Sample records for biochemical reaction kinetics

  1. The Chemical Master Equation Approach to Nonequilibrium Steady-State of Open Biochemical Systems: Linear Single-Molecule Enzyme Kinetics and Nonlinear Biochemical Reaction Networks

    Lisa M. Bishop


    Full Text Available We develop the stochastic, chemical master equation as a unifying approach to the dynamics of biochemical reaction systems in a mesoscopic volume under a living environment. A living environment provides a continuous chemical energy input that sustains the reaction system in a nonequilibrium steady state with concentration fluctuations. We discuss the linear, unimolecular single-molecule enzyme kinetics, phosphorylation-dephosphorylation cycle (PdPC with bistability, and network exhibiting oscillations. Emphasis is paid to the comparison between the stochastic dynamics and the prediction based on the traditional approach based on the Law of Mass Action. We introduce the difference between nonlinear bistability and stochastic bistability, the latter has no deterministic counterpart. For systems with nonlinear bistability, there are three different time scales: (a individual biochemical reactions, (b nonlinear network dynamics approaching to attractors, and (c cellular evolution. For mesoscopic systems with size of a living cell, dynamics in (a and (c are stochastic while that with (b is dominantly deterministic. Both (b and (c are emergent properties of a dynamic biochemical network; We suggest that the (c is most relevant to major cellular biochemical processes such as epi-genetic regulation, apoptosis, and cancer immunoediting. The cellular evolution proceeds with transitions among the attractors of (b in a “punctuated equilibrium” manner.

  2. The chemical master equation approach to nonequilibrium steady-state of open biochemical systems: linear single-molecule enzyme kinetics and nonlinear biochemical reaction networks.

    Qian, Hong; Bishop, Lisa M


    We develop the stochastic, chemical master equation as a unifying approach to the dynamics of biochemical reaction systems in a mesoscopic volume under a living environment. A living environment provides a continuous chemical energy input that sustains the reaction system in a nonequilibrium steady state with concentration fluctuations. We discuss the linear, unimolecular single-molecule enzyme kinetics, phosphorylation-dephosphorylation cycle (PdPC) with bistability, and network exhibiting oscillations. Emphasis is paid to the comparison between the stochastic dynamics and the prediction based on the traditional approach based on the Law of Mass Action. We introduce the difference between nonlinear bistability and stochastic bistability, the latter has no deterministic counterpart. For systems with nonlinear bistability, there are three different time scales: (a) individual biochemical reactions, (b) nonlinear network dynamics approaching to attractors, and (c) cellular evolution. For mesoscopic systems with size of a living cell, dynamics in (a) and (c) are stochastic while that with (b) is dominantly deterministic. Both (b) and (c) are emergent properties of a dynamic biochemical network; We suggest that the (c) is most relevant to major cellular biochemical processes such as epi-genetic regulation, apoptosis, and cancer immunoediting. The cellular evolution proceeds with transitions among the attractors of (b) in a "punctuated equilibrium" manner. PMID:20957107

  3. Biochemical toxicology studies of methomyl and its kinetic reaction with cholinesterase in rats

    The effect of the pesticide methomyl on acetylcholinesterase activities in brain and blood of male rats in vivo and the kinetics involved in their reaction in vitro were studied. Also, its effect on peroxidase action of catalase in vivo was studied using 14C- formate. The results showed that methomyl is a competitive inhibitor for acetylcholinesterase and the concentration levels that caused 50% inhibition of the enzyme activity were 2.1 x 10-2 M and 1.9 x 10-4 for brain and blood- Ache, respectively. The inhibition of acetylcholinesterase activity decreased to 67.5 % at the time of appearance of toxicity symptoms. The radioactivity eliminated in both the expired air and in urine was reduced

  4. Microfluidic Technology Platforms for Synthesizing, Labeling and Measuring the Kinetics of Transport and Biochemical Reactions for Developing Molecular Imaging Probes

    Phelps, Michael E.


    for radiochemistry (macro to micro levels), biochemistry and biology to imaging principles, tracer kinetics, pharmacokinetics and biochemical assays. New generations of radiochemists will be immersed in the biochemistry and biology for which their labeled probes are being developed for assays of these processes. In this program engineers and radio-chemists integrate the principles of microfluidics and radiolabeling along with proper system design and chemistry rule sets to yield Synthesizers enabling biological and pharmaceutical scientists to develop diverse arrays of probes to pursue their interests. This progression would allow also radiochemists to focus on the further evolution of rapid, high yield synthetic reactions with new enabling technologies, rather than everyday production of radiotracers that should be done by technologists. The invention of integrated circuits in electronics established a platform technology that allowed an evolution of ideas and applications far beyond what could have been imagined at the beginning. Rather than provide a technology for the solution to a single problem, it is hoped that microfluidic radiochemistry will be an enabling platform technology for others to solve many problems. As part of this objective, another program goal is to commercialize the technologies that come from this work so that they can be provided to others who wish to use it.

