Carotene Degradation and Isomerization during Thermal Processing: A Review on the Kinetic Aspects.

PubMed

Colle, Ines J P; Lemmens, Lien; Knockaert, Griet; Van Loey, Ann; Hendrickx, Marc

2016-08-17

Kinetic models are important tools for process design and optimization to balance desired and undesired reactions taking place in complex food systems during food processing and preservation. This review covers the state of the art on kinetic models available to describe heat-induced conversion of carotenoids, in particular lycopene and β-carotene. First, relevant properties of these carotenoids are discussed. Second, some general aspects of kinetic modeling are introduced, including both empirical single-response modeling and mechanism-based multi-response modeling. The merits of multi-response modeling to simultaneously describe carotene degradation and isomerization are demonstrated. The future challenge in this research field lies in the extension of the current multi-response models to better approach the real reaction pathway and in the integration of kinetic models with mass transfer models in case of reaction in multi-phase food systems.

Chemical kinetics as a contract sport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolb, C.E.

1990-01-01

Earlier in this century chemical kinetics was a basic physical chemistry research topic widely pursued in leading academic chemistry departments. Chemical kinetics now appears to be a discipline practiced chiefly for its applications to societal problems. The chemical kinetics activities directed by D.M. Golden at SRI International are strikingly successful in generating data for key applied problems while at the same time advancing our understanding of chemical kinetics as a scientific discipline. In this talk, the author will contrast the chemical kinetics activities in two contract R D laboratories, one on the right side of the U.S. (ARI) and themore » other on the left (SRI). Their approach to common applied problems ranging from stratospheric heterogeneous kinetics to plasma etching systems for semiconductor processing will be compared and contrasted. Empirically discovered Golden Rules for the pursuit of quality chemical kinetics research in a contract R D environment will be presented and discussed.« less

Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method.

PubMed

Jia, Gengjie; Stephanopoulos, Gregory N; Gunawan, Rudiyanto

2011-07-15

Time-series measurements of metabolite concentration have become increasingly more common, providing data for building kinetic models of metabolic networks using ordinary differential equations (ODEs). In practice, however, such time-course data are usually incomplete and noisy, and the estimation of kinetic parameters from these data is challenging. Practical limitations due to data and computational aspects, such as solving stiff ODEs and finding global optimal solution to the estimation problem, give motivations to develop a new estimation procedure that can circumvent some of these constraints. In this work, an incremental and iterative parameter estimation method is proposed that combines and iterates between two estimation phases. One phase involves a decoupling method, in which a subset of model parameters that are associated with measured metabolites, are estimated using the minimization of slope errors. Another phase follows, in which the ODE model is solved one equation at a time and the remaining model parameters are obtained by minimizing concentration errors. The performance of this two-phase method was tested on a generic branched metabolic pathway and the glycolytic pathway of Lactococcus lactis. The results showed that the method is efficient in getting accurate parameter estimates, even when some information is missing.

Thermally induced rarefied gas flow in a three-dimensional enclosure with square cross-section

NASA Astrophysics Data System (ADS)

Zhu, Lianhua; Yang, Xiaofan; Guo, Zhaoli

2017-12-01

Rarefied gas flow in a three-dimensional enclosure induced by nonuniform temperature distribution is numerically investigated. The enclosure has a square channel-like geometry with alternatively heated closed ends and lateral walls with a linear temperature distribution. A recently proposed implicit discrete velocity method with a memory reduction technique is used to numerically simulate the problem based on the nonlinear Shakhov kinetic equation. The Knudsen number dependencies of the vortices pattern, slip velocity at the planar walls and edges, and heat transfer are investigated. The influences of the temperature ratio imposed at the ends of the enclosure and the geometric aspect ratio are also evaluated. The overall flow pattern shows similarities with those observed in two-dimensional configurations in literature. However, features due to the three-dimensionality are observed with vortices that are not identified in previous studies on similar two-dimensional enclosures at high Knudsen and small aspect ratios.

Modified Gompertz equation for electrotherapy murine tumor growth kinetics: predictions and new hypotheses.

PubMed

Cabrales, Luis E Bergues; Nava, Juan J Godina; Aguilera, Andrés Ramírez; Joa, Javier A González; Ciria, Héctor M Camué; González, Maraelys Morales; Salas, Miriam Fariñas; Jarque, Manuel Verdecia; González, Tamara Rubio; Mateus, Miguel A O'Farril; Brooks, Soraida C Acosta; Palencia, Fabiola Suárez; Zamora, Lisset Ortiz; Quevedo, María C Céspedes; Seringe, Sarah Edward; Cuitié, Vladimir Crombet; Cabrales, Idelisa Bergues; González, Gustavo Sierra

2010-10-28

Electrotherapy effectiveness at different doses has been demonstrated in preclinical and clinical studies; however, several aspects that occur in the tumor growth kinetics before and after treatment have not yet been revealed. Mathematical modeling is a useful instrument that can reveal some of these aspects. The aim of this paper is to describe the complete growth kinetics of unperturbed and perturbed tumors through use of the modified Gompertz equation in order to generate useful insight into the mechanisms that underpin this devastating disease. The complete tumor growth kinetics for control and treated groups are obtained by interpolation and extrapolation methods with different time steps, using experimental data of fibrosarcoma Sa-37. In the modified Gompertz equation, a delay time is introduced to describe the tumor's natural history before treatment. Different graphical strategies are used in order to reveal new information in the complete kinetics of this tumor type. The first stage of complete tumor growth kinetics is highly non linear. The model, at this stage, shows different aspects that agree with those reported theoretically and experimentally. Tumor reversibility and the proportionality between regions before and after electrotherapy are demonstrated. In tumors that reach partial remission, two antagonistic post-treatment processes are induced, whereas in complete remission, two unknown antitumor mechanisms are induced. The modified Gompertz equation is likely to lead to insights within cancer research. Such insights hold promise for increasing our understanding of tumors as self-organizing systems and, the possible existence of phase transitions in tumor growth kinetics, which, in turn, may have significant impacts both on cancer research and on clinical practice.

The initial value problem in Lagrangian drift kinetic theory

NASA Astrophysics Data System (ADS)

Burby, J. W.

2016-06-01

> Existing high-order variational drift kinetic theories contain unphysical rapidly varying modes that are not seen at low orders. These unphysical modes, which may be rapidly oscillating, damped or growing, are ushered in by a failure of conventional high-order drift kinetic theory to preserve the structure of its parent model's initial value problem. In short, the (infinite dimensional) system phase space is unphysically enlarged in conventional high-order variational drift kinetic theory. I present an alternative, `renormalized' variational approach to drift kinetic theory that manifestly respects the parent model's initial value problem. The basic philosophy underlying this alternate approach is that high-order drift kinetic theory ought to be derived by truncating the all-orders system phase-space Lagrangian instead of the usual `field particle' Lagrangian. For the sake of clarity, this story is told first through the lens of a finite-dimensional toy model of high-order variational drift kinetics; the analogous full-on drift kinetic story is discussed subsequently. The renormalized drift kinetic system, while variational and just as formally accurate as conventional formulations, does not support the troublesome rapidly varying modes.

MAXIMA IN RATE-CONCENTRATION CURVES AND THEIR RELATION TO THE STRUCTURAL ASPECTS OF CELLULAR METABOLISM

PubMed Central

Spiegelman, S.; Reiner, J. M.

1945-01-01

1. Reproducible maxima are exhibited in the rate-concentration curves obtained by studying the effects of ethyl- and phenylurethanes on regeneration rates of hydranths in Tubularia. 2. The general problem of maxima in rate-concentration curves is analyzed in terms of reaction kinetics of relatively simple systems. 3. Certain systems were shown to exhibit this phenomenon. A comparison is made of these with similar ones which fail to do so. 4. The possible rôle in this phenomenon of cellular structure and its attendant geometrical constraints is discussed in terms of the above comparison. PMID:19873428

Investigation on the efficiency of treated Palm Tree waste for removal of organic pollutants

NASA Astrophysics Data System (ADS)

Azoulay, Karima; El HajjajiI, Souad; Dahchour, Abdelmalek

2017-04-01

Development of the industrial sector generates several problems of environmental pollution. This issue rises concern among scientific community and decision makers, in this work; we e interested in water resources polluted by the chemical substances, which can cause various problems of health. As an example, dyes generated by different industrial activities such as textile, cosmetic, metal plating, leather, paper and plastic sectors, constitute an important source of pollution. In this work, we aim at investigating the efficiency of palm tree waste for removal of dyes from polluted solution. Our work presents a double environmental aspect, on one hand it constitutes an attempt for valorization of Palm Tree waste, and on the other hand it provides natural adsorbent. The study focuses on the effectiveness of the waste in removing Methylene Bleu and Methyl Orange taken as models of pollutants from aqueous solution. Kinetics and isotherm experiments were conducted in order to determine the sorption behavior of the examined dye. The effects of initial dye and adsorbent concentrations are considered. The results indicate that the correlation coefficient calculated from pseudo-second order equation was higher than the other kinetic equations, indicating that equilibrium data fitted well with pseudo-second order model where adsorption process was chemisorption. The adsorption equilibrium was well described by Langmuir isotherm model.

Modified Gompertz equation for electrotherapy murine tumor growth kinetics: predictions and new hypotheses

PubMed Central

2010-01-01

Background Electrotherapy effectiveness at different doses has been demonstrated in preclinical and clinical studies; however, several aspects that occur in the tumor growth kinetics before and after treatment have not yet been revealed. Mathematical modeling is a useful instrument that can reveal some of these aspects. The aim of this paper is to describe the complete growth kinetics of unperturbed and perturbed tumors through use of the modified Gompertz equation in order to generate useful insight into the mechanisms that underpin this devastating disease. Methods The complete tumor growth kinetics for control and treated groups are obtained by interpolation and extrapolation methods with different time steps, using experimental data of fibrosarcoma Sa-37. In the modified Gompertz equation, a delay time is introduced to describe the tumor's natural history before treatment. Different graphical strategies are used in order to reveal new information in the complete kinetics of this tumor type. Results The first stage of complete tumor growth kinetics is highly non linear. The model, at this stage, shows different aspects that agree with those reported theoretically and experimentally. Tumor reversibility and the proportionality between regions before and after electrotherapy are demonstrated. In tumors that reach partial remission, two antagonistic post-treatment processes are induced, whereas in complete remission, two unknown antitumor mechanisms are induced. Conclusion The modified Gompertz equation is likely to lead to insights within cancer research. Such insights hold promise for increasing our understanding of tumors as self-organizing systems and, the possible existence of phase transitions in tumor growth kinetics, which, in turn, may have significant impacts both on cancer research and on clinical practice. PMID:21029411

LSENS: A General Chemical Kinetics and Sensitivity Analysis Code for homogeneous gas-phase reactions. Part 3: Illustrative test problems

NASA Technical Reports Server (NTRS)

Bittker, David A.; Radhakrishnan, Krishnan

1994-01-01

LSENS, the Lewis General Chemical Kinetics and Sensitivity Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 3 of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part 3 explains the kinetics and kinetics-plus-sensitivity analysis problems supplied with LSENS and presents sample results. These problems illustrate the various capabilities of, and reaction models that can be solved by, the code and may provide a convenient starting point for the user to construct the problem data file required to execute LSENS. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions.

Application of separable parameter space techniques to multi-tracer PET compartment modeling.

PubMed

Zhang, Jeff L; Michael Morey, A; Kadrmas, Dan J

2016-02-07

Multi-tracer positron emission tomography (PET) can image two or more tracers in a single scan, characterizing multiple aspects of biological functions to provide new insights into many diseases. The technique uses dynamic imaging, resulting in time-activity curves that contain contributions from each tracer present. The process of separating and recovering separate images and/or imaging measures for each tracer requires the application of kinetic constraints, which are most commonly applied by fitting parallel compartment models for all tracers. Such multi-tracer compartment modeling presents challenging nonlinear fits in multiple dimensions. This work extends separable parameter space kinetic modeling techniques, previously developed for fitting single-tracer compartment models, to fitting multi-tracer compartment models. The multi-tracer compartment model solution equations were reformulated to maximally separate the linear and nonlinear aspects of the fitting problem, and separable least-squares techniques were applied to effectively reduce the dimensionality of the nonlinear fit. The benefits of the approach are then explored through a number of illustrative examples, including characterization of separable parameter space multi-tracer objective functions and demonstration of exhaustive search fits which guarantee the true global minimum to within arbitrary search precision. Iterative gradient-descent algorithms using Levenberg-Marquardt were also tested, demonstrating improved fitting speed and robustness as compared to corresponding fits using conventional model formulations. The proposed technique overcomes many of the challenges in fitting simultaneous multi-tracer PET compartment models.

Application of separable parameter space techniques to multi-tracer PET compartment modeling

NASA Astrophysics Data System (ADS)

Zhang, Jeff L.; Morey, A. Michael; Kadrmas, Dan J.

2016-02-01

Multi-tracer positron emission tomography (PET) can image two or more tracers in a single scan, characterizing multiple aspects of biological functions to provide new insights into many diseases. The technique uses dynamic imaging, resulting in time-activity curves that contain contributions from each tracer present. The process of separating and recovering separate images and/or imaging measures for each tracer requires the application of kinetic constraints, which are most commonly applied by fitting parallel compartment models for all tracers. Such multi-tracer compartment modeling presents challenging nonlinear fits in multiple dimensions. This work extends separable parameter space kinetic modeling techniques, previously developed for fitting single-tracer compartment models, to fitting multi-tracer compartment models. The multi-tracer compartment model solution equations were reformulated to maximally separate the linear and nonlinear aspects of the fitting problem, and separable least-squares techniques were applied to effectively reduce the dimensionality of the nonlinear fit. The benefits of the approach are then explored through a number of illustrative examples, including characterization of separable parameter space multi-tracer objective functions and demonstration of exhaustive search fits which guarantee the true global minimum to within arbitrary search precision. Iterative gradient-descent algorithms using Levenberg-Marquardt were also tested, demonstrating improved fitting speed and robustness as compared to corresponding fits using conventional model formulations. The proposed technique overcomes many of the challenges in fitting simultaneous multi-tracer PET compartment models.

Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

NASA Astrophysics Data System (ADS)

Finkelstein, A. V.

1 Introduction 2 Overview of protein architectures and discussion of physical background of their natural selection 2.1 Protein structures 2.2 Physical selection of protein structures 3 Thermodynamic aspects of protein folding 3.1 Reversible denaturation of protein structures 3.2 What do denatured proteins look like? 3.3 Why denaturation of a globular protein is the first-order phase transition 3.4 "Gap" in energy spectrum: The main characteristic that distinguishes protein chains from random polymers 4 Kinetic aspects of protein folding 4.1 Protein folding in vivo 4.2 Protein folding in vitro (in the test-tube) 4.3 Theory of protein folding rates and solution of the Levinthal paradox

Kinetic: A system code for analyzing nuclear thermal propulsion rocket engine transients

NASA Astrophysics Data System (ADS)

Schmidt, Eldon; Lazareth, Otto; Ludewig, Hans

The topics are presented in viewgraph form and include the following: outline of kinetic code; a kinetic information flow diagram; kinetic neutronic equations; turbopump/nozzle algorithm; kinetic heat transfer equations per node; and test problem diagram.

Kinetic energy density and agglomerate abrasion rate during blending of agglomerates into powders.

PubMed

Willemsz, Tofan A; Hooijmaijers, Ricardo; Rubingh, Carina M; Tran, Thanh N; Frijlink, Henderik W; Vromans, Herman; van der Voort Maarschalk, Kees

2012-01-23

Problems related to the blending of a cohesive powder with a free flowing bulk powder are frequently encountered in the pharmaceutical industry. The cohesive powder often forms lumps or agglomerates which are not dispersed during the mixing process and are therefore detrimental to blend uniformity. Achieving sufficient blend uniformity requires that the blending conditions are able to break up agglomerates, which is often an abrasion process. This study was based on the assumption that the abrasion rate of agglomerates determines the required blending time. It is shown that the kinetic energy density of the moving powder bed is a relevant parameter which correlates with the abrasion rate of agglomerates. However, aspects related to the strength of agglomerates should also be considered. For this reason the Stokes abrasion number (St(Abr)) has been defined. This parameter describes the ratio between the kinetic energy density of the moving powder bed and the work of fracture of the agglomerate. The St(Abr) number is shown to predict the abrasion potential of agglomerates in the dry-mixing process. It appeared possible to include effects of filler particle size and impeller rotational rate into this concept. A clear relationship between abrasion rate of agglomerates and the value of St(Abr) was demonstrated. Copyright © 2011 Elsevier B.V. All rights reserved.

LSENS, a general chemical kinetics and sensitivity analysis code for homogeneous gas-phase reactions. 2: Code description and usage

NASA Technical Reports Server (NTRS)

Radhakrishnan, Krishnan; Bittker, David A.

1994-01-01

LSENS, the Lewis General Chemical Kinetics Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 2 of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part 2 describes the code, how to modify it, and its usage, including preparation of the problem data file required to execute LSENS. Code usage is illustrated by several example problems, which further explain preparation of the problem data file and show how to obtain desired accuracy in the computed results. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions. Part 1 (NASA RP-1328) derives the governing equations describes the numerical solution procedures for the types of problems that can be solved by lSENS. Part 3 (NASA RP-1330) explains the kinetics and kinetics-plus-sensitivity-analysis problems supplied with LSENS and presents sample results.

Hydrolysis of Surfactants Containing Ester Bonds: Modulation of Reaction Kinetics and Important Aspects of Surfactant Self-Assembly

ERIC Educational Resources Information Center

Lundberg, Dan; Stjerndahl, Maria

2011-01-01

The effects of self-assembly on the hydrolysis kinetics of surfactants that contain ester bonds are discussed. A number of examples on how reaction rates and apparent reaction orders can be modulated by changes in the conditions, including an instance of apparent zero-order kinetics, are presented. Furthermore, it is shown that the examples on…

A systematic petri net approach for multiple-scale modeling and simulation of biochemical processes.

PubMed

Chen, Ming; Hu, Minjie; Hofestädt, Ralf

2011-06-01

A method to exploit hybrid Petri nets for modeling and simulating biochemical processes in a systematic way was introduced. Both molecular biology and biochemical engineering aspects are manipulated. With discrete and continuous elements, the hybrid Petri nets can easily handle biochemical factors such as metabolites concentration and kinetic behaviors. It is possible to translate both molecular biological behavior and biochemical processes workflow into hybrid Petri nets in a natural manner. As an example, penicillin production bioprocess is modeled to illustrate the concepts of the methodology. Results of the dynamic of production parameters in the bioprocess were simulated and observed diagrammatically. Current problems and post-genomic perspectives were also discussed.

A prospectus on kinetic heliophysics

NASA Astrophysics Data System (ADS)

Howes, Gregory G.

2017-05-01

Under the low density and high temperature conditions typical of heliospheric plasmas, the macroscopic evolution of the heliosphere is strongly affected by the kinetic plasma physics governing fundamental microphysical mechanisms. Kinetic turbulence, collisionless magnetic reconnection, particle acceleration, and kinetic instabilities are four poorly understood, grand-challenge problems that lie at the new frontier of kinetic heliophysics. The increasing availability of high cadence and high phase-space resolution measurements of particle velocity distributions by current and upcoming spacecraft missions and of massively parallel nonlinear kinetic simulations of weakly collisional heliospheric plasmas provides the opportunity to transform our understanding of these kinetic mechanisms through the full utilization of the information contained in the particle velocity distributions. Several major considerations for future investigations of kinetic heliophysics are examined. Turbulent dissipation followed by particle heating is highlighted as an inherently two-step process in weakly collisional plasmas, distinct from the more familiar case in fluid theory. Concerted efforts must be made to tackle the big-data challenge of visualizing the high-dimensional (3D-3V) phase space of kinetic plasma theory through physics-based reductions. Furthermore, the development of innovative analysis methods that utilize full velocity-space measurements, such as the field-particle correlation technique, will enable us to gain deeper insight into these four grand-challenge problems of kinetic heliophysics. A systems approach to tackle the multi-scale problem of heliophysics through a rigorous connection between the kinetic physics at microscales and the self-consistent evolution of the heliosphere at macroscales will propel the field of kinetic heliophysics into the future.

A prospectus on kinetic heliophysics

PubMed Central

2017-01-01

Under the low density and high temperature conditions typical of heliospheric plasmas, the macroscopic evolution of the heliosphere is strongly affected by the kinetic plasma physics governing fundamental microphysical mechanisms. Kinetic turbulence, collisionless magnetic reconnection, particle acceleration, and kinetic instabilities are four poorly understood, grand-challenge problems that lie at the new frontier of kinetic heliophysics. The increasing availability of high cadence and high phase-space resolution measurements of particle velocity distributions by current and upcoming spacecraft missions and of massively parallel nonlinear kinetic simulations of weakly collisional heliospheric plasmas provides the opportunity to transform our understanding of these kinetic mechanisms through the full utilization of the information contained in the particle velocity distributions. Several major considerations for future investigations of kinetic heliophysics are examined. Turbulent dissipation followed by particle heating is highlighted as an inherently two-step process in weakly collisional plasmas, distinct from the more familiar case in fluid theory. Concerted efforts must be made to tackle the big-data challenge of visualizing the high-dimensional (3D-3V) phase space of kinetic plasma theory through physics-based reductions. Furthermore, the development of innovative analysis methods that utilize full velocity-space measurements, such as the field-particle correlation technique, will enable us to gain deeper insight into these four grand-challenge problems of kinetic heliophysics. A systems approach to tackle the multi-scale problem of heliophysics through a rigorous connection between the kinetic physics at microscales and the self-consistent evolution of the heliosphere at macroscales will propel the field of kinetic heliophysics into the future. PMID:29104421

Variations in protein/flavin hydrogen bonding in a LOV domain produce non-Arrhenius kinetics of adduct decay†

PubMed Central

Zoltowski, Brian D.; Nash, Abigail I.; Gardner, Kevin H.

2011-01-01

Light Oxygen Voltage (LOV) domains utilize a conserved blue light-dependent mechanism to control a diverse array of effector domains in biological and engineered proteins. Variations in the kinetics and efficiency of LOV photochemistry fine tune various aspects of the photic response. Characterization of the kinetics of a key aspect of this photochemical mechanism in EL222, a blue-light responsive DNA binding protein from Erythrobacter litoralis HTCC2594, reveals unique non-Arrhenius behavior in the rate of dark state cleavage of the photochemically-generated adduct. Sequence analysis and mutagenesis studies establish that this effect stems from a Gln to Ala mutation unique to EL222 and homologous proteins from marine bacteria. Kinetic and spectroscopic analyses reveal that hydrogen bonding interactions between the FMN N1, O2 and ribityl hydroxyls with the surrounding protein regulate photocycle kinetics and stabilize the LOV active site from temperature-induced alteration in local structure. Substitution of residues interacting with the N1-O2 locus modulates adduct stability, structural flexibility and sequestration of the active site from bulk solvent without perturbation of light-activated DNA binding. Together, these variants link non-Arrhenius behavior to specific alteration of an H-bonding network, while affording tunability of photocycle kinetics. PMID:21923139

Variations in protein-flavin hydrogen bonding in a light, oxygen, voltage domain produce non-Arrhenius kinetics of adduct decay.

PubMed

Zoltowski, Brian D; Nash, Abigail I; Gardner, Kevin H

2011-10-18

Light, oxygen, voltage (LOV) domains utilize a conserved blue light-dependent mechanism to control a diverse array of effector domains in biological and engineered proteins. Variations in the kinetics and efficiency of LOV photochemistry fine-tune various aspects of the photic response. Characterization of the kinetics of a key aspect of this photochemical mechanism in EL222, a blue light responsive DNA binding protein from Erythrobacter litoralis HTCC2594, reveals unique non-Arrhenius behavior in the rate of dark-state cleavage of the photochemically generated adduct. Sequence analysis and mutagenesis studies establish that this effect stems from a Gln to Ala mutation unique to EL222 and homologous proteins from marine bacteria. Kinetic and spectroscopic analyses reveal that hydrogen bonding interactions between the FMN N1, O2, and ribityl hydroxyls and the surrounding protein regulate photocycle kinetics and stabilize the LOV active site from temperature-induced alteration in local structure. Substitution of residues interacting with the N1-O2 locus modulates adduct stability, structural flexibility, and sequestration of the active site from bulk solvent without perturbation of light-activated DNA binding. Together, these variants link non-Arrhenius behavior to specific alteration of an H-bonding network, while affording tunability of photocycle kinetics. © 2011 American Chemical Society

Exploring the kinetic and thermodynamic aspects of four-electron electrochemical reactions: electrocatalysis of oxygen evolution by metal oxides and biological systems.

PubMed

Wang, Vincent C-C

2016-08-10

Finding fundamental and general mechanisms for electrochemical reactions, such as the oxygen evolution reaction (OER) from water and reduction of CO2, plays vital roles in developing the desired electrocatalysts for facilitating solar fuel production. Recently, density functional theory (DFT) calculations have shown that there is a universal scaling relation of adsorption energy between key intermediate species, HO(ad) and HOO(ad), on the surface of metal oxides as OER electrocatalysts. In this paper, a kinetic and thermodynamic model for the four-electron electrochemical reaction based on previous OER mechanisms proposed by DFT calculations is developed to further investigate the electrocatalytic properties over a wide range of metal oxides and photosystem II. The OER activity of metal oxides (i.e. electrocatalytic current) calculated from the DFT-calculated equilibrium potentials with kinetic properties, such as the rate constants for interfacial electron transfer and catalytic turnover, can lead to a volcano-shaped trend that agrees with the results observed in experiments. In addition, the kinetic aspects of the impact on the electrocatalysts are evaluated. Finally, comparing the results of metal oxides and photosystem II, and fitting experimental voltammograms give further insights into kinetic and thermodynamic roles. Here, the general guidelines for designing OER electrocatalysts with unified kinetic and thermodynamic properties are presented.

LSENS, A General Chemical Kinetics and Sensitivity Analysis Code for Homogeneous Gas-Phase Reactions. Part 2; Code Description and Usage

NASA Technical Reports Server (NTRS)

Radhakrishnan, Krishnan; Bittker, David A.

1994-01-01

LSENS, the Lewis General Chemical Kinetics and Sensitivity Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part II of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part II describes the code, how to modify it, and its usage, including preparation of the problem data file required to execute LSENS. Code usage is illustrated by several example problems, which further explain preparation of the problem data file and show how to obtain desired accuracy in the computed results. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions. Part I (NASA RP-1328) derives the governing equations and describes the numerical solution procedures for the types of problems that can be solved by LSENS. Part III (NASA RP-1330) explains the kinetics and kinetics-plus-sensitivity-analysis problems supplied with LSENS and presents sample results.

Application of separable parameter space techniques to multi-tracer PET compartment modeling

PubMed Central

Zhang, Jeff L; Morey, A Michael; Kadrmas, Dan J

2016-01-01

Multi-tracer positron emission tomography (PET) can image two or more tracers in a single scan, characterizing multiple aspects of biological functions to provide new insights into many diseases. The technique uses dynamic imaging, resulting in time-activity curves that contain contributions from each tracer present. The process of separating and recovering separate images and/or imaging measures for each tracer requires the application of kinetic constraints, which are most commonly applied by fitting parallel compartment models for all tracers. Such multi-tracer compartment modeling presents challenging nonlinear fits in multiple dimensions. This work extends separable parameter space kinetic modeling techniques, previously developed for fitting single-tracer compartment models, to fitting multi-tracer compartment models. The multi-tracer compartment model solution equations were reformulated to maximally separate the linear and nonlinear aspects of the fitting problem, and separable least-squares techniques were applied to effectively reduce the dimensionality of the nonlinear fit. The benefits of the approach are then explored through a number of illustrative examples, including characterization of separable parameter space multi-tracer objective functions and demonstration of exhaustive search fits which guarantee the true global minimum to within arbitrary search precision. Iterative gradient-descent algorithms using Levenberg–Marquardt were also tested, demonstrating improved fitting speed and robustness as compared to corresponding fits using conventional model formulations. The proposed technique overcomes many of the challenges in fitting simultaneous multi-tracer PET compartment models. PMID:26788888

Toward multiscale modelings of grain-fluid systems

NASA Astrophysics Data System (ADS)

Chareyre, Bruno; Yuan, Chao; Montella, Eduard P.; Salager, Simon

2017-06-01

Computationally efficient methods have been developed for simulating partially saturated granular materials in the pendular regime. In contrast, one hardly avoid expensive direct resolutions of 2-phase fluid dynamics problem for mixed pendular-funicular situations or even saturated regimes. Following previous developments for single-phase flow, a pore-network approach of the coupling problems is described. The geometry and movements of phases and interfaces are described on the basis of a tetrahedrization of the pore space, introducing elementary objects such as bridge, meniscus, pore body and pore throat, together with local rules of evolution. As firmly established local rules are still missing on some aspects (entry capillary pressure and pore-scale pressure-saturation relations, forces on the grains, or kinetics of transfers in mixed situations) a multi-scale numerical framework is introduced, enhancing the pore-network approach with the help of direct simulations. Small subsets of a granular system are extracted, in which multiphase scenario are solved using the Lattice-Boltzman method (LBM). In turns, a global problem is assembled and solved at the network scale, as illustrated by a simulated primary drainage.

Combined Homogeneous Surface Diffusion Model - Design of experiments approach to optimize dye adsorption considering both equilibrium and kinetic aspects.

PubMed

Muthukkumaran, A; Aravamudan, K

2017-12-15

Adsorption, a popular technique for removing azo dyes from aqueous streams, is influenced by several factors such as pH, initial dye concentration, temperature and adsorbent dosage. Any strategy that seeks to identify optimal conditions involving these factors, should take into account both kinetic and equilibrium aspects since they influence rate and extent of removal by adsorption. Hence rigorous kinetics and accurate equilibrium models are required. In this work, the experimental investigations pertaining to adsorption of acid orange 10 dye (AO10) on activated carbon were carried out using Central Composite Design (CCD) strategy. The significant factors that affected adsorption were identified to be solution temperature, solution pH, adsorbent dosage and initial solution concentration. Thermodynamic analysis showed the endothermic nature of the dye adsorption process. The kinetics of adsorption has been rigorously modeled using the Homogeneous Surface Diffusion Model (HSDM) after incorporating the non-linear Freundlich adsorption isotherm. Optimization was performed for kinetic parameters (color removal time and surface diffusion coefficient) as well as the equilibrium affected response viz. percentage removal. Finally, the optimum conditions predicted were experimentally validated. Copyright © 2017 Elsevier Ltd. All rights reserved.

Program Helps To Determine Chemical-Reaction Mechanisms

NASA Technical Reports Server (NTRS)

Bittker, D. A.; Radhakrishnan, K.

1995-01-01

General Chemical Kinetics and Sensitivity Analysis (LSENS) computer code developed for use in solving complex, homogeneous, gas-phase, chemical-kinetics problems. Provides for efficient and accurate chemical-kinetics computations and provides for sensitivity analysis for variety of problems, including problems involving honisothermal conditions. Incorporates mathematical models for static system, steady one-dimensional inviscid flow, reaction behind incident shock wave (with boundary-layer correction), and perfectly stirred reactor. Computations of equilibrium properties performed for following assigned states: enthalpy and pressure, temperature and pressure, internal energy and volume, and temperature and volume. Written in FORTRAN 77 with exception of NAMELIST extensions used for input.

Alternative kinetic energy metrics for Lagrangian systems

NASA Astrophysics Data System (ADS)

Sarlet, W.; Prince, G.

2010-11-01

We examine Lagrangian systems on \\ {R}^n with standard kinetic energy terms for the possibility of additional, alternative Lagrangians with kinetic energy metrics different to the Euclidean one. Using the techniques of the inverse problem in the calculus of variations we find necessary and sufficient conditions for the existence of such Lagrangians. We illustrate the problem in two and three dimensions with quadratic and cubic potentials. As an aside we show that the well-known anomalous Lagrangians for the Coulomb problem can be removed by switching on a magnetic field, providing an appealing resolution of the ambiguous quantizations of the hydrogen atom.

Accelerated Simulation of Kinetic Transport Using Variational Principles and Sparsity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caflisch, Russel

This project is centered on the development and application of techniques of sparsity and compressed sensing for variational principles, PDEs and physics problems, in particular for kinetic transport. This included derivation of sparse modes for elliptic and parabolic problems coming from variational principles. The research results of this project are on methods for sparsity in differential equations and their applications and on application of sparsity ideas to kinetic transport of plasmas.

