVC and Pseudomonas spp., gave acceptable bacterial estimations at dynamic temperatures, with over 80% of observed counts within the acceptable simulation zone, revealing promising model applicability as a supporting tool for cold chain management. However, further improvement and validation of the models are needed.

  17. Trajectory Calculations for Bergman Cyclization Predict H/D Kinetic Isotope Effects Due to Nonstatistical Dynamics in the Product.

    Science.gov (United States)

    Doubleday, Charles; Boguslav, Mayla; Howell, Caronae; Korotkin, Scott D; Shaked, David

    2016-06-22

    An unusual H/D kinetic isotope effect (KIE) is described, in which isotopic selectivity arises primarily from nonstatistical dynamics in the product. In DFT-based quasiclassical trajectories of Bergman cyclization of (Z)-3-hexen-1,5-diyne (1) at 470 K, the new CC bond retains its energy, and 28% of nascent p-benzyne recrosses back to the enediyne on a vibrational time scale. The competing process of intramolecular vibrational redistribution (IVR) in p-benzyne is too slow to prevent this. Deuteration increases the rate of IVR, which decreases the fraction of recrossing and increases the yield of statistical (trapable) p-benzyne, 2. Trapable yields for three isotopomers of 2 range from 72% to 86%. The resulting KIEs for Bergman cyclization differ substantially from KIEs predicted by transition state theory, which suggests that IVR in this reaction can be studied by conventional KIEs. Leakage of vibrational zero point energy (ZPE) into the reaction coordinate was probed by trajectories in which initial ZPE in the CH/CD stretching modes was reduced by 25%. This did not change the predicted KIEs.

  18. Periodicity in tumor vasculature targeting kinetics of ligand-functionalized nanoparticles studied by dynamic contrast enhanced magnetic resonance imaging and intravital microscopy

    DEFF Research Database (Denmark)

    Hak, Sjoerd; Cebulla, Jana; Huuse, Else Marie

    2014-01-01

    In the past two decades advances in the development of targeted nanoparticles have facilitated their application as molecular imaging agents and targeted drug delivery vehicles. Nanoparticle-enhanced molecular imaging of the angiogenic tumor vasculature has been of particular interest. Not only...... because angiogenesis plays an important role in various pathologies, but also since endothelial cell surface receptors are directly accessible for relatively large circulating nanoparticles. Typically, nanoparticle targeting towards these receptors is studied by analyzing the contrast distribution...... kinetics. These kinetics will not only depend on nanoparticle characteristics, but also on receptor binding and recycling. In this study, we monitored the in vivo targeting kinetics of αvβ3-integrin specific nanoparticles with intravital microscopy and dynamic contrast enhanced magnetic resonance imaging...

  19. Self-Consistent System of Equations for a Kinetic Description of the Low-Pressure Discharges Accounting for the Nonlocal and Collisionless Electron Dynamics

    International Nuclear Information System (INIS)

    Kaganovich, Igor D.; Polomarov, Oleg

    2003-01-01

    In low-pressure discharges, when the electron mean free path is larger or comparable with the discharge length, the electron dynamics is essentially non-local. Moreover, the electron energy distribution function (EEDF) deviates considerably from a Maxwellian. Therefore, an accurate kinetic description of the low-pressure discharges requires knowledge of the non-local conductivity operator and calculation of the non-Maxwellian EEDF. The previous treatments made use of simplifying assumptions: a uniform density profile and a Maxwellian EEDF. In the present study a self-consistent system of equations for the kinetic description of nonlocal, non-uniform, nearly collisionless plasmas of low-pressure discharges is derived. It consists of the nonlocal conductivity operator and the averaged kinetic equation for calculation of the non-Maxwellian EEDF. The importance of accounting for the non-uniform plasma density profile on both the current density profile and the EEDF is demonstrated

  20. Dynamic phase transition in the kinetic spin-1 Blume-Capel model: Phase diagrams in the temperature and crystal-field interaction plane

    International Nuclear Information System (INIS)

    Keskin, M.; Canko, O.; Temizer, U.

    2007-01-01

    Within a mean-field approach, the stationary states of the kinetic spin-1 Blume-Capel model in the presence of a time-dependent oscillating external magnetic field is studied. The Glauber-type stochastic dynamics is used to describe the time evolution of the system and obtain the mean-field dynamic equation of motion. The dynamic phase-transition points are calculated and phase diagrams are presented in the temperature and crystal-field interaction plane. According to the values of the magnetic field amplitude, three fundamental types of phase diagrams are found: One exhibits a dynamic tricritical point, while the other two exhibit a dynamic zero-temperature critical point

  1. Reaction dynamics of the four-centered elimination CH2OH + --> CHO + +H2: Measurement of kinetic energy release distribution and classical trajectory calculation

    Science.gov (United States)

    Lee, Tae Geol; Park, Seung C.; Kim, Myung Soo

    1996-03-01

    Mass-analyzed ion kinetic energy (MIKE) spectrum of CHO+ generated in the unimolecular dissociation of CH2OH+ was measured. Kinetic energy release distribution (KERD) was evaluated by analyzing the spectrum according to the algorithm developed previously. The average kinetic energy release evaluated from the distribution was extraordinarily large, 1.63 eV, corresponding to 75% of the reverse barrier of the reaction. A global analytical potential energy surface was constructed such that the experimental energetics was represented and that various features in the ab initio potential energy surface were closely reproduced. Classical trajectory calculation was carried out with the global analytical potential energy surface to investigate the causes for the extraordinarily large kinetic energy release. Based on the detailed dynamical calculations, it was found that the strained bending forces at the transition state and strengthening of the CO bond from double to triple bond character were mainly responsible for such a significant kinetic energy release. In addition, the dissociation products H2 and CHO+ ion were found to be rotationally excited in the trajectory calculations. This was attributed to the asymmetry of the transition state and the release of asymmetric bending forces. Also, the bending vibrational modes of CHO+ and the H2 stretching mode, which are coupled with the bending coordinates, were found to be moderately excited.

  2. Flow-Induced New Channels of Energy Exchange in Multi-Scale Plasma Dynamics - Revisiting Perturbative Hybrid Kinetic-MHD Theory.

    Science.gov (United States)

    Shiraishi, Junya; Miyato, Naoaki; Matsunaga, Go

    2016-05-10

    It is found that new channels of energy exchange between macro- and microscopic dynamics exist in plasmas. They are induced by macroscopic plasma flow. This finding is based on the kinetic-magnetohydrodynamic (MHD) theory, which analyses interaction between macroscopic (MHD-scale) motion and microscopic (particle-scale) dynamics. The kinetic-MHD theory is extended to include effects of macroscopic plasma flow self-consistently. The extension is realised by generalising an energy exchange term due to wave-particle resonance, denoted by δ WK. The first extension is generalisation of the particle's Lagrangian, and the second one stems from modification to the particle distribution function due to flow. These extensions lead to a generalised expression of δ WK, which affects the MHD stability of plasmas.

  3. Enzyme kinetics and identification of the rate-limiting step of enzymatic arabinoxylan degradation

    DEFF Research Database (Denmark)

    Rasmussen, Louise Enggaard; Xu, Cheng; Sørensen, Jens

    2012-01-01

    This study investigated the kinetics of multi-enzymatic degradation of soluble wheat arabinoxylan by monitoring the release of xylose and arabinose during designed treatments with mono-component enzymes at different substrate concentrations. The results of different combinations of α...... α-l-arabinofuranosidases catalyze liberation of arabinose residues linked 1→3 to singly (AFAn) or doubly (AFBa) substituted xyloses in arabinoxylan, respectively. When added to arabinoxylan at equimolar levels, the AFBa enzyme catalyzed the release of more arabinose, i.e. had a higher rate constant...... than AFAn, but with respect to the xylose release, AFAn – as expected – exhibited a better synergistic effect than AFBa with β-xylosidase. This synergistic effect with AFAn was estimated to increase the number of β-xylosidase catalyzed cuts from ∼3 (with β-xylosidase alone) to ∼7 in each arabinoxylan...

  4. Quasiclassical Theory of Spin Dynamics in Superfluid ^3He: Kinetic Equations in the Bulk and Spin Response of Surface Majorana States

    Science.gov (United States)

    Silaev, M. A.

    2018-06-01

    We develop a theory based on the formalism of quasiclassical Green's functions to study the spin dynamics in superfluid ^3He. First, we derive kinetic equations for the spin-dependent distribution function in the bulk superfluid reproducing the results obtained earlier without quasiclassical approximation. Then, we consider spin dynamics near the surface of fully gapped ^3He-B-phase taking into account spin relaxation due to the transitions in the spectrum of localized fermionic states. The lifetimes of longitudinal and transverse spin waves are calculated taking into account the Fermi-liquid corrections which lead to a crucial modification of fermionic spectrum and spin responses.

  5. Effective-field theory for dynamic phase diagrams of the kinetic spin-3/2 Blume–Capel model under a time oscillating longitudinal field

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-12-15

    Dynamic phase diagrams are presented for the kinetic spin-3/2 Blume–Capel model under a time oscillating longitudinal field by use of the effective-field theory with correlations. The dynamic equation of the average magnetization is obtained for the square lattice by utilizing the Glauber-type stochastic process. Dynamic phase diagrams are presented in the reduced temperature and the magnetic field amplitude plane. We also investigated the effect of longitudinal field frequency. Finally, the discussion and comparison of the phase diagrams are given. - Highlights: • Dynamic behaviors in the spin-3/2 Blume–Capel system is investigated by the effective-field theory based on the Glauber-type stochastic dynamics. • The dynamic phase transitions and dynamic phase diagrams are obtained. • The effects of the longitudinal field frequency on the dynamic phase diagrams of the system are investigated. • Dynamic phase diagrams exhibit several ordered phases, coexistence phase regions and several critical points as well as a re-entrant behavior.

  6. Effective-field theory for dynamic phase diagrams of the kinetic spin-3/2 Blume–Capel model under a time oscillating longitudinal field

    International Nuclear Information System (INIS)

    Ertaş, Mehmet; Kocakaplan, Yusuf; Keskin, Mustafa

    2013-01-01

    Dynamic phase diagrams are presented for the kinetic spin-3/2 Blume–Capel model under a time oscillating longitudinal field by use of the effective-field theory with correlations. The dynamic equation of the average magnetization is obtained for the square lattice by utilizing the Glauber-type stochastic process. Dynamic phase diagrams are presented in the reduced temperature and the magnetic field amplitude plane. We also investigated the effect of longitudinal field frequency. Finally, the discussion and comparison of the phase diagrams are given. - Highlights: • Dynamic behaviors in the spin-3/2 Blume–Capel system is investigated by the effective-field theory based on the Glauber-type stochastic dynamics. • The dynamic phase transitions and dynamic phase diagrams are obtained. • The effects of the longitudinal field frequency on the dynamic phase diagrams of the system are investigated. • Dynamic phase diagrams exhibit several ordered phases, coexistence phase regions and several critical points as well as a re-entrant behavior

  7. Population dynamics of the murine lymphokine activated killer system: precursor frequency and kinetics of maturation and renewal.

    Science.gov (United States)

    Owen-Schaub, L B; Hemstreet, G P; Hemingway, L L; Abraham, S R; DeBault, L E

    1987-11-01

    The proliferation kinetics and population renewal of recombinant interleukin-2 (rIL-2)-induced murine lymphokine activated killers (LAK) arising from splenic precursors was studied. Extensive proliferation has been shown to accompany the de novo generation of LAK cytotoxicity. In this report, a thymidine 'hot pulse' suicide technique was employed to examine the sensitivity of LAK progenitors during various time periods following culture initiation. Hot pulse during the first 24 hr of culture resulted in a 30-35% reduction in lytic activity when assayed on day 5. Pulse periods between days 1 and 4 resulted in almost complete inhibition (90-95%) of lytic function when assayed on day 5. Proliferation of LAK progenitors was documented by limiting dilution analysis comparison of splenic precursors and functionally mature LAK cultures. These studies showed a 75- to 80-fold enrichment of LAK progenitors after 3 days culture in rIL-2. By flow cytometric cell cycle analysis, we demonstrated that the number of cells in the S/G2/M phase increased with the length of rIL-2 culture and represented approximately 40% of the cells by day 4. Finally, we used the rate of decay of lytic activity following irradiation as a factor to define the mean life span of a cytotoxic effector in the absence of cellular input. An exponential decrease to approximately 50% of controls was observed within 8-9 hr after irradiation. Taken together, these results suggest that the LAK system is highly dynamic and requires continuous cellular proliferation for its maintenance.

  8. 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.

  9. Study on a hidden protein-DNA binding in salmon sperm DNA sample by dynamic kinetic capillary isoelectric focusing

    International Nuclear Information System (INIS)

    Liang Liang; Dou Peng; Dong Mingming; Ke Xiaokang; Bian Ningsheng; Liu Zhen

    2009-01-01

    Nuclease P1 is an important enzyme that hydrolyzes RNA or single-stranded DNA into nucleotides, and complete digestion is an essential basis for assays based on this enzyme. To digest a doubled-stranded DNA, the enzyme is usually combined with heat denaturing, which breaks doubled-stranded DNA into single strands. This paper presents an un-expected phenomenon that nuclease P1, in combination with heat denaturing, fails to completely digest a DNA sample extracted from salmon sperm. Under the experimental conditions used, at which nuclease P1 can completely digest calf thymus DNA, the digestion yield of salmon sperm DNA was only 89.5%. Spectrometric measurement indicated that a total protein of 4.7% is present in the DNA sample. To explain the reason for this phenomenon, the dynamic kinetic capillary isoelectric focusing (DK-CIEF) approach proposed previously, which allows for the discrimination of different types of protein-DNA interactions and the measurement of the individual dissociation rate constants, was modified and applied to examine possible protein-DNA interactions involved. It was found that a non-specific DNA-protein binding occurs in the sample, the dissociation rate constant for which was measured to be 7.05 ± 0.83 x 10 -3 s -1 . The formation of DNA-protein complex was suggested to be the main reason for the incomplete digestion of the DNA sample. The modified DK-CIEF approach can be applied as general DNA samples, with the advantages of fast speed and low sample consumption.

  10. Dynamic phase transition in the kinetic spin-32 Blume-Capel model: Phase diagrams in the temperature and crystal-field interaction plane

    International Nuclear Information System (INIS)

    Keskin, Mustafa; Canko, Osman; Deviren, Bayram

    2007-01-01

    We analyze, within a mean-field approach, the stationary states of the kinetic spin-32 Blume-Capel (BC) model by the Glauber-type stochastic dynamics and subject to a time-dependent oscillating external magnetic field. The dynamic phase transition (DPT) points are obtained by investigating the behavior of the dynamic magnetization as a function of temperature and as well as calculating the Liapunov exponent. Phase diagrams are constructed in the temperature and crystal-field interaction plane. We find five fundamental types of phase diagrams for the different values of the reduced magnetic field amplitude parameter (h) in which they present a disordered, two ordered phases and the coexistences phase regions. The phase diagrams also exhibit a dynamic double-critical end point for 0 5.06

  11. Comparison of morphological and kinetic parameters in distinction of benign and malignant breast lesions in dynamic contrast enhanced magnetic resonance imaging

    Directory of Open Access Journals (Sweden)

    Direnç Özlem Aksoy

    2013-12-01

    Full Text Available Objective: To evaluate the value of qualitative morphologicaland kinetic data and quantitative kinetic data indistinction of malignancy in dynamic contrast enhancedmagnetic resonance imaging (DCE-MRI of the breast.Methods: DCE-MRIs of 49 subjects were evaluated.Morphological and contrast enhancement parameters of95 lesions were recorded in these subjects. Post-contrastkinetic behavior of these lesions were also investigated.Among the quantitative parameters, relative enhancements(E1, E2, Epeak, time-to-peak (Tpeak, slope ofcurve (Slope, signal enhancement ratio (SER, and maximumintensity time ratio (MITR were calculated. Theseresults were compared with the pathological diagnosis.Results: Spiculated contour (100%, rim enhancement(97.87%, irregular shape (95.74%, and irregular margin(91.49% were the most specific morphological featuresof malignancy in mass lesions. In non-mass lesions, focalzone (91.49% was the most specific feature of malignancy.74.5% of the benign lesions showed type 1, 77.1%of the malignant lesions showed type 2 and 3 curves accordingto the kinetic curve evaluation. All quantitativeparameters except Epeak were found to be statisticallysignificant in distinction of malignancy.Conclusion: None of the morphological features of thebenign lesions were found to be significantly specific.More specific features can be described for malignantlesions. Early behavior of the kinetic curve is not usefulfor diagnosis of malignancy but the intermediate and latebehavior gives useful information. Quantitative data involvedin this study might be promising.Key words: Morphological, kinetic, breast lesions, magnetic resonance imaging, dynamic

  12. 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.

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

    Science.gov (United States)

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

    2018-03-01

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

  14. 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.

  15. Multi-enzyme catalyzed processes: Next generation biocatalysis

    DEFF Research Database (Denmark)

    Andrade Santacoloma, Paloma de Gracia; Sin, Gürkan; Gernaey, Krist

    2011-01-01

    Biocatalysis has been attracting increasing interest in recent years. Nevertheless, most studies concerning biocatalysis have been carried out using single enzymes (soluble or immobilized). Currently, multiple enzyme mixtures are attractive for the production of many compounds at an industrial...

  16. Enzyme-Catalyzed Regioselective Modification of Starch Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Soma [Polytechnic Univ., Brooklyn, NY (United States). National Science Foundation (NSF) Center for Biocatalysis and Bioprocessing of Macromolecules, Othmer Dept. of Chemical and Biological Science and Engineering; Sahoo, Bishwabhusan [Polytechnic Univ., Brooklyn, NY (United States). National Science Foundation (NSF) Center for Biocatalysis and Bioprocessing of Macromolecules, Othmer Dept. of Chemical and Biological Science and Engineering; Teraoka, Iwao [Polytechnic Univ., Brooklyn, NY (United States). National Science Foundation (NSF) Center for Biocatalysis and Bioprocessing of Macromolecules, Othmer Dept. of Chemical and Biological Science and Engineering; Miller, Lisa M. [Brookhaven National Lab. (BNL), Upton, NY (United States). National Synchrotron Light Source (NSLS); Gross, Richard A. [Polytechnic Univ., Brooklyn, NY (United States). National Science Foundation (NSF) Center for Biocatalysis and Bioprocessing of Macromolecules, Othmer Dept. of Chemical and Biological Science and Engineering

    2004-12-13

    The selective esterification of starch nanoparticles was performed using as catalyst Candida antartica Lipase B (CAL-B) in its immobilized (Novozym 435) and free (SP-525) forms. The starch nanoparticles were made accessible for acylation reactions by formation of Aerosol-OT (AOT, bis(2-ethylhexyl)sodium sulfosuccinate) stabilized microemulsions. Starch nanoparticles in microemulsions were reacted with vinyl stearate, ε-caprolactone, and maleic anhydride at 40 °C for 48 h to give starch esters with degrees of substitution (DS) of 0.8, 0.6, and 0.4, respectively. Substitution occurred regioselectively at the C-6 position of the glucose repeat units. Infrared microspectroscopy (IRMS) revealed that AOT-coated starch nanoparticles diffuse into the outer 50 μm shell of catalyst beads. Thus, even though CAL-B is immobilized within a macroporous resin, CAL-B is sufficiently accessible to the starch nanoparticles. When free CAL-B was incorporated along with starch within AOT-coated reversed micelles, CAL-B was also active and catalyzed the acylation with vinyl stearate (24 h, 40 °C) to give DS = 0.5. After removal of surfactant from the modified starch nanoparticles, they were dispersed in DMSO or water and were shown to retain their nanodimensions.

  17. Microbial enzyme-catalyzed processes in soils and their analysis

    Czech Academy of Sciences Publication Activity Database

    Baldrian, Petr

    2009-01-01

    Roč. 55, č. 9 (2009), s. 370-378 ISSN 1214-1178 R&D Projects: GA MŠk LC06066; GA MŠk OC 155; GA MŠk OC08050; GA MZe QH72216 Institutional research plan: CEZ:AV0Z50200510 Keywords : assay methods * extracellular enzymes * ecology Subject RIV: EE - Microbiology, Virology Impact factor: 0.697, year: 2009

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

    Science.gov (United States)

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

    2013-10-21

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

  19. Measuring dynamic and kinetic information in the previously inaccessible supra-τ(c) window of nanoseconds to microseconds by solution NMR spectroscopy.

    Science.gov (United States)

    Ban, David; Sabo, T Michael; Griesinger, Christian; Lee, Donghan

    2013-09-26

    Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool that has enabled experimentalists to characterize molecular dynamics and kinetics spanning a wide range of time-scales from picoseconds to days. This review focuses on addressing the previously inaccessible supra-tc window (defined as τ(c) supra-τ(c) supra-τ(c) window. In the second section, the current state of the art for RD is analyzed, as well as the considerable progress toward pushing the sensitivity of RD further into the supra-τ(c) scale by up to a factor of two (motion up to 25 μs). From the data obtained with these techniques and methodology, the importance of the supra-τ(c) scale for protein function and molecular recognition is becoming increasingly clearer as the connection between motion on the supra-τ(c) scale and protein functionality from the experimental side is further strengthened with results from molecular dynamics simulations.

  20. Supporting interpretation of dynamic simulation. Application to chemical kinetic models; Aides a l`interpretation de simulations dynamiques. Application aux modeles de cinetique chimique

    Energy Technology Data Exchange (ETDEWEB)

    Braunschweig, B

    1998-04-22

    Numerous scientific and technical domains make constant use of dynamical simulations. Such simulators are put in the hands of a growing number of users. This phenomenon is due both to the extraordinary increase in computing performance, and to better graphical user interfaces which make simulation models easy to operate. But simulators are still computer programs which produce series of numbers from other series of numbers, even if they are displayed graphically. This thesis presents new interaction paradigms between a dynamical simulator and its user. The simulator produces a self-made interpretation of its results, thanks to a dedicated representation of its domain with objects. It shows dominant cyclic mechanisms identified by their instantaneous loop gain estimates, it uses a notion of episodes for splitting the simulation into homogeneous time intervals, and completes this by animations which rely on the graphical structure of the system. These new approaches are demonstrated with examples from chemical kinetics, because of the energic and exemplary characteristics of the encountered behaviors. They are implemented in the Spike software, Software Platform for Interactive Chemical Kinetics Experiments. Similar concepts are also shown in two other domains: interpretation of seismic wave propagation, and simulation of large projects. (author) 95 refs.

  1. Relaxation dynamics and transformation kinetics of deeply supercooled water: Temperature, pressure, doping, and proton/deuteron isotope effects.

    Science.gov (United States)

    Lemke, Sonja; Handle, Philip H; Plaga, Lucie J; Stern, Josef N; Seidl, Markus; Fuentes-Landete, Violeta; Amann-Winkel, Katrin; Köster, Karsten W; Gainaru, Catalin; Loerting, Thomas; Böhmer, Roland

    2017-07-21

    Above its glass transition, the equilibrated high-density amorphous ice (HDA) transforms to the low-density pendant (LDA). The temperature dependence of the transformation is monitored at ambient pressure using dielectric spectroscopy and at elevated pressures using dilatometry. It is found that near the glass transition temperature of deuterated samples, the transformation kinetics is 300 times slower than the structural relaxation, while for protonated samples, the time scale separation is at least 30 000 and insensitive to doping. The kinetics of the HDA to LDA transformation lacks a proton/deuteron isotope effect, revealing that this process is dominated by the restructuring of the oxygen network. The x-ray diffraction experiments performed on samples at intermediate transition stages reflect a linear combination of the LDA and HDA patterns implying a macroscopic phase separation, instead of a local intermixing of the two amorphous states.

  2. Relaxation dynamics and transformation kinetics of deeply supercooled water: Temperature, pressure, doping, and proton/deuteron isotope effects

    Science.gov (United States)

    Lemke, Sonja; Handle, Philip H.; Plaga, Lucie J.; Stern, Josef N.; Seidl, Markus; Fuentes-Landete, Violeta; Amann-Winkel, Katrin; Köster, Karsten W.; Gainaru, Catalin; Loerting, Thomas; Böhmer, Roland

    2017-07-01

    Above its glass transition, the equilibrated high-density amorphous ice (HDA) transforms to the low-density pendant (LDA). The temperature dependence of the transformation is monitored at ambient pressure using dielectric spectroscopy and at elevated pressures using dilatometry. It is found that near the glass transition temperature of deuterated samples, the transformation kinetics is 300 times slower than the structural relaxation, while for protonated samples, the time scale separation is at least 30 000 and insensitive to doping. The kinetics of the HDA to LDA transformation lacks a proton/deuteron isotope effect, revealing that this process is dominated by the restructuring of the oxygen network. The x-ray diffraction experiments performed on samples at intermediate transition stages reflect a linear combination of the LDA and HDA patterns implying a macroscopic phase separation, instead of a local intermixing of the two amorphous states.

  3. Measuring Dynamic and Kinetic Information in the Previously Inaccessible Supra-tc Window of Nanoseconds to Microseconds by Solution NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Donghan Lee

    2013-09-01

    Full Text Available Nuclear Magnetic Resonance (NMR spectroscopy is a powerful tool that has enabled experimentalists to characterize molecular dynamics and kinetics spanning a wide range of time-scales from picoseconds to days. This review focuses on addressing the previously inaccessible supra-τc window (defined as τc < supra-τc < 40 μs; in which τc is the overall tumbling time of a molecule from the perspective of local inter-nuclear vector dynamics extracted from residual dipolar couplings (RDCs and from the perspective of conformational exchange captured by relaxation dispersion measurements (RD. The goal of the first section is to present a detailed analysis of how to extract protein dynamics encoded in RDCs and how to relate this information to protein functionality within the previously inaccessible supra-τc window. In the second section, the current state of the art for RD is analyzed, as well as the considerable progress toward pushing the sensitivity of RD further into the supra-τc scale by up to a factor of two (motion up to 25 ms. From the data obtained with these techniques and methodology, the importance of the supra-τ c scale for protein function and molecular recognition is becoming increasingly clearer as the connection between motion on the supra-τc scale and protein functionality from the experimental side is further strengthened with results from molecular dynamics simulations.

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

    NARCIS (Netherlands)

    Nikerel, I.E.; Van Winden, W.; Van Gulik, W.M.; Heijnen, J.J.

    2006-01-01

    Background: Dynamic modeling of metabolic reaction networks under in vivo conditions is a crucial step in order to obtain a better understanding of the (dis)functioning of living cells. So far dynamic metabolic models generally have been based on mechanistic rate equations which often contain so

  5. Transient analysis of carbon monoxide transport phenomena and adsorption kinetics in HT-PEMFC during dynamic current extraction

    International Nuclear Information System (INIS)

    Raj, Kamal Abdul Rasheedj; Chan, Siew Hwa

    2015-01-01

    Highlights: • Increasing the fuel cell temperature reduces outlet CO concentration. • Increasing the CO inlet (initial) concentration increases outlet CO concentration. • Increasing current density step and dwell time increases outlet CO concentration. • Increasing in the CL and GDL porosities reduces outlet CO concentration. - Abstract: This paper investigates the transport phenomena of carbon monoxide (CO) and adsorption kinetics, in a high-temperature proton exchange membrane fuel cell (HT-PEMFC) during step-wise current extraction (step-change in current extraction). Step-wise current extraction is a common process done to accommodate a sudden power surge during an operation. Since HT-PEMFCs are capable of handling high impurity of CO, hydrogen fuel that is contaminated with trace amount of CO is usually considered for commercial benefits. Thus, a transient three-dimensional isothermal anodic electro-kinetic numerical model is developed to determine the effect of operating parameters such as fuel cell temperature, CO inlet (initial) concentration, step-change of current density and dwell time on the transport phenomena of CO and adsorption kinetics. In addition, geometrical factors such as the catalyst layer (CL) and gas diffusion layer (GDL) porosity are also varied as well. The results show that the above-mentioned operating parameters can affect the maximum CO concentration at the CL, especially at the outlet of the channel. Specifically, a reduction of fuel cell temperature can significantly increase the CO concentration near the outlet, while increasing CO inlet (initial) concentration, step-change amplitude of current density and current density dwell time can cause an increase in CO concentration at the outlet, albeit to different extent. In addition, the increase in the porosity of CL and GDL, results in the reduction of the maximum CO concentration at the outlet, albeit to different extent. In addition, the CO and hydrogen surface coverage

  6. Kinetic Typography

    DEFF Research Database (Denmark)

    van Leeuwen, Theo; Djonov, Emilia

    2014-01-01

    After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images.......After discussing broad cultural drivers behind the development of kinetic typography, the chapter outlines an approach to analysing kinetic typography which is based on Halliday's theory of transitivity, as applied by Kress and Van Leeuwen to visual images....

  7. Quantification of photoinduced bending of dynamic molecular crystals: from macroscopic strain to kinetic constants and activation energies.

    Science.gov (United States)

    Chizhik, Stanislav; Sidelnikov, Anatoly; Zakharov, Boris; Naumov, Panče; Boldyreva, Elena

    2018-02-28

    Photomechanically reconfigurable elastic single crystals are the key elements for contactless, timely controllable and spatially resolved transduction of light into work from the nanoscale to the macroscale. The deformation in such single-crystal actuators is observed and usually attributed to anisotropy in their structure induced by the external stimulus. Yet, the actual intrinsic and external factors that affect the mechanical response remain poorly understood, and the lack of rigorous models stands as the main impediment towards benchmarking of these materials against each other and with much better developed soft actuators based on polymers, liquid crystals and elastomers. Here, experimental approaches for precise measurement of macroscopic strain in a single crystal bent by means of a solid-state transformation induced by light are developed and used to extract the related temperature-dependent kinetic parameters. The experimental results are compared against an overarching mathematical model based on the combined consideration of light transport, chemical transformation and elastic deformation that does not require fitting of any empirical information. It is demonstrated that for a thermally reversible photoreactive bending crystal, the kinetic constants of the forward (photochemical) reaction and the reverse (thermal) reaction, as well as their temperature dependence, can be extracted with high accuracy. The improved kinematic model of crystal bending takes into account the feedback effect, which is often neglected but becomes increasingly important at the late stages of the photochemical reaction in a single crystal. The results provide the most rigorous and exact mathematical description of photoinduced bending of a single crystal to date.

  8. A study on the kinetic behavior of Listeria monocytogenes in ice cream stored under static and dynamic chilling and freezing conditions.

    Science.gov (United States)

    Gougouli, M; Angelidis, A S; Koutsoumanis, K

    2008-02-01

    The kinetic behavior of Listeria monocytogenes in 2 commercial ice cream products (A and B) that were inoculated and stored under static chilling (4 to 16 degrees C), static freezing (-5 to -33 degrees C), dynamic chilling, and dynamic chilling-freezing conditions was studied, simulating conditions of the aging process and of normal or abuse conditions during distribution and storage. The ice cream products A and B had different compositions but similar pH (6.50 and 6.67, respectively) and water activity (0.957 and 0.965, respectively) values. For both chilling and freezing conditions, the kinetic behavior of the pathogen was similar in the 2 products, indicating that the pH and water activity, together with temperature, were the main factors controlling growth. Under chilling conditions, L. monocytogenes grew well at all temperatures tested. Under freezing conditions, no significant changes in the population of the pathogen were observed throughout a 90-d storage period for either of the inoculum levels tested (10(3) and 10(6) cfu/g). Growth data from chilled storage conditions were fitted to a mathematical model, and the calculated maximum specific growth rate was modeled as a function of temperature by using a square root model. The model was further validated under dynamic chilling and dynamic chilling-freezing conditions by using 4 different storage temperature scenarios. Under dynamic chilling conditions, the model accurately predicted the growth of the pathogen in both products, with 99.5% of the predictions lying within the +/- 20% relative error zone. The results from the chilling-freezing storage experiments showed that the pathogen was able to initiate growth within a very short time after a temperature upshift from freezing to chilling temperatures. This indicates that the freezing conditions did not cause a severe stress in L. monocytogenes cells capable of leading to a significant "additional" lag phase during the subsequent growth of the pathogen at

  9. Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori

    Science.gov (United States)

    Wang, Liang-Wei; Liu, Yu-Nan; Lyu, Ping-Chiang; Jackson, Sophie E.; Hsu, Shang-Te Danny

    2015-09-01

    Understanding the mechanism by which a polypeptide chain thread itself spontaneously to attain a knotted conformation has been a major challenge in the field of protein folding. HP0242 is a homodimeric protein from Helicobacter pylori with intertwined helices to form a unique pseudo-knotted folding topology. A tandem HP0242 repeat has been constructed to become the first engineered trefoil-knotted protein. Its small size renders it a model system for computational analyses to examine its folding and knotting pathways. Here we report a multi-parametric study on the folding stability and kinetics of a library of HP0242 variants, including the trefoil-knotted tandem HP0242 repeat, using far-UV circular dichroism and fluorescence spectroscopy. Equilibrium chemical denaturation of HP0242 variants shows the presence of highly populated dimeric and structurally heterogeneous folding intermediates. Such equilibrium folding intermediates retain significant amount of helical structures except those at the N- and C-terminal regions in the native structure. Stopped-flow fluorescence measurements of HP0242 variants show that spontaneous refolding into knotted structures can be achieved within seconds, which is several orders of magnitude faster than previously observed for other knotted proteins. Nevertheless, the complex chevron plots indicate that HP0242 variants are prone to misfold into kinetic traps, leading to severely rolled-over refolding arms. The experimental observations are in general agreement with the previously reported molecular dynamics simulations. Based on our results, kinetic folding pathways are proposed to qualitatively describe the complex folding processes of HP0242 variants.