  5. Propagation of kinetic uncertainties through a canonical topology of the TLR4 signaling network in different regions of biochemical reaction space

    St Laurent Georges


    Full Text Available Abstract Background Signal transduction networks represent the information processing systems that dictate which dynamical regimes of biochemical activity can be accessible to a cell under certain circumstances. One of the major concerns in molecular systems biology is centered on the elucidation of the robustness properties and information processing capabilities of signal transduction networks. Achieving this goal requires the establishment of causal relations between the design principle of biochemical reaction systems and their emergent dynamical behaviors. Methods In this study, efforts were focused in the construction of a relatively well informed, deterministic, non-linear dynamic model, accounting for reaction mechanisms grounded on standard mass action and Hill saturation kinetics, of the canonical reaction topology underlying Toll-like receptor 4 (TLR4-mediated signaling events. This signaling mechanism has been shown to be deployed in macrophages during a relatively short time window in response to lypopolysaccharyde (LPS stimulation, which leads to a rapidly mounted innate immune response. An extensive computational exploration of the biochemical reaction space inhabited by this signal transduction network was performed via local and global perturbation strategies. Importantly, a broad spectrum of biologically plausible dynamical regimes accessible to the network in widely scattered regions of parameter space was reconstructed computationally. Additionally, experimentally reported transcriptional readouts of target pro-inflammatory genes, which are actively modulated by the network in response to LPS stimulation, were also simulated. This was done with the main goal of carrying out an unbiased statistical assessment of the intrinsic robustness properties of this canonical reaction topology. Results Our simulation results provide convincing numerical evidence supporting the idea that a canonical reaction mechanism of the TLR4

  6. Interfacial Reaction Kinetics

    O'Shaughnessy, Ben; Vavylonis, Dimitrios


    We study irreversible A-B reaction kinetics at a fixed interface separating two immiscible bulk phases, A and B. We consider general dynamical exponent $z$, where $x_t\\sim t^{1/z}$ is the rms diffusion distance after time $t$. At short times the number of reactions per unit area, $R_t$, is {\\em 2nd order} in the far-field reactant densities $n_A^{\\infty},n_B^{\\infty}$. For spatial dimensions $d$ above a critical value $d_c=z-1$, simple mean field (MF) kinetics pertain, $R_t\\sim Q_b t n_A^{\\in...

  7. Modelling of biochemical reaction networks

    Gloppen Jørgensen, Arne Gunnar


    This report investigates signalling in reaction kinetic networks. The main topic is signalling between a substance being controlled by another substance and how this can be related to control theory. Different types of so-called natural controllers are compared and certain properties are investigated. Natural controllers are models on how a catalyst enzyme controls, for example the concentration, of a substance. There are sixteen different combinations of signalling between these substanc...

  8. Chemical kinetics of gas reactions

    Kondrat'Ev, V N


    Chemical Kinetics of Gas Reactions explores the advances in gas kinetics and thermal, photochemical, electrical discharge, and radiation chemical reactions. This book is composed of 10 chapters, and begins with the presentation of general kinetic rules for simple and complex chemical reactions. The next chapters deal with the experimental methods for evaluating chemical reaction mechanisms and some theories of elementary chemical processes. These topics are followed by discussions on certain class of chemical reactions, including unimolecular, bimolecular, and termolecular reactions. The rema

  9. Determination of Kinetic Parameters and Metal Ions in Urea-Urease System Based on the Biochemical Reaction Heat Induced Laser Beam Deflection


    A new analytical method for the determination of urea-urease system based on biochemical reaction heat induced laser beam deflection is presented in this paper. With the method, the Michaelis constant (Km) of urease and apparent inhibition constant (Ki) of some metal ion inhibitors were measured respectively. This method was also used for the quantitative determination of metal ions with satisfactory result.

  10. Kinetics of Bio-Reactions

    Villadsen, John


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

  11. Reaction kinetics of polybutylene terephthalate polycondensation reaction

    Darda, P. J.; Hogendoorn, J. A.; Versteeg, G. F.; Souren, F.


    The kinetics of the forward polycondensation reaction of polybutylene terephthalate (PBT) has been investigated using thermogravimetric analysis (TGA). PBT - prepolymer with an initial degree of polymerization of 5.5 was used as starting material. The PBT prepolymer was prepared from dimethyl tereph

  12. Probabilistic sensitivity analysis of biochemical reaction systems

    Zhang, Hong-Xuan; Dempsey, William P.; Goutsias, John


    Sensitivity analysis is an indispensable tool for studying the robustness and fragility properties of biochemical reaction systems as well as for designing optimal approaches for selective perturbation and intervention. Deterministic sensitivity analysis techniques, using derivatives of the system response, have been extensively used in the literature. However, these techniques suffer from several drawbacks, which must be carefully considered before using them in problems of systems biology. ...