Advances in electron kinetics and theory of gas discharges

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolobov, Vladimir I.; The University of Alabama in Huntsville, Huntsville, Alabama 35899

2013-10-15

“Electrons, like people, are fertile and infertile: high-energy electrons are fertile and able to reproduce.”—Lev TsendinModern physics of gas discharges increasingly uses physical kinetics for analysis of non-equilibrium plasmas. The description of underlying physics at the kinetic level appears to be important for plasma applications in modern technologies. In this paper, we attempt to grasp the legacy of Professor Lev Tsendin, who advocated the use of the kinetic approach for understanding fundamental problems of gas discharges. We outline the fundamentals of electron kinetics in low-temperature plasmas, describe elements of the modern kinetic theory of gas discharges, and show examples ofmore » the theoretical approach to gas discharge problems used by Lev Tsendin. Important connections between electron kinetics in gas discharges and semiconductors are also discussed. Using several examples, we illustrate how Tsendin's ideas and methods are currently being developed for the implementation of next generation computational tools for adaptive kinetic-fluid simulations of gas discharges used in modern technologies.« less

A resource facility for kinetic analysis: modeling using the SAAM computer programs.

PubMed

Foster, D M; Boston, R C; Jacquez, J A; Zech, L

1989-01-01

Kinetic analysis and integrated system modeling have contributed significantly to understanding the physiology and pathophysiology of metabolic systems in humans and animals. Many experimental biologists are aware of the usefulness of these techniques and recognize that kinetic modeling requires special expertise. The Resource Facility for Kinetic Analysis (RFKA) provides this expertise through: (1) development and application of modeling technology for biomedical problems, and (2) development of computer-based kinetic modeling methodologies concentrating on the computer program Simulation, Analysis, and Modeling (SAAM) and its conversational version, CONversational SAAM (CONSAM). The RFKA offers consultation to the biomedical community in the use of modeling to analyze kinetic data and trains individuals in using this technology for biomedical research. Early versions of SAAM were widely applied in solving dosimetry problems; many users, however, are not familiar with recent improvements to the software. The purpose of this paper is to acquaint biomedical researchers in the dosimetry field with RFKA, which, together with the joint National Cancer Institute-National Heart, Lung and Blood Institute project, is overseeing SAAM development and applications. In addition, RFKA provides many service activities to the SAAM user community that are relevant to solving dosimetry problems.

Modeling generic aspects of ideal fibril formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michel, D., E-mail: denis.michel@live.fr

Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalities of fibril formation are very disparate, with various intermediate forms which can be reshuffled by minor modifications of physico-chemical conditions or amino-acid sequences. To bypass this complexity, the multifaceted phenomenon of fibril formation is reduced here to its most elementary principles defined for a linear prototype of fibril. Selected generic features, including nucleation, elongation, and conformational recruitment, are modeled using minimalist hypotheses and tools, by separating equilibrium from kinetic aspects and in vitro from in vivo conditions.more » These reductionist approaches allow to bring out known and new rudiments, including the kinetic and equilibrium effects of nucleation, the dual influence of elongation on nucleation, the kinetic limitations on nucleation and fibril numbers, and the accumulation of complexes in vivo by rescue from degradation. Overlooked aspects of these processes are also pointed: the exponential distribution of fibril lengths can be recovered using various models because it is attributable to randomness only. It is also suggested that the same term “critical concentration” is used for different things, involved in either nucleation or elongation.« less

Modeling generic aspects of ideal fibril formation

NASA Astrophysics Data System (ADS)

Michel, D.

2016-01-01

Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalities of fibril formation are very disparate, with various intermediate forms which can be reshuffled by minor modifications of physico-chemical conditions or amino-acid sequences. To bypass this complexity, the multifaceted phenomenon of fibril formation is reduced here to its most elementary principles defined for a linear prototype of fibril. Selected generic features, including nucleation, elongation, and conformational recruitment, are modeled using minimalist hypotheses and tools, by separating equilibrium from kinetic aspects and in vitro from in vivo conditions. These reductionist approaches allow to bring out known and new rudiments, including the kinetic and equilibrium effects of nucleation, the dual influence of elongation on nucleation, the kinetic limitations on nucleation and fibril numbers, and the accumulation of complexes in vivo by rescue from degradation. Overlooked aspects of these processes are also pointed: the exponential distribution of fibril lengths can be recovered using various models because it is attributable to randomness only. It is also suggested that the same term "critical concentration" is used for different things, involved in either nucleation or elongation.

Experiments in Thermodynamics and Kinetics of Phosphine Substitution in (p-Cymene)RuCl[subscript 2](PR[subscript 3])

ERIC Educational Resources Information Center

Ozerov, Oleg V.; Fafard, Claudia M.; Hoffman, Norris W.

2007-01-01

This manuscript describes a set of three experiments that investigates the thermodynamic and kinetic aspects of phosphine substitution at a Ru center. In the first experiment, the students synthesize a Ru organometallic complex containing a phosphine ligand. In the second, equilibria for phosphine substitution involving several different…

New theoretical framework for designing nonionic surfactant mixtures that exhibit a desired adsorption kinetics behavior.

PubMed

Moorkanikkara, Srinivas Nageswaran; Blankschtein, Daniel

2010-12-21

How does one design a surfactant mixture using a set of available surfactants such that it exhibits a desired adsorption kinetics behavior? The traditional approach used to address this design problem involves conducting trial-and-error experiments with specific surfactant mixtures. This approach is typically time-consuming and resource-intensive and becomes increasingly challenging when the number of surfactants that can be mixed increases. In this article, we propose a new theoretical framework to identify a surfactant mixture that most closely meets a desired adsorption kinetics behavior. Specifically, the new theoretical framework involves (a) formulating the surfactant mixture design problem as an optimization problem using an adsorption kinetics model and (b) solving the optimization problem using a commercial optimization package. The proposed framework aims to identify the surfactant mixture that most closely satisfies the desired adsorption kinetics behavior subject to the predictive capabilities of the chosen adsorption kinetics model. Experiments can then be conducted at the identified surfactant mixture condition to validate the predictions. We demonstrate the reliability and effectiveness of the proposed theoretical framework through a realistic case study by identifying a nonionic surfactant mixture consisting of up to four alkyl poly(ethylene oxide) surfactants (C(10)E(4), C(12)E(5), C(12)E(6), and C(10)E(8)) such that it most closely exhibits a desired dynamic surface tension (DST) profile. Specifically, we use the Mulqueen-Stebe-Blankschtein (MSB) adsorption kinetics model (Mulqueen, M.; Stebe, K. J.; Blankschtein, D. Langmuir 2001, 17, 5196-5207) to formulate the optimization problem as well as the SNOPT commercial optimization solver to identify a surfactant mixture consisting of these four surfactants that most closely exhibits the desired DST profile. Finally, we compare the experimental DST profile measured at the surfactant mixture condition identified by the new theoretical framework with the desired DST profile and find good agreement between the two profiles.

Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways.

PubMed

Alves, Rui; Vilaprinyo, Ester; Hernádez-Bermejo, Benito; Sorribas, Albert

2008-01-01

There is a renewed interest in obtaining a systemic understanding of metabolism, gene expression and signal transduction processes, driven by the recent research focus on Systems Biology. From a biotechnological point of view, such a systemic understanding of how a biological system is designed to work can facilitate the rational manipulation of specific pathways in different cell types to achieve specific goals. Due to the intrinsic complexity of biological systems, mathematical models are a central tool for understanding and predicting the integrative behavior of those systems. Particularly, models are essential for a rational development of biotechnological applications and in understanding system's design from an evolutionary point of view. Mathematical models can be obtained using many different strategies. In each case, their utility will depend upon the properties of the mathematical representation and on the possibility of obtaining meaningful parameters from available data. In practice, there are several issues at stake when one has to decide which mathematical model is more appropriate for the study of a given problem. First, one needs a model that can represent the aspects of the system one wishes to study. Second, one must choose a mathematical representation that allows an accurate analysis of the system with respect to different aspects of interest (for example, robustness of the system, dynamical behavior, optimization of the system with respect to some production goal, parameter value determination, etc). Third, before choosing between alternative and equally appropriate mathematical representations for the system, one should compare representations with respect to easiness of automation for model set-up, simulation, and analysis of results. Fourth, one should also consider how to facilitate model transference and re-usability by other researchers and for distinct purposes. Finally, one factor that is important for all four aspects is the regularity in the mathematical structure of the equations because it facilitates computational manipulation. This regularity is a mark of kinetic representations based on approximation theory. The use of approximation theory to derive mathematical representations with regular structure for modeling purposes has a long tradition in science. In most applied fields, such as engineering and physics, those approximations are often required to obtain practical solutions to complex problems. In this paper we review some of the more popular mathematical representations that have been derived using approximation theory and are used for modeling in molecular systems biology. We will focus on formalisms that are theoretically supported by the Taylor Theorem. These include the Power-law formalism, the recently proposed (log)linear and Lin-log formalisms as well as some closely related alternatives. We will analyze the similarities and differences between these formalisms, discuss the advantages and limitations of each representation, and provide a tentative "road map" for their potential utilization for different problems.

Kinetic Modeling of Next-Generation High-Energy, High-Intensity Laser-Ion Accelerators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Albright, Brian James; Yin, Lin; Stark, David James

One of the long-standing problems in the community is the question of how we can model “next-generation” laser-ion acceleration in a computationally tractable way. A new particle tracking capability in the LANL VPIC kinetic plasma modeling code has enabled us to solve this long-standing problem

Aspects of manual wheelchair configuration affecting mobility: a review.

PubMed

Medola, Fausto Orsi; Elui, Valeria Meirelles Carril; Santana, Carla da Silva; Fortulan, Carlos Alberto

2014-02-01

Many aspects relating to equipment configuration affect users' actions in a manual wheelchair, determining the overall mobility performance. Since the equipment components and configuration determine both stability and mobility efficiency, configuring the wheelchair with the most appropriate set-up for individual users' needs is a difficult task. Several studies have shown the importance of seat/backrest assembly and the relative position of the rear wheels to the user in terms of the kinetics and kinematics of manual propulsion. More recently, new studies have brought to light evidence on the inertial properties of different wheelchair configurations. Further new studies have highlighted the handrim as a key component of wheelchair assembly, since it is the interface through which the user drives the chair. In light of the new evidence on wheelchair mechanics and propulsion kinetics and kinematics, this article presents a review of the most important aspects of wheelchair configuration that affect the users' actions and mobility.

Aspects of Manual Wheelchair Configuration Affecting Mobility: A Review

PubMed Central

Medola, Fausto Orsi; Elui, Valeria Meirelles Carril; Santana, Carla da Silva; Fortulan, Carlos Alberto

2014-01-01

Many aspects relating to equipment configuration affect users’ actions in a manual wheelchair, determining the overall mobility performance. Since the equipment components and configuration determine both stability and mobility efficiency, configuring the wheelchair with the most appropriate set-up for individual users’ needs is a difficult task. Several studies have shown the importance of seat/backrest assembly and the relative position of the rear wheels to the user in terms of the kinetics and kinematics of manual propulsion. More recently, new studies have brought to light evidence on the inertial properties of different wheelchair configurations. Further new studies have highlighted the handrim as a key component of wheelchair assembly, since it is the interface through which the user drives the chair. In light of the new evidence on wheelchair mechanics and propulsion kinetics and kinematics, this article presents a review of the most important aspects of wheelchair configuration that affect the users’ actions and mobility. PMID:24648656

Large-N kinetic theory for highly occupied systems

NASA Astrophysics Data System (ADS)

Walz, R.; Boguslavski, K.; Berges, J.

2018-06-01

We consider an effective kinetic description for quantum many-body systems, which is not based on a weak-coupling or diluteness expansion. Instead, it employs an expansion in the number of field components N of the underlying scalar quantum field theory. Extending previous studies, we demonstrate that the large-N kinetic theory at next-to-leading order is able to describe important aspects of highly occupied systems, which are beyond standard perturbative kinetic approaches. We analyze the underlying quasiparticle dynamics by computing the effective scattering matrix elements analytically and solve numerically the large-N kinetic equation for a highly occupied system far from equilibrium. This allows us to compute the universal scaling form of the distribution function at an infrared nonthermal fixed point within a kinetic description, and we compare to existing lattice field theory simulation results.

Novel aspects of plasma control in ITER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humphreys, D.; Jackson, G.; Walker, M.

2015-02-15

ITER plasma control design solutions and performance requirements are strongly driven by its nuclear mission, aggressive commissioning constraints, and limited number of operational discharges. In addition, high plasma energy content, heat fluxes, neutron fluxes, and very long pulse operation place novel demands on control performance in many areas ranging from plasma boundary and divertor regulation to plasma kinetics and stability control. Both commissioning and experimental operations schedules provide limited time for tuning of control algorithms relative to operating devices. Although many aspects of the control solutions required by ITER have been well-demonstrated in present devices and even designed satisfactorily formore » ITER application, many elements unique to ITER including various crucial integration issues are presently under development. We describe selected novel aspects of plasma control in ITER, identifying unique parts of the control problem and highlighting some key areas of research remaining. Novel control areas described include control physics understanding (e.g., current profile regulation, tearing mode (TM) suppression), control mathematics (e.g., algorithmic and simulation approaches to high confidence robust performance), and integration solutions (e.g., methods for management of highly subscribed control resources). We identify unique aspects of the ITER TM suppression scheme, which will pulse gyrotrons to drive current within a magnetic island, and turn the drive off following suppression in order to minimize use of auxiliary power and maximize fusion gain. The potential role of active current profile control and approaches to design in ITER are discussed. Issues and approaches to fault handling algorithms are described, along with novel aspects of actuator sharing in ITER.« less

Novel aspects of plasma control in ITER

DOE PAGES

Humphreys, David; Ambrosino, G.; de Vries, Peter; ...

2015-02-12

ITER plasma control design solutions and performance requirements are strongly driven by its nuclear mission, aggressive commissioning constraints, and limited number of operational discharges. In addition, high plasma energy content, heat fluxes, neutron fluxes, and very long pulse operation place novel demands on control performance in many areas ranging from plasma boundary and divertor regulation to plasma kinetics and stability control. Both commissioning and experimental operations schedules provide limited time for tuning of control algorithms relative to operating devices. Although many aspects of the control solutions required by ITER have been well-demonstrated in present devices and even designed satisfactorily formore » ITER application, many elements unique to ITER including various crucial integration issues are presently under development. We describe selected novel aspects of plasma control in ITER, identifying unique parts of the control problem and highlighting some key areas of research remaining. Novel control areas described include control physics understanding (e.g. current profile regulation, tearing mode suppression (TM)), control mathematics (e.g. algorithmic and simulation approaches to high confidence robust performance), and integration solutions (e.g. methods for management of highly-subscribed control resources). We identify unique aspects of the ITER TM suppression scheme, which will pulse gyrotrons to drive current within a magnetic island, and turn the drive off following suppression in order to minimize use of auxiliary power and maximize fusion gain. The potential role of active current profile control and approaches to design in ITER are discussed. Finally, issues and approaches to fault handling algorithms are described, along with novel aspects of actuator sharing in ITER.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santhanagopalan, Shriram; White, Ralph E.

Rotating ring disc electrode (RRDE) experiments are a classic tool for investigating kinetics of electrochemical reactions. Several standardized methods exist for extracting transport parameters and reaction rate constants using RRDE measurements. Here in this work, we compare some approximate solutions to the convective diffusion used popularly in the literature to a rigorous numerical solution of the Nernst-Planck equations coupled to the three dimensional flow problem. In light of these computational advancements, we explore design aspects of the RRDE that will help improve sensitivity of our parameter estimation procedure to experimental data. We use the oxygen reduction in acidic media involvingmore » three charge transfer reactions and a chemical reaction as an example, and identify ways to isolate reaction currents for the individual processes in order to accurately estimate the exchange current densities.« less

Disequilibrium condensation environments in space - A frontier in thermodynamics

NASA Technical Reports Server (NTRS)

De, B. R.

1979-01-01

The thermal-disequilibrium aspect of the problem of dust-particle formation from a gas phase in an open space environment is discussed in an effort to draw attention to the space condensation environment as an interesting arena for application and extension of the ideas and formalisms of nonequilibrium thermodynamics. It is shown that quasi-steady states with a disequilibrium between the gas-phase kinetic temperature and the condensed-phase internal temperature appear to be the norm of condensation environments in space. Consideration of the case of condensation onto a bulk condensed phase indicates that these quasi-steady states may constitute Prigogine dissipative structures. It is suggested that a proper study of the process of condensation in a space environment should include any effects arising from thermal disequilibrium.

Comparison of detailed and reduced kinetics mechanisms of silane oxidation in the basis of detonation wave structure problem

NASA Astrophysics Data System (ADS)

Fedorov, A. V.; Tropin, D. A.; Fomin, P. A.

2018-03-01

The paper deals with the problem of the structure of detonation waves in the silane-air mixture within the framework of mathematical model of a nonequilibrium gas dynamics. Detailed kinetic scheme of silane oxidation as well as the newly developed reduced kinetic model of detonation combustion of silane are used. On its basis the detonation wave (DW) structure in stoichiometric silane - air mixture and dependences of Chapman-Jouguet parameters of mixture on stoichiometric ratio between the fuel (silane) and an oxidizer (air) were obtained.

A new model for approximating RNA folding trajectories and population kinetics

NASA Astrophysics Data System (ADS)

Kirkpatrick, Bonnie; Hajiaghayi, Monir; Condon, Anne

2013-01-01

RNA participates both in functional aspects of the cell and in gene regulation. The interactions of these molecules are mediated by their secondary structure which can be viewed as a planar circle graph with arcs for all the chemical bonds between pairs of bases in the RNA sequence. The problem of predicting RNA secondary structure, specifically the chemically most probable structure, has many useful and efficient algorithms. This leaves RNA folding, the problem of predicting the dynamic behavior of RNA structure over time, as the main open problem. RNA folding is important for functional understanding because some RNA molecules change secondary structure in response to interactions with the environment. The full RNA folding model on at most O(3n) secondary structures is the gold standard. We present a new subset approximation model for the full model, give methods to analyze its accuracy and discuss the relative merits of our model as compared with a pre-existing subset approximation. The main advantage of our model is that it generates Monte Carlo folding pathways with the same probabilities with which they are generated under the full model. The pre-existing subset approximation does not have this property.

Illustrating the Steady-State Condition and the Single-Molecule Kinetic Method with the NMDA Receptor

ERIC Educational Resources Information Center

Kosman, Daniel J.

2009-01-01

The steady-state is a fundamental aspect of biochemical pathways in cells; indeed, the concept of steady-state is a definition of life itself. In a simple enzyme kinetic scheme, the steady-state condition is easy to define analytically but experimentally often difficult to capture because of its evanescent quality; the initial, constant velocity…

Characteristics in Restructuring High School Students' Frameworks of Gaseous Kinetics in Korea: A Psychological Point of View.

ERIC Educational Resources Information Center

Cho, In-Young; Park, Hyun-Ju; Choi, Byung-Soon

This study was conducted to describe in detail Korean students' conceptual change learning processes in the study of kinetic theory of gases. The study was interpretive, using multiple data sources to achieve a triangulation of data. Three students from a public high school for boys served as representative cases. How epistemological aspect and…

Movement variability in the golf swing.

PubMed

Langdown, Ben L; Bridge, Matt; Li, Francois-Xavier

2012-06-01

Traditionally, golf biomechanics has focused upon achieving consistency in swing kinematics and kinetics, whilst variability was considered to be noise and dysfunctional. There has been a growing argument that variability is an intrinsic aspect of skilled motor performance and plays a functional role. Two types of variability are described: 'strategic shot selection' and 'movement variability'. In 'strategic shot selection', the outcome remains consistent, but the swing kinematics/kinetics (resulting in the desired ball flight) are free to vary; 'movement variability' is the changes in swing kinematics and kinetics from trial to trial when the golfer attempts to hit the same shot. These changes will emerge due to constraints of the golfer's body, the environment, and the task. Biomechanical research has focused upon aspects of technique such as elite versus non-elite kinematics, kinetics, kinematic sequencing, peak angular velocities of body segments, wrist function, ground reaction forces, and electromyography, mainly in the search for greater distance and clubhead velocity. To date very little is known about the impact of variability on this complex motor skill, and it has yet to be fully researched to determine where the trade-off between functional and detrimental variability lies when in pursuit of enhanced performance outcomes.

First-Order or Second-Order Kinetics? A Monte Carlo Answer

ERIC Educational Resources Information Center

Tellinghuisen, Joel

2005-01-01

Monte Carlo computational experiments reveal that the ability to discriminate between first- and second-order kinetics from least-squares analysis of time-dependent concentration data is better than implied in earlier discussions of the problem. The problem is rendered as simple as possible by assuming that the order must be either 1 or 2 and that…

Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

NASA Astrophysics Data System (ADS)

Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.

2014-12-01

Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

Membrane crystallization of lysozyme: kinetic aspects

NASA Astrophysics Data System (ADS)

Profio, Gianluca Di; Curcio, Efrem; Cassetta, Alberto; Lamba, Doriano; Drioli, Enrico

2003-10-01

The relevant kinetic aspects related to an innovative method of biological macromolecules crystallization based on microporous hydrophobic membranes, used both as active surfaces to promote heterogeneous nucleation and as a mass-transfer apparatus to concentrate macromolecular solutions by solvent removal in vapour phase, have been evaluated. Polypropylene membranes, supplied in the form of hollow fibres, have been aligned in a versatile system, designed for an on-line spectrophotometric monitoring of hen egg white lysozyme crystallizing solutions (experimental conditions: 0.1 M NaAc/HAc Buffer pH 4.6, 0.5-5.8% wt/vol NaCl, 20°C). The turbidity measurements have been exploited in order to follow: (i) the induction time of crystallization, (ii) the early stage nucleation kinetics based on the Rayleigh scattering theory, and (iii) the crystal growth rate (coupled with data evaluated from image-analysis carried out by optical microscopy) under a model hypothesis of exponential growth of clusters. The crystals have been qualitatively assessed by an X-ray crystallographic analysis carried out at the synchrotron light laboratory ELETTRA.

Rotational Energy.

ERIC Educational Resources Information Center

Lockett, Keith

1988-01-01

Demonstrates several objects rolling down a slope to explain the energy transition among potential energy, translational kinetic energy, and rotational kinetic energy. Contains a problem from Galileo's rolling ball experiment. (YP)

A hybrid computer program for rapidly solving flowing or static chemical kinetic problems involving many chemical species

NASA Technical Reports Server (NTRS)

Mclain, A. G.; Rao, C. S. R.

1976-01-01

A hybrid chemical kinetic computer program was assembled which provides a rapid solution to problems involving flowing or static, chemically reacting, gas mixtures. The computer program uses existing subroutines for problem setup, initialization, and preliminary calculations and incorporates a stiff ordinary differential equation solution technique. A number of check cases were recomputed with the hybrid program and the results were almost identical to those previously obtained. The computational time saving was demonstrated with a propane-oxygen-argon shock tube combustion problem involving 31 chemical species and 64 reactions. Information is presented to enable potential users to prepare an input data deck for the calculation of a problem.

What can we learn from relaxation measurements of a laser-perturbed atmosphere? A modeling study

NASA Technical Reports Server (NTRS)

Clericetti, Agostino; Vandenbergh, Hubert; Rossi, Michel J.

1994-01-01

The chemical kinetic aspects of a transient increase in OH and HO2 by several orders of magnitude are explored in three model tropospheres. This chemical kinetic modeling effort was undertaken to support the operation of a pump-and-probe LIDAR instrument. A powerful excimer laser pulse perturbs the troposphere after which its relaxation back to steady state is examined by remote sensing, for example by DIAL or LIF. Instead of probing ambient levels of key free radicals, a study of the relaxation kinetics in real time enables chemical mechanistic studies in situ.

Estimating parameters from rotating ring disc electrode measurements

DOE PAGES

Santhanagopalan, Shriram; White, Ralph E.

2017-10-21

Rotating ring disc electrode (RRDE) experiments are a classic tool for investigating kinetics of electrochemical reactions. Several standardized methods exist for extracting transport parameters and reaction rate constants using RRDE measurements. Here in this work, we compare some approximate solutions to the convective diffusion used popularly in the literature to a rigorous numerical solution of the Nernst-Planck equations coupled to the three dimensional flow problem. In light of these computational advancements, we explore design aspects of the RRDE that will help improve sensitivity of our parameter estimation procedure to experimental data. We use the oxygen reduction in acidic media involvingmore » three charge transfer reactions and a chemical reaction as an example, and identify ways to isolate reaction currents for the individual processes in order to accurately estimate the exchange current densities.« less

Scaling laws and size effects for amorphous crystallization kinetics: Constraints imposed by nucleation and growth specificities.

PubMed

Descamps, Marc; Willart, Jean-François

2018-05-05

In the present paper we review different aspects of the crystallization of amorphous compounds in relation to specificities of the nucleation and growth rates. Its main purpose is: i) to underline the interest of a scaling analysis of recrystallization kinetics to identify similarities or disparities of experimental kinetic regimes. ii) to highlight the intrinsic link between the nucleation rate and growth rate with a temperature dependent characteristic transformation time τ(T), and a characteristic size ξ(T). The consequences on the influence of the sample size on kinetics of crystallization is considered. The significance of size effect and confinement for amorphous stabilization in the pharmaceutical sciences is discussed. Copyright © 2018. Published by Elsevier B.V.

ALCHEMIC: Advanced time-dependent chemical kinetics

NASA Astrophysics Data System (ADS)

Semenov, Dmitry A.

2017-08-01

ALCHEMIC solves chemical kinetics problems, including gas-grain interactions, surface reactions, deuterium fractionization, and transport phenomena and can model the time-dependent chemical evolution of molecular clouds, hot cores, corinos, and protoplanetary disks.

Linearized-moment analysis of the temperature jump and temperature defect in the Knudsen layer of a rarefied gas.

PubMed

Gu, Xiao-Jun; Emerson, David R

2014-06-01

Understanding the thermal behavior of a rarefied gas remains a fundamental problem. In the present study, we investigate the predictive capabilities of the regularized 13 and 26 moment equations. In this paper, we consider low-speed problems with small gradients, and to simplify the analysis, a linearized set of moment equations is derived to explore a classic temperature problem. Analytical solutions obtained for the linearized 26 moment equations are compared with available kinetic models and can reliably capture all qualitative trends for the temperature-jump coefficient and the associated temperature defect in the thermal Knudsen layer. In contrast, the linearized 13 moment equations lack the necessary physics to capture these effects and consistently underpredict kinetic theory. The deviation from kinetic theory for the 13 moment equations increases significantly for specular reflection of gas molecules, whereas the 26 moment equations compare well with results from kinetic theory. To improve engineering analyses, expressions for the effective thermal conductivity and Prandtl number in the Knudsen layer are derived with the linearized 26 moment equations.

LSENS: A General Chemical Kinetics and Sensitivity Analysis Code for homogeneous gas-phase reactions. Part 1: Theory and numerical solution procedures

NASA Technical Reports Server (NTRS)

Radhakrishnan, Krishnan

1994-01-01

LSENS, the Lewis General Chemical Kinetics and Sensitivity Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 1 of a series of three reference publications that describe LENS, provide a detailed guide to its usage, and present many example problems. Part 1 derives the governing equations and describes the numerical solution procedures for the types of problems that can be solved. The accuracy and efficiency of LSENS are examined by means of various test problems, and comparisons with other methods and codes are presented. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions.

GPU based 3D feature profile simulation of high-aspect ratio contact hole etch process under fluorocarbon plasmas

NASA Astrophysics Data System (ADS)

Chun, Poo-Reum; Lee, Se-Ah; Yook, Yeong-Geun; Choi, Kwang-Sung; Cho, Deog-Geun; Yu, Dong-Hun; Chang, Won-Seok; Kwon, Deuk-Chul; Im, Yeon-Ho

2013-09-01

Although plasma etch profile simulation has been attracted much interest for developing reliable plasma etching, there still exist big gaps between current research status and predictable modeling due to the inherent complexity of plasma process. As an effort to address this issue, we present 3D feature profile simulation coupled with well-defined plasma-surface kinetic model for silicon dioxide etching process under fluorocarbon plasmas. To capture the realistic plasma surface reaction behaviors, a polymer layer based surface kinetic model was proposed to consider the simultaneous polymer deposition and oxide etching. Finally, the realistic plasma surface model was used for calculation of speed function for 3D topology simulation, which consists of multiple level set based moving algorithm, and ballistic transport module. In addition, the time consumable computations in the ballistic transport calculation were improved drastically by GPU based numerical computation, leading to the real time computation. Finally, we demonstrated that the surface kinetic model could be coupled successfully for 3D etch profile simulations in high-aspect ratio contact hole plasma etching.

Non-focusing optics spectrophotometer, and methods of use

DOEpatents

Kramer, David M.; Sacksteder, Colette A.

2004-11-02

In one aspect, the present invention provides kinetic spectrophotometers that each comprise: (a) a light source; and (b) a compound parabolic concentrator disposed to receive light from the light source and configured to (1) intensify and diffuse the light received from the light source, and (2) direct the intensified and diffused light onto a sample. In other aspects, the present invention provides methods for measuring a photosynthetic parameter, the methods comprising the steps of: (a) illuminating a plant leaf until steady-state photosynthesis is achieved; (b) subjecting the illuminated plant leaf to a period of darkness; (c) using a kinetic spectrophotometer of the invention to collect spectral data from the plant leaf treated in accordance with steps (a) and (b); and (d) determining a value for a photosynthetic parameter from the spectral data.

Co-digestion of municipal sewage sludge and solid waste: modelling of carbohydrate, lipid and protein content influence.

PubMed

Nielfa, A; Cano, R; Pérez, A; Fdez-Polanco, M

2015-03-01

Solid wastes from industrial, commercial and community activities are of growing concern as the total volume of waste produced continues to increase. The knowledge of the specific composition and characteristics of the waste is an important tool in the correct development of the anaerobic digestion process. The problems derived from the anaerobic digestion of sole substrates with high lipid, carbohydrate or protein content lead to the co-digestion of these substrates with another disposed waste, such as sewage sludge. The kinetic of the anaerobic digestion is especially difficult to explain adequately, although some mathematical models are able to represent the main aspects of a biological system, thus improving understanding of the parameters involved in the process. The aim of this work is to evaluate the experimental biochemical methane potential on the co-digestion of sewage sludge with different solid wastes (grease; spent grain and cow manure) through the implementation of four kinetic models. The co-digestion of grease waste and mixed sludge obtained the best improvements from the sole substrates, with additional positive synergistic effects. The Gompertz model fits the experimental biochemical methane potential to an accuracy of 99%, showing a correlation between the percentage of lipid in the substrates and co-digestions and the period of lag phase. © The Author(s) 2015.

Novel degradation pathway and kinetic analysis for buprofezin removal by newly isolated Bacillus sp.

PubMed

Wang, Guangli; Xu, Dayong; Xiong, Minghua; Zhang, Hui; Li, Feng; Liu, Yuan

2016-09-15

Given the intensive and widespread application of the pesticide, buprofezin, its environmental residues potentially pose a problem; yet little is known about buprofezin's kinetic and metabolic behaviors. In this study, a novel gram-positive strain, designated BF-5, isolated from aerobic activated sludge, was found to be capable of metabolizing buprofezin as its sole energy, carbon, and nitrogen source. Based on its physiological and biochemical characteristics, other aspects of its phenotype, and a phylogenetic analysis, strain BF-5 was identified as Bacillus sp. This study investigated the effect of culture conditions on bacterial growth and substrate degradation, such as pH, temperature, initial concentration, different nitrogen source, and additional nitrogen sources as co-substrates. The degradation rate parameters, qmax, Ks, Ki and Sm were determined to be 0.6918 h(-1), 105.4 mg L(-1), 210.5 mg L(-1), and 148.95 mg L(-1) respectively. The capture of unpublished potential metabolites by gas chromatography-mass spectrometry (GC-MS) analysis has led to the proposal of a novel degradation pathway. Taken together, our results clarify buprofezin's biodegradation pathway(s) and highlight the promising potential of strain BF-5 in bioremediation of buprofezin-contaminated environments. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multi-scale simulation of quantum dot formation in Al/Al (110) homoepitaxy

NASA Astrophysics Data System (ADS)

Tiwary, Yogesh; Fichthorn, Kristen

2007-03-01

In experimental studies of Al(110) homoepitaxy, it is observed that over a certain temperature window (330-500K), 3D huts, up to 50 nm high with well defined and smooth (111) and (100) facets, form and self-organize over the micron scale [1]. The factors leading to this kinetic self-organization are currently unclear. To understand how these structures form and evolve, we simulated multi-layer, homoepitaxial growth on Al(110) using ab initio kinetic Monte Carlo (KMC). At the high temperatures, where nano-huts form, the KMC simulations are slow. To tackle this problem, we use a technique developed by Devita & Sander [2], in which isolated adatoms make multiple moves in one step. We achieve high efficiency with this algorithm and we explore very high temperatures on large simulation lattices. We uncover a variety of interesting morphologies (Ripples, mounds, smooth surface, huts) that depend on the growth temperature. By varying the barriers for various rate processes, we discern the factors that determine hut sizes, aspect ratios, and self-organization. [1] F. Buatier de Mongeot, W. Zhu, A. Molle, R. Buzio, C. Boragno, U. Valbusa, E. Wang, and Z. Zhang, Phys. Rev. Lett. 91, 016102 (2003). [2] J.P. Devita & L.M. Sander, Phys. Rev. B 72, 205421 (2005).