  10. Sample Handling and Chemical Kinetics in an Acoustically Levitated Drop Microreactor

    Science.gov (United States)

    2009-01-01

    Accurate measurement of enzyme kinetics is an essential part of understanding the mechanisms of biochemical reactions. The typical means of studying such systems use stirred cuvettes, stopped-flow apparatus, microfluidic systems, or other small sample containers. These methods may prove to be problematic if reactants or products adsorb to or react with the container’s surface. As an alternative approach, we have developed an acoustically-levitated drop reactor eventually intended to study enzyme-catalyzed reaction kinetics related to free radical and oxidative stress chemistry. Microliter-scale droplet generation, reactant introduction, maintenance, and fluid removal are all important aspects in conducting reactions in a levitated drop. A three capillary bundle system has been developed to address these needs. We report kinetic measurements for both luminol chemiluminescence and the reaction of pyruvate with nicotinamide adenine dinucleotide, catalyzed by lactate dehydrogenase, to demonstrate the feasibility of using a levitated drop in conjunction with the developed capillary sample handling system as a microreactor. PMID:19769373

  11. Comparison of the results of the fifth dynamic AER benchmark-a benchmark for coupled thermohydraulic system/three-dimensional hexagonal kinetic core models

    International Nuclear Information System (INIS)

    Kliem, S.

    1998-01-01

    The fifth dynamic benchmark was defined at seventh AER-Symposium, held in Hoernitz, Germany in 1997. It is the first benchmark for coupled thermohydraulic system/three-dimensional hexagonal neutron kinetic core models. In this benchmark the interaction between the components of a WWER-440 NPP with the reactor core has been investigated. The initiating event is a symmetrical break of the main steam header at the end of the first fuel cycle and hot shutdown conditions with one control rod group stucking. This break causes an overcooling of the primary circuit. During this overcooling the scram reactivity is compensated and the scrammed reactor becomes re critical. The calculation was continued until the highly-borated water from the high pressure injection system terminated the power excursion. Each participant used own best-estimate nuclear cross section data. Only the initial subcriticality at the beginning of the transient was given. Solutions were received from Kurchatov Institute Russia with the code BIPR8/ATHLET, VTT Energy Finland with HEXTRAN/SMABRE, NRI Rez Czech Republic with DYN3/ATHLET, KFKI Budapest Hungary with KIKO3D/ATHLET and from FZR Germany with the code DYN3D/ATHLET.In this paper the results are compared. Beside the comparison of global results, the behaviour of several thermohydraulic and neutron kinetic parameters is presented to discuss the revealed differences between the solutions.(Authors)

  12. How Four Scientists Integrate Thermodynamic and Kinetic Theory, Context, Analogies, and Methods in Protein-Folding and Dynamics Research: Implications for Biochemistry Instruction.

    Science.gov (United States)

    Jeffery, Kathleen A; Pelaez, Nancy; Anderson, Trevor R

    2018-01-01

    To keep biochemistry instruction current and relevant, it is crucial to expose students to cutting-edge scientific research and how experts reason about processes governed by thermodynamics and kinetics such as protein folding and dynamics. This study focuses on how experts explain their research into this topic with the intention of informing instruction. Previous research has modeled how expert biologists incorporate research methods, social or biological context, and analogies when they talk about their research on mechanisms. We used this model as a guiding framework to collect and analyze interview data from four experts. The similarities and differences that emerged from analysis indicate that all experts integrated theoretical knowledge with their research context, methods, and analogies when they explained how phenomena operate, in particular by mapping phenomena to mathematical models; they explored different processes depending on their explanatory aims, but readily transitioned between different perspectives and explanatory models; and they explained thermodynamic and kinetic concepts of relevance to protein folding in different ways that aligned with their particular research methods. We discuss how these findings have important implications for teaching and future educational research. © 2018 K. A. Jeffery et al. CBE—Life Sciences Education © 2018 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  13. Ejecta cloud from the AIDA space project kinetic impact on the secondary of a binary asteroid: I. mechanical environment and dynamical model

    Science.gov (United States)

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

    2017-01-01

    An understanding of the post-impact dynamics of ejecta clouds are crucial to the planning of a kinetic impact mission to an asteroid, and also has great implications for the history of planetary formation. The purpose of this article is to track the evolution of ejecta produced by AIDA mission, which targets for kinetic impact the secondary of near-Earth binary asteroid (65803) Didymos on 2022, and to feedback essential informations to AIDA's ongoing phase-A study. We present a detailed dynamic model for the simulation of an ejecta cloud from a binary asteroid that synthesizes all relevant forces based on a previous analysis of the mechanical environment. We apply our method to gain insight into the expected response of Didymos to the AIDA impact, including the subsequent evolution of debris and dust. The crater scaling relations from laboratory experiments are employed to approximate the distributions of ejecta mass and launching speed. The size distribution of fragments is modeled with a power law fitted from observations of real asteroid surface. A full-scale demonstration is simulated using parameters specified by the mission. We report the results of the simulation, which include the computed spread of the ejecta cloud and the recorded history of ejecta accretion and escape. The violent period of the ejecta evolution is found to be short, and is followed by a stage where the remaining ejecta is gradually cleared. Solar radiation pressure proves to be efficient in cleaning dust-size ejecta, and the simulation results after two weeks shows that large debris on polar orbits (perpendicular to the binary orbital plane) has a survival advantage over smaller ejecta and ejecta that keeps to low latitudes.

  14. The dynamics of particle disks. III - Dense and spinning particle disks. [development of kinetic theory for planetary rings

    Science.gov (United States)

    Araki, Suguru

    1991-01-01

    The kinetic theory of planetary rings developed by Araki and Tremaine (1986) and Araki (1988) is extended and refined, with a focus on the implications of finite particle size: (1) nonlocal collisions and (2) finite filling factors. Consideration is given to the derivation of the equations for the local steady state, the low-optical-depth limit, and the steady state at finite filling factors (including the effects of collision inelasticity, spin degrees of freedom, and self-gravity). Numerical results are presented in extensive graphs and characterized in detail. The importance of distinguishing effects (1) and (2) at low optical depths is stressed, and the existence of vertical density profiles with layered structures at high filling factors is demonstrated.

  15. Dynamical and many-body correlation effects in the kinetic energy spectra of isotopes produced in nuclear multifragmentation

    Science.gov (United States)

    Souza, S. R.; Donangelo, R.; Lynch, W. G.; Tsang, M. B.

    2018-03-01

    The properties of the kinetic energy spectra of light isotopes produced in the breakup of a nuclear source and during the de-excitation of its products are examined. The initial stage, at which the hot fragments are created, is modeled by the statistical multifragmentation model, whereas the Weisskopf-Ewing evaporation treatment is adopted to describe the subsequent fragment de-excitation, as they follow their classical trajectories dictated by the Coulomb repulsion among them. The energy spectra obtained are compared to available experimental data. The influence of the fusion cross section entering into the evaporation treatment is investigated and its influence on the qualitative aspects of the energy spectra turns out to be small. Although these aspects can be fairly well described by the model, the underlying physics associated with the quantitative discrepancies remains to be understood.

  16. Absorption of calcium ions on oxidized graphene sheets and study its dynamic behavior by kinetic and isothermal models

    Directory of Open Access Journals (Sweden)

    Mahmoud Fathy

    2016-07-01

    Full Text Available Abstract Sorption of calcium ion from the hard underground water using novel oxidized graphene (GO sheets was studied in this paper. Physicochemical properties and microstructure of graphene sheets were investigated using Raman spectrometer, thermogravimetry analyzer, transmission electron microscope, scanning electron microscope. The kinetics adsorption of calcium on graphene oxide sheets was examined using Lagergren first and second orders. The results show that the Lagergren second-order was the best-fit model that suggests the conception process of calcium ion adsorption on the Go sheets. For isothermal studies, the Langmuir and Freundlich isotherm models were used at temperatures ranging between 283 and 313 K. Thermodynamic parameters resolved at 283, 298 and 313 K indicating that the GO adsorption was exothermic spontaneous process. Finally, the graphene sheets show high partiality toward calcium particles and it will be useful in softening and treatment of hard water.

  17. CFD analysis of the dynamic behaviour of a fuel rod subchannel in a supercritical water reactor with point kinetics

    International Nuclear Information System (INIS)

    Ampomah-Amoako, Emmanuel; Akaho, Edward H.K.; Nyarko, Benjamin J.B.; Ambrosini, Walter

    2013-01-01

    Highlights: • The analysis of flow stability of nuclear fuel subchannels with supercritical water is presented. • The results obtained by a CFD code are compared with those of a system code. • The model includes also heat conduction in the fuel rod and point neutron kinetics. - Abstract: The paper presents the analysis by a CFD code of coupled neutronic–thermal hydraulic instabilities in a subchannel slice belonging to a square lattice assembly. The work represents a further phase in the assessment of the suitability of CFD codes for studies of flow stability of supercritical fluids; the research started in previous work with the analysis of bare 2D circular pipes and already addressed 3D subchannel slices with no allowance for heat conduction or neutronic effects. In the present phase, a more realistic system is considered, dealing with a slice of a fuel assembly subchannel containing the regions of the pellet, the gap and the cladding and including also the effect of inlet and outlet throttling. The adopted neutronic model is a point kinetics one, including six delayed neutron groups with global Doppler and fluid density feedbacks. The response of the model to perturbations applied starting from a steady-state condition at the rated power is compared with that of a similar model developed for a 1D system code. Upward, horizontal and downward flow orientations are addressed making use of a uniform power profile and changing relevant parameters as the gap equivalent conductance and the density reactivity coefficient. A bottom-peaked power profile is also considered in the case of vertical upward flow. Though the adopted model can still be considered simple in comparison with actual details of fuel assemblies, the obtained results demonstrate the potential of the adopted methodology for more accurate analyses to be made with larger computational resources

  18. Low energy ion-molecule reaction dynamics and chemiionization kinetics: Progress report, February 1, 1985-January 31, 1988

    International Nuclear Information System (INIS)

    Farrar, J.M.

    1988-01-01

    The research program at Rochester is devoted to an understanding of the dynamics of elementary gas phase ionic reactions by using the molecular beam methods. We seek to elucidate pathways for energy disposal in elementary reactions, with the goal of using this information to understand the topology of the potential surfaces which govern the reaction, applying the results to ionic channels in combustion systems. We have made significant accomplishments in several distinct areas of research in crossed beam studies of ion-neutral reaction dynamics in the past three years. Our research has focused on the following topics and has resulted in 15 publications and submissions to major journals, with several additional manuscripts in preparation: dynamics of gas phase proton transfer reactions, gas phase carbon and methyl cation chemistry, reactive scattering from double minimum potentials, reactions of highly vibrationally excited ions: NH 3 + + D 2 , and electron and proton transfer reactions of anions. 9 refs

  19. New approach to study mobility in the vicinity of dynamical arrest; exact application to a kinetically constrained model

    Science.gov (United States)

    DeGregorio, P.; Lawlor, A.; Dawson, K. A.

    2006-04-01

    We introduce a new method to describe systems in the vicinity of dynamical arrest. This involves a map that transforms mobile systems at one length scale to mobile systems at a longer length. This map is capable of capturing the singular behavior accrued across very large length scales, and provides a direct route to the dynamical correlation length and other related quantities. The ideas are immediately applicable in two spatial dimensions, and have been applied to a modified Kob-Andersen type model. For such systems the map may be derived in an exact form, and readily solved numerically. We obtain the asymptotic behavior across the whole physical domain of interest in dynamical arrest.

  20. Temperature Dependence of the OH- + CH3I Reaction Kinetics. Experimental and Simulation Studies and Atomic-Level Dynamics (Postprint)

    Science.gov (United States)

    2013-11-25

    reaction time, the core of the flow was sampled through a small orifice in a rounded nose cone, while the bulk of the gas was pumped by an oil free...with direct dynamics simulations,6’ 10’ 11’ 13- 17 have provided an atomistic understanding of the dynamics of gas phase x- + CH3Y reactions. In...OH- was mass selected using a quadrupole mass filter, injected into the flow tube through a Venturi inlet, and carried downstream by a helium

  1. Kinetic analysis of superparamagnetic iron oxide nanoparticles in the liver of body-temperature-controlled mice using dynamic susceptibility contrast magnetic resonance imaging and an empirical mathematical model.

    Science.gov (United States)

    Murase, Kenya; Assanai, Purapan; Takata, Hiroshige; Matsumoto, Nozomi; Saito, Shigeyoshi; Nishiura, Motoko

    2015-06-01

    The purpose of this study was to develop a method for analyzing the kinetic behavior of superparamagnetic iron oxide nanoparticles (SPIONs) in the murine liver under control of body temperature using dynamic susceptibility contrast magnetic resonance imaging (DSC-MRI) and an empirical mathematical model (EMM). First, we investigated the influence of body temperature on the kinetic behavior of SPIONs in the liver by controlling body temperature using our temperature-control system. Second, we investigated the kinetic behavior of SPIONs in the liver when mice were injected with various doses of GdCl3, while keeping the body temperature at 36°C. Finally, we investigated it when mice were injected with various doses of zymosan, while keeping the body temperature at 36°C. We also investigated the effect of these substances on the number of Kupffer cells by immunohistochemical analysis using the specific surface antigen of Kupffer cells (CD68). To quantify the kinetic behavior of SPIONs in the liver, we calculated the upper limit of the relative enhancement (A), the rates of early contrast uptake (α) and washout or late contrast uptake (β), the parameter related to the slope of early uptake (q), the area under the curve (AUC), the maximum change of transverse relaxation rate (ΔR2) (ΔR2(max)), the time to ΔR2(max) (Tmax), and ΔR2 at the last time point (ΔR2(last)) from the time courses of ΔR2 using the EMM. The β and Tmax values significantly decreased and increased, respectively, with decreasing body temperature, suggesting that the phagocytic activity of Kupffer cells is significantly affected by body temperature. The AUC, ΔR2(max), and ΔR2(last) values decreased significantly with increasing dose of GdCl3, which was consistent with the change in the number of CD68-positive cells. They increased with increasing dose of zymosan, which was also consistent with the change in the number of CD68-positive cells. These results suggest that AUC, ΔR2(max), and ΔR2

  2. Sensitivity analysis in molecular dynamics and chemical kinetics and a theory of intramolecular energy transfer in the presence of intense radiation fields

    International Nuclear Information System (INIS)

    Eslava, L.A.

    1983-01-01

    This thesis is an investigation of two topics in the area of molecular and chemical dynamics phenomena. The first topic, Sensitivity Analysis in Molecular Dynamics and Chemical Kinetics, explores the response of the numerical solutions to variation in the input information. After a brief consideration of elementary sensitivity coefficients (i.e. partial derivatives of observables with respect to model parameters), attention is focused on an entire new family of derived coefficients capable of exhibiting important aspects of the underlying dynamics. Each derived sensitivity coefficient has a unique physical interpretation in terms of an experiment or modeling calculation. Also, a fitting model for rotationally inelastic cross sections that accurately predicts cross sections away from the region of parameter space used in the fitting is presented. The global behavior of cross sections in parameter space is examined, and a nonlinear interpolation formula is suggested which utilizes sensitivity information. The second topic, A Theory of Intramolecular Energy Transfer in the Presence of Intense Radiation Fields, represents a theoretical formulation of energy redistribution based on stochastic considerations. The fundamental assumption is that a random phase approximation is valid at specific time intervals. This results in the replacement of the Schrodinger equation by a master-type equation, which is further approximated by a Fokker-Planck diffusion like equation. Energy transfer is described as a flow of probability among the quantum states, and the dissociation of dynamics are embodied in the boundary conditions. By virtue of the continuous character of the Fokker-Planck equation, the computational difficulty of its numerical solution depends only on the number of degrees of freedom and not on the number of states

  3. Dynamic phase transition and multicritical dynamic phase diagrams of the kinetic spin-3/2 Blume Emery Griffiths model with repulsive biquadratic coupling under a time-dependent oscillating external field

    Science.gov (United States)

    Deviren, Bayram; Keskin, Mustafa; Canko, Osman

    2008-03-01

    We extend our recent paper [O. Canko, B. Deviren, M. Keskin, J. Phys.: Condens. Mater 118 (2006) 6635] to present a study, within a mean-field approach, the stationary states of the kinetic spin-3/2 Blume-Emery-Griffiths model with repulsive biquadratic interaction under the presence of a time varying (sinusoidal) magnetic field. We found that the dynamic phase diagrams of the present work exhibit more complex, richer and more topological different types of phase diagrams than our recent paper. Especially, the obtained dynamic phase diagrams show the ferrimagnetic ( i) phase in addition to the ferromagnetic ±3/2 ( f), ferromagnetic ±1/2 ( f), antiquadrupolar or staggered ( a) and disordered ( d) phases, and the f+i, f+d, i+d, f+i+d, a+d and/or f+i+a coexistence regions in addition to the f+f, f+d, f+a, f+d and/or f+a+d coexistence regions, depending on interaction parameters. Moreover, the phase diagrams exhibit dynamic zero-temperature critical, critical end, double critical end, multicritical, and/or pentacritical special points in addition to the dynamic tricritical, double critical end point, triple, quadruple and/or tetracritical special points that depending on the interaction parameters.

  4. In vivo dynamics and kinetics of pKi-67: transition from a mobile to an immobile form at the onset of anaphase.

    Science.gov (United States)

    Saiwaki, Takuya; Kotera, Ippei; Sasaki, Mitsuho; Takagi, Masatoshi; Yoneda, Yoshihiro

    2005-08-01

    A cell proliferation marker protein, pKi-67, distributes to the chromosome periphery during mitosis and nucleolar heterochromatin in the interphase. We report here on the structural domains of pKi-67 that are required for its correct distribution. While both the LR domain and the conserved domain were involved in localization to the nucleolar heterochromatin, both the LR domain and the Ki-67 repeat domain were required for its distribution to the mitotic chromosome periphery. Using in vivo time-lapse microscopy, GFP-pKi-67 was dynamically tracked from the mitotic chromosome periphery to reforming nucleoli via prenucleolar bodies (PNBs). The signals in PNBs then moved towards and fused into the reforming nucleoli with a thin string-like fluorescence during early G1 phase. An analysis of the in vivo kinetics of pKi-67 using photobleaching indicated that the association of pKi-67 with chromatin was progressively altered from "loose" to "tight" after the onset of anaphase. These findings indicate that pKi-67 dynamically alters the nature of the interaction with chromatin structure during the cell cycle, which is closely related to the reformation process of the interphase nucleolar chromatin.

  5. CORTAP: a coupled neutron kinetics-heat transfer digital computer program for the dynamic simulation of the high temperature gas cooled reactor core

    International Nuclear Information System (INIS)

    Cleveland, J.C.

    1977-01-01

    CORTAP (Core Transient Analysis Program) was developed to predict the dynamic behavior of the High Temperature Gas Cooled Reactor (HTGR) core under normal operational transients and postulated accident conditions. CORTAP is used both as a stand-alone component simulation and as part of the HTGR nuclear steam supply (NSS) system simulation code ORTAP. The core thermal neutronic response is determined by solving the heat transfer equations for the fuel, moderator and coolant in an average powered region of the reactor core. The space independent neutron kinetics equations are coupled to the heat transfer equations through a rapidly converging iterative technique. The code has the capability to determine conservative fuel, moderator, and coolant temperatures in the ''hot'' fuel region. For transients involving a reactor trip, the core heat generation rate is determined from an expression for decay heat following a scram. Nonlinear effects introduced by temperature dependent fuel, moderator, and coolant properties are included in the model. CORTAP predictions will be compared with dynamic test results obtained from the Fort St. Vrain reactor owned by Public Service of Colorado, and, based on these comparisons, appropriate improvements will be made in CORTAP

  6. In vivo dynamics and kinetics of pKi-67: Transition from a mobile to an immobile form at the onset of anaphase

    International Nuclear Information System (INIS)

    Saiwaki, Takuya; Kotera, Ippei; Sasaki, Mitsuho; Takagi, Masatoshi; Yoneda, Yoshihiro

    2005-01-01

    A cell proliferation marker protein, pKi-67, distributes to the chromosome periphery during mitosis and nucleolar heterochromatin in the interphase. We report here on the structural domains of pKi-67 that are required for its correct distribution. While both the LR domain and the conserved domain were involved in localization to the nucleolar heterochromatin, both the LR domain and the Ki-67 repeat domain were required for its distribution to the mitotic chromosome periphery. Using in vivo time-lapse microscopy, GFP-pKi-67 was dynamically tracked from the mitotic chromosome periphery to reforming nucleoli via prenucleolar bodies (PNBs). The signals in PNBs then moved towards and fused into the reforming nucleoli with a thin string-like fluorescence during early G1 phase. An analysis of the in vivo kinetics of pKi-67 using photobleaching indicated that the association of pKi-67 with chromatin was progressively altered from 'loose' to 'tight' after the onset of anaphase. These findings indicate that pKi-67 dynamically alters the nature of the interaction with chromatin structure during the cell cycle, which is closely related to the reformation process of the interphase nucleolar chromatin

  7. Modeling chemical kinetics graphically

    NARCIS (Netherlands)

    Heck, A.

    2012-01-01

    In literature on chemistry education it has often been suggested that students, at high school level and beyond, can benefit in their studies of chemical kinetics from computer supported activities. Use of system dynamics modeling software is one of the suggested quantitative approaches that could

  8. Tracer kinetic model selection for dynamic contrast-enhanced magnetic resonance imaging of locally advanced cervical cancer

    DEFF Research Database (Denmark)

    Kallehauge, Jesper Folsted; Tanderup, Kari; Duan, Chong

    2014-01-01

    , the TM was optimal in 17.0%, the ETM was optimal in 2.2%, the C-TU in 23.4% and the 2CXM was optimal in 57.3%. Throughout the tumour, a high correlation was found between Ktrans(TM) and Fp(2CXM), ρ = 0.91. Conclusion. The 2CXM was most often optimal in describing the contrast agent enhancement of pre......Background. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) offers a unique capability to probe tumour microvasculature. Different analysis of the acquired data will possibly lead to different conclusions. Therefore, the objective of this study was to investigate under which...

  9. Absolute quantitation of myocardial blood flow with {sup 201}Tl and dynamic SPECT in canine: optimisation and validation of kinetic modelling

    Energy Technology Data Exchange (ETDEWEB)

    Iida, Hidehiro; Kim, Kyeong-Min; Nakazawa, Mayumi; Sohlberg, Antti; Zeniya, Tsutomu; Hayashi, Takuya; Watabe, Hiroshi [National Cardiovascular Center Research Institute, Department of Investigative Radiology, Suita City, Osaka (Japan); Eberl, Stefan [National Cardiovascular Center Research Institute, Department of Investigative Radiology, Suita City, Osaka (Japan); Royal Prince Alfred Hospital, PET and Nuclear Medicine Department, Camperdown, NSW (Australia); Tamura, Yoshikazu [Akita Kumiai General Hospital, Department of Cardiology, Akita City (Japan); Ono, Yukihiko [Akita Research Institute of Brain, Akita City (Japan)

    2008-05-15

    {sup 201}Tl has been extensively used for myocardial perfusion and viability assessment. Unlike {sup 99m}Tc-labelled agents, such as {sup 99m}Tc-sestamibi and {sup 99m}Tc-tetrofosmine, the regional concentration of {sup 201}Tl varies with time. This study is intended to validate a kinetic modelling approach for in vivo quantitative estimation of regional myocardial blood flow (MBF) and volume of distribution of {sup 201}Tl using dynamic SPECT. Dynamic SPECT was carried out on 20 normal canines after the intravenous administration of {sup 201}Tl using a commercial SPECT system. Seven animals were studied at rest, nine during adenosine infusion, and four after beta-blocker administration. Quantitative images were reconstructed with a previously validated technique, employing OS-EM with attenuation-correction, and transmission-dependent convolution subtraction scatter correction. Measured regional time-activity curves in myocardial segments were fitted to two- and three-compartment models. Regional MBF was defined as the influx rate constant (K{sub 1}) with corrections for the partial volume effect, haematocrit and limited first-pass extraction fraction, and was compared with that determined from radio-labelled microspheres experiments. Regional time-activity curves responded well to pharmacological stress. Quantitative MBF values were higher with adenosine and decreased after beta-blocker compared to a resting condition. MBFs obtained with SPECT (MBF{sub SPECT}) correlated well with the MBF values obtained by the radio-labelled microspheres (MBF{sub MS}) (MBF{sub SPECT} = -0.067 + 1.042 x MBF{sub MS}, p < 0.001). The three-compartment model provided better fit than the two-compartment model, but the difference in MBF values between the two methods was small and could be accounted for with a simple linear regression. Absolute quantitation of regional MBF, for a wide physiological flow range, appears to be feasible using {sup 201}Tl and dynamic SPECT. (orig.)

  10. An 'attachment kinetics-based' volume of fraction method for organic crystallization: a fluid-dynamic approach to macromolecular-crystal engineering

    International Nuclear Information System (INIS)

    Lappa, Marcello

    2003-01-01

    This analysis exhibits a strong interdisciplinary nature and deals with advances in protein (crystal) engineering models and computational methods as well as with novel results on the relative importance of 'controlling forces' in macromolecular crystal growth. The attention is focused in particular on microgravity fluid-dynamic aspects. From a numerical point of view, the growing crystal gives rise to a moving boundary problem. A 'kinetic-coefficient-based' volume tracking method is specifically and carefully developed according to the complex properties and mechanisms of macromolecular protein crystal growth taking into account the possibility of anisotropic (faceted) surface-orientation-dependent growth. The method is used to shed some light on the interplay of surface attachment kinetics and mass transport (diffusive or convective) in liquid phase and on several mechanisms still poorly understood. It is shown that the size of a growing crystal plays a 'critical role' in the relative importance of surface effects and in determining the intensity of convection. Convective effects, in turn, are found to impact growth rates, macroscopic structures of precipitates, particle size and morphology as well as the mechanisms driving growth. The paper introduces a novel computational method (that simulates the growth due to the slow addition of solute molecules to a lattice and can handle the shape of organic growing crystals under the influence of natural convection) and, at the same time, represents a quite exhaustive attempt to help organic crystal growers to discern the complex interrelations among the various parameters under one's control (that are not independent of one another) and to elaborate rational guidelines relating to physical factors that can influence the probability of success in crystallizing protein substances

  11. Effects of pressure, temperature and atomic exchanges on phase separation dynamics in Au/Ni(111) surface alloy: Kinetic Monte Carlo study

    Energy Technology Data Exchange (ETDEWEB)

    Zvejnieks, G. [Institute for Solid State Physics, University of Latvia, Kengaraga 8, LV-1063 Riga (Latvia); Ibenskas, A., E-mail: ibenskas@pfi.lt [Center for Physical Sciences and Technology, Semiconductor Physics Institute, Gostauto 11, LT-01108 Vilnius (Lithuania); Tornau, E.E. [Center for Physical Sciences and Technology, Semiconductor Physics Institute, Gostauto 11, LT-01108 Vilnius (Lithuania)

    2015-11-15

    Instability of the Au/Ni(111) surface alloy is studied in different CO gas pressure, p, and temperature limits using kinetic Monte Carlo simulations. We analyze the reaction front dynamics and formation of Au clusters using the model which takes into account surface adatom pair and three-body interactions, CO adsorption and desorption, catalytic carbonyl formation reaction, Au and Ni adatom diffusion and their concerted exchange. Variation of interaction parameters allows us to identify three possible reaction front propagation limits with different pressure dependencies: (i) slow channel-like flow in agreement with experimental data [1] (step flow rate, R, increases with p), (ii) intermediate regime (weak p–dependence), and (iii) fast homogeneous flow (R decreases with p). We find that only Au–Ni exchange, contrary to both Ni–CO and Au–CO exchanges, significantly reduces the number of screened Ni atoms inside the Au clusters and stimulates the occurrence of Ni-free Au clusters. The size of Au islands depends on both pressure and temperature. At a fixed temperature it decreases with pressure due to an increased step flow rate. In the high temperature limit, despite the step flow rate exponential increase with temperature, the cluster size increases due to an enhanced Au mobility. - Highlights: • Kinetic Monte Carlo study of Au–Ni surface alloy instability to CO pressure and temperature. • Three reaction front propagation regimes. • In channel-like regime, the step flow rate increases with CO pressure as in experiment. • Ni-free Au islands are obtained when Au-Ni adatom exchange mechanism is considered. • The size of Au islands decreases with pressure and increases with temperature.

  12. Effects of pressure, temperature and atomic exchanges on phase separation dynamics in Au/Ni(111) surface alloy: Kinetic Monte Carlo study

    International Nuclear Information System (INIS)

    Zvejnieks, G.; Ibenskas, A.; Tornau, E.E.

    2015-01-01

    Instability of the Au/Ni(111) surface alloy is studied in different CO gas pressure, p, and temperature limits using kinetic Monte Carlo simulations. We analyze the reaction front dynamics and formation of Au clusters using the model which takes into account surface adatom pair and three-body interactions, CO adsorption and desorption, catalytic carbonyl formation reaction, Au and Ni adatom diffusion and their concerted exchange. Variation of interaction parameters allows us to identify three possible reaction front propagation limits with different pressure dependencies: (i) slow channel-like flow in agreement with experimental data [1] (step flow rate, R, increases with p), (ii) intermediate regime (weak p–dependence), and (iii) fast homogeneous flow (R decreases with p). We find that only Au–Ni exchange, contrary to both Ni–CO and Au–CO exchanges, significantly reduces the number of screened Ni atoms inside the Au clusters and stimulates the occurrence of Ni-free Au clusters. The size of Au islands depends on both pressure and temperature. At a fixed temperature it decreases with pressure due to an increased step flow rate. In the high temperature limit, despite the step flow rate exponential increase with temperature, the cluster size increases due to an enhanced Au mobility. - Highlights: • Kinetic Monte Carlo study of Au–Ni surface alloy instability to CO pressure and temperature. • Three reaction front propagation regimes. • In channel-like regime, the step flow rate increases with CO pressure as in experiment. • Ni-free Au islands are obtained when Au-Ni adatom exchange mechanism is considered. • The size of Au islands decreases with pressure and increases with temperature

  13. Physical kinetics

    International Nuclear Information System (INIS)

    Lifschitz, E.M.; Pitajewski, L.P.

    1983-01-01

    The textbook covers the subject under the following headings: kinetic gas theory, diffusion approximation, collisionless plasma, collisions within the plasma, plasma in the magnetic field, theory of instabilities, dielectrics, quantum fluids, metals, diagram technique for nonequilibrium systems, superconductors, and kinetics of phase transformations

  14. Heparin kinetics

    International Nuclear Information System (INIS)

    Swart, C.A.M. de.

    1983-01-01

    The author has studied the kinetics of heparin and heparin fractions after intravenous administration in humans and in this thesis the results of this study are reported. Basic knowledge about the physico-chemical properties of heparin and its interactions with proteins resulting in anticoagulant and lipolytic effects are discussed in a review (chapter II), which also comprises some clinical aspects of heparin therapy. In chapter III the kinetics of the anticoagulant effect are described after intravenous administration of five commercial heparin preparations. A mathematical model is presented that fits best to these kinetics. The kinetics of the anticoagulant and lipolytic effects after intravenous injection of various 35 S-radiolabelled heparin fractions and their relationship with the disappearance of the radiolabel are described in chapter IV. Chapter V gives a description of the kinetics of two radiolabels after injection of in vitro formed complexes consisting of purified, 125 I-radiolabelled antithrombin III and various 35 S-radiolabelled heparin fractions. (Auth.)

  15. Multi-step cure kinetic model of ultra-thin glass fiber epoxy prepreg exhibiting both autocatalytic and diffusion-controlled regimes under isothermal and dynamic-heating conditions

    Science.gov (United States)

    Kim, Ye Chan; Min, Hyunsung; Hong, Sungyong; Wang, Mei; Sun, Hanna; Park, In-Kyung; Choi, Hyouk Ryeol; Koo, Ja Choon; Moon, Hyungpil; Kim, Kwang J.; Suhr, Jonghwan; Nam, Jae-Do

    2017-08-01

    As packaging technologies are demanded that reduce the assembly area of substrate, thin composite laminate substrates require the utmost high performance in such material properties as the coefficient of thermal expansion (CTE), and stiffness. Accordingly, thermosetting resin systems, which consist of multiple fillers, monomers and/or catalysts in thermoset-based glass fiber prepregs, are extremely complicated and closely associated with rheological properties, which depend on the temperature cycles for cure. For the process control of these complex systems, it is usually required to obtain a reliable kinetic model that could be used for the complex thermal cycles, which usually includes both the isothermal and dynamic-heating segments. In this study, an ultra-thin prepreg with highly loaded silica beads and glass fibers in the epoxy/amine resin system was investigated as a model system by isothermal/dynamic heating experiments. The maximum degree of cure was obtained as a function of temperature. The curing kinetics of the model prepreg system exhibited a multi-step reaction and a limited conversion as a function of isothermal curing temperatures, which are often observed in epoxy cure system because of the rate-determining diffusion of polymer chain growth. The modified kinetic equation accurately described the isothermal behavior and the beginning of the dynamic-heating behavior by integrating the obtained maximum degree of cure into the kinetic model development.

