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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 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.

  3. 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...... and at the elevated gelation rates (>100 Pa min−1) gels produced using laccase were stronger (higher G′) than HRP catalyzed gels at similar rates of gelation. Chemical analysis confirmed the formation of ferulic acid dehydrodimers (diFAs) by both enzymes supporting that the gelation was a result of oxidative cross...... activity dosage levels, the two enzymes produced different gelation kinetics and the resulting gels had different rheological properties: HRP (with addition of H2O2) catalyzed a fast rate of gelation compared to laccase (no H2O2 addition), but laccase catalysis produced stronger gels (higher G′). The main...

  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. 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

    2009-03-01

    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 brominate bromophenol red, a novel starting substrate. Substrate and enzyme concentration dependence of this enzyme-catalyzed reaction as followed colorimetrically yielded initial rates of reaction that the students compared with those of their peers. The students worked as collaborative groups partially designing their own experiments and carrying them out. In performing the laboratory experiment, they were minimally guided by the instructor and teaching assistants. To engage the students before the laboratory, a short activity involving the enzyme-induced color change was carried out. At the end of the laboratory session, student groups discussed their results in front of the class and reached their own conclusions. Most students had better understanding of important concepts in enzyme kinetics and showed good attitude toward the overall student-centered laboratory exercise. Copyright © 2009 International Union of Biochemistry and Molecular Biology, 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. Starting D-optimal designs for batch kinetics studies of enzyme-catalyzed reactions in the presence of enzyme deactivation.

    Science.gov (United States)

    Malcata, F X

    1992-09-01

    This paper describes a strategy for the starting experimental design of experiments required by general research in the field of biochemical kinetics. The type of experiments that qualify for this analysis involve batch reactions catalyzed by soluble enzymes where the activity of the enzyme decays with time. Assuming that the catalytic action of the enzyme obeys a Michaelis-Menten rate expression and that the deactivation of the enzyme follows a first-order decay, the present analysis employs the dimensionless, integrated form of the overall rate expression to obtain a criterion (based on the maximization of the determinant of the derivative matrix) that relates the a priori estimates of the parameters with the times at which samples should be withdrawn from the reacting mixture. The analysis indicates that the initial concentration of substrate should be as large as possible, and that the samples should be taken at times corresponding to substrate concentrations of approximately 2/3, 1/4, and I/epsilon of the initial concentration (where epsilon should be as large as possible).

  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. 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.

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

    DEFF Research Database (Denmark)

    Abang Zaidel, Dayang Norulfairuz

    , 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...... 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...... byproduct. In this study we investigated the effect of arabinans backbone length on the kinetics of horseradish peroxidase (EC 1.11.1.7) (HRP) catalyzed oxidative cross-linking of ferulic acid (FA) moieties esterified to ?-(1,5)-linked arabinans; taking into account that FA can be oxidatively cross...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1986-05-01

    The R and S enantionmers of S-adenosyl-3-(/sup 2/H)3-(methylthio)-1-propylamine (decarboxylated S-adenosylmethionine), previously synthesized in this laboratory, were incubated with (1,4-/sup 2/H/sub 4/)-putrescine in the presence of spermidine synthase from E. coli. The resulting chiral (/sup 2/H/sub 5/)spermidines were isolated and converted to their N/sub 1/,N/sub 7/-dibocspermidine-N/sub 4/-(1S,4R)-camphanamides. The derivatives were analyzed by 500 MHz /sup 1/H-NMR and the configuration of the chiral center assigned by correlation with the spectra of synthetic chiral (/sup 2/H/sub 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/sub 3/) in all cases studied to date.

  13. Controlled enzyme catalyzed heteropolysaccharide degradation:Xylans

    OpenAIRE

    Rasmussen, Louise Enggaard; Meyer, Anne S.

    2011-01-01

    The work presented in this PhD thesis has provided a better understanding of the enzyme kinetics and quantitative phenomena of the hydrolysis of xylan substrates by selected pure enzyme preparations. Furthermore, the options for producing specific substituted xylooligosaccharides from selected substrates by specific xylanase treatment have been examined. The kinetics of the enzymatic degradation of water-extractable wheat arabinoxylan (WE-AX) during designed treatments with selected monocompo...

  14. Biodiesel production by enzyme-catalyzed transesterification

    OpenAIRE

    Stamenković Olivera S.; Lazić Miodrag L.; Veljković Vlada B.; Skala Dejan U.

    2005-01-01

    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 appli...

  15. Enzyme-Catalyzed Mutation in Breast Cancer

    Science.gov (United States)

    2014-08-01

    Control   lines  will  be  generated  using  the  catalytically   dead ,  tagged   A3B-­‐E255Q.     Cell  culture...human cancers. Nat Genet 2013, 45:970–976. 10. Bryant HE, Schultz N, Thomas HD, Parker KM, Flower D, Lopez E, Kyle S, Meuth M, Curtin NJ, Helleday T...drinking water. Tumors develop as shown within 100-150 days . Experiments are underway to evaluate the kinetics of therapy resistance using this

  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. 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...... 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...

  18. 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.

  19. Enzyme catalyzed electricity-driven water softening system.

    Science.gov (United States)

    Arugula, Mary A; Brastad, Kristen S; Minteer, Shelley D; He, Zhen

    2012-12-10

    Hardness in water, which is caused by divalent cations such as calcium and magnesium ions, presents a major water quality problem. Because hard water must be softened before use in residential applications, there is great interest in the saltless water softening process because, unlike ion exchange softeners, it does not introduce additional ions into water. In this study, a saltless hardness removal driven by bioelectrochemical energy produced through enzymatic oxidation of glucose was proposed and investigated. Glucose dehydrogenase was coated on a carbon electrode to catalyze glucose oxidation in the presence of NAD⁺ as a cofactor/mediator and methylene green as an electrocatalyst. The results showed that electricity generation stimulated hardness removal compared with non-electricity conditions. The enzymatic water softener worked upon a 6h batch operation per day for eight days, and achieved an average hardness removal of 46% at a high initial concentration of 800 mg/L as CaCO₃. More hardness was removed at a lower initial concentration. For instance, at 200mg/L as CaCO₃ the enzymatic water softener removed 76.4±4.6% of total hardness. The presence of magnesium ions decreased hardness removal because of its larger hydrated radius than calcium ions. The enzymatic water softener removed 70-80% of total hardness from three actual hard water samples. These results demonstrated a proof-of-concept that enzyme catalyzed electricity generation can be used to soften hard water. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. Enzyme-catalyzed biocathode in a photoelectrochemical biofuel cell

    Science.gov (United States)

    Yang, Jing; Hu, Donghua; Zhang, Xiaohuan; Wang, Kunqi; Wang, Bin; Sun, Bo; Qiu, Zhidong

    2014-12-01

    A novel double-enzyme photoelectrochemical biofuel cell (PEBFC) has been developed by taking glucose dehydrogenase (GDH) and horseradish peroxidase (HRP) as the enzyme of the photoanode and biocathode to catalyze the oxidation of glucose and the reduction of oxygen. A H2-mesoporphyrin IX is used as a dye for a TiO2 film electrode to fabricate a photoanode. The horseradish peroxidase (HRP) is immobilized on a glassy carbon (GC) electrode to construct a biocathode which is used to catalyze the reduction of oxygen in the PEBFC for the first time. The biocathode exhibits excellent electrocatalytic activity in the presence of O2. The performances of the PEBFC are obtained by current-voltage and power-voltage curves. The short-circuit current density (Isc), the open-circuit voltage (Voc), maximum power density (Pmax), fill factor (FF) and energy conversion efficiency (η) are 439 μA cm-2, 678 mV, 79 μW cm-2, 0.39 and 0.016%, respectively, and the incident photon-to-collected electron conversion efficiency (IPCE) is 32% at 350 nm. The Isc is higher than that of the PEBFC with Pt cathode, and the Voc is higher than that of the dye-sensitized solar cell or the enzyme-catalyzed biofuel cell operating individually, which demonstrates that the HRP is an efficient catalyst for the biocathode in the PEBFC.

  1. Multistep enzyme catalyzed reactions for unnatural amino acids.

    Science.gov (United States)

    D'Arrigo, Paola; Tessaro, Davide

    2012-01-01

    The use of unnatural amino acids, particularly synthetic α-amino acids, for modern drug discovery research requires the availability of enantiomerically pure isomers. Starting from a racemate, one single enantiomer can be obtained using a deracemization process. The two more common strategies of deracemization are those obtained by stereoinversion and by dynamic kinetic resolution. Both techniques will be here described using as a substrate the D,L-3-(2-naphthyl)-alanine, a non-natural amino acid: the first one employing a multi-enzymatic redox system, the second one combining an hydrolytic enzyme together with a base-catalyzed substrate racemization. In both cases, the final product, L-3-(2-naphthyl)alanine, is recovered with good yield and excellent enantiomeric excess.

  2. Reversed hydroxamate-bearing thermolysin inhibitors mimic a high-energy intermediate along the enzyme-catalyzed proteolytic reaction pathway.

    Science.gov (United States)

    Park, Jung Dae; Kim, Dong H

    2003-10-06

    A series of inhibitors that bear a reversed hydroxamate moiety have been evaluated as transition state analogue inhibitors for thermolysin. A linear correlation is observed between the K(i) values of these inhibitors and the kinetic parameters (K(M)/k(cat)) of the parallel series of related substrates, satisfying the criterion stipulated for transition state analogue inhibitors by Bartlett and Marlowe. Furthermore, examination of the binding mode of a related reversed hydroxamate bearing thermolysin inhibitor, in comparison with a transition state postulated for the enzyme-catalyzed proteolytic reaction revealed that the inhibitors under study mimic the electronic as well as the geometric characteristics of the transition state. On the basis of these results it may be concluded that the hydroxamate-bearing zinc protease inhibitors are a new type of transition state analogue inhibitors.

  3. Quantum kinetic Heisenberg models: a unique dynamics

    International Nuclear Information System (INIS)

    Timonen, J.; Pilling, D.J.; Bullough, R.K.

    1986-01-01

    We suggest that the dynamics Glauber embodied in his kinetic Ising model can be introduced similarly and in an apparently unique way, into the quantum statistical mechanics of the quantum-integrable models like the Heisenberg, sine-Gordon and Massive Thirring models. The latter may suggest an extension of the theory to unique kinetic Ising models in two dimensions. The kinetic repulsive bose gas which is studied in detail in the steady state seems to be a solvable kinetic model. (author)

  4. Optimization of the Enzyme-Catalyzed Transesterification of Hungarian Sunflower Oil with High Oleic Acid Content

    Energy Technology Data Exchange (ETDEWEB)

    Kovacs, Sandor; Krar, Marton; Hancsok, Jenoe (Univ. of Pannonia, Dept. of Hydrocarbon and Coal Processing, H-8201 Veszprem (Hungary)). e-mail: kovacss@almos.uni-pannon.hu

    2008-10-15

    In our research work we defined the optimum parameters (temperature, methanol to triglyceride molar ratio, reaction time, number of methanol feeds, and the amount of Candia Antarctica lipase) of the enzyme-catalyzed transesterification of properly pre-treated high oleic acid containing sunflower oil. The oleic acid content of the previously mentioned sunflower oil was present in the structure of the triglycerides. Characteristics of the produced sunflower oil methyl esters were evaluated according to the requirements of the EN 14214 standard. Our experimental results indicated that enzyme-catalyzed transesterification could be successfully used for the conversion of high oleic sunflower oils, since we have found proper combination of process parameters resulting in high yield (>99%) of monoesters. The applied enzyme can be separated after the transesterification and used again. The glycerine - because its reaction inhibiting effect - was separated continuously by membrane separation

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

    Science.gov (United States)

    Noé, Frank; Clementi, Cecilia

    2015-10-13

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

  6. 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.

  7. 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

  8. Myofilament kinetics in isometric twitch dynamics.

    Science.gov (United States)

    Campbell, K B; Razumova, M V; Kirkpatrick, R D; Slinker, B K

    2001-05-01

    To better understand the relationship between kinetic processes of contraction and the dynamic features of an isometric twitch, studies were conducted using a mathematical model that included: (1) kinetics of cross bridge (XB) cycling; (2) kinetics of thin filament regulatory processes; (3) serial and feedback interactions between these two kinetic processes; and (4) time course of calcium activation. Isometric twitch wave forms were predicted, morphometric features of the predicted twitch wave form were evaluated, and sensitivities of wave form morphometric features to model kinetic parameters were assessed. Initially, the impulse response of the XB cycle alone was analyzed with the findings that dynamic constants of the twitch transient were much faster than turnover number of steady-state XB cycling, and, although speed and duration of the twitch wave form were sensitive to XB cycle kinetic constants. parameters of wave shape were not. When thin filament regulatory unit (RU) kinetics were added to XB cycle kinetics, the system impulse response was slowed with only little effect on wave shape. When cooperative neighbor interactions between RU and XB were added, twitch wave shape (as well as amplitude, speed and duration) proved to be sensitive to variation in cooperativity. Importantly, persistence and shape of the falling phase could be strongly modified. When kinetic coefficients of XB attachment were made to depend on sarcomere length, changes in wave shape occurred that did not occur when only sliding filament mechanisms were operative. Indeed, the force-length relationship proved to be highly sensitive to length-dependent XB attachment in combination with cooperative interactions. These model findings are the basis of hypotheses for the role of specific kinetic events of contraction in generating twitch wave form features.

  9. Modeling of Reactor Kinetics and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Matthew Johnson; Scott Lucas; Pavel Tsvetkov

    2010-09-01

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

  10. Kinetic effects in dynamic wetting

    Science.gov (United States)

    Sprittles, James

    2017-11-01

    The maximum speed at which a liquid can wet a solid is limited by the need to displace gas lubrication films in front of the moving contact line. The characteristic height of these films is often comparable to the mean free path in the gas so that hydrodynamic models do not adequately describe the flow physics. In this talk, I will develop a model which incorporates kinetic effects in the gas, via the Boltzmann equation, and can predict experimentally-observed increases in the maximum speed of wetting when (a) the liquid's viscosity is varied, (b) the ambient gas pressure is reduced or (c) the meniscus is confined. This work was supported by the Leverhulme Trust (Research Project Grant) and the Engineering & Physical Sciences Research Council (Grant EP/N016602/1).

  11. Kinetic Theory of Dynamical Systems

    NARCIS (Netherlands)

    Zon, R. van; Beijeren, H. van; Dorfman, J.R.

    1999-01-01

    It is generally believed that the dynamics of simple fluids can be considered to be chaotic, at least to the extent that they can be modeled as classical systems of particles interacting with short range, repulsive forces. Here we give a brief introduction to those parts of chaos theory that are

  12. Enzyme-catalyzed silver deposition on irregular-shaped gold nanoparticles for electrochemical immunoassay of alpha-fetoprotein.

    Science.gov (United States)

    Lai, Wenqiang; Tang, Dianping; Que, Xiaohua; Zhuang, Junyang; Fu, Libing; Chen, Guonan

    2012-11-28

    A new and disposable electrochemical immunosensor was designed for detection of alpha-fetoprotein (AFP), as a model analyte, with sensitivity enhancement based on enzyme-catalyzed silver deposition onto irregular-shaped gold nanoparticles (ISGNPs). The assay was carried out with a sandwich-type immunoassay protocol by using ISGNP-labeled anti-AFP antibodies conjugated with alkaline phosphatase (ALP-Ab(2)) as detection antibodies. The enzymatically catalytic deposition of silver on the electrode could be measured by stripping analysis in KCl solution due to the Ag/AgCl solid-state voltammetric process. Several labeling protocols including spherical gold nanoparticle-labeled ALP-Ab(2) and ISGNP-labeled ALP-Ab(2) were investigated for determination of AFP, and improved analytical properties were achieved with the ISGNP labeling. With the ISGNP labeling method, the effects of incubation time and incubation temperature for antigen-antibody reaction, and deposition time of silver on the current responses of the electrochemical immunosensors were also monitored. Under optimal conditions, the electrochemical immunosensor exhibited a wide dynamic range from 0.01 ng mL(-1) to 200 ng mL(-1) with a detection limit of 5.0 pg mL(-1) AFP. The immunosensor displayed a good stability and acceptable reproducibility and accuracy. No significant differences at the 95% confidence level were encountered in the analysis of 10 clinical serum samples between the developed immunoassay and the commercially available electrochemiluminescent method for determination of AFP. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Monitoring enzyme-catalyzed reactions in micromachined nanoliter wells using a conventional microscope-based microarray reader

    Science.gov (United States)

    van den Doel, L. Richard; Moerman, R.; van Dedem, G. W. K.; Young, Ian T.; van Vliet, Lucas J.

    2002-06-01

    Yeast-Saccharomyces cerevisiae - it widely used as a model system for other higher eukaryotes, including man. One of the basic fermentation processes in yeast is the glycolytic pathway, which is the conversion of glucose to ethanol and carbon dioxide. This pathway consists of 12 enzyme-catalyzed reactions. With the approach of microarray technology we want to explore the metabolic regulation of this pathway in yeast. This paper will focus on the design of a conventional microscope based microarray reader, which is used to monitor these enzymatic reactions in microarrays. These microarrays are fabricated in silicon and have sizes of 300 by 300 micrometers 2. The depth varies from 20 to 50 micrometers . Enzyme activity levels can be derived by monitoring the production or consumption rate of NAD(P)H, which is excited at 360nm and emits around 450nm. This fluorophore is involved in all 12 reactions of the pathway. The microarray reader is equipped with a back-illuminated CCD camera in order to obtain a high quantum efficiency for the lower wavelengths. The dynamic range of our microarray reader varies form 5(mu) Molar to 1mMolar NAD(P)H. With this microarray reader enzyme activity levels down to 0.01 unit per milliliter can be monitored. The acquisition time per well is 0.1s. The total scan cycle time for a 5 X 5 microarray is less than half a minute. The number of cycles for a proper estimation of the enzyme activity is inversely proportional to the enzyme activity: long measurement times are needed to determine low enzyme activity levels.

  14. 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

  15. Folylpolyglutamate synthetase: direct evidence for an acyl phosphate intermediate in the enzyme-catalyzed reaction

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, R.; McGuire, J.J.; Shane, B.; Coward, J.K.

    1986-05-01

    The nature of the intermediate in the reaction catalyzed by folylpoly-..gamma..-glutamate synthetase (FPGS) has been investigated. Incubation of ..cap alpha..,..gamma..-(/sup 18/O)methotrexate with ATP, glutamate, and FPGS resulted in the formation of (/sup 18/O)phosphate, thus providing strong evidence for the formation of a ..gamma..-glutamyl phosphate during catalysis. The inorganic phosphate formed in the enzyme-catalyzed reaction was separated from other products and substrates by chromatography on DEAE-cellulose, then converted to the trimethyl ester, and analyzed by mass spectroscopy. Stoichiometric formation of (/sup 18/O)phosphate was observed in the case of the E. coli enzyme, isolated from a transformant containing the cloned FPGS-dihydrofolate synthetase (folC) gene. In addition, /sup 31/P-NMR analysis of the phosphate isolated from the reaction using E. coli FPGS showed the expected /sup 18/O-isotopic perturbations due to both singly bonded and doubly bonded P-/sup 18/O species. Similar experiments were carried out with FPGS isolated from hog liver. In this case, the small amounts of pure enzyme available precluded use of the NMR technique. However, mass spectral analysis of the derivatized phosphate product revealed the presence of (/sup 18/O)-trimethyl phosphate, thus indicating that the reaction catalyzed by the mammalian enzyme also proceeds via an acyl phosphate intermediate.

  16. Detoxification of sulfur mustard by enzyme-catalyzed oxidation using chloroperoxidase.

    Science.gov (United States)

    Popiel, S; Nawała, J

    2013-10-10

    One of the most interesting methods for the detoxification of sulfur mustard is enzyme-catalyzed oxidation. This study examined the oxidative destruction of a sulfur mustard by the enzyme chloroperoxidase (EC 1.11.1.10). Chloroperoxidase (CPO) belongs to a group of enzymes that catalyze the oxidation of various organic compounds by peroxide in the presence of a halide ion. The enzymatic oxidation reaction is affected by several factors: pH, presence or absence of chloride ion, temperature, the concentrations of hydrogen peroxide and enzyme and aqueous solubility of the substrate. The optimum reaction conditions were determined by analyzing the effects of all factors, and the following conditions were selected: solvent, Britton-Robinson buffer (pH=3) with tert-butanol (70:30 v/v); CPO concentration, 16U/mL; hydrogen peroxide concentration, 40mmol/L; sodium chloride concentration, 20mmol/L. Under these reaction conditions, the rate constant for the reaction is 0.006s(-1). The Michaelis constant, a measure of the affinity of an enzyme for a particular substrate, is 1.87×10(-3)M for this system. The Michaelis constant for enzymes with a high affinity for their substrate is in the range of 10(-5) to 10(-4)M, so this value indicates that CPO does not have a very high affinity for sulfur mustard. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. 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.

  18. A natural vanishing act: the enzyme-catalyzed degradation of carbon nanomaterials.

    Science.gov (United States)

    Kotchey, Gregg P; Hasan, Saad A; Kapralov, Alexander A; Ha, Seung Han; Kim, Kang; Shvedova, Anna A; Kagan, Valerian E; Star, Alexander

    2012-10-16

    Over the past three decades, revolutionary research in nanotechnology by the scientific, medical, and engineering communities has yielded a treasure trove of discoveries with diverse applications that promise to benefit humanity. With their unique electronic and mechanical properties, carbon nanomaterials (CNMs) represent a prime example of the promise of nanotechnology with applications in areas that include electronics, fuel cells, composites, and nanomedicine. Because of toxicological issues associated with CNMs, however, their full commercial potential may not be achieved. The ex vitro, in vitro, and in vivo data presented in this Account provide fundamental insights into the biopersistence of CNMs, such as carbon nanotubes and graphene, and their oxidation/biodegradation processes as catalyzed by peroxidase enzymes. We also communicate our current understanding of the mechanism for the enzymatic oxidation and biodegradation. Finally, we outline potential future directions that could enhance our mechanistic understanding of the CNM oxidation and biodegradation and could yield benefits in terms of human health and environmental safety. The conclusions presented in this Account may catalyze a rational rethinking of CNM incorporation in diverse applications. For example, armed with an understanding of how and why CNMs undergo enzyme-catalyzed oxidation and biodegradation, researchers can tailor the structure of CNMs to either promote or inhibit these processes. In nanomedical applications such as drug delivery, the incorporation of carboxylate functional groups could facilitate biodegradation of the nanomaterial after delivery of the cargo. On the other hand, in the construction of aircraft, a CNM composite should be stable to oxidizing conditions in the environment. Therefore, pristine, inert CNMs would be ideal for this application. Finally, the incorporation of CNMs with defect sites in consumer goods could provide a facile mechanism that promotes the

  19. Enzyme-catalyzed copolymerization of ε-caprolactone and fumaryl chloride

    International Nuclear Information System (INIS)

    Monteroso, Joan B.; Chakraborty, Soma

    2015-01-01

    Polycaprolactone(PCL) is a polyester that has major applications in the manufacture of films, formulation of copolymers and is widely used as a biomaterial in medical devices, drug delivery and tissue engineering. Polycaprolactone can be synthesized via ring-opening polymerization of ε-caprolactone using a variety of catalysts which includes biocatalysts such as Lipase B from Candida antarctica. Crosslinking polycaprolactone continues to be a challenge due to the lack of functional groups on the polycaprolactone chains. Crosslinking polycaprolactone can improve physical and mechanical properties of the polymer. Gamma-irradiation of polycaprolactone resulted to improved heat resistance and processability of the cross-linked polymer. Radiation crosslinking, however, is not an ideal method of crosslinking since it is not highly selective in breaking and forming new bonds within the polymer chains. For this study, we aim to synthesize a crosslinkable copolymer of ε-caprolactone and fumaryl chloride via enzyme-catalyzed (Lipase B from Candida antarctica) copolymerization of ε-caprolactone (CL) and fumaryl chloride (FCI). The double bonds coming from the fumaryl chloride can serve as the functional group of the synthesized copolymer thereby allowing the polymer to be crosslinkable. Several copolymerization reactions at 70°C were performed by varying the CL, FCl ratios (10 mol % and 20 mol %) and reaction time (4h, 6h, and 12h). As the control sample, polycaprolactone was synthesized via ring-opening of CL. Reactions were catalyzed by Novozyme 435 and no solvent was used for the synthesis. Baeyer's test for unsaturation yielded positive results for polycaprolactonefumarate (PCLF), indicating the successful incorporation of fumaryl chloride into the polymer. IR analysis of the methanol washings of the PCLF samples indicated the presence of unreacted caprolactone. Thermogravimetric analysis of 10% and 20% PCLF samples showed a slight increase in the thermal

  20. 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.

  1. 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...

  2. 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.

  3. 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...... of the progress of enzymatic hydrolysis of different xylan substrates was developed. The method relies on dividing the HPSEC elution profiles into fixed time intervals and utilizing the linear refractive index response (area under the curve) of defined standard compounds. To obtain optimal HPSEC profiles......, 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...

  4. 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…

  5. 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.

  6. 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)

  7. Generic Dynamic Scaling in Kinetic Roughening

    OpenAIRE

    Ramasco, JJ; Lopez, JM; Rodriguez, MA

    2000-01-01

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

  8. 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...... plotted as an Avrami plot. Various reasons for such a low slope are discussed, including possible recrystallization during storage of samples, and the heterogeneous recrystallization kinetics. The effects of heterogeneous recrystallization kinetics are illustrated by a simplified model with a fast...... and a slowly recrystallizing region....

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.)

  14. 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 ...

  15. 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...

  16. 4-wave dynamics in kinetic wave turbulence

    Science.gov (United States)

    Chibbaro, Sergio; Dematteis, Giovanni; Rondoni, Lamberto

    2018-01-01

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

  17. Kinetic simulations of plasmoid chain dynamics

    Science.gov (United States)

    Markidis, S.; Henri, P.; Lapenta, G.; Divin, A.; Goldman, M.; Newman, D.; Laure, E.

    2013-08-01

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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-03-14

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

  4. Energetic Particle Hybrid Simulations for Kinetic Ring Current Dynamics

    Science.gov (United States)

    Amano, T.; Miyoshi, Y.; Seki, K.

    2016-12-01

    The energetic ring current particles dominate the plasma pressure in the inner magnetosphere. Therefore, it is essential to take into account the ring current dynamics in understanding the various inner magnetospheric phenomena. It has been known that the Magnetohydrodynamics (MHD) approximation is not adequate in numerical modeling of the ring current dynamics and the kinetic effect associated with the ring current ions must be included in a self-consistent manner. In particular, the so-called drift-bounce resonance including finite Larmor radius correction has been considered to be a plausible mechanism for internal excitation of ULF waves. However, the scenario has not been confirmed in a self-consistent simulation. We have developed a new three-dimensional numerical simulation code that incorporates the self-consistent coupling between the fully kinetic ring current particle dynamics and the cold background plasma. In other words, it is essentially a hybrid code that solves the ring current ions by using the particle-in-cell method, whereas the two-fluid approximation is adopted for the background electron and proton fluids. The coupling between the two populations has been introduced in a systematic manner. By performing kinetic temperature-anisotropy driven instabilities, we show that the code is indeed capable of describing the kinetic effect associated with the ring current ions. We also discuss three-dimensional simulation results using an approximate magnetosphere-like equilibrium as an initial condition. The initial equilibrium was obtained by iteratively solving a Grad-Shafranov-like equation for an anisotropic bounce-averaged ring current pressure distribution in a two-dimensional dipole-like potential magnetic field. Depending on parameters, we believe that the simulation model should be able to reproduce ULF wave excitation via drift-bounce resonance. Simulation results with different plasma beta, temperature anisotropy, and pressure gradient scale

  5. 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...

  6. 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

  7. 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.

  8. General dynamical properties of cosmological models with nonminimal kinetic coupling

    Science.gov (United States)

    Matsumoto, Jiro; Sushkov, Sergey V.

    2018-01-01

    We consider cosmological dynamics in the theory of gravity with the scalar field possessing the nonminimal kinetic coupling to curvature given as η Gμνphi,μphi,ν, where η is an arbitrary coupling parameter, and the scalar potential V(phi) which assumed to be as general as possible. With an appropriate dimensionless parametrization we represent the field equations as an autonomous dynamical system which contains ultimately only one arbitrary function χ (x)= 8 π | η | V(x/√8 π) with x=√8 πphi. Then, assuming the rather general properties of χ(x), we analyze stationary points and their stability, as well as all possible asymptotical regimes of the dynamical system. It has been shown that for a broad class of χ(x) there exist attractors representing three accelerated regimes of the Universe evolution, including de Sitter expansion (or late-time inflation), the Little Rip scenario, and the Big Rip scenario. As the specific examples, we consider a power-law potential V(phi)=M4(phi/phi0)σ, Higgs-like potential V(phi)=λ/4(phi2‑phi02)2, and exponential potential V(phi)=M4 e‑phi/phi0.

  9. 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.

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

    Science.gov (United States)

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

    2009-08-27

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

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

    Directory of Open Access Journals (Sweden)

    H. Wiechen

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

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

  12. 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.

  13. 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.

  14. 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,…

  15. 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...

  16. Kinetic analysis of oxygen dynamics under a variable work rate.

    Science.gov (United States)

    Artiga Gonzalez, Alexander; Bertschinger, Raphael; Brosda, Fabian; Dahmen, Thorsten; Thumm, Patrick; Saupe, Dietmar

    2017-09-14

    Measurements of oxygen uptake are central to methods for the assessment of physical fitness and endurance capabilities in athletes. Two important parameters extracted from such data of incremental exercise tests are the maximal oxygen uptake and the critical power. A commonly accepted model of the dynamics of oxygen uptake during exercise at a constant work rate comprises a constant baseline oxygen uptake, an exponential fast component, and another exponential slow component for heavy and severe work rates. We have generalized this model to variable load protocols with differential equations that naturally correspond to the standard model for a constant work rate. This provides the means for predicting the oxygen uptake response to variable load profiles including phases of recovery. The model parameters have been fitted for individual subjects from a cycle ergometer test, including the maximal oxygen uptake and critical power. The model predictions have been validated by data collected in separate tests. Our findings indicate that the oxygen kinetics for a variable exercise load can be predicted using the generalized mathematical standard model. Such models can be applied in the field where the constant work rate assumption generally is not valid. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Entropy production in mesoscopic stochastic thermodynamics: nonequilibrium kinetic cycles driven by chemical potentials, temperatures, and mechanical forces.