Fatigue crack layer propagation in silicon-iron

NASA Technical Reports Server (NTRS)

Birol, Y.; Welsch, G.; Chudnovsky, A.

1986-01-01

Fatigue crack propagation in metal is almost always accompanied by plastic deformation unless conditions strongly favor brittle fracture. The analysis of the plastic zone is crucial to the understanding of crack propagation behavior as it governs the crack growth kinetics. This research was undertaken to study the fatigue crack propagation in a silicon iron alloy. Kinetic and plasticity aspects of fatigue crack propagation in the alloy were obtained, including the characterization of damage evolution.

Engineering aspects of rate-related processes in food manufacturing.

PubMed

Adachi, Shuji

2015-01-01

Many rate-related phenomena occur in food manufacturing processes. This review addresses four of them, all of which are topics that the author has studied in order to design food manufacturing processes that are favorable from the standpoint of food engineering. They include chromatographic separation through continuous separation with a simulated moving adsorber, lipid oxidation kinetics in emulsions and microencapsulated systems, kinetic analysis and extraction in subcritical water, and water migration in pasta.

Epidemiological and experimental aspects of metal carcinogenesis: physicochemical properties, kinetics, and the active species.

PubMed Central

Magos, L

1991-01-01

The carcinogenic properties of selected metals and their compounds are reviewed to provide a useful reference for existing knowledge on relationships between physical and chemical forms, kinetics and carcinogenic potential and between epidemiology, bioassays, and short-term tests. Extensive consideration is given to arsenic, beryllium, cadmium, chromium, lead, and nickel. Other metals such as antimony, cobalt, copper, iron, manganese, selenium, and zinc are discussed briefly. PMID:1821370

WKB approximation and tunneling in theories with noncanonical kinetic terms

NASA Astrophysics Data System (ADS)

González, Mariana Carrillo; Masoumi, Ali; Solomon, Adam R.; Trodden, Mark

2017-09-01

Tunneling is a fascinating aspect of quantum mechanics that renders the local minima of a potential meta-stable, with important consequences for particle physics, for the early hot stage of the universe, and more speculatively, for the behavior of the putative multiverse. While this phenomenon has been studied extensively for systems which have canonical kinetic terms, many theories of fundamental physics contain fields with noncanonical kinetic structures. It is therefore desirable to have a detailed framework for calculating tunneling rates and initial states after tunneling for these theories. In this work we present such a rigorous formulation and illustrate its use by applying it to a number of examples.

Navigating ligand protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

NASA Astrophysics Data System (ADS)

Verkhivker, Gennady M.; Rejto, Paul A.; Bouzida, Djamal; Arthurs, Sandra; Colson, Anthony B.; Freer, Stephan T.; Gehlhaar, Daniel K.; Larson, Veda; Luty, Brock A.; Marrone, Tami; Rose, Peter W.

2001-03-01

Thermodynamic and kinetic aspects of ligand-protein binding are studied for the methotrexate-dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand-protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.

Turbulence kinetic energy equation for dilute suspensions

NASA Technical Reports Server (NTRS)

Abou-Arab, T. W.; Roco, M. C.

1989-01-01

A multiphase turbulence closure model is presented which employs one transport equation, namely the turbulence kinetic energy equation. The proposed form of this equation is different from the earlier formulations in some aspects. The power spectrum of the carrier fluid is divided into two regions, which interact in different ways and at different rates with the suspended particles as a function of the particle-eddy size ratio and density ratio. The length scale is described algebraically. A mass/time averaging procedure for the momentum and kinetic energy equations is adopted. The resulting turbulence correlations are modeled under less retrictive assumptions comparative to previous work. The closures for the momentum and kinetic energy equations are given. Comparisons of the predictions with experimental results on liquid-solid jet and gas-solid pipe flow show satisfactory agreement.

On Riemann solvers and kinetic relations for isothermal two-phase flows with surface tension

NASA Astrophysics Data System (ADS)

Rohde, Christian; Zeiler, Christoph

2018-06-01

We consider a sharp interface approach for the inviscid isothermal dynamics of compressible two-phase flow that accounts for phase transition and surface tension effects. Kinetic relations are frequently used to fix the mass exchange and entropy dissipation rate across the interface. The complete unidirectional dynamics can then be understood by solving generalized two-phase Riemann problems. We present new well-posedness theorems for the Riemann problem and corresponding computable Riemann solvers that cover quite general equations of state, metastable input data and curvature effects. The new Riemann solver is used to validate different kinetic relations on physically relevant problems including a comparison with experimental data. Riemann solvers are building blocks for many numerical schemes that are used to track interfaces in two-phase flow. It is shown that the new Riemann solver enables reliable and efficient computations for physical situations that could not be treated before.

A second-order accurate kinetic-theory-based method for inviscid compressible flows

NASA Technical Reports Server (NTRS)

Deshpande, Suresh M.

1986-01-01

An upwind method for the numerical solution of the Euler equations is presented. This method, called the kinetic numerical method (KNM), is based on the fact that the Euler equations are moments of the Boltzmann equation of the kinetic theory of gases when the distribution function is Maxwellian. The KNM consists of two phases, the convection phase and the collision phase. The method is unconditionally stable and explicit. It is highly vectorizable and can be easily made total variation diminishing for the distribution function by a suitable choice of the interpolation strategy. The method is applied to a one-dimensional shock-propagation problem and to a two-dimensional shock-reflection problem.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alvarez-Ramirez, J.; Aguilar, R.; Lopez-Isunza, F.

FCC processes involve complex interactive dynamics which are difficult to operate and control as well as poorly known reaction kinetics. This work concerns the synthesis of temperature controllers for FCC units. The problem is addressed first for the case where perfect knowledge of the reaction kinetics is assumed, leading to an input-output linearizing state feedback. However, in most industrial FCC units, perfect knowledge of reaction kinetics and composition measurements is not available. To address the problem of robustness against uncertainties in the reaction kinetics, an adaptive model-based nonlinear controller with simplified reaction models is presented. The adaptive strategy makes usemore » of estimates of uncertainties derived from calorimetric (energy) balances. The resulting controller is similar in form to standard input-output linearizing controllers and can be tuned analogously. Alternatively, the controller can be tuned using a single gain parameter and is computationally efficient. The performance of the closed-loop system and the controller design procedure are shown with simulations.« less

Kinetic and equilibrium aspects of adsorption and desorption of class II hydrophobins HFBI and HFBII at silicon oxynitride/water and air/water interfaces.

PubMed

Krivosheeva, Olga; Dėdinaitė, Andra; Linder, Markus B; Tilton, Robert D; Claesson, Per M

2013-02-26

Hydrophobins are relatively small globular proteins produced by filamentous fungi. They display unusual high surface activity and are implied as mediators of attachment to surfaces, which has resulted in high scientific and technological interest. In this work we focus on kinetic and equilibrium aspects of adsorption and desorption properties of two representatives of class II hydrophobins, namely HFBI and HFBII, at a negatively charged hydrophilic solid/water interface and at the air/water interface. The layers formed at the air/liquid interface were examined in a Langmuir trough, whereas layers formed at the solid/liquid interface were studied using dual polarization interferometry (DPI) under different flow conditions. For comparison, another globular protein, lysozyme, was also investigated. It was found that both the adsorbed amount and the adsorption kinetics were different for HFBI and HFBII, and the adsorption behavior of both hydrophobins on the negatively charged surface displayed some unusual features. For instance, even though the adsorption rate for HFBI was slowed down with increasing adsorbed amount as expected from packing constraints at the interface, the adsorption kinetics curves for HFBII displayed a region indicating adsorption cooperativity. Further, it was found that hydrophobin layers formed under flow partly desorbed when the flow was stopped, and the desorption rate for HFBII was enhanced in the presence of hydrophobins in solution.

Synthetic oligonucleotide antigens modified with locked nucleic acids detect disease specific antibodies

NASA Astrophysics Data System (ADS)

Samuelsen, Simone V.; Solov'Yov, Ilia A.; Balboni, Imelda M.; Mellins, Elizabeth; Nielsen, Christoffer Tandrup; Heegaard, Niels H. H.; Astakhova, Kira

2016-10-01

New techniques to detect and quantify antibodies to nucleic acids would provide a significant advance over current methods, which often lack specificity. We investigate the potential of novel antigens containing locked nucleic acids (LNAs) as targets for antibodies. Particularly, employing molecular dynamics we predict optimal nucleotide composition for targeting DNA-binding antibodies. As a proof of concept, we address a problem of detecting anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We test the best oligonucleotide binders in surface plasmon resonance studies to analyze binding and kinetic aspects of interactions between antigens and target DNA. These DNA and LNA/DNA sequences showed improved binding in enzyme-linked immunosorbent assay using human samples of pediatric lupus patients. Our results suggest that the novel method is a promising tool to create antigens for research and point-of-care monitoring of anti-DNA antibodies.

Causation and the origin of life. Metabolism or replication first?

PubMed

Pross, Addy

2004-06-01

The conceptual gulf that separates the 'metabolism first' and 'replication first' mechanisms for the emergence of life continues to cloud the origin of life debate. In the present paper we analyze this aspect of the origin of life problem and offer arguments in favor of the 'replication first' school. Utilizing Wicken's two-tier approach to causation we argue that a causal connection between replication and metabolism can only be demonstrated if replication would have preceded metabolism. In conjunction with existing empirical evidence and theoretical reasoning, our analysis concludes that there is no substantive evidence for a 'metabolism first' mechanism for life's emergence, while a coherent case can be made for the 'replication first' group of mechanisms. The analysis reaffirms our conviction that life is an extreme expression of kinetic control, and that the emergence of metabolic pathways can be understood by considering life as a manifestation of 'replicative chemistry'.

Dynamic dual-tracer PET reconstruction.

PubMed

Gao, Fei; Liu, Huafeng; Jian, Yiqiang; Shi, Pengcheng

2009-01-01

Although of important medical implications, simultaneous dual-tracer positron emission tomography reconstruction remains a challenging problem, primarily because the photon measurements from dual tracers are overlapped. In this paper, we propose a simultaneous dynamic dual-tracer reconstruction of tissue activity maps based on guidance from tracer kinetics. The dual-tracer reconstruction problem is formulated in a state-space representation, where parallel compartment models serve as continuous-time system equation describing the tracer kinetic processes of dual tracers, and the imaging data is expressed as discrete sampling of the system states in measurement equation. The image reconstruction problem has therefore become a state estimation problem in a continuous-discrete hybrid paradigm, and H infinity filtering is adopted as the estimation strategy. As H infinity filtering makes no assumptions on the system and measurement statistics, robust reconstruction results can be obtained for the dual-tracer PET imaging system where the statistical properties of measurement data and system uncertainty are not available a priori, even when there are disturbances in the kinetic parameters. Experimental results on digital phantoms, Monte Carlo simulations and physical phantoms have demonstrated the superior performance.

Morphological, kinetic, membrane biochemical and genetic aspects of intestinal enteroplasticity

PubMed Central

Drozdowski, Laurie A; Clandinin, M Tom; Thomson, Alan BR

2009-01-01

The process of intestinal adaptation (“enteroplasticity”) is complex and multifaceted. Although a number of trophic nutrients and non-nutritive factors have been identified in animal studies, successful, reproducible clinical trials in humans are awaited. Understanding mechanisms underlying this adaptive process may direct research toward strategies that maximize intestinal function and impart a true clinical benefit to patients with short bowel syndrome, or to persons in whom nutrient absorption needs to be maximized. In this review, we consider the morphological, kinetic and membrane biochemical aspects of enteroplasticity, focus on the importance of nutritional factors, provide an overview of the many hormones that may alter the adaptive process, and consider some of the possible molecular profiles. While most of the data is derived from rodent studies, wherever possible, the results of human studies of intestinal enteroplasticity are provided. PMID:19230039

Magnetospheric Effects as a New Aspect of the Asteroid Impact Problem: Necessity and Possibilities of Laboratory Simulation Experiments

NASA Astrophysics Data System (ADS)

Zakharov, Yuri P.; Nikitin, Sergei A.; Ponomarenko, Arnold G.; Minami, Shigeyuki

1997-05-01

This paper discusses the possible consequences to the Earth's magnetosphere, when due to too short an advanced warning, attempts at mitigation of a near-Earth object (NEO) must be made in close proximity to the Earth. The energy Eo, and explosive plasma release during impact may be compared with the kinetic energy Ek of the NEO and with the energy, Ee (Ee approximately Ek), needed for NEO deflection by a strong (protective force) explosive, at distances close to the scale of the magnetosphere. If the energy, Em, of the Earth's dipole field latter is relatively small (Em is less than Eo for a NEO size approximately 1 km), global or even catastrophic disturbances could occur. These ecologically important magnetospheric aspects of the NEO impact problem have been discussed recently; particularly in the context of the comet SL-9/Jupiter impact. In the latter case, the effect on Jupiter's magnetosphere of the 'NEO' explosions was very small (x equals Eo/Em approximately 0.001, where Em is the 'outer' magnetic energy of the planetary dipole field) and the corresponding model of its 'fireball' development could be simulated numerically in 'zero' approximation, with the assumption of an undisturbed magnetospheric media as a whole. However, in general, and, in the rather probable case of NEO impacts with values x approximately 1, the development of such 3D, nonstationary MHD or PIC-models at this time. Such information can be obtained from new kinds of simulation experiments with the laboratory magnetosphere, the so-called 'terrella'.

Nano-material aspects of shock absorption in bone joints.

PubMed

Tributsch, H; Copf, F; Copf, P; Hindenlang, U; Niethard, F U; Schneider, R

2010-01-01

This theoretical study is based on a nano-technological evaluation of the effect of pressure on the composite bone fine structure. It turned out, that the well known macroscopic mechano-elastic performance of bones in combination with muscles and tendons is just one functional aspect which is critically supported by additional micro- and nano- shock damping technology aimed at minimising local bone material damage within the joints and supporting spongy bone material. The identified mechanisms comprise essentially three phenomena localised within the three-dimensional spongy structure with channels and so called perforated flexible tensulae membranes of different dimensions intersecting and linking them. Kinetic energy of a mechanical shock may be dissipated within the solid-liquid composite bone structure into heat via the generation of quasi-chaotic hydromechanic micro-turbulence. It may generate electro-kinetic energy in terms of electric currents and potentials. And the resulting specific structural and surface electrochemical changes may induce the compressible intra-osseal liquid to build up pressure dependent free chemical energy. Innovative bone joint prostheses will have to consider and to be adapted to the nano-material aspects of shock absorption in the operated bones.

A third-order gas-kinetic CPR method for the Euler and Navier-Stokes equations on triangular meshes

NASA Astrophysics Data System (ADS)

Zhang, Chao; Li, Qibing; Fu, Song; Wang, Z. J.

2018-06-01

A third-order accurate gas-kinetic scheme based on the correction procedure via reconstruction (CPR) framework is developed for the Euler and Navier-Stokes equations on triangular meshes. The scheme combines the accuracy and efficiency of the CPR formulation with the multidimensional characteristics and robustness of the gas-kinetic flux solver. Comparing with high-order finite volume gas-kinetic methods, the current scheme is more compact and efficient by avoiding wide stencils on unstructured meshes. Unlike the traditional CPR method where the inviscid and viscous terms are treated differently, the inviscid and viscous fluxes in the current scheme are coupled and computed uniformly through the kinetic evolution model. In addition, the present scheme adopts a fully coupled spatial and temporal gas distribution function for the flux evaluation, achieving high-order accuracy in both space and time within a single step. Numerical tests with a wide range of flow problems, from nearly incompressible to supersonic flows with strong shocks, for both inviscid and viscous problems, demonstrate the high accuracy and efficiency of the present scheme.

Kinetic effects in thermal explosion with oscillating ambient conditions.

PubMed

Novozhilov, Vasily

2018-03-05

Thermal explosion problem for a medium with oscillating ambient temperature at its boundaries is a new problem which was introduced in the preceding publication by the present author. It is directly applicable to a range of practical fire autoignition scenarios (e.g. in the storages of organic matter, explosives, propellants, etc.). Effects of kinetic mechanisms, however, need be further investigated as they are expected to alter critical conditions of thermal explosion. We consider several global kinetic mechanisms: first order reaction, second order reaction, and first order autocatalysis. It is demonstrated that kinetic effects related to reactants consumption do indeed shift respective critical boundaries. Effect of kinetics on oscillatory development of thermal explosion is of particular interest. In line with conclusions of the preceding publication, it is confirmed that temperature oscillations may develop during induction phase of thermal explosion when the effect of reactants consumption is properly taken into account. Moreover, development of thermal explosion instability through the prior oscillations is an inevitable and natural scenario. This fact is confirmed by a number of examples. Besides, effects of the other relevant parameter, Zeldovich number on critical conditions are also investigated.

Physical and numerical sources of computational inefficiency in integration of chemical kinetic rate equations: Etiology, treatment and prognosis

NASA Technical Reports Server (NTRS)

Pratt, D. T.; Radhakrishnan, K.

1986-01-01

The design of a very fast, automatic black-box code for homogeneous, gas-phase chemical kinetics problems requires an understanding of the physical and numerical sources of computational inefficiency. Some major sources reviewed in this report are stiffness of the governing ordinary differential equations (ODE's) and its detection, choice of appropriate method (i.e., integration algorithm plus step-size control strategy), nonphysical initial conditions, and too frequent evaluation of thermochemical and kinetic properties. Specific techniques are recommended (and some advised against) for improving or overcoming the identified problem areas. It is argued that, because reactive species increase exponentially with time during induction, and all species exhibit asymptotic, exponential decay with time during equilibration, exponential-fitted integration algorithms are inherently more accurate for kinetics modeling than classical, polynomial-interpolant methods for the same computational work. But current codes using the exponential-fitted method lack the sophisticated stepsize-control logic of existing black-box ODE solver codes, such as EPISODE and LSODE. The ultimate chemical kinetics code does not exist yet, but the general characteristics of such a code are becoming apparent.

Broad-Bandwidth Chiral Sum Frequency Generation Spectroscopy for Probing the Kinetics of Proteins at Interfaces

PubMed Central

2016-01-01

The kinetics of proteins at interfaces plays an important role in biological functions and inspires solutions to fundamental problems in biomedical sciences and engineering. Nonetheless, due to the lack of surface-specific and structural-sensitive biophysical techniques, it still remains challenging to probe protein kinetics in situ and in real time without the use of spectroscopic labels at interfaces. Broad-bandwidth chiral sum frequency generation (SFG) spectroscopy has been recently developed for protein kinetic studies at interfaces by tracking the chiral vibrational signals of proteins. In this article, we review our recent progress in kinetic studies of proteins at interfaces using broad-bandwidth chiral SFG spectroscopy. We illustrate the use of chiral SFG signals of protein side chains in the C–H stretch region to monitor self-assembly processes of proteins at interfaces. We also present the use of chiral SFG signals from the protein backbone in the N–H stretch region to probe the real-time kinetics of proton exchange between protein and water at interfaces. In addition, we demonstrate the applications of spectral features of chiral SFG that are typical of protein secondary structures in both the amide I and the N–H stretch regions for monitoring the kinetics of aggregation of amyloid proteins at membrane surfaces. These studies exhibit the power of broad-bandwidth chiral SFG to study protein kinetics at interfaces and the promise of this technique in research areas of surface science to address fundamental problems in biomedical and material sciences. PMID:26196215

Nonlinear saturation of the slab ITG instability and zonal flow generation with fully kinetic ions

NASA Astrophysics Data System (ADS)

Miecnikowski, Matthew T.; Sturdevant, Benjamin J.; Chen, Yang; Parker, Scott E.

2018-05-01

Fully kinetic turbulence models are of interest for their potential to validate or replace gyrokinetic models in plasma regimes where the gyrokinetic expansion parameters are marginal. Here, we demonstrate fully kinetic ion capability by simulating the growth and nonlinear saturation of the ion-temperature-gradient instability in shearless slab geometry assuming adiabatic electrons and including zonal flow dynamics. The ion trajectories are integrated using the Lorentz force, and the cyclotron motion is fully resolved. Linear growth and nonlinear saturation characteristics show excellent agreement with analogous gyrokinetic simulations across a wide range of parameters. The fully kinetic simulation accurately reproduces the nonlinearly generated zonal flow. This work demonstrates nonlinear capability, resolution of weak gradient drive, and zonal flow physics, which are critical aspects of modeling plasma turbulence with full ion dynamics.

Processes of aggression described by kinetic method

NASA Astrophysics Data System (ADS)

Aristov, V. V.; Ilyin, O.

2014-12-01

In the last decades many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological and historical processes. In the present paper we suggest a model of the Nazi Germany invasion of Poland, France and USSR based on the kinetic theory. We model this process with the Cauchy boundary problem for the two-element kinetic equations with spatial initial conditions. The solution of the problem is given in the form of traveling wave. The propagation velocity of a frontline depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solution of the model can be expressed in terms of quadratures and elementary functions. Finally it is shown that the frontline velocities are complied with the historical data.

BRIEF COMMUNICATION: On the drift kinetic equation driven by plasma flows

NASA Astrophysics Data System (ADS)

Shaing, K. C.

2010-07-01

A drift kinetic equation that is driven by plasma flows has previously been derived by Shaing and Spong 1990 (Phys. Fluids B 2 1190). The terms that are driven by particle speed that is parallel to the magnetic field B have been neglected. Here, such terms are discussed to examine their importance to the equation and to show that these terms do not contribute to the calculations of plasma viscosity in large aspect ratio toroidal plasmas, e.g. tokamaks and stellarators.

Device for data-acquisition from transient signals: kinetic considerations

PubMed Central

Sampedro, A. Sanchez; Vives, S. Sagrado

1990-01-01

This paper reports on the evaluation and testing of a home-made device. Data-acquisition, treatment of transient signals and the hardware and software involved are discussed. Some practical aspects are developed in order to power the autonomy of procedures using the device. Kinetic and multi-signal calculations are considered in order to cover the actual tendencies in continuous-flow analysis. Somepractical advantages versus the use of classical chart recorders or commercial computerized-instrument devices are pointed out. PMID:18925275

Kinetic and mechanistic aspects of sensitized photodegradation of β-lactam antibiotics: microbiological implications.

PubMed

Reynoso, E; Nesci, A; Allegretti, P; Criado, S; Biasutti, M A

2012-01-01

Amoxicillin (Amx) and cephalexin (Cfx) are β-lactam antibiotics widely used in human and veterinary medicine. Two points of interest surrounding these molecules are the photodegradation of the molecules and their microbiological implications, as well as the persistence and bioaccumulation in the environment which may cause resistance to bacterial strains. The kinetic and mechanistic aspects of the photosensitized degradation of Amx and Cfx have been studied in water at pH 7.4 and 10 by stationary and time-resolved methods. Kinetic evidence indicates that the Rose Bengal-sensitized photooxidation of Amx at pH 7.4 proceeds via O(2)((1)Δ(g)) and O(2•-) mechanisms while at pH 10 the degradation path occurs, principally, via O(2)((1)Δ(g)). For Cfx, this process is attributed to O(2)((1)Δ(g)) and O(2•-). Photoproducts, which arise from the addition of oxygen atoms and subsequent oxidation of the groups -CH(3) to -COOH, were detected. For both antibiotics the bacteriostatic activity decreases in parallel to their photodegradation. The results of this study could potentially help scientists to better understand and predict the photodegradability of these antibiotics on living organisms and in different environmental compartments.

Effects of combined pressure and temperature on enzymes related to quality of fruits and vegetables: from kinetic information to process engineering aspects.

PubMed

Ludikhuyze, L; Van Loey, A; Indrawati; Smout, C; Hendrickx, M

2003-01-01

Throughout the last decade, high pressure technology has been shown to offer great potential to the food processing and preservation industry in delivering safe and high quality products. Implementation of this new technology will be largely facilitated when a scientific basis to assess quantitatively the impact of high pressure processes on food safety and quality becomes available. Besides, quantitative data on the effects of pressure and temperature on safety and quality aspects of foods are indispensable for design and evaluation of optimal high pressure processes, i.e., processes resulting in maximal quality retention within the constraints of the required reduction of microbial load and enzyme activity. Indeed it has to be stressed that new technologies should deliver, apart from the promised quality improvement, an equivalent or preferably enhanced level of safety. The present paper will give an overview from a quantitative point of view of the combined effects of pressure and temperature on enzymes related to quality of fruits and vegetables. Complete kinetic characterization of the inactivation of the individual enzymes will be discussed, as well as the use of integrated kinetic information in process engineering.

The applications of chemical thermodynamics and chemical kinetics to planetary atmospheres research

NASA Technical Reports Server (NTRS)

Fegley, Bruce, Jr.

1990-01-01

A review of the applications of chemical thermodynamics and chemical kinetics to planetary atmospheres research during the past four decades is presented with an emphasis on chemical equilibrium models and thermochemical kinetics. Several current problems in planetary atmospheres research such as the origin of the atmospheres of the terrestrial planets, atmosphere-surface interactions on Venus and Mars, deep mixing in the atmospheres of the gas giant planets, and the origin of the atmospheres of outer planet satellites all require laboratory data on the kinetics of thermochemical reactions for their solution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

J.A. Krommes

Fusion physics poses an extremely challenging, practically complex problem that does not yield readily to simple paradigms. Nevertheless, various of the theoretical tools and conceptual advances emphasized at the KaufmanFest 2007 have motivated and/or found application to the development of fusion-related plasma turbulence theory. A brief historical commentary is given on some aspects of that specialty, with emphasis on the role (and limitations) of Hamiltonian/symplectic approaches, variational methods, oscillation-center theory, and nonlinear dynamics. It is shown how to extract a renormalized ponderomotive force from the statistical equations of plasma turbulence, and the possibility of a renormalized K-χ theorem is discussed.more » An unusual application of quasilinear theory to the problem of plasma equilibria in the presence of stochastic magnetic fields is described. The modern problem of zonal-flow dynamics illustrates a confluence of several techniques, including (i) the application of nonlinear-dynamics methods, especially center-manifold theory, to the problem of the transition to plasma turbulence in the face of self-generated zonal flows; and (ii) the use of Hamiltonian formalism to determine the appropriate (Casimir) invariant to be used in a novel wave-kinetic analysis of systems of interacting zonal flows and drift waves. Recent progress in the theory of intermittent chaotic statistics and the generation of coherent structures from turbulence is mentioned, and an appeal is made for some new tools to cope with these interesting and difficult problems in nonlinear plasma physics. Finally, the important influence of the intellectually stimulating research environment fostered by Prof. Allan Kaufman on the author's thinking and teaching methodology is described.« less

Kinetic Aspects of Surfactant-Induced Structural Changes of Proteins - Unsolved Problems of Two-State Model for Protein Denaturation -.

PubMed

Takeda, Kunio; Moriyama, Yoshiko

2015-01-01

The kinetic mechanism of surfactant-induced protein denaturation is discussed on the basis of not only stopped-flow kinetic data but also the changes of protein helicities caused by the surfactants and the discontinuous mobility changes of surfactant-protein complexes. For example, the α-helical structures of bovine serum albumin (BSA) are partially disrupted due to the addition of sodium dodecyl sulfate (SDS). Formation of SDS-BSA complex can lead to only four complex types with specific mobilities depending on the surfactant concentration. On the other hand, the apparent rate constant of the structural change of BSA increases with an increase of SDS concentration, indicating that the rate of the structural change becomes fast as the degree of the change increases. When a certain amount of surfactant ions bind to proteins, their native structures transform directly to particular structures without passing through intermediate stages that might be induced due to the binding of fewer amounts of the surfactant ions. Furthermore, this review brings up a question about two-state and three-state models, N⇌D and N⇌D'⇌D (N: native state, D: denatured sate, D': intermediate between N and D), which have been often adopted without hesitation in discussion on general denaturations of proteins. First of all, doubtful is whether any equilibrium relationship exists in such denaturation reactions. It cannot be disregarded that the D states in these models differ depending on the changes of intensities of the denaturing factors. The authors emphasize that the denaturations or the structural changes of proteins should be discussed assuming one-way reaction models with no backward processes rather than assuming the reversible two-state reaction models or similar modified reaction models.

A theoretical and numerical study of the flow of granular materials down an inclined plane. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rajagopal, K.R.

The mechanics of the flowing granular materials such as coal, agricultural products, at deal of attention as it has fertilizers, dry chemicals, metal ores, etc. have received a great deal of attention as it has relevance to several important technological problems. Despite wide interest and more than five decades of experimental and theoretical investigations, most aspects of the behavior of flowing granular materials are still not well understood. So Experiments have to be devised which quantify and describe the non-linear behavior of the modular materials, and theories developed which can explain the experimentally observed facts. As many models have beenmore » suggested for describing the behavior of granular materials, from both continuum and kinetic theory viewpoints, we proposed to investigate the validity and usefulness of representative models from both the continuum and kinetic theory points of view, by determining the prediction of such a theory, in a representative flow, with respect to existence, non-existence, multiplicity and stability of solutions. The continuum model to be investigated is an outgrowth of a model due to Goodman and Cowin (1971, 1972) and the kinetic theory models being those due to Jenkins and Richman (1985) and Boyle and Massoudi (1989). In this report we present detailed results regarding the same. Interestingly, we find that the predictions of all the theories, in certain parameter space associated with these models, are qualitatively similar. This ofcourse depends on the values assumed for various material parameters in the models, which as yet are unknown, as reliable experiments have not been carried out as yet for their determination.« less

Inflationary magneto-(non)genesis, increasing kinetic couplings, and the strong coupling problem

NASA Astrophysics Data System (ADS)

Bazrafshan Moghaddam, Hossein; McDonough, Evan; Namba, Ryo; Brandenberger, Robert H.

2018-05-01

We study the generation of magnetic fields during inflation making use of a coupling of the inflaton and moduli fields to electromagnetism via the photon kinetic term, and assuming that the coupling is an increasing function of time. We demonstrate that the strong coupling problem of inflationary magnetogenesis can be avoided by incorporating the destabilization of moduli fields after inflation. The magnetic field always dominates over the electric one, and thus the severe constraints on the latter from backreaction, which are the demanding obstacles in the case of a decreasing coupling function, do not apply to the current scenario. However, we show that this loophole to the strong coupling problem comes at a price: the normalization of the amplitude of magnetic fields is determined by this coupling term and is therefore suppressed by a large factor after the moduli destabilization completes. From this we conclude that there is no self-consistent and generic realization of primordial magnetogenesis producing scale-invariant fields in the case of an increasing kinetic coupling.

Turbulence dissipation challenge: particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Roytershteyn, V.; Karimabadi, H.; Omelchenko, Y.; Germaschewski, K.

2015-12-01

We discuss application of three particle in cell (PIC) codes to the problems relevant to turbulence dissipation challenge. VPIC is a fully kinetic code extensively used to study a variety of diverse problems ranging from laboratory plasmas to astrophysics. PSC is a flexible fully kinetic code offering a variety of algorithms that can be advantageous to turbulence simulations, including high order particle shapes, dynamic load balancing, and ability to efficiently run on Graphics Processing Units (GPUs). Finally, HYPERS is a novel hybrid (kinetic ions+fluid electrons) code, which utilizes asynchronous time advance and a number of other advanced algorithms. We present examples drawn both from large-scale turbulence simulations and from the test problems outlined by the turbulence dissipation challenge. Special attention is paid to such issues as the small-scale intermittency of inertial range turbulence, mode content of the sub-proton range of scales, the formation of electron-scale current sheets and the role of magnetic reconnection, as well as numerical challenges of applying PIC codes to simulations of astrophysical turbulence.

CHLORINE DISINFECTION OF AEROMONAS

EPA Science Inventory

The bacterial genus Aeromonas is currently listed on the USEPA's Candidate Contaminant List (CCL). Resistance to chemical disinfection is an essential aspect regarding all microbial groups listed on the CCL. This study was designed to determine the inactivation kinetics of Aeromo...