  16. A two-time-scale dynamic-model approach for magnetic and kinetic profile control in advanced tokamak scenarios on JET

    International Nuclear Information System (INIS)

    Moreau, D.; Mazon, D.; Ariola, M.; Tommasi, G. De; Laborde, L.; Piccolo, F.; Sartori, F.; Zabeo, L.; Boboc, A.; Brix, M.; Challis, C.D.; Felton, R.; Hawkes, N.; Tala, T.; Bouvier, E.; Cordoliani, V.; Brzozowski, J.; Cocilovo, V.; Crisanti, F.; Luna, E. de la

    2008-01-01

    Real-time simultaneous control of several radially distributed magnetic and kinetic plasma parameters is being investigated on JET, in view of developing integrated control of advanced tokamak scenarios. This paper describes the new model-based profile controller which has been implemented during the 2006-2007 experimental campaigns. The controller aims to use the combination of heating and current drive (H and CD) systems-and optionally the poloidal field (PF) system-in an optimal way to regulate the evolution of plasma parameter profiles such as the safety factor, q(x), and gyro-normalized temperature gradient, ρ Te *(x). In the first part of the paper, a technique for the experimental identification of a minimal dynamic plasma model is described, taking into account the physical structure and couplings of the transport equations, but making no quantitative assumptions on the transport coefficients or on their dependences. To cope with the high dimensionality of the state space and the large ratio between the time scales involved, the model identification procedure and the controller design both make use of the theory of singularly perturbed systems by means of a two-time-scale approximation. The second part of the paper provides the theoretical basis for the controller design. The profile controller is articulated around two composite feedback loops operating on the magnetic and kinetic time scales, respectively, and supplemented by a feedforward compensation of density variations. For any chosen set of target profiles, the closest self-consistent state achievable with the available actuators is uniquely defined. It is reached, with no steady state offset, through a near-optimal proportional-integral control algorithm. Conventional optimal control is recovered in the limiting case where the ratio of the plasma confinement time to the resistive diffusion time tends to zero. Closed-loop simulations of the controller response have been performed in preparation for

  17. Quantum kinetic theory

    CERN Document Server

    Bonitz, Michael

    2016-01-01

    This book presents quantum kinetic theory in a comprehensive way. The focus is on density operator methods and on non-equilibrium Green functions. The theory allows to rigorously treat nonequilibrium dynamics in quantum many-body systems. Of particular interest are ultrafast processes in plasmas, condensed matter and trapped atoms that are stimulated by rapidly developing experiments with short pulse lasers and free electron lasers. To describe these experiments theoretically, the most powerful approach is given by non-Markovian quantum kinetic equations that are discussed in detail, including computational aspects.

  18. Kinetic models for crowd dynamics. Comment on "Human behaviours in evacuation crowd dynamics: From modelling to "big data" toward crisis management" by N. Bellomo et al.

    Science.gov (United States)

    Banasiak, J.

    2016-09-01

    There has been a hierarchy of models of crowd behaviour. One can consider the crowd at the so called microscopic level, as a collection of individuals, and derive its description in the form of a (large) system of ordinary differential equations describing the position and velocity of each individual, in parallel to the Newton's description of matter, see e.g. [10]. Another possibility is to describe crowd, in analogy to fluid dynamics, by providing its density and velocity at a given point, see e.g. [11,12]. At the same time, it is recognized that crowd is 'living, social' system that is prone to exhibit rare, not easily predictable, behaviour in response to stress induced by the perception of danger, or of the action of specific agents, see e.g. [1,2]. This high probability of the occurrence of events that are far from average, makes the crowd behaviour similar to the processes with fat-tailed distribution of events. Such unlikely events have been metaphorically termed black swans in [14], or Lévy flights in [13]. While microscopic and macroscopic models can capture many features of crowd dynamics, including obstacles, see [3,8], such models are described by differential equations that inherently are local in space. At the same time, black swan events are often caused by non-local interactions such as self-organization, learning or adherence to some averaged group behaviour. It is known that such interactions are well described by mean field models best represented by integro-differential equations, such as the Boltzmann equation of the rarefied gas theory. This has made plausible to introduce crowd models at the intermediate, (meso) scale by describing the crowd by the one particle distribution function that gives the density of individuals at any particular state; that is, at a given point in the domain and moving with a specific velocity.

  19. Prediction of gasoline yield in a fluid catalytic cracking (FCC riser using k-epsilon turbulence and 4-lump kinetic models: A computational fluid dynamics (CFD approach

    Directory of Open Access Journals (Sweden)

    Muhammad Ahsan

    2015-07-01

    Full Text Available Fluid catalytic cracking (FCC is an essential process for the conversion of gas oil to gasoline. This study is an effort to model the phenomenon numerically using commercial computational fluid dynamics (CFD software, heavy density catalyst and 4-lump kinetic model. Geometry, boundary conditions and dimensions of industrial riser for catalytic cracking unit are conferred for 2D simulation using commercial CFD code FLUENT 6.3. Continuity, momentum, energy and species transport equations, applicable to two phase solid and gas flow, are used to simulate the physical phenomenon as efficient as possible. This study implements and predicts the use of the granular Eulerian multiphase model with species transport. Time accurate transient problem is solved with the prediction of mass fraction profiles of gas oil, gasoline, light gas and coke. The output curves demonstrate the breaking of heavy hydrocarbon in the presence of catalyst. An approach proposed in this study shows good agreement with the experimental and numerical data available in the literature.

  20. Towards a fully kinetic 3D electromagnetic particle-in-cell model of streamer formation and dynamics in high-pressure electronegative gases

    International Nuclear Information System (INIS)

    Rose, D. V.; Welch, D. R.; Clark, R. E.; Thoma, C.; Zimmerman, W. R.; Bruner, N.; Rambo, P. K.; Atherton, B. W.

    2011-01-01

    Streamer and leader formation in high pressure devices is dynamic process involving a broad range of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. Accurate modeling of these physical processes is essential for a number of applications, including high-current, laser-triggered gas switches. Towards this end, we present a new 3D implicit particle-in-cell simulation model of gas breakdown leading to streamer formation in electronegative gases. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge [D. R. Welch, T. C. Genoni, R. E. Clark, and D. V. Rose, J. Comput. Phys. 227, 143 (2007)]. The simulation model is fully electromagnetic, making it capable of following, for example, the evolution of a gas switch from the point of laser-induced localized breakdown of the gas between electrodes through the successive stages of streamer propagation, initial electrode current connection, and high-current conduction channel evolution, where self-magnetic field effects are likely to be important. We describe the model details and underlying assumptions used and present sample results from 3D simulations of streamer formation and propagation in SF 6 .

  1. Towards a fully kinetic 3D electromagnetic particle-in-cell model of streamer formation and dynamics in high-pressure electronegative gases

    Science.gov (United States)

    Rose, D. V.; Welch, D. R.; Clark, R. E.; Thoma, C.; Zimmerman, W. R.; Bruner, N.; Rambo, P. K.; Atherton, B. W.

    2011-09-01

    Streamer and leader formation in high pressure devices is dynamic process involving a broad range of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. Accurate modeling of these physical processes is essential for a number of applications, including high-current, laser-triggered gas switches. Towards this end, we present a new 3D implicit particle-in-cell simulation model of gas breakdown leading to streamer formation in electronegative gases. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge [D. R. Welch, T. C. Genoni, R. E. Clark, and D. V. Rose, J. Comput. Phys. 227, 143 (2007)]. The simulation model is fully electromagnetic, making it capable of following, for example, the evolution of a gas switch from the point of laser-induced localized breakdown of the gas between electrodes through the successive stages of streamer propagation, initial electrode current connection, and high-current conduction channel evolution, where self-magnetic field effects are likely to be important. We describe the model details and underlying assumptions used and present sample results from 3D simulations of streamer formation and propagation in SF6.

  2. Kinetics of CO2 diffusion in human carbonic anhydrase: a study using molecular dynamics simulations and the Markov-state model.

    Science.gov (United States)

    Chen, Gong; Kong, Xian; Lu, Diannan; Wu, Jianzhong; Liu, Zheng

    2017-05-10

    Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO 2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO 2 capture and utilization. The diffusion process in the hydrophobic pocket of hCA-II was illustrated in terms of a two-dimensional free-energy landscape. We found that CO 2 diffusion in hCA-II is a rate-limiting step in the CO 2 diffusion-binding-reaction process. The equilibrium distribution of CO 2 shows its preferential accumulation within a hydrophobic domain in the protein core region. An analysis of the committors and reactive fluxes indicates that the main pathway for CO 2 diffusion into the active site of hCA-II is through a binding pocket where residue Gln 136 contributes to the maximal flux. The simulation results offer a new perspective on the CO 2 hydration kinetics and useful insights toward the development of novel biochemical processes for more efficient CO 2 sequestration and utilization.

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

    Science.gov (United States)

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

    2015-08-10

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

  4. Towards a fully kinetic 3D electromagnetic particle-in-cell model of streamer formation and dynamics in high-pressure electronegative gases

    Energy Technology Data Exchange (ETDEWEB)

    Rose, D. V.; Welch, D. R.; Clark, R. E.; Thoma, C.; Zimmerman, W. R.; Bruner, N. [Voss Scientific, LLC, Albuquerque, New Mexico 87108 (United States); Rambo, P. K.; Atherton, B. W. [Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States)

    2011-09-15

    Streamer and leader formation in high pressure devices is dynamic process involving a broad range of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. Accurate modeling of these physical processes is essential for a number of applications, including high-current, laser-triggered gas switches. Towards this end, we present a new 3D implicit particle-in-cell simulation model of gas breakdown leading to streamer formation in electronegative gases. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge [D. R. Welch, T. C. Genoni, R. E. Clark, and D. V. Rose, J. Comput. Phys. 227, 143 (2007)]. The simulation model is fully electromagnetic, making it capable of following, for example, the evolution of a gas switch from the point of laser-induced localized breakdown of the gas between electrodes through the successive stages of streamer propagation, initial electrode current connection, and high-current conduction channel evolution, where self-magnetic field effects are likely to be important. We describe the model details and underlying assumptions used and present sample results from 3D simulations of streamer formation and propagation in SF{sub 6}.

  5. Dynamic determination of kinetic parameters for the interaction between polypeptide hormones and cell-surface receptors in the perfused rat liver by the multiple-indicator dilution method

    International Nuclear Information System (INIS)

    Sato, H.; Sugiyama, Y.; Sawada, Y.; Iga, T.; Sakamoto, S.; Fuwa, T.; Hanano, M.

    1988-01-01

    Hepatic elimination of epidermal growth factor (EGF) via receptor-mediated endocytosis was studied by a multiple-indicator dilution method in the isolated perfused rat liver, in which cell polarity and spatial organization are maintained. In this method EGF was given with inulin, an extracellular reference, as a bolus into the portal vein, and dilution curves of both compounds in the hepatic vein effluent were analyzed. Analysis of the dilution curve for EGF, compared with that for somatostatin, which showed no specific binding to isolated liver plasma membranes, resulted as follows: (i) both extraction ratio and distribution volume of 125 I-labeled EGF decreased as the injected amount of unlabeled EGF increased; (ii) the ratio plot of the dilution curve for EGF exhibited an upward straight line initially for a short period of time, whereas the ratio plot of somatostatin gradually decreased. The multiple-indicator dilution method was used for other peptides also. Insulin and glucagon, known to have hepatocyte receptors, behaved similarly to EGF in shape of their ratio plots. The kinetic parameters calculated by this analysis were comparable with reported values obtained by in vitro direct binding measurements at equilibrium using liver homogenates. They conclude that the multiple-indicator dilution method is a good tool for analyzing the dynamics of peptide hormones-cell-surface receptor interaction under a condition in which spatial architecture of the liver is maintained

  6. Kinetics and dynamics of nanosecond streamer discharge in atmospheric-pressure gas bubble suspended in distilled water under saturated vapor pressure conditions

    KAUST Repository

    Sharma, Ashish

    2016-09-08

    We perform computational studies of nanosecond streamer discharges generated in helium bubbles immersed in distilled water under atmospheric pressure conditions. The model takes into account the presence of water vapor in the gas bubble for an accurate description of the discharge kinetics. We find that the dynamic characteristics of the streamer discharge are different at low and high positive trigger voltages with the axial streamer evolution dominant for low voltages and a surface hugging mode favored for high voltages. We also find a substantial difference in initiation, transition and evolution stages of discharge for positive and negative trigger voltages with the volumetric distribution of species in the streamer channel much more uniform for negative trigger voltages on account of the presence of multiple streamers. We observe that the presence of water vapor does not affect the breakdown voltage even for oversaturated conditions but significantly influences the composition of dominant species in the trail of the streamer as well as the flux of the dominant species on the bubble surface. © 2016 IOP Publishing Ltd.

  7. IMPROVED DERIVATION OF INPUT FUNCTION IN DYNAMIC MOUSE [18F]FDG PET USING BLADDER RADIOACTIVITY KINETICS

    Science.gov (United States)

    Wong, Koon-Pong; Zhang, Xiaoli; Huang, Sung-Cheng

    2013-01-01

    Purpose Accurate determination of the plasma input function (IF) is essential for absolute quantification of physiological parameters in positron emission tomography (PET). However, it requires an invasive and tedious procedure of arterial blood sampling that is challenging in mice because of the limited blood volume. In this study, a hybrid modeling approach is proposed to estimate the plasma IF of 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG) in mice using accumulated radioactivity in urinary bladder together with a single late-time blood sample measurement. Methods Dynamic PET scans were performed on nine isoflurane-anesthetized male C57BL/6 mice after a bolus injection of [18F]FDG at the lateral caudal vein. During a 60- or 90-min scan, serial blood samples were taken from the femoral artery. Image data were reconstructed using filtered backprojection with CT-based attenuation correction. Total accumulated radioactivity in the urinary bladder was fitted to a renal compartmental model with the last blood sample and a 1-exponential function that described the [18F]FDG clearance in blood. Multiple late-time blood sample estimates were calculated by the blood [18F]FDG clearance equation. A sum of 4-exponentials was assumed for the plasma IF that served as a forcing function to all tissues. The estimated plasma IF was obtained by simultaneously fitting the [18F]FDG model to the time-activity curves (TACs) of liver and muscle and the forcing function to early (0–1 min) left-ventricle data (corrected for delay, dispersion, partial-volume effects and erythrocytes uptake) and the late-time blood estimates. Using only the blood sample acquired at the end of the study to estimate the IF and the use of liver TAC as an alternative IF were also investigated. Results The area under the plasma TACs calculated for all studies using the hybrid approach was not significantly different from that using all blood samples. [18F]FDG uptake constants in brain, myocardium, skeletal

  8. Kinetic Interface

    DEFF Research Database (Denmark)

    2009-01-01

    A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises.......A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises....

  9. Kinetics of the H 2O 2-dependent ligninase-catalyzed oxidation of veratryl alcohol in the presence of cationic surfactant studied by spectrophotometric technique

    Science.gov (United States)

    Liu, Airong; Huang, Xirong; Song, Shaofang; Wang, Dan; Lu, Xuemei; Qu, Yinbo; Gao, Peiji

    2003-09-01

    The kinetics of ligninase-catalyzed oxidation of veratryl alcohol (VA) by H 2O 2 in the aqueous medium containing cationic surfactant cetyltrimethylammonium bromide (CTAB) has been investigated using spectrophotometric technique. Steady-state kinetic studies at different concentrations of CTAB indicate that the reaction follows a ping pong mechanism and the mechanism always holds but the kinetic parameters vary with CTAB concentrations. CTAB is a weak inhibitor for ligninase; it lowers the maximum initial velocity. CTAB also causes the Michaelis constant of H 2O 2 to decrease dramatically and that of VA to increase markedly. Based on the changes in kinetic parameters of the enzyme-catalyzed reaction at different CTAB concentrations (lower than, near to and larger than its critical micelle concentration) and the effects of the CTAB monomer and the micelles on the spectra of VA and its corresponding aldehyde, a conclusion could be made that modification of the enzymatic protein by the surfactant monomer should be responsible for the above-mentioned results.

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

    Science.gov (United States)

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

    2018-04-01

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

  11. Delineation and segmentation of cerebral tumors by mapping blood-brain barrier disruption with dynamic contrast-enhanced CT and tracer kinetics modeling-a feasibility study

    International Nuclear Information System (INIS)

    Bisdas, S.; Vogl, T.J.; Yang, X.; Koh, T.S.; Lim, C.C.T.

    2008-01-01

    Dynamic contrast-enhanced (DCE) imaging is a promising approach for in vivo assessment of tissue microcirculation. Twenty patients with clinical and routine computed tomography (CT) evidence of intracerebral neoplasm were examined with DCE-CT imaging. Using a distributed-parameter model for tracer kinetics modeling of DCE-CT data, voxel-level maps of cerebral blood flow (F), intravascular blood volume (v i ) and intravascular mean transit time (t 1 ) were generated. Permeability-surface area product (PS), extravascular extracellular blood volume (v e ) and extraction ratio (E) maps were also calculated to reveal pathologic locations of tracer extravasation, which are indicative of disruptions in the blood-brain barrier (BBB). All maps were visually assessed for quality of tumor delineation and measurement of tumor extent by two radiologists. Kappa (κ) coefficients and their 95% confidence intervals (CI) were calculated to determine the interobserver agreement for each DCE-CT map. There was a substantial agreement for the tumor delineation quality in the F, v e and t 1 maps. The agreement for the quality of the tumor delineation was excellent for the v i , PS and E maps. Concerning the measurement of tumor extent, excellent and nearly excellent agreement was achieved only for E and PS maps, respectively. According to these results, we performed a segmentation of the cerebral tumors on the base of the E maps. The interobserver agreement for the tumor extent quantification based on manual segmentation of tumor in the E maps vs. the computer-assisted segmentation was excellent (κ = 0.96, CI: 0.93-0.99). The interobserver agreement for the tumor extent quantification based on computer segmentation in the mean images and the E maps was substantial (κ = 0.52, CI: 0.42-0.59). This study illustrates the diagnostic usefulness of parametric maps associated with BBB disruption on a physiology-based approach and highlights the feasibility for automatic segmentation of

  12. Relating the variation of secondary structure of gelatin at fish oil-water interface to adsorption kinetics, dynamic interfacial tension and emulsion stability.

    Science.gov (United States)

    Liu, Huihua; Wang, Bo; Barrow, Colin J; Adhikari, Benu

    2014-01-15

    The objectives of this study were to quantify the relationship between secondary structure of gelatin and its adsorption at the fish-oil/water interface and to quantify the implication of the adsorption on the dynamic interfacial tension (DST) and emulsion stability. The surface hydrophobicity of the gelatin solutions decreased when the pH increased from 4.0 to 6.0, while opposite tend was observed in the viscosity of the solution. The DST values decreased as the pH increased from 4.0 to 6.0, indicating that higher positive charges (measured trough zeta potential) in the gelatin solution tended to result in higher DST values. The adsorption kinetics of the gelatin solution was examined through the calculated diffusion coefficients (Deff). The addition of acid promoted the random coil and β-turn structures at the expense of α-helical structure. The addition of NaOH decreased the β-turn and increased the α-helix and random coil. The decrease in the random coil and triple helix structures in the gelatin solution resulted into increased Deff values. The highest diffusion coefficients, the highest emulsion stability and the lowest amount of random coil and triple helix structures were observed at pH=4.8. The lowest amount of random coil and triple helix structures in the interfacial protein layer correlated with the highest stability of the emulsion (highest ESI value). The lower amount of random coil and triple helix structures allowed higher coverage of the oil-water interface by relatively highly ordered secondary structure of gelatin. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Kinetics and

    Directory of Open Access Journals (Sweden)

    Mojtaba Ahmadi

    2016-11-01

    Full Text Available The aqueous degradation of Reactive Yellow 84 (RY84 by potassium peroxydisulfate (K2S2O8 has been studied in laboratory scale experiments. The effect of the initial concentrations of potassium peroxydisulfate and RY84, pH and temperature on RY84 degradation were also examined. Experimental data were analyzed using first and second-order kinetics. The degradation kinetics of RY84 of the potassium peroxydisulfate process followed the second-order reaction kinetics. These rate constants have an extreme values similar to of 9.493 mM−1min−1 at a peroxydisulfate dose of 4 mmol/L. Thermodynamic parameters such as activation (Ea and Gibbs free energy (ΔG° were also evaluated. The negative value of ΔGo and Ea shows the spontaneous reaction natural conditions and exothermic nature.

  14. Granulocyte kinetics

    International Nuclear Information System (INIS)

    Peters, A.M.; Lavender, J.P.; Saverymuttu, S.H.

    1985-01-01

    By using density gradient materials enriched with autologous plasma, the authors have been able to isolate granulocutes from other cellular elements and label them with In-111 without separation from a plasma environment. The kinetic behavior of these cells suggests that phenomena attributed to granulocyte activation are greatly reduced by this labeling. Here, they review their study of granulocyte kinetics in health and disease in hope of quantifying sites of margination and identifying principal sites of destruction. The three principle headings of the paper are distribution, life-span, and destruction

  15. Catecholase activity of dicopper(II)-bispidine complexes: stabilities and structures of intermediates, kinetics and reaction mechanism.

    Science.gov (United States)

    Born, Karin; Comba, Peter; Daubinet, André; Fuchs, Alexander; Wadepohl, Hubert

    2007-01-01

    A mechanism for the oxidation of 3,5-di-tert-butylcatechol (dtbc) with dioxygen to the corresponding quinone (dtbq), catalyzed by bispidine-dicopper complexes (bispidines are various mono- and dinucleating derivatives of 3,7-diazabicyclo[3.3.1]nonane with bis-tertiary-amine-bispyridyl or bis-tertiary-amine-trispyridyl donor sets), is proposed on the basis of (1) the stoichiometry of the reaction as well as the stabilities and structures [X-ray, density functional theory (B3LYP, TZV)] of the bispidine-dicopper(II)-3,4,5,6-tetrachlorcatechol intermediates, (2) formation kinetics and structures (molecular mechanics, MOMEC) of the end-on peroxo-dicopper(II) complexes and (3) kinetics of the stoichiometric (anaerobic) and catalytic (aerobic) copper-complex-assisted oxidation of dtbc. This involves (1) the oxidation of the dicopper(I) complexes with dioxygen to the corresponding end-on peroxo-dicopper(II) complexes, (2) coordination of dtbc as a bridging ligand upon liberation of H(2)O(2) and (3) intramolecular electron transfer to produce dtbq, which is liberated, and the dicopper(I) catalyst. Although the bispidine complexes have reactivities comparable to those of recently published catalysts with macrocyclic ligands, which seem to reproduce the enzyme-catalyzed process in various reaction sequences, a strikingly different oxidation mechanism is derived from the bispidine-dicopper-catalyzed reaction.

  16. Physisorption kinetics

    CERN Document Server

    Kreuzer, Hans Jürgen

    1986-01-01

    This monograph deals with the kinetics of adsorption and desorption of molecules physisorbed on solid surfaces. Although frequent and detailed reference is made to experiment, it is mainly concerned with the theory of the subject. In this, we have attempted to present a unified picture based on the master equation approach. Physisorption kinetics is by no means a closed and mature subject; rather, in writing this monograph we intended to survey a field very much in flux, to assess its achievements so far, and to give a reasonable basis from which further developments can take off. For this reason we have included many papers in the bibliography that are not referred to in the text but are of relevance to physisorption. To keep this monograph to a reasonable size, and also to allow for some unity in the presentation of the material, we had to omit a number of topics related to physisorption kinetics. We have not covered to any extent the equilibrium properties of physisorbed layers such as structures, phase tr...

  17. Stochastic kinetics

    International Nuclear Information System (INIS)

    Colombino, A.; Mosiello, R.; Norelli, F.; Jorio, V.M.; Pacilio, N.

    1975-01-01

    A nuclear system kinetics is formulated according to a stochastic approach. The detailed probability balance equations are written for the probability of finding the mixed population of neutrons and detected neutrons, i.e. detectrons, at a given level for a given instant of time. Equations are integrated in search of a probability profile: a series of cases is analyzed through a progressive criterium. It tends to take into account an increasing number of physical processes within the chosen model. The most important contribution is that solutions interpret analytically experimental conditions of equilibrium (moise analysis) and non equilibrium (pulsed neutron measurements, source drop technique, start up procedures)

  18. Quantum kinetic Ising models

    International Nuclear Information System (INIS)

    Augusiak, R; Cucchietti, F M; Lewenstein, M; Haake, F

    2010-01-01

    In this paper, we introduce a quantum generalization of classical kinetic Ising models (KIM), described by a certain class of quantum many-body master equations. Similarly to KIMs with detailed balance that are equivalent to certain Hamiltonian systems, our models reduce to a set of Hamiltonian systems determining the dynamics of the elements of the many-body density matrix. The ground states of these Hamiltonians are well described by the matrix product, or pair entangled projected states. We discuss critical properties of such Hamiltonians, as well as entanglement properties of their low-energy states.

  19. Tolrestat kinetics

    International Nuclear Information System (INIS)

    Hicks, D.R.; Kraml, M.; Cayen, M.N.; Dubuc, J.; Ryder, S.; Dvornik, D.

    1984-01-01

    The kinetics of tolrestat, a potent inhibitor of aldose reductase, were examined. Serum concentrations of tolrestat and of total 14 C were measured after dosing normal subjects and subjects with diabetes with 14 C-labeled tolrestat. In normal subjects, tolrestat was rapidly absorbed and disappearance from serum was biphasic. Distribution and elimination t 1/2s were approximately 2 and 10 to 12 hr, respectively, after single and multiple doses. Unchanged tolrestat accounted for the major portion of 14 C in serum. Radioactivity was rapidly and completely excreted in urine and feces in an approximate ratio of 2:1. Findings were much the same in subjects with diabetes. In normal subjects, the kinetics of oral tolrestat were independent of dose in the 10 to 800 mg range. Repetitive dosing did not result in unexpected cumulation. Tolrestat was more than 99% bound to serum protein; it did not compete with warfarin for binding sites but was displaced to some extent by high concentrations of tolbutamide or salicylate

  20. Some concepts in condensed phase chemical kinetics

    International Nuclear Information System (INIS)

    Adelman, S.A.

    1986-01-01

    Some concepts in condensed phase chemical kinetics which have emerged from a recent rigorous statistical mechanical treatment of condensed phase chemical reaction dynamics (S.A. Adelman, Adv. Chem. Phys.53:61 (1983)) are discussed in simple physical terms

  1. Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

    Science.gov (United States)

    Flamholz, Avi; Reznik, Ed; Liebermeister, Wolfram; Milo, Ron

    2014-01-01

    In metabolism research, thermodynamics is usually used to determine the directionality of a reaction or the feasibility of a pathway. However, the relationship between thermodynamic potentials and fluxes is not limited to questions of directionality: thermodynamics also affects the kinetics of reactions through the flux-force relationship, which states that the logarithm of the ratio between the forward and reverse fluxes is directly proportional to the change in Gibbs energy due to a reaction (ΔrG′). Accordingly, if an enzyme catalyzes a reaction with a ΔrG′ of -5.7 kJ/mol then the forward flux will be roughly ten times the reverse flux. As ΔrG′ approaches equilibrium (ΔrG′ = 0 kJ/mol), exponentially more enzyme counterproductively catalyzes the reverse reaction, reducing the net rate at which the reaction proceeds. Thus, the enzyme level required to achieve a given flux increases dramatically near equilibrium. Here, we develop a framework for quantifying the degree to which pathways suffer these thermodynamic limitations on flux. For each pathway, we calculate a single thermodynamically-derived metric (the Max-min Driving Force, MDF), which enables objective ranking of pathways by the degree to which their flux is constrained by low thermodynamic driving force. Our framework accounts for the effect of pH, ionic strength and metabolite concentration ranges and allows us to quantify how alterations to the pathway structure affect the pathway's thermodynamics. Applying this methodology to pathways of central metabolism sheds light on some of their features, including metabolic bypasses (e.g., fermentation pathways bypassing substrate-level phosphorylation), substrate channeling (e.g., of oxaloacetate from malate dehydrogenase to citrate synthase), and use of alternative cofactors (e.g., quinone as an electron acceptor instead of NAD). The methods presented here place another arrow in metabolic engineers' quiver, providing a simple means of evaluating

  2. WE-FG-206-06: Dual-Input Tracer Kinetic Modeling and Its Analog Implementation for Dynamic Contrast-Enhanced (DCE-) MRI of Malignant Mesothelioma (MPM)

    Energy Technology Data Exchange (ETDEWEB)

    Lee, S; Rimner, A; Hayes, S; Hunt, M; Deasy, J; Zauderer, M; Rusch, V; Tyagi, N [Memorial Sloan Kettering Cancer Center, New York, NY (United States)

    2016-06-15

    Purpose: To use dual-input tracer kinetic modeling of the lung for mapping spatial heterogeneity of various kinetic parameters in malignant MPM Methods: Six MPM patients received DCE-MRI as part of their radiation therapy simulation scan. 5 patients had the epitheloid subtype of MPM, while one was biphasic. A 3D fast-field echo sequence with TR/TE/Flip angle of 3.62ms/1.69ms/15° was used for DCE-MRI acquisition. The scan was collected for 5 minutes with a temporal resolution of 5-9 seconds depending on the spatial extent of the tumor. A principal component analysis-based groupwise deformable registration was used to co-register all the DCE-MRI series for motion compensation. All the images were analyzed using five different dual-input tracer kinetic models implemented in analog continuous-time formalism: the Tofts-Kety (TK), extended TK (ETK), two compartment exchange (2CX), adiabatic approximation to the tissue homogeneity (AATH), and distributed parameter (DP) models. The following parameters were computed for each model: total blood flow (BF), pulmonary flow fraction (γ), pulmonary blood flow (BF-pa), systemic blood flow (BF-a), blood volume (BV), mean transit time (MTT), permeability-surface area product (PS), fractional interstitial volume (vi), extraction fraction (E), volume transfer constant (Ktrans) and efflux rate constant (kep). Results: Although the majority of patients had epitheloid histologies, kinetic parameter values varied across different models. One patient showed a higher total BF value in all models among the epitheloid histologies, although the γ value was varying among these different models. In one tumor with a large area of necrosis, the TK and ETK models showed higher E, Ktrans, and kep values and lower interstitial volume as compared to AATH and DP and 2CX models. Kinetic parameters such as BF-pa, BF-a, PS, Ktrans values were higher in surviving group compared to non-surviving group across most models. Conclusion: Dual-input tracer

  3. Li+ solvation and kinetics of Li+-BF4-/PF6- ion pairs in ethylene carbonate. A molecular dynamics study with classical rate theories

    Science.gov (United States)

    Chang, Tsun-Mei; Dang, Liem X.

    2017-10-01

    Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ethylene carbonate (EC) exchange process between the first and second solvation shells around Li+ and the dissociation kinetics of ion pairs Li+-[BF4] and Li+-[PF6] in this solvent. We calculate the exchange rates using transition state theory and correct them with transmission coefficients computed by the reactive flux, Impey, Madden, and McDonald approaches, and Grote-Hynes theory. We found that the residence times of EC around Li+ ions varied from 60 to 450 ps, depending on the correction method used. We found that the relaxation times changed significantly from Li+-[BF4] to Li+-[PF6] ion pairs in EC. Our results also show that, in addition to affecting the free energy of dissociation in EC, the anion type also significantly influences the dissociation kinetics of ion pairing.

  4. Dynamical influence of gravity waves generated by the Vestfjella Mountains in Antarctica: radar observations, fine-scale modelling and kinetic energy budget analysis

    Directory of Open Access Journals (Sweden)

    Joel Arnault

    2012-02-01

    Full Text Available Gravity waves generated by the Vestfjella Mountains (in western Droning Maud Land, Antarctica, southwest of the Finnish/Swedish Aboa/Wasa station have been observed with the Moveable atmospheric radar for Antarctica (MARA during the SWEDish Antarctic Research Programme (SWEDARP in December 2007/January 2008. These radar observations are compared with a 2-month Weather Research Forecast (WRF model experiment operated at 2 km horizontal resolution. A control simulation without orography is also operated in order to separate unambiguously the contribution of the mountain waves on the simulated atmospheric flow. This contribution is then quantified with a kinetic energy budget analysis computed in the two simulations. The results of this study confirm that mountain waves reaching lower-stratospheric heights break through convective overturning and generate inertia gravity waves with a smaller vertical wavelength, in association with a brief depletion of kinetic energy through frictional dissipation and negative vertical advection. The kinetic energy budget also shows that gravity waves have a strong influence on the other terms of the budget, i.e. horizontal advection and horizontal work of pressure forces, so evaluating the influence of gravity waves on the mean-flow with the vertical advection term alone is not sufficient, at least in this case. We finally obtain that gravity waves generated by the Vestfjella Mountains reaching lower stratospheric heights generally deplete (create kinetic energy in the lower troposphere (upper troposphere–lower stratosphere, in contradiction with the usual decelerating effect attributed to gravity waves on the zonal circulation in the upper troposphere–lower stratosphere.