    Science.gov (United States)

    Qian, Hong; Kjelstrup, Signe; Kolomeisky, Anatoly B; Bedeaux, Dick

    2016-04-20

    Nonequilibrium thermodynamics (NET) investigates processes in systems out of global equilibrium. On a mesoscopic level, it provides a statistical dynamic description of various complex phenomena such as chemical reactions, ion transport, diffusion, thermochemical, thermomechanical and mechanochemical fluxes. In the present review, we introduce a mesoscopic stochastic formulation of NET by analyzing entropy production in several simple examples. The fundamental role of nonequilibrium steady-state cycle kinetics is emphasized. The statistical mechanics of Onsager's reciprocal relations in this context is elucidated. Chemomechanical, thermomechanical, and enzyme-catalyzed thermochemical energy transduction processes are discussed. It is argued that mesoscopic stochastic NET in phase space provides a rigorous mathematical basis of fundamental concepts needed for understanding complex processes in chemistry, physics and biology. This theory is also relevant for nanoscale technological advances.

  18. Entropy production in mesoscopic stochastic thermodynamics: nonequilibrium kinetic cycles driven by chemical potentials, temperatures, and mechanical forces

    Science.gov (United States)

    Qian, Hong; Kjelstrup, Signe; Kolomeisky, Anatoly B.; Bedeaux, Dick

    2016-04-01

    Nonequilibrium thermodynamics (NET) investigates processes in systems out of global equilibrium. On a mesoscopic level, it provides a statistical dynamic description of various complex phenomena such as chemical reactions, ion transport, diffusion, thermochemical, thermomechanical and mechanochemical fluxes. In the present review, we introduce a mesoscopic stochastic formulation of NET by analyzing entropy production in several simple examples. The fundamental role of nonequilibrium steady-state cycle kinetics is emphasized. The statistical mechanics of Onsager’s reciprocal relations in this context is elucidated. Chemomechanical, thermomechanical, and enzyme-catalyzed thermochemical energy transduction processes are discussed. It is argued that mesoscopic stochastic NET in phase space provides a rigorous mathematical basis of fundamental concepts needed for understanding complex processes in chemistry, physics and biology. This theory is also relevant for nanoscale technological advances.

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

    Directory of Open Access Journals (Sweden)

    Anup Kumar Singh

    2009-11-01

    Full Text Available 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, pseudokinetic and endpoint analyses, in optical turn on or turn off modes, under acidic or basic conditions. Reactions in microwell plates and 100 μL 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 μM respectively, with linear trend lines over 3 to 4 orders of magnitude. Coniferyl alcohol oxidation was evident within 10 minutes or with 0.01 μg/mL laccase and 2 minutes or 0.001 μg/mL peroxidase. Detection limit improved to 1.0 μM coniferyl alcohol with Km of 978.7 ± 150.7 μM when examined at 260 nm following 30 minutes oxidation with 1.0 μg/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.

  20. Atmospheric corrosion kinetics and dynamics of karachi onshore areas

    International Nuclear Information System (INIS)

    Khan, M.I.; Bano, H.

    2015-01-01

    Atmospheric corrosion kinetics and dynamics (rate and factors) of Karachi coastal city was ascertained at a couple of locations in the vicinity of Arabian seashore i.e. Hawksbay and Seaview Township by complying ISO 9223, ASTM G01 and ASTM G50 norms. Both exposure test sites were located at west to south-westward wind corridor. Data was collected for exposure of mild steel coupons at these two locations and their meteorological conditions were logged for a period from March 2005 to April 2007. Chloride and Sulfur dioxide were measured by employing ISO 9225 standard. Severe degree of material depletion for mild steel coupons was observed at both test locations. Mass loss was higher at Hawksbay test site than at Sea view Township. Maximum mass loss was observed during monsoon period probably due to rainfall and strong sea wave action which produced enriched marine aerosols and boosted chloride deposition rates. Although paucity of rainfall was observed but substantial relative humidity level was recorded during test period. Comparison of the results indicated that corrosion rate was higher at Hawksbay test site as compared to Seaview test site. Goethite and lepidocrocite were identified as major corrosion products by Scanning electron microscopy while it was also revealed that major portion of lepidocrocite phase was transformed into goethite at Seaview test site. As goethite phase is thermodynamically more stable and less vulnerable to further recurrence of corrosion as compared to lepidocrocite phase which may be attributed to less corrosion rate measured at Seaview test site. Since corrosion rate at both locations were gauged in the range of 65> rcorr <= 150 in terms of mu m.year-1 so this study ranked the corrosivity of these two test locations as C5 i.e. very high marine corrosivity. (author)

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

    Science.gov (United States)

    Grossman, Max; Willacy, Karen; Allen, Mark

    2011-01-01

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

  2. Binding energy and catalysis by D-xylose isomerase: kinetic, product, and X-ray crystallographic analysis of enzyme-catalyzed isomerization of (R)-glyceraldehyde.

    Science.gov (United States)

    Toteva, Maria M; Silvaggi, Nicholas R; Allen, Karen N; Richard, John P

    2011-11-22

    D-Xylose isomerase (XI) and triosephosphate isomerase (TIM) catalyze the aldose-ketose isomerization reactions of D-xylose and d-glyceraldehyde 3-phosphate (DGAP), respectively. D-Glyceraldehyde (DGA) is the triose fragment common to the substrates for XI and TIM. The XI-catalyzed isomerization of DGA to give dihydroxyacetone (DHA) in D(2)O was monitored by (1)H nuclear magnetic resonance spectroscopy, and a k(cat)/K(m) of 0.034 M(-1) s(-1) was determined for this isomerization at pD 7.0. This is similar to the k(cat)/K(m) of 0.017 M(-1) s(-1) for the TIM-catalyzed carbon deprotonation reaction of DGA in D(2)O at pD 7.0 [Amyes, T. L., O'Donoghue, A. C., and Richard, J. P. (2001) J. Am. Chem. Soc. 123, 11325-11326]. The much larger activation barrier for XI-catalyzed isomerization of D-xylose (k(cat)/K(m) = 490 M(-1) s(-1)) versus that for the TIM-catalyzed isomerization of DGAP (k(cat)/K(m) = 9.6 × 10(6) M(-1) s(-1)) is due to (i) the barrier to conversion of cyclic d-xylose to the reactive linear sugar (5.4 kcal/mol) being larger than that for conversion of DGAP hydrate to the free aldehyde (1.7 kcal/mol) and (ii) the intrinsic binding energy [Jencks, W. P. (1975) Adv. Enzymol. Relat. Areas Mol. Biol. 43, 219-410] of the terminal ethylene glycol fragment of D-xylose (9.3 kcal/mol) being smaller than that of the phosphodianion group of DGAP (~12 kcal/mol). The XI-catalyzed isomerization of DGA in D(2)O at pD 7.0 gives a 90% yield of [1-(1)H]DHA and a 10% yield of [1-(2)H]DHA, the product of isomerization with incorporation of deuterium from solvent D(2)O. By comparison, the transfer of (3)H from the labeled hexose substrate to solvent is observed only once in every 10(9) turnovers for the XI-catalyzed isomerization of [2-(3)H]glucose in H(2)O [Allen, K. N., Lavie, A., Farber, G. K., Glasfeld, A., Petsko, G. A., and Ringe, D. (1994) Biochemistry 33, 1481-1487]. We propose that truncation of the terminal ethylene glycol fragment of d-xylose to give DGA results in a large decrease in the rate of XI-catalyzed isomerization with hydride transfer compared with that for proton transfer. An ultra-high-resolution (0.97 Å) X-ray crystal structure was determined for the complex obtained by soaking crystals of XI with 50 mM DGA. The triose binds to XI as the unreactive hydrate, but ligand binding induces metal cofactor movement and conformational changes in active site residues similar to those observed for XI·sugar complexes. © 2011 American Chemical Society

  3. Binding Energy and Catalysis by D-Xylose Isomerase: Kinetic, Product and X-Ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde‡, ¶

    Science.gov (United States)

    Toteva, Maria M.; Silvaggi, Nicholas R.; Allen, Karen N.; Richard, John P.

    2011-01-01

    D-Xylose isomerase (XI) and triosephosphate isomerase (TIM) catalyze the aldose-ketose isomerization reactions of D-xylose and D-glyceraldehyde 3-phosphate (DGAP), respectively. D-Glyceraldehyde (DGA) is the triose fragment common to the substrates for XI and TIM. The XI-catalyzed isomerization of DGA to give dihydroxyacetone (DHA) in D2O was monitored by 1H NMR spectroscopy and kcat/Km = 0.034 M−1 s−1 was determined for this isomerization at pD 7.0. This is similar to kcat/Km = 0.017 M−1 s−1 for the TIM-catalyzed carbon deprotonation reaction of DGA in D2O at pD 7.0 [Amyes, T. L.; O’Donoghue, A. C. and Richard J. P. (2001) J. Am. Chem. Soc. 123, 11325–11326]. The much larger activation barrier for XI-catalyzed isomerization of D-xylose (kcat/Km = 490 M−1 s−1) than for the TIM-catalyzed isomerization of DGAP (kcat/Km = 9.6 x 106 M−1 s−1) is due to: (i) The larger barrier to conversion of cyclic D-xylose to the reactive linear sugar (5.4 kcal/mol) than for conversion of DGAP hydrate to the free aldehyde (1.7 kcal/mol). (ii) The smaller intrinsic binding energy [Jencks, W. P. (1975) Adv. Enzymol. Relat. Areas Mol. Biol. 43, 219–410] of the terminal ethylene glycol fragment of D-xylose (9.3 kcal/mol) than of the phosphodianion group of DGAP (ca. 12 kcal/mol). The XI-catalyzed isomerization of DGA in D2O at pD 7.0 gives a 90% yield of [1-1H]-DHA and a 10% yield of [1-2H]-DHA, the product of isomerization with deuterium incorporation from solvent D2O. By comparison, the transfer of 3H from labeled hexose substrate to solvent is observed only once in every 109 turnovers for the XI-catalyzed isomerization of [2-3H]-glucose in H2O [Allen, K. N., Lavie, A., Farber, G. K., Glasfeld, A., Petsko, G. A., and Ringe, D. (1994), Biochemistry 33, 1481–1487]. We propose that truncation of the terminal ethylene glycol fragment of D-xylose to give DGA results in a large decrease in the rate of XI-catalyzed isomerization with hydride transfer compared with that for proton transfer. An ultra-high resolution (0.97 Å) X-ray crystal structure was determined for the complex obtained by soaking crystals of XI with 50 mM DGA. The triose binds to XI as the unreactive hydrate, but ligand binding induces metal cofactor movement and conformational changes in active site residues similar to those observed for XI•sugar complexes. PMID:21995300

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

    DEFF Research Database (Denmark)

    Flyvbjerg, H.; Jobs, E.

    1997-01-01

    Inverse scattering theory describes the conditions necessary and sufficient to determine an unknown potential from known scattering data. No similar theory exists for when and how one may deduce the kinetics of an unknown chemical reaction from quantitative information about its final state and its...... various initial concentrations of monomers. Distinct mathematical properties of the kinetics of the unknown reaction pathway are found. These properties are shown to restrict the kinetics to a single model that generalizes Oosawa's classical nucleation-polymerization model. The methods used here...

  5. The kinetics and dynamics of the coma of Halley's comet

    Science.gov (United States)

    Combi, Michael R.

    1994-01-01

    This grant to the University of Michigan supported the efforts of Michael R. Combi to serve as a co-investigator in collaboration with a larger effort by the principal investigator, William Smyth of Atmospheric and Environmental Research, Inc. The overall objective of this project was to analyze in a self-consistent manner unique optical O((sup 1)D) and NH2 ultra-high resolution line profile data of excellent quality and other supporting lower-resolution spectral data for the coma of comet P/Halley by using highly developed and physically-based cometary coma models in order to determine and explain in terms of physical processes the actual dynamics and photochemical kinetics that occur in the coma. The justification for this work is that it provides a valuable and underlying physical base from which to interpret significantly different types of coma observations in a self-consistent manner and hence bring into agreement (or avoid) apparent inconsistencies that arise from non-physically based interpretations. The level of effort for the Michigan component amounted to less than three person-months over a planned period of three years. The period had been extended at no extra cost to four years because the Michigan grant and the AER contract did not have coincident time periods. An effort of somewhat larger scope was undertaken by the PI. The importance of the O((sup 1)D) profiles is that they provide a direct trace of the water distribution in comets. The line profile shape is produced by the convolution of the outflow velocity and thermal dispersion of the parent water molecules with the photokinetic ejection of the oxygen atoms upon photodissociation of the parent water molecules. Our understanding of the NH2 and its precursor ammonia are important for comet-to-comet composition variations as they relate to the cosmo-chemistry of the early solar nebula. Modeling of the distribution of NH2 is necessary in order to infer the ammonia production rates from NH2

  6. Dynamic kinetic resolution: alternative approach in optimizing S-ibuprofen production.

    Science.gov (United States)

    Fazlena, H; Kamaruddin, A H; Zulkali, M M D

    2006-03-01

    A lipase catalysed enantioselective hydrolysis process under in situ racemization of the remaining (R)-ibuprofen ester substrate with sodium hydroxide as the catalyst was developed for the production of S-ibuprofen from (R,S)-ibuprofen ester in isooctane. Detailed investigations on parameters study indicated that 0.5 M NaOH, addition of 20% (v/v) co-solvent (dimethyl sulphoxide), operating temperature of 45 degrees C, and 40 mmol/L substrate gave 86% conversion and 99.4% optical purity of S-ibuprofen in dynamic kinetic resolution. Meanwhile, in common enzymatic kinetic resolution process, only 42% conversion of the racemate and 93% enantiomeric excess of the product was obtained which are of lower values as compared to dynamic kinetic resolution. The S-ibuprofen produced during each process was evaluated and approximately 50% increment in concentration of S-acid product was produced when dynamic kinetic resolution was applied into the process.

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

    Directory of Open Access Journals (Sweden)

    Bangji Zhang

    2016-01-01

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

  8. Controlled enzyme catalyzed heteropolysaccharide degradation

    DEFF Research Database (Denmark)

    Rasmussen, Louise Enggaard

    of the progress of enzymatic hydrolysis of different xylan substrates was developed. The method relies on dividing the HPSEC elution profiles into fixed time intervals and utilizing the linear refractive index response (area under the curve) of defined standard compounds. In order to obtain optimal high...... by BsX addition alone on these substrates, nor without FM or BsX addition, the results indicate the presence of endogenous β-D-xylosidase and α-Larabinofuranosidase activities in FM. FM also exhibited activity on both p-nitrophenyl α-Larabinofuranoside (pNPA) and p-nitrophenyl β-D-xylopyranoside (p...

  9. 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

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

    Science.gov (United States)

    Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto

    2012-01-01

    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. PMID:24957767

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Kinetics of colloidal fractal aggregation by differential dynamic microscopy

    Science.gov (United States)

    Ferri, F.; D'Angelo, A.; Lee, M.; Lotti, A.; Pigazzini, M. C.; Singh, K.; Cerbino, R.

    2011-11-01

    We study the kinetics of an aggregation process induced by adding salt to a stable colloidal suspension of 73 nm (diameter) particles. Despite the subdiffraction size of the colloidal particles, the process is monitored via optical microscopy, which is used here to obtain time-resolved scattering information about the colloidal aggregates. The radius of the aggregates is determined as a function of time and their fractal dimension is extracted. Our results are compatible with a diffusion limited aggregation process, as independently confirmed by spectral turbidimetry measurements on the same sample.

  16. CO rebinding kinetics and molecular dynamics simulations highlight dynamic regulation of internal cavities in human cytoglobin.

    Directory of Open Access Journals (Sweden)

    Matteo Gabba

    Full Text Available Cytoglobin (Cygb was recently discovered in the human genome and localized in different tissues. It was suggested to play tissue-specific protective roles, spanning from scavenging of reactive oxygen species in neurons to supplying oxygen to enzymes in fibroblasts. To shed light on the functioning of such versatile machinery, we have studied the processes supporting transport of gaseous heme ligands in Cygb. Carbon monoxide rebinding shows a complex kinetic pattern with several distinct reaction intermediates, reflecting rebinding from temporary docking sites, second order recombination, and formation (and dissociation of a bis-histidyl heme hexacoordinated reaction intermediate. Ligand exit to the solvent occurs through distinct pathways, some of which exploit temporary docking sites. The remarkable change in energetic barriers, linked to heme bis-histidyl hexacoordination by HisE7, may be responsible for active regulation of the flux of reactants and products to and from the reaction site on the distal side of the heme. A substantial change in both protein dynamics and inner cavities is observed upon transition from the CO-liganded to the pentacoordinated and bis-histidyl hexacoordinated species, which could be exploited as a signalling state. These findings are consistent with the expected versatility of the molecular activity of this protein.

  17. Direct observation of the kinetics and dynamics of molecular desorption from liquid surfaces

    Science.gov (United States)

    Quintella, Cristina M.; McCaffery, Anthony J.; Zidan, Mohammed D.

    1993-11-01

    We report measurement of the kinetics and dynamics of I 2 molecules scattered off liquid polydimethylsiloxane. Time-resolved LIF spectra give number densities and quantum state populations throughout the trapping and desorption process. Temperature dependence yields desorption enthalpy Ed=30(±4) kJ mol -1, frequency factor 3 × 10 10. Dynamical behaviour indicates more than one mechanism for activation of trapped species, i.e. conversion of internal energy into translation and energising via interaction with liquid molecules.

  18. 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

  19. Lipase/Ruthenium-Catalyzed Dynamic Kinetic Resolution of β-Hydroxyalkyl ferrocene Derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Han Ki; Ahn, Yang Soo [Pohang University of Science and Technology, Pohang (Korea, Republic of)

    2004-10-15

    An efficient dynamic kinetic resolution of racemic β-hydroxyalkyl ferrocene and 1,1'-bis(β-hydroxyalkyl)- ferrocene derivatives was achieved using lipase/ruthenium-catalyzed transesterification in the presence of an acyl donor. The racemic β-hydroxyalkyl ferrocene derivatives were successfully transformed to the corresponding chiral acetates of high optical purities in high yields.

  20. Clinical effects of proton pump inhibitors: Focus on pharmacogenetics, kinetics and dynamics

    NARCIS (Netherlands)

    N.G.M. Hunfeld (Nicole)

    2010-01-01

    textabstractThis thesis describes the clinical effects of proton pump inhibitors, with focus on pharmacogenetics, kinetics and dynamics. The aims were to investigate the occurence of Rebound Acid Hypersecretion and to investigate the speed of onset, the duration of effect and the difference in

  1. 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.

  2. Suggested Courseware for the Non-Calculus Physics Student: Fluid Dynamics, Kinetic Theory, and Thermal Properties.

    Science.gov (United States)

    Grable-Wallace, Lisa; And Others

    1989-01-01

    Evaluates seven courseware packages covering the topics of fluid dynamics, kinetic theory, and thermal properties. Discusses the price range, sub-topics, program type, interaction, time, calculus required, graphics, and comments of each courseware. Selects some packages based on the criteria. (YP)

  3. 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.

  4. Using simulations and kinetic network models to reveal the dynamics and functions of riboswitches.

    Science.gov (United States)

    Lin, Jong-Chin; Yoon, Jeseong; Hyeon, Changbong; Thirumalai, D

    2015-01-01

    Riboswitches, RNA elements found in the untranslated region, regulate gene expression by binding to target metaboloites with exquisite specificity. Binding of metabolites to the conserved aptamer domain allosterically alters the conformation in the downstream expression platform. The fate of gene expression is determined by the changes in the downstream RNA sequence. As the metabolite-dependent cotranscriptional folding and unfolding dynamics of riboswitches are the key determinant of gene expression, it is important to investigate both the thermodynamics and kinetics of riboswitches both in the presence and absence of metabolite. Single molecule force experiments that decipher the free energy landscape of riboswitches from their mechanical responses, theoretical and computational studies have recently shed light on the distinct mechanism of folding dynamics in different classes of riboswitches. Here, we first discuss the dynamics of water around riboswitch, highlighting that water dynamics can enhance the fluctuation of nucleic acid structure. To go beyond native state fluctuations, we used the Self-Organized Polymer model to predict the dynamics of add adenine riboswitch under mechanical forces. In addition to quantitatively predicting the folding landscape of add-riboswitch, our simulations also explain the difference in the dynamics between pbuE adenine- and add adenine-riboswitches. In order to probe the function in vivo, we use the folding landscape to propose a system level kinetic network model to quantitatively predict how gene expression is regulated for riboswitches that are under kinetic control. © 2015 Elsevier Inc. All rights reserved.

  5. Developing the enzyme-machine analogy: a non-mathematical approach to teaching Michaelis-Menten kinetics

    Directory of Open Access Journals (Sweden)

    Simon Brown

    2010-06-01

    Full Text Available The behavior of enzyme-catalyzed reactions is not made clear to many students by the standard mathematical description of enzyme kinetics. An enzyme-machine analogy is described that has made the details of the Michaelis-Menten mechanism and the associated kinetics more accessible with minimal use of mathematics. Students taught using the analogy appear to have fewer of the misconceptions than those taught using a more mathematical approach.

  6. 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

  7. Lifetime of dynamic heterogeneity in strong and fragile kinetically constrained spin models

    International Nuclear Information System (INIS)

    Leonard, Sebastien; Berthier, Ludovic

    2005-01-01

    Kinetically constrained spin models are schematic coarse-grained models for the glass transition which represent an efficient theoretical tool to study detailed spatio-temporal aspects of dynamic heterogeneity in supercooled liquids. Here, we study how spatially correlated dynamic domains evolve with time and compare our results to various experimental and numerical investigations. We find that strong and fragile models yield different results. In particular, the lifetime of dynamic heterogeneity remains constant and roughly equal to the alpha relaxation time in strong models, while it increases more rapidly in fragile models when the glass transition is approached

  8. Plasmoid Chain Dynamics in Three-Dimensional Kinetic Simulations

    Science.gov (United States)

    Markidis, S.; Henri, P.; Lapenta, G.; Divin, A.; Goldman, M.; Newman, D.; Laure, E.

    2013-10-01

    We study the dynamics of a plasmoid chain with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The plasmoid chain forms by spontaneous magnetic reconnection: the tearing instability rapidly disrupts the initial current sheet generating several small-scale plasmoids, that rapidly grow in size coalescing and kinking. The plasmoid kink is mainly driven by the coalescence process. The presence of guide field strongly influences the evolution of the plasmoid chain. Without a guide field, a main reconnection site dominates and smaller reconnection regions are included in larger ones, leading to an hierarchical structure of the plasmoid-dominated current sheet. On the contrary in presence of a guide field, plasmoids have approximately the same size and the hierarchical structure does not emerge, a strong core magnetic field develops in the center of the plasmoid in the direction of the existing guide field, and bump-on-tail instability, leading to the formation of electron holes, is detected in proximity of the plasmoids. The present work is supported by NASA MMS Grant NNX08AO84G. Additional support rom the European Commission's Seventh Framework Programme under the grant agreement no. 287703 (CRESTA, cresta-project.eu).

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Kinetic Selectivity and Thermodynamic Features of Competitive Imine Formation in Dynamic Covalent Chemistry.

    Science.gov (United States)

    Kulchat, Sirinan; Chaur, Manuel N; Lehn, Jean-Marie

    2017-08-16

    The kinetic and thermodynamic selectivities of imine formation have been investigated for several dynamic covalent libraries of aldehydes and amines. Two systems were examined, involving the reaction of different types of primary amino groups (aliphatic amines, alkoxy-amines, hydrazides and hydrazines) with two types of aldehydes, sulfobenzaldehyde and pyridoxal phosphate in aqueous solution at different pD (5.0, 8.5, 11.4) on one hand, 2-pyridinecarboxaldehyde and salicylaldehyde in organic solvents on the other hand. The reactions were performed separately for given amine/aldehyde pairs as well as in competitive conditions between an aldehyde and a mixture of amines. In the latter case, the time evolution of the dynamic covalent libraries generated was followed, taking into consideration the operation of both kinetic and thermodynamic selectivities. The results showed that, in aqueous solution, the imine of the aliphatic amine was not stable, but oxime and hydrazone formed well in a pH dependent way. On the other hand, in organic solvents, the kinetic product was the imine derived from an aliphatic amine and the thermodynamic products were oxime and hydrazone. The insights gained from these experiments provide a basis for the implementation of imine formation in selective derivatization of mono-amines in mixtures as well as of polyfunctional compounds presenting different types of amino groups. They may in principle be extended to other dynamic covalent chemistry systems. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. 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

  17. 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.

  18. 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.

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

    Science.gov (United States)

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

    2015-11-01

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

  20. 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.

  1. 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)

  2. Viral kinetics and exhaled droplet size affect indoor transmission dynamics of influenza infection.

    Science.gov (United States)

    Chen, S C; Chio, C P; Jou, L J; Liao, C M

    2009-10-01

    The purpose of this paper was to investigate the effects of viral kinetics and exhaled droplet size on indoor transmission dynamics of influenza infection. The target cell-limited model with delayed virus production was adopted to strengthen the inner mechanisms of virus infection on human epithelial cell. The particle number and volume involved in the viral kinetics were linked with Wells-Riley mathematical equation to quantify the infection risk. We investigated population dynamics in a specific elementary school by using the seasonal susceptible - exposed - infected - recovery (SEIR) model. We found that exhaled pulmonary bioaerosol of sneeze (particle diameter generation. By linking the viral kinetics and different exposure parameters and environmental factors in a proposed school setting with five age groups, the influenza infection risk can be estimated. On the other hand, we implicated a new simple means of inhaling to mitigate exhaled bioaerosols through an inhaled non-toxic aerosol. The proposed predictive model may serve as a tool for further investigation of specific control measure such as the personal protection masks to alter the particle size and number concentration characteristics and minimize the exhaled bioaerosol droplet to decrease the infection risk in indoor environment settings.

  3. 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…

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

    Science.gov (United States)

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

    2014-05-16

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

  5. Effects of arterial input function selection on kinetic parameters in brain dynamic contrast-enhanced MRI.

    Science.gov (United States)

    Keil, Vera C; Mädler, Burkhard; Gieseke, Jürgen; Fimmers, Rolf; Hattingen, Elke; Schild, Hans H; Hadizadeh, Dariusch R

    2017-07-01

    Kinetic parameters derived from dynamic contrast-enhanced MRI (DCE-MRI) were suggested as a possible instrument for multi-parametric lesion characterization, but have not found their way into clinical practice yet due to inconsistent results. The quantification is heavily influenced by the definition of an appropriate arterial input functions (AIF). Regarding brain tumor DCE-MRI, there are currently several co-existing methods to determine the AIF frequently including different brain vessels as sources. This study quantitatively and qualitatively analyzes the impact of AIF source selection on kinetic parameters derived from commonly selected AIF source vessels compared to a population-based AIF model. 74 patients with brain lesions underwent 3D DCE-MRI. Kinetic parameters [transfer constants of contrast agent efflux and reflux K trans and k ep and, their ratio, v e, that is used to measure extravascular-extracellular volume fraction and plasma volume fraction v p ] were determined using extended Tofts model in 821 ROI from 4 AIF sources [the internal carotid artery (ICA), the closest artery to the lesion, the superior sagittal sinus (SSS), the population-based Parker model]. The effect of AIF source alteration on kinetic parameters was evaluated by tissue type selective intra-class correlation (ICC) and capacity to differentiate gliomas by WHO grade [area under the curve analysis (AUC)]. Arterial AIF more often led to implausible v e >100% values (pkinetic parameters (pkinetic parameters of different AIF sources and tissues were variable (0.08-0.87) and only consistent >0.5 between arterial AIF derived kinetic parameters. Differentiation between WHO III and II glioma was exclusively possible with v p derived from an AIF in the SSS (p=0.03; AUC 0.74). The AIF source has a significant impact on absolute kinetic parameters in DCE-MRI, which limits the comparability of kinetic parameters derived from different AIF sources. The effect is also tissue-dependent. The SSS

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

    Science.gov (United States)

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

    2014-06-25

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

  7. 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.

  8. Comparison of growth kinetics between static and dynamic cultures of human induced pluripotent stem cells.

    Science.gov (United States)

    Kato, Yuma; Kim, Mee-Hae; Kino-Oka, Masahiro

    2018-02-02

    Understanding the fundamental mechanisms that govern the growth kinetics of human induced pluripotent stem cells (hiPSCs) contributes to culture design strategies to improve large-scale production. Two hiPSC lines (Tic and 253G1) were cultured under static and dynamic suspension conditions, and growth kinetics were compared during early (24-48 h), middle (48-72 h), and late (72-96 h) stages. In 2D static culture, similar growth profiles were observed for both hiPSC lines. However, there were significant differences in growth profile patterns and aggregate morphologies between hiPSC lines grown in 3D static and dynamic cultures. Based on immunostaining comparing the two hiPSC lines, surface distribution of collagen type I was observed in aggregates of the Tic line, but not in those of the 253G1 line. Compared to that in 3D static culture, the numbers of cells at 96 h were significantly decreased in 3D dynamic culture. The apparent specific growth rate (μ app ) of the Tic line was maintained continuously throughout culture, whereas that of the 253G1 line decreased gradually with culture until the late phase, at which time this parameter was reduced to μ app  = (0.85 ± 0.71) × 10 -2  h -1 . This indicates that during the growth of hiPSCs in 3D dynamic culture, cells were damaged by liquid flow, which disrupted the cell-synthesized extracellular matrix (ECM). These results demonstrate that cell-synthesized ECM is an important factor affecting cell growth and morphology, and that changes to the ECM within aggregates lead to reduced growth abilities in dynamic culture. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  9. 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.