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Solution of Linearized Drift Kinetic Equations in Neoclassical Transport Theory by the Method of Matched Asymptotic Expansions

NASA Astrophysics Data System (ADS)

Wong, S. K.; Chan, V. S.; Hinton, F. L.

2001-10-01

The classic solution of the linearized drift kinetic equations in neoclassical transport theory for large-aspect-ratio tokamak flux-surfaces relies on the variational principle and the choice of ``localized" distribution functions as trialfunctions.(M.N. Rosenbluth, et al., Phys. Fluids 15) (1972) 116. Somewhat unclear in this approach are the nature and the origin of the ``localization" and whether the results obtained represent the exact leading terms in an asymptotic expansion int he inverse aspect ratio. Using the method of matched asymptotic expansions, we were able to derive the leading approximations to the distribution functions and demonstrated the asymptotic exactness of the existing results. The method is also applied to the calculation of angular momentum transport(M.N. Rosenbluth, et al., Plasma Phys. and Contr. Nucl. Fusion Research, 1970, Vol. 1 (IAEA, Vienna, 1971) p. 495.) and the current driven by electron cyclotron waves.

A path-independent integral for the characterization of solute concentration and flux at biofilm detachments

USGS Publications Warehouse

Moran, B.; Kulkarni, S.S.; Reeves, H.W.

2007-01-01

A path-independent (conservation) integral is developed for the characterization of solute concentration and flux in a biofilm in the vicinity of a detachment or other flux limiting boundary condition. Steady state conditions of solute diffusion are considered and biofilm kinetics are described by an uptake term which can be expressed in terms of a potential (Michaelis-Menten kinetics). An asymptotic solution for solute concentration at the tip of the detachment is obtained and shown to be analogous to that of antiplane crack problems in linear elasticity. It is shown that the amplitude of the asymptotic solution can be calculated by evaluating a path-independent integral. The special case of a semi-infinite detachment in an infinite strip is considered and the amplitude of the asymptotic field is related to the boundary conditions and problem parameters in closed form for zeroth and first order kinetics and numerically for Michaelis-Menten kinetics. ?? Springer Science+Business Media, Inc. 2007.

Theory and Simulation of Reconnection. In memoriam Harry Petschek

NASA Astrophysics Data System (ADS)

Büchner, J.

2006-06-01

Reconnection is a major commonality of solar and magnetospheric physics. It was conjectured by Giovanelli in 1946 to explain particle acceleration in solar flares near magnetic neutral points. Since than it has been broadly applied in space physics including magnetospheric physics. In a special way this is due to Harry Petschek, who in 1994 published his ground breaking solution for a 2D magnetized plasma flow in regions containing singularities of vanishing magnetic field. Petschek’s reconnection theory was questioned in endless disputes and arguments, but his work stimulated the further investigation of this phenomenon like no other. However, there are questions left open. We consider two of them “anomalous” resistivity in collisionless space plasma and the nature of reconnection in three dimensions. The CLUSTER and SOHO missions address these two aspects of reconnection in a complementary way -- the resistivity problem in situ in the magnetosphere and the 3D aspect by remote sensing of the Sun. We demonstrate that the search for answers to both questions leads beyond the applicability of analytical theories and that appropriate numerical approaches are necessary to investigate the essentially nonlinear and nonlocal processes involved. Necessary are both micro-physical, kinetic Vlasov-equation based methods of investigation as well as large scale (MHD) simulations to obtain the geometry and topology of the acting fields and flows.

Nonlinear theory of diffusive acceleration of particles by shock waves

NASA Astrophysics Data System (ADS)

Malkov, M. A.; Drury, L. O'C.

2001-04-01

Among the various acceleration mechanisms which have been suggested as responsible for the nonthermal particle spectra and associated radiation observed in many astrophysical and space physics environments, diffusive shock acceleration appears to be the most successful. We review the current theoretical understanding of this process, from the basic ideas of how a shock energizes a few reactionless particles to the advanced nonlinear approaches treating the shock and accelerated particles as a symbiotic self-organizing system. By means of direct solution of the nonlinear problem we set the limit to the test-particle approximation and demonstrate the fundamental role of nonlinearity in shocks of astrophysical size and lifetime. We study the bifurcation of this system, proceeding from the hydrodynamic to kinetic description under a realistic condition of Bohm diffusivity. We emphasize the importance of collective plasma phenomena for the global flow structure and acceleration efficiency by considering the injection process, an initial stage of acceleration and, the related aspects of the physics of collisionless shocks. We calculate the injection rate for different shock parameters and different species. This, together with differential acceleration resulting from nonlinear large-scale modification, determines the chemical composition of accelerated particles. The review concentrates on theoretical and analytical aspects but our strategic goal is to link the fundamental theoretical ideas with the rapidly growing wealth of observational data.

Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes.

PubMed

Gao, Jiali; Major, Dan T; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu

2008-01-01

A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.

Kinetics and thermodynamics of living copolymerization processes

PubMed Central

2016-01-01

Theoretical advances are reported on the kinetics and thermodynamics of free and template-directed living copolymerizations. Until recently, the kinetic theory of these processes had only been established in the fully irreversible regime, in which the attachment rates are only considered. However, the entropy production is infinite in this regime and the approach to thermodynamic equilibrium cannot be investigated. For this purpose, the detachment rates should also be included. Inspite of this complication, the kinetics can be exactly solved in the regimes of steady growth and depolymerization. In this way, analytical expressions are obtained for the mean growth velocity, the statistical properties of the copolymer sequences, as well as the thermodynamic entropy production. The results apply to DNA replication, transcription and translation, allowing us to understand important aspects of molecular evolution. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’. PMID:27698043

Kinetics and thermodynamics of living copolymerization processes.

PubMed

Gaspard, Pierre

2016-11-13

Theoretical advances are reported on the kinetics and thermodynamics of free and template-directed living copolymerizations. Until recently, the kinetic theory of these processes had only been established in the fully irreversible regime, in which the attachment rates are only considered. However, the entropy production is infinite in this regime and the approach to thermodynamic equilibrium cannot be investigated. For this purpose, the detachment rates should also be included. Inspite of this complication, the kinetics can be exactly solved in the regimes of steady growth and depolymerization. In this way, analytical expressions are obtained for the mean growth velocity, the statistical properties of the copolymer sequences, as well as the thermodynamic entropy production. The results apply to DNA replication, transcription and translation, allowing us to understand important aspects of molecular evolution.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

Effect of grain morphology on gas bubble swelling in UMo fuels – A 3D microstructure dependent Booth model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Shenyang; Burkes, Douglas; Lavender, Curt A.

2016-11-01

A three dimensional microstructure dependent swelling model is developed for studying the fission gas swelling kinetics in irradiated nuclear fuels. The model is extended from the Booth model [1] in order to investigate the effect of heterogeneous microstructures on gas bubble swelling kinetics. As an application of the model, the effect of grain morphology, fission gas diffusivity, and spatial dependent fission rate on swelling kinetics are simulated in UMo fuels. It is found that the decrease of grain size, the increase of grain aspect ratio for the grain having the same volume, and the increase of fission gas diffusivity (fissionmore » rate) cause the increase of swelling kinetics. Other heterogeneities such as second phases and spatial dependent thermodynamic properties including diffusivity of fission gas, sink and source strength of defects could be naturally integrated into the model to enhance the model capability.« less

Kinetics and thermodynamics of living copolymerization processes

NASA Astrophysics Data System (ADS)

Gaspard, Pierre

2016-11-01

Theoretical advances are reported on the kinetics and thermodynamics of free and template-directed living copolymerizations. Until recently, the kinetic theory of these processes had only been established in the fully irreversible regime, in which the attachment rates are only considered. However, the entropy production is infinite in this regime and the approach to thermodynamic equilibrium cannot be investigated. For this purpose, the detachment rates should also be included. Inspite of this complication, the kinetics can be exactly solved in the regimes of steady growth and depolymerization. In this way, analytical expressions are obtained for the mean growth velocity, the statistical properties of the copolymer sequences, as well as the thermodynamic entropy production. The results apply to DNA replication, transcription and translation, allowing us to understand important aspects of molecular evolution. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Assembly kinetics determine the architecture of α-actinin crosslinked F-actin networks.

PubMed

Falzone, Tobias T; Lenz, Martin; Kovar, David R; Gardel, Margaret L

2012-05-29

The actin cytoskeleton is organized into diverse meshworks and bundles that support many aspects of cell physiology. Understanding the self-assembly of these actin-based structures is essential for developing predictive models of cytoskeletal organization. Here we show that the competing kinetics of bundle formation with the onset of dynamic arrest arising from filament entanglements and crosslinking determine the architecture of reconstituted actin networks formed with α-actinin crosslinks. Crosslink-mediated bundle formation only occurs in dilute solutions of highly mobile actin filaments. As actin polymerization proceeds, filament mobility and bundle formation are arrested concomitantly. By controlling the onset of dynamic arrest, perturbations to actin assembly kinetics dramatically alter the architecture of biochemically identical samples. Thus, the morphology of reconstituted F-actin networks is a kinetically determined structure similar to those formed by physical gels and glasses. These results establish mechanisms controlling the structure and mechanics in diverse semiflexible biopolymer networks.

Effects of electrostatic interactions on ligand dissociation kinetics

NASA Astrophysics Data System (ADS)

Erbaş, Aykut; de la Cruz, Monica Olvera; Marko, John F.

2018-02-01

We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a 1000-fold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH) (or implicit ions, i.e., use of an electrostatic potential with a prescribed decay length) level and by the more precise approach of considering all ionic species explicitly in the simulations. We find that the DH approach systematically overestimates unbinding rates, relative to the calculations where all ion pairs are present explicitly in solution, although many aspects of the two types of calculation are qualitatively similar. For facilitated dissociation (FD) (acceleration of unbinding by free ligands in solution) explicit-ion simulations lead to unbinding at lower free-ligand concentrations. Our simulations predict a variety of FD regimes as a function of free-ligand and ion concentrations; a particularly interesting regime is at intermediate concentrations of ligands where nonelectrostatic binding strength controls FD. We conclude that explicit-ion electrostatic modeling is an essential component to quantitatively tackle problems in molecular ligand dissociation, including nucleic-acid-binding proteins.

Aspects of effective supersymmetric theories

NASA Astrophysics Data System (ADS)

Tziveloglou, Panteleimon

This work consists of two parts. In the first part we construct the complete extension of the Minimal Supersymmetric Standard Model by higher dimensional effective operators and then study its phenomenology. These operators encapsulate the effects on LHC physics of any kind of new degrees of freedom at the multiTeV scale. The effective analysis includes the case where the multiTeV physics is the supersymmetry breaking sector itself. In that case the appropriate framework is nonlinear supersymmetry. We choose to realize the nonlinear symmetry by the method of constrained superfields. Beyond the new effective couplings, the analysis suggests an interpretation of the 'little hierarchy problem' as an indication of new physics at multiTeV scale. In the second part we explore the power of constrained superfields in extended supersymmetry. It is known that in N = 2 supersymmetry the gauge kinetic function cannot depend on hypermultiplet scalars. However, it is also known that the low energy effective action of a D-brane in an N = 2 supersymmetric bulk includes the DBI action, where the gauge kinetic function does depend on the dilaton. We show how the nonlinearization of the second SUSY (imposed by the presence of the D-brane) opens this possibility, by constructing the global N = 1 linear + 1 nonlinear invariant coupling of a hypermultiplet with a gauge multiplet. The constructed theory enjoys interesting features, including a novel super-Higgs mechanism without gravity.

Exact solutions of a hierarchy of mixing speeds models

NASA Astrophysics Data System (ADS)

Cornille, H.; Platkowski, T.

1992-07-01

This paper presents several new aspects of discrete kinetic theory (DKT). First a hierarchy of d-dimensional (d=1,2,3) models is proposed with (2d+3) velocities and three moduli speeds: 0, 2, and a third one that can be arbitrary. It is assumed that the particles at rest have an internal energy which, for microscopic collisions, supplies for the loss of the kinetic energy. In a more general way than usual, collisions are allowed that mix particles with different speeds. Second, for the (1+1)-dimensional restriction of the systems of PDE for these models which have two independent quadratic collision terms we construct different exact solutions. The usual types of exact solutions are studied: periodic solutions and shock wave solutions obtained from the standard linearization of the scalar Riccati equations called Riccatian shock waves. Then other types of solutions of the coupled Riccati equations are found called non-Riccatian shock waves and they are compared with the previous ones. The main new result is that, between the upstream and downstream states, these new solutions are not necessarily monotonous. Further, for the shock problem, a two-dimensional dynamical system of ODE is solved numerically with limit values corresponding to the upstream and downstream states. As a by-product of this study two new linearizations for the Riccati coupled equations with two functions are proposed.

Electrochemical metallization memories--fundamentals, applications, prospects.

PubMed

Valov, Ilia; Waser, Rainer; Jameson, John R; Kozicki, Michael N

2011-06-24

This review focuses on electrochemical metallization memory cells (ECM), highlighting their advantages as the next generation memories. In a brief introduction, the basic switching mechanism of ECM cells is described and the historical development is sketched. In a second part, the full spectra of materials and material combinations used for memory device prototypes and for dedicated studies are presented. In a third part, the specific thermodynamics and kinetics of nanosized electrochemical cells are described. The overlapping of the space charge layers is found to be most relevant for the cell properties at rest. The major factors determining the functionality of the ECM cells are the electrode reaction and the transport kinetics. Depending on electrode and/or electrolyte material electron transfer, electro-crystallization or slow diffusion under strong electric fields can be rate determining. In the fourth part, the major device characteristics of ECM cells are explained. Emphasis is placed on switching speed, forming and SET/RESET voltage, R(ON) to R(OFF) ratio, endurance and retention, and scaling potentials. In the last part, circuit design aspects of ECM arrays are discussed, including the pros and cons of active and passive arrays. In the case of passive arrays, the fundamental sneak path problem is described and as well as a possible solution by two anti-serial (complementary) interconnected resistive switches per cell. Furthermore, the prospects of ECM with regard to further scalability and the ability for multi-bit data storage are addressed.

Electrochemical metallization memories—fundamentals, applications, prospects

NASA Astrophysics Data System (ADS)

Valov, Ilia; Waser, Rainer; Jameson, John R.; Kozicki, Michael N.

2011-06-01

This review focuses on electrochemical metallization memory cells (ECM), highlighting their advantages as the next generation memories. In a brief introduction, the basic switching mechanism of ECM cells is described and the historical development is sketched. In a second part, the full spectra of materials and material combinations used for memory device prototypes and for dedicated studies are presented. In a third part, the specific thermodynamics and kinetics of nanosized electrochemical cells are described. The overlapping of the space charge layers is found to be most relevant for the cell properties at rest. The major factors determining the functionality of the ECM cells are the electrode reaction and the transport kinetics. Depending on electrode and/or electrolyte material electron transfer, electro-crystallization or slow diffusion under strong electric fields can be rate determining. In the fourth part, the major device characteristics of ECM cells are explained. Emphasis is placed on switching speed, forming and SET/RESET voltage, RON to ROFF ratio, endurance and retention, and scaling potentials. In the last part, circuit design aspects of ECM arrays are discussed, including the pros and cons of active and passive arrays. In the case of passive arrays, the fundamental sneak path problem is described and as well as a possible solution by two anti-serial (complementary) interconnected resistive switches per cell. Furthermore, the prospects of ECM with regard to further scalability and the ability for multi-bit data storage are addressed.

Continuum-Kinetic Models and Numerical Methods for Multiphase Applications

NASA Astrophysics Data System (ADS)

Nault, Isaac Michael

This thesis presents a continuum-kinetic approach for modeling general problems in multiphase solid mechanics. In this context, a continuum model refers to any model, typically on the macro-scale, in which continuous state variables are used to capture the most important physics: conservation of mass, momentum, and energy. A kinetic model refers to any model, typically on the meso-scale, which captures the statistical motion and evolution of microscopic entitites. Multiphase phenomena usually involve non-negligible micro or meso-scopic effects at the interfaces between phases. The approach developed in the thesis attempts to combine the computational performance benefits of a continuum model with the physical accuracy of a kinetic model when applied to a multiphase problem. The approach is applied to modeling a single particle impact in Cold Spray, an engineering process that intimately involves the interaction of crystal grains with high-magnitude elastic waves. Such a situation could be classified a multiphase application due to the discrete nature of grains on the spatial scale of the problem. For this application, a hyper elasto-plastic model is solved by a finite volume method with approximate Riemann solver. The results of this model are compared for two types of plastic closure: a phenomenological macro-scale constitutive law, and a physics-based meso-scale Crystal Plasticity model.

Processes of aggression described by kinetic method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aristov, V. V.; Ilyin, O.

In the last decades many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological and historical processes. In the present paper we suggest a model of the Nazi Germany invasion of Poland, France and USSR based on the kinetic theory. We model this process with the Cauchy boundary problem for the two-element kinetic equations with spatial initial conditions. The solution of the problem is given in the form of traveling wave. The propagation velocity of a frontline depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solutionmore » of the model can be expressed in terms of quadratures and elementary functions. Finally it is shown that the frontline velocities are complied with the historical data.« less

Kinetic models for historical processes of fast invasion and aggression

NASA Astrophysics Data System (ADS)

Aristov, Vladimir V.; Ilyin, Oleg V.

2015-04-01

In the last few decades many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological, and historical processes. In the present paper we suggest a model of the Nazi Germany invasion of Poland, France, and the USSR based on kinetic theory. We simulate this process with the Cauchy boundary problem for two-element kinetic equations. The solution of the problem is given in the form of a traveling wave. The propagation velocity of a front line depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solution of the model can be expressed in terms of quadratures and elementary functions. Finally it is shown that the front-line velocities agree with the historical data.

Implicit Plasma Kinetic Simulation Using The Jacobian-Free Newton-Krylov Method

NASA Astrophysics Data System (ADS)

Taitano, William; Knoll, Dana; Chacon, Luis

2009-11-01

The use of fully implicit time integration methods in kinetic simulation is still area of algorithmic research. A brute-force approach to simultaneously including the field equations and the particle distribution function would result in an intractable linear algebra problem. A number of algorithms have been put forward which rely on an extrapolation in time. They can be thought of as linearly implicit methods or one-step Newton methods. However, issues related to time accuracy of these methods still remain. We are pursuing a route to implicit plasma kinetic simulation which eliminates extrapolation, eliminates phase-space from the linear algebra problem, and converges the entire nonlinear system within a time step. We accomplish all this using the Jacobian-Free Newton-Krylov algorithm. The original research along these lines considered particle methods to advance the distribution function [1]. In the current research we are advancing the Vlasov equations on a grid. Results will be presented which highlight algorithmic details for single species electrostatic problems and coupled ion-electron electrostatic problems. [4pt] [1] H. J. Kim, L. Chac'on, G. Lapenta, ``Fully implicit particle in cell algorithm,'' 47th Annual Meeting of the Division of Plasma Physics, Oct. 24-28, 2005, Denver, CO

Use of fly ash, phosphogypsum and red mud as a liner material for the disposal of hazardous zinc leach residue waste.

PubMed

Coruh, Semra; Ergun, Osman Nuri

2010-01-15

Increasing amounts of residues and waste materials coming from industrial activities in different processes have become an increasingly urgent problem for the future. The release of large quantities of heavy metals into the environment has resulted in a number of environmental problems. The present study investigated the safe disposal of the zinc leach residue waste using industrial residues such as fly ash, phosphogypsum and red mud. In the study, leachability of heavy metals from the zinc leach residue has been evaluated by mine water leaching procedure (MWLP) and toxicity characteristic leaching procedure (TCLP). Zinc removal from leachate was studied using fly ash, phosphogypsum and red mud. The adsorption capacities and adsorption efficiencies were determined. The adsorption rate data was analyzed according to the pseudo-second-order kinetic, Elovich kinetic and intra-particle diffusion kinetic models. The pseudo-second-order kinetic was the best fit kinetic model for the experimental data. The results show that addition of fly ash, phosphogypsum and red mud to the zinc leach residue drastically reduces the heavy metal content in the leachate and could be used as liner materials.

Review of chemical-kinetic problems of future NASA missions. I - Earth entries

NASA Technical Reports Server (NTRS)

Park, Chul

1993-01-01

A number of chemical-kinetic problems related to phenomena occurring behind a shock wave surrounding an object flying in the earth atmosphere are discussed, including the nonequilibrium thermochemical relaxation phenomena occurring behind a shock wave surrounding the flying object, problems related to aerobraking maneuver, the radiation phenomena for shock velocities of up to 12 km/sec, and the determination of rate coefficients for ionization reactions and associated electron-impact ionization reactions. Results of experiments are presented in form of graphs and tables, giving data on the reaction rate coefficients for air, the ionization distances, thermodynamic properties behind a shock wave, radiative heat flux calculations, Damkoehler numbers for the ablation-product layer, together with conclusions.

Self-Paced Physics, Segment 18.

ERIC Educational Resources Information Center

New York Inst. of Tech., Old Westbury.

Eighty-seven problems are included in this volume which is arranged to match study segments 2 through 14. The subject matter is related to projectiles, simple harmonic motion, kinetic friction, multiple pulley arrangements, motion on inclined planes, circular motion, potential energy, kinetic energy, center of mass, Newton's laws, elastic and…

3D nozzle flow simulations including state-to-state kinetics calculation

NASA Astrophysics Data System (ADS)

Cutrone, L.; Tuttafesta, M.; Capitelli, M.; Schettino, A.; Pascazio, G.; Colonna, G.

2014-12-01

In supersonic and hypersonic flows, thermal and chemical non-equilibrium is one of the fundamental aspects that must be taken into account for the accurate characterization of the plasma. In this paper, we present an optimized methodology to approach plasma numerical simulation by state-to-state kinetics calculations in a fully 3D Navier-Stokes CFD solver. Numerical simulations of an expanding flow are presented aimed at comparing the behavior of state-to-state chemical kinetics models with respect to the macroscopic thermochemical non-equilibrium models that are usually used in the numerical computation of high temperature hypersonic flows. The comparison is focused both on the differences in the numerical results and on the computational effort associated with each approach.

LSENS - GENERAL CHEMICAL KINETICS AND SENSITIVITY ANALYSIS CODE

NASA Technical Reports Server (NTRS)

Bittker, D. A.

1994-01-01

LSENS has been developed for solving complex, homogeneous, gas-phase, chemical kinetics problems. The motivation for the development of this program is the continuing interest in developing detailed chemical reaction mechanisms for complex reactions such as the combustion of fuels and pollutant formation and destruction. A reaction mechanism is the set of all elementary chemical reactions that are required to describe the process of interest. Mathematical descriptions of chemical kinetics problems constitute sets of coupled, nonlinear, first-order ordinary differential equations (ODEs). The number of ODEs can be very large because of the numerous chemical species involved in the reaction mechanism. Further complicating the situation are the many simultaneous reactions needed to describe the chemical kinetics of practical fuels. For example, the mechanism describing the oxidation of the simplest hydrocarbon fuel, methane, involves over 25 species participating in nearly 100 elementary reaction steps. Validating a chemical reaction mechanism requires repetitive solutions of the governing ODEs for a variety of reaction conditions. Analytical solutions to the systems of ODEs describing chemistry are not possible, except for the simplest cases, which are of little or no practical value. Consequently, there is a need for fast and reliable numerical solution techniques for chemical kinetics problems. In addition to solving the ODEs describing chemical kinetics, it is often necessary to know what effects variations in either initial condition values or chemical reaction mechanism parameters have on the solution. Such a need arises in the development of reaction mechanisms from experimental data. The rate coefficients are often not known with great precision and in general, the experimental data are not sufficiently detailed to accurately estimate the rate coefficient parameters. The development of a reaction mechanism is facilitated by a systematic sensitivity analysis which provides the relationships between the predictions of a kinetics model and the input parameters of the problem. LSENS provides for efficient and accurate chemical kinetics computations and includes sensitivity analysis for a variety of problems, including nonisothermal conditions. LSENS replaces the previous NASA general chemical kinetics codes GCKP and GCKP84. LSENS is designed for flexibility, convenience and computational efficiency. A variety of chemical reaction models can be considered. The models include static system, steady one-dimensional inviscid flow, reaction behind an incident shock wave including boundary layer correction, and the perfectly stirred (highly backmixed) reactor. In addition, computations of equilibrium properties can be performed for the following assigned states, enthalpy and pressure, temperature and pressure, internal energy and volume, and temperature and volume. For static problems LSENS computes sensitivity coefficients with respect to the initial values of the dependent variables and/or the three rates coefficient parameters of each chemical reaction. To integrate the ODEs describing chemical kinetics problems, LSENS uses the packaged code LSODE, the Livermore Solver for Ordinary Differential Equations, because it has been shown to be the most efficient and accurate code for solving such problems. The sensitivity analysis computations use the decoupled direct method, as implemented by Dunker and modified by Radhakrishnan. This method has shown greater efficiency and stability with equal or better accuracy than other methods of sensitivity analysis. LSENS is written in FORTRAN 77 with the exception of the NAMELIST extensions used for input. While this makes the code fairly machine independent, execution times on IBM PC compatibles would be unacceptable to most users. LSENS has been successfully implemented on a Sun4 running SunOS and a DEC VAX running VMS. With minor modifications, it should also be easily implemented on other platforms with FORTRAN compilers which support NAMELIST input. LSENS required 4Mb of RAM under SunOS 4.1.1 and 3.4Mb of RAM under VMS 5.5.1. The standard distribution medium for LSENS is a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format. It is also available on a 1600 BPI 9-track magnetic tape or a TK50 tape cartridge in DEC VAX BACKUP format. Alternate distribution media and formats are available upon request. LSENS was developed in 1992.

A minimal dissipation type-based classification in irreversible thermodynamics and microeconomics

NASA Astrophysics Data System (ADS)

Tsirlin, A. M.; Kazakov, V.; Kolinko, N. A.

2003-10-01

We formulate the problem of finding classes of kinetic dependencies in irreversible thermodynamic and microeconomic systems for which minimal dissipation processes belong to the same type. We show that this problem is an inverse optimal control problem and solve it. The commonality of this problem in irreversible thermodynamics and microeconomics is emphasized.

A mixed fluid-kinetic solver for the Vlasov-Poisson equations

NASA Astrophysics Data System (ADS)

Cheng, Yongtao

Plasmas are ionized gases that appear in a wide range of applications including astrophysics and space physics, as well as in laboratory settings such as in magnetically confined fusion. There are two prevailing types of modeling strategies to describe a plasma system: kinetic models and fluid models. Kinetic models evolve particle probability density distributions (PDFs) in phase space, which are accurate but computationally expensive. Fluid models evolve a small number of moments of the distribution function and reduce the dimension of the solution. However, some approximation is necessary to close the system, and finding an accurate moment closure that correctly captures the dynamics away from thermodynamic equilibrium is a difficult and still open problem. The main contributions of the present work can be divided into two main parts: (1) a new class of moment closures, based on a modification of existing quadrature-based moment-closure methods, is developed using bi-B-spline and bi-bubble representations; and (2) a novel mixed solver that combines a fluid and a kinetic solver is proposed, which uses the new class of moment-closure methods described in the first part. For the newly developed quadrature-based moment-closure based on bi-B-spline and bi-bubble representation, the explicit form of flux terms and the moment-realizability conditions are given. It is shown that while the bi-delta system is weakly hyperbolic, the newly proposed fluid models are strongly hyperbolic. Using a high-order Runge-Kutta discontinuous Galerkin method together with Strang operator splitting, the resulting models are applied to the Vlasov-Poisson-Fokker-Planck system in the high field limit. In the second part of this work, results from kinetic solver are used to provide a corrected closure to the fluid model. This correction keeps the fluid model hyperbolic and gives fluid results that match the moments as computed from the kinetic solution. Furthermore, a prolongation operation based on the bi-bubble moment-closure is used to make the first few moments of the kinetic and fluid solvers match. This results in a kinetic solver that exactly conserves mass and total energy. This mixed fluid-kinetic solver is applied to standard test problems for the Vlasov-Poisson system, including two-stream-instability problem and Landau damping.

Nano-Material Aspects of Shock Absorption in Bone Joints

PubMed Central

Tributsch, H; Copf, F; Copf, p; Hindenlang, U; Niethard, F.U; Schneider, R

2010-01-01

This theoretical study is based on a nano-technological evaluation of the effect of pressure on the composite bone fine structure. It turned out, that the well known macroscopic mechano-elastic performance of bones in combination with muscles and tendons is just one functional aspect which is critically supported by additional micro- and nano- shock damping technology aimed at minimising local bone material damage within the joints and supporting spongy bone material. The identified mechanisms comprise essentially three phenomena localised within the three–dimensional spongy structure with channels and so called perforated flexible tensulae membranes of different dimensions intersecting and linking them. Kinetic energy of a mechanical shock may be dissipated within the solid-liquid composite bone structure into heat via the generation of quasi-chaotic hydromechanic micro-turbulence. It may generate electro-kinetic energy in terms of electric currents and potentials. And the resulting specific structural and surface electrochemical changes may induce the compressible intra-osseal liquid to build up pressure dependent free chemical energy. Innovative bone joint prostheses will have to consider and to be adapted to the nano-material aspects of shock absorption in the operated bones. PMID:21625375

Tense and aspect in word problems about motion: diagram, gesture, and the felt experience of time

NASA Astrophysics Data System (ADS)

de Freitas, Elizabeth; Zolkower, Betina

2015-09-01

Word problems about motion contain various conjugated verb forms. As students and teachers grapple with such word problems, they jointly operationalize diagrams, gestures, and language. Drawing on findings from a 3-year research project examining the social semiotics of classroom interaction, we show how teachers and students use gesture and diagram to make sense of complex verb forms in such word problems. We focus on the grammatical category of "aspect" for how it broadens the concept of verb tense. Aspect conveys duration and completion or frequency of an event. The aspect of a verb defines its temporal flow (or lack thereof) and the location of a vantage point for making sense of this durational process.

SORPTION AND DESORPTION BY IDEAL TWO-COMPARTMENT SYSTEMS: UNUSUAL BEHAVIOR AND DATA INTERPRETATION PROBLEMS

EPA Science Inventory

This paper presents an evaluation of the results of fitting curves to isotherm and kinetic data for idealized two-compartment systems of soil or sediment. Data were produced by numerically solving sets of Freundlich isotherm and first-order kinetics equations for mixtures of up ...

Nonisothermal Analysis of Solution Kinetics by Spreadsheet Simulation

ERIC Educational Resources Information Center

de Levie, Robert

2012-01-01

A fast and generally applicable alternative solution to the problem of determining the useful shelf life of medicinal solutions is described. It illustrates the power and convenience of the combination of numerical simulation and nonlinear least squares with a practical pharmaceutical application of chemical kinetics and thermodynamics, validated…

Enzyme Kinetics and the Michaelis-Menten Equation

ERIC Educational Resources Information Center

Biaglow, Andrew; Erickson, Keith; McMurran, Shawnee

2010-01-01

The concepts presented in this article represent the cornerstone of classical mathematical biology. The central problem of the article relates to enzyme kinetics, which is a biochemical system. However, the theoretical underpinnings that lead to the formation of systems of time-dependent ordinary differential equations have been applied widely to…

Kinetic phase transitions and reactive windows in reactions of monomers on two-dimensional lattices

NASA Astrophysics Data System (ADS)

Cortés, Joaquín; Puschmann, Heinrich; Valencia, Eliana

1997-01-01

Some conceptual considerations are made and Monte Carlo simulation studies are carried out to analyze a series of catalytic reactions of two and three monomers on a square lattice of sites. Two aspects are considered: The increase in the system's degrees of freedom, leading to the formation of reactive sites that allow a change in the character of one of the kinetic phase transitions from the first order to a second order transition, and the classification and reactivity of the new system class.

Effect of medium acidity on the thermodynamics and kinetics of the reaction of pyridoxal 5'-phosphate with isoniazid in an aqueous solution

NASA Astrophysics Data System (ADS)

Gamov, G. A.; Zavalishin, M. N.; Usacheva, T. R.; Sharnin, V. A.

2017-05-01

Thermodynamic characteristics of the formation of the Schiff base between isoniazid and pyridoxal 5'-phosphate in an aqueous solution at different pH values of a medium are determined by means of spectrophotometry and calorimetric titration. The process kinetics is studied spectrophotometrically, and the reaction rate constants for the formation of the imine at different acidities of a medium are determined. Biochemical aspects of the binding of pyridoxal 5'-phosphate into stable compounds are discussed.