  5. Biological-clinical study of radiosensitivity and chemosensitivity of squamous cell carcinoma of the mouth. Growth and regression rates, dynamic histology, and cell kinetics

    International Nuclear Information System (INIS)

    Friedman, M.; Nervi, C.

    1974-01-01

    Effects of combined methotrexate and radiotherapy were studied in 22 patients with advanced squamous cell cancer of the upper air passages. Studies included clinical growth rate of tumor volume prior to treatment, cell kinetics before treatment, electron microscope studies of serial biopsies, response of tumor to methotrexate and radiation, and time and rate of recurrences. Case histories are described for four different types of tumors and results are discussed. (U.S.)

  6. Mechanistic investigations of the hydrolysis of amides, oxoesters and thioesters via kinetic isotope effects and positional isotope exchange.

    Science.gov (United States)

    Robins, Lori I; Fogle, Emily J; Marlier, John F

    2015-11-01

    The hydrolysis of amides, oxoesters and thioesters is an important reaction in both organic chemistry and biochemistry. Kinetic isotope effects (KIEs) are one of the most important physical organic methods for determining the most likely transition state structure and rate-determining step of these reaction mechanisms. This method induces a very small change in reaction rates, which, in turn, results in a minimum disturbance of the natural mechanism. KIE studies were carried out on both the non-enzymatic and the enzyme-catalyzed reactions in an effort to compare both types of mechanisms. In these studies the amides and esters of formic acid were chosen because this molecular structure allowed development of methodology to determine heavy-atom solvent (nucleophile) KIEs. This type of isotope effect is difficult to measure, but is rich in mechanistic information. Results of these investigations point to transition states with varying degrees of tetrahedral character that fit a classical stepwise mechanism. This article is part of a special issue entitled: Enzyme Transition States from Theory and Experiment. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Investigation of Spark Ignition and Autoignition in Methane and Air Using Computational Fluid Dynamics and Chemical Reaction Kinetics. A numerical Study of Ignition Processes in Internal Combustion Engines

    Energy Technology Data Exchange (ETDEWEB)

    Nordrik, R.

    1993-12-01

    The processes in the combustion chamber of internal combustion engines have received increased attention in recent years because their efficiencies are important both economically and environmentally. This doctoral thesis studies the ignition phenomena by means of numerical simulation methods. The fundamental physical relations include flow field conservation equations, thermodynamics, chemical reaction kinetics, transport properties and spark modelling. Special attention is given to the inclusion of chemical kinetics in the flow field equations. Using his No Transport of Radicals Concept method, the author reduces the computational efforts by neglecting the transport of selected intermediate species. The method is validated by comparison with flame propagation data. A computational method is described and used to simulate spark ignition in laminar premixed methane-air mixtures and the autoignition process of a methane bubble surrounded by hot air. The spark ignition simulation agrees well with experimental results from the literature. The autoignition simulation identifies the importance of diffusive and chemical processes acting together. The ignition delay times exceed the experimental values found in the literature for premixed ignition delay, presumably because of the mixing process and lack of information on low temperature reactions in the skeletal kinetic mechanism. Transient turbulent methane jet autoignition is simulated by means of the KIVA-II code. Turbulent combustion is modelled by the Eddy Dissipation Concept. 90 refs., 81 figs., 3 tabs.

  8. The coke drum thermal kinetic effects

    Energy Technology Data Exchange (ETDEWEB)

    Aldescu, Maria M.; Romero, Sim; Larson, Mel [KBC Advanced Technologies plc, Surrey (United Kingdom)

    2012-07-01

    The coke drum thermal kinetic dynamics fundamentally affect the coker unit yields as well as the coke product properties and unit reliability. In the drum the thermal cracking and polymerization or condensation reactions take place in a semi-batch environment. Understanding the fundamentals of the foaming kinetics that occur in the coke drums is key to avoiding a foam-over that could result in a unit shutdown for several months. Although the most dynamic changes with time occur during drum filling, other dynamics of the coker process will be discussed as well. KBC has contributed towards uncovering and modelling the complexities of heavy oil thermal dynamics. (author)

  9. Real-time relationship between PKA biochemical signal network dynamics and increased action potential firing rate in heart pacemaker cells: Kinetics of PKA activation in heart pacemaker cells.

    Science.gov (United States)

    Yaniv, Yael; Ganesan, Ambhighainath; Yang, Dongmei; Ziman, Bruce D; Lyashkov, Alexey E; Levchenko, Andre; Zhang, Jin; Lakatta, Edward G

    2015-09-01

    cAMP-PKA protein kinase is a key nodal signaling pathway that regulates a wide range of heart pacemaker cell functions. These functions are predicted to be involved in regulation of spontaneous action potential (AP) generation of these cells. Here we investigate if the kinetics and stoichiometry of increase in PKA activity match the increase in AP firing rate in response to β-adrenergic receptor (β-AR) stimulation or phosphodiesterase (PDE) inhibition, that alters the AP firing rate of heart sinoatrial pacemaker cells. In cultured adult rabbit pacemaker cells infected with an adenovirus expressing the FRET sensor AKAR3, the EC50 in response to graded increases in the intensity of β-AR stimulation (by Isoproterenol) the magnitude of the increases in PKA activity and the spontaneous AP firing rate were similar (0.4±0.1nM vs. 0.6±0.15nM, respectively). Moreover, the kinetics (t1/2) of the increases in PKA activity and spontaneous AP firing rate in response to β-AR stimulation or PDE inhibition were tightly linked. We characterized the system rate-limiting biochemical reactions by integrating these experimentally derived data into a mechanistic-computational model. Model simulations predicted that phospholamban phosphorylation is a potent target of the increase in PKA activity that links to increase in spontaneous AP firing rate. In summary, the kinetics and stoichiometry of increases in PKA activity in response to a physiological (β-AR stimulation) or pharmacological (PDE inhibitor) stimuli match those of changes in the AP firing rate. Thus Ca(2+)-cAMP/PKA-dependent phosphorylation limits the rate and magnitude of increase in spontaneous AP firing rate. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. The cross-bridge dynamics is determined by two length-independent kinetics: Implications on muscle economy and Frank-Starling Law.

    Science.gov (United States)

    Amiad Pavlov, Daria; Landesberg, Amir

    2016-01-01

    The cellular mechanisms underlying the Frank-Starling Law of the heart and the skeletal muscle force-length relationship are not clear. This study tested the effects of sarcomere length (SL) on the average force per cross-bridge and on the rate of cross-bridge cycling in intact rat cardiac trabeculae (n=9). SL was measured by laser diffraction and controlled with a fast servomotor to produce varying initial SLs. Tetanic contractions were induced by addition of cyclopiazonic acid, to maintain a constant activation. Stress decline and redevelopment in response to identical ramp shortenings, starting at various initial SLs, was analyzed. Both stress decline and redevelopment responses revealed two distinct kinetics: a fast and a slower phase. The duration of the rapid phases (4.2 ± 0.1 msec) was SL-independent. The second slower phase depicted a linear dependence of the rate of stress change on the instantaneous stress level. Identical slopes (70.5 ± 1.6 [1/s], p=0.33) were obtained during ramp shortening at all initial SLs, indicating that the force per cross-bridge and cross-bridge cycling kinetics are length-independent. A decrease in the slope at longer SLs was obtained during stress redevelopment, due to internal shortening. The first phase is attributed to rapid changes in the average force per cross-bridge. The second phase is ascribed to both cross-bridge cycling between its strong and weak conformations and to changes in the number of strong cross-bridges. Cross-bridge cycling kinetics and muscle economy are length-independent and the Frank-Starling Law cannot be attributed to changes in the force per cross-bridge or in the single cross-bridge cycling rates. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Contrast enhancement kinetics of normal breast parenchyma in dynamic MR mammography: effects of menopausal status, oral contraceptives, and postmenopausal hormone therapy

    International Nuclear Information System (INIS)

    Hegenscheid, Katrin; Seipel, Rebecca; Laqua, Rene; Hosten, Norbert; Puls, Ralf; Schmidt, Carsten O.; Ohlinger, Ralf

    2012-01-01

    To investigate effects of menopausal status, oral contraceptives (OC), and postmenopausal hormone therapy (HT) on normal breast parenchymal contrast enhancement (CE) and non-mass-like enhancing areas in magnetic resonance mammography (MRM). A total of 459 female volunteers (mean age 49.1 ± 12.5 years) underwent T1-weighted 3D MRM 1-5 min after bolus injection of gadobutrol. Quantitative analysis was performed in normal breast parenchyma by manually tracing regions of interest and calculating percentage CE. Semiquantitative analysis was performed in non-mass-like enhancing areas, and signal intensity changes were characterised by five predefined kinetic curve types. The influence of OC (n = 69) and HT (n = 24) on CE was studied using random effects models. Breast parenchymal enhancement was significantly higher in premenopausal than in postmenopausal women (P < 0.001). CE decreased significantly with the use of OC (P = 0.01), while HT had negligible effects (P = 0.52). Prevalence of kinetic curve types of non-mass-like enhancement differed strongly between pre- and postmenopausal women (P < 0.0001), but was similar in OC users and non-OC users (P = 0.61) as well as HT users and non-HT users (P = 0.77). Normal breast parenchymal enhancement and non-mass-like enhancing areas were strongly affected by menopausal status, while they were not affected by HT use and only moderately by OC use. (orig.)

  12. Contrast enhancement kinetics of normal breast parenchyma in dynamic MR mammography: effects of menopausal status, oral contraceptives, and postmenopausal hormone therapy

    Energy Technology Data Exchange (ETDEWEB)

    Hegenscheid, Katrin; Seipel, Rebecca; Laqua, Rene; Hosten, Norbert; Puls, Ralf [Ernst-Moritz-Arndt University Medical Center Greifswald, Department of Diagnostic Radiology and Neuroradiology, Greifswald (Germany); Schmidt, Carsten O. [Ernst-Moritz-Arndt University Medical Center Greifswald, Institute for Community Medicine, Greifswald (Germany); Ohlinger, Ralf [Ernst-Moritz-Arndt University Medical Center Greifswald, Department of Gynecology and Obstetrics, Greifswald (Germany)

    2012-12-15

    To investigate effects of menopausal status, oral contraceptives (OC), and postmenopausal hormone therapy (HT) on normal breast parenchymal contrast enhancement (CE) and non-mass-like enhancing areas in magnetic resonance mammography (MRM). A total of 459 female volunteers (mean age 49.1 {+-} 12.5 years) underwent T1-weighted 3D MRM 1-5 min after bolus injection of gadobutrol. Quantitative analysis was performed in normal breast parenchyma by manually tracing regions of interest and calculating percentage CE. Semiquantitative analysis was performed in non-mass-like enhancing areas, and signal intensity changes were characterised by five predefined kinetic curve types. The influence of OC (n = 69) and HT (n = 24) on CE was studied using random effects models. Breast parenchymal enhancement was significantly higher in premenopausal than in postmenopausal women (P < 0.001). CE decreased significantly with the use of OC (P = 0.01), while HT had negligible effects (P = 0.52). Prevalence of kinetic curve types of non-mass-like enhancement differed strongly between pre- and postmenopausal women (P < 0.0001), but was similar in OC users and non-OC users (P = 0.61) as well as HT users and non-HT users (P = 0.77). Normal breast parenchymal enhancement and non-mass-like enhancing areas were strongly affected by menopausal status, while they were not affected by HT use and only moderately by OC use. (orig.)

  13. Kinetic theory and transport phenomena

    CERN Document Server

    Soto, Rodrigo

    2016-01-01

    This textbook presents kinetic theory, which is a systematic approach to describing nonequilibrium systems. The text is balanced between the fundamental concepts of kinetic theory (irreversibility, transport processes, separation of time scales, conservations, coarse graining, distribution functions, etc.) and the results and predictions of the theory, where the relevant properties of different systems are computed. The book is organised in thematic chapters where different paradigmatic systems are studied. The specific features of these systems are described, building and analysing the appropriate kinetic equations. Specifically, the book considers the classical transport of charges, the dynamics of classical gases, Brownian motion, plasmas, and self-gravitating systems, quantum gases, the electronic transport in solids and, finally, semiconductors. Besides these systems that are studied in detail, concepts are applied to some modern examples including the quark–gluon plasma, the motion of bacterial suspen...

  14. Dynamic compensation temperature in the kinetic spin-1 Ising model in an oscillating external magnetic field on alternate layers of a hexagonal lattice

    International Nuclear Information System (INIS)

    Temizer, Umuet; Keskin, Mustafa; Canko, Osman

    2009-01-01

    The dynamic behavior of a two-sublattice spin-1 Ising model with a crystal-field interaction (D) in the presence of a time-varying magnetic field on a hexagonal lattice is studied by using the Glauber-type stochastic dynamics. The lattice is formed by alternate layers of spins σ=1 and S=1. For this spin arrangement, any spin at one lattice site has two nearest-neighbor spins on the same sublattice, and four on the other sublattice. The intersublattice interaction is antiferromagnetic. We employ the Glauber transition rates to construct the mean-field dynamical equations. Firstly, we study time variations of the average magnetizations in order to find the phases in the system, and the temperature dependence of the average magnetizations in a period, which is also called the dynamic magnetizations, to obtain the dynamic phase transition (DPT) points as well as to characterize the nature (continuous and discontinuous) of transitions. Then, the behavior of the total dynamic magnetization as a function of the temperature is investigated to find the types of the compensation behavior. Dynamic phase diagrams are calculated for both DPT points and dynamic compensation effect. Phase diagrams contain the paramagnetic (p) and antiferromagnetic (af) phases, the p+af and nm+p mixed phases, nm is the non-magnetic phase, and the compensation temperature or the L-type behavior that strongly depend on the interaction parameters. For D 0 >3.8275, H 0 is the magnetic field amplitude, the compensation effect does not appear in the system.

  15. Dynamic compensation temperature in the kinetic spin-1 Ising model in an oscillating external magnetic field on alternate layers of a hexagonal lattice

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-10-15

    The dynamic behavior of a two-sublattice spin-1 Ising model with a crystal-field interaction (D) in the presence of a time-varying magnetic field on a hexagonal lattice is studied by using the Glauber-type stochastic dynamics. The lattice is formed by alternate layers of spins {sigma}=1 and S=1. For this spin arrangement, any spin at one lattice site has two nearest-neighbor spins on the same sublattice, and four on the other sublattice. The intersublattice interaction is antiferromagnetic. We employ the Glauber transition rates to construct the mean-field dynamical equations. Firstly, we study time variations of the average magnetizations in order to find the phases in the system, and the temperature dependence of the average magnetizations in a period, which is also called the dynamic magnetizations, to obtain the dynamic phase transition (DPT) points as well as to characterize the nature (continuous and discontinuous) of transitions. Then, the behavior of the total dynamic magnetization as a function of the temperature is investigated to find the types of the compensation behavior. Dynamic phase diagrams are calculated for both DPT points and dynamic compensation effect. Phase diagrams contain the paramagnetic (p) and antiferromagnetic (af) phases, the p+af and nm+p mixed phases, nm is the non-magnetic phase, and the compensation temperature or the L-type behavior that strongly depend on the interaction parameters. For D<2.835 and H{sub 0}>3.8275, H{sub 0} is the magnetic field amplitude, the compensation effect does not appear in the system.

  16. Dynamics

    CERN Document Server

    Goodman, Lawrence E

    2001-01-01

    Beginning text presents complete theoretical treatment of mechanical model systems and deals with technological applications. Topics include introduction to calculus of vectors, particle motion, dynamics of particle systems and plane rigid bodies, technical applications in plane motions, theory of mechanical vibrations, and more. Exercises and answers appear in each chapter.

  17. Resonance transport and kinetic entropy

    International Nuclear Information System (INIS)

    Ivanov, Yu.B.; Knoll, J.; Voskresensky, D.N.

    2000-01-01

    We continue the description of the dynamics of unstable particles within the real-time formulation of nonequilibrium field theory initiated in a previous paper . There we suggest to use Baym's PHI-functional method in order to achieve approximation schemes with 'built in' consistency with respect to conservation laws and thermodynamics even in the case of particles with finite damping width. Starting from Kadanoff-Baym equations we discuss a consistent first order gradient approach to transport which preserves the PHI-derivable properties. The validity conditions for the resulting quantum four-phase-space kinetic theory are discussed under the perspective to treat particles with broad damping widths. This non-equilibrium dynamics naturally includes all those quantum features already inherent in the corresponding equilibrium limit (e.g. Matsubara formalism) at the same level of PHI-derivable approximation. Various collision-term diagrams are discussed including those of higher order which lead to memory effects. As an important novel part we derive a generalized nonequilibrium expression for the kinetic entropy flow, which includes contributions from fluctuations and mass-width effects. In special cases an H-theorem is derived implying that the entropy can only increase with time. Memory effects in the kinetic terms provide contributions to the kinetic entropy flow that in the equilibrium limit recover the famous bosonic type T 3 lnT correction to the specific heat in the case of Fermi liquids like Helium-3

  18. Clinical evaluation of iterative reconstruction (ordered-subset expectation maximization) in dynamic positron emission tomography: quantitative effects on kinetic modeling with N-13 ammonia in healthy subjects

    DEFF Research Database (Denmark)

    Hove, Jens D; Rasmussen, Rune; Freiberg, Jacob

    2008-01-01

    BACKGROUND: The purpose of this study was to investigate the quantitative properties of ordered-subset expectation maximization (OSEM) on kinetic modeling with nitrogen 13 ammonia compared with filtered backprojection (FBP) in healthy subjects. METHODS AND RESULTS: Cardiac N-13 ammonia positron...... emission tomography (PET) studies from 20 normal volunteers at rest and during dipyridamole stimulation were analyzed. Image data were reconstructed with either FBP or OSEM. FBP- and OSEM-derived input functions and tissue curves were compared together with the myocardial blood flow and spillover values...... and OSEM flow values were observed with a flow underestimation of 45% (rest/dipyridamole) in the septum and of 5% (rest) and 15% (dipyridamole) in the lateral myocardial wall. CONCLUSIONS: OSEM reconstruction of myocardial perfusion images with N-13 ammonia and PET produces high-quality images for visual...

  19. Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Li, Minjing [School of Environmental Studies, China University of Geosciences, Wuhan 430074 People' s Republic of China; Gao, Yuqian [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Qian, Wei-Jun [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Shi, Liang [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Liu, Yuanyuan [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Nelson, William C. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Nicora, Carrie D. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Resch, Charles T. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Thompson, Christopher [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Yan, Sen [School of Environmental Studies, China University of Geosciences, Wuhan 430074 People' s Republic of China; Fredrickson, James K. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Zachara, John M. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Liu, Chongxuan [Pacific Northwest National Laboratory, Richland, WA 99354 USA; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055 People' s Republic of China

    2017-07-13

    Microbially mediated biogeochemical processes are catalyzed by enzymes that control the transformation of carbon, nitrogen, and other elements in environment. The dynamic linkage between enzymes and biogeochemical species transformation has, however, rarely been investigated because of the lack of analytical approaches to efficiently and reliably quantify enzymes and their dynamics in soils and sediments. Herein, we developed a signature peptide-based technique for sensitively quantifying dissimilatory and assimilatory enzymes using nitrate-reducing enzymes in a hyporheic zone sediment as an example. Moreover, the measured changes in enzyme concentration were found to correlate with the nitrate reduction rate in a way different from that inferred from biogeochemical models based on biomass or functional genes as surrogates for functional enzymes. This phenomenon has important implications for understanding and modeling the dynamics of microbial community functions and biogeochemical processes in environments. Our results also demonstrate the importance of enzyme quantification for the identification and interrogation of those biogeochemical processes with low metabolite concentrations as a result of faster enzyme-catalyzed consumption of metabolites than their production. The dynamic enzyme behaviors provide a basis for the development of enzyme-based models to describe the relationship between the microbial community and biogeochemical processes.

  20. Kinetics of Social Contagion

    Science.gov (United States)

    Ruan, Zhongyuan; Iñiguez, Gerardo; Karsai, Márton; Kertész, János

    2015-11-01

    Diffusion of information, behavioral patterns or innovations follows diverse pathways depending on a number of conditions, including the structure of the underlying social network, the sensitivity to peer pressure and the influence of media. Here we study analytically and by simulations a general model that incorporates threshold mechanism capturing sensitivity to peer pressure, the effect of "immune" nodes who never adopt, and a perpetual flow of external information. While any constant, nonzero rate of dynamically introduced spontaneous adopters leads to global spreading, the kinetics by which the asymptotic state is approached shows rich behavior. In particular, we find that, as a function of the immune node density, there is a transition from fast to slow spreading governed by entirely different mechanisms. This transition happens below the percolation threshold of network fragmentation, and has its origin in the competition between cascading behavior induced by adopters and blocking due to immune nodes. This change is accompanied by a percolation transition of the induced clusters.

  1. Transition-state analysis of a Vmax mutant of AMP nucleosidase by the application of heavy-atom kinetic isotope effects

    International Nuclear Information System (INIS)

    Parkin, D.W.; Mentch, F.; Banks, G.A.; Horenstein, B.A.; Schramm, V.L.

    1991-01-01

    The transition state of the V max mutant of AMP nucleosidase from Azotobacter vinelandii has been characterized by heavy-atom kinetic isotope effects in the presence and absence of MgATP, the allosteric activator. The enzyme catalyzes hydrolysis of the N-glycosidic bond of AMP at approximately 2% of the rate of the normal enzyme with only minor changes in the K m for substrate, the activation constant for MgATP, and the K i for formycin 5'-phosphate, a tight-binding competitive inhibitor. Isotope effects were measured as a function of the allosteric activator concentration that increases the turnover number of the enzyme from 0.006 s -1 . The kinetic isotope effects were measured with the substrates [1'- 3 H]AMP, [2'- 2 H]AMP, [9- 15 N]AMP, and [1',9- 14 C, 15 N]AMP. All substrates gave significant kinetic isotope effects in a pattern that establishes that the reaction expresses intrinsic kinetic isotope effects in the presence or absence of MgATP. Transition-state analysis using bond-energy and bond-order vibrational analysis indicated that the transition state for the mutant enzyme has a similar position in the reaction coordinate compared to that for the normal enzyme. The mutant enzyme is less effective in stabilizing the carbocation-like intermediate and in the ability to protonate N7 of adenine to create a better leaving group. This altered transition-state structure was confirmed by an altered substrate specificity for the mutant protein

  2. Improved evaluation of antivascular cancer therapy using constrained tracer-kinetic modeling for multi-agent dynamic contrast-enhanced MRI

    NARCIS (Netherlands)

    Hectors, Stefanie; Jacobs, Igor; Lok, Jasper; Peters, Johannes; Bussink, Johan; Hoeben, Freek J. M.; Keizer, Henk; Janssen, Henk M.; Nicolay, Klaas; Schabel, Matthias; Strijkers, Gustav

    2018-01-01

    Dynamic contrast-enhanced MRI (DCE-MRI) is a promising technique for assessing the response of tumor vasculature to anti-vascular therapies. Multi-agent DCE-MRI employs a combination of low and high molecular weight contrast agents, which potentially improves the accuracy of estimation of tumor

  3. Extraction, purification, kinetic and thermodynamic properties of urease from germinating Pisum Sativum L. seeds

    Science.gov (United States)

    2014-01-01

    Background Urease, one of the highly efficient known enzymes, catalyzes the hydrolysis of urea into ammonia and carbon dioxide. The present study aimed to extract urease from pea seeds (Pisum Sativum L). The enzyme was then purified in three consequence steps: acetone precipitation, DEAE-cellulose ion-exchange chromatography, and gel filtration chromatography (Sephacryl S-200 column). Results The purification fold was 12.85 with a yield of 40%. The molecular weight of the isolated urease was estimated by chromatography to be 269,000 Daltons. Maximum urease activity (190 U/g) was achieved at the optimum conditions of 40°C and pH of 7.5 after 5 min of incubation. The kinetic parameters, K m and V max , were estimated by Lineweaver-Burk fits and found to be 500 mM and 333.3 U/g, respectively. The thermodynamic constants of activation, ΔH, E a , and ΔS, were determined using Arrhenius plot and found to be 21.20 kJ/mol, 23.7 kJ/mol, and 1.18 kJ/mol/K, respectively. Conclusions Urease was purified from germinating Pisum Sativum L. seeds. The purification fold, yield, and molecular weight were determined. The effects of pH, concentration of enzyme, temperature, concentration of substrate, and storage period on urease activity were examined. This may provide an insight on the various aspects of the property of the enzyme. The significance of extracting urease from different sources could play a good role in understanding the metabolism of urea in plants. PMID:25065975

  4. Flash kinetics in liquefied noble gases: Studies of alkane activation and ligand dynamics at rhodium carbonyl centers, and a search for xenon-carbene adducts

    Energy Technology Data Exchange (ETDEWEB)

    Yeston, Jake Simon [Univ. of California, Berkeley, CA (United States)

    2001-01-01

    A general introduction is given to place the subsequent chapters in context for the nonspecialist. Results are presented from a low temperature infrared (IR) flash kinetic study of C-H bond activation via photoinduced reaction of Cp*Rh(CO)2 (1) with linear and cyclic alkanes in liquid krypton and liquid xenon solution. No reaction was observed with methane; for all other hydrocarbons studied, the rate law supports fragmentation of the overall reaction into an alkane binding step followed by an oxidative addition step. For the binding step, larger alkanes within each series (linear and cyclic) interact more strongly than smaller alkanes with the Rh center. The second step, oxidative addition of the C-H bond across Rh, exhibits very little variance in the series of linear alkanes, while in the cyclic series the rate decreases with increasing alkane size. Results are presented from an IR flash kinetic study of the photoinduced chemistry of Tp*Rh(CO)2 (5; Tp* = hydridotris(3,5-dimethylpyrazolyl)borato) in liquid xenon solution at –50 °C. IR spectra of the solution taken 2 μs after 308 nm photolysis exhibit two transient bands at 1972-1980 cm-1 and 1992-2000 cm-1, respectively. These bands were assigned to (η3-Tp*)Rh(CO)•Xe and (η2-Tp*)Rh(CO)•Xe solvates on the basis of companion studies using Bp*Rh(CO)2 (9; Bp* = dihydridobis(3,5-dimethyl pyrazolyl)borato). Preliminary kinetic data for reaction of 5 with cyclohexane in xenon solution indicate that both transient bands still appear and that their rates of decay correlate with formation of the product Tp*Rh(CO)(C6H11)(H). The preparation and reactivity of the new complex Bp*Rh(CO)(pyridine) (11) are described. The complex reacts with CH3I to yield the novel Rh carbene hydride complex HB(Me2pz)2Rh(H)(I)(C5H5N)(C(O)Me) (12), resulting from formal addition of CH

  5. Degradation of pharmaceuticals in UV (LP)/H₂O₂ reactors simulated by means of kinetic modeling and computational fluid dynamics (CFD).

    Science.gov (United States)

    Wols, B A; Harmsen, D J H; Wanders-Dijk, J; Beerendonk, E F; Hofman-Caris, C H M

    2015-05-15

    UV/H2O2 treatment is a well-established technique to degrade organic micropollutants. A CFD model in combination with an advanced kinetic model is presented to predict the degradation of organic micropollutants in UV (LP)/H2O2 reactors, accounting for the hydraulics, fluence rate, complex (photo)chemical reactions in the water matrix and the interactions between these processes. The model incorporates compound degradation by means of direct UV photolysis, OH radical and carbonate radical reactions. Measurements of pharmaceutical degradations in pilot-scale UV/H2O2 reactors are presented under different operating conditions. A comparison between measured and modeled degradation for a group of 35 pharmaceuticals resulted in good model predictions for most of the compounds. The research also shows that the degradation of organic micropollutants can be dependent on temperature, which is relevant for full-scale installations that are operated at different temperatures over the year. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. The influence of precipitation kinetics on trace element partitioning between solid and liquid solutions: A coupled fluid dynamics/thermodynamics framework to predict distribution coefficients

    Science.gov (United States)

    Kavner, A.

    2017-12-01

    In a multicomponent multiphase geochemical system undergoing a chemical reaction such as precipitation and/or dissolution, the partitioning of species between phases is determined by a combination of thermodynamic properties and transport processes. The interpretation of the observed distribution of trace elements requires models integrating coupled chemistry and mechanical transport. Here, a framework is presented that predicts the kinetic effects on the distribution of species between two reacting phases. Based on a perturbation theory combining Navier-Stokes fluid flow and chemical reactivity, the framework predicts rate-dependent partition coefficients in a variety of different systems. We present the theoretical framework, with applications to two systems: 1. species- and isotope-dependent Soret diffusion of species in a multicomponent silicate melt subjected to a temperature gradient, and 2. Elemental partitioning and isotope fractionation during precipitation of a multicomponent solid from a multicomponent liquid phase. Predictions will be compared with results from experimental studies. The approach has applications for understanding chemical exchange in at boundary layers such as the Earth's surface magmatic systems and at the core/mantle boundary.

  7. Cesium removal and kinetics equilibrium: Precipitation kinetics

    International Nuclear Information System (INIS)

    Barnes, M.J.

    1999-01-01

    This task consisted of both non-radioactive and radioactive (tracer) tests examining the influence of potentially significant variables on cesium tetraphenylborate precipitation kinetics. The work investigated the time required to reach cesium decontamination and the conditions that affect the cesium precipitation kinetics

  8. Kinetic Stability May Determine the Interaction Dynamics of the Bifunctional Protein DCoH1, the Dimerization Cofactor of the Transcription Factor HNF-1[alpha

    Energy Technology Data Exchange (ETDEWEB)

    Rho, H.; Jones, C.N.; Rose, R.B. (NCSU)

    2010-12-07

    The two disparate functions of DCoH1 (dimerization cofactor of HNF-1)/PCD (pterin-4a-carbinolamine dehydratase) are associated with a change in oligomeric state. DCoH dimers enhance the activity of the diabetes-associated transcription factor HNF-1{alpha} (hepatocyte nuclear factor-1{alpha}), while the PCD activity of DCoH1 homotetramers aids in aromatic amino acid metabolism. These complexes compete for the same interface of the DCoH dimer. Formation of the DCoH1/HNF-1{alpha} complex requires cofolding. The homotetramer of the DCoH1 paralogue, DCoH2, interacts with HNF-1{alpha} through simple mixing. To further investigate regulation of DCoH/HNF-1{alpha} complex formation, we measured the stability of the DCoH1 homotetramer through unfolding studies by intrinsic tryptophan fluorescence. DCoH2 unfolding is reversible. Surprisingly, the DCoH1 homotetramer is resistant to guanidine unfolding but refolds at a much lower guanidine concentration. We show that a point mutation at the DCoH1 tetramer interface, Thr 51 Ser, overcomes the dissociation barrier of the homotetramer and increases the interaction with HNF-1{alpha}. The 1.8 {angstrom} resolution crystal structure of DCoH1 T51S shows the presence of an ordered water molecule at the tetramer interface, as in DCoH2, which may destabilize the homotetramer. The equilibrium unfolding data were fit to a two-state model with no apparent intermediate. Folding intermediates were detectable by size exclusion chromatography. For wild-type DCoH1 the intermediates changed with time, suggesting a kinetic origin for the unfolding barrier of the homotetramer. We propose an unfolding pathway in which the tetramer unfolds slowly, but the dimer folds reversibly. Implications for regulation of DCoH1/HNF-1{alpha} complex formation are discussed.

  9. Global genome response of Escherichia coli O157∶H7 Sakai during dynamic changes in growth kinetics induced by an abrupt downshift in water activity.

    Directory of Open Access Journals (Sweden)

    Chawalit Kocharunchitt

    Full Text Available The present study was undertaken to investigate growth kinetics and time-dependent change in global expression of Escherichia coli O157∶H7 Sakai upon an abrupt downshift in water activity (aw. Based on viable count data, shifting E. coli from aw 0.993 to aw 0.985 or less caused an apparent loss, then recovery, of culturability. Exponential growth then resumed at a rate characteristic for the aw imposed. To understand the responses of this pathogen to abrupt osmotic stress, we employed an integrated genomic and proteomic approach to characterize its cellular response during exposure to a rapid downshift but still within the growth range from aw 0.993 to aw 0.967. Of particular interest, genes and proteins with cell envelope-related functions were induced during the initial loss and subsequent recovery of culturability. This implies that cells undergo remodeling of their envelope composition, enabling them to adapt to osmotic stress. Growth at low aw, however, involved up-regulating additional genes and proteins, which are involved in the biosynthesis of specific amino acids, and carbohydrate catabolism and energy generation. This suggests their important role in facilitating growth under such stress. Finally, we highlighted the ability of E. coli to activate multiple stress responses by transiently inducing the RpoE and RpoH regulons to control protein misfolding, while simultaneously activating the master stress regulator RpoS to mediate long-term adaptation to hyperosmolality. This investigation extends our understanding of the potential mechanisms used by pathogenic E. coli to adapt, survive and grow under osmotic stress, which could potentially be exploited to aid the selection and/or development of novel strategies to inactivate this pathogen.