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

    Science.gov (United States)

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

    2018-01-01

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

  11. Respiratory dynamics of fresh baby corn (Zea mays L.) under modified atmospheres based on enzyme kinetics.

    Science.gov (United States)

    Singh, Manpreet; Kumar, Ashok; Kaur, Preetinder

    2014-09-01

    The respiratory behaviour of baby corn - whole and end-cut, under different temperatures and gas conditions was evaluated to study its respiratory dynamics based upon enzyme kinetics. The dependence of respiration rate on the O2 and CO2 concentrations has been described assuming the enzyme kinetics model for combined type of inhibition caused by CO2. Various respiratory parameters viz. maximal O2 consumption rate Michaelis-Menten constants, Inhibition constants under the specified environmental conditions of 5, 12.5, 20°C and 75% relative humidity (RH) were estimated using non-linear regression technique. The enzyme kinetics parameters were analyzed according to Arrhenius law to study their temperature dependence. Based upon the overall analysis, it was found that storage temperature had substantial affect on the partial pressures within the closed containers and subsequently the respiration rates. The concentration of O2 inside the container and surrounding temperature had synergistic effect on the rate of respiration and respiratory parameters. Though the inhibition by evolved CO2 was observed to be of combined type, it changed from predominantly competitive at 5°C to predominantly uncompetitive at 12.5 and 20°C. This study can be utilized for design of modified atmosphere packages for storage of fresh and minimally processed baby corn.

  12. 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

  13. Modeling Fluid Dynamics and Growth Kinetics in Fluidized Bed Spray Granulation

    Directory of Open Access Journals (Sweden)

    Zhen Li

    2010-12-01

    Full Text Available Fluidized bed spray granulation is used to produce spherical granules from suspensions, solutions and melts. Experimental investigations revealed that fluid dynamics in the granulator plays a crucial role, in particular in the jet. The jet causes the particle movement as well as drop propagation and deposition on the particles. In this work the “Two Fluid Model” (TFM is used to simulate the multiphase fluid dynamics in the fluidized bed. The results of simulations were validated by measuring the particle velocity using Laser Doppler Velocimetry (LDV. From the TFM-simulations with implemented growth mechanisms the growth kinetics is obtained and is used to describe the transient states of various granulation processes by solving the appropriate population balances.

  14. Mass fluctuation kinetics: analysis and computation of equilibria and local dynamics.

    Science.gov (United States)

    Azunre, P; Gómez-Uribe, C; Verghese, G

    2011-11-01

    The mass fluctuation kinetics (MFK) model is a set of coupled ordinary differential equations approximating the time evolution of means and covariances of species concentrations in chemical reaction networks. It generalises classical mass action kinetics (MAK), in which fluctuations around the mean are ignored. MFK may be used to approximate stochasticity in system trajectories when stochastic simulation methods are prohibitively expensive computationally. This study presents a set of tools to aid in the analysis of systems within the MFK framework. A closed-form expression for the MFK Jacobian matrix is derived. This expression facilitates the computation of MFK equilibria and the characterisation of the dynamics of small deviations from the equilibria (i.e. local dynamics). Software developed in MATLAB to analyse systems within the MFK framework is also presented. The authors outline a homotopy continuation method that employs the Jacobian for bifurcation analysis, that is, to generate a locus of steady-state Jacobian eigenvalues corresponding to changing a chosen MFK parameter such as system volume or a rate constant. This method is applied to study the effect of small-volume stochasticity on local dynamics at equilibria in a pair of example systems, namely the formation and dissociation of an enzyme-substrate complex and a genetic oscillator. For both systems, this study reveals volume regimes where MFK provides a quantitatively and/or qualitatively correct description of system behaviour, and regimes where the MFK approximation is inaccurate. Moreover, our analysis provides evidence that decreasing volume from the MAK regime (infinite volume) has a destabilising effect on system dynamics.

  15. Biochemical thermodynamics and rapid-equilibrium enzyme kinetics.

    Science.gov (United States)

    Alberty, Robert A

    2010-12-30

    Biochemical thermodynamics is based on the chemical thermodynamics of aqueous solutions, but it is quite different because pH is used as an independent variable. A transformed Gibbs energy G' is used, and that leads to transformed enthalpies H' and transformed entropies S'. Equilibrium constants for enzyme-catalyzed reactions are referred to as apparent equilibrium constants K' to indicate that they are functions of pH in addition to temperature and ionic strength. Despite this, the most useful way to store basic thermodynamic data on enzyme-catalyzed reactions is to give standard Gibbs energies of formation, standard enthalpies of formation, electric charges, and numbers of hydrogen atoms in species of biochemical reactants like ATP. This makes it possible to calculate standard transformed Gibbs energies of formation, standard transformed enthalpies of formation of reactants (sums of species), and apparent equilibrium constants at desired temperatures, pHs, and ionic strengths. These calculations are complicated, and therefore, a mathematical application in a computer is needed. Rapid-equilibrium enzyme kinetics is based on biochemical thermodynamics because all reactions in the mechanism prior to the rate-determining reaction are at equilibrium. The expression for the equilibrium concentration of the enzyme-substrate complex that yields products can be derived by applying Solve in a computer to the expressions for the equilibrium constants in the mechanism and the conservation equation for enzymatic sites. In 1979, Duggleby pointed out that the minimum number of velocities of enzyme-catalyzed reactions required to estimate the values of the kinetic parameters is equal to the number of kinetic parameters. Solve can be used to do this with steady-state rate equations as well as rapid-equilibrium rate equations, provided that the rate equation is a polynomial. Rapid-equilibrium rate equations can be derived for complicated mechanisms that involve several reactants

  16. 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.

  17. STADEERS: a software package for the statistical design of experiments pertaining to the estimation of parameters in rate expressions that describe enzyme-catalyzed processes.

    Science.gov (United States)

    Balcão, V M; Malcata, F X

    1993-12-01

    This paper describes a computational algorithm (STADEERS--STAtistical Design of Experiments in Enzyme ReactorS) for the statistical design of biochemical engineering experiments. The type of experiment that qualifies for this package involves a batch reaction catalyzed by a soluble enzyme where the activity of the enzyme decays with time. Assuming that both the catalytic action and the deactivation of the enzyme obey known rate expressions, the present code is helpful in the process of obtaining estimates of the kinetic parameters by providing as output the times at which samples should be withdrawn from the reacting mixture. Starting D-optimal design is used as a basis for the statistical approach. This BASIC code is a powerful tool when fitting a rate expression to data because it increases the effectiveness of experimentation by helping the biochemical kineticist obtain data points with the largest possible informational content.

  18. 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

  19. 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.

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

    Science.gov (United States)

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

    2017-09-01

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

  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. 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.

  4. 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.

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

    Science.gov (United States)

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

    2015-11-01

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

  6. 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

  7. 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.

  8. The kinetics of molecular oxygen migration in the isolated α chains of human hemoglobin as revealed by molecular dynamics simulations and laser kinetic spectroscopy.

    Science.gov (United States)

    Lepeshkevich, Sergei V; Biziuk, Sergey A; Lemeza, Alexander M; Dzhagarov, Boris M

    2011-10-01

    Bimolecular and germinate molecular oxygen (O(2)) rebinding to isolated α chains of human adult hemoglobin in solutions is analyzed. Multiple extended molecular dynamics (MD) simulations of the O(2) migration within the protein after dissociation are described. Computational modeling is exploited to identify hydrophobic pockets within the αchains and internal O(2) migration pathways associated with the experimentally observed ligand rebinding kinetics. To initiate dissociation, trajectories of the liganded protein are interrupted, the iron-dioxygen bond is broken, and the parameters of the iron-nitrogen bonds are simultaneously altered to produce a deoxyheme conformation. MD simulations provide 140 essentially independent trajectories (up to 25-ns long) of the O(2) migration in the protein. The time dependence of cavities occupancy, obtained by the MD simulations, and the kinetics of O(2) rebinding, measured by flash-photolysis techniques, allow us to obtain the kinetics of the entire O(2) migration process within the nanosecond time range and construct an explicit kinetic model of the O(2) migration and rebinding process. The amino acids that have the most pronounced effect on the ligand migration within the α chain matrix are predicted. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. 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.

  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. 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.

  14. 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

  15. 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.

  16. 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...

  17. Direct dynamic kinetic analysis and computer simulation of growth of Clostridium perfringens in cooked turkey during cooling

    Science.gov (United States)

    This research applied a new one-step methodology to directly construct a tertiary model for describing the growth of C. perfringens in cooked turkey meat under dynamically cooling conditions. The kinetic parameters of the growth models were determined by numerical analysis and optimization using mu...

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

    Science.gov (United States)

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

  19. Chemical kinetics with electrical and gas dynamics modelization for NOx removal in an air corona discharge

    International Nuclear Information System (INIS)

    Eichwald, O.; Guntoro, N.A.; Yousfi, M.; Benhenni, M.

    2002-01-01

    A non-stationary reactive gas dynamics model in a mono-dimensional geometry, including radial mass diffusion, gas temperature variation and chemical kinetics, is developed in this paper. The aim is to analyse the spatio-temporal evolution of the main neutral species involved in a corona discharge used for NO pollution control in polluted air at atmospheric pressure and ambient temperature. The present reactive gas dynamics model takes into account 16 neutral chemical species (including certain metastable species) reacting following 110 selected chemical reactions. The initial concentration of each neutral species is obtained from a 1.5D electrical discharge model. The gas temperature variations are due to direct Joule heating during the discharge phase, and also result from the delayed heating due to the relaxation of the vibrational energy into a random thermal energy during the post-discharge phase. The simulation conditions are those of an existing experimental setup (anode voltage of 10 kV in the case of a point to plane geometry with an interelectrode distance of 10 mm). The obtained results show that the diffusion phenomena and the gas temperature rise affect quite well the gas reactivity and the neutral species evolution. This allows us to better understand the different reaction processes and transport phenomena affecting the NO concentration magnitude inside the discharge channel. (author)

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Kinetic compensation and the role of cations in pectinesterase catalysis.

    Science.gov (United States)

    Sun, D; Wicker, L

    1999-04-01

    The catalytic rate constant of thermostable pectinesterase (TS-PE) from Marsh grapefruit pulp was determined at pH 7 at temperatures between 25 and 60 degrees C. TS-PE activity was measured at NaCl concentrations of 0.05, 0.10, 0.15, and 0.20 M and at CaCl(2) concentrations of 0.005, 0.010, 0.015, and 0.020 M. For sodium- and calcium-added conditions, the kinetic functions of this reaction agreed with kinetic compensation relations. The isokinetic temperatures for sodium- and calcium-added conditions were 327.8 and 312.4 K, respectively. Different isokinetic temperatures and compensation parameters suggest that sodium and calcium uniquely affect TS-PE catalysis. This is the first demonstration of kinetic compensation in an enzyme-catalyzed reaction.

  6. 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

  7. 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.

  8. Species-Specific Inactivation of Triosephosphate Isomerase from Trypanosoma brucei: Kinetic and Molecular Dynamics Studies

    Directory of Open Access Journals (Sweden)

    Alejandra Vázquez-Raygoza

    2017-11-01

    Full Text Available Human African Trypanosomiasis (HAT, a disease that provokes 2184 new cases a year in Sub-Saharan Africa, is caused by Trypanosoma brucei. Current treatments are limited, highly toxic, and parasite strains resistant to them are emerging. Therefore, there is an urgency to find new drugs against HAT. In this context, T. brucei depends on glycolysis as the unique source for ATP supply; therefore, the enzyme triosephosphate isomerase (TIM is an attractive target for drug design. In the present work, three new benzimidazole derivatives were found as TbTIM inactivators (compounds 1, 2 and 3 with an I50 value of 84, 82 and 73 µM, respectively. Kinetic analyses indicated that the three molecules were selective when tested against human TIM (HsTIM activity. Additionally, to study their binding mode in TbTIM, we performed a 100 ns molecular dynamics simulation of TbTIM-inactivator complexes. Simulations showed that the binding of compounds disturbs the structure of the protein, affecting the conformations of important domains such as loop 6 and loop 8. In addition, the physicochemical and drug-like parameters showed by the three compounds suggest a good oral absorption. In conclusion, these molecules will serve as a guide to design more potent inactivators that could be used to obtain new drugs against HAT.

  9. 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.

  10. 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

  11. ENZYME-CATALYZED MUTATION IN BREAST CANCER

    Science.gov (United States)

    2015-10-01

    Biotechnologies Inc. The other authors declare no competing financial interests. This does not alter the authors’ adherence to PLOS ONE policies on sharing data...brain, liver, or lungs. Adjuvant systemic therapies effectively reduce the risk of recurrence at these dis- tant metastatic sites by treating preexisting...potential contri - butions large enough to prevent the significant association between A3B expression levels and clinical outcomes for ER+ breast

  12. 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.

  13. 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...... to a dynamical modification of the properties of the system within an excitation pulse duration. We calculate the excitation kinetics of a biased quantum well and the dependency of resulting electronic and optical properties on the excitation pulse fluence, quantum well width,and initial bias field strength. Our...... 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...

  14. 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...

  15. 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

  16. 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.

  17. Kinetics and critical conditions for initiation of dynamic recrystallization during hot compression deformation of AISI 321 austenitic stainless steel

    Science.gov (United States)

    Ghazani, Mehdi Shaban; Eghbali, Beitallah; Ebrahimi, Gholamreza

    2017-09-01

    Dynamic recrystallization behavior of AISI 321 austenitic stainless steel were studied using hot compression tests over the range of temperatures from 900 °C to 1200 °C and strain rates from 0.001 s-1 to 1 s-1. The critical strain and stress for initiation of dynamic recrystallization were determined by plotting strain hardening rate vs. stress curves and a constitutive equation describing the flow stress at strains lower than peak strain. Also, the strain at maximum flow softening was obtained and the effect of deformation conditions (Z parameter) on the critical strain and stress were analyzed. Finally, the volume fraction of dynamic recrystallization was calculated at different deformation conditions using these critical values. Results showed that the model used for predicting the kinetics of dynamic recrystallization has a great consistency with the data, in the form of θ-ɛ curves, directly acquired from experimental flow curves.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. The effects of open and closed kinetic chain exercises on the static and dynamic balance of the ankle joints in young healthy women.

    Science.gov (United States)

    Kim, Mi-Kyoung; Yoo, Kyung-Tae

    2017-05-01

    [Purpose] The purpose of the present study was to analyze the effects of open kinetic chain and closed kinetic chain exercises on the static and dynamic balance of ankle joints in young healthy women. [Subjects and Methods] Twenty women in their 20s were randomly assigned to two groups of ten women each: an open kinetic chain exercise group and a closed kinetic chain exercise group. Each group performed five sets of exercises three times per week for four weeks. Exercise intensity was increased once after two weeks. The subjects' Romberg's test results and their limits of stability were measured to evaluate their static and dynamic balance. The data were analyzed using a two-way repeated measures analysis of variance test. [Results] In the results of Romberg's test, the main effect of the time showed a significant difference in the trace length with eyes closed (Effect size: d=0.97). In the result of limits of stability, the interaction effect showed a significant difference in the backward, and the main effect of the group showed a significant difference in the forward. [Conclusion] The open kinetic chain and closed kinetic chain exercises both improved the balance of the subjects. The closed kinetic chain exercise was more effective at improving the dynamic balance of young healthy women than the open kinetic chain exercise.

  4. 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.

  5. 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

  6. Dynamic kinetic resolution of allylic sulfoxides by Rh-catalyzed hydrogenation: a combined theoretical and experimental mechanistic study.

    Science.gov (United States)

    Dornan, Peter K; Kou, Kevin G M; Houk, K N; Dong, Vy M

    2014-01-08

    A dynamic kinetic resolution (DKR) of allylic sulfoxides has been demonstrated by combining the Mislow [2,3]-sigmatropic rearrangement with catalytic asymmetric hydrogenation. The efficiency of our DKR was optimized by using low pressures of hydrogen gas to decrease the rate of hydrogenation relative to the rate of sigmatropic rearrangement. Kinetic studies reveal that the rhodium complex acts as a dual-role catalyst and accelerates the substrate racemization while catalyzing olefin hydrogenation. Scrambling experiments and theoretical modeling support a novel mode of sulfoxide racemization which occurs via a rhodium π-allyl intermediate in polar solvents. In nonpolar solvents, however, the substrate racemization is primarily uncatalyzed. Computational studies suggest that the sulfoxide binds to rhodium via O-coordination throughout the catalytic cycle for hydrogenation.

  7. [The accuracy of rapid equilibrium assumption in steady-state enzyme kinetics is the function of equilibrium segment structure and properties].

    Science.gov (United States)

    Vrzheshch, P V

    2015-01-01

    Quantitative evaluation of the accuracy of the rapid equilibrium assumption in the steady-state enzyme kinetics was obtained for an arbitrary mechanism of an enzyme-catalyzed reaction. This evaluation depends only on the structure and properties of the equilibrium segment, but doesn't depend on the structure and properties of the rest (stationary part) of the kinetic scheme. The smaller the values of the edges leaving equilibrium segment in relation to values of the edges within the equilibrium segment, the higher the accuracy of determination of intermediate concentrations and reaction velocity in a case of the rapid equilibrium assumption.

  8. Stimuli-Directed Dynamic Reconfiguration in Self-Organized Helical Superstructures Enabled by Chemical Kinetics of Chiral Molecular Motors.

    Science.gov (United States)

    Sun, Jian; Lan, Ruochen; Gao, Yanzi; Wang, Meng; Zhang, Wanshu; Wang, Ling; Zhang, Lanying; Yang, Zhou; Yang, Huai

    2018-02-01

    Dynamic controllability of self-organized helical superstructures in spatial dimensions is a key step to promote bottom-up artificial nanoarchitectures and functional devices for diverse applications in a variety of areas. Here, a light-driven chiral overcrowded alkene molecular motor with rod-like substituent is designed and synthesized, and its thermal isomerization reaction exhibits an increasing structural entropy effect on chemical kinetic analysis in anisotropic achiral liquid crystal host than that in isotropic organic liquid. Interestingly, the stimuli-directed angular orientation motion of helical axes in the self-organized helical superstructures doped with the chiral motors enables the dynamic reconfiguration between the planar (thermostationary) and focal conic (photostationary) states. The reversible micromorphology deformation processes are compatible with the free energy fluctuation of self-organized helical superstructures and the chemical kinetics of chiral motors under different conditions. Furthermore, stimuli-directed reversible nonmechanical beam steering is achieved in dynamic hidden periodic photopatterns with reconfigurable attributes prerecorded with a corresponding photomask and photoinduced polymerization.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. Dynamic force spectroscopy of DNA hairpins: I. Force kinetics and free energy landscapes

    International Nuclear Information System (INIS)

    Mossa, A; Manosas, M; Forns, N; Huguet, J M; Ritort, F

    2009-01-01

    We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force dependent Kramers–Bell rates. To test the theory we have designed a specific DNA hairpin sequence that shows two-state cooperative folding under mechanical tension and carried out pulling experiments using optical tweezers. We show how we can determine the parameters that characterize the molecular free energy landscape of such sequences from rupture force kinetic studies. Finally we combine such kinetic studies with experimental investigations of the Crooks fluctuation relation to derive the free energy of formation of the hairpin at zero force

  14. 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

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

    Science.gov (United States)

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

    1989-04-01

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

  16. Dynamics of competing diffusion processes in a bias electric field: kinetic Ising model approach and phenomenological descriptions

    CERN Document Server

    Aldrin-Denny, R

    1998-01-01

    The methodology of formulating spatio-temporal diffusion-migration equations in an applied electric field for two competing diffusion processes is outlined using kinetic Ising model versions with the help of spin-exchange dynamics due to Kawasaki. The two transport processes considered here correspond to bounded displacement of species attached to supramolecular structures and electron hopping between spatially separated electron transfer active centres. The dependence of the diffusion coefficient on number density as well as the microscopic basis underlying phenomenological diffusion-migration equations are pointed out. (author)

  17. The dynamics of local kinetic parameters of glutamate dehydrogenase in rat liver

    NARCIS (Netherlands)

    Jonker, A.; Geerts, W. J.; Charles, R.; Lamers, W. H.; van Noorden, C. J.

    1996-01-01

    Kinetic parameters of glutamate dehydrogenase (GDH, EC 1.4.1.2) for glutamate were determined in periportal and pericentral zones of adult male and female rat liver lobules under normal fed conditions and after starvation for 24 h. GDH activity was measured as formazan production over time against a

  18. 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 ...

  19. 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

  20. 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.

  1. A novel dynamic kinetic model of oxygen isotopic exchange on a supported metal catalyst

    Energy Technology Data Exchange (ETDEWEB)

    Galdikas, Arvaidas; Duprez, Daniel; Descorme, Claude

    2004-09-15

    A time-resolved kinetic analysis has been developed for modeling experimental results of {sup 18}O/{sup 16}O isotopic exchange over oxide-supported metal catalysts. Model is based on two very important points: (1) the parallel calculation of surface and bulk diffusion and (2) the implication of certain O species such as superoxides. The model includes adsorption-desorption processes on metal clusters and oxygen spillover from the metal to the surface of support and vice versa. Different mechanisms of exchange were also taken into account via mononuclear (O atoms, O{sup -}, OH) or binuclear (superoxides) oxygen species. A refined model taking into account surface diffusion, direct exchange on surface of support by binuclear oxygen species and bulk diffusion was also developed. Kinetic (reaction rates and diffusion coefficients) as well as thermodynamic parameters (activation energies) were derived by fitting theoretical and experimental curves of {sup 18}O{sub 2}, {sup 18}O{sup 16}O and {sup 16}O{sub 2} gas phase concentrations versus time. The experimental results of Pt/CeZrO{sub 2} catalyst samples obtained in the 200-450 deg. C range of temperatures are examined. The refined model provides a very good fitting of the kinetic curves recorded with ceria-zirconia-supported catalysts. Moreover, values of diffusion coefficients and activation energies are in good agreement with already published values found by other methods. For a better understanding of all the steps of exchange, the kinetics of {sup 18}O and {sup 16}O distribution on the surface of metal clusters and on the surface of support are calculated and analyzed. On the basis of this model, a computer code is developed for analysis and calculations of kinetic and thermodynamic parameters of automotive catalysts.

  2. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-15

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

  4. 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

  5. Aging kinetics of levoglucosan orientational glass as a rate dispersion process and consequences for the heterogeneous dynamics view.

    Science.gov (United States)

    Righetti, Maria Cristina; Tombari, Elpidio; Johari, G P

    2016-08-07

    Aging kinetics of a glass is currently modeled in terms of slowing of its α-relaxation dynamics, whose features are interpreted in terms of dynamic heterogeneity, i.e., formation and decay of spatially and temporally distinct nm-size regions. To test the merits of this view, we studied the calorimetric effects of aging an orientational glass of levoglucosan crystal in which such regions would not form in the same way as they form in liquids, and persist in structural glasses, because there is no liquid-like molecular diffusion in the crystal. By measuring the heat capacity, Cp, we determined the change in the enthalpy, H, and the entropy, S, during two aging-protocols: (a) keeping the samples isothermally at temperature, Ta, and measuring the changes after different aging times, ta, and (b) keeping the samples at different Tas and measuring the changes after the same ta. A model-free analysis of the data shows that as ta is increased (procedure (a)), H and S decrease according to a dispersive rate kinetics, and as Ta is increased (procedure (b)), H and S first increase, reach a local maximum at a certain Ta, and then decrease. Even though there is no translational diffusion to produce (liquid-like) free volume, and no translational-rotational decoupling, the aging features are indistinguishable from those of structural glasses. We also find that the Kohlrausch parameter, originally fitted to the glass-aging data, decreases with decrease in Ta, which is incompatible with the current use of the aging data for estimating the α-relaxation time. We argue that the vibrational state of a glass is naturally incompatible with its configurational state, and both change on aging until they are compatible, in the equilibrium liquid. So, dipolar fluctuations seen as the α-relaxation would not be the same motions that cause aging. We suggest that aging kinetics is intrinsically dispersive with its own characteristic rate constant and it does not yield the α-relaxation rate

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

    Science.gov (United States)

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

    2011-08-01

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

  7. 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.

  8. 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.

  9. 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...

  10. 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...... 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...

  11. A robust methodology for kinetic model parameter estimation for biocatalytic reactions

    DEFF Research Database (Denmark)

    Al-Haque, Naweed; Andrade Santacoloma, Paloma de Gracia; Lima Afonso Neto, Watson

    2012-01-01

    Effective estimation of parameters in biocatalytic reaction kinetic expressions are very important when building process models to enable evaluation of process technology options and alternative biocatalysts. The kinetic models used to describe enzyme-catalyzed reactions generally include several...... parameters, which are strongly correlated with each other. State-of-the-art methodologies such as nonlinear regression (using progress curves) or graphical analysis (using initial rate data, for example, the Lineweaver-Burke plot, Hanes plot or Dixon plot) often incorporate errors in the estimates and rarely...... lead to globally optimized parameter values. In this article, a robust methodology to estimate parameters for biocatalytic reaction kinetic expressions is proposed. The methodology determines the parameters in a systematic manner by exploiting the best features of several of the current approaches...

  12. 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

  13. 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...

  14. Exploring the dynamics of kinetic/multi-ion effects and ion-electron equilibration rates in ICF plasmas at OMEGA

    Science.gov (United States)

    Sio, H.

    2017-10-01

    During the last few years, an increasing number of experiments have shown that kinetic and multi-ion-fluid effects do impact the performance of an ICF implosion. Observations include: increasing yield degradation as the implosion becomes more kinetic; thermal decoupling between ion species; anomalous yield scaling for different fuel mixtures; ion diffusion; and fuel stratification. The common theme in these experiments is that the results are based on time-integrated nuclear observables that are affected by an accumulation of effects throughout the implosion, which complicate interpretation of the data. A natural extension of these studies is therefore to conduct time-resolved measurements of multiple nuclear-burn histories to explore the dynamics of kinetic/multi-ion effects in the fuel and their impact on the implosion performance. This was accomplished through simultaneous, high-precision measurements of the relative timing of the onset, bang time and duration of DD, D3He, DT and T3He burn from T3He (with trace D) or D3He gas-filled implosions using the new Particle X-ray Temporal Diagnostic (PXTD) on OMEGA. As the different reactions have different temperature sensitivities, Ti(t) was determined from the data. Uniquely to the PXTD, several x-ray emission histories (in different energy bands) were also measured, from which a spatially averaged Te(t) was also determined. The inferred Ti(t) and Te(t) data have been used to experimentally explore ion-electron equilibration rates and the Coulomb Logarithm for various plasma conditions. Finally, the implementation and use of PXTD, which represents a significant advance at OMEGA, have laid the foundation for implementing a Te(t) measurement in support of the main cryogenic DT programs at OMEGA and the NIF. This work was supported in part by the US DOE, LLE, LLNL, and DOE NNSA SSGF.

  15. Dynamic instabilities in the kinetics of growth and disassembly of microtubules

    OpenAIRE

    Katrukha, Eugene

    2016-01-01

    Dynamic instability of microtubules is considered using frameworks of non-linear thermodynamics and non-equilibrium reaction-diffusion systems. Stochastic assembly/disassembly phases in the polymerization dynamics of microtubules are treated as a result of collective clusterization of microdefects (holes in structure). The model explains experimentally observed power law dependence of catastrophe frequency from the microtubule growth rate. Additional reaction-diffusion-precipitation model is ...

  16. Dynamic kinetic resolution of amino acid amide catalyzed by D-aminopeptidase and alpha-amino-epsilon-caprolactam racemase.

    Science.gov (United States)

    Asano, Yasuhisa; Yamaguchi, Shigenori

    2005-06-01

    Amino acid amide racemizing activity was discovered in alpha-amino-epsilon-caprolactam (ACL) racemase (EC 5. 1. 1. 15) from Achromobacter obae. The enzymatic synthesis of d-alanine from l-alanine amide has been demonstrated by use of d-aminopeptidase (DAP; EC 3. 4. 11. 19) from Ochrobactrum anthropi C1-38 and ACL racemase. The conversion of 45 mM l-alanine amide was carried out at 30 degrees C for 7 h; l-alanine amide was completely converted to d-alanine, and no l-alanine was detected. The result of successive enzymatic reaction shows that the combination of ACL racemase and DAP can be applied for dynamic kinetic resolution of dl-amino acid amides to yield d-amino acids.

  17. Unique pH dynamics in GABAergic synaptic vesicles illuminates the mechanism and kinetics of GABA loading.

    Science.gov (United States)

    Egashira, Yoshihiro; Takase, Miki; Watanabe, Shoji; Ishida, Junji; Fukamizu, Akiyoshi; Kaneko, Ryosuke; Yanagawa, Yuchio; Takamori, Shigeo

    2016-09-20

    GABA acts as the major inhibitory neurotransmitter in the mammalian brain, shaping neuronal and circuit activity. For sustained synaptic transmission, synaptic vesicles (SVs) are required to be recycled and refilled with neurotransmitters using an H(+) electrochemical gradient. However, neither the mechanism underlying vesicular GABA uptake nor the kinetics of GABA loading in living neurons have been fully elucidated. To characterize the process of GABA uptake into SVs in functional synapses, we monitored luminal pH of GABAergic SVs separately from that of excitatory glutamatergic SVs in cultured hippocampal neurons. By using a pH sensor optimal for the SV lumen, we found that GABAergic SVs exhibited an unexpectedly higher resting pH (∼6.4) than glutamatergic SVs (pH ∼5.8). Moreover, unlike glutamatergic SVs, GABAergic SVs displayed unique pH dynamics after endocytosis that involved initial overacidification and subsequent alkalization that restored their resting pH. GABAergic SVs that lacked the vesicular GABA transporter (VGAT) did not show the pH overshoot and acidified further to ∼6.0. Comparison of luminal pH dynamics in the presence or absence of VGAT showed that VGAT operates as a GABA/H(+) exchanger, which is continuously required to offset GABA leakage. Furthermore, the kinetics of GABA transport was slower (τ > 20 s at physiological temperature) than that of glutamate uptake and may exceed the time required for reuse of exocytosed SVs, allowing reuse of incompletely filled vesicles in the presence of high demand for inhibitory transmission.