Methods for determining the physiological state of a plant

DOEpatents

Kramer, David M.; Sacksteder, Colette

2003-09-23

The present invention provides methods for measuring a photosynthetic parameter. The methods of the invention include the steps of: (a) illuminating a plant leaf until steady-state photosynthesis is achieved; (b) subjecting the illuminated plant leaf to a period of darkness; (c) using a kinetic spectrophotometer or kinetic spectrophotometer/fluorimeter to collect spectral data from the plant leaf treated in accordance with steps (a) and (b); and (d) determining a photosynthetic parameter from the spectral data. In another aspect, the invention provides methods for determining the physiological state of a plant.

Radiation Sensitization in Cancer Therapy.

ERIC Educational Resources Information Center

Greenstock, Clive L.

1981-01-01

Discusses various aspects of radiation damage to biological material, including free radical mechanisms, radiation sensitization and protection, tumor hypoxia, mechanism of hypoxic cell radiosensitization, redox model for radiation modification, sensitizer probes of cellular radiation targets, pulse radiolysis studies of free radical kinetics,…

Lectures on combustion theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burstein, S.Z.; Lax, P.D.; Sod, G.A.

1978-09-01

Eleven lectures are presented on mathematical aspects of combustion: fluid dynamics, deflagrations and detonations, chemical kinetics, gas flows, combustion instability, flame spread above solids, spark ignition engines, burning rate of coal particles and hydrocarbon oxidation. Separate abstracts were prepared for three of the lectures. (DLC)

Do Scaffolded Supports between Aspects of Problem Solving Enhance Assessment Usability?

ERIC Educational Resources Information Center

McCoy, Jan D.; Braun-Monegan, Jenelle; Bettesworth, Leanne; Tindal, Gerald

2015-01-01

While problem solving as an instructional technique is widely advocated, educators are often challenged in effectively assessing student skill in this area. Students failing to solve a problem might fail in any of several aspects of the effort. The purpose of this research was to validate a scaffolded technique for assessing problem solving in…

Mind over matter? I: philosophical aspects of the mind-brain problem.

PubMed

Schimmel, P

2001-08-01

To conceptualize the essence of the mind-body or mind-brain problem as one of metaphysics rather than science, and to propose a formulation of the problem in the context of current scientific knowledge and its limitations. The background and conceptual parameters of the mind-body problem are delineated, and the limitations of brain research in formulating a solution identified. The problem is reformulated and stated in terms of two propositions. These constitute a 'double aspect theory'. The problem appears to arise as a consequence of the conceptual limitations of the human mind, and hence remains essentially a metaphysical one. A 'double aspect theory' recognizes the essential unity of mind and brain, while remaining consistent with the dualism inherent in human experience.

Coping with jealousy: the association between maladaptive aspects of jealousy and drinking problems is mediated by drinking to cope.

PubMed

Dibello, Angelo M; Neighbors, Clayton; Rodriguez, Lindsey M; Lindgren, Kristen

2014-01-01

Previous research has shown that both alcohol use and jealousy are related to negative relationship outcomes. Little work, however, has examined direct associations between alcohol use and jealousy. The current study was aimed to build upon existing research examining alcohol use and jealousy. More specifically, findings from current jealousy literature indicate that jealousy is a multifaceted construct with both maladaptive and adaptive aspects. The current study examined the association between maladaptive and adaptive feelings of jealousy and alcohol-related problems in the context of drinking to cope. Given the relationship between coping motives and alcohol-related problems, our primary interest was in predicting alcohol-related problems, but alcohol consumption was also investigated. Undergraduate students at a large Northwestern university (N=657) in the US participated in the study. They completed measures of jealousy, drinking to cope, alcohol use, and alcohol-related problems. Analyses examined associations between jealousy subscales, alcohol use, drinking to cope, and drinking problems. Results indicated that drinking to cope mediated the association between some, but not all, aspects of jealousy and problems with alcohol use. In particular, the more negative or maladaptive aspects of jealousy were related to drinking to cope and drinking problems, while the more adaptive aspects were not, suggesting a more complex view of jealousy than previously understood. © 2013. Published by Elsevier Ltd. All rights reserved.

Coping with Jealousy: The Association between Maladaptive Aspects of Jealousy and Drinking Problems are Mediated by Drinking to Cope

PubMed Central

DiBello, Angelo M.; Neighbors, Clayton; Rodriguez, Lindsey M.; Lindgren, Kristen

2013-01-01

Previous research has shown that both alcohol use and jealousy are related to negative relationship outcomes. Little work, however, has examined direct associations between alcohol use and jealousy. The current study aimed to build upon existing research examining alcohol use and jealousy. More specifically, findings from current jealousy literature indicate that jealousy is a multifaceted construct with both maladaptive and adaptive aspects. The current study examined the association between maladaptive and adaptive feelings of jealousy and alcohol-related problems in the context of drinking to cope. Given the relationship between coping motives and alcohol-related problems, our primary interest was in predicting alcohol-related problems, but alcohol consumption was also investigated. Undergraduate students at a large Northwestern university (N = 657) in the US participated in the study. They completed measures of jealousy, drinking to cope, alcohol use, and alcohol-related problems. Analyses examined associations between jealousy subscales, alcohol use, drinking to cope, and drinking problems. Results indicated that drinking to cope mediated the association between some, but not all, aspects of jealousy and problems with alcohol use. In particular, the more negative or maladaptive aspects of jealousy were related to drinking to cope and drinking problems, while the more adaptive aspects were not, suggesting a more complex view of jealousy than previously understood. PMID:24138965

A critical analysis of the accuracy of several numerical techniques for combustion kinetic rate equations

NASA Technical Reports Server (NTRS)

Radhadrishnan, Krishnan

1993-01-01

A detailed analysis of the accuracy of several techniques recently developed for integrating stiff ordinary differential equations is presented. The techniques include two general-purpose codes EPISODE and LSODE developed for an arbitrary system of ordinary differential equations, and three specialized codes CHEMEQ, CREK1D, and GCKP4 developed specifically to solve chemical kinetic rate equations. The accuracy study is made by application of these codes to two practical combustion kinetics problems. Both problems describe adiabatic, homogeneous, gas-phase chemical reactions at constant pressure, and include all three combustion regimes: induction, heat release, and equilibration. To illustrate the error variation in the different combustion regimes the species are divided into three types (reactants, intermediates, and products), and error versus time plots are presented for each species type and the temperature. These plots show that CHEMEQ is the most accurate code during induction and early heat release. During late heat release and equilibration, however, the other codes are more accurate. A single global quantity, a mean integrated root-mean-square error, that measures the average error incurred in solving the complete problem is used to compare the accuracy of the codes. Among the codes examined, LSODE is the most accurate for solving chemical kinetics problems. It is also the most efficient code, in the sense that it requires the least computational work to attain a specified accuracy level. An important finding is that use of the algebraic enthalpy conservation equation to compute the temperature can be more accurate and efficient than integrating the temperature differential equation.

Multiplexed immunosensing and kinetics monitoring in nanofluidic devices with highly enhanced target capture efficiency

PubMed Central

Lin, Yii-Lih; Huang, Yen-Jun; Teerapanich, Pattamon; Leïchlé, Thierry

2016-01-01

Nanofluidic devices promise high reaction efficiency and fast kinetic responses due to the spatial constriction of transported biomolecules with confined molecular diffusion. However, parallel detection of multiple biomolecules, particularly proteins, in highly confined space remains challenging. This study integrates extended nanofluidics with embedded protein microarray to achieve multiplexed real-time biosensing and kinetics monitoring. Implementation of embedded standard-sized antibody microarray is attained by epoxy-silane surface modification and a room-temperature low-aspect-ratio bonding technique. An effective sample transport is achieved by electrokinetic pumping via electroosmotic flow. Through the nanoslit-based spatial confinement, the antigen-antibody binding reaction is enhanced with ∼100% efficiency and may be directly observed with fluorescence microscopy without the requirement of intermediate washing steps. The image-based data provide numerous spatially distributed reaction kinetic curves and are collectively modeled using a simple one-dimensional convection-reaction model. This study represents an integrated nanofluidic solution for real-time multiplexed immunosensing and kinetics monitoring, starting from device fabrication, protein immobilization, device bonding, sample transport, to data analysis at Péclet number less than 1. PMID:27375819

Kinetic models of controllable pore growth of anodic aluminum oxide membrane

NASA Astrophysics Data System (ADS)

Huang, Yan; Zeng, Hong-yan; Zhao, Ce; Qu, Ye-qing; Zhang, Pin

2012-06-01

An anodized Al2O3 (AAO) membrane with apertures about 72 nm in diameter was prepared by two-step anodic oxidation. The appearance and pore arrangement of the AAO membrane were characterized by energy dispersive x-ray spectroscopy and scanning electron microscopy. It was confirmed that the pores with high pore aspect ratio were parallel, well-ordered, and uniform. The kinetics of pores growth in the AAO membrane was derived, and the kinetic models showed that pores stopped developing when the pressure ( σ) trended to equal the surface tension at the end of anodic oxidation. During pore expansion, the effects of the oxalic acid concentration and expansion time on the pore size were investigated, and the kinetic behaviors were explained with two kinetic models derived in this study. They showed that the pore size increased with extended time ( r= G· t+ G'), but decreased with increased concentration ( r = - K·ln c- K') through the derived mathematic formula. Also, the values of G, G', K, and K' were derived from our experimental data.

Challenges for mass production of nematodes in submerged culture.

PubMed

de la Torre, Mayra

2003-08-01

Nematodes of Steinernema and Heterorhabditis genera are used as agents in insect biocontrol programs. They are associated with specific bacteria which are also involved in the mechanism of pathogenicity and which are consumed by nematodes as living food. S. feltiae has various developmental stages in its life cycle, including four juvenile stages, adults and the free living form. During mating, males coil themselves around the female, which is around 1 cm long. Successful commercialization of nematode-bacteria biocontrol products depends on the ability to produce sufficient quantities of these products at competitive prices for a full pest control program. This could be feasible if high cell density submerged cultures are designed and implemented; however, major problems related to nematodes mass production in a bioreactor remain unsolved due to the lack of knowledge about the physiological aspects of the nematode, bacteria and nematode-bacteria association, interaction between the three phases present in the bioreactor (liquid, gas, nematodes-bacteria), possibility of mating under hydrodynamic stress conditions, etc. We have found that the two most important engineering aspects to take into account the mass propagation of nematodes are oxygen transfer rate and hydrodynamics to allow mating and to avoid mechanical damage of juveniles in stage 2. This article focuses on several aspects related to the fermentation system such as kinetics of growth, shear stress, hydrodynamics fields in the bioreactor and oxygen demand. Also, results published by other groups, together with those of our own, will be discussed in relation to the main challenges found during the fermentation process.

Compactness and robustness: Applications in the solution of integral equations for chemical kinetics and electromagnetic scattering

NASA Astrophysics Data System (ADS)

Zhou, Yajun

This thesis employs the topological concept of compactness to deduce robust solutions to two integral equations arising from chemistry and physics: the inverse Laplace problem in chemical kinetics and the vector wave scattering problem in dielectric optics. The inverse Laplace problem occurs in the quantitative understanding of biological processes that exhibit complex kinetic behavior: different subpopulations of transition events from the "reactant" state to the "product" state follow distinct reaction rate constants, which results in a weighted superposition of exponential decay modes. Reconstruction of the rate constant distribution from kinetic data is often critical for mechanistic understandings of chemical reactions related to biological macromolecules. We devise a "phase function approach" to recover the probability distribution of rate constants from decay data in the time domain. The robustness (numerical stability) of this reconstruction algorithm builds upon the continuity of the transformations connecting the relevant function spaces that are compact metric spaces. The robust "phase function approach" not only is useful for the analysis of heterogeneous subpopulations of exponential decays within a single transition step, but also is generalizable to the kinetic analysis of complex chemical reactions that involve multiple intermediate steps. A quantitative characterization of the light scattering is central to many meteoro-logical, optical, and medical applications. We give a rigorous treatment to electromagnetic scattering on arbitrarily shaped dielectric media via the Born equation: an integral equation with a strongly singular convolution kernel that corresponds to a non-compact Green operator. By constructing a quadratic polynomial of the Green operator that cancels out the kernel singularity and satisfies the compactness criterion, we reveal the universality of a real resonance mode in dielectric optics. Meanwhile, exploiting the properties of compact operators, we outline the geometric and physical conditions that guarantee a robust solution to the light scattering problem, and devise an asymptotic solution to the Born equation of electromagnetic scattering for arbitrarily shaped dielectric in a non-perturbative manner.

Fully Parallel MHD Stability Analysis Tool

NASA Astrophysics Data System (ADS)

Svidzinski, Vladimir; Galkin, Sergei; Kim, Jin-Soo; Liu, Yueqiang

2014-10-01

Progress on full parallelization of the plasma stability code MARS will be reported. MARS calculates eigenmodes in 2D axisymmetric toroidal equilibria in MHD-kinetic plasma models. It is a powerful tool for studying MHD and MHD-kinetic instabilities and it is widely used by fusion community. Parallel version of MARS is intended for simulations on local parallel clusters. It will be an efficient tool for simulation of MHD instabilities with low, intermediate and high toroidal mode numbers within both fluid and kinetic plasma models, already implemented in MARS. Parallelization of the code includes parallelization of the construction of the matrix for the eigenvalue problem and parallelization of the inverse iterations algorithm, implemented in MARS for the solution of the formulated eigenvalue problem. Construction of the matrix is parallelized by distributing the load among processors assigned to different magnetic surfaces. Parallelization of the solution of the eigenvalue problem is made by repeating steps of the present MARS algorithm using parallel libraries and procedures. Initial results of the code parallelization will be reported. Work is supported by the U.S. DOE SBIR program.

Simulation of 2D rarefied gas flows based on the numerical solution of the Boltzmann equation

NASA Astrophysics Data System (ADS)

Poleshkin, Sergey O.; Malkov, Ewgenij A.; Kudryavtsev, Alexey N.; Shershnev, Anton A.; Bondar, Yevgeniy A.; Kohanchik, A. A.

2017-10-01

There are various methods for calculating rarefied gas flows, in particular, statistical methods and deterministic methods based on the finite-difference solutions of the Boltzmann nonlinear kinetic equation and on the solutions of model kinetic equations. There is no universal method; each has its disadvantages in terms of efficiency or accuracy. The choice of the method depends on the problem to be solved and on parameters of calculated flows. Qualitative theoretical arguments help to determine the range of parameters of effectively solved problems for each method; however, it is advisable to perform comparative tests of calculations of the classical problems performed by different methods and with different parameters to have quantitative confirmation of this reasoning. The paper provides the results of the calculations performed by the authors with the help of the Direct Simulation Monte Carlo method and finite-difference methods of solving the Boltzmann equation and model kinetic equations. Based on this comparison, conclusions are made on selecting a particular method for flow simulations in various ranges of flow parameters.

Tumorigenic action of beta, proton, alpha and electron radiation on the rat skin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burns, F.J.

1980-01-01

Rat skin is utilized as a model system for studying dose and time related aspects of the oncogenic action of ionizing radiation, ultraviolet light and polycyclic aromatic hydrocarbons. Molecular lesions in the DNA of the epidermis, including strand breaks and thymine dimers, are measured and compared to the temporal and dose related aspects of tumor induction. The induction and repair kinetics of molecular lesions are compared to split dose recovery as modified by sensitizers and type of radition of oncogenic damage.

Pathway-engineering for highly-aligned block copolymer arrays

DOE PAGES

Choo, Youngwoo; Majewski, Paweł W.; Fukuto, Masafumi; ...

2017-12-06

While kinetic aspects of self-assembly can hinder ordering, non-equilibirum effects can also be exploited to enforce a particular kind of order. We develop a pathway-engineering approach, using it to select a particular arrangement of a block copolymer cylinder phase.

Pathway-engineering for highly-aligned block copolymer arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choo, Youngwoo; Majewski, Paweł W.; Fukuto, Masafumi

While kinetic aspects of self-assembly can hinder ordering, non-equilibirum effects can also be exploited to enforce a particular kind of order. We develop a pathway-engineering approach, using it to select a particular arrangement of a block copolymer cylinder phase.

The Characterization of Cognitive Processes Involved in Chemical Kinetics Using a Blended Processing Framework

ERIC Educational Resources Information Center

Bain, Kinsey; Rodriguez, Jon-Marc G.; Moon, Alena; Towns, Marcy H.

2018-01-01

Chemical kinetics is a highly quantitative content area that involves the use of multiple mathematical representations to model processes and is a context that is under-investigated in the literature. This qualitative study explored undergraduate student integration of chemistry and mathematics during problem solving in the context of chemical…

Kinetic Tetrazolium Microtiter Assay

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Stowe, Raymond; Koenig, David

1993-01-01

Kinetic tetrazolium microtiter assay (KTMA) involves use of tetrazolium salts and Triton X-100 (or equivalent), nontoxic, in vitro color developer solubilizing colored metabolite formazan without injuring or killing metabolizing cells. Provides for continuous measurement of metabolism and makes possible to determine rate of action of antimicrobial agent in real time as well as determines effective inhibitory concentrations. Used to monitor growth after addition of stimulatory compounds. Provides for kinetic determination of efficacy of biocide, greatly increasing reliability and precision of results. Also used to determine relative effectiveness of antimicrobial agent as function of time. Capability of generating results on day of test extremely important in treatment of water and waste, disinfection of hospital rooms, and in pharmaceutical, agricultural, and food-processing industries. Assay also used in many aspects of cell biology.

Analysis of energy relaxation kinetics for control of the electron energy distributions in capacitively coupled RF discharges

NASA Astrophysics Data System (ADS)

Lee, Jung Yeol; Verboncoeur, John P.; Lee, Hae June

2018-04-01

The transition of electron energy probability functions (EEPFs) through the change of heating mode is an important issue in plasma science. A well-known example is that the increase of gas pressure, which was analyzed in terms of the ratio of the energy relaxation mean free path to the electrode gap distance, changes the EEPF from bi-Maxwellian to Maxwellian or Druyvesteyn. In this study, a new aspect of the temporal decay of kinetic energy during the energy relaxation time is theoretically analyzed and compared with a particle-in-cell Monte Carlo collision simulation of capacitively coupled plasmas. A fully kinetic description of electron transport and collisions shows drastic changes of EEPFs with the variation of the driving frequency due to the heating mode transition.

Physical interpretation of antigravity

NASA Astrophysics Data System (ADS)

Bars, Itzhak; James, Albin

2016-02-01

Geodesic incompleteness is a problem in both general relativity and string theory. The Weyl-invariant Standard Model coupled to general relativity (SM +GR ), and a similar treatment of string theory, are improved theories that are geodesically complete. A notable prediction of this approach is that there must be antigravity regions of spacetime connected to gravity regions through gravitational singularities such as those that occur in black holes and cosmological bang/crunch. Antigravity regions introduce apparent problems of ghosts that raise several questions of physical interpretation. It was shown that unitarity is not violated, but there may be an instability associated with negative kinetic energies in the antigravity regions. In this paper we show that the apparent problems can be resolved with the interpretation of the theory from the perspective of observers strictly in the gravity region. Such observers cannot experience the negative kinetic energy in antigravity directly, but can only detect in and out signals that interact with the antigravity region. This is no different from a spacetime black box for which the information about its interior is encoded in scattering amplitudes for in/out states at its exterior. Through examples we show that negative kinetic energy in antigravity presents no problems of principles but is an interesting topic for physical investigations of fundamental significance.

Occurrence of dead core in catalytic particles containing immobilized enzymes: analysis for the Michaelis-Menten kinetics and assessment of numerical methods.

PubMed

Pereira, Félix Monteiro; Oliveira, Samuel Conceição

2016-11-01

In this article, the occurrence of dead core in catalytic particles containing immobilized enzymes is analyzed for the Michaelis-Menten kinetics. An assessment of numerical methods is performed to solve the boundary value problem generated by the mathematical modeling of diffusion and reaction processes under steady state and isothermal conditions. Two classes of numerical methods were employed: shooting and collocation. The shooting method used the ode function from Scilab software. The collocation methods included: that implemented by the bvode function of Scilab, the orthogonal collocation, and the orthogonal collocation on finite elements. The methods were validated for simplified forms of the Michaelis-Menten equation (zero-order and first-order kinetics), for which analytical solutions are available. Among the methods covered in this article, the orthogonal collocation on finite elements proved to be the most robust and efficient method to solve the boundary value problem concerning Michaelis-Menten kinetics. For this enzyme kinetics, it was found that the dead core can occur when verified certain conditions of diffusion-reaction within the catalytic particle. The application of the concepts and methods presented in this study will allow for a more generalized analysis and more accurate designs of heterogeneous enzymatic reactors.

Verification of kinetic schemes of hydrogen ignition and combustion in air

NASA Astrophysics Data System (ADS)

Fedorov, A. V.; Fedorova, N. N.; Vankova, O. S.; Tropin, D. A.

2018-03-01

Three chemical kinetic models for hydrogen combustion in oxygen and three gas-dynamic models for reactive mixture flow behind the initiating SW front were analyzed. The calculated results were compared with experimental data on the dependences of the ignition delay on the temperature and the dilution of the mixture with argon or nitrogen. Based on detailed kinetic mechanisms of nonequilibrium chemical transformations, a mathematical technique for describing the ignition and combustion of hydrogen in air was developed using the ANSYS Fluent code. The problem of ignition of a hydrogen jet fed coaxially into supersonic flow was solved numerically. The calculations were carried out using the Favre-averaged Navier-Stokes equations for a multi-species gas taking into account chemical reactions combined with the k-ω SST turbulence model. The problem was solved in several steps. In the first step, verification of the calculated and experimental data for the three kinetic schemes was performed without considering the conicity of the flow. In the second step, parametric calculations were performed to determine the influence of the conicity of the flow on the mixing and ignition of hydrogen in air using a kinetic scheme consisting of 38 reactions. Three conical supersonic nozzles for a Mach number M = 2 with different expansion angles β = 4°, 4.5°, and 5° were considered.

Integer Linear Programming for Constrained Multi-Aspect Committee Review Assignment

PubMed Central

Karimzadehgan, Maryam; Zhai, ChengXiang

2011-01-01

Automatic review assignment can significantly improve the productivity of many people such as conference organizers, journal editors and grant administrators. A general setup of the review assignment problem involves assigning a set of reviewers on a committee to a set of documents to be reviewed under the constraint of review quota so that the reviewers assigned to a document can collectively cover multiple topic aspects of the document. No previous work has addressed such a setup of committee review assignments while also considering matching multiple aspects of topics and expertise. In this paper, we tackle the problem of committee review assignment with multi-aspect expertise matching by casting it as an integer linear programming problem. The proposed algorithm can naturally accommodate any probabilistic or deterministic method for modeling multiple aspects to automate committee review assignments. Evaluation using a multi-aspect review assignment test set constructed using ACM SIGIR publications shows that the proposed algorithm is effective and efficient for committee review assignments based on multi-aspect expertise matching. PMID:22711970

A tensor Banach algebra approach to abstract kinetic equations

NASA Astrophysics Data System (ADS)

Greenberg, W.; van der Mee, C. V. M.

The study deals with a concrete algebraic construction providing the existence theory for abstract kinetic equation boundary-value problems, when the collision operator A is an accretive finite-rank perturbation of the identity operator in a Hilbert space H. An algebraic generalization of the Bochner-Phillips theorem is utilized to study solvability of the abstract boundary-value problem without any regulatory condition. A Banach algebra in which the convolution kernel acts is obtained explicitly, and this result is used to prove a perturbation theorem for bisemigroups, which then plays a vital role in solving the initial equations.

Nanoscale Properties of Rocks and Subduction Zone Rheology: Inferences for the Mechanisms of Deep Earthquakes

NASA Astrophysics Data System (ADS)

Riedel, M. R.

2007-12-01

Grain boundaries are the key for the understanding of mineral reaction kinetics. More generally, nanometer scale processes involved in breaking and establishing bonds at reaction sites determine how and at which rate bulk rock properties change in response to external tectonic forcing and possibly feed back into various geodynamic processes. A particular problem is the effects of grain-boundary energy on the kinetics of the olivine-spinel phase transformation in subducting slabs. Slab rheology is affected in many ways by this (metastable) mineral phase change. Sluggish kinetics due to metastable hindrance is likely to cause particular difficulties, because of possible strong non-linear feedback loops between strain-rate and change of creep properties during transformation. In order to get these nanoscale properties included into thermo-mechanical models, reliable kinetic data is required. The measurement of grain-boundary energies is, however, a rather difficult problem. Conventional methods of grain boundary surface tension measurement include (a) equilibrium angles at triple junction (b) rotating ball method (c) thermal groove method, and others (Gottstein & Shvindlerman, 1999). Here I suggest a new method that allows for the derivation of grain-boundary energies for an isochemical phase transformation based on experimental (in-situ) kinetic data in combination with a corresponding dynamic scaling law (Riedel and Karato, 1997). The application of this method to the olivine-spinel phase transformation in subducting slabs provides a solution to the extrapolation problem of measured kinetic data: Any kinetic phase boundary measured at the laboratory time scale can be "scaled" to the correct critical isotherm at subduction zones, under experimentelly "forbidden" conditions (Liou et al., 2000). Consequences for the metastability hypothesis that relates deep seismicity with olivine metastability are derived and discussed. References: Gottstein G, Shvindlerman LS (1999) Grain Boundary Migration in Metals, CRC Press, 385 pp., New York. Riedel MR, Karato S (1997) Grain-Size Evolution in Subducted Oceanic Lithosphere Associated with the Olivine- Spinel Transformation and Its Effects on Rheology. EPSL 148: 27-43. Liou JG, Hacker BR, Zhang RY (2000) Into the forbidden zone. Science 287, 1215-1216.

Hydrogen interactions with metals

NASA Technical Reports Server (NTRS)

Mclellan, R. B.; Harkins, C. G.

1975-01-01

Review of the literature on the nature and extent of hydrogen interactions with metals and the role of hydrogen in metal failure. The classification of hydrogen-containing systems is discussed, including such categories as covalent hydrides, volatile hydrides, polymeric hydrides, and transition metal hydride complexes. The use of electronegativity as a correlating parameter in determining hydride type is evaluated. A detailed study is made of the thermodynamics of metal-hydrogen systems, touching upon such aspects as hydrogen solubility, the positions occupied by hydrogen atoms within the solvent metal lattice, the derivation of thermodynamic functions of solid solutions from solubility data, and the construction of statistical models for hydrogen-metal solutions. A number of theories of hydrogen-metal bonding are reviewed, including the rigid-band model, the screened-proton model, and an approach employing the augmented plane wave method to solve the one-electron energy band problem. Finally, the mechanism of hydrogen embrittlement is investigated on the basis of literature data concerning stress effects and the kinetics of hydrogen transport to critical sites.

How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1

PubMed Central

2017-01-01

Abstract Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA. For the first time, we describe the spontaneous formation of a sequence-specific native protein–DNA complex in atomistic detail, and study the mechanism by which proteins avoid off-target binding while retaining high affinity for target sites. Our calculated free energy landscapes reproduce the thermodynamics of sequence-specific binding, while statistical approaches allow for a comprehensive description of intermediate stages of complex formation. PMID:28633355

State of the art for the biosorption process--a review.

PubMed

Michalak, Izabela; Chojnacka, Katarzyna; Witek-Krowiak, Anna

2013-07-01

In recent years, biosorption process has become an economic and eco-friendly alternative treatment technology in the water and wastewater industry. In this light, a number of biosorbents were developed and are successfully employed for treating various pollutants including metals, dyes, phenols, fluoride, and pharmaceuticals in solutions (aqueous/oil). However, still there are few technical barriers in the biosorption process that impede its commercialization and thus to overcome these problems there has been a steadily growing interest in this research field. This resulted in large numbers of publications and patents each year. This review reports the state of the art in biosorption research. In this review, we provide a compendium of know-how in laboratory methodology, mathematical modeling of equilibrium and kinetics, identification of the biosorption mechanism. Various mathematical models of biosorption were discussed: the process in packed-bed column arrangement, as well as by suspended biomass. Particular attention was paid to patents in biosorption and pilot-scale systems. In addition, we provided future aspects in biosorption research.

Atmospheric Oxygen Photoabsorption

NASA Technical Reports Server (NTRS)

Slanger, Tom G.

1996-01-01

The work conducted on this grant was devoted to various aspects of the photophysics and photochemistry of the oxygen molecule. Predissociation linewidths were measured for several vibrational levels in the O2(B3 Sigma(sub u)(sup -)) state, providing good agreement with other groups working on this important problem. Extensive measurements were made on the loss kinetics of vibrationally excited oxygen, where levels between v = 5 and v = 22 were investigated. Cavity ring-down spectroscopy was used to measure oscillator strengths in the oxygen Herzberg bands. The great sensitivity of this technique made it possible to extend the known absorption bands to the dissociation limit as well as providing many new absorption lines that seem to be associated with new O2 transitions. The literature concerning the Herzberg band strengths was evaluated in light of our new measurements, and we made recommendations for the appropriate Herzberg continuum cross sections to be used in stratospheric chemistry. The transition probabilities for all three Herzberg band systems were re-evaluated, and we are recommending a new set of values.

Psychosocial work aspects, stress and musculoskeletal pain among musicians. A systematic review in search of correlates and predictors of playing-related pain.

PubMed

Jacukowicz, Aleksandra

2016-06-16

Musicians face numerous psychosocial and physical demands at work resulting in high prevalence of musculoskeletal problems. Unlike physical risks, little is known about psychosocial work factors influencing such health problems in this particular group. The paper aimed to identify psychosocial work demands resulting in musculoskeletal problems among musicians. A systematic review was undertaken to find data linking psychosocial work demands or stress with musculoskeletal disorders among musicians. The exploration of databases resulted in nine research studies linking psychosocial aspects of work or stress with musculoskeletal problems among musicians. The analyzed studies linked psychosocial aspects with musculoskeletal problems in three ways - showing proportions of people indicating particular causes of pain, indicating correlations between these variables or performing regression analysis showing psychosocial predictors of musculoskeletal pain. Only a few studies have undertaken the issue of psychosocial risk factors for musculoskeletal problems among musicians. The results revealed that some psychosocial aspects of work, e.g. long hours at work, work content, high job demands, low control/influence, lack of social support, were related to musculoskeletal pain, however, the methods and results were inconsistent. The extant studies employed variety of definitions of psychosocial aspects that hindered the possibility for consistent conclusions. Basing on those conclusions, future directions were offered.

On electron bunching and stratification of glow discharges

DOE Office of Scientific and Technical Information (OSTI.GOV)

Golubovskii, Yuri B.; Kolobov, Vladimir I.; Nekuchaev, Vladimir O.

2013-10-15

Plasma stratification and excitation of ionization waves is one of the fundamental problems in gas discharge physics. Significant progress in this field is associated with the name of Lev Tsendin. He advocated the need for the kinetic approach to this problem contrary to the traditional hydrodynamic approach, introduced the idea of electron bunching in spatially periodic electric fields, and developed a theory of kinetic resonances for analysis of moving striations in rare gases. The present paper shows how Tsendin's ideas have been further developed and applied for understanding the nature of the well-known S-, P-, and R-striations observed in glowmore » discharges of inert gases at low pressures and currents. We review numerical solutions of a Fokker-Planck kinetic equation in spatially periodic electric fields under the effects of elastic and inelastic collisions of electrons with atoms. We illustrate the formation of kinetic resonances at specific field periods for different shapes of injected Electron Distribution Functions (EDF). Computer simulations illustrate how self-organization of the EDFs occurs under nonlocal conditions and how Gaussian-like peaks moving along resonance trajectories are formed in a certain range of discharge conditions. The calculated EDFs agree well with the experimentally measured EDFs for the S, P, and R striations in noble gases. We discuss how kinetic resonances affect dispersion characteristics of moving striations and mention some non-linear effects associated with glow discharge stratification. We propose further studies of stratification phenomena combining physical kinetics and non-linear physics.« less

Sample Handling and Chemical Kinetics in an Acoustically Levitated Drop Microreactor

PubMed Central

2009-01-01

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

Assembly Kinetics Determine the Architecture of α-actinin Crosslinked F-actin Networks

PubMed Central

Falzone, Tobias T.; Lenz, Martin; Kovar, David R.; Gardel, Margaret L.