  10. Plasma kinetic theory

    International Nuclear Information System (INIS)

    Elliott, J.A.

    1993-01-01

    Plasma kinetic theory is discussed and a comparison made with the kinetic theory of gases. The plasma is described by a modified set of fluid equations and it is shown how these fluid equations can be derived. (UK)

  11. Photo-crosslinkable cyanoacrylate bioadhesive: shrinkage kinetics, dynamic mechanical properties, and biocompatibility of adhesives containing TMPTMA and POSS nanostructures as crosslinking agents.

    Science.gov (United States)

    Ghasaban, S; Atai, M; Imani, M; Zandi, M; Shokrgozar, M-A

    2011-11-01

    The study investigates the photo-polymerization shrinkage behavior, dynamic mechanical properties, and biocompatibility of cyanoacrylate bioadhesives containing POSS nanostructures and TMPTMA as crosslinking agents. Adhesives containing 2-octyl cyanoacrylate (2-OCA) and different percentages of POSS nanostructures and TMPTMA as crosslinking agents were prepared. The 1-phenyl-1, 2-propanedione (PPD) was incorporated as photo-initiator into the adhesive in 1.5, 3, and 4 wt %. The shrinkage strain of the specimens was measured using bonded-disk technique. Shrinkage strain, shrinkage strain rate, maximum and time at maximum shrinkage strain rate were measured and compared. Mechanical properties of the adhesives were also studied using dynamic mechanical thermal analysis (DMTA). Biocompatibility of the adhesives was examined by MTT method. The results showed that shrinkage strain increased with increasing the initiator concentration up to 3 wt % in POSS-containing and 1.5 wt % in TMPTMA-containing specimens and plateaued out at higher concentrations. By increasing the crosslinking agent, shrinkage strain, and shrinkage strain rate increased and the time at maximum shrinkage strain rate decreased. The study indicates that the incorporation of crosslinking agents into the cyanoacrylate adhesives resulted in improved mechanical properties. Preliminary MTT studies also revealed better biocompatibility profile for the adhesives containing crosslinking agents comparing to the neat specimens. Copyright © 2011 Wiley Periodicals, Inc.

  12. Sheared Rotation Effects on Kinetic Stability in Enhanced Confinement Tokamak Plasmas, and Nonlinear Dynamics of Fluctuations and Flows in Axisymmetric Plasmas

    International Nuclear Information System (INIS)

    Beer, M.A.; Chance, M.S.; Hahm, T.S.; Lin, Z.; Rewoldt, G.; Tang, W.M.

    1997-01-01

    Sheared rotation dynamics are widely believed to have signficant influence on experimentally observed confinement transitions in advanced operating modes in major tokamak experiments, such as the Tokamak Fusion Test Reactor (TFTR) [D.J. Grove and D.M. Meade, Nuclear Fusion 25, 1167 (1985)], with reversed magnetic shear regions in the plasma interior. The high-n toroidal drift modes destabilized by the combined effects of ion temperature gradients and trapped particles in toroidal geometry can be strongly affected by radially sheared toroidal and poloidal plasma rotation. In previous work with the FULL linear microinstability code, a simplified rotation model including only toroidal rotation was employed, and results were obtained. Here, a more complete rotation model, that includes contributions from toroidal and poloidal rotation and the ion pressure gradient to the total radial electric field, is used for a proper self-consistent treatment of this key problem. Relevant advanced operating mode cases for TFTR are presented. In addition, the complementary problem of the dynamics of fluctuation-driven E x B flow is investigated by an integrated program of gyrokinetic simulation in annulus geometry and gyrofluid simulation in flux tube geometry

  13. Relationship between morphological features and kinetic patterns of enhancement of the dynamic breast magnetic resonance imaging and clinico-pathological and biological factors in invasive breast cancer

    International Nuclear Information System (INIS)

    Fernández-Guinea, Oscar; Andicoechea, Alejandro; González, Luis O; González-Reyes, Salomé; Merino, Antonio M; Hernández, Luis C; López-Muñiz, Alfonso; García-Pravia, Paz; Vizoso, Francisco J

    2010-01-01

    To investigate the relationship between the magnetic resonance imaging (MRI) features of breast cancer and its clinicopathological and biological factors. Dynamic MRI parameters of 68 invasive breast carcinomas were investigated. We also analyzed microvessel density (MVD), estrogen and progesterone receptor status, and expression of p53, HER2, ki67, VEGFR-1 and 2. Homogeneous enhancement was significantly associated with smaller tumor size (T1: < 2 cm) (p = 0.015). Tumors with irregular or spiculated margins had a significantly higher MVD than tumors with smooth margins (p = 0.038). Tumors showing a maximum enhancement peak at two minutes, or longer, after injecting the contrast, had a significantly higher MVD count than those which reached this point sooner (p = 0.012). The percentage of tumors with vascular invasion or high mitotic index was significantly higher among those showing a low percentage (≤ 150%) of maximum enhancement before two minutes than among those ones showing a high percentage (>150%) of enhancement rate (p = 0.016 and p = 0.03, respectively). However, there was a significant and positive association between the mitotic index and the peak of maximum intensity (p = 0.036). Peritumor inflammation was significantly associated with washout curve type III (p = 0.042). Variations in the early phase of dynamic MRI seem to be associated with parameters indicatives of tumor aggressiveness in breast cancer

  14. Mild and Highly Flexible Enzyme-Catalyzed Modification of Poly (ethersulfone) Membranes

    NARCIS (Netherlands)

    Nady, N.; Schroën, C.G.P.H.; Franssen, M.C.R.; Lagen, van B.; Murali, S.; Boom, R.M.; Mohyeldin, M.S.; Zuilhof, H.

    2011-01-01

    Poly(ethersulfone) (PES) membranes are widely used in industry for separation and purification purposes. However, the drawback of this type of membranes is fouling by proteins. For that reason, modification of PES membranes has been studied to enhance their protein repellence. This paper presents

  15. Enzyme-catalyzed modification of PES surfaces: Reduction in adsorption of BSA, dextrin and tannin

    NARCIS (Netherlands)

    Nady, N.; Schroën, C.G.P.H.; Franssen, M.C.R.; Fokkink, R.G.; Mohy Eldin, M.S.; Zuilhof, H.; Boom, R.M.

    2012-01-01

    Poly(ethersulfone) (PES) can be modified in a flexible manner using mild, environmentally benign components such as 4-hydroxybenzoic acid and gallic acid, which can be attached to the surface via catalysis by the enzyme laccase. This leads to grafting of mostly linear polymeric chains (for

  16. Influence of the reaction conditions on the enzyme catalyzed transesterification of castor oil

    DEFF Research Database (Denmark)

    Andrade, Thalles Allan; Errico, Massimiliano; Christensen, Knud Villy

    2017-01-01

    The identification of the influence of the reaction parameters is of paramount importance when defining a process design. In this work, non-edible castor oil was reacted with methanol to produce a possible component for biodiesel blends, using liquid enzymes as the catalyst. Temperature, alcohol......-to-oil molar ratio, enzyme and added water contents were the reaction parameters evaluated in the transesterification reactions. The optimal conditions, giving the optimal final FAME yield and FFA content in the methyl ester-phase was identified. At 35 °C, 6.0 methanol-to-oil molar ratio, 5 wt% of enzyme and 5...... wt% of water contents, 94 % of FAME yield and 6.1 % of FFA in the final composition were obtained. The investigation was completed with the analysis of the component profiles, showing that at least 8 hours are necessary to reach a satisfactory FAME yield together with a minor FFA content....

  17. Enzyme-catalyzed synthesis of unsaturated aliphatic polyesters based on green monomers from renewable resources

    NARCIS (Netherlands)

    Jiang, Yi; Woortman, Albert J J; van Ekenstein, Gert O R Alberda; Loos, Katja

    2013-01-01

    Bio-based commercially available succinate, itaconate and 1,4-butanediol are enzymatically co-polymerized in solution via a two-stage method, using Candida antarctica Lipase B (CALB, in immobilized form as Novozyme® 435) as the biocatalyst. The chemical structures of the obtained products,

  18. Enzyme-catalyzed hydrolysis of dentin adhesives containing a new urethane-based trimethacrylate monomer

    Science.gov (United States)

    Park, Jong-Gu; Ye, Qiang; Topp, Elizabeth M.; Spencer, Paulette

    2009-01-01

    A new trimethacrylate monomer with urethane-linked groups, 1,1,1-tri-[4-(methacryloxyethylamino-carbonyloxy)-phenyl]ethane (MPE), was synthesized, characterized, and used as a co-monomer in dentin adhesives. Dentin adhesives containing 2-hydroxyethyl methacrylate (HEMA, 45% w/w) and 2,2-bis[4(2-hydroxy-3-methacryloyloxy-propyloxy)-phenyl] propane (BisGMA, 30% w/w) in addition to MPE (25% w/w) were formulated with H2O at 0 (MPE0), 8 (MPE8) and 16 wt % water (MPE16) to simulate the wet demineralized dentin matrix and compared with controls [HEMA/BisGMA, 45/55 w/w, at 0 (C0), 8 (C8) and 16 wt% water (C16)]. The new adhesive showed a degree of double bond conversion and mechanical properties comparable with control, with good penetration into the dentin surface and a uniform adhesive/dentin interface. On exposure to porcine liver esterase, the net cumulative methacrylic acid (MAA) release from the new adhesives was dramatically (P < 0.05) decreased relative to the control, suggesting that the new monomer improves esterase resistance. PMID:19582843

  19. Enzyme-Catalyzed Oxidation of 17β-Estradiol Using Immobilized Laccase from Trametes versicolor

    Science.gov (United States)

    Cardinal-Watkins, Chantale; Nicell, Jim A.

    2011-01-01

    Many natural and synthetic estrogens are amenable to oxidation through the catalytic action of oxidative enzymes such as the fungal laccase Trametes versicolor. This study focused on characterizing the conversion of estradiol (E2) using laccase that had been immobilized by covalent bonding onto silica beads contained in a bench-scale continuous-flow packed bed reactor. Conversion of E2 accomplished in the reactor declined when the temperature of the system was changed from room temperature to just above freezing at pH 5 as a result of a reduced rate of reaction rather than inactivation of the enzyme. Similarly, conversion increased when the system was brought to warmer temperatures. E2 conversion increased when the pH of the influent to the immobilized laccase reactor was changed from pH 7 to pH 5, but longer-term experiments showed that the enzyme is more stable at pH 7. Results also showed that the immobilized laccase maintained its activity when treating a constant supply of aqueous E2 at a low mean residence time over a 12-hour period and when treating a constant supply of aqueous E2 at a high mean residence time over a period of 9 days. PMID:21869925

  20. The effect of oxidation on the enzyme-catalyzed hydrolytic biodegradation of poly(urethane)s.

    Science.gov (United States)

    Labow, Rosalind S; Tang, Yiwen; McCloskey, Christopher B; Santerre, J Paul

    2002-01-01

    Although the biodegradation of polyurethanes (PU) by oxidative and hydrolytic agents has been studied extensively, few investigations have reported on the combination of their effects. Since neutrophils (PMN) arrive at an implanted device first and release HOCl, followed by monocyte-derived macrophages (MDM) which have potent esterase activities and oxidants of their own, the combined effect of oxidative and hydrolytic degradation on radiolabeled polycarbonate-polyurethanes (PCNU)s was investigated and compared to that of a polyester-PU (PESU) and a polyether-PU (PEU). The PCNUs were synthesized with PCN (MW = 1,000), and butanediol (14C-BD) and one of two diisocyanates, hexane-1,6-diisocyanate (14C-HDI) or methylene bis-p-phenyl diisocyanate (MDI). The PESU and PEU were synthesized using toluene-diisocyanate (14C-TDI), with polycaprolactone and polytetramethylene oxide as soft segments respectively, and ethylene diamine as the chain extender. The effect of pre-treatment with 0.1 mM HOC1 for 1 week on the HDI-based PCNUs and both TDI-based PUs resulted in a significant inhibition of radiolabel release (RR) elicited by cholesterol esterase (CE), when compared to buffer alone, whereas the MDI-based PCNU showed a small but significant increase. When PMN were activated on the HDI-based PCNU surface with phorbol myristate acetate (PMA), HOCl was released for 3 h, and was almost completely abolished by sodium azide (AZ). Simultaneously, the PMN-elicited RR, shown previously to be due to the esterolytic cleavage by serine proteases, was inhibited approximately 75% by PMA-activation of the cells, but significantly increased relative to the latter when AZ was added. Both in vitro oxidation by HOCl and the release of HOCI by PMN were associated with the inhibition of RR and suggest perturbations between oxidative and hydrolytic mechanisms of biodegradation.

  1. Synthesis of 2-monoacylglycerols and structured triacylglycerols rich in polyunsaturated fatty acids by enzyme catalyzed reactions.

    Science.gov (United States)

    Rodríguez, Alicia; Esteban, Luis; Martín, Lorena; Jiménez, María José; Hita, Estrella; Castillo, Beatriz; González, Pedro A; Robles, Alfonso

    2012-08-10

    This paper studies the synthesis of structured triacylglycerols (STAGs) by a four-step process: (i) obtaining 2-monoacylglycerols (2-MAGs) by alcoholysis of cod liver oil with several alcohols, catalyzed by lipases Novozym 435, from Candida antartica and DF, from Rhizopus oryzae, (ii) purification of 2-MAGs, (iii) formation of STAGs by esterification of 2-MAGs with caprylic acid catalyzed by lipase DF, from R. oryzae, and (iv) purification of these STAGs. For the alcoholysis of cod liver oil, absolute ethanol, ethanol 96% (v/v) and 1-butanol were compared; the conditions with ethanol 96% were then optimized and 2-MAG yields of around 54-57% were attained using Novozym 435. In these 2-MAGs, DHA accounted for 24-31% of total fatty acids. In the operational conditions this lipase maintained a stable level of activity over at least 11 uses. These results were compared with those obtained with lipase DF, which deactivated after only three uses. The alcoholysis of cod liver oil and ethanol 96% catalyzed by Novozym 435 was scaled up by multiplying the reactant amounts 100-fold and maintaining the intensity of treatment constant (IOT=3g lipase h/g oil). In these conditions, the 2-MAG yield attained was about 67%; these 2-MAGs contained 36.6% DHA. The synthesized 2-MAGs were separated and purified from the alcoholysis reaction products by solvent extraction using solvents of low toxicity (ethanol and hexane); 2-MAG recovery yield and purity of the target product were approximately 96.4% and 83.9%, respectively. These 2-MAGs were transformed to STAGs using the optimal conditions obtained in a previous work. After synthesis and purification, 93% pure STAGs were obtained, containing 38% DHA at sn-2 position and 60% caprylic acid (CA) at sn-1,3 positions (of total fatty acids at these positions), i.e. the major TAG is the STAG with the structure CA-DHA-CA. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. The Effect of Temperature on the Enzyme-Catalyzed Reaction: Insights from Thermodynamics

    Science.gov (United States)

    Aledo, Juan Carlos; Jimenez-Riveres, Susana; Tena, Manuel

    2010-01-01

    When teaching the effect of temperature on biochemical reactions, the problem is usually oversimplified by confining the thermal effect to the catalytic constant, which is identified with the rate constant of the elementary limiting step. Therefore, only positive values for activation energies and values greater than 1 for temperature coefficients…

  3. Enzyme-Catalyzed Synthesis of Saccharide Acrylate Monomers from Nonedible Biomass

    NARCIS (Netherlands)

    Kloosterman, Wouter M. J.; Brouwer, Sander; Loos, Katja

    Various cellulase preparations were found to catalyze the transglycosidation between cotton linters and 2-hydroxyethyl acrylate. The conversion and enzyme activity were found to be optimal in reaction mixtures that contained 5 vol% of the acrylate. The structures of the products were revealed by

  4. Identification of Critical Parameters in Liquid Enzyme-Catalyzed Biodiesel Production

    DEFF Research Database (Denmark)

    Nordblad, Mathias; Silva, Vanessa T. L.; Nielsen, Per Munk

    2014-01-01

    CalleraTM Trans L, a liquid formulation of Thermomyces lanuginosus lipase, has recently shown great promise as a cost-efficient catalyst for methanolysis of triglyceride substrates, specifically in the BioFAME process. However, identifying the right combination of temperature and concentrations o...

  5. Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions

    International Nuclear Information System (INIS)

    Malik, Radhika; Viola, Ronald E.

    2010-01-01

    The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2 (angstrom) resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg 2+ and NADH. This TDH structure from Pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. However, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identification of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate intermediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH.

  6. Beta-D-xylosidase from Selenomonas ruminantium: thermodynamics of enzyme-catalyzed and noncatalyzed reactions

    Science.gov (United States)

    Beta-D-xylosidase/alpha-L-arabinofuranosidase from Selenomonas ruminantium (SXA) is the most active enzyme known for catalyzing hydrolysis of 1,4-beta-D-xylooligosaccharides to D-xylose. Temperature dependence for hydrolysis of 4-nitrophenyl-beta-D-xylopyranoside (4NPX), 4-nitrophenyl-alpha-L-arabi...

  7. Principles of magnetoplasma dynamics

    International Nuclear Information System (INIS)

    Woods, L.C.

    1987-01-01

    A self-contained account is given of magnetoplasma dynamics covering fluid dynamics, thermodynamics, kinetic theory of gases, particle dynamics and electromagnetism. The six chapter headings are, basic concepts, magnetohydrodynamics, dynamics of charged particles, transport in a magnetoplasma, magnetoplasma shock waves, and transport in tokamaks. There are 231 references. (U.K.)

  8. Dynamic disorder in single-molecule Michaelis-Menten kinetics: The reaction-diffusion formalism in the Wilemski-Fixman approximation

    Science.gov (United States)

    Chaudhury, Srabanti; Cherayil, Binny J.

    2007-09-01

    Single-molecule equations for the Michaelis-Menten [Biochem. Z. 49, 333 (1913)] mechanism of enzyme action are analyzed within the Wilemski-Fixman [J. Chem. Phys. 58, 4009 (1973); 60, 866 (1974)] approximation after the effects of dynamic disorder—modeled by the anomalous diffusion of a particle in a harmonic well—are incorporated into the catalytic step of the reaction. The solution of the Michaelis-Menten equations is used to calculate the distribution of waiting times between successive catalytic turnovers in the enzyme β-galactosidase. The calculated distribution is found to agree qualitatively with experimental results on this enzyme obtained at four different substrate concentrations. The calculations are also consistent with measurements of correlations in the fluctuations of the fluorescent light emitted during the course of catalysis, and with measurements of the concentration dependence of the randomness parameter.

  9. Use of 3H-colesterol and its kinetics to assess the dynamics of the cholesterol metabolism in human lipoprotein fractions

    International Nuclear Information System (INIS)

    Grossmann, K.D.; Marek, H.; Fieber, R.S.

    1982-01-01

    The assessment of the dynamics of 3 H cholesterols in very low, low and high density lipoproteins, resp. lipoproteins after oral administration in normal subjects and in patients with hyperlipoproteinemia type II a and II b is described. Specific activity-time-curves of the lipoprotein fractions isolated by means of discontinuous ultracentrifugation were recorded. In order to optimize the centrifugation activity-electrophoresis-profiles of the separating steps were recorded. The fractions obtained were characterized by the determination of cholesterol, agarose electrophoresis and radioactivity measurement. The turnover of the tracer in the lipoproteins was determined on the basis of the maximum values of the specific activity-time-curves. Hyperlipoproteinemia patients showed time shifts of the maximum values especially with regard to esterized cholesterols and high density lipoprotein cholesterol as compared to healthy persons. (author)

  10. Kinetic approach to relativistic dissipation

    Science.gov (United States)

    Gabbana, A.; Mendoza, M.; Succi, S.; Tripiccione, R.

    2017-08-01

    Despite a long record of intense effort, the basic mechanisms by which dissipation emerges from the microscopic dynamics of a relativistic fluid still elude complete understanding. In particular, several details must still be finalized in the pathway from kinetic theory to hydrodynamics mainly in the derivation of the values of the transport coefficients. In this paper, we approach the problem by matching data from lattice-kinetic simulations with analytical predictions. Our numerical results provide neat evidence in favor of the Chapman-Enskog [The Mathematical Theory of Non-Uniform Gases, 3rd ed. (Cambridge University Press, Cambridge, U.K., 1970)] procedure as suggested by recent theoretical analyses along with qualitative hints at the basic reasons why the Chapman-Enskog expansion might be better suited than Grad's method [Commun. Pure Appl. Math. 2, 331 (1949), 10.1002/cpa.3160020403] to capture the emergence of dissipative effects in relativistic fluids.

  11. Probing the effect of the non-active-site mutation Y229W in New Delhi metallo-β-lactamase-1 by site-directed mutagenesis, kinetic studies, and molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Jiao Chen

    Full Text Available New Delhi metallo-β-lactamase-1 (NDM-1 has attracted extensive attention for its high catalytic activities of hydrolyzing almost all β-lactam antibiotics. NDM-1 shows relatively higher similarity to subclass B1 metallo-β-lactamases (MβLs, but its residue at position 229 is identical to that of B2/B3 MβLs, which is a Tyr instead of a B1-MβL-conserved Trp. To elucidate the possible role of Y229 in the bioactivity of NDM-1, we performed mutagenesis study and molecular dynamics (MD simulations. Although residue Y229 is spatially distant from the active site and not contacting directly with the substrate or zinc ions, the Y229W mutant was found to have higher kcat and Km values than those of wild-type NDM-1, resulting in 1 ∼ 7 fold increases in k(cat /K(m values against tested antibiotics. In addition, our MD simulations illustrated the enhanced flexibility of Loop 2 upon Y229W mutation, which could increase the kinetics of both substrate entrance (kon and product egress (koff. The enhanced flexibility of Loop 2 might allow the enzyme to adjust the geometry of its active site to accommodate substrates with different structures, broadening its substrate spectrum. This study indicated the possible role of the residue at position 229 in the evolution of NDM-1.

  12. Growth kinetics and structural perfection of (InN){sub 1}/(GaN){sub 1–20} short-period superlattices on +c-GaN template in dynamic atomic layer epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Kusakabe, Kazuhide; Hashimoto, Naoki; Wang, Ke; Imai, Daichi [Center for SMART Green Innovation Research, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522 (Japan); Itoi, Takaomi [Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522 (Japan); Yoshikawa, Akihiko, E-mail: yoshi@faculty.chiba-u.jp [Center for SMART Green Innovation Research, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522 (Japan); Graduate School of Engineering, Kogakuin University, Hachioji, Tokyo 192-0015 (Japan)

    2016-04-11

    The growth kinetics and structural perfection of (InN){sub 1}/(GaN){sub 1–20} short-period superlattices (SPSs) were investigated with their application to ordered alloys in mind. The SPSs were grown on +c-GaN template at 650 °C by dynamic atomic layer epitaxy in conventional plasma-assisted molecular beam epitaxy. It was found that coherent structured InN/GaN SPSs could be fabricated when the thickness of the GaN barrier was 4 ML or above. Below 3 ML, the formation of SPSs was quite difficult owing to the increased strain in the SPS structure caused by the use of GaN as a template. The effective or average In composition of the (InN){sub 1}/(GaN){sub 4} SPSs was around 10%, and the corresponding InN coverage in the ∼1 ML-thick InN wells was 50%. It was found that the effective InN coverage in ∼1 ML-thick InN wells could be varied with the growth conditions. In fact, the effective In composition could be increased up to 13.5%, i.e., the corresponding effective InN coverage was about 68%, by improving the capping/freezing speed by increasing the growth rate of the GaN barrier layer.

  13. Growth kinetics and structural perfection of (InN)_1/(GaN)_1_–_2_0 short-period superlattices on +c-GaN template in dynamic atomic layer epitaxy

    International Nuclear Information System (INIS)

    Kusakabe, Kazuhide; Hashimoto, Naoki; Wang, Ke; Imai, Daichi; Itoi, Takaomi; Yoshikawa, Akihiko

    2016-01-01

    The growth kinetics and structural perfection of (InN)_1/(GaN)_1_–_2_0 short-period superlattices (SPSs) were investigated with their application to ordered alloys in mind. The SPSs were grown on +c-GaN template at 650 °C by dynamic atomic layer epitaxy in conventional plasma-assisted molecular beam epitaxy. It was found that coherent structured InN/GaN SPSs could be fabricated when the thickness of the GaN barrier was 4 ML or above. Below 3 ML, the formation of SPSs was quite difficult owing to the increased strain in the SPS structure caused by the use of GaN as a template. The effective or average In composition of the (InN)_1/(GaN)_4 SPSs was around 10%, and the corresponding InN coverage in the ∼1 ML-thick InN wells was 50%. It was found that the effective InN coverage in ∼1 ML-thick InN wells could be varied with the growth conditions. In fact, the effective In composition could be increased up to 13.5%, i.e., the corresponding effective InN coverage was about 68%, by improving the capping/freezing speed by increasing the growth rate of the GaN barrier layer.

  14. Molecular and Silica-Supported Molybdenum Alkyne Metathesis Catalysts: Influence of Electronics and Dynamics on Activity Revealed by Kinetics, Solid-State NMR, and Chemical Shift Analysis.

    Science.gov (United States)

    Estes, Deven P; Gordon, Christopher P; Fedorov, Alexey; Liao, Wei-Chih; Ehrhorn, Henrike; Bittner, Celine; Zier, Manuel Luca; Bockfeld, Dirk; Chan, Ka Wing; Eisenstein, Odile; Raynaud, Christophe; Tamm, Matthias; Copéret, Christophe

    2017-12-06

    Molybdenum-based molecular alkylidyne complexes of the type [MesC≡Mo{OC(CH 3 ) 3-x (CF 3 ) x } 3 ] (MoF 0 , x = 0; MoF 3 , x = 1; MoF 6 , x = 2; MoF 9 , x = 3; Mes = 2,4,6-trimethylphenyl) and their silica-supported analogues are prepared and characterized at the molecular level, in particular by solid-state NMR, and their alkyne metathesis catalytic activity is evaluated. The 13 C NMR chemical shift of the alkylidyne carbon increases with increasing number of fluorine atoms on the alkoxide ligands for both molecular and supported catalysts but with more shielded values for the supported complexes. The activity of these catalysts increases in the order MoF 0 molecular and supported species. Detailed solid-state NMR analysis of molecular and silica-supported metal alkylidyne catalysts coupled with DFT/ZORA calculations rationalize the NMR spectroscopic signatures and discernible activity trends at the frontier orbital level: (1) increasing the number of fluorine atoms lowers the energy of the π*(M≡C) orbital, explaining the more deshielded chemical shift values; it also leads to an increased electrophilicity and higher reactivity for catalysts up to MoF 6 , prior to a sharp decrease in reactivity for MoF 9 due to the formation of stable metallacyclobutadiene intermediates; (2) the silica-supported catalysts are less active than their molecular analogues because they are less electrophilic and dynamic, as revealed by their 13 C NMR chemical shift tensors.

  15. Design and Fabrication of an Instrumented Handrim to Measure the Kinetic and Kinematic Information by the Hand of User for 3D Analysis of Manual Wheelchair Propulsion Dynamics

    Science.gov (United States)

    Mallakzadeh, Mohammadreza; Akbari, Hossein

    2014-01-01

    The repetitious nature of propelling a wheelchair has been associated with the high incidence of injury among manual wheelchair users (MWUs), mainly in the shoulder, elbow and wrist. Recent literature has found a link between handrim biomechanics and risk of injury to the upper extremity. The valid measurement of three-dimensional net joint forces and torques, however, can lead to a better understanding of the mechanisms of injury, the development of prevention techniques, and the reduction of serious injuries to the joints. In this project, an instrumented wheel system was developed to measure the applied loads dynamically by the hand of the user and the angular position of the wheelchair user's hand on the handrim during the propulsion phase. The system is composed of an experimental six-axis load cell, and a wireless eight channel data logger mounted on a wheel hub. The angular position of the wheel is measured by an absolute magnetic encoder. The angular position of the wheelchair user's hand on the handrim during the propulsion phase (ɸ) or point of force application (PFA) is calculated by means of a new-experimental method using 36 pairs of infrared emitter/receiver diodes mounted around the handrim. In this regard, the observed data extracted from an inexperienced able-bodied subject pushed a wheelchair with the instrumented handrim are presented to show the output behavior of the instrumented handrim. The recorded forces and torques were in agreement with previously reported magnitudes. However, this paper can provide readers with some technical insights into possible solutions for measuring the manual wheelchair propulsion biomechanical data. PMID:25426429

  16. Predictive value of modeled AUC(AFP-hCG), a dynamic kinetic parameter characterizing serum tumor marker decline in patients with nonseminomatous germ cell tumor.

    Science.gov (United States)

    You, Benoit; Fronton, Ludivine; Boyle, Helen; Droz, Jean-Pierre; Girard, Pascal; Tranchand, Brigitte; Ribba, Benjamin; Tod, Michel; Chabaud, Sylvie; Coquelin, Henri; Fléchon, Aude

    2010-08-01

    The early decline profile of alpha-fetoprotein (AFP) and human chorionic gonadotropin (hCG) in patients with nonseminomatous germ cell tumors (NSGCT) treated with chemotherapy may be related to the risk of relapse. We assessed the predictive values of areas under the curve of hCG (AUC(hCG)) and AFP (AUC(AFP)) of modeled concentration-time equations on progression-free survival (PFS). Single-center retrospective analysis of hCG and AFP time-points from 65 patients with IGCCCG intermediate-poor risk NSGCT treated with 4 cycles of bleomycin-etoposide-cisplatin (BEP). To determine AUC(hCG) and AUC(AFP) for D0-D42, AUCs for D0-D7 were calculated using the trapezoid rule and AUCs for D7-D42 were calculated using the mathematic integrals of equations modeled with NONMEM. Combining AUC(AFP) and AUC(hCG) enabled us to define 2 predictive groups: namely, patients with favorable and unfavorable AUC(AFP-hCG). Survival analyses and ROC curves assessed the predictive values of AUC(AFP-hCG) groups regarding progression-free survival (PFS) and compared them with those of half-life (HL) and time-to-normalization (TTN). Mono-exponential models best fit the patterns of marker decreases. Patients with a favorable AUC(AFP-hCG) had a significantly better PFS (100% vs 71.5%, P = .014). ROC curves confirmed the encouraging predictive accuracy of AUC(AFP-hCG) against HL or TTN regarding progression risk (ROC AUCs = 79.6 vs 71.9 and 70.2 respectively). Because of the large number of patients with missing data, multivariate analysis could not be performed. AUC(AFP-hCG) is a dynamic parameter characterizing tumor marker decline in patients with NSGCT during BEP treatment. Its value as a promising predictive factor should be validated. Copyright 2010 Elsevier Inc. All rights reserved.

  17. Design and Fabrication of an Instrumented Handrim to Measure the Kinetic and Kinematic Information by the Hand of User for 3D Analysis of Manual Wheelchair Propulsion Dynamics.

    Science.gov (United States)

    Mallakzadeh, Mohammadreza; Akbari, Hossein

    2014-10-01

    The repetitious nature of propelling a wheelchair has been associated with the high incidence of injury among manual wheelchair users (MWUs), mainly in the shoulder, elbow and wrist. Recent literature has found a link between handrim biomechanics and risk of injury to the upper extremity. The valid measurement of three-dimensional net joint forces and torques, however, can lead to a better understanding of the mechanisms of injury, the development of prevention techniques, and the reduction of serious injuries to the joints. In this project, an instrumented wheel system was developed to measure the applied loads dynamically by the hand of the user and the angular position of the wheelchair user's hand on the handrim during the propulsion phase. The system is composed of an experimental six-axis load cell, and a wireless eight channel data logger mounted on a wheel hub. The angular position of the wheel is measured by an absolute magnetic encoder. The angular position of the wheelchair user's hand on the handrim during the propulsion phase (ɸ) or point of force application (PFA) is calculated by means of a new-experimental method using 36 pairs of infrared emitter/receiver diodes mounted around the handrim. In this regard, the observed data extracted from an inexperienced able-bodied subject pushed a wheelchair with the instrumented handrim are presented to show the output behavior of the instrumented handrim. The recorded forces and torques were in agreement with previously reported magnitudes. However, this paper can provide readers with some technical insights into possible solutions for measuring the manual wheelchair propulsion biomechanical data.

  18. Longitudinal studies of the 18F-FDG kinetics after ipilimumab treatment in metastatic melanoma patients based on dynamic FDG PET/CT.