  13. Kinetics of actinide complexation reactions

    Though the literature records extensive compilations of the thermodynamics of actinide complexation reactions, the kinetics of complex formation and dissociation reactions of actinide ions in aqueous solutions have not been extensively investigated. In light of the central role played by such reactions in actinide process and environmental chemistry, this situation is somewhat surprising. The authors report herein a summary of what is known about actinide complexation kinetics. The systems include actinide ions in the four principal oxidation states (III, IV, V, and VI) and complex formation and dissociation rates with both simple and complex ligands. Most of the work reported was conducted in acidic media, but a few address reactions in neutral and alkaline solutions. Complex formation reactions tend in general to be rapid, accessible only to rapid-scan and equilibrium perturbation techniques. Complex dissociation reactions exhibit a wider range of rates and are generally more accessible using standard analytical methods. Literature results are described and correlated with the known properties of the individual ions

  14. Simulation methods with extended stability for stiff biochemical Kinetics

    Rué Pau


    Full Text Available Abstract Background With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (biochemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA. The key quantity is the step size, or waiting time, τ, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where τ can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called τ-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as τ grows. Results In this paper we extend Poisson τ-leap methods to a general class of Runge-Kutta (RK τ-leap methods. We show that with the proper selection of the coefficients, the variance of the extended τ-leap can be well-behaved, leading to significantly larger step sizes. Conclusions The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original τ-leap method. The approach paves the way to explore new multiscale methods to simulate (biochemical systems.

  15. Combustion kinetics and reaction pathways

    Klemm, R.B.; Sutherland, J.W. [Brookhaven National Laboratory, Upton, NY (United States)


    This project is focused on the fundamental chemistry of combustion. The overall objectives are to determine rate constants for elementary reactions and to elucidate the pathways of multichannel reactions. A multitechnique approach that features three independent experiments provides unique capabilities in performing reliable kinetic measurements over an exceptionally wide range in temperature, 300 to 2500 K. Recent kinetic work has focused on experimental studies and theoretical calculations of the methane dissociation system (CH{sub 4} + Ar {yields} CH{sub 3} + H + Ar and H + CH{sub 4} {yields} CH{sub 3} + H{sub 2}). Additionally, a discharge flow-photoionization mass spectrometer (DF-PIMS) experiment is used to determine branching fractions for multichannel reactions and to measure ionization thresholds of free radicals. Thus, these photoionization experiments generate data that are relevant to both reaction pathways studies (reaction dynamics) and fundamental thermochemical research. Two distinct advantages of performing PIMS with high intensity, tunable vacuum ultraviolet light at the National Synchrotron Light Source are high detection sensitivity and exceptional selectivity in monitoring radical species.

  16. Chemical reaction network approaches to Biochemical Systems Theory.

    Arceo, Carlene Perpetua P; Jose, Editha C; Marin-Sanguino, Alberto; Mendoza, Eduardo R


    This paper provides a framework to represent a Biochemical Systems Theory (BST) model (in either GMA or S-system form) as a chemical reaction network with power law kinetics. Using this representation, some basic properties and the application of recent results of Chemical Reaction Network Theory regarding steady states of such systems are shown. In particular, Injectivity Theory, including network concordance [36] and the Jacobian Determinant Criterion [43], a "Lifting Theorem" for steady states [26] and the comprehensive results of Müller and Regensburger [31] on complex balanced equilibria are discussed. A partial extension of a recent Emulation Theorem of Cardelli for mass action systems [3] is derived for a subclass of power law kinetic systems. However, it is also shown that the GMA and S-system models of human purine metabolism [10] do not display the reactant-determined kinetics assumed by Müller and Regensburger and hence only a subset of BST models can be handled with their approach. Moreover, since the reaction networks underlying many BST models are not weakly reversible, results for non-complex balanced equilibria are also needed. PMID:26363083

  17. Practical Enzyme Kinetics: A Biochemical Laboratory Experiment.

    Rowe, H. Alan; Brown, Morris


    Describes an experiment that provides a fundamental understanding of the kinetics of the enzyme papain. Discusses background, materials, procedures and results. Mentions analogous experiments that can be conducted with enzymatic contact-lens cleaning solutions. (CW)

  18. Kinetics of heterogeneous catalytic reactions

    Boudart, Michel


    This book is a critical account of the principles of the kinetics of heterogeneous catalytic reactions in the light of recent developments in surface science and catalysis science. Originally published in 1984. The Princeton Legacy Library uses the latest print-on-demand technology to again make available previously out-of-print books from the distinguished backlist of Princeton University Press. These paperback editions preserve the original texts of these important books while presenting them in durable paperback editions. The goal of the Princeton Legacy Library is to vastly increase acc

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

    Maggi, F.M.; Riley, W.J.