2013-01-01

The actin cytoskeleton is organized into diverse meshworks and bundles that support many aspects of cell physiology. Understanding the self-assembly of these actin-based structures is essential for developing predictive models of cytoskeletal organization. Here we show that the competing kinetics of bundle formation with the onset of dynamic arrest arising from filament entanglements and cross-linking determine the architecture of reconstituted actin networks formed with α-actinin cross-links. Cross-link mediated bundle formation only occurs in dilute solutions of highly mobile actin filaments. As actin polymerization proceeds, filament mobility and bundle formation are arrested concomitantly. By controlling the onset of dynamic arrest, perturbations to actin assembly kinetics dramatically alter the architecture of biochemically identical samples. Thus, the morphology of reconstituted F-actin networks is a kinetically determined structure similar to those formed by physical gels and glasses. These results establish mechanisms controlling the structure and mechanics in diverse semi-flexible biopolymer networks. PMID:22643888

Charging of nanoparticles in stationary plasma in a gas aggregation cluster source

NASA Astrophysics Data System (ADS)

Blažek, J.; Kousal, J.; Biederman, H.; Kylián, O.; Hanuš, J.; Slavínská, D.

2015-10-01

Clusters that grow into nanoparticles near the magnetron target of the gas aggregation cluster source (GAS) may acquire electric charge by collecting electrons and ions or through other mechanisms like secondary- or photo-electron emissions. The region of the GAS close to magnetron may be considered as stationary plasma. The steady state charge distribution on nanoparticles can be determined by means of three possible models—fluid model, kinetic model and model employing Monte Carlo simulations—of cluster charging. In the paper the mathematical and numerical aspects of these models are analyzed in detail and close links between them are clarified. Among others it is shown that Monte Carlo simulation may be considered as a particular numerical technique of solving kinetic equations. Similarly the equations of the fluid model result, after some approximation, from averaged kinetic equations. A new algorithm solving an in principle unlimited set of kinetic equations is suggested. Its efficiency is verified on physical models based on experimental input data.

Kinetic energy partition method applied to ground state helium-like atoms.

PubMed

Chen, Yu-Hsin; Chao, Sheng D

2017-03-28

We have used the recently developed kinetic energy partition (KEP) method to solve the quantum eigenvalue problems for helium-like atoms and obtain precise ground state energies and wave-functions. The key to treating properly the electron-electron (repulsive) Coulomb potential energies for the KEP method to be applied is to introduce a "negative mass" term into the partitioned kinetic energy. A Hartree-like product wave-function from the subsystem wave-functions is used to form the initial trial function, and the variational search for the optimized adiabatic parameters leads to a precise ground state energy. This new approach sheds new light on the all-important problem of solving many-electron Schrödinger equations and hopefully opens a new way to predictive quantum chemistry. The results presented here give very promising evidence that an effective one-electron model can be used to represent a many-electron system, in the spirit of density functional theory.

Integrating Multiple Approaches to Solving Solar Wind Turbulence Problems (Invited)

NASA Astrophysics Data System (ADS)

Karimabadi, H.; Roytershteyn, V.

2013-12-01

The ultimate understanding of the solar wind turbulence must explain the physical process and their connection at all scales ranging from the largest down to electron kinetic scales. This is a daunting task and as a result a more piecemeal approach to the problem has been followed. For example, the role of each wave has been explored in isolation and in simulations with scales limited to those of the underlying waves. In this talk, we present several issues with this approach and offer an alternative with an eye towards more realistic simulations of solar wind turbulence. The main simulation techniques used have been MHD, Hall MHD, hybrid, fully kinetic, and gyrokinetic. We examine the limitations of each approach and their viability for studies of solar wind turbulence. Finally, the effect of initial conditions on the resulting turbulence and their comparison with solar wind are demonstrated through several kinetic simulations.

Analytical solutions for coagulation and condensation kinetics of composite particles

NASA Astrophysics Data System (ADS)

Piskunov, Vladimir N.

2013-04-01

The processes of composite particles formation consisting of a mixture of different materials are essential for many practical problems: for analysis of the consequences of accidental releases in atmosphere; for simulation of precipitation formation in clouds; for description of multi-phase processes in chemical reactors and industrial facilities. Computer codes developed for numerical simulation of these processes require optimization of computational methods and verification of numerical programs. Kinetic equations of composite particle formation are given in this work in a concise form (impurity integrated). Coagulation, condensation and external sources associated with nucleation are taken into account. Analytical solutions were obtained in a number of model cases. The general laws for fraction redistribution of impurities were defined. The results can be applied to develop numerical algorithms considerably reducing the simulation effort, as well as to verify the numerical programs for calculation of the formation kinetics of composite particles in the problems of practical importance.

Studies of fission fragment properties at the Los Alamos Neutron Science Center (LANSCE)

NASA Astrophysics Data System (ADS)

Tovesson, Fredrik; Mayorov, Dmitriy; Duke, Dana; Manning, Brett; Geppert-Kleinrath, Verena

2017-09-01

Nuclear data related to the fission process are needed for a wide variety of research areas, including fundamental science, nuclear energy and non-proliferation. While some of the relevant data have been measured to the required accuracies there are still many aspects of fission that need further investigation. One such aspect is how Total Kinetic Energy (TKE), fragment yields, angular distributions and other fission observables depend on excitation energy of the fissioning system. Another question is the correlation between mass, charge and energy of fission fragments. At the Los Alamos Neutron Science Center (LANSCE) we are studying neutron-induced fission at incident energies from thermal up to hundreds of MeV using the Lujan Center and Weapons Neutron Research (WNR) facilities. Advanced instruments such as SPIDER (time-of-flight and kinetic energy spectrometer), the NIFFTE Time Projection Chamber (TPC), and Frisch grid Ionization Chambers (FGIC) are used to investigate the properties of fission fragments, and some important results for the major actinides have been obtained.

Studies of fission fragment properties at the Los Alamos Neutron Science Center (LANSCE)

DOE PAGES

Tovesson, Fredrik; Mayorov, Dmitriy; Duke, Dana; ...

2017-09-13

Nuclear data related to the fission process are needed for a wide variety of research areas, including fundamental science, nuclear energy and non-proliferation. While some of the relevant data have been measured to the required accuracies there are still many aspects of fission that need further investigation. One such aspect is how Total Kinetic Energy (TKE), fragment yields, angular distributions and other fission observables depend on excitation energy of the fissioning system. Another question is the correlation between mass, charge and energy of fission fragments. At the Los Alamos Neutron Science Center (LANSCE) we are studying neutron-induced fission at incidentmore » energies from thermal up to hundreds of MeV using the Lujan Center and Weapons Neutron Research (WNR) facilities. Advanced instruments such as SPIDER (time-of-flight and kinetic energy spectrometer), the NIFFTE Time Projection Chamber (TPC), and Frisch grid Ionization Chambers (FGIC) are used to investigate the properties of fission fragments, and some important results for the major actinides have been obtained.« less

The effect of salt on the melting of ice: A molecular dynamics simulation study.

PubMed

Kim, Jun Soo; Yethiraj, Arun

2008-09-28

The effect of added salt (NaCl) on the melting of ice is studied using molecular dynamics simulations. The equilibrium freezing point depression observed in the simulations is in good agreement with experimental data. The kinetic aspects of melting are investigated in terms of the exchange of water molecules between ice and the liquid phase. The ice/liquid equilibrium is a highly dynamic process with frequent exchange of water molecules between ice and the liquid phase. The balance is disturbed when ice melts and the melting proceeds in two stages; the inhibition of the association of water molecules to the ice surface at short times, followed by the increased dissociation of water molecules from the ice surface at longer times. We also find that Cl(-) ions penetrate more deeply into the interfacial region than Na(+) ions during melting. This study provides an understanding of the kinetic aspects of melting that could be useful in other processes such as the inhibition of ice growth by antifreeze proteins.

Studies of fission fragment properties at the Los Alamos Neutron Science Center (LANSCE)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tovesson, Fredrik; Mayorov, Dmitriy; Duke, Dana

Nuclear data related to the fission process are needed for a wide variety of research areas, including fundamental science, nuclear energy and non-proliferation. While some of the relevant data have been measured to the required accuracies there are still many aspects of fission that need further investigation. One such aspect is how Total Kinetic Energy (TKE), fragment yields, angular distributions and other fission observables depend on excitation energy of the fissioning system. Another question is the correlation between mass, charge and energy of fission fragments. At the Los Alamos Neutron Science Center (LANSCE) we are studying neutron-induced fission at incidentmore » energies from thermal up to hundreds of MeV using the Lujan Center and Weapons Neutron Research (WNR) facilities. Advanced instruments such as SPIDER (time-of-flight and kinetic energy spectrometer), the NIFFTE Time Projection Chamber (TPC), and Frisch grid Ionization Chambers (FGIC) are used to investigate the properties of fission fragments, and some important results for the major actinides have been obtained.« less

Explicit integration with GPU acceleration for large kinetic networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brock, Benjamin; Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830; Belt, Andrew

2015-12-01

We demonstrate the first implementation of recently-developed fast explicit kinetic integration algorithms on modern graphics processing unit (GPU) accelerators. Taking as a generic test case a Type Ia supernova explosion with an extremely stiff thermonuclear network having 150 isotopic species and 1604 reactions coupled to hydrodynamics using operator splitting, we demonstrate the capability to solve of order 100 realistic kinetic networks in parallel in the same time that standard implicit methods can solve a single such network on a CPU. This orders-of-magnitude decrease in computation time for solving systems of realistic kinetic networks implies that important coupled, multiphysics problems inmore » various scientific and technical fields that were intractable, or could be simulated only with highly schematic kinetic networks, are now computationally feasible.« less

Enhancing the solubility and bioavailability of poorly water-soluble drugs using supercritical antisolvent (SAS) process.

PubMed

Abuzar, Sharif Md; Hyun, Sang-Min; Kim, Jun-Hee; Park, Hee Jun; Kim, Min-Soo; Park, Jeong-Sook; Hwang, Sung-Joo

2018-03-01

Poor water solubility and poor bioavailability are problems with many pharmaceuticals. Increasing surface area by micronization is an effective strategy to overcome these problems, but conventional techniques often utilize solvents and harsh processing, which restricts their use. Newer, green technologies, such as supercritical fluid (SCF)-assisted particle formation, can produce solvent-free products under relatively mild conditions, offering many advantages over conventional methods. The antisolvent properties of the SCFs used for microparticle and nanoparticle formation have generated great interest in recent years, because the kinetics of the precipitation process and morphologies of the particles can be accurately controlled. The characteristics of the supercritical antisolvent (SAS) technique make it an ideal tool for enhancing the solubility and bioavailability of poorly water-soluble drugs. This review article focuses on SCFs and their properties, as well as the fundamentals of overcoming poorly water-soluble drug properties by micronization, crystal morphology control, and formation of composite solid dispersion nanoparticles with polymers and/or surfactants. This article also presents an overview of the main aspects of the SAS-assisted particle precipitation process, its mechanism, and parameters, as well as our own experiences, recent advances, and trends in development. Copyright © 2017 Elsevier B.V. All rights reserved.

Thermodynamics versus Kinetics Dichotomy in the Linear Self-Assembly of Mixed Nanoblocks.

PubMed

Ruiz, L; Keten, S

2014-06-05

We report classical and replica exchange molecular dynamics simulations that establish the mechanisms underpinning the growth kinetics of a binary mix of nanorings that form striped nanotubes via self-assembly. A step-growth coalescence model captures the growth process of the nanotubes, which suggests that high aspect ratio nanostructures can grow by obeying the universal laws of self-similar coarsening, contrary to systems that grow through nucleation and elongation. Notably, striped patterns do not depend on specific growth mechanisms, but are governed by tempering conditions that control the likelihood of depropagation and fragmentation.

Fission fragment yields and total kinetic energy release in neutron-induced fission of235,238U,and239Pu

NASA Astrophysics Data System (ADS)

Tovesson, F.; Duke, D.; Geppert-Kleinrath, V.; Manning, B.; Mayorov, D.; Mosby, S.; Schmitt, K.

2018-03-01

Different aspects of the nuclear fission process have been studied at Los Alamos Neutron Science Center (LANSCE) using various instruments and experimental techniques. Properties of the fragments emitted in fission have been investigated using Frisch-grid ionization chambers, a Time Projection Chamber (TPC), and the SPIDER instrument which employs the 2v-2E method. These instruments and experimental techniques have been used to determine fission product mass yields, the energy dependent total kinetic energy (TKE) release, and anisotropy in neutron-induced fission of U-235, U-238 and Pu-239.

Sodium dopants in helium clusters: Structure, equilibrium and submersion kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Calvo, F.

Alkali impurities bind to helium nanodroplets very differently depending on their size and charge state, large neutral or charged dopants being wetted by the droplet whereas small neutral impurities prefer to reside aside. Using various computational modeling tools such as quantum Monte Carlo and path-integral molecular dynamics simulations, we have revisited some aspects of the physical chemistry of helium droplets interacting with sodium impurities, including the onset of snowball formation in presence of many-body polarization forces, the transition from non-wetted to wetted behavior in larger sodium clusters, and the kinetics of submersion of small dopants after sudden ionization.

Enhanced Sampling Methods for the Computation of Conformational Kinetics in Macromolecules

NASA Astrophysics Data System (ADS)

Grazioli, Gianmarc

Calculating the kinetics of conformational changes in macromolecules, such as proteins and nucleic acids, is still very much an open problem in theoretical chemistry and computational biophysics. If it were feasible to run large sets of molecular dynamics trajectories that begin in one configuration and terminate when reaching another configuration of interest, calculating kinetics from molecular dynamics simulations would be simple, but in practice, configuration spaces encompassing all possible configurations for even the simplest of macromolecules are far too vast for such a brute force approach. In fact, many problems related to searches of configuration spaces, such as protein structure prediction, are considered to be NP-hard. Two approaches to addressing this problem are to either develop methods for enhanced sampling of trajectories that confine the search to productive trajectories without loss of temporal information, or coarse-grained methodologies that recast the problem in reduced spaces that can be exhaustively searched. This thesis will begin with a description of work carried out in the vein of the second approach, where a Smoluchowski diffusion equation model was developed that accurately reproduces the rate vs. force relationship observed in the mechano-catalytic disulphide bond cleavage observed in thioredoxin-catalyzed reduction of disulphide bonds. Next, three different novel enhanced sampling methods developed in the vein of the first approach will be described, which can be employed either separately or in conjunction with each other to autonomously define a set of energetically relevant subspaces in configuration space, accelerate trajectories between the interfaces dividing the subspaces while preserving the distribution of unassisted transition times between subspaces, and approximate time correlation functions from the kinetic data collected from the transitions between interfaces.

A Simple Simulator to Teach Enzyme Kinetics Dynamics. Application in a Problem-Solving Exercise

ERIC Educational Resources Information Center

Torres, Néstor; Santos, Guido

2017-01-01

Enzyme kinetics is an essential part of biochemistry programs, which have been gaining importance in recent years for their applications in biotechnology and biomedicine. The teaching and learning of these issues has been traditionally hampered by difficulties that stem mainly from the dynamic and mathematical nature of the topic and the…

Structural aspects of digestion of medium chain triglycerides studied in real time using sSAXS and Cryo-TEM.

PubMed

Phan, Stephanie; Hawley, Adrian; Mulet, Xavier; Waddington, Lynne; Prestidge, Clive A; Boyd, Ben J

2013-12-01

The purpose of this study was to investigate the colloidal structures formed on digestion of medium chain triglyceride (MCT) with a specific objective of identifying and characterizing a previously reported vesicular phase, which has been linked to supersaturation and anomalous digestion kinetics, and to evaluate the influence of lipid mass and enzyme inhibition on self assembled structure. MCT was digested in vitro and nanostructure was monitored in real time using synchrotron small angle X-ray scattering (sSAXS), and morphology was studied using cryogenic transmission electron microscopy (cryo-TEM). Formation of the putative vesicular phase formed on digestion of MCT was confirmed and its structural attributes were determined. Vesicle formation was dependent on lipid mass and bile salt concentration. The use of enzyme inhibitor for offline analysis of lipolysis samples did influence structural aspects of the digestion medium when compared to real time evaluation. The formation of a vesicular phase was directly linked to the kinetics of lipid digestion. Vesicle formation is linked to lipid mass, or more specifically the ratio of lipid to bile salts present in the digestion mixture. Inhibition of lipase to halt digestion during sampling for offline analysis must be done with caution as structural aspects were shown to differ for the MCT digests with and without inhibitor present.

Modeling the Inner Magnetosphere: Radiation Belts, Ring Current, and Composition

NASA Technical Reports Server (NTRS)

Glocer, Alex

2011-01-01

The space environment is a complex system defined by regions of differing length scales, characteristic energies, and physical processes. It is often difficult, or impossible, to treat all aspects of the space environment relative to a particular problem with a single model. In our studies, we utilize several models working in tandem to examine this highly interconnected system. The methodology and results will be presented for three focused topics: 1) Rapid radiation belt electron enhancements, 2) Ring current study of Energetic Neutral Atoms (ENAs), Dst, and plasma composition, and 3) Examination of the outflow of ionospheric ions. In the first study, we use a coupled MHD magnetosphere - kinetic radiation belt model to explain recent Akebono/RDM observations of greater than 2.5 MeV radiation belt electron enhancements occurring on timescales of less than a few hours. In the second study, we present initial results of a ring current study using a newly coupled kinetic ring current model with an MHD magnetosphere model. Results of a dst study for four geomagnetic events are shown. Moreover, direct comparison with TWINS ENA images are used to infer the role that composition plays in the ring current. In the final study, we directly model the transport of plasma from the ionosphere to the magnetosphere. We especially focus on the role of photoelectrons and and wave-particle interactions. The modeling methodology for each of these studies will be detailed along with the results.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marinov, N.M.; Westbrook, C.K.; Cloutman, L.D.

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 dynamicmore » 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.« less

Secondary flow in turbulent ducts with increasing aspect ratio

NASA Astrophysics Data System (ADS)

Vinuesa, R.; Schlatter, P.; Nagib, H. M.

2018-05-01

Direct numerical simulations of turbulent duct flows with aspect ratios 1, 3, 5, 7, 10, and 14.4 at a center-plane friction Reynolds number Reτ,c≃180 , and aspect ratios 1 and 3 at Reτ,c≃360 , were carried out with the spectral-element code nek5000. The aim of these simulations is to gain insight into the kinematics and dynamics of Prandtl's secondary flow of the second kind and its impact on the flow physics of wall-bounded turbulence. The secondary flow is characterized in terms of the cross-plane component of the mean kinetic energy, and its variation in the spanwise direction of the flow. Our results show that averaging times of around 3000 convective time units (based on duct half-height h ) are required to reach a converged state of the secondary flow, which extends up to a spanwise distance of around ≃5 h measured from the side walls. We also show that if the duct is not wide enough to accommodate the whole extent of the secondary flow, then its structure is modified as reflected through a different spanwise distribution of energy. Another confirmation of the extent of the secondary flow is the decay rate of kinetic energy of any remnant secondary motions for zc/h >5 (where zc is the spanwise distance from the corner) in aspect ratios 7, 10, and 14.4, which exhibits a decreasing level of energy with increasing averaging time ta, and in its rapid rate of decay given by ˜ta-1 . This is the same rate of decay observed in a spanwise-periodic channel simulation, which suggests that at the core, the kinetic energy of the secondary flow integrated over the cross-sectional area, , behaves as a random variable with zero mean, with rate of decay consistent with central limit theorem. Long-time averages of statistics in a region of rectangular ducts extending about the width of a well-designed channel simulation (i.e., extending about ≃3 h on each side of the center plane) indicate that ducts or experimental facilities with aspect ratios larger than 10 may, if properly designed, exhibit good agreement with results obtained from spanwise-periodic channel computations.

Non-Markovian renormalization of kinetic coefficients for drift-type turbulence in magnetized plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zagorodny, A.; Weiland, J.

2009-05-15

The problem of derivation of the kinetic equations for inhomogeneous plasma in an external magnetic field is considered. The Fokker-Planck-type equations with the non-Markovian kinetic coefficients are proposed. In the time-local limit (small correlation times with respect to the distribution function relaxation time) the relations obtained recover the results known from the appropriate quasilinear theory and the Dupree-Weinstock theory of plasma turbulence. Kinetic calculations of the dielectric response function are also performed with regard to the influence of turbulent fields on particle motion. The equations proposed are used to describe zonal flow generation and to estimate the diffusion coefficient formore » saturated turbulence.« less

Role of Kinetic Modeling in Biomedical Imaging

PubMed Central

Huang, Sung-Cheng

2009-01-01

Biomedical imaging can reveal clear 3-dimensional body morphology non-invasively with high spatial resolution. Its efficacy, in both clinical and pre-clinical settings, is enhanced with its capability to provide in vivo functional/biological information in tissue. The role of kinetic modeling in providing biological/functional information in biomedical imaging is described. General characteristics and limitations in extracting biological information are addressed and practical approaches to solve the problems are discussed and illustrated with examples. Some future challenges and opportunities for kinetic modeling to expand the capability of biomedical imaging are also presented. PMID:20640185

Limitations of bootstrap current models

DOE PAGES

Belli, Emily A.; Candy, Jefferey M.; Meneghini, Orso; ...

2014-03-27

We assess the accuracy and limitations of two analytic models of the tokamak bootstrap current: (1) the well-known Sauter model and (2) a recent modification of the Sauter model by Koh et al. For this study, we use simulations from the first-principles kinetic code NEO as the baseline to which the models are compared. Tests are performed using both theoretical parameter scans as well as core- to-edge scans of real DIII-D and NSTX plasma profiles. The effects of extreme aspect ratio, large impurity fraction, energetic particles, and high collisionality are studied. In particular, the error in neglecting cross-species collisional couplingmore » – an approximation inherent to both analytic models – is quantified. Moreover, the implications of the corrections from kinetic NEO simulations on MHD equilibrium reconstructions is studied via integrated modeling with kinetic EFIT.« less

Kinetic Adaptations of Myosins for their Diverse Cellular Functions

PubMed Central

Heissler, Sarah M.; Sellers, James R.

2016-01-01

Members of the myosin superfamily are involved in all aspects of eukaryotic life. Their function ranges from the transport of organelles and cargos to the generation of membrane tension, and the contraction of muscle. The diversity of physiological functions is remarkable, given that all enzymatically active myosins follow a conserved mechanoenzymatic cycle in which the hydrolysis of ATP to ADP and inorganic phosphate is coupled to either actin-based transport or tethering of actin to defined cellular compartments. Kinetic capacities and limitations of a myosin are determined by the extent to with actin can accelerate the hydrolysis of ATP and the release of the hydrolysis products and are indispensably linked to its physiological tasks. This review focuses on kinetic competencies that – together with structural adaptations – result in myosins with unique mechanoenzymatic properties targeted to their diverse cellular function. PMID:26929436

A new hybrid code (CHIEF) implementing the inertial electron fluid equation without approximation

NASA Astrophysics Data System (ADS)

Muñoz, P. A.; Jain, N.; Kilian, P.; Büchner, J.

2018-03-01

We present a new hybrid algorithm implemented in the code CHIEF (Code Hybrid with Inertial Electron Fluid) for simulations of electron-ion plasmas. The algorithm treats the ions kinetically, modeled by the Particle-in-Cell (PiC) method, and electrons as an inertial fluid, modeled by electron fluid equations without any of the approximations used in most of the other hybrid codes with an inertial electron fluid. This kind of code is appropriate to model a large variety of quasineutral plasma phenomena where the electron inertia and/or ion kinetic effects are relevant. We present here the governing equations of the model, how these are discretized and implemented numerically, as well as six test problems to validate our numerical approach. Our chosen test problems, where the electron inertia and ion kinetic effects play the essential role, are: 0) Excitation of parallel eigenmodes to check numerical convergence and stability, 1) parallel (to a background magnetic field) propagating electromagnetic waves, 2) perpendicular propagating electrostatic waves (ion Bernstein modes), 3) ion beam right-hand instability (resonant and non-resonant), 4) ion Landau damping, 5) ion firehose instability, and 6) 2D oblique ion firehose instability. Our results reproduce successfully the predictions of linear and non-linear theory for all these problems, validating our code. All properties of this hybrid code make it ideal to study multi-scale phenomena between electron and ion scales such as collisionless shocks, magnetic reconnection and kinetic plasma turbulence in the dissipation range above the electron scales.

Distinct mechanisms coordinate transcription and translation under carbon and nitrogen starvation in Escherichia coli.

PubMed

Iyer, Sukanya; Le, Dai; Park, Bo Ryoung; Kim, Minsu

2018-05-14

Bacteria adapt to environmental stress by producing proteins that provide stress protection. However, stress can severely perturb the kinetics of gene expression, disrupting protein production. Here, we characterized how Escherichia coli mitigates such perturbations under nutrient stress through the kinetic coordination of transcription and translation. We observed that, when translation became limiting under nitrogen starvation, transcription elongation slowed accordingly. This slowdown was mediated by (p)ppGpp, the alarmone whose primary role is thought to be promoter regulation. This kinetic coordination by (p)ppGpp was critical for the robust synthesis of gene products. Surprisingly, under carbon starvation, (p)ppGpp was dispensable for robust synthesis. Characterization of the underlying kinetics revealed that under carbon starvation, transcription became limiting, and translation aided transcription elongation. This mechanism naturally coordinated transcription with translation, alleviating the need for (p)ppGpp as a mediator. These contrasting mechanisms for coordination resulted in the condition-dependent effects of (p)ppGpp on global protein synthesis and starvation survival. Our findings reveal a kinetic aspect of gene expression plasticity, establishing (p)ppGpp as a condition-dependent global effector of gene expression.

Separation of aflatoxin B1 from synthetic physiological fluids using talc and diatomite: Kinetic and isotherm aspects.

PubMed

Sprynskyy, Myroslav; Krzemień-Konieczka, Iwona; Gadzała-Kopciuch, Renata; Buszewski, Bogusław

2018-01-01

The objective of the study was to examine adsorption of the aflatoxin B1 from synthetic gastric fluid and synthetic intestinal fluid by talc, raw and calcined diatomite. The kinetic and equilibrium adsorption processes were studied in the batch adsorption experiments applying high performance liquid chromatography for the aflatoxin B1 determination. The kinetic study showed a very fast adsorption of the aflatoxin B1 onto the selected adsorbents from the both physiological fluids with reaching equilibrium within 1-15min. The aflatoxin B1 was almost completely adsorbed in initial linear step of the kinetic process that can be described well by the zero-order kinetics model. The experimental data of the equilibrium adsorption were characterized using the Langmuir and Freundlich isotherm models. The high adsorption effectiveness was found in a range of 90%-100% and 60%-100% for the diatomite samples and the talc respectively at the initial concentrations of the aflatoxin B1 as 31-300ng/mL. The possible mechanisms of the aflatoxin adsorption onto the used mineral adsorbents are also discussed in the work. Copyright © 2017 Elsevier B.V. All rights reserved.

Fully Parallel MHD Stability Analysis Tool

NASA Astrophysics Data System (ADS)

Svidzinski, Vladimir; Galkin, Sergei; Kim, Jin-Soo; Liu, Yueqiang

2015-11-01

Progress on full parallelization of the plasma stability code MARS will be reported. MARS calculates eigenmodes in 2D axisymmetric toroidal equilibria in MHD-kinetic plasma models. It is a powerful tool for studying MHD and MHD-kinetic instabilities and it is widely used by fusion community. Parallel version of MARS is intended for simulations on local parallel clusters. It will be an efficient tool for simulation of MHD instabilities with low, intermediate and high toroidal mode numbers within both fluid and kinetic plasma models, already implemented in MARS. Parallelization of the code includes parallelization of the construction of the matrix for the eigenvalue problem and parallelization of the inverse iterations algorithm, implemented in MARS for the solution of the formulated eigenvalue problem. Construction of the matrix is parallelized by distributing the load among processors assigned to different magnetic surfaces. Parallelization of the solution of the eigenvalue problem is made by repeating steps of the present MARS algorithm using parallel libraries and procedures. Results of MARS parallelization and of the development of a new fix boundary equilibrium code adapted for MARS input will be reported. Work is supported by the U.S. DOE SBIR program.

Bounds on stochastic chemical kinetic systems at steady state

NASA Astrophysics Data System (ADS)

Dowdy, Garrett R.; Barton, Paul I.

2018-02-01

The method of moments has been proposed as a potential means to reduce the dimensionality of the chemical master equation (CME) appearing in stochastic chemical kinetics. However, attempts to apply the method of moments to the CME usually result in the so-called closure problem. Several authors have proposed moment closure schemes, which allow them to obtain approximations of quantities of interest, such as the mean molecular count for each species. However, these approximations have the dissatisfying feature that they come with no error bounds. This paper presents a fundamentally different approach to the closure problem in stochastic chemical kinetics. Instead of making an approximation to compute a single number for the quantity of interest, we calculate mathematically rigorous bounds on this quantity by solving semidefinite programs. These bounds provide a check on the validity of the moment closure approximations and are in some cases so tight that they effectively provide the desired quantity. In this paper, the bounded quantities of interest are the mean molecular count for each species, the variance in this count, and the probability that the count lies in an arbitrary interval. At present, we consider only steady-state probability distributions, intending to discuss the dynamic problem in a future publication.

Formation of co-crystals: Kinetic and thermodynamic aspects

NASA Astrophysics Data System (ADS)

Gagnière, E.; Mangin, D.; Puel, F.; Rivoire, A.; Monnier, O.; Garcia, E.; Klein, J. P.

2009-04-01

Co-crystallisation is a recent method of great interest for the pharmaceutical industry, since pharmaceutical co-crystals represent useful materials for drug products. In this study, an active pharmaceutical ingredient (carbamazepine (CBZ)) co-crystallized with a vitamin (nicotinamide (NCT)) was chosen as a model substance. This work was focused on the construction of a phase diagram for the system CBZ/NCT, split in six domains for kinetic reasons (the different solid phases which might appear during the crystallisation) and in four domains according to thermodynamic aspects (the stable final phase obtained). Although co-crystals are not ionic compounds, the supersaturation of co-crystals can be evaluated by considering the solubility product. Batch crystallisation operations were carried out in a stirred vessel equipped with an in situ video probe. This latter device was a powerful analysis tool to monitor the CBZ/NCT co-crystals and single CBZ crystals since these two crystalline phases grown in ethanol exhibited needle and platelet habits. As concerns kinetics, the different solid phases which might appear during the experiments were observed and competed against each others. In accordance with thermodynamics, the stable solid form was obtained at the end of the operation. Finally some preliminary results indicate that the nucleation of co-crystals may be favoured by the presence of CBZ crystals. Epitaxial relationships between CBZ/NCT co-crystals and CBZ crystals were suspected.

Sensitivity of Polar Stratospheric Ozone Loss to Uncertainties in Chemical Reaction Kinetics

NASA Technical Reports Server (NTRS)

Kawa, S. Randolph; Stolarksi, Richard S.; Douglass, Anne R.; Newman, Paul A.

2008-01-01

Several recent observational and laboratory studies of processes involved in polar stratospheric ozone loss have prompted a reexamination of aspects of our understanding for this key indicator of global change. To a large extent, our confidence in understanding and projecting changes in polar and global ozone is based on our ability to simulate these processes in numerical models of chemistry and transport. The fidelity of the models is assessed in comparison with a wide range of observations. These models depend on laboratory-measured kinetic reaction rates and photolysis cross sections to simulate molecular interactions. A typical stratospheric chemistry mechanism has on the order of 50- 100 species undergoing over a hundred intermolecular reactions and several tens of photolysis reactions. The rates of all of these reactions are subject to uncertainty, some substantial. Given the complexity of the models, however, it is difficult to quantify uncertainties in many aspects of system. In this study we use a simple box-model scenario for Antarctic ozone to estimate the uncertainty in loss attributable to known reaction kinetic uncertainties. Following the method of earlier work, rates and uncertainties from the latest laboratory evaluations are applied in random combinations. We determine the key reactions and rates contributing the largest potential errors and compare the results to observations to evaluate which combinations are consistent with atmospheric data. Implications for our theoretical and practical understanding of polar ozone loss will be assessed.

Technical and economic aspects of hydrogen storage in metal hydrides

NASA Technical Reports Server (NTRS)

Schmitt, R.

1981-01-01

The recovery of hydrogen from such metal hydrides as LiH, MgH2, TiH2, CaH2 and FeTiH compounds is studied, with the aim of evaluating the viability of the technique for the storage of hydrogen fuel. The pressure-temperature dependence of the reactions, enthalpies of formation, the kinetics of the hydrogen absorption and desorption, and the mechanical and chemical stability of the metal hydrides are taken into account in the evaluation. Economic aspects are considered. Development of portable metal hydride hydrogen storage reservoirs is also mentioned.

Kinetic and mechanistic aspects of hydroxyl radical‒mediated degradation of naproxen and reaction intermediates.