    Science.gov (United States)

    Sachpekidis, Christos; Anwar, Hoda; Winkler, Julia K; Kopp-Schneider, Annette; Larribere, Lionel; Haberkorn, Uwe; Hassel, Jessica C; Dimitrakopoulou-Strauss, Antonia

    2018-06-05

    Immunotherapy has raised the issue of appropriate treatment response evaluation, due to the unique mechanism of action of the immunotherapeutic agents. Aim of this analysis is to evaluate the potential role of quantitative analysis of 2-deoxy-2-( 18 F)fluoro-D-glucose ( 18 F-FDG) positron emission tomography/computed tomography (PET/CT) data in monitoring of patients with metastatic melanoma undergoing ipilimumab therapy. 25 patients with unresectable metastatic melanoma underwent dynamic PET/CT (dPET/CT) of the thorax and upper abdomen as well as static, whole body PET/CT with 18 F-FDG before the start of ipilimumab treatment (baseline PET/CT), after two cycles of treatment (interim PET/CT) and at the end of treatment after four cycles (late PET/CT). The evaluation of dPET/CT studies was based on semi-quantitative (standardized uptake value, SUV) calculation as well as quantitative analysis, based on two-tissue compartment modeling and a fractal approach. Patients' best clinical response, assessed at a mean of 59 weeks, was used as reference. According to their best clinical response, patients were dichotomized in those demonstrating clinical benefit (CB, n = 16 patients) and those demonstrating no clinical benefit (no-CB, n = 9 patients). No statistically significant differences were observed between CB and no-CB regarding either semi-quantitative or quantitative parameters in all scans. On contrary, the application of the recently introduced PET response evaluation criteria for immunotherapy (PERCIMT) led to a correct classification rate of 84% (21/25 patients). Quantitative analysis of 18 F-FDG PET data does not provide additional information in treatment response evaluation of metastatic melanoma patients receiving ipilimumab. PERCIMT criteria correlated better with clinical response.

  19. Fundamental aspects of plasma chemical physics kinetics

    CERN Document Server

    Capitelli, Mario; Colonna, Gianpiero; Esposito, Fabrizio; Gorse, Claudine; Hassouni, Khaled; Laricchiuta, Annarita; Longo, Savino

    2016-01-01

    Describing non-equilibrium "cold" plasmas through a chemical physics approach, this book uses the state-to-state plasma kinetics, which considers each internal state as a new species with its own cross sections. Extended atomic and molecular master equations are coupled with Boltzmann and Monte Carlo methods to solve the electron energy distribution function. Selected examples in different applied fields, such as microelectronics, fusion, and aerospace, are presented and discussed including the self-consistent kinetics in RF parallel plate reactors, the optimization of negative ion sources and the expansion of high enthalpy flows through nozzles of different geometries. The book will cover the main aspects of the state-to-state kinetic approach for the description of nonequilibrium cold plasmas, illustrating the more recent achievements in the development of kinetic models including the self-consistent coupling of master equations and Boltzmann equation for electron dynamics. To give a complete portrayal, the...

  20. A discontinuous Galerkin method on kinetic flocking models

    OpenAIRE

    Tan, Changhui

    2014-01-01

    We study kinetic representations of flocking models. They arise from agent-based models for self-organized dynamics, such as Cucker-Smale and Motsch-Tadmor models. We prove flocking behavior for the kinetic descriptions of flocking systems, which indicates a concentration in velocity variable in infinite time. We propose a discontinuous Galerkin method to treat the asymptotic $\\delta$-singularity, and construct high order positive preserving scheme to solve kinetic flocking systems.

  1. Kinetic theory of radiation effects

    International Nuclear Information System (INIS)

    Mansur, L.K.

    1987-01-01

    To help achieve the quantitative and mechanistic understanding of these processes, the kinetic theory of radiation effects has been developed in the DOE basic energy sciences radiation effects and fusion reactor materials programs, as well as in corresponding efforts in other countries. This discipline grapples with a very wide range of phenomena and draws on numerous sub-fields of theory such as defect physics, diffusion, elasticity, chemical reaction rates, phase transformations and thermodynamics. The theory is cast in a mathematical framework of continuum dynamics. Issues particularly relevant to the present inquiry can be viewed from the standpoints of applications of the theory and areas requiring further progress

  2. Principles of chemical kinetics

    CERN Document Server

    House, James E

    2007-01-01

    James House's revised Principles of Chemical Kinetics provides a clear and logical description of chemical kinetics in a manner unlike any other book of its kind. Clearly written with detailed derivations, the text allows students to move rapidly from theoretical concepts of rates of reaction to concrete applications. Unlike other texts, House presents a balanced treatment of kinetic reactions in gas, solution, and solid states. The entire text has been revised and includes many new sections and an additional chapter on applications of kinetics. The topics covered include quantitative rela

  3. Introduction to chemical kinetics

    CERN Document Server

    Soustelle, Michel

    2013-01-01

    This book is a progressive presentation of kinetics of the chemical reactions. It provides complete coverage of the domain of chemical kinetics, which is necessary for the various future users in the fields of Chemistry, Physical Chemistry, Materials Science, Chemical Engineering, Macromolecular Chemistry and Combustion. It will help them to understand the most sophisticated knowledge of their future job area. Over 15 chapters, this book present the fundamentals of chemical kinetics, its relations with reaction mechanisms and kinetic properties. Two chapters are then devoted to experimental re

  4. Improved Kinetic Models for High-Speed Combustion Simulation

    National Research Council Canada - National Science Library

    Montgomery, C. J; Tang, Q; Sarofim, A. F; Bockelie, M. J; Gritton, J. K; Bozzelli, J. W; Gouldin, F. C; Fisher, E. M; Chakravarthy, S

    2008-01-01

    Report developed under an STTR contract. The overall goal of this STTR project has been to improve the realism of chemical kinetics in computational fluid dynamics modeling of hydrocarbon-fueled scramjet combustors...

  5. Nonlinear Kinetics on Lattices Based on the Kinetic Interaction Principle

    Directory of Open Access Journals (Sweden)

    Giorgio Kaniadakis

    2018-06-01

    Full Text Available Master equations define the dynamics that govern the time evolution of various physical processes on lattices. In the continuum limit, master equations lead to Fokker–Planck partial differential equations that represent the dynamics of physical systems in continuous spaces. Over the last few decades, nonlinear Fokker–Planck equations have become very popular in condensed matter physics and in statistical physics. Numerical solutions of these equations require the use of discretization schemes. However, the discrete evolution equation obtained by the discretization of a Fokker–Planck partial differential equation depends on the specific discretization scheme. In general, the discretized form is different from the master equation that has generated the respective Fokker–Planck equation in the continuum limit. Therefore, the knowledge of the master equation associated with a given Fokker–Planck equation is extremely important for the correct numerical integration of the latter, since it provides a unique, physically motivated discretization scheme. This paper shows that the Kinetic Interaction Principle (KIP that governs the particle kinetics of many body systems, introduced in G. Kaniadakis, Physica A 296, 405 (2001, univocally defines a very simple master equation that in the continuum limit yields the nonlinear Fokker–Planck equation in its most general form.

  6. Kinetic equation solution by inverse kinetic method

    International Nuclear Information System (INIS)

    Salas, G.

    1983-01-01

    We propose a computer program (CAMU) which permits to solve the inverse kinetic equation. The CAMU code is written in HPL language for a HP 982 A microcomputer with a peripheral interface HP 9876 A ''thermal graphic printer''. The CAMU code solves the inverse kinetic equation by taking as data entry the output of the ionization chambers and integrating the equation with the help of the Simpson method. With this program we calculate the evolution of the reactivity in time for a given disturbance

  7. Intramolecular and nonlinear dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Davis, M.J. [Argonne National Laboratory, IL (United States)

    1993-12-01

    Research in this program focuses on three interconnected areas. The first involves the study of intramolecular dynamics, particularly of highly excited systems. The second area involves the use of nonlinear dynamics as a tool for the study of molecular dynamics and complex kinetics. The third area is the study of the classical/quantum correspondence for highly excited systems, particularly systems exhibiting classical chaos.

  8. Studies in Chemical Dynamics

    International Nuclear Information System (INIS)

    Rabitz, Herschel; Ho, Tak-San

    2003-01-01

    This final report draws together the research carried from February, 1986 through January, 2003 concerning a series of topics in chemical dynamics. The specific areas of study include molecular collisions, chemical kinetics, data inversion to extract potential energy surfaces, and model reduction of complex kinetic systems

  9. Kinetics in radiation chemistry

    International Nuclear Information System (INIS)

    Hummel, A.

    1987-01-01

    In this chapter the authors first briefly review the kinetics of first- and second-order processes for continuous and pulsed irradiation, without taking the effects of nonhomogeneous formation of the species into consideration. They also discuss diffusion controlled reactions under conditions where interactions of more than two particles can be neglected, first the kinetics of the diffusion-controlled reaction of randomly generated species (homogeneous reaction) and then that of isolated pairs of reactants. The latter is often called geminate kinetics when dealing with pairs of oppositely charged species; they shall use this term for the kinetics of isolated pairs in general. In the last section they discuss briefly the kinetics of groups of more than two reactants

  10. Enzyme Catalysis and the Gibbs Energy

    Science.gov (United States)

    Ault, Addison

    2009-01-01

    Gibbs-energy profiles are often introduced during the first semester of organic chemistry, but are less often presented in connection with enzyme-catalyzed reactions. In this article I show how the Gibbs-energy profile corresponds to the characteristic kinetics of a simple enzyme-catalyzed reaction. (Contains 1 figure and 1 note.)

  11. Adhesion kinetics of human primary monocytes, dendritic cells, and macrophages: Dynamic cell adhesion measurements with a label-free optical biosensor and their comparison with end-point assays.

    Science.gov (United States)

    Orgovan, Norbert; Ungai-Salánki, Rita; Lukácsi, Szilvia; Sándor, Noémi; Bajtay, Zsuzsa; Erdei, Anna; Szabó, Bálint; Horvath, Robert

    2016-09-01

    Monocytes, dendritic cells (DCs), and macrophages (MFs) are closely related immune cells that differ in their main functions. These specific functions are, to a considerable degree, determined by the differences in the adhesion behavior of the cells. To study the inherently and essentially dynamic aspects of the adhesion of monocytes, DCs, and MFs, dynamic cell adhesion assays were performed with a high-throughput label-free optical biosensor [Epic BenchTop (BT)] on surfaces coated with either fibrinogen (Fgn) or the biomimetic copolymer PLL-g-PEG-RGD. Cell adhesion profiles typically reached their maximum at ∼60 min after cell seeding, which was followed by a monotonic signal decrease, indicating gradually weakening cell adhesion. According to the biosensor response, cell types could be ordered by increasing adherence as monocytes, MFs, and DCs. Notably, all three cell types induced a larger biosensor signal on Fgn than on PLL-g-PEG-RGD. To interpret this result, the molecular layers were characterized by further exploiting the potentials of the biosensor: by measuring the adsorption signal induced during the surface coating procedure, the authors could estimate the surface density of adsorbed molecules and, thus, the number of binding sites potentially presented for the adhesion receptors. Surfaces coated with PLL-g-PEG-RGD presented less RGD sites, but was less efficient in promoting cell spreading than those coated with Fgn; hence, other binding sites in Fgn played a more decisive role in determining cell adherence. To support the cell adhesion data obtained with the biosensor, cell adherence on Fgn-coated surfaces 30-60 min after cell seeding was measured with three complementary techniques, i.e., with (1) a fluorescence-based classical adherence assay, (2) a shear flow chamber applying hydrodynamic shear stress to wash cells away, and (3) an automated micropipette using vacuum-generated fluid flow to lift cells up. These techniques confirmed the results

  12. Non-kinetic capabilities: complementing the kinetic prevalence to targeting

    OpenAIRE

    Ducheine, P.

    2014-01-01

    Targeting is used in military doctrine to describe a military operational way, using (military) means to influence a target (or addressee) in order to achieve designated political and/or military goals. The four factors italicized are used to analyse non-kinetic targeting, complementing our knowledge and understanding of the kinetic prevalence. Paradoxically, non-kinetic targeting is not recognized as a separate concept: kinetic and non-kinetic are intertwined facets of targeting. Kinetic tar...

  13. Kinetics of phase transformations

    International Nuclear Information System (INIS)

    Thompson, M.O.; Aziz, M.J.; Stephenson, G.B.

    1992-01-01

    This volume contains papers presented at the Materials Research Society symposium on Kinetics of Phase Transformations held in Boston, Massachusetts from November 26-29, 1990. The symposium provided a forum for research results in an exceptionally broad and interdisciplinary field. Presentations covered nearly every major class of transformations including solid-solid, liquid-solid, transport phenomena and kinetics modeling. Papers involving amorphous Si, a dominant topic at the symposium, are collected in the first section followed by sections on four major areas of transformation kinetics. The symposium opened with joint sessions on ion and electron beam induced transformations in conjunction with the Surface Chemistry and Beam-Solid Interactions: symposium. Subsequent sessions focused on the areas of ordering and nonlinear diffusion kinetics, solid state reactions and amorphization, kinetics and defects of amorphous silicon, and kinetics of melting and solidification. Seven internationally recognized invited speakers reviewed many of the important problems and recent results in these areas, including defects in amorphous Si, crystal to glass transformations, ordering kinetics, solid-state amorphization, computer modeling, and liquid/solid transformations

  14. Modeling in applied sciences a kinetic theory approach

    CERN Document Server

    Pulvirenti, Mario

    2000-01-01

    Modeling complex biological, chemical, and physical systems, in the context of spatially heterogeneous mediums, is a challenging task for scientists and engineers using traditional methods of analysis Modeling in Applied Sciences is a comprehensive survey of modeling large systems using kinetic equations, and in particular the Boltzmann equation and its generalizations An interdisciplinary group of leading authorities carefully develop the foundations of kinetic models and discuss the connections and interactions between model theories, qualitative and computational analysis and real-world applications This book provides a thoroughly accessible and lucid overview of the different aspects, models, computations, and methodology for the kinetic-theory modeling process Topics and Features * Integrated modeling perspective utilized in all chapters * Fluid dynamics of reacting gases * Self-contained introduction to kinetic models * Becker–Doring equations * Nonlinear kinetic models with chemical reactions * Kinet...

  15. Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data

    NARCIS (Netherlands)

    Kotasidis, F. A.; Mehranian, A.; Zaidi, H.

    2016-01-01

    Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from

  16. Irreversible processes kinetic theory

    CERN Document Server

    Brush, Stephen G

    2013-01-01

    Kinetic Theory, Volume 2: Irreversible Processes deals with the kinetic theory of gases and the irreversible processes they undergo. It includes the two papers by James Clerk Maxwell and Ludwig Boltzmann in which the basic equations for transport processes in gases are formulated, together with the first derivation of Boltzmann's ""H-theorem"" and a discussion of this theorem, along with the problem of irreversibility.Comprised of 10 chapters, this volume begins with an introduction to the fundamental nature of heat and of gases, along with Boltzmann's work on the kinetic theory of gases and s

  17. SHORT COMMUNICATION CATALYTIC KINETIC ...

    African Journals Online (AJOL)

    IV) catalyzes the discoloring reaction of DBS-arsenazo oxidized by potassium bromate, a new catalytic kinetic spectrophotometric method for the determination of trace titanium (IV) was developed. The linear range of the determination of ...

  18. Kinetic mechanism for modeling of electrochemical reactions.

    Science.gov (United States)

    Cervenka, Petr; Hrdlička, Jiří; Přibyl, Michal; Snita, Dalimil

    2012-04-01

    We propose a kinetic mechanism of electrochemical interactions. We assume fast formation and recombination of electron donors D- and acceptors A+ on electrode surfaces. These mediators are continuously formed in the electrode matter by thermal fluctuations. The mediators D- and A+, chemically equivalent to the electrode metal, enter electrochemical interactions on the electrode surfaces. Electrochemical dynamics and current-voltage characteristics of a selected electrochemical system are studied. Our results are in good qualitative agreement with those given by the classical Butler-Volmer kinetics. The proposed model can be used to study fast electrochemical processes in microsystems and nanosystems that are often out of the thermal equilibrium. Moreover, the kinetic mechanism operates only with the surface concentrations of chemical reactants and local electric potentials, which facilitates the study of electrochemical systems with indefinable bulk.

  19. Exercise: Kinetic considerations for gas exchange.

    Science.gov (United States)

    Rossiter, Harry B

    2011-01-01

    The activities of daily living typically occur at metabolic rates below the maximum rate of aerobic energy production. Such activity is characteristic of the nonsteady state, where energy demands, and consequential physiological responses, are in constant flux. The dynamics of the integrated physiological processes during these activities determine the degree to which exercise can be supported through rates of O₂ utilization and CO₂ clearance appropriate for their demands and, as such, provide a physiological framework for the notion of exercise intensity. The rate at which O₂ exchange responds to meet the changing energy demands of exercise--its kinetics--is dependent on the ability of the pulmonary, circulatory, and muscle bioenergetic systems to respond appropriately. Slow response kinetics in pulmonary O₂ uptake predispose toward a greater necessity for substrate-level energy supply, processes that are limited in their capacity, challenge system homeostasis and hence contribute to exercise intolerance. This review provides a physiological systems perspective of pulmonary gas exchange kinetics: from an integrative view on the control of muscle oxygen consumption kinetics to the dissociation of cellular respiration from its pulmonary expression by the circulatory dynamics and the gas capacitance of the lungs, blood, and tissues. The intensity dependence of gas exchange kinetics is discussed in relation to constant, intermittent, and ramped work rate changes. The influence of heterogeneity in the kinetic matching of O₂ delivery to utilization is presented in reference to exercise tolerance in endurance-trained athletes, the elderly, and patients with chronic heart or lung disease. © 2011 American Physiological Society.

  20. Modeling the degradation kinetics of ascorbic acid.

    Science.gov (United States)

    Peleg, Micha; Normand, Mark D; Dixon, William R; Goulette, Timothy R

    2018-06-13

    Most published reports on ascorbic acid (AA) degradation during food storage and heat preservation suggest that it follows first-order kinetics. Deviations from this pattern include Weibullian decay, and exponential drop approaching finite nonzero retention. Almost invariably, the degradation rate constant's temperature-dependence followed the Arrhenius equation, and hence the simpler exponential model too. A formula and freely downloadable interactive Wolfram Demonstration to convert the Arrhenius model's energy of activation, E a , to the exponential model's c parameter, or vice versa, are provided. The AA's isothermal and non-isothermal degradation can be simulated with freely downloadable interactive Wolfram Demonstrations in which the model's parameters can be entered and modified by moving sliders on the screen. Where the degradation is known a priori to follow first or other fixed order kinetics, one can use the endpoints method, and in principle the successive points method too, to estimate the reaction's kinetic parameters from considerably fewer AA concentration determinations than in the traditional manner. Freeware to do the calculations by either method has been recently made available on the Internet. Once obtained in this way, the kinetic parameters can be used to reconstruct the entire degradation curves and predict those at different temperature profiles, isothermal or dynamic. Comparison of the predicted concentration ratios with experimental ones offers a way to validate or refute the kinetic model and the assumptions on which it is based.

  1. A Comparison of Kinetic Energy and Momentum in Special Relativity and Classical Mechanics

    Science.gov (United States)

    Riggs, Peter J.

    2016-01-01

    Kinetic energy and momentum are indispensable dynamical quantities in both the special theory of relativity and in classical mechanics. Although momentum and kinetic energy are central to understanding dynamics, the differences between their relativistic and classical notions have not always received adequate treatment in undergraduate teaching.…

  2. The first example of a Hoogsteen base-paired DNA duplex in dynamic equilibrium with a Watson-Crick base-paired duplex--a structural (NMR), kinetic and thermodynamic study.

    Science.gov (United States)

    Isaksson, J; Zamaratski, E; Maltseva, T V; Agback, P; Kumar, A; Chattopadhyaya, J

    2001-06-01

    A single-point substitution of the O4' oxygen by a CH2 group at the sugar residue of A6 (i.e. 2'-deoxyaristeromycin moiety) in a self-complementary DNA duplex, 5'-d(C1G2C3G4A5A6T7T8C9G10C11G12)2(-3), has been shown to steer the fully Watson-Crick basepaired DNA duplex (1A), akin to the native counterpart, to a doubly A6:T7 Hoogsteen basepaired (1B) B-type DNA duplex, resulting in a dynamic equilibrium of (1A)(1B): Keq = k1/k(-1) = 0.56+/-0.08. The dynamic conversion of the fully Watson-Crick basepaired (1A) to the partly Hoogsteen basepaired (1B) structure is marginally kinetically and thermodynamically disfavoured [k1 (298K) = 3.9 0.8 sec(-1); deltaHdegrees++ = 164+/-14 kJ/mol; -TdeltaS degrees++ (298K) = -92 kJ/mol giving a deltaG degrees++ 298 of 72 kJ/mol. Ea (k1) = 167 14 kJ/mol] compared to the reverse conversion of the Hoogsteen (1B) to the Watson-Crick (1A) structure [k-1 (298K) = 7.0 0.6 sec-1, deltaH degrees++ = 153 13 kJ/mol; -TdeltaSdegrees++ (298K) = -82 kJ/mol giving a deltaGdegrees++(298) of 71 kJ/mol. Ea (k-1) = 155 13 kJ/mol]. Acomparison of deltaGdegrees++(298) of the forward (k1) and backward (k-1) conversions, (1A)(1B), shows that there is ca 1 kJ/mol preference for the Watson-Crick (1A) over the double Hoogsteen basepaired (1B) DNA duplex, thus giving an equilibrium ratio of almost 2:1 in favour of the fully Watson-Crick basepaired duplex. The chemical environments of the two interconverting DNA duplexes are very different as evident from their widely separated sets of chemical shifts connected by temperature-dependent exchange peaks in the NOESY and ROESY spectra. The fully Watson-Crick basepaired structure (1A) is based on a total of 127 intra, 97 inter and 17 cross-strand distance constraints per strand, whereas the double A6:T7 Hoogsteen basepaired (1B) structure is based on 114 intra, 92 inter and 15 cross-strand distance constraints, giving an average of 22 and 20 NOE distance constraints per residue and strand, respectively. In addition

  3. Combustion kinetics and reaction pathways

    Energy Technology Data Exchange (ETDEWEB)

    Klemm, R.B.; Sutherland, J.W. [Brookhaven National Laboratory, Upton, NY (United States)

    1993-12-01

    This project is focused on the fundamental chemistry of combustion. The overall objectives are to determine rate constants for elementary reactions and to elucidate the pathways of multichannel reactions. A multitechnique approach that features three independent experiments provides unique capabilities in performing reliable kinetic measurements over an exceptionally wide range in temperature, 300 to 2500 K. Recent kinetic work has focused on experimental studies and theoretical calculations of the methane dissociation system (CH{sub 4} + Ar {yields} CH{sub 3} + H + Ar and H + CH{sub 4} {yields} CH{sub 3} + H{sub 2}). Additionally, a discharge flow-photoionization mass spectrometer (DF-PIMS) experiment is used to determine branching fractions for multichannel reactions and to measure ionization thresholds of free radicals. Thus, these photoionization experiments generate data that are relevant to both reaction pathways studies (reaction dynamics) and fundamental thermochemical research. Two distinct advantages of performing PIMS with high intensity, tunable vacuum ultraviolet light at the National Synchrotron Light Source are high detection sensitivity and exceptional selectivity in monitoring radical species.

  4. Analysis of kinetic reaction mechanisms

    CERN Document Server

    Turányi, Tamás

    2014-01-01

    Chemical processes in many fields of science and technology, including combustion, atmospheric chemistry, environmental modelling, process engineering, and systems biology, can be described by detailed reaction mechanisms consisting of numerous reaction steps. This book describes methods for the analysis of reaction mechanisms that are applicable in all these fields. Topics addressed include: how sensitivity and uncertainty analyses allow the calculation of the overall uncertainty of simulation results and the identification of the most important input parameters, the ways in which mechanisms can be reduced without losing important kinetic and dynamic detail, and the application of reduced models for more accurate engineering optimizations. This monograph is invaluable for researchers and engineers dealing with detailed reaction mechanisms, but is also useful for graduate students of related courses in chemistry, mechanical engineering, energy and environmental science and biology.

  5. Nuclear reactor kinetics and control

    International Nuclear Information System (INIS)

    Lewins, J.

    1978-01-01

    A consistent, integrated account of modern developments in the study of nuclear reactor kinetics and the problem of their efficient and safe control. It aims to prepare the student for advanced study and research or practical work in the field. Special features include treatments of noise theory, reliability theory and safety related studies. It covers all aspects of the operation and control of nuclear reactors, power and research and is complete in providing physical data methods of calculation and solution including questions of equipment reliability. The work uses illustrations of the main types of reactors in use in the UK, USA and Europe. Each chapter contains problems and worked examples suitable for course work and study. The subject is covered in chapters, entitled: introductory review; neutron and precursor equations; elementary solutions at low power; linear reactor process dynamics with feedback; power reactor control systems; fluctuations and reactor noise; safety and reliability; nonlinear systems (safety and control); analogue computing. (author)

  6. The Balescu kinetic equation with exchange interaction

    International Nuclear Information System (INIS)

    Belyi, V V; Kukharenko, Yu A

    2009-01-01

    Starting with the quantum BBGKY hierarchy for the distribution functions, we have obtained the quantum kinetic equation including the dynamical screening of the interaction potential, which exactly takes into account the exchange scattering in the plasma. The collision integral is expressed in terms of the Green function of the linearized Hartree–Fock equation. The potential energy takes into account the polarization and exchange interaction too

  7. A stochastic model of enzyme kinetics

    Science.gov (United States)

    Stefanini, Marianne; Newman, Timothy; McKane, Alan

    2003-10-01

    Enzyme kinetics is generally modeled by deterministic rate equations, and in the simplest case leads to the well-known Michaelis-Menten equation. It is plausible that stochastic effects will play an important role at low enzyme concentrations. We have addressed this by constructing a simple stochastic model which can be exactly solved in the steady-state. Throughout a wide range of parameter values Michaelis-Menten dynamics is replaced by a new and simple theoretical result.

  8. Relativistic Chiral Kinetic Theory

    International Nuclear Information System (INIS)

    Stephanov, Mikhail

    2016-01-01

    This very brief review of the recent progress in chiral kinetic theory is based on the results of Refs. [J.-Y. Chen, D. T. Son, M. A. Stephanov, H.-U. Yee, Y. Yin, Lorentz Invariance in Chiral Kinetic Theory, Phys. Rev. Lett. 113 (18) (2014) 182302. doi: (10.1103/PhysRevLett.113.182302); J.-Y. Chen, D. T. Son, M. A. Stephanov, Collisions in Chiral Kinetic Theory, Phys. Rev. Lett. 115 (2) (2015) 021601. doi: (10.1103/PhysRevLett.115.021601); M. A. Stephanov, H.-U. Yee, The no-drag frame for anomalous chiral fluid, Phys. Rev. Lett. 116 (12) (2016) 122302. doi: (10.1103/PhysRevLett.116.122302)].

  9. Relativistic Chiral Kinetic Theory

    Energy Technology Data Exchange (ETDEWEB)

    Stephanov, Mikhail

    2016-12-15

    This very brief review of the recent progress in chiral kinetic theory is based on the results of Refs. [J.-Y. Chen, D. T. Son, M. A. Stephanov, H.-U. Yee, Y. Yin, Lorentz Invariance in Chiral Kinetic Theory, Phys. Rev. Lett. 113 (18) (2014) 182302. doi: (10.1103/PhysRevLett.113.182302); J.-Y. Chen, D. T. Son, M. A. Stephanov, Collisions in Chiral Kinetic Theory, Phys. Rev. Lett. 115 (2) (2015) 021601. doi: (10.1103/PhysRevLett.115.021601); M. A. Stephanov, H.-U. Yee, The no-drag frame for anomalous chiral fluid, Phys. Rev. Lett. 116 (12) (2016) 122302. doi: (10.1103/PhysRevLett.116.122302)].

  10. Erbium hydride decomposition kinetics.

    Energy Technology Data Exchange (ETDEWEB)

    Ferrizz, Robert Matthew

    2006-11-01

    Thermal desorption spectroscopy (TDS) is used to study the decomposition kinetics of erbium hydride thin films. The TDS results presented in this report are analyzed quantitatively using Redhead's method to yield kinetic parameters (E{sub A} {approx} 54.2 kcal/mol), which are then utilized to predict hydrogen outgassing in vacuum for a variety of thermal treatments. Interestingly, it was found that the activation energy for desorption can vary by more than 7 kcal/mol (0.30 eV) for seemingly similar samples. In addition, small amounts of less-stable hydrogen were observed for all erbium dihydride films. A detailed explanation of several approaches for analyzing thermal desorption spectra to obtain kinetic information is included as an appendix.

  11. Kinetic and Structural Characterization of a Heterohexamer 4-Oxalocrotonate Tautomerase from Chloroflexus aurantiacus J-10-fl: Implications for Functional and Structural Diversity in the Tautomerase Superfamily

    International Nuclear Information System (INIS)

    Burks, Elizabeth A.; Fleming, Christopher D.; Mesecar, Andrew D.; Whitman, Christian P.; Pegan, Scott D.

    2010-01-01

    4-Oxalocrotonate tautomerase (4-OT) isozymes play prominent roles in the bacterial utilization of aromatic hydrocarbons as sole carbon sources. These enzymes catalyze the conversion of 2-hydroxy-2,4-hexadienedioate (or 2-hydroxymuconate) to 2-oxo-3-hexenedioate, where Pro-1 functions as a general base and shuttles a proton from the 2-hydroxyl group of the substrate to the C-5 position of the product. 4-OT, a homohexamer from Pseudomonas putida mt-2, is the most extensively studied 4-OT isozyme and the founding member of the tautomerase superfamily. A search of five thermophilic bacterial genomes identified a coded amino acid sequence in each that had been annotated as a tautomerase-like protein but lacked Pro-1. However, a nearby sequence has Pro-1, but the sequence is not annotated as a tautomerase-like protein. To characterize this group of proteins, two genes from Chloroflexus aurantiacus J-10-fl were cloned, and the corresponding proteins were expressed. Kinetic, biochemical, and X-ray structural analyses show that the two expressed proteins form a functional heterohexamer 4-OT (hh4-OT), composed of three αβ dimers. Like the P. putida enzyme, hh4-OT requires the amino-terminal proline and two arginines for the conversion of 2-hydroxymuconate to the product, implicating an analogous mechanism. In contrast to 4-OT, hh4-OT does not exhibit the low-level activity of another tautomerase superfamily member, the heterohexamer trans-3-chloroacrylic acid dehalogenase (CaaD). Characterization of hh4-OT enables functional assignment of the related enzymes, highlights the diverse ways the β-α-β building block can be assembled into an active enzyme, and provides further insight into the molecular basis of the low-level CaaD activity in 4-OT.

  12. Relativistic Kinetic Theory

    Science.gov (United States)

    Vereshchagin, Gregory V.; Aksenov, Alexey G.

    2017-02-01

    Preface; Acknowledgements; Acronyms and definitions; Introduction; Part I. Theoretical Foundations: 1. Basic concepts; 2. Kinetic equation; 3. Averaging; 4. Conservation laws and equilibrium; 5. Relativistic BBGKY hierarchy; 6. Basic parameters in gases and plasmas; Part II. Numerical Methods: 7. The basics of computational physics; 8. Direct integration of Boltzmann equations; 9. Multidimensional hydrodynamics; Part III. Applications: 10. Wave dispersion in relativistic plasma; 11. Thermalization in relativistic plasma; 12. Kinetics of particles in strong fields; 13. Compton scattering in astrophysics and cosmology; 14. Self-gravitating systems; 15. Neutrinos, gravitational collapse and supernovae; Appendices; Bibliography; Index.

  13. The Einstein-Vlasov System/Kinetic Theory.

    Science.gov (United States)

    Andréasson, Håkan

    2011-01-01

    The main purpose of this article is to provide a guide to theorems on global properties of solutions to the Einstein-Vlasov system. This system couples Einstein's equations to a kinetic matter model. Kinetic theory has been an important field of research during several decades in which the main focus has been on non-relativistic and special relativistic physics, i.e., to model the dynamics of neutral gases, plasmas, and Newtonian self-gravitating systems. In 1990, Rendall and Rein initiated a mathematical study of the Einstein-Vlasov system. Since then many theorems on global properties of solutions to this system have been established. This paper gives introductions to kinetic theory in non-curved spacetimes and then the Einstein-Vlasov system is introduced. We believe that a good understanding of kinetic theory in non-curved spacetimes is fundamental to a good comprehension of kinetic theory in general relativity.

  14. Kinetic Modifications to MHD Phenomena in Toroidal Plasmas

    International Nuclear Information System (INIS)

    Cheng, C.Z.; Gorelenkov, N.N.; Kramer, G.J.; Fredrickson, E.