  18. Monomer Dynamics of Alzheimer Peptides and Kinetic Control of Early Aggregation in Alzheimer's Disease.

    Science.gov (United States)

    Acharya, Srabasti; Srivastava, Kinshuk R; Nagarajan, Sureshbabu; Lapidus, Lisa J

    2016-11-04

    The rate of reconfiguration-or intramolecular diffusion-of monomeric Alzheimer (Aβ) peptides is measured and, under conditions that aggregation is more likely, peptide diffusion slows down significantly, which allows bimolecular associations to be initiated. By using the method of Trp-Cys contact quenching, the rate of reconfiguration is observed to be about five times faster for Aβ 40 , which aggregates slowly, than that for Aβ 42 , which aggregates quickly. Furthermore, the rate of reconfiguration for Aβ 42 speeds up at higher pH, which slows aggregation, and in the presence of the aggregation inhibitor curcumin. The measured reconfiguration rates are able to predict the early aggregation behavior of the Aβ peptide and provide a kinetic basis for why Aβ 42 is more prone to aggregation than Aβ 40 , despite a difference of only two amino acids. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Dynamic kinetic resolution of suprofen thioester via coupled trioctylamine and lipase catalysis.

    Science.gov (United States)

    Lin, C N; Tsai, S W

    2000-07-05

    A lipase-catalyzed enantioselective hydrolysis process under conditions of continuous in situ racemization of substrate with trioctylamine as the catalyst was developed for the production of (S)-suprofen from (R,S)-suprofen 2,2,2-trifluoroethyl thioester in isooctane. A detailed investigation of trioctylamine concentration on the enzyme activation and stability as well as the kinetic behaviors of the thioester in racemization and enzymatic reaction was conducted, in which good agreement between the experimental data and theoretical results was observed. A complete conversion of the racemate for the desired (S)-suprofen in 95% ee(P) was obtained. Moreover, the recovery of the acid product by extraction and reuse of the organic solution were reported. Copyright 2000 John Wiley & Sons, Inc.

  20. 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.

  1. 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

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

    NARCIS (Netherlands)

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

    2000-01-01

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

  3. 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.

  4. 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…

  5. The effect of alpha-ketoglutaric acid on tyrosinase activity and conformation: Kinetics and molecular dynamics simulation study.

    Science.gov (United States)

    Gou, Lin; Lee, Jinhyuk; Yang, Jun-Mo; Park, Yong-Doo; Zhou, Hai-Meng; Zhan, Yi; Lü, Zhi-Rong

    2017-12-01

    Alpha-ketoglutaric acid (AKG) is naturally found in organisms and is a well-known intermediate in the production of ATP or GTP in the Krebs cycle. We elucidated the effects of AKG on tyrosinase activity and conformation via methods of inhibition kinetics integrated with molecular dynamics (MD) simulations. AKG was found to be a reversible inhibitor of tyrosinase (IC 50 =15±0.5mM) and induced parabolic slope mixed-type inhibition. Based on our newly established equation, the dissociation constant (K islope ) was determined to be 7.93±0.31mM. The spectrofluorimetry studies showed that AKG mainly induced regional changes in the active site of tyrosinase, which reflects the flexibility of the active site. The computational docking and molecular dynamics (MD) simulations further demonstrated that AKG could interact with several residues near the substrate-binding site located in the tyrosinase active site pocket. Our study provides insight into the mechanism by which energy-producing intermediates such as AKG inhibit tyrosinase through its ketone groups. Also, AKG could be a potential natural antipigmentation agent due to its non-toxic property. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Assessment of myocardial perfusion by dynamic N-13 ammonia PET imaging: comparison of 2 tracer kinetic models.

    Science.gov (United States)

    Khorsand, Aliasghar; Graf, Senta; Pirich, Christian; Muzik, Otto; Kletter, Kurt; Dudczak, Robert; Maurer, Gerald; Sochor, Heinz; Schuster, Ernst; Porenta, Gerold

    2005-01-01

    Measurement of myocardial blood flow (MBF) by dynamic nitrogen 13 ammonia (NH(3)) positron emission tomography (PET) uses tracer kinetic modeling to analyze time-activity curves. We compared 2 commonly used models with 2 compartments (2C) and 3 compartments (3C) for quantification of MBF and coronary flow reserve (CFR). Seventy-seven patients underwent NH(3) PET at rest and during hyperemia. Time-activity curves for blood pool and myocardial segments were obtained from short-axis images of dynamic sequences. Model fitting of the 2C and 3C models was performed to estimate regional MBF. MBF values calculated by 2C and 3C models were 0.98 +/- 0.31 mL.min(-1).g(-1) and 1.11 +/- 0.37 mL.min(-1).g(-1), respectively, at rest (P models for calculation of resting MBF (r = 0.78), hyperemic MBF (r = 0.68), and CFR (r = 0.68). Measurements of MBF and CFR by 2C and 3C models are significantly related. However, quantification of MBF and CFR significantly differs between the methods. This difference needs to be considered when normal values are established or when measurements obtained with different methods need to be compared.

  7. 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.

  8. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gimbert, Frederic [University of Franche-Comte, Department of Environmental Biology, EA 3184 MR UsC INRA, Place Leclerc, 25030 Besancon Cedex (France); Mench, Michel [UMR BIOGECO INRA 1202, Ecology of Communities, University Bordeaux 1, Avenue des Facultes, 33405 Talence (France); Coeurdassier, Michael; Badot, Pierre-Marie [University of Franche-Comte, Department of Environmental Biology, EA 3184 MR UsC INRA, Place Leclerc, 25030 Besancon Cedex (France); Vaufleury, Annette de [University of Franche-Comte, Department of Environmental Biology, EA 3184 MR UsC INRA, Place Leclerc, 25030 Besancon Cedex (France)], E-mail: annette.devaufleury@univ-fcomte.fr

    2008-04-15

    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{sup -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.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures with...... the kinetic Monte Carlo approach in a three-dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system....... with tailored properties, for example, bacteria colonies of cells or nanodevices with desired properties. Theoretical studies and simulations provide an important tool for unraveling the principles of self-organization and, therefore, have recently gained an increasing interest. The present article features...... an extension of a popular code MBN EXPLORER (MesoBioNano Explorer) aiming to provide a universal approach to study self-assembly phenomena in biology and nanoscience. In particular, this extension involves a highly parallelized module of MBN EXPLORER that allows simulating stochastic processes using...

  11. 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'.

  12. Dynamic dual-energy chest radiography: a potential tool for lung tissue motion monitoring and kinetic study

    Science.gov (United States)

    Xu, Tong; Ducote, Justin L.; Wong, Jerry T.; Molloi, Sabee

    2011-02-01

    Dual-energy chest radiography has the potential to provide better diagnosis of lung disease by removing the bone signal from the image. Dynamic dual-energy radiography is now possible with the introduction of digital flat-panel detectors. The purpose of this study is to evaluate the feasibility of using dynamic dual-energy chest radiography for functional lung imaging and tumor motion assessment. The dual-energy system used in this study can acquire up to 15 frames of dual-energy images per second. A swine animal model was mechanically ventilated and imaged using the dual-energy system. Sequences of soft-tissue images were obtained using dual-energy subtraction. Time subtracted soft-tissue images were shown to be able to provide information on regional ventilation. Motion tracking of a lung anatomic feature (a branch of pulmonary artery) was performed based on an image cross-correlation algorithm. The tracking precision was found to be better than 1 mm. An adaptive correlation model was established between the above tracked motion and an external surrogate signal (temperature within the tracheal tube). This model is used to predict lung feature motion using the continuous surrogate signal and low frame rate dual-energy images (0.1-3.0 frames per second). The average RMS error of the prediction was (1.1 ± 0.3) mm. The dynamic dual energy was shown to be potentially useful for lung functional imaging such as regional ventilation and kinetic studies. It can also be used for lung tumor motion assessment and prediction during radiation therapy.

  13. Dynamic dual-energy chest radiography: a potential tool for lung tissue motion monitoring and kinetic study

    Energy Technology Data Exchange (ETDEWEB)

    Xu Tong [Department of Physics, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S5B6 (Canada); Ducote, Justin L; Wong, Jerry T; Molloi, Sabee, E-mail: txu@physics.carleton.ca [Department of Radiological Sciences, University of California, Irvine, CA 92697 (United States)

    2011-02-21

    Dual-energy chest radiography has the potential to provide better diagnosis of lung disease by removing the bone signal from the image. Dynamic dual-energy radiography is now possible with the introduction of digital flat-panel detectors. The purpose of this study is to evaluate the feasibility of using dynamic dual-energy chest radiography for functional lung imaging and tumor motion assessment. The dual-energy system used in this study can acquire up to 15 frames of dual-energy images per second. A swine animal model was mechanically ventilated and imaged using the dual-energy system. Sequences of soft-tissue images were obtained using dual-energy subtraction. Time subtracted soft-tissue images were shown to be able to provide information on regional ventilation. Motion tracking of a lung anatomic feature (a branch of pulmonary artery) was performed based on an image cross-correlation algorithm. The tracking precision was found to be better than 1 mm. An adaptive correlation model was established between the above tracked motion and an external surrogate signal (temperature within the tracheal tube). This model is used to predict lung feature motion using the continuous surrogate signal and low frame rate dual-energy images (0.1-3.0 frames per second). The average RMS error of the prediction was (1.1 {+-} 0.3) mm. The dynamic dual energy was shown to be potentially useful for lung functional imaging such as regional ventilation and kinetic studies. It can also be used for lung tumor motion assessment and prediction during radiation therapy.

  14. Towards Binding Mechanism of Cu2+ on Creatine Kinase from Pelodiscus sinensis: Molecular Dynamics Simulation Integrating Inhibition Kinetics Study.

    Science.gov (United States)

    Cai, Yan; Lee, Jinhyuk; Wang, Wei; Park, Yong-Doo; Qian, Guo-Ying

    2017-01-01

    Cu2+ is well known to play important roles in living organisms having bifacial distinction: essential microelement that is necessary for a wide range of metabolic processes but hyper-accumulation of Cu2+ can be toxic. The physiological function of Cu2+ in ectothermic animals such as Pelodiscus sinensis (Chinese soft-shelled turtle) has not been elucidated. In this study, we elucidated effect of Cu2+ on the energy producing metabolic enzyme creatine kinase (CK), which might directly affect energy metabolism and homeostasis of P. sinensis. We first conducted molecular dynamics (MD) simulations between P-CK and Cu2+ and conducted the inactivation kinetics including spectrofluorimetry study. MD simulation showed that Cu2+ blocked the binding site of the ATP cofactor, indicating that Cu2+ could directly inactivate P-CK. We prepared the muscle type of CK (P-CK) and confirmed that Cu2+ conspicuously inactivated the activity of P-CK (IC50 = 24.3 μM) and exhibited non-competitive inhibition manner with creatine and ATP in a first-order kinetic process. This result was well matched to the MD simulation results that Cu2+-induced non-competitive inactivation of P-CK. The spectrofluorimetry study revealed that Cu2+ induced tertiary structure changes in PCK accompanying with the exposure of hydrophobic surfaces. Interestingly, the addition of osmolytes (glycine, proline, and liquaemin) effectively restored activity of the Cu2+-inactivated P-CK. Our study illustrates the Cu2+-mediated unfolding of P-CK with disruption of the enzymatic function and the protective restoration role of osmolytes on P-CK inactivation. This study provides information of interest on P-CK as a metabolic enzyme of ectothermic animal in response to Cu2+ binding. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  15. 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

  16. 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.

  17. 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)

  18. 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

  19. Bacterial community dynamics, lactic acid bacteria species diversity and metabolite kinetics of traditional Romanian vegetable fermentations.

    Science.gov (United States)

    Wouters, Dorrit; Grosu-Tudor, Silvia; Zamfir, Medana; De Vuyst, Luc

    2013-03-15

    Artisanal vegetable fermentations are very popular in Eastern European countries. Fresh vegetables undergo a spontaneous fermentation in the presence of salt, which is mainly carried out by lactic acid bacteria (LAB). Culture-dependent and culture-independent analyses of end-samples of various spontaneous vegetable fermentations carried out in houses of the Chiodju region (central Romania) revealed Lactobacillus plantarum and Lactobacillus brevis as the most frequently isolated LAB species. Leuconostoc mesenteroides and Leuconostoc citreum were also found. Furthermore, the community dynamics of spontaneous cauliflower and mixed-vegetable (green tomatoes, carrots and cauliflower) fermentations revealed three steps: an initial phase characterised by the presence of Enterobacteriaceae and a wide LAB species diversity, encompassing Weissella species; a second phase from day 3 onwards wherein L. citreum and Lb. brevis occurred; and a final phase characterised by the prevalence of Lb. brevis and Lb. plantarum. Metabolite target analysis revealed that glucose and fructose were mostly depleted at the end of fermentation. The main products of carbohydrate metabolism were lactic acid, acetic acid, ethanol and small amounts of mannitol, indicating heterolactate fermentation. Given their prevalence at the end of vegetable fermentations, Lb. brevis and Lb. plantarum appear to be good candidate starter cultures for controlled vegetable fermentation processes. © 2012 Society of Chemical Industry.

  20. 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.

  1. Tris(trimethylsilyl)silane as a co-initiator for dental adhesive: Photo-polymerization kinetics and dynamic mechanical property.

    Science.gov (United States)

    Song, Linyong; Ye, Qiang; Ge, Xueping; Misra, Anil; Spencer, Paulette

    2016-01-01

    The purpose of this study was to evaluate the polymerization behavior of a model dentin adhesive with tris(trimethylsilyl)silane (TTMSS) as a co-initiator, and to investigate the polymerization kinetics and mechanical properties of copolymers in dry and wet conditions. A co-monomer mixture based on HEMA/BisGMA (45/55, w/w) was used as a model dentin adhesive. The photoinitiator system included camphorquinone (CQ) as the photosensitizer and the co-initiator was ethyl-4-(dimethylamino) benzoate (EDMAB) or TTMSS. Iodonium salt, diphenyliodonium hexafluorophosphate (DPIHP) serving as a catalyst, was selectively added into the adhesive formulations. The control and the experimental formulations were characterized with regard to the degree of conversion (DC) and dynamic mechanical properties under dry and wet conditions. In two-component photoinitiator system (CQ/TTMSS), with an increase of TTMSS concentration, the polymerization rate and DC of CC double bond increased, and showed a dependence on the irradiation time and curing light intensity. The copolymers that contained the three-component photoinitiator system (CQ/TTMSS/DPIHP) showed similar dynamic mechanical properties, under both dry and wet conditions, to the EDMAB-containing system. The DC of formulations using TTMSS as co-initiator showed a strong dependence on irradiation time. With the addition of TTMSS, the maximum polymerization rate can be adjusted and the network structure became more homogenous. The results indicated that the TTMSS could be used as a substitute for amine-type co-initiator in visible-light induced free radical polymerization of methacrylate-based dentin adhesives. Copyright © 2015 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

  2. Solvent dynamical effects in electron transfer: Predicted consequences of non-Debye relaxation processes and some comparisons with experimental kinetics

    Science.gov (United States)

    McManis, George E.; Weaver, Michael J.

    1989-01-01

    The consequences of non-Debye solvent relaxation upon the barrier-crossing dynamics of adiabatic electron-transfer processes have been explored numerically using a rate formulation due to Hynes for several common forms of the dielectric response function Ê(s), with the objective of assessing the likely experimental importance of such effects. For the ``multiple Debye'' form of Ê(s), analytic expressions for the required time-correlation function can be obtained, whereas for the Davidson-Cole and Cole-Cole forms numerical solutions to the inverse Laplace transform were required. Illustrative numerical results are presented of the increases in the adiabatic barrier-crossing frequency, νn, predicted to be engendered by the presence of higher-frequency relaxation components for dielectric conditions of likely experimental relevance. Substantial (five- to ten fold) rate enhancements are often obtained, resulting from the disproportionately large influence upon νn predicted to arise from the higher-frequency components of Ê(s). Neither νn, nor the non-Debye influence upon νn, are found to be affected greatly by alterations in the shape of the barrier top caused by variations in the electronic coupling matrix element. Comparisons between these numerical predictions and corresponding experimental solvent-dependent νn values extracted from metallocene self-exchange kinetics indicate that the former can account for a substantial fraction of the νn accelerations observed in alcohols and other non-Debye solvents. Roughly concordant non-Debye effects are also predicted from some other, but not all, recent rate formulations. The desirability of utilizing subpicosecond dynamical solvation information from fluorescence Stokes shifts to predict non-Debye effects upon electron-transfer barrier-crossing frequencies is pointed out.

  3. 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

  4. Stereodirectional Origin of anti-Arrhenius Kinetics for a Tetraatomic Hydrogen Exchange Reaction: Born-Oppenheimer Molecular Dynamics for OH + HBr.

    Science.gov (United States)

    Coutinho, Nayara D; Aquilanti, Vincenzo; Silva, Valter H C; Camargo, Ademir J; Mundim, Kleber C; de Oliveira, Heibbe C B

    2016-07-14

    Among four-atom processes, the reaction OH + HBr → H2O + Br is one of the most studied experimentally: its kinetics has manifested an unusual anti-Arrhenius behavior, namely, a marked decrease of the rate constant as the temperature increases, which has intrigued theoreticians for a long time. Recently, salient features of the potential energy surface have been characterized and most kinetic aspects can be considered as satisfactorily reproduced by classical trajectory simulations. Motivation of the work reported in this paper is the investigation of the stereodirectional dynamics of this reaction as the prominent reason for the peculiar kinetics: we started in a previous Letter ( J. Phys. Chem. Lett. 2015 , 6 , 1553 - 1558 ) a first-principles Born-Oppenheimer "canonical" molecular dynamics approach. Trajectories are step-by-step generated on a potential energy surface quantum mechanically calculated on-the-fly and are thermostatically equilibrated to correspond to a specific temperature. Here, refinements of the method permitted a major increase of the number of trajectories and the consideration of four temperatures -50, +200, +350, and +500 K, for which the sampling of initial conditions allowed us to characterize the stereodynamical effect. The role is documented of the adjustment of the reactants' mutual orientation to encounter the entrance into the "cone of acceptance" for reactivity. The aperture angle of this cone is dictated by a range of directions of approach compatible with the formation of the specific HOH angle of the product water molecule; and consistently the adjustment is progressively less effective the higher the kinetic energy. Qualitatively, this emerging picture corroborates experiments on this reaction, involving collisions of aligned and oriented molecular beams, and covering a range of energies higher than the thermal ones. The extraction of thermal rate constants from this molecular dynamics approach is discussed and the systematic

  5. Integration of biological kinetics and computational fluid dynamics to model the growth of Nannochloropsis salina in an open channel raceway.

    Science.gov (United States)

    Park, Stephen; Li, Yebo

    2015-05-01

    Microalgal growth and systemic productivity is not only affected by environmental conditions such as temperature, irradiance, and nutrient concentrations, but also by physical processes such as fluid flow and particulate sedimentation. Modeling and simulating the system is a cost-effective way to predict the growth behavior under various environmental and physical conditions while determining effective engineering approaches to maximize productivity. Many mathematical models have been proposed to describe microalgal growth, while computational fluid dynamics (CFD) have been used to model the behavior of many fluid systems. Integrating the growth kinetics into a CFD model can help researchers understand the impact of a variety of parameters and determine what measures can be taken to overcome some obstacles in the aquaculture industry--self-shading, biomass sedimentation, and contamination--which prevent the production of high biomass yields. The aim of this study was to integrate physical and environmental effects to predict space- and time-dependent algal growth in industrial scale raceways. A commercial CFD software, ANSYS-Fluent 14.5, was used to solve the proposed models in regards to fluid flow, heat transfer, and nutrient balance. User-defined functions written in C language were used to incorporate the kinetic equations into a three-dimensional standard k-ε turbulence model of an open channel raceway system driven by a single paddlewheel. Simulated results were compared with light intensity, temperature, nutrient concentration, and algal biomass data acquired for 56 day from an industrial scale raceway pond constructed for the growth of Nannochloropsis salina and were observed to be in good agreement with one another. There was up to a 17.6% increase in simulated productivity when the incoming CO2 concentration was increased from 0.0006 to 0.150 g L(-1), while the effect of paddlewheel velocity was not significant. Sensitivity analysis showed that the model

  6. Dynamic kinetic resolution of 1,3-dihydro-2H-isoindole-1-carboxylic acid methyl ester: asymmetric transformations toward isoindoline carbamates.

    Science.gov (United States)

    Morán-Ramallal, Roberto; Gotor-Fernández, Vicente; Laborda, Pedro; Sayago, Francisco J; Cativiela, Carlos; Gotor, Vicente

    2012-04-06

    Asymmetric syntheses of isoindoline carbamates have been successfully achieved through enzyme-mediated dynamic kinetic resolution processes and without requirement of metal or acid-base catalyst for the substrate racemization. Optically active carbamates were obtained in good yields and an excellent degree of stereoselectivity when Pseudomonas cepacia lipase (PSL) was used as biocatalyst, with diallyl or dibenzyl carbonates being both adequate reagents in alkoxycarbonylation reactions.

  7. Development of a concise, asymmetric synthesis of a smoothened receptor (SMO) inhibitor: enzymatic transamination of a 4-piperidinone with dynamic kinetic resolution.

    Science.gov (United States)

    Peng, Zhihui; Wong, John W; Hansen, Eric C; Puchlopek-Dermenci, Angela L A; Clarke, Hugh J

    2014-02-07

    A concise, asymmetric synthesis of a smoothened receptor inhibitor (1) is described. The synthesis features an enzymatic transamination with concurrent dynamic kinetic resolution (DKR) of a 4-piperidone (4) to establish the two stereogenic centers required in a single step. This efficient reaction affords the desired anti amine (3) in >10:1 dr and >99% ee. The title compound is prepared in only five steps with 40% overall yield.

  8. 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.

  9. 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

  10. The influence of shape on the glassy dynamics of hard nonspherical particle fluids. II. Barriers, relaxation, fragility, kinetic vitrification, and universality

    Science.gov (United States)

    Tripathy, Mukta; Schweizer, Kenneth S.

    2009-06-01

    We extend and apply the nonlinear Langevin equation theory of activated barrier hopping dynamics in glassy fluids and colloidal suspensions to study broad families of one-, two-, and three-dimensional hard nonspherical particles. Beyond the ideal kinetic arrest volume fraction, entropic barriers emerge with heights (alpha relaxation times, inverse diffusion constants) that increase nonlinearly (nonexponentially) with volume fraction and in a manner that becomes stronger with particle dimensionality. Partial collapse of the volume fraction dependence of barrier heights and reduced relaxation times of different particle shapes within a fixed dimensionality class are achieved based on a difference volume fraction variable that quantifies the distance from the ideal mode coupling theory dynamic crossover. However, the barrier, alpha relaxation time, and self-diffusion constant results of all shapes are remarkably well collapsed onto a single universal master curve based on a theoretically motivated coupling constant which quantifies the renormalized mean square force on a tagged particle. The latter is determined mainly by the square of the intermolecular site-site contact value of the pair correlation function, thereby providing an explicit microscopic connection between local packing, binary collisions, and slow dynamics. A large variation of the dynamic fragility with particle shape is found with compact cluster particles being the most fragile. A kinetic glass transition map is constructed that is relevant to vitrification of laboratory colloidal suspensions. The possible relevance of the hard particle results for understanding the dynamic fragility of thermal van der Waals liquids is discussed.

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

    Energy Technology Data Exchange (ETDEWEB)

    Liang Liang; Dou Peng; Dong Mingming; Ke Xiaokang; Bian Ningsheng [School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093 (China); Liu Zhen, E-mail: zhenliu@nju.edu.cn [School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093 (China)

    2009-09-14

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

  12. Tissue Distribution Dynamics of Human NK Cells Inferred from Peripheral Blood Depletion Kinetics after Sphingosine-1-Phosphate Receptor Blockade.

    Science.gov (United States)

    Mehling, M; Burgener, A-V; Brinkmann, V; Bantug, G R; Dimeloe, S; Hoenger, G; Kappos, L; Hess, C

    2015-11-01

    Human natural killer (NK) cell subsets differentially distribute throughout the organism. While CD56(dim) and CD56(bright) NK cell subsets similarly reside in the bone marrow (BM), the CD56(dim) population predominantly accumulates in non-lymphoid tissues and the CD56(bright) counterpart in lymphoid tissue (LT). The dynamics with which these NK cell subsets redistribute to tissues remains unexplored. Here, we studied individuals newly exposed to fingolimod, a drug that efficiently blocks sphingosine-1-phosphate (S1P)-directed lymphocyte - including NK cell - egress from tissue to blood. During an observation period of 6h peripheral blood depletion of CD56(bright) NK cells was observed 3 h after first dose of fingolimod, with 40-50% depletion after 6 h, while a decrease of the numbers of CD56(dim) NK cells did not reach the level of statistical significance. In vitro, CD56(bright) and CD56(dim) NK cells responded comparably to the BM-homing chemokine CXCL12, while CD56(bright) NK cells migrated more efficiently in gradients of the LT-homing chemokines CCL19 and CCL21. In conjuncture with these in vitro studies, the indirectly observed subset-specific depletion kinetics from blood are compatible with preferential and more rapid redistribution of CD56(bright) NK cells from blood to peripheral tissue such as LT and possibly also the inflamed central nervous system. These data shed light on an unexplored level at which access of NK cells to LT, and thus, for example antigen-presenting cells, is regulated. © 2015 The Foundation for the Scandinavian Journal of Immunology.

  13. Dynamics and kinetics of Si/Si(1-x)Ge(x) MBE studies by reflectance spectroscopy

    International Nuclear Information System (INIS)

    Lees, A.

    1998-01-01

    Reflectance anisotropy (RA) and reflection high energy electron diffraction (RHEED) have been used simultaneously to study the growth of Si and Si (1-x) Ge x on Si(001) surfaces by gas source molecular beam epitaxy (GSMBE). Dynamic oscillatory changes in the RA response have been investigated and attributed to periodic changes in the domain coverage of the (2x1) and (1x2) reconstructions. These measurements demonstrate that RA gives a more direct measure of domain coverage variations on the Si(001) surface than RHEED, which may include ordering and multiple scattering effects. RA was used to investigate domain coverage variations as a function of substrate temperature and as a result of growth interruption. The temperature dependence of the change in the RA response is interpreted as a growth mode change at higher temperatures and a change in the electronic configuration of the surface dimers due to chemisorbed hydrogen at low substrate temperatures. The change in the RA response during deposition of Si (1-x) Ge x are also investigated as a function of Ge concentration. Reflectance anisotropy spectroscopy (RAS) has been used to monitor changes in the surface hydrogen coverage during growth and the difference between the RA spectra obtained before and after hydrogen exposure has been used to quantify monohydride coverage as a function of substrate temperature, flux and hydrogen source. The kinetics of Si growth have also been investigated and isothermal hydrogen desorption measurements have been made. Interruption of the disilane supply leads to a change in the RA response which can be attributed to the associative desorption of molecular hydrogen. Subsequent to the interruption of growth, the hydrogen coverage is found to vary linearly with time, changing to an exponential like dependence as the hydrogen coverage approaches zero. This zeroth order coverage dependence of hydrogen desorption is attributed to a desorption pathway incorporating a saturated and

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. Optimal clustering of kinetic patterns on malignant breast lesions: comparison between K-means clustering and three-time-points method in dynamic contrast-enhanced MRI.

    Science.gov (United States)

    Lee, S H; Kim, J H; Kim, K G; Park, J S; Park, S J; Moon, W K

    2007-01-01

    Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is useful for breast cancer diagnosis and treatment planning. Nevertheless, due to the multi-temporal nature of DCE-MRI data, the assessment of early stage breast cancer is a challenging task. In this study, we applied an unsupervised clustering approach and cluster validation technique to the analysis of malignant intral-tumoral kinetic curves in DCE-MRI. K-means cluster analysis was performed from real world malignant tumor cases and the data were transformed into an optimal number of reference patterns representative each cluster. The optimal number of clusters was estimated by a cluster validation index, which was calculated with the ratio of inter-class scatter to intra-class scatter. This technique then classifies tumor specific patterns from a given MRI data by measuring the vector distances from the reference pattern set, and compared the result from the k-means clustering with that from three-time-points (3TP) method, which represents a clinical standard protocol for analysis of tumor kinetics. The evaluation of twenty five cases indicates that optimal k-means clustering reflects partitioning intra-tumoral kinetic patterns better than the 3TP technique. This method will greatly enhance the capability of radiologists to identify and characterize internal kinetic heterogeneity and vascular change of a tumor in breast DCE-MRI.

  20. 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...

  1. Trickling filter for urea and bio-waste processing - dynamic modelling of nitrogen cycle

    Science.gov (United States)

    Zhukov, Anton; Hauslage, Jens; Tertilt, Gerin; Bornemann, Gerhild

    Mankind’s exploration of the solar system requires reliable Life Support Systems (LSS) enabling long duration manned space missions. In the absence of frequent resupply missions, closure of the LSS will play a very important role and its maximisation will to a large extent drive the selection of appropriate LSS architectures. One of the significant issues on the way to full closure is to effectively utilise biological wastes such as urine, inedible biomass etc. A very promising concept of biological waste reprocessing is the use of trickling filters which are currently being developed and investigated by DLR, Cologne, Germany. The concept is called Combined Regenerative Organic-Food Production (C.R.O.P.) and is based on the microbiological treatment of biological wastes and reprocessing them into aqueous fertilizer which can directly be used in a greenhouse for food production. Numerous experiments have been and are being conducted by DLR in order to fully understand and characterize the process. The human space exploration group of the Technical University of Munich (TUM) in cooperation with DLR has started to establish a dynamic model of the trickling filter system to be able to assess its performance on the LSS level. In the first development stage the model covers the nitrogen cycle enabling to simulate urine processing. This paper describes briefly the C.R.O.P. concept and the status of the trickling filter model development. The model is based on enzyme-catalyzed reaction kinetics for the fundamental microbiological reaction chain and is created in MATLAB. Verification and correlation of the developed model with experiment results has been performed. Several predictive studies for batch sequencing behavior have been performed, demonstrating a good capability of C.R.O.P. concept to be used in closed LSS. Achieved results are critically discussed and way forward is presented.

  2. 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

    conditions the Tofts (TM), extended Tofts (ETM), compartmental tissue uptake model (C-TU) and 2-compartment exchange model (2CXM) were the optimal tracer kinetic models (TKMs) for the analysis of DCE-MRI in patients with cervical cancer. Material and methods. Ten patients with locally advanced cervical...

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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...

  8. Enzyme-catalyzed synthesis of polyamides and polypeptides

    Science.gov (United States)

    Polyamides and polypeptides are important polymers in biological systems and industrial processes. Usually polyamides are produced via chemical synthesis, whereas polypeptides and proteins are isolated from living systems or produced from Merrifield synthesis. An area of active research is to use ...