PubMed

Luo, Shuang; Gao, Lingwei; Wei, Zongsu; Spinney, Richard; Dionysiou, Dionysios D; Hu, Wei-Ping; Chai, Liyuan; Xiao, Ruiyang

2018-06-15

Hydroxyl radical ( • OH) based advanced oxidation technologies (AOTs) are effective for removing non‒steroidal anti-inflammatory drugs (NSAIDs) during water treatment. In this study, we systematically investigated the degradation kinetics of naproxen (NAP), a representative NSAID, with a combination of experimental and theoretical approaches. The second-order rate constant (k) of • OH oxidation of NAP was measured to be (4.32 ± 0.04) × 10 9  M -1  s -1 , which was in a reasonable agreement with transition state theory calculated k value (1.08 × 10 9  M -1  s -1 ) at SMD/M05-2X/6-311++G**//M05-2X/6-31+G** level of theory. The calculated result revealed that the dominant reaction intermediate is 2‒(5‒hydroxy‒6‒methoxynaphthalen‒2‒yl)propanoic acid (HMNPA) formed via radical adduct formation pathway, in which • OH addition onto the ortho site of the methoxy-substituted benzene ring is the most favorable pathway for the NAP oxidation. We further investigated the subsequent • OH oxidation of HMNPA via a kinetic modelling technique. The k value of the reaction of HMNPA and • OH was determined to be 2.22 × 10 9  M -1  s -1 , exhibiting a similar reactivity to the parent NAP. This is the first study on the kinetic and mechanistic aspects of NAP and its reaction intermediates. The current results are valuable in future study evaluating and extending the application of • OH based AOTs to degrade NAP and other NSAIDs of concern in water treatment plants. Copyright © 2018 Elsevier Ltd. All rights reserved.

Filtering analysis of a direct numerical simulation of the turbulent Rayleigh-Benard problem

NASA Technical Reports Server (NTRS)

Eidson, T. M.; Hussaini, M. Y.; Zang, T. A.

1990-01-01

A filtering analysis of a turbulent flow was developed which provides details of the path of the kinetic energy of the flow from its creation via thermal production to its dissipation. A low-pass spatial filter is used to split the velocity and the temperature field into a filtered component (composed mainly of scales larger than a specific size, nominally the filter width) and a fluctuation component (scales smaller than a specific size). Variables derived from these fields can fall into one of the above two ranges or be composed of a mixture of scales dominated by scales near the specific size. The filter is used to split the kinetic energy equation into three equations corresponding to the three scale ranges described above. The data from a direct simulation of the Rayleigh-Benard problem for conditions where the flow is turbulent are used to calculate the individual terms in the three kinetic energy equations. This is done for a range of filter widths. These results are used to study the spatial location and the scale range of the thermal energy production, the cascading of kinetic energy, the diffusion of kinetic energy, and the energy dissipation. These results are used to evaluate two subgrid models typically used in large-eddy simulations of turbulence. Subgrid models attempt to model the energy below the filter width that is removed by a low-pass filter.

Explicit integration with GPU acceleration for large kinetic networks

DOE PAGES

Brock, Benjamin; Belt, Andrew; Billings, Jay Jay; ...

2015-09-15

In this study, we demonstrate the first implementation of recently-developed fast explicit kinetic integration algorithms on modern graphics processing unit (GPU) accelerators. Taking as a generic test case a Type Ia supernova explosion with an extremely stiff thermonuclear network having 150 isotopic species and 1604 reactions coupled to hydrodynamics using operator splitting, we demonstrate the capability to solve of order 100 realistic kinetic networks in parallel in the same time that standard implicit methods can solve a single such network on a CPU. In addition, this orders-of-magnitude decrease in computation time for solving systems of realistic kinetic networks implies thatmore » important coupled, multiphysics problems in various scientific and technical fields that were intractable, or could be simulated only with highly schematic kinetic networks, are now computationally feasible.« less

Choose Wisely: Static or Kinetic Friction--The Power of Dimensionless Plots

ERIC Educational Resources Information Center

Ludwigsen, Daniel; Svinarich, Kathryn

2009-01-01

Consider a problem of sliding blocks, one stacked atop the other, resting on a frictionless table. If the bottom block is pulled horizontally, nature makes a choice: if the applied force is small, static friction between the blocks accelerates the blocks together, but with a large force the blocks slide apart. In that case, kinetic friction still…

Langevin equation versus kinetic equation: Subdiffusive behavior of charged particles in a stochastic magnetic field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balescu, R.; Wang, H.; Misguich, J.H.

1994-12-01

The running diffusion coefficient [ital D]([ital t]) is evaluated for a system of charged particles undergoing the effect of a fluctuating magnetic field and of their mutual collisions. The latter coefficient can be expressed either in terms of the mean square displacement (MSD) of a test particle, or in terms of a correlation between a fluctuating distribution function and the magnetic field fluctuation. In the first case a stochastic differential equation of Langevin type for the position of a test particle must be solved; the second problem requires the determination of the distribution function from a kinetic equation. Using suitablemore » simplifications, both problems are amenable to exact analytic solution. The conclusion is that the equivalence of the two approaches is by no means automatically guaranteed. A new type of object, the hybrid kinetic equation'' is constructed: it automatically ensures the equivalence with the Langevin results. The same conclusion holds for the generalized Fokker--Planck equation. The (Bhatnagar--Gross--Krook) (BGK) model for the collisions yields a completely wrong result. A linear approximation to the hybrid kinetic equation yields an inexact behavior, but represents an acceptable approximation in the strongly collisional limit.« less

Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures.

PubMed

Kurata, Hiroyuki; Sugimoto, Yurie

2018-02-01

Many kinetic models of Escherichia coli central metabolism have been built, but few models accurately reproduced the dynamic behaviors of wild type and multiple genetic mutants. In 2016, our latest kinetic model improved problems of existing models to reproduce the cell growth and glucose uptake of wild type, ΔpykA:pykF and Δpgi in a batch culture, while it overestimated the glucose uptake and cell growth rates of Δppc and hardly captured the typical characteristics of the glyoxylate and TCA cycle fluxes for Δpgi and Δppc. Such discrepancies between the simulated and experimental data suggested biological complexity. In this study, we overcame these problems by assuming critical mechanisms regarding the OAA-regulated isocitrate dehydrogenase activity, aceBAK gene regulation and growth suppression. The present model accurately predicts the extracellular and intracellular dynamics of wild type and many gene knockout mutants in batch and continuous cultures. It is now the most accurate, detailed kinetic model of E. coli central carbon metabolism and will contribute to advances in mathematical modeling of cell factories. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

A nonlocal fluid closure for antiparallel reconnection

NASA Astrophysics Data System (ADS)

Ng, J.; Hakim, A.; Bhattacharjee, A.

2016-12-01

The integration of kinetic effects in fluid models is an important problem in global simulations of the Earth's magnetosphere and space weather modelling. In particular, it has been shown that ion kinetics play an important role in the dynamics of large reconnecting systems, and that fluid models can account of some of these effects[1,2] . Here we introduce a new fluid model and closure for collisionless magnetic reconnection and more general applications. Taking moments of the kinetic equation, we evolve the full pressure tensor for electrons and ions, which includes the off diagonal terms necessary for reconnection. Kinetic effects are recovered by using a nonlocal heat flux closure, which approximates linear Landau damping in the fluid framework [3]. Using the island coalescence problem as a test, we show how the nonlocal ion closure improves on the typical collisional closures used for ten-moment models and circumvents the need for a colllisional free parameter. Finally, we extend the closure to study guide-field reconnection and discuss the implementation of a twenty-moment model.[1] A. Stanier et al. Phys Rev Lett (2015)[2] J. Ng et al. Phys Plasmas (2015)[3] G. Hammett et al. Phys Rev Lett (1990)

A Method for Decomposition of the Basic Reaction of Biological Macromolecules into Exponential Components

NASA Astrophysics Data System (ADS)

Barabash, Yu. M.; Lyamets, A. K.

2016-12-01

The structural and dynamical properties of biological macromolecules under non-equilibrium conditions determine the kinetics of their basic reaction to external stimuli. This kinetics is multiexponential in nature. This is due to the operation of various subsystems in the structure of macromolecules, as well as the effect of the basic reaction on the structure of macromolecules. The situation can be interpreted as a manifestation of the stationary states of macromolecules, which are represented by monoexponential components of the basic reaction (Monod-Wyman-Changeux model) Monod et al. (J Mol Cell Biol 12:88-118, 1965). The representation of multiexponential kinetics of the basic reaction in the form of a sum of exponential functions (A(t)={sum}_{i=1}^n{a}_i{e}^{-{k}_it}) is a multidimensional optimization problem. To solve this problem, a gradient method of optimization with software determination of the amount of exponents and reasonable calculation time is developed. This method is used to analyze the kinetics of photoinduced electron transport in the reaction centers (RC) of purple bacteria and the fluorescence induction in the granum thylakoid membranes which share a common function of converting light energy.

KINETIC ASPECTS OF CATION-ENHANCED AGGREGATION IN AQUEOUS HUMIC ACIDS. (R822832)

EPA Science Inventory

The cation-enhanced formation of hydrophobic domains in aqueous humic acids has been shown to be a slow process, consistent with the evolution and disintegration of humic acid configurations over periods lasting from days to weeks. After the addition of a magnesium salt to a humi...

INTERACTIONS OF LIGHT AND CHEMICAL REACTIONS IN THE AQUATIC ENVIRONMENT: KINETIC AND MECHANISTIC ASPECTS

EPA Science Inventory

Changes in the ozone layer over the past two decades have resulted in increases in solar ultraviolet (UV) radiation that reaches the surface of aquatic environments. Recent studies have demonstrated that these UV increases cause changes in photochemical reactions that affect the...

Numerical Problem Solving Using Mathcad in Undergraduate Reaction Engineering

ERIC Educational Resources Information Center

Parulekar, Satish J.

2006-01-01

Experience in using a user-friendly software, Mathcad, in the undergraduate chemical reaction engineering course is discussed. Example problems considered for illustration deal with simultaneous solution of linear algebraic equations (kinetic parameter estimation), nonlinear algebraic equations (equilibrium calculations for multiple reactions and…

Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

PubMed Central

Mannan, Ahmad A.; Toya, Yoshihiro; Shimizu, Kazuyuki; McFadden, Johnjoe; Kierzek, Andrzej M.; Rocco, Andrea

2015-01-01

An understanding of the dynamics of the metabolic profile of a bacterial cell is sought from a dynamical systems analysis of kinetic models. This modelling formalism relies on a deterministic mathematical description of enzyme kinetics and their metabolite regulation. However, it is severely impeded by the lack of available kinetic information, limiting the size of the system that can be modelled. Furthermore, the subsystem of the metabolic network whose dynamics can be modelled is faced with three problems: how to parameterize the model with mostly incomplete steady state data, how to close what is now an inherently open system, and how to account for the impact on growth. In this study we address these challenges of kinetic modelling by capitalizing on multi-‘omics’ steady state data and a genome-scale metabolic network model. We use these to generate parameters that integrate knowledge embedded in the genome-scale metabolic network model, into the most comprehensive kinetic model of the central carbon metabolism of E. coli realized to date. As an application, we performed a dynamical systems analysis of the resulting enriched model. This revealed bistability of the central carbon metabolism and thus its potential to express two distinct metabolic states. Furthermore, since our model-informing technique ensures both stable states are constrained by the same thermodynamically feasible steady state growth rate, the ensuing bistability represents a temporal coexistence of the two states, and by extension, reveals the emergence of a phenotypically heterogeneous population. PMID:26469081

Collisionless plasma expansion into vacuum: Two new twists on an old problem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arefiev, Alexey V.; Breizman, Boris N.

The paper deals with a generic problem of collisionless plasma expansion into vacuum in the regimes where the expanding plasma consists of hot electrons and cold ions. The expansion is caused by electron pressure and serves as an energy transfer mechanism from electrons to ions. This process is often described under the assumption of Maxwellian electrons, which easily fails in the absence of collisions. The paper discusses two systems with a naturally occurring non-Maxwellian distribution: an expanding laser-irradiated nanoplasma and a supersonic jet coming out of a magnetic nozzle. The presented rigorous kinetic description demonstrates how the deviation from themore » Maxwellian distribution fundamentally alters the process of ion acceleration during plasma expansion. This result points to the critical importance of a fully kinetic treatment in problems with collisionless plasma expansion.« less

Numerical solutions of nonlinear STIFF initial value problems by perturbed functional iterations

NASA Technical Reports Server (NTRS)

Dey, S. K.

1982-01-01

Numerical solution of nonlinear stiff initial value problems by a perturbed functional iterative scheme is discussed. The algorithm does not fully linearize the system and requires only the diagonal terms of the Jacobian. Some examples related to chemical kinetics are presented.

Determination of thermophysical characteristics of vulcanizable rubber products by the mathematical modeling method

NASA Astrophysics Data System (ADS)

Tikhomirov, S. G.; Pyatakov, Y. V.; Karmanova, O. V.; Maslov, A. A.

2018-03-01

The studies of the vulcanization kinetics of elastomers were carried out using a Truck tyre tread rubber compound. The formal kinetic scheme of vulcanization of rubbers sulfur-accelerator curing system was used which generalizes the set of reactions occurring in the curing process. A mathematical model is developed for determining the thermal parameters vulcanizable mixture comprising algorithms for solving direct and inverse problems for system of equations of heat conduction and kinetics of the curing process. The performance of the model is confirmed by the results of numerical experiments on model examples.

Energy spectrum and kinetics of the fusing particles

NASA Astrophysics Data System (ADS)

Ryutov, D. D.; Putvinski, s. V.; Yushmanov, P. N.; TAE Team

2017-10-01

The fusing particles (e.g., D and T, or p and 11B) contribution to the reaction rate can be found by the integration of the fusion reactivity over the particle distribution functions. The distribution function (e.g., Maxwellian) is depleted in the energy range determined by the highest reactivity and has to be replenished by particle collisions. The kinetics of the replenishment process may affect the rate of fusion energy release. We present a simple analysis of the corresponding kinetic problems for the conditions typical for the standard and advanced-fuel fusion reactions and assess the possible effect on the reaction yield.

Comparison between different adsorption-desorption kinetics schemes in two dimensional lattice gas

NASA Astrophysics Data System (ADS)

Huespe, V. J.; Belardinelli, R. E.; Pereyra, V. D.; Manzi, S. J.

2017-12-01

Monte Carlo simulation is used to study the adsorption-desorption kinetics in the framework of the kinetic lattice-gas model. Three schemes of the so-called hard dynamics and five schemes of the so called soft dynamics were used for this purpose. It is observed that for the hard dynamic schemes, the equilibrium and non-equilibrium observable, such as adsorption isotherms, sticking coefficients, and thermal desorption spectra, have a normal or physical sustainable behavior. While for the soft dynamics schemes, with the exception of the transition state theory, the equilibrium and non-equilibrium observables have several problems.

Kinetic exchange models: From molecular physics to social science

NASA Astrophysics Data System (ADS)

Patriarca, Marco; Chakraborti, Anirban

2013-08-01

We discuss several multi-agent models that have their origin in the kinetic exchange theory of statistical mechanics and have been recently applied to a variety of problems in the social sciences. This class of models can be easily adapted for simulations in areas other than physics, such as the modeling of income and wealth distributions in economics and opinion dynamics in sociology.

Mathematical Modeling and Data Analysis of NMR Experiments using Hyperpolarized 13C Metabolites

PubMed Central

Pagès, Guilhem; Kuchel, Philip W.

2013-01-01

Rapid-dissolution dynamic nuclear polarization (DNP) has made significant impact in the characterization and understanding of metabolism that occurs on the sub-minute timescale in several diseases. While significant efforts have been made in developing applications, and in designing rapid-imaging radiofrequency (RF) and magnetic field gradient pulse sequences, very few groups have worked on implementing realistic mathematical/kinetic/relaxation models to fit the emergent data. The critical aspects to consider when modeling DNP experiments depend on both nuclear magnetic resonance (NMR) and (bio)chemical kinetics. The former constraints are due to the relaxation of the NMR signal and the application of ‘read’ RF pulses, while the kinetic constraints include the total amount of each molecular species present. We describe the model-design strategy we have used to fit and interpret our DNP results. To our knowledge, this is the first report on a systematic analysis of DNP data. PMID:25114541

Efficient chemoenzymatic dynamic kinetic resolution of 1-heteroaryl ethanols.

PubMed

Vallin, Karl S A; Wensbo Posaric, David; Hamersak, Zdenko; Svensson, Mats A; Minidis, Alexander B E

2009-12-18

The scope and limitation of the combined ruthenium-lipase induced dynamic kinetic resolution (DKR) through O-acetylation of racemic heteroaromatic secondary alcohols, i.e., 1-heteroaryl substituted ethanols, was investigated. After initial screening of reaction conditions, Candida antarctica lipase B (Novozyme 435, N435) together with 4-chloro-phenylacetate as acetyl-donor for kinetic resolution (KR), in conjunction with the ruthenium-based Shvo catalyst for substrate racemization in toluene at 80 degrees C, enabled DKR with high yields and stereoselectivity of various 1-heteroaryl ethanols, such as oxadiazoles, isoxazoles, 1H-pyrazole, or 1H-imidazole. In addition, DFT calculations based on a simplified catalyst complex model for the catalytic (de)hydrogenation step are in agreement with the previously reported outer sphere mechanism. These results support the further understanding of the mechanistic aspects behind the difference in reactivity of 1-heteroaryl substituted ethanols in comparison to reference substrates, as often referred to in the literature.

Some aspects of modeling hydrocarbon oxidation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gal, D.; Botar, L.; Danoczy, E.

1981-01-01

A modeling procedure for the study of hydrocarbon oxidation is suggested, and its effectiveness for the oxidation of ethylbenzene is demonstrated. As a first step in modeling, systematization involves compilation of possible mechanisms. Then, by introduction of the concept of kinetic communication, the chaotic set of possible mechanisms is systematized into a network. Experimentation serves both as feedback to the systematic arrangement of information and source of new information. Kinetic treatment of the possible mechanism has been accomplished by two different approaches: by classical inductive calculations starting with a small mechanism and using kinetic approximations, and by computer simulation. Themore » authors have compiled a so-called Main Contributory Mechanism, involving processes - within the possible mechanism - which contribute basically to the formation and consumption of the intermediates, to the consumption of the starting compounds and to the formation of the end products. 24 refs.« less

Energy transfer and kinetics in mechanochemistry.

PubMed

Chen, Zhiliang; Lu, Shengyong; Mao, Qiongjing; Buekens, Alfons; Wang, Yuting; Yan, Jianhua

2017-11-01

Mechanochemistry (MC) exerts extraordinary degradation and decomposition effects on many chlorinated, brominated, and even fluorinated persistent organic pollutants (POPs). However, its application is still limited by inadequate study of its reaction kinetic aspects. In the present work, the ball motion and energy transfer in planetary ball mill are investigated in some detail. Almost all milling parameters are summarised in a single factor-total effective impact energy. Furthermore, the MC kinetic between calcium oxide/Al and hexachlorobenzene is well established and modelled. The results indicate that total effective impact energy and reagent ratio are the two factors sufficient for describing the MC degradation degree of POPs. The reaction rate constant only depends on the chemical properties of reactants, so it could be used as an important index to appraise the quality of MC additives. This model successfully predicts the reaction rate for different operating conditions, indicating that it could be suitably applied for conducting MC reactions in other reactors.

The influence of different space-related physiological variations on exercise capacity determined by oxygen uptake kinetics.

PubMed

Stegemann, J

1992-07-01

Oxygen uptake kinetics, following defined variations of work load changes allow to estimate the contribution of aerob and anaerob energy supply which is the base for determining work capacity. Under the aspect of long duration missions with application of adequate dosed countermeasures, a reliable estimate of the astronaut's work capacity is important to adjust the necessary inflight training. Since the kinetics of oxygen uptake originate in the working muscle group itself, while measurements are performed at the mouth, various influences within the oxygen transport system might disturb the determinations. There are not only detraining effects but also well-known other influences, such as blood- and fluid shifts induced by weightlessness. They might have an impact on the circulatory system. Some of these factors have been simulated by immersion, blood donation, and changing of the body position.

The influence of different space-related physiological variations on exercise capacity determined by oxygen uptake kinetics

NASA Astrophysics Data System (ADS)

Stegemann, J.

Oxygen uptake kinetics, following defined variations of work load changes allow to estimate the contribution of aerob and anaerob energy supply which is the base for determining work capacity. Under the aspect of long duration missions with application of adequate dosed countermeasures, a reliable estimate of the astronaut's work capacity is important to adjust the necessary inflight training. Since the kinetics of oxygen uptake originate in the working muscle group itself, while measurements are performed at the mouth, various influences within the oxygen transport system might disturb the determinations. There are not only detraining effects but also well-known other influences, such as blood- and fluid shifts induced by weightlessness. They might have an impact on the circulatory system. Some of these factors have been simulated by immersion, blood donation, and changing of the body position.

From particle systems to learning processes. Comment on "Collective learning modeling based on the kinetic theory of active particles" by Diletta Burini, Silvana De Lillo, and Livio Gibelli

NASA Astrophysics Data System (ADS)

Lachowicz, Mirosław

2016-03-01

The very stimulating paper [6] discusses an approach to perception and learning in a large population of living agents. The approach is based on a generalization of kinetic theory methods in which the interactions between agents are described in terms of game theory. Such an approach was already discussed in Ref. [2-4] (see also references therein) in various contexts. The processes of perception and learning are based on the interactions between agents and therefore the general kinetic theory is a suitable tool for modeling them. However the main question that rises is how the perception and learning processes may be treated in the mathematical modeling. How may we precisely deliver suitable mathematical structures that are able to capture various aspects of perception and learning?

"Oh" + Apology + Solution: A Practice for Managing the Concomitant Presence of a Possible Offense and a Problem-to-Be-Solved

ERIC Educational Resources Information Center

Pino, Marco; Pozzuoli, Loredana; Riccioni, Ilaria; Castellarin, Valentine

2016-01-01

In this article we examine a turn construction ("oh"+apology+solution) that speakers use to deal with the concomitant presence of a possible offense and a problem-to-be-solved in the immediately preceding interactional environment. We show that speakers collaborate in differentiating the offense aspect and the problem aspect of an…

Identification and temporal behavior of radical intermediates formed during the combustion and pyrolysis of gaseous fuels: Kinetic pathways to soot formation. Final performance report, July 1, 1994--June 30, 1997

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kern, R.D.

1998-09-01

The authors have developed software in-house to automate the processing of peak heights recorded from the shock tube: time-of-flight mass spectrometer (TOF) experiments in a format suitable for the modeling programs and have performed numerous ab initio calculations to provide energy barrier values and thermodynamic data for several key reactions in various reaction mechanisms. Each of the studies described here has contributed to the understanding of the detailed kinetics of the reactions of acyclic fuels, the thermal decompositions of aromatic ring compounds, the shock tube techniques dedicated to combustion science problems, and the role of theoretical chemistry in providing essentialmore » thermodynamic and kinetics information necessary for constructing plausible reaction mechanisms. The knowledge derived from these investigations is applicable not only to the area of pre-particle soot formation chemistry, but also to various incineration and coal pyrolysis problems.« less

Utilization of integrated Michaelis-Menten equations for enzyme inhibition diagnosis and determination of kinetic constants using Solver supplement of Microsoft Office Excel.

PubMed

Bezerra, Rui M F; Fraga, Irene; Dias, Albino A

2013-01-01

Enzyme kinetic parameters are usually determined from initial rates nevertheless, laboratory instruments only measure substrate or product concentration versus reaction time (progress curves). To overcome this problem we present a methodology which uses integrated models based on Michaelis-Menten equation. The most severe practical limitation of progress curve analysis occurs when the enzyme shows a loss of activity under the chosen assay conditions. To avoid this problem it is possible to work with the same experimental points utilized for initial rates determination. This methodology is illustrated by the use of integrated kinetic equations with the well-known reaction catalyzed by alkaline phosphatase enzyme. In this work nonlinear regression was performed with the Solver supplement (Microsoft Office Excel). It is easy to work with and track graphically the convergence of SSE (sum of square errors). The diagnosis of enzyme inhibition was performed according to Akaike information criterion. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Research on rechargeable oxygen electrodes.

NASA Technical Reports Server (NTRS)

Giner, J.; Holleck, G.; Malachesky, P. A.

1970-01-01

A research program is described which consisted of studying the effects of electrode cycling in very pure KOH solutions, with and without controlled additions of impurities, on oxide formation, oxygen evolution kinetics, oxygen reduction kinetics (including hydrogen peroxide formation), and changes in electrode structure. Bright platinum, platinized platinum, and Teflon-bonded platinum black electrodes were studied. Three main problem areas are identified: the buildup of a refractory anodic layer on prolonged cycling, which leads to a degradation of performance; the dissolution and subsequent deposition of dendritic platinum in the separator, leading to short-circuit ing and loss of electrocatalyst; and the disruptive effect of bubbling during gas evolution on charge. Each of these problem areas is analyzed, and remedial solutions are proposed.

Correlation between oxidant concentrations, morphological aspects and etching kinetics of silicon nanowires during silver-assist electroless etching

NASA Astrophysics Data System (ADS)

Moumni, Besma; Jaballah, Abdelkader Ben

2017-12-01

Silicon porosification by silver assisted chemical etching (Ag-ACE) for a short range of H2O2 concentration is reported. We experimentally show that porous silicon (PSi) is obtained for 1% H2O2, whereas silicon nanowires (SiNWs) appeared by simply tuning the concentration of H2O2 to relatively high concentrations up to 8%. The morphological aspects are claimed by scanning electron microscopy proving that the kinetics of SiNWs formation display nonlinear relationships versus H2O2 concentration and etching time. A semi-qualitative electrochemical etching model based on local anodic, Ic, and cathodic, Ia, currents is proposed to explain the different morphological changes, and to unveil the formation pathways of both PS and SiNWs. More importantly, an efficient antireflective character for silicon solar cell (reflectance close to 2%) is realized at 8% H2O2. In addition, the luminescence of the prepared Si-nanostructures is claimed by photoluminescence which exhibit a large enhancement of the intensity and a blue shift for narrow and deep SiNWs.

3D Study of the Morphology and Dynamics of Zeolite Nucleation.

PubMed

Melinte, Georgian; Georgieva, Veselina; Springuel-Huet, Marie-Anne; Nossov, Andreï; Ersen, Ovidiu; Guenneau, Flavien; Gedeon, Antoine; Palčić, Ana; Bozhilov, Krassimir N; Pham-Huu, Cuong; Qiu, Shilun; Mintova, Svetlana; Valtchev, Valentin

2015-12-07

The principle aspects and constraints of the dynamics and kinetics of zeolite nucleation in hydrogel systems are analyzed on the basis of a model Na-rich aluminosilicate system. A detailed time-series EMT-type zeolite crystallization study in the model hydrogel system was performed to elucidate the topological and temporal aspects of zeolite nucleation. A comprehensive set of analytical tools and methods was employed to analyze the gel evolution and complement the primary methods of transmission electron microscopy (TEM) and nuclear magnetic resonance (NMR) spectroscopy. TEM tomography reveals that the initial gel particles exhibit a core-shell structure. Zeolite nucleation is topologically limited to this shell structure and the kinetics of nucleation is controlled by the shell integrity. The induction period extends to the moment when the shell is consumed and the bulk solution can react with the core of the gel particles. These new findings, in particular the importance of the gel particle shell in zeolite nucleation, can be used to control the growth process and properties of zeolites formed in hydrogels. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamics of Phonological Cognition

ERIC Educational Resources Information Center

Gafos, Adamantios I.; Benus, Stefan

2006-01-01

A fundamental problem in spoken language is the duality between the continuous aspects of phonetic performance and the discrete aspects of phonological competence. We study 2 instances of this problem from the phenomenon of voicing neutralization and vowel harmony. In each case, we present a model where the experimentally observed continuous…

Parameter estimation in tree graph metabolic networks.

PubMed

Astola, Laura; Stigter, Hans; Gomez Roldan, Maria Victoria; van Eeuwijk, Fred; Hall, Robert D; Groenenboom, Marian; Molenaar, Jaap J

2016-01-01

We study the glycosylation processes that convert initially toxic substrates to nutritionally valuable metabolites in the flavonoid biosynthesis pathway of tomato (Solanum lycopersicum) seedlings. To estimate the reaction rates we use ordinary differential equations (ODEs) to model the enzyme kinetics. A popular choice is to use a system of linear ODEs with constant kinetic rates or to use Michaelis-Menten kinetics. In reality, the catalytic rates, which are affected among other factors by kinetic constants and enzyme concentrations, are changing in time and with the approaches just mentioned, this phenomenon cannot be described. Another problem is that, in general these kinetic coefficients are not always identifiable. A third problem is that, it is not precisely known which enzymes are catalyzing the observed glycosylation processes. With several hundred potential gene candidates, experimental validation using purified target proteins is expensive and time consuming. We aim at reducing this task via mathematical modeling to allow for the pre-selection of most potential gene candidates. In this article we discuss a fast and relatively simple approach to estimate time varying kinetic rates, with three favorable properties: firstly, it allows for identifiable estimation of time dependent parameters in networks with a tree-like structure. Secondly, it is relatively fast compared to usually applied methods that estimate the model derivatives together with the network parameters. Thirdly, by combining the metabolite concentration data with a corresponding microarray data, it can help in detecting the genes related to the enzymatic processes. By comparing the estimated time dynamics of the catalytic rates with time series gene expression data we may assess potential candidate genes behind enzymatic reactions. As an example, we show how to apply this method to select prominent glycosyltransferase genes in tomato seedlings.

Coarsening of Ni(3)Si precipitates in binary Ni-Si alloys

NASA Astrophysics Data System (ADS)

Cho, Jin-Hoon

The coarsening behavior of coherent gammasp'\\ (Nisb3Si) precipitates with volume fractions, f, ranging from 0.017 to 0.32 in binary Ni-Si alloys was investigated. All of the alloys were aged at 650sp° C for times as long as 2760 h and measurements were made of the kinetics of coarsening, particle size distributions and the evolution of particle morphologies using transmission electron microscopy. The kinetics of solute depletion were investigated using measurements of the ferromagnetic Curie temperature. We successfully overcame the difficulties in obtaining uniform spatial distributions of precipitates at small f by employing an up-quenching treatment; alloys with f less than 0.1 were pre-aged at 530sp° C prior to re-aging at the normal aging temperature of 650sp° C. Almost identical coarsening behavior exhibited by an alloy subjected to both isothermal and up-quenching treatments confirm that the up-quenching treatments do not affect any aspect of the coarsening behavior. Consistent with previous studies, the particles are spherical in shape when small and evolve to a cuboidal shape, with flat faces parallel to {}, as they grow. This shape transition was characterized quantitatively by analyzing the intensity distributions of Fast Fourier Transform spectra generated from the digitized images of TEM micrographs. The precipitates display no tendency towards becoming plate-shaped and they resist coalescence even at the largest sizes, which approach 400 nm in diameter at 2760 h of aging for higher volume fraction alloys. For f < 0.1, the kinetics of coarsening and solute depletion as well as the standard deviation of the particle size distributions decrease as f increases. This anomalous behavior has been documented previously by other investigators, but is contrary to the predictions of theories that incorporate the volume fraction effect in coarsening kinetics. We find no convincing evidence to suggest that f influences any aspect of the coarsening behavior at larger f. It is suggested that the lack of agreement between the volume fraction effects observed experimentally and those predicted theoretically stems from the elastic interactions having a strong influence on the kinetics of coarsening, effectively counteracting the accelerating influence of f on the coarsening kinetics predicted by the theories.

Unified implicit kinetic scheme for steady multiscale heat transfer based on the phonon Boltzmann transport equation

NASA Astrophysics Data System (ADS)

Zhang, Chuang; Guo, Zhaoli; Chen, Songze

2017-12-01

An implicit kinetic scheme is proposed to solve the stationary phonon Boltzmann transport equation (BTE) for multiscale heat transfer problem. Compared to the conventional discrete ordinate method, the present method employs a macroscopic equation to accelerate the convergence in the diffusive regime. The macroscopic equation can be taken as a moment equation for phonon BTE. The heat flux in the macroscopic equation is evaluated from the nonequilibrium distribution function in the BTE, while the equilibrium state in BTE is determined by the macroscopic equation. These two processes exchange information from different scales, such that the method is applicable to the problems with a wide range of Knudsen numbers. Implicit discretization is implemented to solve both the macroscopic equation and the BTE. In addition, a memory reduction technique, which is originally developed for the stationary kinetic equation, is also extended to phonon BTE. Numerical comparisons show that the present scheme can predict reasonable results both in ballistic and diffusive regimes with high efficiency, while the memory requirement is on the same order as solving the Fourier law of heat conduction. The excellent agreement with benchmark and the rapid converging history prove that the proposed macro-micro coupling is a feasible solution to multiscale heat transfer problems.