    2004-01-01

    Particle kinetic effects involving small spatial and fast temporal scales can strongly affect MHD phenomena and the long time behavior of plasmas. In particular, kinetic effects such as finite ion gyroradii, trapped particle dynamics, and wave-particle resonances have been shown to greatly modify the stability of MHD modes. Here, the kinetic effects of trapped electron dynamics and finite ion gyroradii are shown to have a large stabilizing effect on kinetic ballooning modes in low aspect ratio toroidal plasmas such as NSTX [National Spherical Torus Experiment]. We also present the analysis of Toroidicity-induced Alfven Eigenmodes (TAEs) destabilized by fast neutral-beam injected ions in NSTX experiments and TAE stability in ITER due to alpha-particles and MeV negatively charged neutral beam injected ions

  15. Modelling opinion formation by means of kinetic equations

    OpenAIRE

    Boudin , Laurent; Salvarani , Francesco

    2010-01-01

    In this chapter, we review some mechanisms of opinion dynamics that can be modelled by kinetic equations. Beside the sociological phenomenon of compromise, naturally linked to collisional operators of Boltzmann kind, many other aspects, already mentioned in the sociophysical literature or no, can enter in this framework. While describing some contributions appeared in the literature, we enlighten some mathematical tools of kinetic theory that can be useful in the context of sociophysics.

  16. Relaxation and kinetics in scalar field theories

    International Nuclear Information System (INIS)

    Boyanovsky, D.; Lawrie, I.D.; Lee, D.

    1996-01-01

    A new approach to the dynamics of relaxation and kinetics of thermalization in a scalar field theory is presented that incorporates the relevant time scales through the resummation of hard thermal loops. An alternative derivation of the kinetic equations for the open-quote open-quote quasiparticle close-quote close-quote distribution functions is obtained that allows a clear understanding of the different open-quote open-quote coarse-graining close-quote close-quote approximations usually involved in a kinetic description. This method leads to a systematic perturbative expansion to obtain the kinetic equations including hard thermal loop resummation and to an improvement including renormalization, off-shell effects, and contributions that change chemical equilibrium on short time scales. As a by-product of these methods we establish the equivalence between the relaxation time scale in the linearized equation of motion of the quasiparticles and the thermalization time scale of the quasiparticle distribution function in the open-quote open-quote relaxation time approximation close-quote close-quote including hard thermal loop effects. Hard thermal loop resummation dramatically modifies the scattering rate for long wavelength modes as compared to the usual (semi)classical estimate. Relaxation and kinetics are studied both in the unbroken and broken symmetry phases of the theory. The broken symmetry phase also provides the setting to obtain the contribution to the kinetic equations from processes that involve decay of a heavy scalar into light scalar particles in the medium. copyright 1996 The American Physical Society

  17. Oxidative desulfurization: kinetic modelling.

    Science.gov (United States)

    Dhir, S; Uppaluri, R; Purkait, M K

    2009-01-30

    Increasing environmental legislations coupled with enhanced production of petroleum products demand, the deployment of novel technologies to remove organic sulfur efficiently. This work represents the kinetic modeling of ODS using H(2)O(2) over tungsten-containing layered double hydroxide (LDH) using the experimental data provided by Hulea et al. [V. Hulea, A.L. Maciuca, F. Fajula, E. Dumitriu, Catalytic oxidation of thiophenes and thioethers with hydrogen peroxide in the presence of W-containing layered double hydroxides, Appl. Catal. A: Gen. 313 (2) (2006) 200-207]. The kinetic modeling approach in this work initially targets the scope of the generation of a superstructure of micro-kinetic reaction schemes and models assuming Langmuir-Hinshelwood (LH) and Eley-Rideal (ER) mechanisms. Subsequently, the screening and selection of above models is initially based on profile-based elimination of incompetent schemes followed by non-linear regression search performed using the Levenberg-Marquardt algorithm (LMA) for the chosen models. The above analysis inferred that Eley-Rideal mechanism describes the kinetic behavior of ODS process using tungsten-containing LDH, with adsorption of reactant and intermediate product only taking place on the catalyst surface. Finally, an economic index is presented that scopes the economic aspects of the novel catalytic technology with the parameters obtained during regression analysis to conclude that the cost factor for the catalyst is 0.0062-0.04759 US $ per barrel.

  18. Oxidative desulfurization: Kinetic modelling

    International Nuclear Information System (INIS)

    Dhir, S.; Uppaluri, R.; Purkait, M.K.

    2009-01-01

    Increasing environmental legislations coupled with enhanced production of petroleum products demand, the deployment of novel technologies to remove organic sulfur efficiently. This work represents the kinetic modeling of ODS using H 2 O 2 over tungsten-containing layered double hydroxide (LDH) using the experimental data provided by Hulea et al. [V. Hulea, A.L. Maciuca, F. Fajula, E. Dumitriu, Catalytic oxidation of thiophenes and thioethers with hydrogen peroxide in the presence of W-containing layered double hydroxides, Appl. Catal. A: Gen. 313 (2) (2006) 200-207]. The kinetic modeling approach in this work initially targets the scope of the generation of a superstructure of micro-kinetic reaction schemes and models assuming Langmuir-Hinshelwood (LH) and Eley-Rideal (ER) mechanisms. Subsequently, the screening and selection of above models is initially based on profile-based elimination of incompetent schemes followed by non-linear regression search performed using the Levenberg-Marquardt algorithm (LMA) for the chosen models. The above analysis inferred that Eley-Rideal mechanism describes the kinetic behavior of ODS process using tungsten-containing LDH, with adsorption of reactant and intermediate product only taking place on the catalyst surface. Finally, an economic index is presented that scopes the economic aspects of the novel catalytic technology with the parameters obtained during regression analysis to conclude that the cost factor for the catalyst is 0.0062-0.04759 US $ per barrel

  19. CATALYTIC KINETIC SPECTROPHOTOMETRIC DETERMINATION ...

    African Journals Online (AJOL)

    Preferred Customer

    acetylchlorophosphonazo(CPApA) by hydrogen peroxide in 0.10 M phosphoric acid. A novel catalytic kinetic-spectrophotometric method is proposed for the determination of copper based on this principle. Copper(II) can be determined spectrophotometrically ...

  20. Kinetic energy budget details

    Indian Academy of Sciences (India)

    Abstract. This paper presents the detailed turbulent kinetic energy budget and higher order statistics of flow behind a surface-mounted rib with and without superimposed acoustic excitation. Pattern recognition technique is used to determine the large-scale structure magnitude. It is observed that most of the turbulence ...

  1. Point kinetics modeling

    International Nuclear Information System (INIS)

    Kimpland, R.H.

    1996-01-01

    A normalized form of the point kinetics equations, a prompt jump approximation, and the Nordheim-Fuchs model are used to model nuclear systems. Reactivity feedback mechanisms considered include volumetric expansion, thermal neutron temperature effect, Doppler effect and void formation. A sample problem of an excursion occurring in a plutonium solution accidentally formed in a glovebox is presented

  2. LLNL Chemical Kinetics Modeling Group

    Energy Technology Data Exchange (ETDEWEB)

    Pitz, W J; Westbrook, C K; Mehl, M; Herbinet, O; Curran, H J; Silke, E J

    2008-09-24

    The LLNL chemical kinetics modeling group has been responsible for much progress in the development of chemical kinetic models for practical fuels. The group began its work in the early 1970s, developing chemical kinetic models for methane, ethane, ethanol and halogenated inhibitors. Most recently, it has been developing chemical kinetic models for large n-alkanes, cycloalkanes, hexenes, and large methyl esters. These component models are needed to represent gasoline, diesel, jet, and oil-sand-derived fuels.

  3. Kinetic theory for strongly coupled Coulomb systems

    Science.gov (United States)

    Dufty, James; Wrighton, Jeffrey

    2018-01-01

    The calculation of dynamical properties for matter under extreme conditions is a challenging task. The popular Kubo-Greenwood model exploits elements from equilibrium density-functional theory (DFT) that allow a detailed treatment of electron correlations, but its origin is largely phenomenological; traditional kinetic theories have a more secure foundation but are limited to weak ion-electron interactions. The objective here is to show how a combination of the two evolves naturally from the short-time limit for the generator of the effective single-electron dynamics governing time correlation functions without such limitations. This provides a theoretical context for the current DFT-related approach, the Kubo-Greenwood model, while showing the nature of its corrections. The method is to calculate the short-time dynamics in the single-electron subspace for a given configuration of the ions. This differs from the usual kinetic theory approach in which an average over the ions is performed as well. In this way the effective ion-electron interaction includes strong Coulomb coupling and is shown to be determined from DFT. The correlation functions have the form of the random-phase approximation for an inhomogeneous system but with renormalized ion-electron and electron-electron potentials. The dynamic structure function, density response function, and electrical conductivity are calculated as examples. The static local field corrections in the dielectric function are identified in this way. The current analysis is limited to semiclassical electrons (quantum statistical potentials), so important quantum conditions are excluded. However, a quantization of the kinetic theory is identified for broader application while awaiting its detailed derivation.

  4. Kinetic energy absorbing pad

    International Nuclear Information System (INIS)

    Bricmont, R.J.; Hamilton, P.A.; Ming Long Ting, R.

    1981-01-01

    Reactors, fuel processing plants etc incorporate pipes and conduits for fluids under high pressure. Fractures, particularly adjacent to conduit elbows, produce a jet of liquid which whips the broken conduit at an extremely high velocity. An enormous impact load would be applied to any stationary object in the conduit's path. The design of cellular, corrugated metal impact pads to absorb the kinetic energy of the high velocity conduits is given. (U.K.)

  5. Kinetic Line Voronoi Operations and Their Reversibility

    DEFF Research Database (Denmark)

    Mioc, Darka; Anton, François; Gold, Christopher

    2010-01-01

    In Geographic Information Systems the reversibility of map update operations has not been explored yet. In this paper we are using the Voronoi based Quad-edge data structure to define reversible map update operations. The reversibility of the map operations has been formalised at the lowest level...... mechanisms and dynamic map visualisations. In order to use the reversibility within the kinetic Voronoi diagram of points and open oriented line segments, we need to assure that reversing the map commands will produce exactly the changes in the map equivalent to the previous map states. To prove...... that reversing the map update operations produces the exact reverse changes, we show an isomorphism between the set of complex operations on the kinetic Voronoi diagram of points and open oriented line segments and the sets of numbers of new / deleted Voronoi regions induced by these operations, and its...

  6. Kinetics of the chiral phase transition

    Energy Technology Data Exchange (ETDEWEB)

    Hees, Hendrik van [Johann-Wolfgang-Goethe-Universitaet Frankfurt, Institut fuer Theoretische Physik, Frankfurt (Germany); Frankfurt Institute for Advanced Studies (FIAS), Frankfurt (Germany); Wesp, Christian; Meistrenko, Alex; Greiner, Carsten [Johann-Wolfgang-Goethe-Universitaet Frankfurt, Institut fuer Theoretische Physik, Frankfurt (Germany)

    2016-07-01

    We simulate the kinetics of the chiral phase transition in hot and dense strongly interacting matter within a novel kinetic-theory approach. Employing an effective linear σ model for quarks, σ mesons, and pions we treat the quarks within a test-particle ansatz for solving the Boltzmann transport equation and the mesons in terms of classical fields. The decay-recombination processes like σ <-> anti q+q are treated using a kind of wave-particle dualism using the exact conservation of energy and momentum. After demonstrating the correct thermodynamic limit for particles and fields in a ''box calculation'' we apply the simulation to the dynamics of an expanding fireball similar to the medium created in ultrarelativistic heavy-ion collisions.

  7. Kinetic modeling in PET imaging of hypoxia

    Science.gov (United States)

    Li, Fan; Joergensen, Jesper T; Hansen, Anders E; Kjaer, Andreas

    2014-01-01

    Tumor hypoxia is associated with increased therapeutic resistance leading to poor treatment outcome. Therefore the ability to detect and quantify intratumoral oxygenation could play an important role in future individual personalized treatment strategies. Positron Emission Tomography (PET) can be used for non-invasive mapping of tissue oxygenation in vivo and several hypoxia specific PET tracers have been developed. Evaluation of PET data in the clinic is commonly based on visual assessment together with semiquantitative measurements e.g. standard uptake value (SUV). However, dynamic PET contains additional valuable information on the temporal changes in tracer distribution. Kinetic modeling can be used to extract relevant pharmacokinetic parameters of tracer behavior in vivo that reflects relevant physiological processes. In this paper, we review the potential contribution of kinetic analysis for PET imaging of hypoxia. PMID:25250200

  8. The kinetics of denitrification in permeable sediments

    DEFF Research Database (Denmark)

    Evrard, Victor; Glud, Ronnie N.; Cook, Perran L. M.

    2013-01-01

    Permeable sediments comprise the majority of shelf sediments, yet the rates of denitrification remain highly uncertain in these environments. Computational models are increasingly being used to understand the dynamics of denitrification in permeable sediments, which are complex environments...... on sediments taken from six shallow coastal sites in Port Phillip Bay, Victoria, Australia. The results showed that denitrification commenced rapidly (within 30 min) after the onset of anoxia and the kinetics could be well described by Michaelis-Menten kinetics with half saturation constants (apparent K...... in cohesive sediments despite organic carbon contents one order of magnitude lower for the sediments studied here. The ratio of sediment O-2 consumption to V-max was in the range of 0.02-0.09, and was on average much lower than the theoretical ratio of 0.8. As a consequence, models implemented...

  9. Calcite Dissolution Kinetics

    Science.gov (United States)

    Berelson, W.; Subhas, A.; Dong, S.; Naviaux, J.; Adkins, J. F.

    2016-12-01

    A geological buffer for high atmospheric CO2 concentrations is neutralization via reaction with CaCO3. We have been studying the dissolution kinetics of carbonate minerals using labeled 13C calcite and Picarro-based measurements of 13C enrichments in solution DIC. This methodology has greatly facilitated our investigation of dissolution kinetics as a function of water carbonate chemistry, temperature and pressure. One can adjust the saturation state Omega by changing the ion activity product (e.g. adjusting carbonate ion concentration), or by changing the solubility product (e.g. adjusting temperature or pressure). The canonical formulation of dissolution rate vs. omega has been refined (Subhas et al. 2015) and shows distinct non-linear behavior near equilibrium and rates in sea water of 1-3 e-6 g/cm2day at omega = 0.8. Carbonic anhydrase (CA), an enzyme that catalyzes the hydration of dissolved CO2 to carbonic acid, was shown (in concentrations 500x. This result points to the importance of carbonic acid in enhancing dissolution at low degrees of undersaturation. CA activity and abundance in nature must be considered regarding the role it plays in catalyzing dissolution. We also have been investigating the role of temperature on dissolution kinetics. An increase of 16C yields an order of magnitude increase in dissolution rate. Temperature (and P) also change Omega critical, the saturation state where dissolution rates change substantially. Increasing pressure (achieved in a pressure reaction chamber we built) also shifts Omega critical closer to equilibrium and small pressure increases have large impact on dissolution kinetics. Dissolution rates are enhanced by an order of magnitude for a change in pressure of 1500 psi relative to the dissolution rate achieved by water chemistry effects alone for an omega of 0.8. We've shown that the thermodynamic determination of saturation state does not adequately describe the kinetics of dissolution. The interplay of mineral

  10. Performance of neutron kinetics models for ADS transient analyses

    International Nuclear Information System (INIS)

    Rineiski, A.; Maschek, W.; Rimpault, G.

    2002-01-01

    Within the framework of the SIMMER code development, neutron kinetics models for simulating transients and hypothetical accidents in advanced reactor systems, in particular in Accelerator Driven Systems (ADSs), have been developed at FZK/IKET in cooperation with CE Cadarache. SIMMER is a fluid-dynamics/thermal-hydraulics code, coupled with a structure model and a space-, time- and energy-dependent neutronics module for analyzing transients and accidents. The advanced kinetics models have also been implemented into KIN3D, a module of the VARIANT/TGV code (stand-alone neutron kinetics) for broadening application and for testing and benchmarking. In the paper, a short review of the SIMMER and KIN3D neutron kinetics models is given. Some typical transients related to ADS perturbations are analyzed. The general models of SIMMER and KIN3D are compared with more simple techniques developed in the context of this work to get a better understanding of the specifics of transients in subcritical systems and to estimate the performance of different kinetics options. These comparisons may also help in elaborating new kinetics models and extending existing computation tools for ADS transient analyses. The traditional point-kinetics model may give rather inaccurate transient reaction rate distributions in an ADS even if the material configuration does not change significantly. This inaccuracy is not related to the problem of choosing a 'right' weighting function: the point-kinetics model with any weighting function cannot take into account pronounced flux shape variations related to possible significant changes in the criticality level or to fast beam trips. To improve the accuracy of the point-kinetics option for slow transients, we have introduced a correction factor technique. The related analyses give a better understanding of 'long-timescale' kinetics phenomena in the subcritical domain and help to evaluate the performance of the quasi-static scheme in a particular case. One

  11. On the kinetic theory of the one-component plasma

    International Nuclear Information System (INIS)

    Cohen, J.S.

    1984-01-01

    In this thesis, kinetic theory is applied to transport phenomena of a one-component plasma. Existing kinetic equations, containing both dynamical screening effects and close binary collisions do not suffer from divergencies. Recently an approximation for the pair correlation function has been proposed that is valid for small values of the plasma collision parameter. Upon insertion of this expression into the general form of the collision integral, one obtains another convergent kinetic equation. This thesis shows that both kinetic equations yield the same coefficient of heat conductivity and viscosity; and that for a hot dilute plasma the arbitrary transport coefficient is rather insensitive to the pair correlation function. In the second part, the author studies the diffusion of a tagged particle in an external magnetic field. It is found that the longitudinal self-diffusion coefficient contra-varies monotonically with the magnetic field strength. (Auth.)

  12. Control of DNA strand displacement kinetics using toehold exchange.

    Science.gov (United States)

    Zhang, David Yu; Winfree, Erik

    2009-12-02

    DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Many of these enzyme-free constructions function by DNA strand displacement reactions. The kinetics of strand displacement can be modulated by toeholds, short single-stranded segments of DNA that colocalize reactant DNA molecules. Recently, the toehold exchange process was introduced as a method for designing fast and reversible strand displacement reactions. Here, we characterize the kinetics of DNA toehold exchange and model it as a three-step process. This model is simple and quantitatively predicts the kinetics of 85 different strand displacement reactions from the DNA sequences. Furthermore, we use toehold exchange to construct a simple catalytic reaction. This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices.

  13. Kinetics of tetrataenite disordering

    International Nuclear Information System (INIS)

    Dos Santos, E.; Gattacceca, J.; Rochette, P.; Fillion, G.; Scorzelli, R.B.

    2015-01-01

    Tetrataenite is a chemically ordered L1 0 -type Fe 50 Ni 50 alloy detected for the first time in 1977 by 57 Fe Mössbauer spectroscopy studies in iron meteorites. The thermal history of meteorites, in particular short thermal events like those associated to hypervelocity impacts, can be constrained by tracing the presence of tetrataenite or its disordering into taenite. The knowledge of the disordering kinetics of tetrataenite, that is associated with changes in its magnetic properties, is still very fragmentary so that the time–temperature history of these meteorites cannot be constrained in details. Furthermore, knowledge of disordering kinetics is important due to potential technological application of tetrataenite as a rare-earth free strong magnet. Thus, this work provides the first time–temperature data for disordering reaction of tetrataenite. We have shown that disordering is not an instantaneous process but is a kinetic limited reaction. It was shown that disordering may take place at any temperature above the order–disorder transition for L 10 superstructure phase (∼320 °C) when the appropriate time-scale is considered. This result means that the apparent Curie point for tetrataenite is not an absolute property in the sense that any estimate of this parameter should be referred to a given time-scale. - Highlights: • The first time–temperature data for tetrataenite disordering reaction is provided. • Previous works does not give a complete picture of tetrataenite disordering. • Apparent Curie temperature of tetrataenite should be referred to a time-scale. • Tetrataenite can be used as a probe to detect thermal/shock events recorded in meteorites

  14. Li + solvation and kinetics of Li+–BF4-/PF 6 - ion pairs in ethylene carbonate. A molecular dynamics study with classical rate theories

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Tsun-Mei [Department of Chemistry, University of Wisconsin–Parkside, Kenosha, Wisconsin 53141, USA; Dang, Liem X. [Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 93352, USA

    2017-10-28

    Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ethylene carbonate (EC) exchange process between the first and second solvation shells around Li+ and the dissociation kinetics of ion pairs Li+-[BF4] and Li+-[PF6] in this solvent. We calculate the exchange rates using transition state theory and correct them with transmission coefficients computed by the reactive flux; Impey, Madden, and McDonald approaches; and Grote-Hynes theory. We found the residence times of EC around Li+ ions varied from 70 to 450 ps, depending on the correction method used. We found the relaxation times changed significantly from Li+-[BF4] to Li+-[PF6] ion pairs in EC. Our results also show that, in addition to affecting the free energy of dissociation in EC, the anion type also significantly influence the dissociation kinetics of ion pairing. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.

  15. Vlasov simulations of kinetic Alfvén waves at proton kinetic scales

    Energy Technology Data Exchange (ETDEWEB)

    Vásconez, C. L. [Dipartimento di Fisica, Università della Calabria, I-87036 Cosenza (Italy); Observatorio Astronómico de Quito, Escuela Politécnica Nacional, Quito (Ecuador); Valentini, F.; Veltri, P. [Dipartimento di Fisica, Università della Calabria, I-87036 Cosenza (Italy); Camporeale, E. [Centrum Wiskunde and Informatica, Amsterdam (Netherlands)

    2014-11-15

    Kinetic Alfvén waves represent an important subject in space plasma physics, since they are thought to play a crucial role in the development of the turbulent energy cascade in the solar wind plasma at short wavelengths (of the order of the proton gyro radius ρ{sub p} and/or inertial length d{sub p} and beyond). A full understanding of the physical mechanisms which govern the kinetic plasma dynamics at these scales can provide important clues on the problem of the turbulent dissipation and heating in collisionless systems. In this paper, hybrid Vlasov-Maxwell simulations are employed to analyze in detail the features of the kinetic Alfvén waves at proton kinetic scales, in typical conditions of the solar wind environment (proton plasma beta β{sub p} = 1). In particular, linear and nonlinear regimes of propagation of these fluctuations have been investigated in a single-wave situation, focusing on the physical processes of collisionless Landau damping and wave-particle resonant interaction. Interestingly, since for wavelengths close to d{sub p} and β{sub p} ≃ 1 (for which ρ{sub p} ≃ d{sub p}) the kinetic Alfvén waves have small phase speed compared to the proton thermal velocity, wave-particle interaction processes produce significant deformations in the core of the particle velocity distribution, appearing as phase space vortices and resulting in flat-top velocity profiles. Moreover, as the Eulerian hybrid Vlasov-Maxwell algorithm allows for a clean almost noise-free description of the velocity space, three-dimensional plots of the proton velocity distribution help to emphasize how the plasma departs from the Maxwellian configuration of thermodynamic equilibrium due to nonlinear kinetic effects.

  16. Chemical kinetic modeling of H{sub 2} applications

    Energy Technology Data Exchange (ETDEWEB)

    Marinov, N.M.; Westbrook, C.K.; Cloutman, L.D. [Lawrence Livermore National Lab., CA (United States)] [and others

    1995-09-01

    Work being carried out at LLNL has concentrated on studies of the role of chemical kinetics in a variety of problems related to hydrogen combustion in practical combustion systems, with an emphasis on vehicle propulsion. Use of hydrogen offers significant advantages over fossil fuels, and computer modeling provides advantages when used in concert with experimental studies. Many numerical {open_quotes}experiments{close_quotes} can be carried out quickly and efficiently, reducing the cost and time of system development, and many new and speculative concepts can be screened to identify those with sufficient promise to pursue experimentally. This project uses chemical kinetic and fluid dynamic computational modeling to examine the combustion characteristics of systems burning hydrogen, either as the only fuel or mixed with natural gas. Oxidation kinetics are combined with pollutant formation kinetics, including formation of oxides of nitrogen but also including air toxics in natural gas combustion. We have refined many of the elementary kinetic reaction steps in the detailed reaction mechanism for hydrogen oxidation. To extend the model to pressures characteristic of internal combustion engines, it was necessary to apply theoretical pressure falloff formalisms for several key steps in the reaction mechanism. We have continued development of simplified reaction mechanisms for hydrogen oxidation, we have implemented those mechanisms into multidimensional computational fluid dynamics models, and we have used models of chemistry and fluid dynamics to address selected application problems. At the present time, we are using computed high pressure flame, and auto-ignition data to further refine the simplified kinetics models that are then to be used in multidimensional fluid mechanics models. Detailed kinetics studies have investigated hydrogen flames and ignition of hydrogen behind shock waves, intended to refine the detailed reactions mechanisms.

  17. Effective potential kinetic theory for strongly coupled plasmas

    Science.gov (United States)

    Baalrud, Scott D.; Daligault, Jérôme

    2016-11-01

    The effective potential theory (EPT) is a recently proposed method for extending traditional plasma kinetic and transport theory into the strongly coupled regime. Validation from experiments and molecular dynamics simulations have shown it to be accurate up to the onset of liquid-like correlation parameters (corresponding to Γ ≃ 10-50 for the one-component plasma, depending on the process of interest). Here, this theory is briefly reviewed along with comparisons between the theory and molecular dynamics simulations for self-diffusivity and viscosity of the one-component plasma. A number of new results are also provided, including calculations of friction coefficients, energy exchange rates, stopping power, and mobility. The theory is also cast in the Landau and Fokker-Planck kinetic forms, which may prove useful for enabling efficient kinetic computations.

  18. Kinetic coefficients in isotopically disordered crystals

    International Nuclear Information System (INIS)

    Zhernov, Arkadii P; Inyushkin, Alexander V

    2002-01-01

    Peculiarities of the behavior of kinetic coefficients, like thermal conductivity, electric conductivity, and thermoelectric power, in isotopically disordered materials are reviewed in detail. New experimental and theoretical results on the isotope effects in the thermal conductivity of diamond, Ge, and Si semiconductors are presented. The suppression effect of phonon-drag thermopower in the isotopically disordered Ge crystals is discussed. The influence of dynamic and static crystal lattice deformations on the electric conductivity of metals as well as on the ordinary phonon spectrum deformations is considered. (reviews of topical problems)

  19. Kinetics of coal pyrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Seery, D.J.; Freihaut, J.D.; Proscia, W.M. (United Technologies Research Center, East Hartford, CT (USA)); Howard, J.B.; Peters, W.; Hsu, J.; Hajaligol, M.; Sarofim, A. (Massachusetts Inst. of Tech., Cambridge, MA (USA)); Jenkins, R.; Mallin, J.; Espindola-Merin, B. (Pennsylvania State Univ., University Park, PA (USA)); Essenhigh, R.; Misra, M.K. (Ohio State Univ., Columbus, OH (USA))

    1989-07-01

    This report contains results of a coordinated, multi-laboratory investigation of coal devolatilization. Data is reported pertaining to the devolatilization for bituminous coals over three orders of magnitude in apparent heating rate (100 to 100,000 + {degree}C/sec), over two orders of magnitude in particle size (20 to 700 microns), final particle temperatures from 400 to 1600{degree}C, heat transfer modes ranging from convection to radiative, ambient pressure ranging from near vacuum to one atmosphere pressure. The heat transfer characteristics of the reactors are reported in detail. It is assumed the experimental results are to form the basis of a devolatilization data base. Empirical rate expressions are developed for each phase of devolatilization which, when coupled to an awareness of the heat transfer rate potential of a particular devolatilization reactor, indicate the kinetics emphasized by a particular system reactor plus coal sample. The analysis indicates the particular phase of devolatilization that will be emphasized by a particular reactor type and, thereby, the kinetic expressions appropriate to that devolatilization system. Engineering rate expressions are developed from the empirical rate expressions in the context of a fundamental understanding of coal devolatilization developed in the course of the investigation. 164 refs., 223 figs., 44 tabs.

  20. Repair kinetics in tissues

    International Nuclear Information System (INIS)

    Thames, H.D.

    1989-01-01

    Monoexponential repair kinetics is based on the assumption of a single, dose-independent rate of repair of sublethal injury in the target cells for tissue injury after exposure to ionizing radiation. Descriptions of the available data based on this assumption have proved fairly successful for both acutely responding (skin, lip mucosa, gut) and late-responding (lung, spinal cord) normal tissues. There are indications of biphasic exponential repair in both categories, however. Unfortunately, the data usually lack sufficient resolution to permit unambiguous determination of the repair rates. There are also indications that repair kinetics may depend on the size of the dose. The data are conflicting on this account, however, with suggestions of both faster and slower repair after larger doses. Indeed, experiments that have been explicitly designed to test this hypothesis show either no effect (gut, spinal cord), faster repair after higher doses (lung, kidney), or slower repair after higher doses (skin). Monoexponential repair appears to be a fairly accurate description that provides an approximation to a more complicated picture, the elucidation of whose details will, however, require very careful and extensive experimental study. (author). 30 refs.; 1 fig

  1. Diffusion Influenced Adsorption Kinetics.

    Science.gov (United States)

    Miura, Toshiaki; Seki, Kazuhiko

    2015-08-27

    When the kinetics of adsorption is influenced by the diffusive flow of solutes, the solute concentration at the surface is influenced by the surface coverage of solutes, which is given by the Langmuir-Hinshelwood adsorption equation. The diffusion equation with the boundary condition given by the Langmuir-Hinshelwood adsorption equation leads to the nonlinear integro-differential equation for the surface coverage. In this paper, we solved the nonlinear integro-differential equation using the Grünwald-Letnikov formula developed to solve fractional kinetics. Guided by the numerical results, analytical expressions for the upper and lower bounds of the exact numerical results were obtained. The upper and lower bounds were close to the exact numerical results in the diffusion- and reaction-controlled limits, respectively. We examined the validity of the two simple analytical expressions obtained in the diffusion-controlled limit. The results were generalized to include the effect of dispersive diffusion. We also investigated the effect of molecular rearrangement of anisotropic molecules on surface coverage.

  2. Enzymes catalyzing pre-hydrolysis facilitated the anaerobic fermentation of waste activated sludge with acidogenic and microbiological perspectives.

    Science.gov (United States)

    Xin, Xiaodong; He, Junguo; Li, Lin; Qiu, Wei

    2018-02-01

    This study investigated acidogenic and microbiological perspectives in the anaerobic fermentation (AF) of waste activated sludge (WAS) pre-hydrolyzed by enzymes catalysis. The enzymes catalysis boosted WAS biodegradability dramatically with nearly 8500 mg/L soluble chemical oxygen demand (SCOD) increase just within 4 h. The volatile fatty acids (VFAs) in the acidogenesis were accumulated effectively with over 3200 mg COD/L in 12 d, which reached 0.687 kWh/kg VSS electricity conversion efficiency (2.5 times higher than the control test). The fermentation process favored the compression of fermentative sludge with the distribution spread index (DSI) rising. The core populations of bacteria and archaea shifting enlarged the dissimilarity of communities at different fermentation stages. Increase of community diversity contributed to VFAs accumulation stability. Moreover, the intermediate bacterial community evenness favored VFAs accumulation potentially. The enzymes catalysis might be a promising solution for strengthening VFAs accumulation in the WAS fermentation with boosting the electricity conversion potential. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Data characterizing the energetics of enzyme-catalyzed hydrolysis and transglycosylation reactions by DFT cluster model calculations

    Directory of Open Access Journals (Sweden)

    Jitrayut Jitonnom

    2018-04-01

    Full Text Available The data presented in this paper are related to the research article entitled “QM/MM modeling of the hydrolysis and transfructosylation reactions of fructosyltransferase from Aspergillus japonicas, an enzyme that produces prebiotic fructooligosaccharide” (Jitonnom et al., 2018 [1]. This paper presents the procedure and data for characterizing the whole relative energy profiles of hydrolysis and transglycosylation reactions whose elementary steps differ in chemical composition. The data also reflects the choices of the QM cluster model, the functional/basis set method and the equations in determining the reaction energetics.

  4. A plant gene for photolyase: an enzyme catalyzing the repair of UV-light-induced DNA damage

    International Nuclear Information System (INIS)

    Batschauer, A.

    1993-01-01

    Photolyases are thought to be critical components of the defense of plants against damage to DNA by solar ultraviolet light, but nothing is known about their molecular or enzymatic nature. The molecular cloning of a photolyase from mustard (Sinapis alba) described here is intended to increase the knowledge about this important repair mechanism in plant species at a molecular level. The gene encodes a polypeptide of 501 amino acids with a predicted molecular mass of 57 kDa. There is a strong sequence similarity to bacterial and yeast photolyases, with a close relationship to enzymes with a deazaflavin chromophor. The plant photolyase is shown to be functional in Escherichia coli which also indicates conservation of photolyases during evolution. It is demonstrated that photolyase expression in plants is light induced, thus providing good evidence for the adaptation of plants to their environment in order to diminish the harmful effects of sunlight. (author)

  5. ESolvent-free, enzyme-catalyzed biodiesel production from mango, neem, and shea oils via response surface methodology.