  9. 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

  10. 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

  11. Kinetic Typography

    DEFF Research Database (Denmark)

    van Leeuwen, Theo; Djonov, Emilia

    2014-01-01

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

  12. 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.

  13. 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....

  14. Ordering kinetics of lamella-forming block copolymers under the guidance of various external fields studied by dynamic self-consistent field theory.

    Science.gov (United States)

    Wan, Xiaomin; Gao, Tong; Zhang, Liangshun; Lin, Jiaping

    2017-03-01

    Self-consistent field theory with a dynamic extension is exploited to investigate the kinetics of the lamellar formation of symmetric block copolymers under the direction of external fields. In particular, three types of directed self-assembly methods - a permanent field for chemo-epitaxy, a dynamic field for zone annealing and an integrated permanent/dynamic field - are examined. For the chemo-epitaxy involving sparsely prepatterned substrates or zone annealing, the block copolymers generally develop into polycrystalline nanostructures with multiple orientations due to the lack of strong driving forces for eliminating the long-lived imperfections in a limited time. As the integrated chemo-epitaxy and zone annealing method is applied to the block copolymer systems, single-crystalline nanostructures with precisely registered orientations are achieved in a short annealing time owing to the mutual acceleration of defect annihilations, which cannot be produced by the conventional techniques alone. Furthermore, the integrated method allows the rapid fabrication of well-ordered nanostructures on the extremely sparse prepatterned substrates. Our theoretical work may serve to rationalize the faster modern nanolithographic fabrication of smaller microelectronic components using lower-spatial-frequency templates.

  15. Intracellular kinetics of ATX-S10·Na(II) and its correlation with photochemical reaction dynamics during a pulsed photosensitization process: effect of pulse repetition rate

    Science.gov (United States)

    Kawauchi, Satoko; Sato, Shunichi; Morimoto, Yuji; Kikuchi, Makoto

    2006-01-01

    Although photodynamic therapy with pulsed light excitation has interesting characteristics, its photosensitization mechanism has not been fully elucidated. In this study, we showed that the intracellular kinetics of ATX-S10.Na(II), a lysosomal sensitizer, was closely related to photochemical reaction dynamics during photodynamic treatment of A549 cells with nanosecond pulsed light. Fluorescence microscopy revealed that at high frequencies of 10 and 30 Hz the sensitizer initially localized mainly in lysosomes but that it started to be redistributed to the cytosol in certain ranges of radiant exposures. These ranges were found to coincide with a regime of fluorescence degradation with limited oxygen consumption. On the other hand, at 5 Hz, there was no such a discontinuous behavior in the sensitizer redistribution characteristics throughout the period of irradiation; this was consistent with the fact that no reaction switching was observed. Two possible reasons for the appearance of the regime with limited oxygen consumption are discussed: participation of an oxygen-independent reaction and change in the microenvironment for the sensitizer caused by lysosomal photodamage. The pulse frequency-dependent intracellular kinetics of the sensitizer also explains our previous results showing higher cytotoxicity at 5 Hz than at 10 and 30 Hz.

  16. 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.; Bruner, N.; Clark, R. E.; Genoni, T. C.; Thoma, C.; Zimmerman, W. R.; Rambo, P. K.; Atherton, B. W.

    2011-10-01

    Streamer and leader formation in high pressure devices is a dynamic process involving a hierarchy of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. We present a new 3D fully EM 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 [D. R. Welch, et al., J. Comp. Phys. 227, 143 (2007)] that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge. This work is funded by the US Department of Energy through Sandia National Laboratories.

  17. Direct observation of preferential processing of clustered abasic DNA damages with APE1 in TATA box and CpG island by reaction kinetics and fluorescence dynamics.

    Science.gov (United States)

    Singh, Vandana; Kumari, Bhavini; Maity, Banibrata; Seth, Debabrata; Das, Prolay

    2014-01-01

    Sequences like the core element of TATA box and CpG island are frequently encountered in the genome and related to transcription. The fate of repair of clustered abasic sites in such sequences of genomic importance is largely unknown. This prompted us to investigate the sequence dependence of cleavage efficiency of APE1 enzyme at abasic sites within the core sequences of TATA box and CpG island using fluorescence dynamics and reaction kinetics. Simultaneous molecular dynamics study through steady state and time resolved fluorescence spectroscopy using unique ethidium bromide dye release assay confirmed an elevated amount of abasic site cleavage of the TATA box sequence as compared to the core CpG island. Reaction kinetics showed that catalytic efficiency of APE1 for abasic site cleavage of core CpG island sequence was ∼4 times lower as compared to that of the TATA box. Higher value of Km was obtained from the core CpG island sequence than the TATA box sequence. This suggests a greater binding effect of APE1 enzyme on TATA sequence that signifies a prominent role of the sequence context of the DNA substrate. Evidently, a faster response from APE1 was obtained for clustered abasic damage repair of TATA box core sequences than CpG island consensus sequences. The neighboring bases of the abasic sites in the complementary DNA strand were found to have significant contribution in addition to the flanking bases in modulating APE1 activity. The repair refractivity of the bistranded clustered abasic sites arise from the slow processing of the second abasic site, consequently resulting in decreased overall production of potentially lethal double strand breaks. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. 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.

  19. 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

  20. 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

  1. 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

    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...

  2. Cluster dynamics modeling of He accumulation kinetics in W exposed to low-energy He plasma exposure

    Science.gov (United States)

    Blondel, Sophie; Maroudas, Dimitrios; Hu, Lin; Hammond, Karl; Wirth, Brian; PSI SciDAC Collaboration

    2015-11-01

    We report a hierarchical multi-scale modeling study of implanted helium segregation to surfaces of tungsten, considered as a plasma facing component in nuclear fusion reactors. We employ a hierarchy of atomic-scale simulations based on a reliable interatomic interaction potential, including molecular-statics and molecular dynamics simulations to understand the origin of helium surface segregation. The near-surface cluster dynamics found in these simulations have significant effects on the surface morphology, near-surface defect structures, and the amount of helium retained in the material upon plasma exposure. We integrate the findings of such atomic-scale simulations into a properly parameterized and validated spatially-dependent, continuum-scale reaction-diffusion cluster dynamics model, capable of predicting implanted helium evolution, surface segregation, and its near-surface effects in tungsten. This cluster-dynamics model sets the stage for development of fully atomistically informed coarse-grained models for computationally efficient simulation predictions, toward optimal design of plasma facing components.

  3. Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions.

    Science.gov (United States)

    Bryan, Louise C; Weilandt, Daniel R; Bachmann, Andreas L; Kilic, Sinan; Lechner, Carolin C; Odermatt, Pascal D; Fantner, Georg E; Georgeon, Sandrine; Hantschel, Oliver; Hatzimanikatis, Vassily; Fierz, Beat

    2017-10-13

    Chromatin recruitment of effector proteins involved in gene regulation depends on multivalent interaction with histone post-translational modifications (PTMs) and structural features of the chromatin fiber. Due to the complex interactions involved, it is currently not understood how effectors dynamically sample the chromatin landscape. Here, we dissect the dynamic chromatin interactions of a family of multivalent effectors, heterochromatin protein 1 (HP1) proteins, using single-molecule fluorescence imaging and computational modeling. We show that the three human HP1 isoforms are recruited and retained on chromatin by a dynamic exchange between histone PTM and DNA bound states. These interactions depend on local chromatin structure, the HP1 isoforms as well as on PTMs on HP1 itself. Of the HP1 isoforms, HP1α exhibits the longest residence times and fastest binding rates due to DNA interactions in addition to PTM binding. HP1α phosphorylation further increases chromatin retention through strengthening of multivalency while reducing DNA binding. As DNA binding in combination with specific PTM recognition is found in many chromatin effectors, we propose a general dynamic capture mechanism for effector recruitment. Multiple weak protein and DNA interactions result in a multivalent interaction network that targets effectors to a specific chromatin modification state, where their activity is required. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. 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.

  5. New enzymatic method of chiral amino acid synthesis by dynamic kinetic resolution of amino acid amides: use of stereoselective amino acid amidases in the presence of alpha-amino-epsilon-caprolactam racemase.

    Science.gov (United States)

    Yamaguchi, Shigenori; Komeda, Hidenobu; Asano, Yasuhisa

    2007-08-01

    D- and L-amino acids were produced from L- and D-amino acid amides by D-aminopeptidase from Ochrobactrum anthropi C1-38 and L-amino acid amidase from Pseudomonas azotoformans IAM 1603, respectively, in the presence of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae as the catalyst by dynamic kinetic resolution of amino acid amides.

  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. Formation of ultrafine and dense {alpha}-Al{sub 2}O{sub 3} nanoparticles via kinetic phase change in a dynamic process

    Energy Technology Data Exchange (ETDEWEB)

    Liu, I-Lung; Shen, Pouyan [National Sun Yat-sen University, Department of Materials and Optoelectronic Science, Institute of Materials Science and Engineering (China); Chen, Shuei-Yuan, E-mail: steven@isu.edu.t [I-Shou University, Department of Mechanical and Automation Engineering (China)

    2010-10-15

    Ultrafine (5 nm) Al{sub 2}O{sub 3} nanoparticles having a predominant {alpha}-type structure and with an internal compressive stress up to ca. 15 GPa were synthesized by pulsed laser ablation on Al target under a very high power density (1.8 x 10{sup 12} W/cm{sup 2}) with oxygen flow in vacuum. The ultrafine {alpha}-Al{sub 2}O{sub 3} was alternatively formed from the minor {gamma}-Al{sub 2}O{sub 3} nanocondensates upon electron irradiation. In such a case, the polymorphs follow a special crystallographic relationship with a mixed mismatch strain yet nonparallel close-packed planes indicating a reconstructive-type transformation. The formation of metastable {alpha}-Al{sub 2}O{sub 3} in the dynamic processes can be rationalized by the kinetic phase change from the amorphous lamellar and/or {gamma}-Al{sub 2}O{sub 3} depending on their free energy versus cell volume curves. The dense and ultrafine-sized Al{sub 2}O{sub 3} polymorphs with a rather low minimum band gap of 3.7 eV shed light on their natural occurrence in dynamic settings and abrasive as well as catalytic/optoelectronic applications.

  8. 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

  9. 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

  10. Kinetic sculpture

    OpenAIRE

    Joneta Witabora; Jonata Witabora

    2014-01-01

    Kinetic Sculpture was born from a long process of searching new approach in sculpture. The artists tried to escape from 'static' paradigm and tried to implement movement into their works: a sculpture that is mobile. Movement is always a fascinating phenomenon to eyes. Kinetic sculpture strength lies in its unique character in combining science and art. Kinetic Sculptures are really interesting pieces of art. It succeeds to fascinate human everytime. 

  11. 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.)

  12. Development of a predictive model for the growth kinetics of aerobic microbial population on pomegranate marinated chicken breast fillets under isothermal and dynamic temperature conditions.

    Science.gov (United States)

    Lytou, Anastasia; Panagou, Efstathios Z; Nychas, George-John E

    2016-05-01

    The aim of this study was the development of a model to describe the growth kinetics of aerobic microbial population of chicken breast fillets marinated in pomegranate juice under isothermal and dynamic temperature conditions. Moreover, the effect of pomegranate juice on the extension of the shelf life of the product was investigated. Samples (10 g) of chicken breast fillets were immersed in marinades containing pomegranate juice for 3 h at 4 °C following storage under aerobic conditions at 4, 10, and 15 °C for 10 days. Total Viable Counts (TVC), Pseudomonas spp and lactic acid bacteria (LAB) were enumerated, in parallel with sensory assessment (odor and overall appearance) of marinated and non-marinated samples. The Baranyi model was fitted to the growth data of TVC to calculate the maximum specific growth rate (μmax) that was further modeled as a function of temperature using a square root-type model. The validation of the model was conducted under dynamic temperature conditions based on two fluctuating temperature scenarios with periodic changes from 6 to 13 °C. The shelf life was determined both mathematically and with sensory assessment and its temperature dependence was modeled by an Arrhenius type equation. Results showed that the μmax of TVC of marinated samples was significantly lower compared to control samples regardless temperature, while under dynamic temperature conditions the model satisfactorily predicted the growth of TVC in both control and marinated samples. The shelf-life of marinated samples was significantly extended compared to the control (5 days extension at 4 °C). The calculated activation energies (Ea), 82 and 52 kJ/mol for control and marinated samples, respectively, indicated higher temperature dependence of the shelf life of control samples compared to marinated ones. The present results indicated that pomegranate juice could be used as an alternative ingredient in marinades to prolong the shelf life of chicken. Copyright © 2015

  13. Kinetic suppression of microtubule dynamic instability by griseofulvin: Implications for its possible use in the treatment of cancer

    Science.gov (United States)

    Panda, Dulal; Rathinasamy, K.; Santra, Manas K.; Wilson, Leslie

    2005-01-01

    The antifungal drug griseofulvin inhibits mitosis strongly in fungal cells and weakly in mammalian cells by affecting mitotic spindle microtubule (MT) function. Griseofulvin also blocks cell-cycle progression at G2/M and induces apoptosis in human tumor cell lines. Despite extensive study, the mechanism by which the drug inhibits mitosis in human cells remains unclear. Here, we analyzed the ability of griseofulvin to inhibit cell proliferation and mitosis and to affect MT polymerization and organization in HeLa cells together with its ability to affect MT polymerization and dynamic instability in vitro. Griseofulvin inhibited cell-cycle progression at prometaphase/anaphase of mitosis in parallel with its ability to inhibit cell proliferation. At its mitotic IC50 of 20 μM, spindles in blocked cells displayed nearly normal quantities of MTs and MT organization similar to spindles blocked by more powerful MT-targeted drugs. Similar to previously published data, we found that very high concentrations of griseofulvin (>100 μM) were required to inhibit MT polymerization in vitro. However, much lower drug concentrations (1–20 μM) strongly suppressed the dynamic instability behavior of the MTs. We suggest that the primary mechanism by which griseofulvin inhibits mitosis in human cells is by suppressing spindle MT dynamics in a manner qualitatively similar to that of much more powerful antimitotic drugs, including the vinca alkaloids and the taxanes. In view of griseofulvin's lack of significant toxicity in humans, we further suggest that it could be useful as an adjuvant in combination with more powerful drugs for the treatment of cancer. PMID:15985553

  14. Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis MR-1.

    Directory of Open Access Journals (Sweden)

    Xueyang Feng

    2012-02-01

    Full Text Available Shewanella oneidensis MR-1 sequentially utilizes lactate and its waste products (pyruvate and acetate during batch culture. To decipher MR-1 metabolism, we integrated genome-scale flux balance analysis (FBA into a multiple-substrate Monod model to perform the dynamic flux balance analysis (dFBA. The dFBA employed a static optimization approach (SOA by dividing the batch time into small intervals (i.e., ∼400 mini-FBAs, then the Monod model provided time-dependent inflow/outflow fluxes to constrain the mini-FBAs to profile the pseudo-steady-state fluxes in each time interval. The mini-FBAs used a dual-objective function (a weighted combination of "maximizing growth rate" and "minimizing overall flux" to capture trade-offs between optimal growth and minimal enzyme usage. By fitting the experimental data, a bi-level optimization of dFBA revealed that the optimal weight in the dual-objective function was time-dependent: the objective function was constant in the early growth stage, while the functional weight of minimal enzyme usage increased significantly when lactate became scarce. The dFBA profiled biologically meaningful dynamic MR-1 metabolisms: 1. the oxidative TCA cycle fluxes increased initially and then decreased in the late growth stage; 2. fluxes in the pentose phosphate pathway and gluconeogenesis were stable in the exponential growth period; and 3. the glyoxylate shunt was up-regulated when acetate became the main carbon source for MR-1 growth.

  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. Development and validation of a variance model for dynamic PET: uses in fitting kinetic data and optimizing the injected activity

    Energy Technology Data Exchange (ETDEWEB)

    Walker, M D; Matthews, J C; Asselin, M-C; Julyan, P J [School of Cancer and Enabling Sciences, Wolfson Molecular Imaging Centre, MAHSC, University of Manchester, M20 3LJ (United Kingdom); Watson, C C [Siemens Medical Solutions Molecular Imaging, Knoxville, TN 37932 (United States); Saleem, A; Dickinson, C; Charnley, N; Price, P M; Jones, T, E-mail: matthew.walker@manchester.ac.u [Academic Department of Radiation Oncology, Christie NHS Foundation Trust, University of Manchester, M20 4BX (United Kingdom)

    2010-11-21

    The precision of biological parameter estimates derived from dynamic PET data can be limited by the number of acquired coincidence events (prompts and randoms). These numbers are affected by the injected activity (A{sub 0}). The benefits of optimizing A{sub 0} were assessed using a new model of data variance which is formulated as a function of A{sub 0}. Seven cancer patients underwent dynamic [{sup 15}O]H{sub 2}O PET scans (32 scans) using a Biograph PET-CT scanner (Siemens), with A{sub 0} varied (142-839 MBq). These data were combined with simulations to (1) determine the accuracy of the new variance model, (2) estimate the improvements in parameter estimate precision gained by optimizing A{sub 0}, and (3) examine changes in precision for different size regions of interest (ROIs). The new variance model provided a good estimate of the relative variance in dynamic PET data across a wide range of A{sub 0}s and time frames for FBP reconstruction. Patient data showed that relative changes in estimate precision with A{sub 0} were in reasonable agreement with the changes predicted by the model: Pearson's correlation coefficients were 0.73 and 0.62 for perfusion (F) and the volume of distribution (V{sub T}), respectively. The between-scan variability in the parameter estimates agreed with the estimated precision for small ROIs (<5 mL). An A{sub 0} of 500-700 MBq was near optimal for estimating F and V{sub T} from abdominal [{sup 15}O]H{sub 2}O scans on this scanner. This optimization improved the precision of parameter estimates for small ROIs (<5 mL), with an injection of 600 MBq reducing the standard error on F by a factor of 1.13 as compared to the injection of 250 MBq, but by the more modest factor of 1.03 as compared to A{sub 0} = 400 MBq.

  17. Kinetic approach

    Indian Academy of Sciences (India)

    Collapse of a Bose gas: Kinetic approach ... Thermodynamical, statistical and static properties of condensates; Ultracold and trapped gases; matter waves. ... of a harmonically trapped attractively interacting Bose gas below the condensation point by introducing a kinetic approach within the Hartee-Fock approximation.

  18. 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.)

  19. 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.

  20. Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations.

    Science.gov (United States)

    Díaz, Natalia; Suárez, Dimas; Suárez, Ernesto

    2010-01-01

    Herein, we examine computationally the binding and hydrolysis reaction of the MMP-2 enzyme with two peptide substrates selected by the enzyme from a phage peptide library. Molecular dynamics simulations of the Michaelis complexes (25 ns) allow us to characterize the main enzyme/substrate contacts. Subsequently MM-PBSA calculations using independent trajectories for the complexes and the free substrates provide relative binding energies in good agreement with the experimental K(M) results. Computational alanine scanning analyses of the enzyme/substrate interaction energies confirm the relevance of the P(3), P(2), and P(1)' side chains for ligand binding. Finally, the hydrolysis of both peptides taking place at the MMP-2 active site is explored by means of hybrid quantum mechanical/molecular mechanics calculations. The computed reaction mechanisms result in rate-determining energy barriers being in consonance with the experimental k(cat) values. Overall, the computational protocol seems to capture the subtle differences in binding and catalysis experimentally observed for the two peptide substrates. Some implications of our results for the future design of novel and more specific MMP-2 inhibitors are also discussed. (c) 2009 Wiley-Liss, Inc.

  1. Exploring the multiscale signaling behavior of phototropin1 from Chlamydomonas reinhardtii using a full-residue space kinetic Monte Carlo molecular dynamics technique.

    Science.gov (United States)

    Peter, Emanuel; Dick, Bernhard; Stambolic, Ivan; Baeurle, Stephan A

    2014-09-01

    Devising analysis tools for elucidating the regulatory mechanism of complex enzymes has been a challenging task for many decades. It generally requires the determination of the structural-dynamical information of protein solvent systems far from equilibrium over multiple length and time scales, which is still difficult both theoretically and experimentally. To cope with the problem, we introduce a full-residue space multiscale simulation method based on a combination of the kinetic Monte Carlo and molecular dynamics techniques, in which the rates of the rate-determining processes are evaluated from a biomolecular forcefield on the fly during the simulation run by taking into account the full space of residues. To demonstrate its reliability and efficiency, we explore the light-induced functional behavior of the full-length phototropin1 from Chlamydomonas reinhardtii (Cr-phot1) and its various subdomains. Our results demonstrate that in the dark state the light oxygen voltage-2-Jα (LOV2-Jα) photoswitch inhibits the enzymatic activity of the kinase, whereas the LOV1-Jα photoswitch controls the dimerization with the LOV2 domain. This leads to the repulsion of the LOV1-LOV2 linker out of the interface region between both LOV domains, which results in a positively charged surface suitable for cell-membrane interaction. By contrast, in the light state, we observe that the distance between both LOV domains is increased and the LOV1-LOV2 linker forms a helix-turn-helix (HTH) motif, which enables gene control through nucleotide binding. Finally, we find that the kinase is activated through the disruption of the Jα-helix from the LOV2 domain, which is followed by a stretching of the activation loop (A-loop) and broadening of the catalytic cleft of the kinase. © 2014 Wiley Periodicals, Inc.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Species Diversity, Community Dynamics, and Metabolite Kinetics of the Microbiota Associated with Traditional Ecuadorian Spontaneous Cocoa Bean Fermentations▿

    Science.gov (United States)

    Papalexandratou, Zoi; Falony, Gwen; Romanens, Edwina; Jimenez, Juan Carlos; Amores, Freddy; Daniel, Heide-Marie; De Vuyst, Luc

    2011-01-01

    Traditional fermentations of the local Ecuadorian cocoa type Nacional, with its fine flavor, are carried out in boxes and on platforms for a short time. A multiphasic approach, encompassing culture-dependent and -independent microbiological analyses of fermenting cocoa pulp-bean samples, metabolite target analyses of both cocoa pulp and beans, and sensory analysis of chocolates produced from the respective fermented dry beans, was applied for the investigation of the influence of these fermentation practices on the yeast and bacterial species diversity and community dynamics during cocoa bean fermentation. A wide microbial species diversity was found during the first 3 days of all fermentations carried out. The prevailing ethanol-producing yeast species were Pichia kudriavzevii and Pichia manshurica, followed by Saccharomyces cerevisiae. Leuconostoc pseudomesenteroides (glucose and fructose fermenting), Fructobacillus tropaeoli-like (fructose fermenting), and Lactobacillus fermentum (citrate converting, mannitol producing) represented the main lactic acid bacterial species in the fermentations studied, resulting in intensive heterolactate metabolism of the pulp substrates. Tatumella saanichensis and Tatumella punctata were among the members of the family Enterobacteriaceae present during the initial phase of the cocoa bean fermentations and could be responsible for the production of gluconic acid in some cases. Also, a potential new yeast species was isolated, namely, Candida sorbosivorans-like. Acetic acid bacteria, whose main representative was Acetobacter pasteurianus, generally appeared later during fermentation and oxidized ethanol to acetic acid. However, acetic acid bacteria were not always present during the main course of the platform fermentations. All of the data taken together indicated that short box and platform fermentation methods caused incomplete fermentation, which had a serious impact on the quality of the fermented dry cocoa beans. PMID

  7. Species diversity, community dynamics, and metabolite kinetics of the microbiota associated with traditional ecuadorian spontaneous cocoa bean fermentations.

    Science.gov (United States)

    Papalexandratou, Zoi; Falony, Gwen; Romanens, Edwina; Jimenez, Juan Carlos; Amores, Freddy; Daniel, Heide-Marie; De Vuyst, Luc

    2011-11-01

    Traditional fermentations of the local Ecuadorian cocoa type Nacional, with its fine flavor, are carried out in boxes and on platforms for a short time. A multiphasic approach, encompassing culture-dependent and -independent microbiological analyses of fermenting cocoa pulp-bean samples, metabolite target analyses of both cocoa pulp and beans, and sensory analysis of chocolates produced from the respective fermented dry beans, was applied for the investigation of the influence of these fermentation practices on the yeast and bacterial species diversity and community dynamics during cocoa bean fermentation. A wide microbial species diversity was found during the first 3 days of all fermentations carried out. The prevailing ethanol-producing yeast species were Pichia kudriavzevii and Pichia manshurica, followed by Saccharomyces cerevisiae. Leuconostoc pseudomesenteroides (glucose and fructose fermenting), Fructobacillus tropaeoli-like (fructose fermenting), and Lactobacillus fermentum (citrate converting, mannitol producing) represented the main lactic acid bacterial species in the fermentations studied, resulting in intensive heterolactate metabolism of the pulp substrates. Tatumella saanichensis and Tatumella punctata were among the members of the family Enterobacteriaceae present during the initial phase of the cocoa bean fermentations and could be responsible for the production of gluconic acid in some cases. Also, a potential new yeast species was isolated, namely, Candida sorbosivorans-like. Acetic acid bacteria, whose main representative was Acetobacter pasteurianus, generally appeared later during fermentation and oxidized ethanol to acetic acid. However, acetic acid bacteria were not always present during the main course of the platform fermentations. All of the data taken together indicated that short box and platform fermentation methods caused incomplete fermentation, which had a serious impact on the quality of the fermented dry cocoa beans.

  8. Kinetic and mechanistic characterization of the Sphingomyelinases D from Loxosceles intermedia spider venom.

    Science.gov (United States)

    de Andrade, Sonia A; Murakami, Mario T; Cavalcante, Danielle P; Arni, Raghuvir K; Tambourgi, Denise V

    2006-03-15

    Envenomation by arachnids of the genus Loxosceles leads to local dermonecrosis and serious systemic toxicity mainly induced by sphingomyelinases D (SMase D). These enzymes catalyze the hydrolysis of sphingomyelin resulting in the formation of ceramide-phosphate and choline as well as the cleavage of lysophosphatidyl choline generating the lipid mediator lysophosphatidic acid. We have, previously, cloned and expressed two functional SMase D isoforms, named P1 and P2, from Loxosceles intermedia venom and comparative protein sequence analysis revealed that they are highly homologous to SMase I from Loxosceles laeta which folds to form an (alpha/beta)8 barrel. In order to further characterize these proteins, pH dependence kinetic experiments and chemical modification of the two active SMases D isoforms were performed. We show here that the amino acids involved in catalysis and in the metal ion binding sites are strictly conserved in the SMase D isoforms from L. intermedia. However, the kinetic studies indicate that SMase P1 hydrolyzes sphingomyelin less efficiently than P2, which can be attributed to a substitution at position 203 (Pro-Leu) and local amino acid substitutions in the hydrophobic channel that could probably play a role in the substrate recognition and binding.

  9. 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....

  10. New Enzymatic Method of Chiral Amino Acid Synthesis by Dynamic Kinetic Resolution of Amino Acid Amides: Use of Stereoselective Amino Acid Amidases in the Presence of α-Amino-ɛ-Caprolactam Racemase▿

    Science.gov (United States)

    Yamaguchi, Shigenori; Komeda, Hidenobu; Asano, Yasuhisa

    2007-01-01

    d- and l-amino acids were produced from l- and d-amino acid amides by d-aminopeptidase from Ochrobactrum anthropi C1-38 and l-amino acid amidase from Pseudomonas azotoformans IAM 1603, respectively, in the presence of α-amino-ɛ-caprolactam racemase from Achromobacter obae as the catalyst by dynamic kinetic resolution of amino acid amides. PMID:17586677

  11. Kinetic transport in crystals

    OpenAIRE

    Marklof, Jens

    2009-01-01

    One of the central challenges in kinetic theory is the derivation of macroscopic evolution equations--describing, for example, the dynamics of an electron gas--from the underlying fundamental microscopic laws of classical or quantum mechanics. An iconic mathematical model in this research area is the Lorentz gas, which describes an ensemble of non-interacting point particles in an infinite array of spherical scatterers. In the case of a disordered scatterer configuration, the classical result...

  12. 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

  13. Optimized time-resolved imaging of contrast kinetics (TRICKS) in dynamic contrast-enhanced MRI after peptide receptor radionuclide therapy in small animal tumor models.

    Science.gov (United States)

    Haeck, Joost; Bol, Karin; Bison, Sander; van Tiel, Sandra; Koelewijn, Stuart; de Jong, Marion; Veenland, Jifke; Bernsen, Monique

    2015-01-01

    Anti-tumor efficacy of targeted peptide-receptor radionuclide therapy (PRRT) relies on several factors, including functional tumor vasculature. Little is known about the effect of PRRT on tumor vasculature. With dynamic contrast-enhanced (DCE-) MRI, functional vasculature is imaged and quantified using contrast agents. In small animals DCE-MRI is a challenging application. We optimized a clinical sequence for fast hemodynamic acquisitions, time-resolved imaging of contrast kinetics (TRICKS), to obtain DCE-MRI images at both high spatial and high temporal resolution in mice and rats. Using TRICKS, functional vasculature was measured prior to PRRT and longitudinally to investigate the effect of treatment on tumor vascular characteristics. Nude mice bearing H69 tumor xenografts and rats bearing syngeneic CA20948 tumors were used to study perfusion following PRRT administration with (177) lutetium octreotate. Both semi-quantitative and quantitative parameters were calculated. Treatment efficacy was measured by tumor-size reduction. Optimized TRICKS enabled MRI at 0.032 mm(3) voxel size with a temporal resolution of less than 5 s and large volume coverage, a substantial improvement over routine pre-clinical DCE-MRI studies. Tumor response to therapy was reflected in changes in tumor perfusion/permeability parameters. The H69 tumor model showed pronounced changes in DCE-derived parameters following PRRT. The rat CA20948 tumor model showed more heterogeneity in both treatment outcome and perfusion parameters. TRICKS enabled the acquisition of DCE-MRI at both high temporal resolution (Tres ) and spatial resolutions relevant for small animal tumor models. With the high Tres enabled by TRICKS, accurate pharmacokinetic data modeling was feasible. DCE-MRI parameters revealed changes over time and showed a clear relationship between tumor size and Ktrans . Copyright © 2015 John Wiley & Sons, Ltd.