Rectangular subsonic jet flow field measurements

NASA Technical Reports Server (NTRS)

Morrison, Gerald L.; Swan, David H.

1990-01-01

Flow field measurements of three subsonic rectangular cold air jets are presented. The three cases had aspect ratios of 1x2, 1x4 at a Mach number of 0.09 and an aspect ratio of 1x2 at a Mach number of 0.9. All measurements were made using a 3-D laser Doppler anemometer system. The data includes the mean velocity vector, all Reynolds stress tensor components, turbulent kinetic energy and velocity correlation coefficients. The data are presented in tabular and graphical form. No analysis of the measured data or comparison to other published data is made.

Oxidative desulfurization: kinetic modelling.

PubMed

Dhir, S; Uppaluri, R; Purkait, M K

2009-01-30

Increasing environmental legislations coupled with enhanced production of petroleum products demand, the deployment of novel technologies to remove organic sulfur efficiently. This work represents the kinetic modeling of ODS using H(2)O(2) over tungsten-containing layered double hydroxide (LDH) using the experimental data provided by Hulea et al. [V. Hulea, A.L. Maciuca, F. Fajula, E. Dumitriu, Catalytic oxidation of thiophenes and thioethers with hydrogen peroxide in the presence of W-containing layered double hydroxides, Appl. Catal. A: Gen. 313 (2) (2006) 200-207]. The kinetic modeling approach in this work initially targets the scope of the generation of a superstructure of micro-kinetic reaction schemes and models assuming Langmuir-Hinshelwood (LH) and Eley-Rideal (ER) mechanisms. Subsequently, the screening and selection of above models is initially based on profile-based elimination of incompetent schemes followed by non-linear regression search performed using the Levenberg-Marquardt algorithm (LMA) for the chosen models. The above analysis inferred that Eley-Rideal mechanism describes the kinetic behavior of ODS process using tungsten-containing LDH, with adsorption of reactant and intermediate product only taking place on the catalyst surface. Finally, an economic index is presented that scopes the economic aspects of the novel catalytic technology with the parameters obtained during regression analysis to conclude that the cost factor for the catalyst is 0.0062-0.04759 US $ per barrel.

Continuous monitoring of enzymatic activity within native electrophoresis gels: Application to mitochondrial oxidative phosphorylation complexes

PubMed Central

Covian, Raul; Chess, David; Balaban, Robert S.

2012-01-01

Native gel electrophoresis allows the separation of very small amounts of protein complexes while retaining aspects of their activity. In-gel enzymatic assays are usually performed by using reaction-dependent deposition of chromophores or light scattering precipitates quantified at fixed time points after gel removal and fixation, limiting the ability to analyze enzyme reaction kinetics. Herein, we describe a custom reaction chamber with reaction media recirculation and filtering and an imaging system that permits the continuous monitoring of in-gel enzymatic activity even in the presence of turbidity. Images were continuously collected using time-lapse high resolution digital imaging, and processing routines were developed to obtain kinetic traces of the in-gel activities and analyze reaction time courses. This system also permitted the evaluation of enzymatic activity topology within the protein bands of the gel. This approach was used to analyze the reaction kinetics of two mitochondrial complexes in native gels. Complex IV kinetics showed a short initial linear phase where catalytic rates could be calculated, whereas Complex V activity revealed a significant lag phase followed by two linear phases. The utility of monitoring the entire kinetic behavior of these reactions in native gels, as well as the general application of this approach, is discussed. PMID:22975200

Toward a Multi-scale Phase Transition Kinetics Methodology: From Non-Equilibrium Statistical Mechanics to Hydrodynamics

NASA Astrophysics Data System (ADS)

Belof, Jonathan; Orlikowski, Daniel; Wu, Christine; McLaughlin, Keith

2013-06-01

Shock and ramp compression experiments are allowing us to probe condensed matter under extreme conditions where phase transitions and other non-equilibrium aspects can now be directly observed, but first principles simulation of kinetics remains a challenge. A multi-scale approach is presented here, with non-equilibrium statistical mechanical quantities calculated by molecular dynamics (MD) and then leveraged to inform a classical nucleation and growth kinetics model at the hydrodynamic scale. Of central interest is the free energy barrier for the formation of a critical nucleus, with direct NEMD presenting the challenge of relatively long timescales necessary to resolve nucleation. Rather than attempt to resolve the time-dependent nucleation sequence directly, the methodology derived here is built upon the non-equilibrium work theorem in order to bias the formation of a critical nucleus and thus construct the nucleation and growth rates. Having determined these kinetic terms from MD, a hydrodynamics implementation of Kolmogorov-Johnson-Mehl-Avrami (KJMA) kinetics and metastabilty is applied to the dynamic compressive freezing of water and compared with recent ramp compression experiments [Dolan et al., Nature (2007)] Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344.

Continuous monitoring of enzymatic activity within native electrophoresis gels: application to mitochondrial oxidative phosphorylation complexes.

PubMed

Covian, Raul; Chess, David; Balaban, Robert S

2012-12-01

Native gel electrophoresis allows the separation of very small amounts of protein complexes while retaining aspects of their activity. In-gel enzymatic assays are usually performed by using reaction-dependent deposition of chromophores or light-scattering precipitates quantified at fixed time points after gel removal and fixation, limiting the ability to analyze the enzyme reaction kinetics. Herein, we describe a custom reaction chamber with reaction medium recirculation and filtering and an imaging system that permits the continuous monitoring of in-gel enzymatic activity even in the presence of turbidity. Images were continuously collected using time-lapse high-resolution digital imaging, and processing routines were developed to obtain kinetic traces of the in-gel activities and analyze reaction time courses. This system also permitted the evaluation of enzymatic activity topology within the protein bands of the gel. This approach was used to analyze the reaction kinetics of two mitochondrial complexes in native gels. Complex IV kinetics showed a short initial linear phase in which catalytic rates could be calculated, whereas Complex V activity revealed a significant lag phase followed by two linear phases. The utility of monitoring the entire kinetic behavior of these reactions in native gels, as well as the general application of this approach, is discussed. Published by Elsevier Inc.

Self-Paced Physics, Segments 6-10.

ERIC Educational Resources Information Center

New York Inst. of Tech., Old Westbury.

Five segments of the Self-Paced Physics Course materials are presented in this problems and solutions book for use as the second part of student course work. The subject-matter topics are related to circular motion, work, power, kinetic energy, potential energy, conservative forces, conservation of energy, spring problems, center of mass, and…

Energy and the Confused Student V: The Energy/Momentum Approach to Problems Involving Rotating and Deformable Systems

ERIC Educational Resources Information Center

Jewett, John W., Jr.

2008-01-01

Energy is a critical concept in physics problem-solving, but is often a major source of confusion for students if the presentation is not carefully crafted by the instructor or the textbook. A common approach to problems involving deformable or rotating systems that has been discussed in the literature is to employ the work-kinetic energy theorem…

Waves and instabilities in plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, L.

1987-01-01

The contents of this book are: Plasma as a Dielectric Medium; Nyquist Technique; Absolute and Convective Instabilities; Landau Damping and Phase Mixing; Particle Trapping and Breakdown of Linear Theory; Solution of Viasov Equation via Guilding-Center Transformation; Kinetic Theory of Magnetohydrodynamic Waves; Geometric Optics; Wave-Kinetic Equation; Cutoff and Resonance; Resonant Absorption; Mode Conversion; Gyrokinetic Equation; Drift Waves; Quasi-Linear Theory; Ponderomotive Force; Parametric Instabilities; Problem Sets for Homework, Midterm and Final Examinations.

Bootstrap current for the edge pedestal plasma in a diverted tokamak geometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koh, S.; Choe, W.; Chang, C. S.

The edge bootstrap current plays a critical role in the equilibrium and stability of the steep edge pedestal plasma. The pedestal plasma has an unconventional and difficult neoclassical property, as compared with the core plasma. It has a narrow passing particle region in velocity space that can be easily modified or destroyed by Coulomb collisions. At the same time, the edge pedestal plasma has steep pressure and electrostatic potential gradients whose scale-lengths are comparable with the ion banana width, and includes a magnetic separatrix surface, across which the topological properties of the magnetic field and particle orbits change abruptly. Amore » drift-kinetic particle code XGC0, equipped with a mass-momentum-energy conserving collision operator, is used to study the edge bootstrap current in a realistic diverted magnetic field geometry with a self-consistent radial electric field. When the edge electrons are in the weakly collisional banana regime, surprisingly, the present kinetic simulation confirms that the existing analytic expressions [represented by O. Sauter et al., Phys. Plasmas 6, 2834 (1999)] are still valid in this unconventional region, except in a thin radial layer in contact with the magnetic separatrix. The agreement arises from the dominance of the electron contribution to the bootstrap current compared with ion contribution and from a reasonable separation of the trapped-passing dynamics without a strong collisional mixing. However, when the pedestal electrons are in plateau-collisional regime, there is significant deviation of numerical results from the existing analytic formulas, mainly due to large effective collisionality of the passing and the boundary layer trapped particles in edge region. In a conventional aspect ratio tokamak, the edge bootstrap current from kinetic simulation can be significantly less than that from the Sauter formula if the electron collisionality is high. On the other hand, when the aspect ratio is close to unity, the collisional edge bootstrap current can be significantly greater than that from the Sauter formula. Rapid toroidal rotation of the magnetic field lines at the high field side of a tight aspect-ratio tokamak is believed to be the cause of the different behavior. A new analytic fitting formula, as a simple modification to the Sauter formula, is obtained to bring the analytic expression to a better agreement with the edge kinetic simulation results.« less

Simultaneous versus sequential optimal experiment design for the identification of multi-parameter microbial growth kinetics as a function of temperature.

PubMed

Van Derlinden, E; Bernaerts, K; Van Impe, J F

2010-05-21

Optimal experiment design for parameter estimation (OED/PE) has become a popular tool for efficient and accurate estimation of kinetic model parameters. When the kinetic model under study encloses multiple parameters, different optimization strategies can be constructed. The most straightforward approach is to estimate all parameters simultaneously from one optimal experiment (single OED/PE strategy). However, due to the complexity of the optimization problem or the stringent limitations on the system's dynamics, the experimental information can be limited and parameter estimation convergence problems can arise. As an alternative, we propose to reduce the optimization problem to a series of two-parameter estimation problems, i.e., an optimal experiment is designed for a combination of two parameters while presuming the other parameters known. Two different approaches can be followed: (i) all two-parameter optimal experiments are designed based on identical initial parameter estimates and parameters are estimated simultaneously from all resulting experimental data (global OED/PE strategy), and (ii) optimal experiments are calculated and implemented sequentially whereby the parameter values are updated intermediately (sequential OED/PE strategy). This work exploits OED/PE for the identification of the Cardinal Temperature Model with Inflection (CTMI) (Rosso et al., 1993). This kinetic model describes the effect of temperature on the microbial growth rate and encloses four parameters. The three OED/PE strategies are considered and the impact of the OED/PE design strategy on the accuracy of the CTMI parameter estimation is evaluated. Based on a simulation study, it is observed that the parameter values derived from the sequential approach deviate more from the true parameters than the single and global strategy estimates. The single and global OED/PE strategies are further compared based on experimental data obtained from design implementation in a bioreactor. Comparable estimates are obtained, but global OED/PE estimates are, in general, more accurate and reliable. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Aspects of the Cognitive Model of Physics Problem Solving.

ERIC Educational Resources Information Center

Brekke, Stewart E.

Various aspects of the cognitive model of physics problem solving are discussed in detail including relevant cues, encoding, memory, and input stimuli. The learning process involved in the recognition of familiar and non-familiar sensory stimuli is highlighted. Its four components include selection, acquisition, construction, and integration. The…

On the design of high-rise buildings with a specified level of reliability

NASA Astrophysics Data System (ADS)

Dolganov, Andrey; Kagan, Pavel

2018-03-01

High-rise buildings have a specificity, which significantly distinguishes them from traditional buildings of high-rise and multi-storey buildings. Steel structures in high-rise buildings are advisable to be used in earthquake-proof regions, since steel, due to its plasticity, provides damping of the kinetic energy of seismic impacts. These aspects should be taken into account when choosing a structural scheme of a high-rise building and designing load-bearing structures. Currently, modern regulatory documents do not quantify the reliability of structures. Although the problem of assigning an optimal level of reliability has existed for a long time. The article shows the possibility of designing metal structures of high-rise buildings with specified reliability. Currently, modern regulatory documents do not quantify the reliability of high-rise buildings. Although the problem of assigning an optimal level of reliability has existed for a long time. It is proposed to establish the value of reliability 0.99865 (3σ) for constructions of buildings and structures of a normal level of responsibility in calculations for the first group of limiting states. For increased (construction of high-rise buildings) and reduced levels of responsibility for the provision of load-bearing capacity, it is proposed to assign respectively 0.99997 (4σ) and 0.97725 (2σ). The coefficients of the use of the cross section of a metal beam for different levels of security are given.

Problems associated with gene transfer and opportunities for microgravity environments

NASA Astrophysics Data System (ADS)

Tennessen, Daniel J.

1997-01-01

The method of crop improvement by gene transfer is becoming increasingly routine with transgenic foods and ornamental crops now being marketed to consumers. However, biological processes of plants, and the physical barriers of current protocols continue to limit the application of gene transfer in many commercial crops. The goal of this paper is to outline the current limitations of gene transfer and to hypothesize possible opportunities for use of microgravity to overcome such limitations. The limitations detailed in this paper include host-range specificity of Agrobacterium mediated transformation, probability of gene insertion, position effects of the inserted genes, gene copy number, stability of foreign gene expression in host plants, and regeneration of recalcitrant plant species. Microgravity offers an opportunity for gene transfer where cell growth kinetics, DNA synthesis, and genetic recombination rates can be altered. Such biological conditions may enhance the ability for recombination of reporter genes and other genes of interest to agriculture. Proposed studies would be useful for understanding instability of foreign gene expression and may lead to stable transformed plants. Other aspects of gene transfer in microgravity are discussed.

Alginate-immobilized bentonite clay: adsorption efficacy and reusability for Cu(II) removal from aqueous solution.

PubMed

Tan, Wei Shang; Ting, Adeline Su Yien

2014-05-01

This study evaluated the use of alginate-immobilized bentonite to remove Cu(II) as an alternative to mitigate clogging problems. The adsorption efficacy (under the influence of time, pH and initial Cu(II) concentration) and reusability of immobilized-bentonite (1% w/v bentonite) was tested against plain alginate beads. Results revealed that immobilized bentonite demonstrated significantly higher sorption efficacy compared to plain alginate beads with 114.70 and 94.04 mg Cu(II) adsorbed g(-1) adsorbent, respectively. Both sorbents were comparable in other aspects where sorption equilibrium was achieved within 6 h, with optimum pH between pH 4 and 5 for adsorption, displayed maximum adsorption capacity at initial Cu(II) concentrations of 400 mg l(-1), and demonstrated excellent reusability potential with desorption greater than 90% throughout three consecutive adsorption-desorption cycles. Both sorbents also conformed to Langmuir isotherm and pseudo-second order kinetic model. Immobilized bentonite is therefore recommended for use in water treatments to remove Cu(II) without clogging the system. Copyright © 2013 Elsevier Ltd. All rights reserved.

Object-oriented code SUR for plasma kinetic simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Levchenko, V.D.; Sigov, Y.S.

1995-12-31

We have developed a self-consistent simulation code based on object-oriented model of plasma (OOMP) for solving the Vlasov/Poisson (V/P), Vlasov/Maxwell (V/M), Bhatnagar-Gross-Krook (BGK) as well as Fokker-Planck (FP) kinetic equations. The application of an object-oriented approach (OOA) to simulation of plasmas and plasma-like media by means of splitting methods permits to uniformly describe and solve the wide circle of plasma kinetics problems, including those being very complicated: many-dimensional, relativistic, with regard for collisions, specific boundary conditions etc. This paper gives the brief description of possibilities of the SUR code, as a concrete realization of OOMP.

On the Boltzmann Equation with Stochastic Kinetic Transport: Global Existence of Renormalized Martingale Solutions

NASA Astrophysics Data System (ADS)

Punshon-Smith, Samuel; Smith, Scott

2018-02-01

This article studies the Cauchy problem for the Boltzmann equation with stochastic kinetic transport. Under a cut-off assumption on the collision kernel and a coloring hypothesis for the noise coefficients, we prove the global existence of renormalized (in the sense of DiPerna/Lions) martingale solutions to the Boltzmann equation for large initial data with finite mass, energy, and entropy. Our analysis includes a detailed study of weak martingale solutions to a class of linear stochastic kinetic equations. This study includes a criterion for renormalization, the weak closedness of the solution set, and tightness of velocity averages in {{L}1}.

CREKID: A computer code for transient, gas-phase combustion of kinetics

NASA Technical Reports Server (NTRS)

Pratt, D. T.; Radhakrishnan, K.

1984-01-01

A new algorithm was developed for fast, automatic integration of chemical kinetic rate equations describing homogeneous, gas-phase combustion at constant pressure. Particular attention is paid to the distinguishing physical and computational characteristics of the induction, heat-release and equilibration regimes. The two-part predictor-corrector algorithm, based on an exponentially-fitted trapezoidal rule, includes filtering of ill-posed initial conditions, automatic selection of Newton-Jacobi or Newton iteration for convergence to achieve maximum computational efficiency while observing a prescribed error tolerance. The new algorithm was found to compare favorably with LSODE on two representative test problems drawn from combustion kinetics.

Design of Spacecraft Missions to Test Kinetic Impact for Asteroid Deflection

NASA Technical Reports Server (NTRS)

Barbee, Brent W.; Hernandez, Sonia

2012-01-01

Earth has previously been struck with devastating force by near-Earth asteroids (NEAs) and will be struck again. Telescopic search programs aim to provide advance warning of such an impact, but no techniques or systems have yet been tested for deflecting an incoming NEA. To begin addressing this problem, we have analyzed the more than 8000 currently known NEAs to identify those that offer opportunities for safe and meaningful near-term tests of the proposed kinetic impact asteroid deflection technique. In this paper we present our methodology and results, including complete mission designs for the best kinetic impactor test mission opportunities.

Analysis of expert validation on developing integrated science worksheet to improve problem solving skills of natural science prospective teachers

NASA Astrophysics Data System (ADS)

Widodo, W.; Sudibyo, E.; Sari, D. A. P.

2018-04-01

This study aims to develop student worksheets for higher education that apply integrated science learning in discussing issues about motion in humans. These worksheets will guide students to solve the problem about human movement. They must integrate their knowledge about biology, physics, and chemistry to solve the problem. The worksheet was validated by three experts in Natural Science Integrated Science, especially in Human Movement topic. The aspects of the validation were feasibility of the content, the construction, and the language. This research used the Likert scale to measure the validity of each aspect, which is 4.00 for very good validity criteria, 3.00 for good validity criteria, 2.00 for more or less validity criteria, and 1.00 for not good validity criteria. Data showed that the validity for each aspect were in the range of good validity and very good validity criteria (3.33 to 3.67 for the content aspect, 2.33 to 4.00 for the construction aspect, and 3.33 to 4.00 for language aspect). However, there was a part of construction aspect that needed to improve. Overall, this students’ worksheet can be applied in classroom after some revisions based on suggestions from the validators.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models.

PubMed

Cotten, Cameron; Reed, Jennifer L

2013-01-30

Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

PubMed Central

2013-01-01

Background Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. Results In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. Conclusions This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets. PMID:23360254

Interchange mode excited by trapped energetic ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishimura, Seiya, E-mail: n-seiya@kobe-kosen.ac.jp

2015-07-15

The kinetic energy principle describing the interaction between ideal magnetohydrodynamic (MHD) modes with trapped energetic ions is revised. A model is proposed on the basis of the reduced ideal MHD equations for background plasmas and the bounce-averaged drift-kinetic equation for trapped energetic ions. The model is applicable to large-aspect-ratio toroidal devices. Specifically, the effect of trapped energetic ions on the interchange mode in helical systems is analyzed. Results show that the interchange mode is excited by trapped energetic ions, even if the equilibrium states are stable to the ideal interchange mode. The energetic-ion-induced branch of the interchange mode might bemore » associated with the fishbone mode in helical systems.« less

Kinetic Activation-Relaxation Technique and Self-Evolving Atomistic Kinetic Monte Carlo: Comparison of on-the-fly kinetic Monte Carlo algorithms

DOE PAGES

Beland, Laurent Karim; Osetskiy, Yury N.; Stoller, Roger E.; ...

2015-02-07

Here, we present a comparison of the Kinetic Activation–Relaxation Technique (k-ART) and the Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC), two off-lattice, on-the-fly Kinetic Monte Carlo (KMC) techniques that were recently used to solve several materials science problems. We show that if the initial displacements are localized the dimer method and the Activation–Relaxation Technique nouveau provide similar performance. We also show that k-ART and SEAKMC, although based on different approximations, are in agreement with each other, as demonstrated by the examples of 50 vacancies in a 1950-atom Fe box and of interstitial loops in 16,000-atom boxes. Generally speaking, k-ART’s treatment ofmore » geometry and flickers is more flexible, e.g. it can handle amorphous systems, and rigorous than SEAKMC’s, while the later’s concept of active volumes permits a significant speedup of simulations for the systems under consideration and therefore allows investigations of processes requiring large systems that are not accessible if not localizing calculations.« less

Analysis of energy dissipation and deposition in elastic bodies impacting at hypervelocities

NASA Technical Reports Server (NTRS)

Medina, David F.; Allahdadi, Firooz A.

1992-01-01

A series of impact problems were analyzed using the Eulerian hydrocode CTH. The objective was to quantify the amount of energy dissipated locally by a projectile-infinite plate impact. A series of six impact problems were formulated such that the mass and speed of each projectile were varied in order to allow for increasing speed with constant kinetic energy. The properties and dimensions of the plate were the same for each projectile impact. The resulting response of the plate was analyzed for global Kinetic Energy, global momentum, and local maximum shear stress. The percentage of energy dissipated by the various hypervelocity impact phenomena appears as a relative change of shear stress at a point away from the impact in the plate.

Enhancing the Effectiveness of Carbon Dioxide Flooding by Managing Asphaltene Precipitation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deo, Milind D.

2002-02-21

This project was undertaken to understand fundamental aspects of carbon dioxide (CO2) induced asphaltene precipitation. Oil and asphaltene samples from the Rangely field in Colorado were used for most of the project. The project consisted of pure component and high-pressure, thermodynamic experiments, thermodynamic modeling, kinetic experiments and modeling, targeted corefloods and compositional modeling.

Kinetic Analysis of Amylase Using Quantitative Benedict's and Iodine Starch Reagents

ERIC Educational Resources Information Center

Cochran, Beverly; Lunday, Deborah; Miskevich, Frank

2008-01-01

Quantitative analysis of carbohydrates is a fundamental analytical tool used in many aspects of biology and chemistry. We have adapted a technique developed by Mathews et al. using an inexpensive scanner and open-source image analysis software to quantify amylase activity using both the breakdown of starch and the appearance of glucose. Breakdown…

Profile of student’s understanding in Kinetic Theory of Gases

NASA Astrophysics Data System (ADS)

Putri, E. E. R.; Sukarmin; Cari

2018-04-01

Students in eleven grade had a different style for answering the physics problems. They could do anything to solve the problem. The way they thought and revealed it into the answer in many styles could be used as a data to know their conception. One of the sub-chapter in physics was the effective velocity of gases. It included in Kinetic Theory of Gases. It was one of the most difficult scientific theories to accept. This research aimed to identify student’s understanding in effective velocity of gases problem. The research was qualitative research. It was taken place at MAN Yogyakarta I in semester two on grade eleven. The obtained datas were collected by test sheet that contained of essay form. The respondents were all of the students in XI MIA 3. The data was analyzed by quantitative analysis using rubric of scoring in essay test and it contained of two problems. The results were the students had resolved the test and it was divided into three categories which are high 10,42%, medium 29,17%, and low 50,00%.

Constructive methods of invariant manifolds for kinetic problems

NASA Astrophysics Data System (ADS)

Gorban, Alexander N.; Karlin, Iliya V.; Zinovyev, Andrei Yu.

2004-06-01

The concept of the slow invariant manifold is recognized as the central idea underpinning a transition from micro to macro and model reduction in kinetic theories. We present the Constructive Methods of Invariant Manifolds for model reduction in physical and chemical kinetics, developed during last two decades. The physical problem of reduced description is studied in the most general form as a problem of constructing the slow invariant manifold. The invariance conditions are formulated as the differential equation for a manifold immersed in the phase space ( the invariance equation). The equation of motion for immersed manifolds is obtained ( the film extension of the dynamics). Invariant manifolds are fixed points for this equation, and slow invariant manifolds are Lyapunov stable fixed points, thus slowness is presented as stability. A collection of methods to derive analytically and to compute numerically the slow invariant manifolds is presented. Among them, iteration methods based on incomplete linearization, relaxation method and the method of invariant grids are developed. The systematic use of thermodynamics structures and of the quasi-chemical representation allow to construct approximations which are in concordance with physical restrictions. The following examples of applications are presented: nonperturbative deviation of physically consistent hydrodynamics from the Boltzmann equation and from the reversible dynamics, for Knudsen numbers Kn∼1; construction of the moment equations for nonequilibrium media and their dynamical correction (instead of extension of list of variables) to gain more accuracy in description of highly nonequilibrium flows; determination of molecules dimension (as diameters of equivalent hard spheres) from experimental viscosity data; model reduction in chemical kinetics; derivation and numerical implementation of constitutive equations for polymeric fluids; the limits of macroscopic description for polymer molecules, etc.

A study of dynamical behavior of space environment

NASA Technical Reports Server (NTRS)

Wu, S. T.

1974-01-01

Studies have covered a wide range of problems in the space environment, such as the problems of the dynamical behavior of the thermosphere, hydromagnetic wave propagation in the ionosphere, and interplanetary space environment. The theories used to analyze these problems range from a continuum theory of magnetohydrodynamics to the kinetic theory of free molecular flow. This is because the problems encountered covered the entire range of the Knudsen number (i.e., the ratio of mean free path to the characteristic length). Significant results are summarized.

SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration

DOE PAGES

Tang, Jin-Yun; Riley, William J.

2017-09-05

Several land biogeochemical models used for studying carbon–climate feedbacks have begun explicitly representing microbial dynamics. However, to our knowledge, there has been no theoretical work on how to achieve a consistent scaling of the complex biogeochemical reactions from microbial individuals to populations, communities, and interactions with plants and mineral soils. We focus here on developing a mathematical formulation of the substrate–consumer relationships for consumer-mediated redox reactions of the form A +  B E→  products, where products could be, e.g., microbial biomass or bioproducts. Under the quasi-steady-state approximation, these substrate–consumer relationships can be formulated as the computationally difficult full equilibrium chemistrymore » problem or approximated analytically with the dual Monod (DM) or synthesizing unit (SU) kinetics. We find that DM kinetics is scaling inconsistently for reaction networks because (1) substrate limitations are not considered, (2) contradictory assumptions are made regarding the substrate processing rate when transitioning from single- to multi-substrate redox reactions, and (3) the product generation rate cannot be scaled from one to multiple substrates. In contrast, SU kinetics consistently scales the product generation rate from one to multiple substrates but predicts unrealistic results as consumer abundances reach large values with respect to their substrates. We attribute this deficit to SU's failure to incorporate substrate limitation in its derivation. To address these issues, we propose SUPECA (SU plus the equilibrium chemistry approximation – ECA) kinetics, which consistently imposes substrate and consumer mass balance constraints. We show that SUPECA kinetics satisfies the partition principle, i.e., scaling invariance across a network of an arbitrary number of reactions (e.g., as in Newton's law of motion and Dalton's law of partial pressures). We tested SUPECA kinetics with the equilibrium chemistry solution for some simple problems and found SUPECA outperformed SU kinetics. As an example application, we show that a steady-state SUPECA-based approach predicted an aerobic soil respiration moisture response function that agreed well with laboratory observations. We conclude that, as an extension to SU and ECA kinetics, SUPECA provides a robust mathematical representation of complex soil substrate–consumer interactions and can be applied to improve Earth system model (ESM) land models.« less

SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Jin-Yun; Riley, William J.

Several land biogeochemical models used for studying carbon–climate feedbacks have begun explicitly representing microbial dynamics. However, to our knowledge, there has been no theoretical work on how to achieve a consistent scaling of the complex biogeochemical reactions from microbial individuals to populations, communities, and interactions with plants and mineral soils. We focus here on developing a mathematical formulation of the substrate–consumer relationships for consumer-mediated redox reactions of the form A +  B E→  products, where products could be, e.g., microbial biomass or bioproducts. Under the quasi-steady-state approximation, these substrate–consumer relationships can be formulated as the computationally difficult full equilibrium chemistrymore » problem or approximated analytically with the dual Monod (DM) or synthesizing unit (SU) kinetics. We find that DM kinetics is scaling inconsistently for reaction networks because (1) substrate limitations are not considered, (2) contradictory assumptions are made regarding the substrate processing rate when transitioning from single- to multi-substrate redox reactions, and (3) the product generation rate cannot be scaled from one to multiple substrates. In contrast, SU kinetics consistently scales the product generation rate from one to multiple substrates but predicts unrealistic results as consumer abundances reach large values with respect to their substrates. We attribute this deficit to SU's failure to incorporate substrate limitation in its derivation. To address these issues, we propose SUPECA (SU plus the equilibrium chemistry approximation – ECA) kinetics, which consistently imposes substrate and consumer mass balance constraints. We show that SUPECA kinetics satisfies the partition principle, i.e., scaling invariance across a network of an arbitrary number of reactions (e.g., as in Newton's law of motion and Dalton's law of partial pressures). We tested SUPECA kinetics with the equilibrium chemistry solution for some simple problems and found SUPECA outperformed SU kinetics. As an example application, we show that a steady-state SUPECA-based approach predicted an aerobic soil respiration moisture response function that agreed well with laboratory observations. We conclude that, as an extension to SU and ECA kinetics, SUPECA provides a robust mathematical representation of complex soil substrate–consumer interactions and can be applied to improve Earth system model (ESM) land models.« less

SUPECA kinetics for scaling redox reactions in networks of mixed substrates and consumers and an example application to aerobic soil respiration

NASA Astrophysics Data System (ADS)

Tang, Jin-Yun; Riley, William J.

2017-09-01

Several land biogeochemical models used for studying carbon-climate feedbacks have begun explicitly representing microbial dynamics. However, to our knowledge, there has been no theoretical work on how to achieve a consistent scaling of the complex biogeochemical reactions from microbial individuals to populations, communities, and interactions with plants and mineral soils. We focus here on developing a mathematical formulation of the substrate-consumer relationships for consumer-mediated redox reactions of the form A + BE→ products, where products could be, e.g., microbial biomass or bioproducts. Under the quasi-steady-state approximation, these substrate-consumer relationships can be formulated as the computationally difficult full equilibrium chemistry problem or approximated analytically with the dual Monod (DM) or synthesizing unit (SU) kinetics. We find that DM kinetics is scaling inconsistently for reaction networks because (1) substrate limitations are not considered, (2) contradictory assumptions are made regarding the substrate processing rate when transitioning from single- to multi-substrate redox reactions, and (3) the product generation rate cannot be scaled from one to multiple substrates. In contrast, SU kinetics consistently scales the product generation rate from one to multiple substrates but predicts unrealistic results as consumer abundances reach large values with respect to their substrates. We attribute this deficit to SU's failure to incorporate substrate limitation in its derivation. To address these issues, we propose SUPECA (SU plus the equilibrium chemistry approximation - ECA) kinetics, which consistently imposes substrate and consumer mass balance constraints. We show that SUPECA kinetics satisfies the partition principle, i.e., scaling invariance across a network of an arbitrary number of reactions (e.g., as in Newton's law of motion and Dalton's law of partial pressures). We tested SUPECA kinetics with the equilibrium chemistry solution for some simple problems and found SUPECA outperformed SU kinetics. As an example application, we show that a steady-state SUPECA-based approach predicted an aerobic soil respiration moisture response function that agreed well with laboratory observations. We conclude that, as an extension to SU and ECA kinetics, SUPECA provides a robust mathematical representation of complex soil substrate-consumer interactions and can be applied to improve Earth system model (ESM) land models.