    Science.gov (United States)

    Nde, Divine Bup; Astete, Carlos; Boldor, Dorin

    2015-12-01

    Mango, neem and shea kernels produce non-conventional oils whose potentials are not fully exploited. To give an added value to these oils, they were transesterified into biodiesel in a solvent-free system using immobilized enzyme lipozyme from Mucor miehei. The Doehlert experimental design was used to evaluate the methyl ester (ME) yields as influenced by enzyme concentration-EC, temperature-T, added water content-AWC, and reaction time-RT. Biodiesel yields were quantified by (1)H NMR spectroscopy and subsequently modeled by a second order polynomial equation with interactions. Lipozyme enzymes were more tolerant to high temperatures in neem and shea oils reaction media compared to that of mango oil. The optimum reaction conditions EC, T, AWC, and RT assuring near complete conversion were as follows: mango oil 7.25 %, 36.6 °C, 10.9 %, 36.4 h; neem oil EC = 7.19 %, T = 45.7 °C, AWC = 8.43 %, RT = 25.08 h; and shea oil EC = 4.43 %, T = 45.65 °C, AWC = 6.21 % and RT = 25.08 h. Validation experiments of these optimum conditions gave ME yields of 98.1 ± 1.0, 98.5 ± 1.6 and 99.3 ± 0.4 % for mango, neem and shea oils, respectively, which all met ASTM biodiesel standards.

  6. ESolvent-free, enzyme-catalyzed biodiesel production from mango, neem, and shea oils via response surface methodology

    OpenAIRE

    Nde, Divine Bup; Astete, Carlos; Boldor, Dorin

    2015-01-01

    Mango, neem and shea kernels produce non-conventional oils whose potentials are not fully exploited. To give an added value to these oils, they were transesterified into biodiesel in a solvent-free system using immobilized enzyme lipozyme from Mucor miehei. The Doehlert experimental design was used to evaluate the methyl ester (ME) yields as influenced by enzyme concentration?EC, temperature?T, added water content?AWC, and reaction time?RT. Biodiesel yields were quantified by 1H NMR spectrosc...

  7. Influence of the reaction conditions on the enzyme catalyzed transesterification of castor oil: A possible step in biodiesel production.

    Science.gov (United States)

    Andrade, Thalles A; Errico, Massimiliano; Christensen, Knud V

    2017-11-01

    The identification of the influence of the reaction parameters is of paramount importance when defining a process design. In this work, non-edible castor oil was reacted with methanol to produce a possible component for biodiesel blends, using liquid enzymes as the catalyst. Temperature, alcohol-to-oil molar ratio, enzyme and added water contents were the reaction parameters evaluated in the transesterification reactions. The optimal conditions, giving the optimal final FAME yield and FFA content in the methyl ester-phase was identified. At 35°C, 6.0 methanol-to-oil molar ratio, 5wt% of enzyme and 5wt% of water contents, 94% of FAME yield and 6.1% of FFA in the final composition were obtained. The investigation was completed with the analysis of the component profiles, showing that at least 8h are necessary to reach a satisfactory FAME yield together with a minor FFA content. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Iron-Dependent Enzyme Catalyzes the Initial Step in Biodegradation of N-Nitroglycine by Variovorax sp. Strain JS1663.

    Science.gov (United States)

    Mahan, Kristina M; Zheng, Hangping; Fida, Tekle T; Parry, Ronald J; Graham, David E; Spain, Jim C

    2017-08-01

    Nitramines are key constituents of most of the explosives currently in use and consequently contaminate soil and groundwater at many military facilities around the world. Toxicity from nitramine contamination poses a health risk to plants and animals. Thus, understanding how nitramines are biodegraded is critical to environmental remediation. The biodegradation of synthetic nitramine compounds such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has been studied for decades, but little is known about the catabolism of naturally produced nitramine compounds. In this study, we report the isolation of a soil bacterium, Variovorax sp. strain JS1663, that degrades N -nitroglycine (NNG), a naturally produced nitramine, and the key enzyme involved in its catabolism. Variovorax sp. JS1663 is a Gram-negative, non-spore-forming motile bacterium isolated from activated sludge based on its ability to use NNG as a sole growth substrate under aerobic conditions. A single gene ( nnlA ) encodes an iron-dependent enzyme that releases nitrite from NNG through a proposed β-elimination reaction. Bioinformatics analysis of the amino acid sequence of NNG lyase identified a PAS (Per-Arnt-Sim) domain. PAS domains can be associated with heme cofactors and function as signal sensors in signaling proteins. This is the first instance of a PAS domain present in a denitration enzyme. The NNG biodegradation pathway should provide the basis for the identification of other enzymes that cleave the N-N bond and facilitate the development of enzymes to cleave similar bonds in RDX, nitroguanidine, and other nitramine explosives. IMPORTANCE The production of antibiotics and other allelopathic chemicals is a major aspect of chemical ecology. The biodegradation of such chemicals can play an important ecological role in mitigating or eliminating the effects of such compounds. N -Nitroglycine (NNG) is produced by the Gram-positive filamentous soil bacterium Streptomyces noursei This study reports the isolation of a Gram-negative soil bacterium, Variovorax sp. strain JS1663, that is able to use NNG as a sole growth substrate. The proposed degradation pathway occurs via a β-elimination reaction that releases nitrite from NNG. The novel NNG lyase requires iron(II) for activity. The identification of a novel enzyme and catabolic pathway provides evidence of a substantial and underappreciated flux of the antibiotic in natural ecosystems. Understanding the NNG biodegradation pathway will help identify other enzymes that cleave the N-N bond and facilitate the development of enzymes to cleave similar bonds in synthetic nitramine explosives. Copyright © 2017 American Society for Microbiology.

  9. Chemical kinetics and reaction mechanism

    International Nuclear Information System (INIS)

    Jung, Ou Sik; Park, Youn Yeol

    1996-12-01

    This book is about chemical kinetics and reaction mechanism. It consists of eleven chapters, which deal with reaction and reaction speed on reaction mechanism, simple reaction by rate expression, reversible reaction and simultaneous reaction, successive reaction, complicated reaction mechanism, assumption for reaction mechanism, transition state theory, successive reaction and oscillating reaction, reaction by solution, research method high except kinetics on reaction mechanism, high reaction of kinetics like pulsed radiolysis.

  10. Chemical kinetics of gas reactions

    CERN Document Server

    Kondrat'Ev, V N

    2013-01-01

    Chemical Kinetics of Gas Reactions explores the advances in gas kinetics and thermal, photochemical, electrical discharge, and radiation chemical reactions. This book is composed of 10 chapters, and begins with the presentation of general kinetic rules for simple and complex chemical reactions. The next chapters deal with the experimental methods for evaluating chemical reaction mechanisms and some theories of elementary chemical processes. These topics are followed by discussions on certain class of chemical reactions, including unimolecular, bimolecular, and termolecular reactions. The rema

  11. Determination of kinetic coefficients for proton-nucleus collisions at high energy

    International Nuclear Information System (INIS)

    Rizzato, C.M.

    1987-01-01

    From the effective proton dynamics, the approximations in the context of high energy collisions which lead to the Boltzmann equation, are established. From this equation, general expressions for the kinetic coefficients are deduced. Using a simple model, analytical expressions for kinetic coefficients are obtained. The importance of the effect of Pauli blocking is also shown. (author) [pt

  12. Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks

    DEFF Research Database (Denmark)

    Saa, Pedro A.; Nielsen, Lars K.

    2017-01-01

    Kinetic models are critical to predict the dynamic behaviour of metabolic networks. Mechanistic kinetic models for large networks remain uncommon due to the difficulty of fitting their parameters. Recent modelling frameworks promise new ways to overcome this obstacle while retaining predictive ca...

  13. Interrelationships of glycosylation and aggregation kinetics for Peniophora lycii phytase

    DEFF Research Database (Denmark)

    Høiberg-Nielsen, R.; Fuglsang, C.C.; Arleth, L.

    2006-01-01

    The kinetics of thermally induced aggregation of the glycoprotein Peniophora lycii phytase (Phy) and a deglycosylated form (dgPhy) was studied by dynamic (DLS) and static (SLS) light scattering. This provided a detailed insight into the time course of the formation of small aggregates (similar...

  14. Adsorption analysis equilibria and kinetics

    CERN Document Server

    Do, Duong D

    1998-01-01

    This book covers topics of equilibria and kinetics of adsorption in porous media. Fundamental equilibria and kinetics are dealt with for homogeneous as well as heterogeneous particles. Five chapters of the book deal with equilibria and eight chapters deal with kinetics. Single component as well as multicomponent systems are discussed. In kinetics analysis, we deal with the various mass transport processes and their interactions inside a porous particle. Conventional approaches as well as the new approach using Maxwell-Stefan equations are presented. Various methods to measure diffusivity, such

  15. Kinetic constrained optimization of the golf swing hub path.

    Science.gov (United States)

    Nesbit, Steven M; McGinnis, Ryan S

    2014-12-01

    This study details an optimization of the golf swing, where the hand path and club angular trajectories are manipulated. The optimization goal was to maximize club head velocity at impact within the interaction kinetic limitations (force, torque, work, and power) of the golfer as determined through the analysis of a typical swing using a two-dimensional dynamic model. The study was applied to four subjects with diverse swing capabilities and styles. It was determined that it is possible for all subjects to increase their club head velocity at impact within their respective kinetic limitations through combined modifications to their respective hand path and club angular trajectories. The manner of the modifications, the degree of velocity improvement, the amount of kinetic reduction, and the associated kinetic limitation quantities were subject dependent. By artificially minimizing selected kinetic inputs within the optimization algorithm, it was possible to identify swing trajectory characteristics that indicated relative kinetic weaknesses of a subject. Practical implications are offered based upon the findings of the study. Key PointsThe hand path trajectory is an important characteristic of the golf swing and greatly affects club head velocity and golfer/club energy transfer.It is possible to increase the energy transfer from the golfer to the club by modifying the hand path and swing trajectories without increasing the kinetic output demands on the golfer.It is possible to identify relative kinetic output strengths and weakness of a golfer through assessment of the hand path and swing trajectories.Increasing any one of the kinetic outputs of the golfer can potentially increase the club head velocity at impact.The hand path trajectory has important influences over the club swing trajectory.

  16. Feedback-controlled electro-kinetic traps for single-molecule ...

    Indian Academy of Sciences (India)

    2014-01-11

    Jan 11, 2014 ... limited residence time of a given molecule within the detection volume. A common ... information on individual folding pathways, as well as to the internal dynamics between ..... Essentials for building an electro-kinetic trap.

  17. The temperature hydration kinetics

    Directory of Open Access Journals (Sweden)

    Mircea Oroian

    2017-07-01

    Full Text Available The aim of this study is to evaluate the hydration kinetics of lentil seeds (Lens culinaris in water at different temperatures (25, 32.5, 40, 55, 70 and 80 °C for assessing the adequacy of models for describing the absorption phenomena during soaking. The diffusion coefficient values were calculated using Fick’s model for spherical and hemispherical geometries and the values were in the range of 10−6 m2/s. The experimental data were fitted to Peleg, Sigmoidal, Weibull and Exponential models. The models adequacy was determined using regression coefficients (R2, root mean square error (RMSE and reduced chi-square (χ2. The Peleg model is the suitable one for predicting the experimental data. Temperature had a positive and significant effect on the water absorption capacities and absorption was an endothermic process.

  18. Kinetics model development of cocoa bean fermentation

    Science.gov (United States)

    Kresnowati, M. T. A. P.; Gunawan, Agus Yodi; Muliyadini, Winny

    2015-12-01

    Although Indonesia is one of the biggest cocoa beans producers in the world, Indonesian cocoa beans are oftenly of low quality and thereby frequently priced low in the world market. In order to improve the quality, adequate post-harvest cocoa processing techniques are required. Fermentation is the vital stage in series of cocoa beans post harvest processing which could improve the quality of cocoa beans, in particular taste, aroma, and colours. During the fermentation process, combination of microbes grow producing metabolites that serve as the precursors for cocoa beans flavour. Microbial composition and thereby their activities will affect the fermentation performance and influence the properties of cocoa beans. The correlation could be reviewed using a kinetic model that includes unstructured microbial growth, substrate utilization and metabolic product formation. The developed kinetic model could be further used to design cocoa bean fermentation process to meet the expected quality. Further the development of kinetic model of cocoa bean fermentation also serve as a good case study of mixed culture solid state fermentation, that has rarely been studied. This paper presents the development of a kinetic model for solid-state cocoa beans fermentation using an empirical approach. Series of lab scale cocoa bean fermentations, either natural fermentations without starter addition or fermentations with mixed yeast and lactic acid bacteria starter addition, were used for model parameters estimation. The results showed that cocoa beans fermentation can be modelled mathematically and the best model included substrate utilization, microbial growth, metabolites production and its transport. Although the developed model still can not explain the dynamics in microbial population, this model can sufficiently explained the observed changes in sugar concentration as well as metabolic products in the cocoa bean pulp.

  19. Photochemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Moore, B.C. [Lawrence Berkeley Laboratory, Livermore, CA (United States)

    1993-12-01

    The purpose of the program is to develop a fundamental understanding of unimolecular and bimolecular reaction dynamics with application in combustion and energy systems. The energy dependence in ketene isomerization, ketene dissociation dynamics, and carbonyl substitution on organometallic rhodium complexes in liquid xenon have been studied. Future studies concerning unimolecular processes in ketene as well as energy transfer and kinetic studies of methylene radicals are discussed.

  20. Kinetic theory of Jeans instability

    NARCIS (Netherlands)

    Trigger, S.A.; Ershkovic, A.I.; Heijst, van G.J.F.; Schram, P.P.J.M.

    2004-01-01

    Kinetic treatment of the Jeans gravitational instability, with collisions taken into account, is presented. The initial-value problem for the distribution function which obeys the kinetic equation, with the collision integral conserving the number of particles, is solved. Dispersion relation is

  1. Thermodynamics and kinetics of vesicles formation processes.

    Science.gov (United States)

    Guida, Vincenzo

    2010-12-15

    Vesicles are hollow aggregates, composed of bilayers of amphiphilic molecules, dispersed into and filled with a liquid solvent. These aggregates can be formed either as equilibrium or as out of equilibrium meta-stable structures and they exhibit a rich variety of different morphologies. The surprising richness of structures, the vast range of industrial applications and the presence of vesicles in a number of biological systems have attracted the interest of numerous researchers and scientists. In this article, we review both the thermodynamics and the kinetics aspects of the phenomena of formation of vesicles. We start presenting the thermodynamics of bilayer membranes formation and deformation, with the aim of deriving the conditions for the existence of equilibrium vesicles. Specifically, we use the results from continuum thermodynamics to discuss the possibility of formation of stable equilibrium vesicles, from both mixed amphiphiles and single component systems. We also link the bilayer membrane properties to the molecular structure of the starting amphiphiles. In the second part of this article, we focus on the dynamics and kinetics of vesiculation. We review the process of vesicles formation both from planar lamellar phase under shear and from isotropic micelles. In order to clarify the physical mechanisms of vesicles formation, we continuously draw a parallel between emulsification and vesiculation processes. Specifically, we compare the experimental results, the driving forces and the relative scaling laws identified for the two processes. Describing the dynamics of vesicles formation, we also discuss why non equilibrium vesicles can be formed by kinetics control and why they are meta-stable. Understanding how to control the properties, the stability and the formation process of vesicles is of fundamental importance for a vast number of industrial applications. Copyright © 2009. Published by Elsevier B.V.

  2. Kinetic Constrained Optimization of the Golf Swing Hub Path

    Directory of Open Access Journals (Sweden)

    Steven M. Nesbit

    2014-12-01

    Full Text Available This study details an optimization of the golf swing, where the hand path and club angular trajectories are manipulated. The optimization goal was to maximize club head velocity at impact within the interaction kinetic limitations (force, torque, work, and power of the golfer as determined through the analysis of a typical swing using a two-dimensional dynamic model. The study was applied to four subjects with diverse swing capabilities and styles. It was determined that it is possible for all subjects to increase their club head velocity at impact within their respective kinetic limitations through combined modifications to their respective hand path and club angular trajectories. The manner of the modifications, the degree of velocity improvement, the amount of kinetic reduction, and the associated kinetic limitation quantities were subject dependent. By artificially minimizing selected kinetic inputs within the optimization algorithm, it was possible to identify swing trajectory characteristics that indicated relative kinetic weaknesses of a subject. Practical implications are offered based upon the findings of the study.

  3. Kinetics of depletion interactions

    NARCIS (Netherlands)

    Vliegenthart, G.A.; Schoot, van der P.P.A.M.

    2003-01-01

    Depletion interactions between colloidal particles dispersed in a fluid medium are effective interactions induced by the presence of other types of colloid. They are not instantaneous but built up in time. We show by means of Brownian dynamics simulations that the static (mean-field) depletion force

  4. Cluster growth kinetics

    International Nuclear Information System (INIS)

    Dubovik, V.M.; Gal'perin, A.G.; Rikhvitskij, V.S.; Lushnikov, A.A.

    2000-01-01

    Processes of some traffic blocking coming into existence are considered as probabilistic ones. We study analytic solutions for models for the dynamics of both cluster growth and cluster growth with fragmentation in the systems of finite number of objects. Assuming rates constancy of both coalescence and fragmentation, the models under consideration are linear on the probability functions

  5. Kinetic Theory of Granular Gases

    Energy Technology Data Exchange (ETDEWEB)

    Trizac, Emmanuel [Center of Theoretical Biological Physics, UC San Diego, La Jolla, CA 92093-0374 (United States); Laboratoire de Physique Theorique et Modeles Statistiques, Campus Universitaire, 91405 Orsay (France)

    2005-11-25

    Granular gases are composed of macroscopic bodies kept in motion by an external energy source such as a violent shaking. The behaviour of such systems is quantitatively different from that of ordinary molecular gases: due to the size of the constituents, external fields have a stronger effect on the dynamics and, more importantly, the kinetic energy of the gas is no longer a conserved quantity. The key role of the inelasticity of collisions has been correctly appreciated for about fifteen years, and the ensuing consequences in terms of phase behaviour or transport properties studied in an increasing and now vast body of literature. The purpose of this book is to help the newcomer to the field in acquiring the essential theoretical tools together with some numerical techniques. As emphasized by the authors-who were among the pioneers in the domain- the content could be covered in a one semester course for advanced undergraduates, or it could be incorporated in a more general course dealing with the statistical mechanics of dissipative systems. The book is self-contained, clear, and avoids mathematical complications. In order to elucidate the main physical ideas, heuristic points of views are sometimes preferred to a more rigorous route that would lead to a longer discussion. The 28 chapters are short; they offer exercises and worked examples, solved at the end of the book. Each part is supplemented with a relevant foreword and a useful summary including take-home messages. The editorial work is of good quality, with very few typographical errors. In spite of the title, kinetic theory stricto sensu is not the crux of the matter covered. The authors discuss the consequences of the molecular chaos assumption both at the individual particle level and in terms of collective behaviour. The first part of the book addresses the mechanics of grain collisions. It is emphasized that considering the coefficient of restitution {epsilon} -a central quantity governing the

  6. Kinetic Theory of Granular Gases

    International Nuclear Information System (INIS)

    Trizac, Emmanuel

    2005-01-01

    Granular gases are composed of macroscopic bodies kept in motion by an external energy source such as a violent shaking. The behaviour of such systems is quantitatively different from that of ordinary molecular gases: due to the size of the constituents, external fields have a stronger effect on the dynamics and, more importantly, the kinetic energy of the gas is no longer a conserved quantity. The key role of the inelasticity of collisions has been correctly appreciated for about fifteen years, and the ensuing consequences in terms of phase behaviour or transport properties studied in an increasing and now vast body of literature. The purpose of this book is to help the newcomer to the field in acquiring the essential theoretical tools together with some numerical techniques. As emphasized by the authors-who were among the pioneers in the domain- the content could be covered in a one semester course for advanced undergraduates, or it could be incorporated in a more general course dealing with the statistical mechanics of dissipative systems. The book is self-contained, clear, and avoids mathematical complications. In order to elucidate the main physical ideas, heuristic points of views are sometimes preferred to a more rigorous route that would lead to a longer discussion. The 28 chapters are short; they offer exercises and worked examples, solved at the end of the book. Each part is supplemented with a relevant foreword and a useful summary including take-home messages. The editorial work is of good quality, with very few typographical errors. In spite of the title, kinetic theory stricto sensu is not the crux of the matter covered. The authors discuss the consequences of the molecular chaos assumption both at the individual particle level and in terms of collective behaviour. The first part of the book addresses the mechanics of grain collisions. It is emphasized that considering the coefficient of restitution ε -a central quantity governing the inelasticity of

  7. Recrystallization of deformed copper - kinetics and microstructural evolution

    DEFF Research Database (Denmark)

    Lin, Fengxiang

    The objective of this study is to investigate the recrystallization kinetics and microstructural evolution in copper deformed to high strains, including copper deformed by cold-rolling and copper deformed by dynamic plastic deformation (DPD). Various characterization techniques were used, including...... electron backscatter diffraction (EBSD), Vickers hardness test, 3D X-ray diffraction (3DXRD) and differential scanning calorimetry (DSC). For the cold-rolled samples, a series of initial parameters was investigated for their effects on the recrystallization kinetics and textures, including initial grain...

  8. Kinetics of thyroid hormones

    International Nuclear Information System (INIS)

    Inada, Mitsuo; Nishikawa, Mitsushige; Naito, Kimikazu; Ishii, Hitoshi; Tanaka, Kiyoshi

    1980-01-01

    Kinetics of thyroid hormones were outlined, and recent progress in metabolism of these hormones was also described. Recently, not only T 4 and T 3 but also rT 3 , 3,3'-T 2 , 3',5'-T 2 , and 3,5-T 2 can be measured by RIA. To clarify metabolic pathways of these hormones, metabolic clearance rate and production rate of these hormones were calculated. As single-compartment analysis was insufficient to clarify disappearance curves of thyroid hormones in blood such as T 3 and T 2 of which metabolic speed was so fast, multi-compartment analysis or non-compartment analysis were also performed. Thyroid hormones seemed to be measured more precisely by constant infusion method. At the first step of T 4 metabolism, T 3 was formed by 5'-monodeiodination of T 4 , and rT 3 was formed by 5-monodeiodination of T 4 . As metabolic pathways of T 3 and rT 3 , conversion of them to 3,3'-T 2 or to 3',5'-T 2 and 3,5-T 2 was supposed. This subject will be an interesting research theme in future. (Tsunoda, M.)

  9. Kinetic effects on magnetohydrodynamic phenomena

    International Nuclear Information System (INIS)

    Naito, Hiroshi; Matsumoto, Taro

    2001-01-01

    Resistive and ideal magnetohydrodynamic (MHD) theories are insufficient to adequately explain MHD phenomena in the high-temperature plasma. Recent progress in numerical simulations concerning kinetic effects on magnetohydrodynamic phenomena is summarized. The following three topics are studied using various models treating extended-MHD phenomena. (1) Kinetic modifications of internal kink modes in tokamaks with normal and reversed magnetic shear configurations. (2) Temporal evolution of the toroidal Alfven eigenmode and fishbone mode in tokamaks with energetic ions. (3) Kinetic stabilization of a title mode in field-reversed configurations by means of anchoring ions and beam ions. (author)

  10. Introduction to dynamics

    CERN Document Server

    Pfeiffer, Friedrich

    2015-01-01

    This concise textbook for students preferably of a postgraduate level, but also for engineers in practice, contains the basic kinematical and kinetic structures of dynamics together with carefully selected applications. The book is a condensed introduction to the fundamental laws of kinematics and kinetics, on the most important principles of mechanics and presents the equations of motion in the form of Lagrange and Newton-Euler. Selected problems of linear and nonlinear dynamics are treated, as well as problems of vibration formation. The presented selection of topics gives a useful basis for stepping into more advanced problems of dynamics. The contents of this book represent the result of a regularly revised course, which has been and still is given for masters students at the Technische Universität München. .

  11. Bicarbonate kinetics in Indian males

    Indian Academy of Sciences (India)

    Madhu

    ized kinetics of bicarbonate using a three-compartment model, to assess which compartmental fluxes changed dur- .... total VCO2 was < 3 % and the average respiratory quotient ..... a part of the nonrespiratory losses of 13CO2 occur to this.

  12. Kinetic equations in dirty superconductors

    International Nuclear Information System (INIS)

    Kraehenbuehl, Y.

    1981-01-01

    Kinetic equations for superconductors in the dirty limit are derived using a method developed for superfluid systems, which allows a systematic expansion in small parameters; exact charge conservation is obeyed. (orig.)

  13. Kinetics of bacterial fluorescence staining with 3,3'-diethylthiacyanine.

    Science.gov (United States)

    Thomas, Marlon S; Nuñez, Vicente; Upadhyayula, Srigokul; Zielins, Elizabeth R; Bao, Duoduo; Vasquez, Jacob M; Bahmani, Baharak; Vullev, Valentine I

    2010-06-15

    For more than a century, colorimetric and fluorescence staining have been the foundation of a broad range of key bioanalytical techniques. The dynamics of such staining processes, however, still remains largely unexplored. We investigated the kinetics of fluorescence staining of two gram-negative and two gram-positive species with 3,3'-diethylthiacyanine (THIA) iodide. An increase in the THIA fluorescence quantum yield, induced by the bacterial dye uptake, was the principal reason for the observed emission enhancement. The fluorescence quantum yield of THIA depended on the media viscosity and not on the media polarity, which suggested that the microenvironment of the dye molecules taken up by the cells was restrictive. The kinetics of fluorescence staining did not manifest a statistically significant dependence neither on the dye concentration, nor on the cell count. In the presence of surfactant additives, however, the fluorescence-enhancement kinetic patterns manifested species specificity with statistically significant discernibility.

  14. Internal Diffusion-Controlled Enzyme Reaction: The Acetylcholinesterase Kinetics.

    Science.gov (United States)

    Lee, Sangyun; Kim, Ji-Hyun; Lee, Sangyoub

    2012-02-14

    Acetylcholinesterase is an enzyme with a very high turnover rate; it quenches the neurotransmitter, acetylcholine, at the synapse. We have investigated the kinetics of the enzyme reaction by calculating the diffusion rate of the substrate molecule along an active site channel inside the enzyme from atomic-level molecular dynamics simulations. In contrast to the previous works, we have found that the internal substrate diffusion is the determinant of the acetylcholinesterase kinetics in the low substrate concentration limit. Our estimate of the overall bimolecular reaction rate constant for the enzyme is in good agreement with the experimental data. In addition, the present calculation provides a reasonable explanation for the effects of the ionic strength of solution and the mutation of surface residues of the enzyme. The study suggests that internal diffusion of the substrate could be a key factor in understanding the kinetics of enzymes of similar characteristics.

  15. Kinetic computer modeling of microwave surface-wave plasma production

    International Nuclear Information System (INIS)

    Ganachev, Ivan P.

    2004-01-01

    Kinetic computer plasma modeling occupies an intermediate position between the time consuming rigorous particle dynamic simulation and the fast but rather rough cold- or warm-plasma fluid models. The present paper reviews the kinetic modeling of microwave surface-wave discharges with accent on recent kinetic self-consistent models, where the external input parameters are reduced to the necessary minimum (frequency and intensity of the applied microwave field and pressure and geometry of the discharge vessel). The presentation is limited to low pressures, so that Boltzmann equation is solved in non-local approximation and collisional electron heating is neglected. The numerical results reproduce correctly the bi-Maxwellian electron energy distribution functions observed experimentally. (author)

  16. Cell kinetics and therapeutic efficiency

    International Nuclear Information System (INIS)

    Andreeff, M.; Abenhardt, W.; Gruner, B.; Stoffner, D.; Mainz Univ.

    1976-01-01

    The study shows that cell kinetics effects correlate with the effects of cytostatic drugs in the tumour model investigated here. It should, however, be noted that even genetically related tumour cell types may react differently to the same cytostatic drug, and that the cell kinetics effects, due to the changes in the cell cycle, cannot be predicted but should be followed with a very fast method, e.g. sequential flan fluorescence cytophotometry, for optimal therapeutic results. (orig./GSE) [de

  17. Kinetic parameters from thermogravimetric analysis

    Science.gov (United States)

    Kiefer, Richard L.

    1993-01-01

    High performance polymeric materials are finding increased use in aerospace applications. Proposed high speed aircraft will require materials to withstand high temperatures in an oxidative atmosphere for long periods of time. It is essential that accurate estimates be made of the performance of these materials at the given conditions of temperature and time. Temperatures of 350 F (177 C) and times of 60,000 to 100,000 hours are anticipated. In order to survey a large number of high performance polymeric materials on a reasonable time scale, some form of accelerated testing must be performed. A knowledge of the rate of a process can be used to predict the lifetime of that process. Thermogravimetric analysis (TGA) has frequently been used to determine kinetic information for degradation reactions in polymeric materials. Flynn and Wall studied a number of methods for using TGA experiments to determine kinetic information in polymer reactions. Kinetic parameters, such as the apparent activation energy and the frequency factor, can be determined in such experiments. Recently, researchers at the McDonnell Douglas Research Laboratory suggested that a graph of the logarithm of the frequency factor against the apparent activation energy can be used to predict long-term thermo-oxidative stability for polymeric materials. Such a graph has been called a kinetic map. In this study, thermogravimetric analyses were performed in air to study the thermo-oxidative degradation of several high performance polymers and to plot their kinetic parameters on a kinetic map.

  18. Impact of the Glymphatic System on the Kinetic and Distribution of Gadodiamide in the Rat Brain: Observations by Dynamic MRI and Effect of Circadian Rhythm on Tissue Gadolinium Concentrations.

    Science.gov (United States)

    Taoka, Toshiaki; Jost, Gregor; Frenzel, Thomas; Naganawa, Shinji; Pietsch, Hubertus

    2018-04-12

    The glymphatic system is a recently hypothesized waste clearance system of the brain in which perivascular space constitutes a pathway similar to the lymphatic system in other body regions. Sleep and anesthesia are reported to influence the activity of the glymphatic system. Because rats are nocturnal animals, the glymphatic system is expected to be more active during the day. We attempted to elucidate the influence of the glymphatic system for intravenously injected gadodiamide in the rat brain by 2 experiments. One was a magnetic resonance imaging (MRI) experiment to evaluate the short-term dynamics of signal intensity changes after gadodiamide administration. The other was a quantification experiment to evaluate the concentration of retained gadolinium within the rat brain after repeated intravenous administration of gadodiamide at different times of day and levels of anesthesia. The imaging experiment was performed on 6 rats that received an intravenous injection of gadodiamide (1 mmol/kg) and dynamic MRI for 3 hours at 2.4-minute intervals. The time course of the signal intensity changes was evaluated for different brain structures. The tissue quantification experiment was performed on 24 rats divided into 4 groups by injection time (morning, late afternoon) and anesthesia (none, short, long) during administration. All animals received gadodiamide (1.8 mmol/kg, 8 times over 2 weeks). Gadolinium concentration of dissected brain tissues was quantified 5 weeks after the last administration by inductively coupled plasma mass spectrometry. In the imaging experiment, muscle and the fourth ventricle showed an instantaneous signal intensity increase immediately after gadodiamide injection. The signal curve of the cerebral cortex and deep cerebellar nuclei reached the peak signal intensity later than the fourth ventricle but earlier than that of the prepontine cistern. In the gadolinium quantification experiment, the concentration in the group with the morning

  19. Biodegradation kinetics for pesticide exposure assessment.

    Science.gov (United States)

    Wolt, J D; Nelson, H P; Cleveland, C B; van Wesenbeeck, I J

    2001-01-01

    Understanding pesticide risks requires characterizing pesticide exposure within the environment in a manner that can be broadly generalized across widely varied conditions of use. The coupled processes of sorption and soil degradation are especially important for understanding the potential environmental exposure of pesticides. The data obtained from degradation studies are inherently variable and, when limited in extent, lend uncertainty to exposure characterization and risk assessment. Pesticide decline in soils reflects dynamically coupled processes of sorption and degradation that add complexity to the treatment of soil biodegradation data from a kinetic perspective. Additional complexity arises from study design limitations that may not fully account for the decline in microbial activity of test systems, or that may be inadequate for considerations of all potential dissipation routes for a given pesticide. Accordingly, kinetic treatment of data must accommodate a variety of differing approaches starting with very simple assumptions as to reaction dynamics and extending to more involved treatments if warranted by the available experimental data. Selection of the appropriate kinetic model to describe pesticide degradation should rely on statistical evaluation of the data fit to ensure that the models used are not overparameterized. Recognizing the effects of experimental conditions and methods for kinetic treatment of degradation data is critical for making appropriate comparisons among pesticide biodegradation data sets. Assessment of variability in soil half-life among soils is uncertain because for many pesticides the data on soil degradation rate are limited to one or two soils. Reasonable upper-bound estimates of soil half-life are necessary in risk assessment so that estimated environmental concentrations can be developed from exposure models. Thus, an understanding of the variable and uncertain distribution of soil half-lives in the environment is

  20. On the dynamics of k-essence models

    International Nuclear Information System (INIS)

    Jorge, Pedro; Mimoso, Jose P; Wands, David

    2007-01-01

    We investigate cosmological dynamics of models with higher-order corrections to the canonical (second-order) kinetic lagrangian for a scalar field, which have been termed k -essence . We study the qualitative dynamics of simple purely kinetic k-essence models and find that the simplest attempts to construct non-singular cosmological models by including higher-order terms in the kinetic lagrangian fail because of a different type of singularity where the scalar field theory becomes ill-defined