  14. Field-theoretic calculation of kinetic helicity flux

    Indian Academy of Sciences (India)

    In the inertial range the kinetic helicity flux is found to be constant and forward. The universal constant KH appearing in the spectrum of kinetic helicity was found to be. 2.47. Keywords. Kinetic helicity; helical turbulence. PACS Nos 47.27.Ak; 47.27.Gs. Kinetic helicity plays an important role in the dynamics of turbulence.

  15. Hydrogen exchange dynamics of the P22 virion determined by time-resolved Raman spectroscopy. Effects of chromosome packaging on the kinetics of nucleotide exchanges.

    Science.gov (United States)

    Reilly, K E; Thomas, G J

    1994-08-05

    We describe the application of laser Raman spectroscopy to probe hydrogen isotope exchange dynamics of nucleic acid and protein constituents in a double-stranded DNA virus, the icosahedral bacteriophage P22. The Raman dynamic method employs a dialysis flow cell to control D2O efflux into an H2O solution of the virus sample while the rates of deuterium exchange of protons in the viral nucleic acid and protein molecules are measured spectrophotometrically in real time. The method provides structural and kinetic information about three different and distinct classes of exchangeable protons of the native virion: (1) labile imino (NH) and amino (NH2) protons of the bases which participate in Watson-Crick hydrogen bonding in the packaged genome; (2) pseudolabile purinic (8CH) protons that line the major groove of packaged P22 DNA; and (3) main-chain amide (NH) protons of viral subunits comprising the shell that encapsidates the DNA. The results obtained on P22 demonstrate that interchange of aqueous solvent with the virion interior is rapid and complete. We find that while labile protons of packaged DNA exchange rapidly, most amide protons in capsid subunits are resistant to solvent-catalyzed exchange. Further, stereospecific retardation of exchange is observed for major-groove protons of the packaged P22 genome. The quantitative measurements can be summarized and interpreted as follows. (1) Imino and amino protons of all bases in packaged P22 DNA exchange more rapidly (approximately 2-fold faster) than the corresponding protons in unpackaged P22 DNA. Remarkably, packaging actually accelerates labile imino and amino hydrogen exchanges of the viral DNA, an effect which can be attributed to selective stabilization in the packaged chromosome of a base-pair open state (breathing model). (2) Conversely, purine 8CH exchange rates in packaged P22 DNA are significantly retarded in comparison to those of unpackaged P22 DNA. The observed 8CH exchange retardation effects are

  16. 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.

  17. 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.

  18. Kinetic bridges.

    Science.gov (United States)

    1980-01-01

    This report on kinetic bridges is essentially a state-of-the-art study on two types of bridges whose location or physical characteristics are designed to be time dependent. The first type, called a "relocatable bridge", is essentially for use as a te...

  19. Application of Photoacoustic Effect to Chemical Kinetics in Solution.

    Science.gov (United States)

    Cheng, Huy-Zu.

    The application of the pulsed photoacoustic technique (PA) to the study of chemical kinetics in very dilute solutions is demonstrated with three different reactions: A bidental ligand substitution of 1,2-bi(diphenylphosphino) ethane on the five-coordinate cobalt dithiolene complex, a nucleophilic addition of tributyl phosphite to (p-(dimethylamino)triphenyl)methyl cation, and an enzyme catalyzed reduction of nicotinamide adenine dinucleotide by glucose-6-phosphate. Photoacoustic detection is shown to be 100 times more sensitive than spectrophotometric detection. As a consequence, it allows one to use lower reactant concentrations so that the time scale for the corresponding fast reactions can be lengthened. The pulsed PA technique also provides an alternative method for the direct determination of reverse rate constants and equilibrium constants of reactions. Moreover, Michaelis constants of biochemical reactions, especially for enzymes whose K_{rm m} values is below 1.0 muM, can be measured more accurately using photoacoustic detection than using spectrophotometric detection. Additionally, the pulsed PA method can be very valuable for the study of reactions that are restricted by the low solubility, availability, or high cost of reactants. The sensitivity of the PA method is found to be limited by the background signal resulting from solvents. Photoacoustic signals generated in strongly absorbing media are also studied and results are in agreement with the theory developed by G. J. Diebold. From the time profile of the acoustic signal, the absorption coefficient of strongly absorbing medium can be determined provided the sound speed is known. Since the pulse shape of the acoustic transient depends upon the relative density and the acoustic velocity of the transparent and the strongly absorbing media, the physical properties of the transparent medium can also be determined with the use of the PA technique.

  20. Modelling non-equilibrium secondary organic aerosol formation and evaporation with the aerosol dynamics, gas- and particle-phase chemistry kinetic multilayer model ADCHAM

    Science.gov (United States)

    Roldin, P.; Eriksson, A. C.; Nordin, E. Z.; Hermansson, E.; Mogensen, D.; Rusanen, A.; Boy, M.; Swietlicki, E.; Svenningsson, B.; Zelenyuk, A.; Pagels, J.

    2014-08-01

    We have developed the novel Aerosol Dynamics, gas- and particle-phase chemistry model for laboratory CHAMber studies (ADCHAM). The model combines the detailed gas-phase Master Chemical Mechanism version 3.2 (MCMv3.2), an aerosol dynamics and particle-phase chemistry module (which considers acid-catalysed oligomerization, heterogeneous oxidation reactions in the particle phase and non-ideal interactions between organic compounds, water and inorganic ions) and a kinetic multilayer module for diffusion-limited transport of compounds between the gas phase, particle surface and particle bulk phase. In this article we describe and use ADCHAM to study (1) the evaporation of liquid dioctyl phthalate (DOP) particles, (2) the slow and almost particle-size-independent evaporation of α-pinene ozonolysis secondary organic aerosol (SOA) particles, (3) the mass-transfer-limited uptake of ammonia (NH3) and formation of organic salts between ammonium (NH4+) and carboxylic acids (RCOOH), and (4) the influence of chamber wall effects on the observed SOA formation in smog chambers. ADCHAM is able to capture the observed α-pinene SOA mass increase in the presence of NH3(g). Organic salts of ammonium and carboxylic acids predominantly form during the early stage of SOA formation. In the smog chamber experiments, these salts contribute substantially to the initial growth of the homogeneously nucleated particles. The model simulations of evaporating α-pinene SOA particles support the recent experimental findings that these particles have a semi-solid tar-like amorphous-phase state. ADCHAM is able to reproduce the main features of the observed slow evaporation rates if the concentration of low-volatility and viscous oligomerized SOA material at the particle surface increases upon evaporation. The evaporation rate is mainly governed by the reversible decomposition of oligomers back to monomers. Finally, we demonstrate that the mass-transfer-limited uptake of condensable organic compounds

  1. Two different ways that hydrogen ions are involved in the thermodynamics and rapid-equilibrium kinetics of the enzymatic catalysis of S=P and S+H2O=P.

    Science.gov (United States)

    Alberty, Robert A

    2007-07-01

    Hydrogen ions are involved in two different ways in the thermodynamics and rapid-equilibrium kinetics of enzyme-catalyzed reactions. The two ways are through pKs and through the production or consumption of hydrogen ions in the mechanism. These ways are examined for the catalyzed reactions S=P and S+H2O=P. Since the apparent equilibrium constant K' can be calculated from the kinetic parameters by use of the Haldane equation, the treatment of the effects of pH must be consistent in thermodynamics and kinetics. This leads to a new kind of Haldane equation that involves 10(pH) or 10(-pH) in addition to the kinetic parameters when hydrogen ions are produced or consumed. These concepts are applicable to more complicated reactions and rate equations. Derivations of equations for calculating these two types of pH effects are discussed in thermodynamics and rapid-equilibrium kinetics. A computer program is used to make four plots of apparent equilibrium constants and changes in the binding of hydrogen ions in the catalyzed reaction.

  2. Applicability of two-step models in estimating nitrification kinetics from batch respirograms under different relative dynamics of ammonia and nitrite oxidation.

    Science.gov (United States)

    Chandran, K; Smets, B F

    2000-10-05

    A mechanistically based nitrification model was formulated to facilitate determination of both NH(4)(+)-N to NO(2)(-)-N and NO(2)(-)-N to NO(3)(-)-N oxidation kinetics from a single NH(4)(+)-N to NO(3)(-)-N batch-oxidation profile by explicitly considering the kinetics of each oxidation step. The developed model incorporated a novel convention for expressing the concentrations of nitrogen species in terms of their nitrogenous oxygen demand (NOD). Stoichiometric coefficients relating nitrogen removal, oxygen uptake, and biomass synthesis were derived from an electron-balanced equation.%A parameter identifiability analysis of the developed two-step model revealed a decrease in correlation and an increase in the precision of the kinetic parameter estimates when NO(2)(-)-N oxidation kinetics became increasingly rate-limiting. These findings demonstrate that two-step models describe nitrification kinetics adequately only when NH(4)(+)-N to NO(3)(-)-N oxidation profiles contain sufficient information pertaining to both nitrification steps. Thus, the rate-determining step in overall nitrification must be identified before applying conventionally used models to describe batch nitrification respirograms.

  3. 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...

  4. 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)

  5. Kinetic energy driven pairing in cuprate superconductors

    NARCIS (Netherlands)

    Maier, TA; Jarrell, M; Macridin, A; Slezak, C

    2004-01-01

    Pairing occurs in conventional superconductors through a reduction of the electronic potential energy accompanied by an increase in kinetic energy. In the underdoped cuprates, optical experiments show that pairing is driven by a reduction of the electronic kinetic energy. Using the dynamical cluster

  6. 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

  7. 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

  8. Kinetic buffers.

    Science.gov (United States)

    Alibrandi, Giuseppe; Fabbrizzi, Luigi; Licchelli, Maurizio; Puglisi, Antonio

    2015-01-12

    This paper proposes a new type of molecular device that is able to act as an inverse proton sponge to slowly decrease the pH inside a reaction vessel. This makes the automatic monitoring of the concentration of pH-sensitive systems possible. The device is a composite formed of an alkyl chloride, which kinetically produces acidity, and a buffer that thermodynamically modulates the variation in pH value. Profiles of pH versus time (pH-t plots) have been generated under various experimental conditions by computer simulation, and the device has been tested by carrying out automatic spectrophotometric titrations, without using an autoburette. To underline the wide variety of possible applications, this new system has been used to realize and monitor HCl uptake by a di-copper(II) bistren complex in a single run, in a completely automatic experiment. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. 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.

  10. 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.

  11. 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)

  12. A mathematical model on germinal center kinetics andtermination

    DEFF Research Database (Denmark)

    Kesmir, Can; De Boer, R.J.

    1999-01-01

    We devise a mathematical model to study germinal center (GC) kinetics. Earlier models for GC kinetics areextended by explicitly modeling 1) the cell division history of centroblasts, 2) the Ag uptake by centrocytes,and 3) T cell dynamics. Allowing for T cell kinetics and T-B cell interactions, we...

  13. Pathway thermodynamics highlights kinetic obstacles in central metabolism.

    Science.gov (United States)

    Noor, Elad; Bar-Even, Arren; Flamholz, Avi; Reznik, Ed; Liebermeister, Wolfram; Milo, Ron

    2014-02-01

    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 the

  14. Pathway thermodynamics highlights kinetic obstacles in central metabolism.

    Directory of Open Access Journals (Sweden)

    Elad Noor

    2014-02-01

    Full Text Available 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

  15. 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

  16. 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.

  17. 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.

  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 Dahlgaard; Rasmussen, R.; Freiberg, J.

    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...... 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. The transformation of triclosan by laccase: Effect of humic acid on the reaction kinetics, products and pathway.

    Science.gov (United States)

    Dou, Rong-Ni; Wang, Jing-Hao; Chen, Yuan-Cai; Hu, Yong-You

    2018-03-01

    This study systematically explored the effect of humic acid (HA) (as model of natural organic matter) on the kinetics, products and transformation pathway of triclosan (TCS) by laccase-catalyzed oxidation. It was found that TCS could be effectively transformed by laccase-catalysis, with the apparent second-order rate constant being 0.056 U -1 mL min -1 . HA inhibited the removal rate of TCS. HA-induced inhibition was negatively correlated with HA concentration in the range of 0-10 mg L -1 and pH-dependent from 3.5 to 9.5. FT-IR and 13 C NMR spectra showed a decrease of aromatic hydroxyl (phenolic) groups and an increase of aromatic ether groups, indicating the cross-linking of HA via C-O-C and C-N-C bonds during enzyme-catalyzed oxidation. Ten principle oxidative products, including two quinone-like products (2-chlorohydroquinone, 2-chloro-5-(2,4-dichlodichlorophenoxy)-(1,4)benzoquinone), one chlorinated phenol (2,4-dichlorophenol (2,4-DCP)), three dimers, two trimmers and two tetramers, were detected by gas chromatograghy/mass spectrometry (GC-MS) and high performance liquid chromatography/quadrupole time-of-flight/mass spectrometry (HPLC/Q-TOF/MS). The presence of HA induced significantly lesser generation of self-polymers and enhanced cross-coupling between HA and self-polymers via C-O-C, C-N-C and C-C coupling pathways. A plausible transformation pathway was proposed as follows: TCS was initially oxidized to form reactive phenoxyl radicals, which self-coupled to each other subsequently by C-C and C-O pathway, yielding self-polymers. In addition, the scission of ether bond was also observed. The presence of HA can promote scission of ether bond and further oxidation of phenoxyl radicals, forming hydroxylated or quinone-like TCS. This study shed light on the behavior of TCS in natural environment and engineered processes, as well provided a perspective for the water/wastewater treatment using enzyme-catalyzed oxidation techniques. Copyright © 2017 Elsevier Ltd

  20. 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.)

  1. 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.)

  2. Dynamic modeling in ovarian cancer: an original approach linking early changes in modeled longitudinal CA-125 kinetics and survival to help decisions in early drug development.

    Science.gov (United States)

    Wilbaux, Mélanie; Hénin, Emilie; Oza, Amit; Colomban, Olivier; Pujade-Lauraine, Eric; Freyer, Gilles; Tod, Michel; You, Benoit

    2014-06-01

    Early prediction of the expected benefit of treatment in recurrent ovarian cancer (ROC) patients may help in drug development decisions. The actual value of 50% CA-125 decrease is being reconsidered. The main objective of the present study was to quantify the links between longitudinal assessments of CA-125 kinetics and progression-free survival (PFS) in treated recurrent ovarian cancer (ROC) patients. The CALYPSO randomized phase III trial database comparing two platinum-based regimens in ROC patients was randomly split into a "learning dataset" and a "validation dataset". A parametric survival model was developed to associate longitudinal modeled CA-125 changes (ΔCA125), predictive factors, and PFS. The predictive performance of the model was evaluated with simulations. The PFS of 534 ROC patients were properly characterized by a parametric mathematical model. The modeled ΔCA125 from baseline to week 6 was a better predictor of PFS than the modeled fractional change in tumor size. Simulations confirmed the model's predictive performance. We present the first parametric survival model quantifying the relationship between PFS and longitudinal CA-125 kinetics in treated ROC patients. The model enabled calculation of the increase in ΔCA125 required to observe a predetermined benefit in PFS to compare therapeutic strategies in populations. Therefore, ΔCA125 may be a predictive marker of the expected gain in PFS and an early predictive tool in drug development decisions. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. Is the Gas-phase OH+H2CO Reaction a Source of HCO in Interstellar Cold Dark Clouds? A Kinetic, Dynamic, and Modeling Study

    Science.gov (United States)

    Ocaña, A. J.; Jiménez, E.; Ballesteros, B.; Canosa, A.; Antiñolo, M.; Albaladejo, J.; Agúndez, M.; Cernicharo, J.; Zanchet, A.; del Mazo, P.; Roncero, O.; Aguado, A.

    2017-11-01

    The chemical kinetics of neutral-neutral gas-phase reactions at ultralow temperatures is a fascinating research subject with important implications on the chemistry of complex organic molecules in the interstellar medium (T ˜ 10-100 K). Scarce kinetic information is currently available for these kinds of reactions at T values greatly increase from 2.1 × 10-11 cm3 s-1 at 107 K to 1.2 × 10-10 cm3 s-1 at 22 K. This is also confirmed by quasi-classical trajectories (QCT) at collision energies down to 0.1 meV performed using a new full dimension and ab initio potential energy surface that generates highly accurate potential and includes long-range dipole-dipole interactions. QCT calculations indicate that at low temperatures HCO is the exclusive product for the OH+H2CO reaction. In order to revisit the chemistry of HCO in cold dense clouds, k is reasonably extrapolated from the experimental results at 10 K (2.6 × 10-10 cm3 s-1). The modeled abundances of HCO are in agreement with the observations in cold dark clouds for an evolving time of 105-106 yr. The different sources of production of HCO are presented and the uncertainties in the chemical networks are discussed. The present reaction is shown to account for a few percent of the total HCO production rate. This reaction can be expected to be a competitive process in the chemistry of prestellar cores. Extensions to photodissociation regions and diffuse cloud environments are also addressed.

  8. 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.

  9. 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

  10. 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

  11. Learning dynamics: A fundamental building block in social models. Comment on "Collective learning modeling based on the kinetic theory of active particles" by D. Burini et al.

    Science.gov (United States)

    Knopoff, Damián A.

    2016-03-01

    In the last several years there has been an increasing interest in the development of mathematical tools to study a vast number of social phenomena. The recent paper by Burini, De Lillo and Gibelli [7] constitutes a novel and valuable contribution on the modelling of learning dynamics over networks. In the spectrum of social sciences, this approach will surely provide new and useful tools for the progress of this field of interdisciplinary science.

  12. Thermodynamically Feasible Kinetic Models of Reaction Networks

    OpenAIRE

    Ederer, Michael; Gilles, Ernst Dieter

    2007-01-01

    The dynamics of biological reaction networks are strongly constrained by thermodynamics. An holistic understanding of their behavior and regulation requires mathematical models that observe these constraints. However, kinetic models may easily violate the constraints imposed by the principle of detailed balance, if no special care is taken. Detailed balance demands that in thermodynamic equilibrium all fluxes vanish. We introduce a thermodynamic-kinetic modeling (TKM) formalism that adapts th...

  13. Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

    Science.gov (United States)

    Luk, Louis Y. P.; Javier Ruiz-Pernía, J.; Dawson, William M.; Roca, Maite; Loveridge, E. Joel; Glowacki, David R.; Harvey, Jeremy N.; Mulholland, Adrian J.; Tuñón, Iñaki; Moliner, Vicent; Allemann, Rudolf K.

    2013-01-01

    Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy (15N, 13C, 2H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy enzyme reflects differences in environmental coupling to the hydride transfer step. Importantly, the barrier and contribution of quantum tunneling are not affected, indicating no significant role for “promoting motions” in driving tunneling or modulating the barrier. The chemical step is slower in the heavy enzyme because protein motions coupled to the reaction coordinate are slower. The fact that the heavy enzyme is only slightly less active than its light counterpart shows that protein dynamics have a small, but measurable, effect on the chemical reaction rate. PMID:24065822

  14. Complex kinetics of fluctuating enzymes: phase diagram characterization of a minimal kinetic scheme.

    Science.gov (United States)

    Min, Wei; Jiang, Liang; Xie, X Sunney

    2010-05-03

    Enzyme molecules are dynamic entities with stochastic fluctuation in both protein conformation and enzymatic activity. However, such a notion of fluctuating enzymes, best characterized by recent single-molecule experiments, was not considered in the classic Michaelis-Menten (MM) kinetic scheme. Here we incorporate the fluctuation concept into the reversible MM scheme, and solve analytically all the possible kinetics (i.e., substrate concentration dependent enzymatic velocity) for a minimal model of fluctuating enzymes. Such a minimal model is found to display a variety of distinct kinetic behaviors (phases) in addition to the classic MM kinetics; excess substrate inhibition, sigmoidal kinetics, and concave biphasic kinetics. We find that all these kinetic phases are interrelated and unified under the framework of fluctuating enzymes and can be adequately described by a phase diagram that consists of two master parameters. Functionally, substrate inhibition, sigmoidal kinetics, and convex biphasic phases exhibit positive cooperativity, whereas concave biphasic phases display negative cooperativity. Remarkably, all these complex kinetics are produced by fluctuating enzymes with single substrate binding site, but the two conformations are, therefore, fundamentally different from the classic MWC and KNF models that require multiple subunit or binding sites. This model also suggests that, for a given enzyme/substrate pair, the non-MM behaviors could undergo transitions among different kinetic phases induced by varying product concentrations, owing to the fundamental Haldane symmetry in the reversible MM scheme.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. The Nonlinear Magnetosphere: Expressions in MHD and in Kinetic Models

    Science.gov (United States)

    Hesse, Michael; Birn, Joachim

    2011-01-01

    Like most plasma systems, the magnetosphere of the Earth is governed by nonlinear dynamic evolution equations. The impact of nonlinearities ranges from large scales, where overall dynamics features are exhibiting nonlinear behavior, to small scale, kinetic, processes, where nonlinear behavior governs, among others, energy conversion and dissipation. In this talk we present a select set of examples of such behavior, with a specific emphasis on how nonlinear effects manifest themselves in MHD and in kinetic models of magnetospheric plasma dynamics.

  20. 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

  1. Maintenance of the mean kinetic energy in the global ocean by the barotropic and baroclinic energy routes: the roles of JEBAR and Ekman dynamics

    Science.gov (United States)

    Aiki, Hidenori; Richards, Kelvin J.; Sakuma, Hirofumi

    2011-05-01

    In order to determine the maintenance mechanisms of the currents of the global ocean, this study investigates the budget of the annual mean kinetic energy (KE) in a high-resolution (0.1° × 0.1°) semi-global ocean simulation. The analysis is based on a separation of the mean KE using the barotropic (i.e., depth-averaged) and baroclinic (the residual) components of velocity. The barotropic and baroclinic KEs dominate in higher and lower latitudes, respectively, with their global average being comparable to each other. The working rates of wind forcing on the barotropic and baroclinic circulations in the global ocean are 243 and 747 gigawatts, respectively. This study presents at least three new results for the budget of the barotropic KE. Firstly, an energy diagram is rederived to show that the work of the barotropic component of the horizontal pressure gradient (HPG) is connected to the work related to the joint effect of baroclinicity and bottom relief (JEBAR), and then to the budget of potential energy (PE). Secondly, the model analysis shows that the globally averaged work of the barotropic HPG (which is connected to the work related to JEBAR and then to the budget of the PE) is nearly zero. This indicates that the wind- and buoyancy-induced barotropic circulations in the global ocean are of the same strength with opposite sign. Thirdly, it is found that the work of the wind forcing on the barotropic component of the simulated Antarctic Circumpolar Current (ACC) is canceled by the combined effect, in equal measure, of the work of the barotropic HPG and the work of dissipative processes for mean KE. This result makes a significant contribution to the discussion on the depth-integrated momentum balance of the ACC. The barotropic KE is dissipated by the effects of bottom frictional stress, lateral frictional stress, and the Reynolds stress, of which more than half is attributed to an unexpectedly large contribution from biharmonic horizontal friction. Future

  2. Methods of nonlinear kinetics

    OpenAIRE

    Gorban, A. N.; Karlin, I. V.

    2003-01-01

    Nonlinear kinetic equations are reviewed for a wide audience of specialists and postgraduate students in physics, mathematical physics, material science, chemical engineering and interdisciplinary research. Contents: The Boltzmann equation, Phenomenology and Quasi-chemical representation of the Boltzmann equation, Kinetic models, Discrete velocity models, Direct simulation, Lattice Gas and Lattice Boltzmann models, Minimal Boltzmann models for flows at low Knudsen number, Other kinetic equati...

  3. Kinetic theory for interacting Luttinger liquids

    Science.gov (United States)

    Buchhold, Michael; Diehl, Sebastian

    2015-10-01

    We derive a closed set of equations for the kinetics and non-equilibrium dynamics of interacting Luttinger Liquids with cubic resonant interactions. In the presence of these interactions, the Luttinger phonons become dressed but still well defined quasi-particles, characterized by a life-time much larger then the inverse energy. This enables the separation of forward time dynamics and relative time dynamics into slow and fast dynamics and justifies the so-called Wigner approximation, which can be seen as a "local-time approximation" for the relative dynamics. Applying field theoretical methods in the Keldysh framework, i.e. kinetic and Dyson-Schwinger equations, we derive a closed set of dynamic equations, describing the kinetics of normal and anomalous phonon densities, the phonon self-energy and vertex corrections for a Gaussian non-equilibrium initial state. In the limit of low phonon densities, the results from self-consistent Born approximation are recaptured, including Andreev's scaling solution for the quasi-particle life-time in a thermal state. As an application, we compute the relaxation of an excited state to its thermal equilibrium. While the intermediate time dynamics displays exponentially fast relaxation, the last stages of thermalization are governed by algebraic laws. This can be traced back to the importance of energy and momentum conservation at the longest times, which gives rise to dynamical slow modes.

  4. 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)

  5. 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.

  6. 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.

  7. 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 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.

  8. Growth kinetics and structural perfection of (InN)1/(GaN)1–20 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) 1–20 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) 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.

  9. 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.

  10. An analysis of whole body tracer kinetics in dynamic PET studies with application to image-based blood input function extraction.

    Science.gov (United States)

    Huang, Jian; O'Sullivan, Finbarr

    2014-05-01

    In a positron emission tomography (PET) study, the local uptake of the tracer is dependent on vascular delivery and retention. For dynamic studies the measured uptake time-course information can be best interpreted when knowledge of the time-course of tracer in the blood is available. This is certainly true for the most established tracers such as 18F-Fluorodeoxyglucose (FDG) and 15O-Water (H2O). Since direct sampling of blood as part of PET studies is increasingly impractical, there is ongoing interest in image-extraction of blood time-course information. But analysis of PET-measured blood pool signals is complicated because they will typically involve a combination of arterial, venous and tissue information. Thus, a careful appreciation of these components is needed to interpret the available data. To facilitate this process, we propose a novel Markov chain model for representation of the circulation of a tracer atom in the body. The model represents both arterial and venous time-course patterns. Under reasonable conditions equilibration of tracer activity in arterial and venous blood is achieved by the end of the PET study-consistent with empirical measurement. Statistical inference for Markov model parameters is a challenge. A penalized nonlinear least squares process, incorporating a generalized cross-validation score, is proposed. Random effects analysis is used to adaptively specify the structure of the penalty function based on historical samples of directly measured blood data. A collection of arterially sampled data from PET studies with FDG and H2O is used to illustrate the methodology. These data analyses are highly supportive of the overall modeling approach. An adaptation of the model to the problem of extraction of arterial blood signals from imaging data is also developed and promising preliminary results for cerebral and thoracic imaging studies with FDG and H2O are obtained.

  11. 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

  12. The Complex Kinetics of Protein Folding in Wide Temperature Ranges

    OpenAIRE

    Wang, Jin

    2004-01-01

    The complex protein folding kinetics in wide temperature ranges is studied through diffusive dynamics on the underlying energy landscape. The well-known kinetic chevron rollover behavior is recovered from the mean first passage time, with the U-shape dependence on temperature. The fastest folding temperature T0 is found to be smaller than the folding transition temperature Tf. We found that the fluctuations of the kinetics through the distribution of first passage time show rather universal b...

  13. 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.

  14. 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...

  15. 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...

  16. 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

  17. 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

  18. Thermodynamics of enzyme-catalyzed esterifications: I. Succinic acid esterification with ethanol.

    Science.gov (United States)

    Altuntepe, Emrah; Greinert, Thorsten; Hartmann, Felix; Reinhardt, Annika; Sadowski, Gabriele; Held, Christoph

    2017-08-01

    Succinic acid (SA) was esterified with ethanol using Candida antarctica lipase B immobilized on acrylic resin at 40 and 50 °C. Enzyme activity in the reaction medium was assured prior to reaction experiments. Reaction-equilibrium experiments were performed for varying initial molalities of SA and water in the reaction mixtures. This allowed calculating the molality-based apparent equilibrium constant K m as function of concentration and temperature. K m was shown to depend strongly on the molality of water and SA as well as on temperature. It could be concluded that increasing the molality of SA shifted the reaction equilibrium towards the products. Water had a strong effect on the activity of the enzyme and on K m . The concentration dependence of K m values was explained by the activity coefficients of the reacting agents. These were predicted with the thermodynamic models Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT), NRTL, and Universal Quasichemical Functional Group Activity Coefficients (UNIFAC), yielding the ratio of activity coefficients of products and reactants K γ . All model parameters were taken from literature. The models yielded K γ values between 25 and 115. Thus, activity coefficients have a huge impact on the consistent determination of the thermodynamic equilibrium constants K th . Combining K m and PC-SAFT-predicted K γ allowed determining K th and the standard Gibbs energy of reaction as function of temperature. This value was shown to be in very good agreement with results obtained from group contribution methods for Gibbs energy of formation. In contrast, inconsistencies were observed for K th using K γ values from the classical g E -models UNIFAC and NRTL. The importance of activity coefficients opens the door for an optimized reaction setup for enzymatic esterifications.

  19. 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.

  20. 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…

  1. Enzyme-catalyzed DNA unwinding: studies on Escherichia coli rep protein.

    Science.gov (United States)

    Yarranton, G T; Gefter, M L

    1979-04-01

    Replication in vitro of the replicative form (RF) I DNA of bacteriophage varphiX174 requires the phage-induced cistron A (cisA) protein, the host rep protein, DNA-binding protein, ATP, and DNA polymerase III plus replication factors. The rep protein is a single-stranded DNA-dependent ATPase. In this paper we show that varphiX174 RF I DNA cut by the cisA protein acts as a duplex DNA cofactor for the rep protein ATPase activity, provided that DNA-binding protein is present. In this latter reaction the duplex DNA is unwound by the rep protein with concomitant hydrolysis of ATP. The extents of ATP hydrolysis, DNA unwinding, and, where appropriate, DNA synthesis are proportional to the amounts of DNA-binding protein present. Two ATP molecules are hydrolyzed per base pair unwound. We propose that the obligatory requirement for the cisA protein in the unwinding of varphiX174 RF I DNA is not simply due to its endonuclease activity but rather is due to its provision of a site for the binding of the rep protein. The rep protein in the presence of DNA-binding protein, but in the absence of cisA protein, unwinds duplex DNA when one strand extends to generate a single-stranded leader region preceding the duplex. We show that rep protein translocates along the leader single strand in a 5'-to-3' direction only and then invades the duplex DNA. The rep protein shows a directional specificity for translocation and unwinding. A model is presented to explain the mechanism of DNA unwinding catalyzed by the rep protein.

  2. Enzyme-Catalyzed Oxidation of 5-Hydroxymethylfurfural to Furan-2,5-dicarboxylic Acid

    NARCIS (Netherlands)

    Dijkman, Willem P.; Groothuis, Daphne E.; Fraaije, Marco W.

    Furan-2,5-dicarboxylic acid (FDCA) is a biobased platform chemical for the production of polymers. In the past few years, numerous multistep chemical routes have been reported on the synthesis of FDCA by oxidation of 5-hydroxymethylfurfural (HMF). Recently we identified an FAD-dependent enzyme which

  3. 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...

  4. 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

  5. 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...

  6. 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,

  7. 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...

  8. Thermodynamics of enzyme-catalyzed esterifications: II. Levulinic acid esterification with short-chain alcohols.

    Science.gov (United States)

    Altuntepe, Emrah; Emel'yanenko, Vladimir N; Forster-Rotgers, Maximilian; Sadowski, Gabriele; Verevkin, Sergey P; Held, Christoph

    2017-10-01

    Levulinic acid was esterified with methanol, ethanol, and 1-butanol with the final goal to predict the maximum yield of these equilibrium-limited reactions as function of medium composition. In a first step, standard reaction data (standard Gibbs energy of reaction Δ R g 0 ) were determined from experimental formation properties. Unexpectedly, these Δ R g 0 values strongly deviated from data obtained with classical group contribution methods that are typically used if experimental standard data is not available. In a second step, reaction equilibrium concentrations obtained from esterification catalyzed by Novozym 435 at 323.15 K were measured, and the corresponding activity coefficients of the reacting agents were predicted with perturbed-chain statistical associating fluid theory (PC-SAFT). The so-obtained thermodynamic activities were used to determine Δ R g 0 at 323.15 K. These results could be used to cross-validate Δ R g 0 from experimental formation data. In a third step, reaction-equilibrium experiments showed that equilibrium position of the reactions under consideration depends strongly on the concentration of water and on the ratio of levulinic acid: alcohol in the initial reaction mixtures. The maximum yield of the esters was calculated using Δ R g 0 data from this work and activity coefficients of the reacting agents predicted with PC-SAFT for varying feed composition of the reaction mixtures. The use of the new Δ R g 0 data combined with PC-SAFT allowed good agreement to the measured yields, while predictions based on Δ R g 0 values obtained with group contribution methods showed high deviations to experimental yields.

  9. Enzyme-catalyzed synthesis of unsaturated aliphatic polyesters based on green monomers from renewable resources.

    Science.gov (United States)

    Jiang, Yi; Woortman, Albert J J; van Ekenstein, Gert O R Alberda; Loos, Katja

    2013-08-12

    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, poly(butylene succinate) (PBS) and poly(butylene succinate-co-itaconate) (PBSI), are confirmed by 1H- and 13C-NMR. The effects of the reaction conditions on the CALB-catalyzed synthesis of PBSI are fully investigated, and the optimal polymerization conditions are obtained. With the established method, PBSI with tunable compositions and satisfying reaction yields is produced. The 1H-NMR results confirm that carbon-carbon double bonds are well preserved in PBSI. The differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA) results indicate that the amount of itaconate in the co-polyesters has no obvious effects on the glass-transition temperature and the thermal stability of PBS and PBSI, but has significant effects on the melting temperature.

  10. 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

  11. 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

  12. 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.

  13. 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

  14. Equilibrium position, kinetics, and reactor concepts for the adipyl-7-ADCA-hydrolysis process

    NARCIS (Netherlands)

    Schroën, C.G.P.H.; Wiel, van de S.; Kroon, P.J.; Vroom, de E.; Janssen, A.E.M.; Tramper, J.

    2000-01-01

    One of the building blocks of cephalosporin antibiotics is 7-amino-deacetoxycephalosporanic acid (7-ADCA). It is currently produced from penicillin G using an elaborate chemical ring-expansion step followed by an enzyme-catalyzed hydrolysis. However, 7-ADCA-like components can also be produced by

  15. Reduction Kinetics of 3-Hydroxybenzoate 6-Hydroxylase from Rhodococcus jostii RHA1

    NARCIS (Netherlands)

    Sucharitakul, J.; Wongnate, T.; Montersino, S.; Berkel, van W.J.H.; Chaiyen, P.

    2012-01-01

    3-Hydroxybenzoate 6-hydroxylase (3HB6H) from Rhodococcus jostii RHA1 is a nicotinamide adenine dinucleotide (NADH)-specific flavoprotein monooxygenase involved in microbial aromatic degradation. The enzyme catalyzes the para hydroxylation of 3-hydroxybenzoate (3-HB) to 2,5-dihydroxybenzoate

  16. 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

  17. Polymer Fluid Dynamics.

    Science.gov (United States)

    Bird, R. Byron

    1980-01-01

    Problems in polymer fluid dynamics are described, including development of constitutive equations, rheometry, kinetic theory, flow visualization, heat transfer studies, flows with phase change, two-phase flow, polymer unit operations, and drag reduction. (JN)

  18. A Pre-Steady State Kinetic Analysis of the αY60W mutant of trans-3-Chloroacrylic Acid Dehalogenase: Implications for the Mechanism of the Wild-type Enzyme†

    Science.gov (United States)

    Huddleston, Jamison P.; Schroeder, Gottfried K.; Johnson, Kenneth A.; Whitman, Christian P.

    2012-01-01

    The bacterial degradation of the nematicide 1,3-dichloropropene, an isomeric mixture, requires the action of trans- and cis-3-chloracrylic acid dehalogenase (CaaD and cis-CaaD, respectively). Both enzymes are tautomerase superfamily members and share a core catalytic mechanism for the hydrolytic dehalogenation of the respective isomer of 3-haloacrylate. The observation that cis-CaaD requires two additional residues raises the question of how CaaD carries out a comparable reaction with fewer catalytic residues. As part of an effort to determine the basis for the apparently simpler CaaD-catalyzed reaction, the kinetic mechanism was determined by stopped-flow and chemical quench techniques using a fluorescent mutant form of the enzyme, αY60W-CaaD, and trans-3-bromoacrylate as the substrate. The data from these experiments as well as bromide inhibition studies are best accommodated by a six-step model that provides individual rate constants for substrate binding, chemistry, and a proposed conformational change occurring after chemistry followed by release of malonate semialdehyde and bromide. The conformational change and product release rates are comparable and together they limit the rate of turnover. The kinetic analysis and modeling studies validate the αY60W-CaaD mutant as an accurate reporter of active site events during the course of the enzyme-catalyzed reaction. The kinetic mechanism for the αY60W-CaaD-catalyzed reaction is comparable to that obtained for the cis-CaaD-catalyzed reaction. The kinetic model and the validated αY60W-CaaD mutant set the stage for an analysis of active site mutants to explore the contributions of individual catalytic residues and the basis for the simplicity of the reaction. PMID:23110338

  19. 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

  20. 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...

  1. Enzymatic dynamic kinetic resolution of epihalohydrins

    NARCIS (Netherlands)

    Lutje Spelberg, Jeffrey H.; Tang, Lixia; Kellogg, Richard M.; Janssen, Dick B.

    2004-01-01

    The haloalcohol dehalogenase from Agrobacterium radiobacter AD1 catalyses the reversible ring closure of vicinal haloalcohols to produce epoxides and halides. In the ring opening of epoxides, nonhalide nucleophiles such as N3- are accepted. The enantioselective irreversible ring opening of an

  2. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II.

    Science.gov (United States)

    Taraphder, Srabani; Maupin, C Mark; Swanson, Jessica M J; Voth, Gregory A

    2016-08-25

    The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II. Special attention has been placed on whether the motion of an excess proton is correlated with fluctuations in the surrounding protein and solvent matrix, which may be rare on the picosecond and subpicosecond time scales of molecular motions. It is found that several active site residues, which do not directly participate in the proton transport event, have a significant impact on the dynamics of the excess proton. These secondary participants are shown to strongly influence the active site environment, resulting in the creation of water clusters that are conducive to fast, moderately slow, or slow proton transport events. The identification and characterization of these secondary participants illuminates the role of protein dynamics in the catalytic efficiency of HCA II.

  3. 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...

  4. 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

  5. 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...... capabilities. In this review, we present an overview of the relevant mathematical frameworks for kinetic formulation, construction and analysis. Starting with kinetic formalisms, we next review statistical methods for parameter inference, as well as recent computational frameworks applied to the construction...

  6. Kinetic Line Voronoi Operations and Their Reversibility

    DEFF Research Database (Denmark)

    Mioc, Darka; Anton, François; Gold, Christopher

    2010-01-01

    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...... explanation using the finite field of residual classes of integers modulo 5: F 5 = ℤ/5ℤ. We show also an isomorphism between the set of complex operations on the kinetic Voronoi diagram of points and open oriented line segments and the set of differences of new and deleted Quad-Edge edges induced...

  7. Thermal kinetic inductance detector

    Science.gov (United States)

    Cecil, Thomas; Gades, Lisa; Miceli, Antonio; Quaranta, Orlando

    2016-12-20

    A microcalorimeter for radiation detection that uses superconducting kinetic inductance resonators as the thermometers. The detector is frequency-multiplexed which enables detector systems with a large number of pixels.

  8. 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.

  9. Mechanisms of kinetic stabilization by the drugs paclitaxel and vinblastine.

    Science.gov (United States)

    Castle, Brian T; McCubbin, Seth; Prahl, Louis S; Bernens, Jordan N; Sept, David; Odde, David J

    2017-05-01

    Microtubule-targeting agents (MTAs), widely used as biological probes and chemotherapeutic drugs, bind directly to tubulin subunits and "kinetically stabilize" microtubules, suppressing the characteristic self-assembly process of dynamic instability. However, the molecular-level mechanisms of kinetic stabilization are unclear, and the fundamental thermodynamic and kinetic requirements for dynamic instability and its elimination by MTAs have yet to be defined. Here we integrate a computational model for microtubule assembly with nanometer-scale fluorescence microscopy measurements to identify the kinetic and thermodynamic basis of kinetic stabilization by the MTAs paclitaxel, an assembly promoter, and vinblastine, a disassembly promoter. We identify two distinct modes of kinetic stabilization in live cells, one that truly suppresses on-off kinetics, characteristic of vinblastine, and the other a "pseudo" kinetic stabilization, characteristic of paclitaxel, that nearly eliminates the energy difference between the GTP- and GDP-tubulin thermodynamic states. By either mechanism, the main effect of both MTAs is to effectively stabilize the microtubule against disassembly in the absence of a robust GTP cap. © 2017 Castle et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication 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).

  10. 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.…

  11. 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.

  12. 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.)

  13. 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)

  14. 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.

  15. A Simple "Boxed Molecular Kinetics" Approach To Accelerate Rare Events in the Stochastic Kinetic Master Equation.

    Science.gov (United States)

    Shannon, Robin; Glowacki, David R

    2018-02-15

    The chemical master equation is a powerful theoretical tool for analyzing the kinetics of complex multiwell potential energy surfaces in a wide range of different domains of chemical kinetics spanning combustion, atmospheric chemistry, gas-surface chemistry, solution phase chemistry, and biochemistry. There are two well-established methodologies for solving the chemical master equation: a stochastic "kinetic Monte Carlo" approach and a matrix-based approach. In principle, the results yielded by both approaches are identical; the decision of which approach is better suited to a particular study depends on the details of the specific system under investigation. In this Article, we present a rigorous method for accelerating stochastic approaches by several orders of magnitude, along with a method for unbiasing the accelerated results to recover the "true" value. The approach we take in this paper is inspired by the so-called "boxed molecular dynamics" (BXD) method, which has previously only been applied to accelerate rare events in molecular dynamics simulations. Here we extend BXD to design a simple algorithmic strategy for accelerating rare events in stochastic kinetic simulations. Tests on a number of systems show that the results obtained using the BXD rare event strategy are in good agreement with unbiased results. To carry out these tests, we have implemented a kinetic Monte Carlo approach in MESMER, which is a cross-platform, open-source, and freely available master equation solver.

  16. 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

  17. 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.

  18. Multiple alternative substrate kinetics.

    Science.gov (United States)

    Anderson, Vernon E

    2015-11-01

    The specificity of enzymes for their respective substrates has been a focal point of enzyme kinetics since the initial characterization of metabolic chemistry. Various processes to quantify an enzyme's specificity using kinetics have been utilized over the decades. Fersht's definition of the ratio kcat/Km for two different substrates as the "specificity constant" (ref [7]), based on the premise that the important specificity existed when the substrates were competing in the same reaction, has become a consensus standard for enzymes obeying Michaelis-Menten kinetics. The expansion of the theory for the determination of the relative specificity constants for a very large number of competing substrates, e.g. those present in a combinatorial library, in a single reaction mixture has been developed in this contribution. The ratio of kcat/Km for isotopologs has also become a standard in mechanistic enzymology where kinetic isotope effects have been measured by the development of internal competition experiments with extreme precision. This contribution extends the theory of kinetic isotope effects to internal competition between three isotopologs present at non-tracer concentrations in the same reaction mix. This article is part of a special issue titled: Enzyme Transition States from Theory and Experiment. Published by Elsevier B.V.

  19. 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.

  20. The Einstein-Vlasov System/Kinetic Theory

    Directory of Open Access Journals (Sweden)

    Håkan Andréasson

    2011-05-01

    Full Text Available 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.

  1. 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.

  2. 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.

  3. Posture and theophylline kinetics.

    OpenAIRE

    Warren, J B; Cuss, F; Barnes, P J

    1985-01-01

    The effect of posture on theophylline kinetics was examined in six healthy men who took 450 mg slow-release aminophylline orally at the same time of day on two separate occasions. On one day they remained standing and on the other supine throughout. Plasma theophylline was measured hourly for 6 h from ingestion. Mean theophylline levels were significantly higher in the standing position at all times (P less than 0.01). We conclude that diurnal variation in theophylline kinetics can be explain...

  4. Tebuconazole photocatalytic degradation kinetics

    OpenAIRE

    Prestes, Thiago de Hermann; Gibbon, Danielle de Oliveira; Lansarin, Marla Azário; Moro, Celso Camilo

    2010-01-01

    The tebuconazole photocatalytic degradation kinetics was studied in a batch reactor using TiO2 (P25-Degussa) as catalyst and a high pressure mercury lamp. The photolysis, adsorption and irradiation effects in the reaction rate were evaluated. Afterward, the suspension catalyst concentration and initial pH to the maximum reaction rate was determined. It was observed that the reaction rate can be approached by a pseudo-first order, with a maximum kinetics constant at 260 mg L-1catalyst concentr...

  5. On the kinetic temperature of He/++/ in the solar wind.

    Science.gov (United States)

    Barnes, A.; Hung, R. J.

    1973-01-01

    Observations of solar-wind He(++) can be useful for studying dynamical processes in the interplanetary medium. Several processes which may influence the kinetic temperature are considered, and an attempt is made to inquire whether they can account for the observed fact that the kinetic temperature exceeds the proton temperature. Resonant heating is discussed qualitatively, and equations of resonant heating are developed. The proton and He(++) heating rates are determined for the least damped magnetoacoustic wave under various conditions.

  6. 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 ...

  7. 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 ...

  8. Kinetics and Catalysis Demonstrations.

    Science.gov (United States)

    Falconer, John L.; Britten, Jerald A.

    1984-01-01

    Eleven videotaped kinetics and catalysis demonstrations are described. Demonstrations include the clock reaction, oscillating reaction, hydrogen oxidation in air, hydrogen-oxygen explosion, acid-base properties of solids, high- and low-temperature zeolite reactivity, copper catalysis of ammonia oxidation and sodium peroxide decomposition, ammonia…

  9. SHORT COMMUNICATION KINETIC SPECTROPHOTOMETRIC ...

    African Journals Online (AJOL)

    Preferred Customer

    gingili paste, oat slice, sleeve-fish silk food samples. The determined results were in agreement with those by atomic absorption spectrometry. KEY WORDS: KEY WORDS: Iron, Catalytic kinetic spectrophotometry, p–Acetylarsenazo, Potassium periodate. INTRODUCTION. Iron is an important component for the human body.

  10. 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

  11. CATALYTIC KINETIC SPECTROPHOTOMETRIC DETERMINATION ...

    African Journals Online (AJOL)

    Based on the property that in 0.12 M sulfuric acid medium titanium(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 titanium is

  12. Development of a Procedure to Apply Detailed Chemical Kinetic Mechanisms to CFD Simulations as Post Processing

    DEFF Research Database (Denmark)

    Skjøth-Rasmussen, Martin Skov; Glarborg, Peter; Jensen, Anker

    2003-01-01

    It is desired to make detailed chemical kinetic mechanisms applicable to the complex geometries of practical combustion devices simulated with computational fluid dynamics tools. This work presents a novel general approach to combining computational fluid dynamics and a detailed chemical kinetic...... mechanism. It involves post-processing of data extracted from computational fluid dynamics simulations. Application of this approach successfully describes combustion chemistry in a standard swirl burner, the so-called Harwell furnace. Nevertheless, it needs validation against more complex combustion models...

  13. 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.

  14. Kinetic Damage from Meteorites

    Science.gov (United States)

    Cooke, W.; Brown, P.; Matney, M.

    2017-01-01

    Comparing the natural meteorite flux at the Earth's surface to that of space debris, re-entering debris is 2 orders of magnitude less of a kinetic hazard at all but the very largest (and therefore rarest) sizes compared to natural impactors. Debris re-entries over several metric tonnes are roughly as frequent as natural impactors, but the survival fraction is expected to be much higher. Kinetic hazards from meteorites are very small, with only one recorded (indirect) injury reported. We expect fatalities to be even more rare, on the order of one person killed per several millennia. That several reports exist of small fragments/sand hitting people during meteorite falls is consistent with our prediction that this should occur every decade or so.

  15. 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.)

  16. A MATLAB toolbox for structural kinetic modeling.

    Science.gov (United States)

    Girbig, Dorothee; Selbig, Joachim; Grimbs, Sergio

    2012-10-01

    Structural kinetic modeling (SKM) enables the analysis of dynamical properties of metabolic networks solely based on topological information and experimental data. Current SKM-based experiments are hampered by the time-intensive process of assigning model parameters and choosing appropriate sampling intervals for Monte-Carlo experiments. We introduce a toolbox for the automatic and efficient construction and evaluation of structural kinetic models (SK models). Quantitative and qualitative analyses of network stability properties are performed in an automated manner. We illustrate the model building and analysis process in detailed example scripts that provide toolbox implementations of previously published literature models. The source code is freely available for download at http://bioinformatics.uni-potsdam.de/projects/skm. girbig@mpimp-golm.mpg.de.

  17. Kinetics of Peptide Folding in Lipid Membranes

    Science.gov (United States)

    Oh, Kwang-Im; Smith-Dupont, Kathryn B.; Markiewicz, Beatrice N.; Gai, Feng

    2015-01-01

    Despite our extensive understanding of water-soluble protein folding kinetics, much less is known about the folding dynamics and mechanisms of membrane proteins. However, recent studies have shown that for relatively simple systems, such as peptides that form a transmembrane α-helix, helical dimer, or helix-turn-helix, it is possible to assess the kinetics of several important steps, including peptide binding to the membrane from aqueous solution, peptide folding on the membrane surface, helix insertion into the membrane, and helix-helix association inside the membrane. Herein, we provide a brief review of these studies and also suggest new initiation and probing methods that could lead to improved temporal and structural resolution in future experiments. PMID:25808575

  18. 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.

  19. 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

  20. 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

  1. 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.)

  2. Modelling and dynamic simulation of a pilot-scale moving bed bioreactor for the treatment of municipal wastewater: model concepts and the use of respirometry for the estimation of kinetic parameters.

    Science.gov (United States)

    Plattes, M; Fiorelli, D; Gillé, S; Girard, C; Henry, E; Minette, F; O'Nagy, O; Schosseler, P M

    2007-01-01

    A model for the simulation of a moving bed bioreactor (MBBR) used for the treatment of municipal wastewater is proposed. The model includes attachment of particulates to the biofilm and detachment of biofilm into the bulk liquid. The growth kinetics are modelled with the activated sludge model no. 1 (ASM1). Respirometry was used for the estimation of kinetic parameters. The resulting respirograms featured the typical endogenous and exogenous respiration phases and the respirogram shapes were as expected from analogous respirometry with activated sludge. The estimated parameter set was used for modelling and simulation of the pilot-scale MBBR. The main proportion of biomass in the MBBR was found to be attached as biofilm on the carrier elements (4.1 -4.6 g dm-3) and only a small amount was suspended in the bulk liquid (0.15gdm(-3)). Attachment and detachment rates were estimated to be 4.8-7.5g m(-2) d(-1) 1for attachment and 6.5-7.5g m(-2) d(-1) for detachment. The biofilm age was estimated to be 1.8-2.7d. The model was used to predict effluent quality parameters and a good fit of the simulated data to the measured data originating from a four-days-long measurement campaign was obtained.

  3. 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.

  4. Jacques Polieri: Kinetic Theatre Space

    Directory of Open Access Journals (Sweden)

    Juan Ignacio Prieto López

    2015-10-01

    Full Text Available Between the First and Second World War the definition of the new type of theater building was one of the main tasks of the European Avantgarde. In its design and theoretical formulation were poets, playwrights, theater directors, architects, painters, actors, engineers… from different countries and art movements. Despite the collaboration of the leading members of the Avant-garde like Marinetti, Moholy-Nagy, Kiesler, El Lissitzky, Gropius… none of these proposals were built because of their radical and utopian characteristics. It was a young French theater director, Jacques Polieri, who became the main compiler and prompter of those proposals in postwar Europe in two issues of the French journal Aujourd´hui, art et architecture. The first of them published in May 1958, under the title “Cinquante ans de recherches dans le spectacle” collected the most important experiences in theory, scenography, technic, and theater architecture in the interwar period. Polieri worked with different architects in several projects for theater buildings, whose main feature was the mobility of all their elements and components, trying to get a dynamic experience during the performance. Those proposals related to Kinetic Art, were published in a second issue of Aujourd´hui, art et architecture entitled “Scénographie Nouvelle” in October 1963.

  5. 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

  6. Kinetics of tetrataenite disordering

    Energy Technology Data Exchange (ETDEWEB)

    Dos Santos, E., E-mail: edisanfi@cbpf.br [Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro (Brazil); Gattacceca, J.; Rochette, P. [Centre Européen de Recherche et d’Enseignement des Géosciences de l’Environnement, UM34, CNRS/Aix-Marseille University, Aix-en-Provence (France); Fillion, G. [Laboratoire National des Champs Magnétiques Intenses (LNCMI), CNRS, UJF, 38042 Grenoble (France); Scorzelli, R.B. [Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro (Brazil)

    2015-02-01

    Tetrataenite is a chemically ordered L1{sub 0}-type Fe{sub 50}Ni{sub 50} alloy detected for the first time in 1977 by {sup 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{sub 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.

  7. Kinetics of stress fibers

    International Nuclear Information System (INIS)

    Stachowiak, Matthew R; O'Shaughnessy, Ben

    2008-01-01

    Stress fibers are contractile cytoskeletal structures, tensile actomyosin bundles which allow sensing and production of force, provide cells with adjustable rigidity and participate in various processes such as wound healing. The stress fiber is possibly the best characterized and most accessible multiprotein cellular contractile machine. Here we develop a quantitative model of the structure and relaxation kinetics of stress fibers. The principal experimentally known features are incorporated. The fiber has a periodic sarcomeric structure similar to muscle fibers with myosin motor proteins exerting contractile force by pulling on actin filaments. In addition the fiber contains the giant spring-like protein titin. Actin is continuously renewed by exchange with the cytosol leading to a turnover time of several minutes. In order that steady state be possible, turnover must be regulated. Our model invokes simple turnover and regulation mechanisms: actin association and dissociation occur at filament ends, while actin filament overlap above a certain threshold in the myosin-containing regions augments depolymerization rates. We use the model to study stress fiber relaxation kinetics after stimulation, as observed in a recent experimental study where some fiber regions were contractile and others expansive. We find that two distinct episodes ensue after stimulation: the turnover-overlap system relaxes rapidly in seconds, followed by the slow relaxation of sarcomere lengths in minutes. For parameter values as they have been characterized experimentally, we find the long time relaxation of sarcomere length is set by the rate at which actin filaments can grow or shrink in response to the forces exerted by the elastic and contractile elements. Consequently, the stress fiber relaxation time scales inversely with both titin spring constant and the intrinsic actin turnover rate. The model's predicted sarcomere velocities and contraction-expansion kinetics are in good

  8. Kinetics of stress fibers

    Energy Technology Data Exchange (ETDEWEB)

    Stachowiak, Matthew R; O' Shaughnessy, Ben [Department of Chemical Engineering, Columbia University, New York, NY 10027 (United States)], E-mail: bo8@columbia.edu

    2008-02-15

    Stress fibers are contractile cytoskeletal structures, tensile actomyosin bundles which allow sensing and production of force, provide cells with adjustable rigidity and participate in various processes such as wound healing. The stress fiber is possibly the best characterized and most accessible multiprotein cellular contractile machine. Here we develop a quantitative model of the structure and relaxation kinetics of stress fibers. The principal experimentally known features are incorporated. The fiber has a periodic sarcomeric structure similar to muscle fibers with myosin motor proteins exerting contractile force by pulling on actin filaments. In addition the fiber contains the giant spring-like protein titin. Actin is continuously renewed by exchange with the cytosol leading to a turnover time of several minutes. In order that steady state be possible, turnover must be regulated. Our model invokes simple turnover and regulation mechanisms: actin association and dissociation occur at filament ends, while actin filament overlap above a certain threshold in the myosin-containing regions augments depolymerization rates. We use the model to study stress fiber relaxation kinetics after stimulation, as observed in a recent experimental study where some fiber regions were contractile and others expansive. We find that two distinct episodes ensue after stimulation: the turnover-overlap system relaxes rapidly in seconds, followed by the slow relaxation of sarcomere lengths in minutes. For parameter values as they have been characterized experimentally, we find the long time relaxation of sarcomere length is set by the rate at which actin filaments can grow or shrink in response to the forces exerted by the elastic and contractile elements. Consequently, the stress fiber relaxation time scales inversely with both titin spring constant and the intrinsic actin turnover rate. The model's predicted sarcomere velocities and contraction-expansion kinetics are in good

  9. 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.

  10. 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.

  11. Kinetic theory of photophoresis

    International Nuclear Information System (INIS)

    Beresnev, S.A.; Chernyak, V.G.; Fomyagin, G.A.

    1988-01-01

    The force acting on an aerosol particle in one-sided illumination is calculated on the basis of solving a linearized gas-kinetic equation. A closed system of integral-moment equations describing photophoresis with arbitrary values of the Knudsen number and an arbitrary ratio of the particle and gas thermal conductivities is constructed. The possibility of arbitrary accommodation of the momentum and energy with interaction between the gas molecules and the particle surface is taken into account. The distribution of heat sources inside the radiation-absorbing particle is described by Mie theory. The results obtained are compared with the known theoretical and experimental data

  12. Chemical kinetics modeling

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, C.K.; Pitz, W.J. [Lawrence Livermore National Laboratory, CA (United States)

    1993-12-01

    This project emphasizes numerical modeling of chemical kinetics of combustion, including applications in both practical combustion systems and in controlled laboratory experiments. Elementary reaction rate parameters are combined into mechanisms which then describe the overall reaction of the fuels being studied. Detailed sensitivity analyses are used to identify those reaction rates and product species distributions to which the results are most sensitive and therefore warrant the greatest attention from other experimental and theoretical research programs. Experimental data from a variety of environments are combined together to validate the reaction mechanisms, including results from laminar flames, shock tubes, flow systems, detonations, and even internal combustion engines.

  13. 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)

  14. Simulation of Adaptive Kinetic Architectural Structures

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning

    2010-01-01

    to obtain the control forces that must be known in order to control the shape of a real variable geometry truss structure. An experimental test of the of the shape control approach has been implemented using VGT truss structure and a low-cost data acquisition system based on the open-source Arduino......This project deals with shape control of kinetic structures within the field of adaptable architecture. Here a variable geometry truss cantilever structure is analyzed using MATLAB/SIMULINK and the multibody dynamic software MSC Adams. Active shape control of a structure requires that the kinematic...

  15. 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

  16. Kinetic mesh-free method for flutter prediction in turbomachines

    Indian Academy of Sciences (India)

    Kinetic mesh-free method for flutter prediction in turbomachines. V RAMESH1,∗ and S M DESHPANDE2. 1Council for Scientific and Industrial Research, National Aerospace Laboratories,. Computational and Theoretical Fluid Dynamics Division, Bangalore 560 017, India. 2Engineering Mechanics Unit, Jawaharlal Nehru ...

  17. Excited state kinetics of anthracene-bridge-aniline intramolecular exciplexes

    DEFF Research Database (Denmark)

    Thyrhaug, Erling; Hammershøj, Peter; Kjær, Kasper Skov

    2014-01-01

    of the excited state dynamics, the presence of this state required the development of a numerical three-excited-state kinetic model to replace the commonly used two-excited-state model. The experimental results shows that the reaction rates are strongly influenced both by substituents and solvent, illustrating...

  18. 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

  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. Evaluation of Kinetic Entropy of Breast Masses Initially Found on MRI using Whole-lesion Curve Distribution Data: Comparison with the Standard Kinetic Analysis.

    Science.gov (United States)

    Shimauchi, Akiko; Abe, Hiroyuki; Schacht, David V; Yulei, Jian; Pineda, Federico D; Jansen, Sanaz A; Ganesh, Rajiv; Newstead, Gillian M

    2015-08-01

    To quantify kinetic heterogeneity of breast masses that were initially detected with dynamic contrast-enhanced MRI, using whole-lesion kinetic distribution data obtained from computer-aided evaluation (CAE), and to compare that with standard kinetic curve analysis. Clinical MR images from 2006 to 2011 with breast masses initially detected with MRI were evaluated with CAE. The relative frequencies of six kinetic patterns (medium-persistent, medium-plateau, medium-washout, rapid-persistent, rapid-plateau, rapid-washout) within the entire lesion were used to calculate kinetic entropy (KE), a quantitative measure of enhancement pattern heterogeneity. Initial uptake (IU) and signal enhancement ratio (SER) were obtained from the most-suspicious kinetic curve. Mann-Whitney U test and ROC analysis were conducted for differentiation of malignant and benign masses. Forty benign and 37 malignant masses comprised the case set. IU and SER were not significantly different between malignant and benign masses, whereas KE was significantly greater for malignant than benign masses (p = 0.748, p = 0.083, and p kinetic heterogeneity of whole-lesion time-curve data with KE has the potential to improve differentiation of malignant from benign breast masses on breast MRI. • Kinetic heterogeneity can be quantified by computer-aided evaluation of breast MRI • Kinetic entropy was greater in malignant masses than benign masses • Kinetic entropy has the potential to improve differentiation of breast masses.

  1. 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

  2. Structure and dynamics of graphite intercalation compounds. Pt. 2. Kinetics of formation of C/sub 8/KDsub(2/3) and C/sub 8/KHsub(2/3)

    Energy Technology Data Exchange (ETDEWEB)

    Beaufils, J.P. (Institut Max von Laue - Paul Langevin, 38 - Grenoble (France)); Trewern, T.; Thomas, R.K.; White, J.W. (Oxford Univ. (UK). Physical Chemistry Lab.)

    1982-08-01

    The kinetics of the intercalation of hydrogen and deuterium into C/sub 8/K have been studied by neutron powder diffraction. There appear to be two different mechanisms for the reaction of hydrogen or deuterium with C/sub 8/K depending upon the temperature. Below ca. 370 K the activation energy derived from the Arrhenius plots is ca. 50 kJ mol/sup -1/ and the reaction order is < 1. In this range the ratio of the rates for hydrogen and deuterium is large. At high temperatures the activation energy was not measurable and the order of the reaction is rather higher, possibly 2. In this temperature range also the isotope effect has decreased. A mechanism involving dissociation and diffusion is invoked to explain these results.

  3. 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.

  4. 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.

  5. Intrinsic kinetics in heavy ion reactions in the strong-coupling limit

    Energy Technology Data Exchange (ETDEWEB)

    Isaev, P.N. (AN SSSR, Novosibirsk. Inst. Yadernoj Fiziki)

    1985-02-01

    A quantum statistical description is suggested for the intrinsic kinetics of nuclear systems with a strong coupling between the collective (global) dynamics and intrinsic degrees of freedom (for a double nuclear system in heavy ion reactions and mother nucleus at the descent stage of fission). The influence of the ''memory'' of the system concerning pre-history of the kinetic process on the form of the kinetic equation is studied in detail. It is shown that Markov's regime is realized at practically all evolution stages of the double nuclear system (and, certainly, in fission). The kinetic equation is written and discussed in this regime.

  6. Dimensional enhancement of kinetic energies

    DEFF Research Database (Denmark)

    Schleich, W.P.; Dahl, Jens Peder

    2002-01-01

    Simple thermodynamics considers kinetic energy to be an extensive variable which is proportional to the number N of particles. We present a quantum state of N noninteracting particles for which the kinetic energy increases quadratically with N. This enhancement effect is tied to the quantum...

  7. Evolution of Enzyme Kinetic Mechanisms.

    Science.gov (United States)

    Ulusu, Nuriye Nuray

    2015-06-01

    This review paper discusses the reciprocal kinetic behaviours of enzymes and the evolution of structure-function dichotomy. Kinetic mechanisms have evolved in response to alterations in ecological and metabolic conditions. The kinetic mechanisms of single-substrate mono-substrate enzyme reactions are easier to understand and much simpler than those of bi-bi substrate enzyme reactions. The increasing complexities of kinetic mechanisms, as well as the increasing number of enzyme subunits, can be used to shed light on the evolution of kinetic mechanisms. Enzymes with heterogeneous kinetic mechanisms attempt to achieve specific products to subsist. In many organisms, kinetic mechanisms have evolved to aid survival in response to changing environmental factors. Enzyme promiscuity is defined as adaptation to changing environmental conditions, such as the introduction of a toxin or a new carbon source. Enzyme promiscuity is defined as adaptation to changing environmental conditions, such as the introduction of a toxin or a new carbon source. Enzymes with broad substrate specificity and promiscuous properties are believed to be more evolved than single-substrate enzymes. This group of enzymes can adapt to changing environmental substrate conditions and adjust catalysing mechanisms according to the substrate's properties, and their kinetic mechanisms have evolved in response to substrate variability.

  8. Calcium kinetics in parathyroid disease

    International Nuclear Information System (INIS)

    Dymling, J.F.

    1964-01-01

    This paper reports a study of calcium kinetics in twelve cases of parathyroid disease. The data suggest that hyperparathyroidism usually causes increased bone turnover. The study of calcium kinetics may be a valuable tool in the differential diagnosis of primary hyperparathyroidism and in evaluating treatment of secondary hyperparathyroidism. The bone turnover in one case of hypoparathyroidism was extremely low. 1 fig., 1 tab

  9. Quantum kinetic theory of the chiral anomaly

    Science.gov (United States)

    Sekine, Akihiko; Culcer, Dimitrie; MacDonald, Allan H.

    2017-12-01

    We present a general quantum kinetic theory of low-field magnetotransport in weakly disordered crystals that accounts fully for the interplay between electric-field-induced interband coherence, Bloch-state scattering, and an external magnetic field. The quantum kinetic equation we derive for the Bloch-state density matrix naturally incorporates the momentum-space Berry phase effects whose influence on Bloch-state wave-packet dynamics is normally incorporated into transport theory in an ad hoc manner. The Berry phase correction to the momentum-space density of states in the presence of an external magnetic field implied by semiclassical wave-packet dynamics is captured by our theory as an intrinsic density-matrix response to a magnetic field. We propose a simple and general procedure for expanding the linear response of the Bloch-state density matrix to an electric field in powers of magnetic field. As an illustration, we apply our theory to magnetotransport in Weyl semimetals. We show that the chiral anomaly (positive magnetoconductivity quadratic in magnetic field) that appears when separate Fermi surface pockets surround distinct Weyl points survives only when intervalley scattering is very weak compared to intravalley scattering.

  10. Kinetics of Bio-Reactions

    DEFF Research Database (Denmark)

    Villadsen, John

    2015-01-01

    . The models can be used in mass balances for design of processes under process conditions not yet studied experimentally. The value of the predictive kinetic model depends on the quality of the experimental data on which the model is based, and well-founded kinetic models for enzyme reactions have...... a considerable predictive power. This is also true for cell reaction models, when the model is used in its proper context. The chapter first discusses the kinetics for enzymatically catalyzed reactions (“enzyme reactions”). The kinetics can be derived from a mechanistic model. Then, the chapter derives empirical......his chapter predicts the specific rates of reaction by means of a mathematical expression, the kinetics of the reaction. This expression can be derived through a mechanistic interpretation of an enzymatically catalyzed reaction, but it is essentially of empirical nature for cell reactions...

  11. 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...

  12. 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

  13. Efficient use of single molecule time traces to resolve kinetic rates, models and uncertainties

    Science.gov (United States)

    Schmid, Sonja; Hugel, Thorsten

    2018-03-01

    Single molecule time traces reveal the time evolution of unsynchronized kinetic systems. Especially single molecule Förster resonance energy transfer (smFRET) provides access to enzymatically important time scales, combined with molecular distance resolution and minimal interference with the sample. Yet the kinetic analysis of smFRET time traces is complicated by experimental shortcomings—such as photo-bleaching and noise. Here we recapitulate the fundamental limits of single molecule fluorescence that render the classic, dwell-time based kinetic analysis unsuitable. In contrast, our Single Molecule Analysis of Complex Kinetic Sequences (SMACKS) considers every data point and combines the information of many short traces in one global kinetic rate model. We demonstrate the potential of SMACKS by resolving the small kinetic effects caused by different ionic strengths in the chaperone protein Hsp90. These results show an unexpected interrelation between conformational dynamics and ATPase activity in Hsp90.

  14. Influence of a cyclic load on the embrittlement kinetics of alloys by the example of the 475 C embrittlement of duplex steel and the dynamic embrittlement of a nickel base alloy

    International Nuclear Information System (INIS)

    Wackermann, Ken

    2015-01-01

    The objective of this study was to investigate the dependence of high temperature embrittlement mechanisms on high temperature fatigue and vice versa. As model embrittlement mechanisms the 475 C Embrittlement of ferritic austenitic duplex stainless steel (1.4462) and the Dynamic Embrittlement of nickel-based superalloys (IN718) were selected. The 475 C Embrittlement is a thermally activated decomposition of the ferritic phase which hardens the material. In contrast to this a cyclic plastic deformation weakens the steel by a deformation-induced dissolution of the decomposition. Fatigue tests with different frequencies, loading amplitudes at room temperature and at 475 C with Duplex Stainless Steel in different states of embrittlement show that the ongoing 475 C Embrittlement and the deformation-induced dissolution are competing mechanisms. It depends on the frequency, the loading amplitude and the temperature which mechanism is dominant. Applying the model of the yield stress distribution function to the hysteresis branches of the fatigue tests allows an analysis of the fatigue behaviour of each phase individually. This analysis shows that the global fatigue behaviour for the test conditions applied in this study is mainly controlled by the ferritic phase. According to the existing understanding of Dynamic Embrittlement it is an oxygen grain boundary diffusion arising by tensile stress at elevated temperatures with the result of a fast intercrystalline crack propagation. In reference tests under vacuum conditions without oxygen grain boundary diffusion, a slow transcrystalline fracture appears. To analyse the Dynamic Embrittlement, the crack propagation was tested at 650 C with different frequencies and superimposed hold times in the fatigue cycle at maximum stress. The results shows that the existing model of Dynamic Embrittlement needs to be adapted to the effects of cyclic plastic deformation. In hold times, the oxygen grain boundary diffusion in front of the

  15. 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. .

  16. 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)

  17. Remarkable diversity in the enzymes catalyzing the last step in synthesis of the pimelate moiety of biotin.

    Directory of Open Access Journals (Sweden)

    Madelyn M Shapiro

    Full Text Available Biotin synthesis in Escherichia coli requires the functions of the bioH and bioC genes to synthesize the precursor pimelate moiety by use of a modified fatty acid biosynthesis pathway. However, it was previously noted that bioH has been replaced with bioG or bioK within the biotin synthetic gene clusters of other bacteria. We report that each of four BioG proteins from diverse bacteria and two cyanobacterial BioK proteins functionally replace E. coli BioH in vivo. Moreover, purified BioG proteins have esterase activity against pimeloyl-ACP methyl ester, the physiological substrate of BioH. Two of the BioG proteins block biotin synthesis when highly expressed and these toxic proteins were shown to have more promiscuous substrate specificities than the non-toxic BioG proteins. A postulated BioG-BioC fusion protein was shown to functionally replace both the BioH and BioC functions of E. coli. Although the BioH, BioG and BioK esterases catalyze a common reaction, the proteins are evolutionarily distinct.

  18. Enzyme-catalyzed Michael addition for the synthesis of warfarin and its determination via fluorescence quenching of L-tryptophan

    Science.gov (United States)

    Yuan, Yusheng; Yang, Liu; Liu, Shaopu; Yang, Jidong; Zhang, Hui; Yan, Jingjing; Hu, Xiaoli

    2017-04-01

    A sensitive fluorescence sensor for warfarin was proposed via quenching the fluorescence of L-tryptophan due to the interaction between warfarin and L-tryptophan. Warfarin, as one of the most effective anticoagulants, was designed and synthesized via lipase from porcine pancreas (PPL) as a biocatalyst to catalyze the Michael addition of 4-hydroxycoumarin to α, β-unsaturated enones in organic medium in the presence of water. Furthermore, the spectrofluorometry was used to detect the concentration of warfarin with a linear range and detection limit (3σ/k) of 0.04-12.0 μmol L- 1 (R2 = 0.994) and 0.01 μmol L- 1, respectively. Herein, this was the first application of bio-catalytic synthesis and fluorescence for the determination of warfarin. The proposed method was applied to determine warfarin of the drug in tablets with satisfactory results.

  19. A specific affinity reagent to distinguish aldehyde dehydrogenases and oxidases. Enzymes catalyzing aldehyde oxidation in an adult moth

    International Nuclear Information System (INIS)

    Tasayco, M.L.; Prestwich, G.D.

    1990-01-01

    Aldehyde dehydrogenase (ALDH) and oxidase (AO) enzymes from the tissue extracts of male and female tobacco budworm moth (Heliothis virescens) were identified after electrophoretic protein separation. AO activity was visualized using formazan- or horseradish peroxidase-mediated staining coupled to the AO-catalyzed oxidation of benzaldehyde. A set of six soluble AO enzymes with isoelectric points from pI 4.6 to 5.3 were detected primarily in the antennal extracts. Partially purified antennal AO enzymes also oxidized both (Z)-9-tetradecenal and (Z)-11-hexadecenal, the two major pheromone components of this moth. ALDH activity was detected using a tritium-labeled affinity reagent based on a known irreversible inhibitor of this enzyme. This labeled vinyl ketone, [3H](Z)-1,11-hexadecadien-3-one, was synthesized and used to covalently modify the soluble ALDH enzymes from tissue extracts. Molecular subunits of potential ALDH enzymes were visualized in the fluorescence autoradiograms of sodium dodecyl sulfate-polyacrylamide gel electrophoresis-separated proteins of the antenna, head, and leg tissues. Covalent modification of these protein subunits decreased specifically in the presence of excess pheromone aldehyde or benzaldehyde. Labeled vinyl ketones are thus novel tools for the identification of molecular subunits of ALDH enzymes

  20. 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.

  1. Kinetics of Levoglucosenone Isomerization.

    Science.gov (United States)

    Krishna, Siddarth H; Walker, Theodore W; Dumesic, James A; Huber, George W

    2017-01-10

    We studied the acid-catalyzed isomerization of levoglucosenone (LGO) to 5-hydroxymethylfurfural (HMF) and developed a reaction kinetics model that describes the experimental data across a range of conditions (100-150 °C, 50-100 mm H 2 SO 4 , 50-150 mm LGO). LGO and its hydrated derivative exist in equilibrium under these reaction conditions. Thermal and catalytic degradation of HMF are the major sources of carbon loss. Within the range of conditions studied, higher temperatures and shorter reaction times favor the production of HMF. The yields of HMF and levulinic acid decrease monotonically as tetrahydrofuran is added to the aqueous solvent system, indicating that water plays a role in the LGO isomerization reaction. Initial-rate analyses show that HMF is produced solely from LGO rather than from the hydrated derivative of LGO. The results of this study are consistent with a mechanism for LGO isomerization that proceeds through hydration of the anhydro bridge, followed by ring rearrangement analogous to the isomerization of glucose to fructose. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. 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.)

  3. On the relationships between Michaelis-Menten kinetics, reverse Michaelis-Menten kinetics, Equilibrium Chemistry Approximation kinetics and quadratic kinetics

    Science.gov (United States)

    Tang, J. Y.

    2015-09-01

    The Michaelis-Menten kinetics and the reverse Michaelis-Menten kinetics are two popular mathematical formulations used in many land biogeochemical models to describe how microbes and plants would respond to changes in substrate abundance. However, the criteria of when to use which of the two are often ambiguous. Here I show that these two kinetics are special approximations to the Equilibrium Chemistry Approximation kinetics, which is the first order approximation to the quadratic kinetics that solves the equation of enzyme-substrate complex exactly for a single enzyme single substrate biogeochemical reaction with the law of mass action and the assumption of quasi-steady-state for the enzyme-substrate complex and that the product genesis from enzyme-substrate complex is much slower than the equilibration between enzyme-substrate complexes, substrates and enzymes. In particular, I showed that the derivation of the Michaelis-Menten kinetics does not consider the mass balance constraint of the substrate, and the reverse Michaelis-Menten kinetics does not consider the mass balance constraint of the enzyme, whereas both of these constraints are taken into account in the Equilibrium Chemistry Approximation kinetics. By benchmarking against predictions from the quadratic kinetics for a wide range of substrate and enzyme concentrations, the Michaelis-Menten kinetics was found to persistently under-predict the normalized sensitivity ∂ ln v / ∂ ln k2+ of the reaction velocity v with respect to the maximum product genesis rate k2+, persistently over-predict the normalized sensitivity ∂ ln v / ∂ ln k1+ of v with respect to the intrinsic substrate affinity k1+, persistently over-predict the normalized sensitivity ∂ ln v / ∂ ln [ E ]T of v with respect the total enzyme concentration [ E ]T and persistently under-predict the normalized sensitivity ∂ ln v / ∂ ln [ S ]T of v with respect to the total substrate concentration [ S ]T. Meanwhile, the reverse Michaelis

  4. Kinetic electrons in global electromagnetic gyrokinetic particle simulations

    Science.gov (United States)

    Nishimura, Y.; Wang, W.

    2005-10-01

    Employing an electromagnetic gyrokinetic simulation model,ootnotetextZ. Lin and L. Chen, Phys. Plasmas 8, 1447 (2001). kinetic electron dynamics in global tokamak geometry is investigated. The massless fluid electron model is developed as a base. We further evolve gyrokinetic equations for non-adiabatic kinetic electrons. To obtain the magnetic perturbation, the fluid-kinetic hybrid electron model^1 employs the inverse of the Faraday's law. Instead, the Ampere's law is used as a closure relation to avoid uncertainties in estimating ue|, the moment of the electron velocities. The physics goal is to investigate the finite beta effects on the turbulent transport, as well as α particle driven turbulence.ootnotetextI. Holod, Z. Lin, et al., this conference. This work is supported by Department of Energy (DOE) Cooperative Agreement No. DE-FC02-03ER54695 (UCI), DOE Contract No. DE-AC02-76CH03073 (PPPL).

  5. 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)

  6. 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.

  7. How hydrophobic drying forces impact the kinetics of molecular recognition.

    Science.gov (United States)

    Mondal, Jagannath; Morrone, Joseph A; Berne, B J

    2013-08-13

    A model of protein-ligand binding kinetics, in which slow solvent dynamics results from hydrophobic drying transitions, is investigated. Molecular dynamics simulations show that solvent in the receptor pocket can fluctuate between wet and dry states with lifetimes in each state that are long enough for the extraction of a separable potential of mean force and wet-to-dry transitions. We present a diffusive surface hopping model that is represented by a 2D Markovian master equation. One dimension is the standard reaction coordinate, the ligand-pocket separation, and the other is the solvent state in the region between ligand and binding pocket which specifies whether it is wet or dry. In our model, the ligand diffuses on a dynamic free-energy surface which undergoes kinetic transitions between the wet and dry states. The model yields good agreement with results from explicit solvent molecular dynamics simulation and an improved description of the kinetics of hydrophobic assembly. Furthermore, it is consistent with a "non-Markovian Brownian theory" for the ligand-pocket separation coordinate alone.

  8. Gas Kinetics of Traffic Jam

    Science.gov (United States)

    Nagatani, Takashi

    1997-04-01

    The kinetics of one-dimensional traffic flow is descibed in terms of Boltzmann-like gas kinetic equation. Paveri-Fontana's gas kinetic equation is modified to take into account the desired velocity depending on the car density. A discrete version of the gas kinetic equation is derived to numerically solve the equation. The velocity distributions are calculated by a numerical method. It is found that the traffic jam is formed in the congested traffic flow when the car density is higher than the critical value. The traffic jam propagates backward, its propagation velocity increases with the accerelation and the density within the jam decreases with increasing accerelation. It is shown that the velocity distributions change significantly before and after the traffic jam.

  9. 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

  10. Effective-field theory on the kinetic Ising model

    International Nuclear Information System (INIS)

    Shi Xiaoling; Wei Guozhu; Li Lin

    2008-01-01

    As an analytical method, the effective-field theory (EFT) is used to study the dynamical response of the kinetic Ising model in the presence of a sinusoidal oscillating field. The effective-field equations of motion of the average magnetization are given for the square lattice (Z=4) and the simple cubic lattice (Z=6), respectively. The dynamic order parameter, the hysteresis loop area and the dynamic correlation are calculated. In the field amplitude h 0 /ZJ-temperature T/ZJ plane, the phase boundary separating the dynamic ordered and the disordered phase has been drawn, and the dynamical tricritical point has been observed. We also make the compare results of EFT with that given by using the mean field theory (MFT)

  11. 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

  12. The effect of light and temperature on the dynamic state of Rhodobacter sphaeroides reaction centers proteins determined from changes in tryptophan fluorescence lifetime and P+QA-recombination kinetics.

    Science.gov (United States)

    Knox, Peter P; Gorokhov, Vladimir V; Korvatovskiy, Boris N; Lukashev, Eugene P; Goryachev, Sergey N; Paschenko, Vladimir Z; Rubin, Andrew B

    2018-02-06

    The temperature dependencies of the rate of dark recombination of separated charges between the photoactive bacteriochlorophyll and the primary quinone acceptor (Q A ) in photosynthetic reaction centers (RCs) of the purple bacteria Rhodobacter sphaeroides (Rb. sphaeroides) were investigated. Measurements were performed in water-glycerol and trehalose environments after freezing to -180 °C in the dark and under actinic light with subsequent heating. Simultaneously, the RC tryptophanyl fluorescence lifetime in the spectral range between 323 and 348 nm was measured under these conditions. A correlation was found between the temperature dependencies of the functional and dynamic parameters of RCs in different solvent mixtures. For the first time, differences in the average fluorescence lifetime of tryptophanyl residues were measured between RCs frozen in the dark and in the actinic light. The obtained results can be explained by the RC transitions between different conformational states and the dynamic processes in the structure of the hydrogen bonds of RCs. We assumed that RCs exist in two main microconformations - "fast" and "slow", which are characterized by different rates of P + and Q A - recombination reactions. The "fast" conformation is induced in frozen RCs in the dark, while the "slow" conformation of RC occurs when the RC preparation is frozen under actinic light. An explanation of the temperature dependencies of tryptophan fluorescence lifetimes in RC proteins was made under the assumption that temperature changes affect mainly the electron transfer from the indole ring of the tryptophan molecule to the nearest amide or carboxyl groups. Copyright © 2018. Published by Elsevier B.V.

  13. On the need for and the possibility of a unified description of kinetic and hydrodynamic processes

    International Nuclear Information System (INIS)

    Klimontovich, Yu.L.

    1993-01-01

    The aim of the paper is to demonstrate the possibility of a unified description of kinetic and hydrodynamic processes on the basis of a generalized kinetic equation without the use of perturbation theory with respect to the Knudsen number. The derivation of the generalized kinetic equation is based on a concrete definition of a continuous medium in the kinetic and hydrodynamic description of nonequilibrium processes in a Boltzmann gas and in a fully ionized plasma. The concept of a open-quotes pointclose quotes of a continuous medium is introduced through the definition of corresponding physically infinitesimally small volumes. A definition is given of a Gibbs ensemble to the description of nonequilibrium processes in statistical theory. Boltzmann's H theorem is proven for the generalized kinetic equation. The entropy production is determined by the sum of two positive contributions. The entropy flux also consists of two terms. The presence of the second term makes it possible to give a general definition of a heat flux for arbitrary Knudsen numbers. For small Knudsen numbers and slow processes, it reduces to Fourier's law. The equations of gas dynamics follow from the generalized kinetic equation without the use of perturbation theory with respect to the Knudsen number. The region of applicability of the equations of gas dynamics is discussed. Generalized kinetic equations are obtained for the distribution functions of the states of the electrons and ions of a partly ionized plasma. Kinetic equations for active media and in the theory of Brownian motion are discussed. 29 refs

  14. The Einstein-Vlasov System/Kinetic Theory

    Directory of Open Access Journals (Sweden)

    Håkan Andréasson

    2002-12-01

    Full Text Available 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 nonrelativistic 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. The Vlasov equation describes matter phenomenologically, and it should be stressed that most of the theorems presented in this article are not presently known for other such matter models (i.e., fluid models. 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 good comprehension of kinetic theory in general relativity.

  15. Effect of surfactant on kinetics of thinning of capillary bridges

    Science.gov (United States)

    Nowak, Emilia; Kovalchuk, Nina; Simmons, Mark

    2015-11-01

    Kinetics of thinning of capillary bridges is of great scientific and industrial interest being of vital importance for example in various emulsification and microfluidic processes. It is well known that the rate of bridge thinning is proportional to the interfacial tension. Therefore it is expected that the process should slow down by addition of surfactant. The kinetics of capillary bridges in the presence of surfactant was studied by the dripping of liquid from a capillary tip under conditions of nearly zero flow rate (We personal care products. The viscosity, surfactant activity and adsorption kinetics have been controlled by addition of glycerol and sodium chloride. The study has shown that the kinetics of capillary bridges are determined by dynamic surface tension rather than by its equilibrium value. In particular, the kinetics of the bridge thinning for the 0.1 g L-1 aqueous SLES solution is practically the same as that of pure water despite twice lower equilibrium surface tension. EPSRC Programme Grant, MEMPHIS, EP/K0039761/1.

  16. The Einstein-Vlasov System/Kinetic Theory

    Directory of Open Access Journals (Sweden)

    Andréasson Håkan

    2005-01-01

    Full Text Available 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 nonrelativistic 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. The Vlasov equation describes matter phenomenologically, and it should be stressed that most of the theorems presented in this article are not presently known for other such matter models (i.e. fluid models. 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 good comprehension of kinetic theory in general relativity.

  17. Understanding the kinetic mechanism of RNA single base pair formation.

    Science.gov (United States)

    Xu, Xiaojun; Yu, Tao; Chen, Shi-Jie

    2016-01-05

    RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model.

  18. Plasmadynamics and ionization kinetics of thermionic energy conversion

    Energy Technology Data Exchange (ETDEWEB)

    Lawless, J.L. Jr.; Lam, S.H.

    1982-02-01

    To reduce the plasma arc-drop, thermionic energy conversion is studied with both analytical and numerical tools. Simplifications are made in both the plasmadynamic and ionization-recombination theories. These are applied to a scheme proposed presently using laser irradiation to enhance the ionization kinetics of the thermionic plasma and thereby reduce the arc-drop. It is also predicted that it is possible to generate the required laser light from a thermionic-type cesium plasma. The analysis takes advantage of theoretical simplifications derived for the ionization-recombination kinetics. It is shown that large laser ionization enhancements can occur and that collisional cesium recombination lasing is expected. To complement the kinetic theory, a numerical method is developed to solve the thermionic plasma dynamics. To combine the analysis of ionization-recombination kinetics with the plasma dynamics of thermionic conversion, a finite difference computer program is constructed. It is capable of solving for both unsteady and steady thermionic converter behavior including possible laser ionization enhancement or atomic recombination lasing. A proposal to improve thermionic converter performance using laser radiation is considered. In this proposed scheme, laser radiation impinging on a thermionic plasma enhances the ionization process thereby raising the plasma density and reducing the plasma arc-drop. A source for such radiation may possibly be a cesium recombination laser operating in a different thermionic converter. The possibility of this being an energy efficient process is discussed. (WHK)

  19. Gyrocenter-gauge kinetic theory

    International Nuclear Information System (INIS)

    Qin, H.; Tang, W.M.; Lee, W.W.

    2000-01-01

    Gyrocenter-gauge kinetic theory is developed as an extension of the existing gyrokinetic theories. In essence, the formalism introduced here is a kinetic description of magnetized plasmas in the gyrocenter coordinates which is fully equivalent to the Vlasov-Maxwell system in the particle coordinates. In particular, provided the gyroradius is smaller than the scale-length of the magnetic field, it can treat high frequency range as well as the usual low frequency range normally associated with gyrokinetic approaches. A significant advantage of this formalism is that it enables the direct particle-in-cell simulations of compressional Alfven waves for MHD applications and of RF waves relevant to plasma heating in space and laboratory plasmas. The gyrocenter-gauge kinetic susceptibility for arbitrary wavelength and arbitrary frequency electromagnetic perturbations in a homogeneous magnetized plasma is shown to recover exactly the classical result obtained by integrating the Vlasov-Maxwell system in the particle coordinates. This demonstrates that all the waves supported by the Vlasov-Maxwell system can be studied using the gyrocenter-gauge kinetic model in the gyrocenter coordinates. This theoretical approach is so named to distinguish it from the existing gyrokinetic theory, which has been successfully developed and applied to many important low-frequency and long parallel wavelength problems, where the conventional meaning of gyrokinetic has been standardized. Besides the usual gyrokinetic distribution function, the gyrocenter-gauge kinetic theory emphasizes as well the gyrocenter-gauge distribution function, which sometimes contains all the physics of the problems being studied, and whose importance has not been realized previously. The gyrocenter-gauge distribution function enters Maxwell's equations through the pull-back transformation of the gyrocenter transformation, which depends on the perturbed fields. The efficacy of the gyrocenter-gauge kinetic approach is

  20. Designing Antibacterial Peptides with Enhanced Killing Kinetics

    Directory of Open Access Journals (Sweden)

    Faiza H. Waghu

    2018-02-01

    Full Text Available Antimicrobial peptides (AMPs are gaining attention as substitutes for antibiotics in order to combat the risk posed by multi-drug resistant pathogens. Several research groups are engaged in design of potent anti-infective agents using natural AMPs as templates. In this study, a library of peptides with high sequence similarity to Myeloid Antimicrobial Peptide (MAP family were screened using popular online prediction algorithms. These peptide variants were designed in a manner to retain the conserved residues within the MAP family. The prediction algorithms were found to effectively classify peptides based on their antimicrobial nature. In order to improve the activity of the identified peptides, molecular dynamics (MD simulations, using bilayer and micellar systems could be used to design and predict effect of residue substitution on membranes of microbial and mammalian cells. The inference from MD simulation studies well corroborated with the wet-lab observations indicating that MD-guided rational design could lead to discovery of potent AMPs. The effect of the residue substitution on membrane activity was studied in greater detail using killing kinetic analysis. Killing kinetics studies on Gram-positive, negative and human erythrocytes indicated that a single residue change has a drastic effect on the potency of AMPs. An interesting outcome was a switch from monophasic to biphasic death rate constant of Staphylococcus aureus due to a single residue mutation in the peptide.