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

  20. Exact Results for Kinetics of Catalytic Reactions

    Frachebourg, L.; Krapivsky, P. L.


    The kinetics of an irreversible catalytic reaction on substrate of arbitrary dimension is examined. In the limit of infinitesimal reaction rate (reaction-controlled limit), we solve the dimer-dimer surface reaction model (or voter model) exactly in arbitrary dimension $D$. The density of reactive interfaces is found to exhibit a power law decay for $D

  1. Turing-Hopf instability in biochemical reaction networks arising from pairs of subnetworks.

    Mincheva, Maya; Roussel, Marc R


    Network conditions for Turing instability in biochemical systems with two biochemical species are well known and involve autocatalysis or self-activation. On the other hand general network conditions for potential Turing instabilities in large biochemical reaction networks are not well developed. A biochemical reaction network with any number of species where only one species moves is represented by a simple digraph and is modeled by a reaction-diffusion system with non-mass action kinetics. A graph-theoretic condition for potential Turing-Hopf instability that arises when a spatially homogeneous equilibrium loses its stability via a single pair of complex eigenvalues is obtained. This novel graph-theoretic condition is closely related to the negative cycle condition for oscillations in ordinary differential equation models and its generalizations, and requires the existence of a pair of subnetworks, each containing an even number of positive cycles. The technique is illustrated with a double-cycle Goodwin type model. PMID:22698892

  2. Reaction kinetics of isopropyl palmitate synthesis

    Lili Fu; Yinge Bai; Gaozhi L; Denggao Jiang


    In this study, the kinetics of isopropyl palmitate synthesis including the reaction mechanism was studied based on the two-step noncatalytic method. The liquid-phase diffusion effect on the reaction process was eliminated by adjusting the stirring rate. The results showed that the two-step reaction followed a tetrahedral mechanism and conformed to second-order reaction kinetics. Nucleophilic attack on the carbonyl carbon afforded an intermedi-ate, containing a tetrahedral carbon center. The intermediate ultimately decomposed by elimination of the leav-ing group, affording isopropyl palmitate. The experimental data were analyzed at different temperatures by the integral method. The kinetic equations of the each step were deduced, and the activation energy and frequency factor were obtained. Experiments were performed to verify the feasibility of kinetic equations, and the result showed that the kinetic equations were reliable. This study could be very significant to both industrial application and determining the continuous production of isopropyl palmitate.

  3. Kinetic studies of elementary chemical reactions

    Durant, J.L. Jr. [Sandia National Laboratories, Livermore, CA (United States)


    This program concerning kinetic studies of elementary chemical reactions is presently focussed on understanding reactions of NH{sub x} species. To reach this goal, the author is pursuing experimental studies of reaction rate coefficients and product branching fractions as well as using electronic structure calculations to calculate transition state properties and reaction rate calculations to relate these properties to predicted kinetic behavior. The synergy existing between the experimental and theoretical studies allow one to gain a deeper insight into more complex elementary reactions.

  4. Non-Markovian polymer reaction kinetics

    Guérin, Thomas; Voituriez, Raphaël; 10.1038/NCHEM.1378


    Describing the kinetics of polymer reactions, such as the formation of loops and hairpins in nucleic acids or polypeptides, is complicated by the structural dynamics of their chains. Although both intramolecular reactions, such as cyclization, and intermolecular reactions have been studied extensively, both experimentally and theoretically, there is to date no exact explicit analytical treatment of transport-limited polymer reaction kinetics, even in the case of the simplest (Rouse) model of monomers connected by linear springs. We introduce a new analytical approach to calculate the mean reaction time of polymer reactions that encompasses the non-Markovian dynamics of monomer motion. This requires that the conformational statistics of the polymer at the very instant of reaction be determined, which provides, as a by-product, new information on the reaction path. We show that the typical reactive conformation of the polymer is more extended than the equilibrium conformation, which leads to reaction times sign...

  5. Hydrogen electrode reaction: A complete kinetic description

    The kinetic description of the hydrogen electrode reaction (HER) in the whole range of overpotentials (-0.2 < η (V) < 0.40) is presented. The Volmer-Heyrovsky-Tafel mechanism was solved considering simultaneously the following items: (i) the diffusional contribution of the molecular hydrogen from and towards the electrode surface, (ii) the forward and backward reaction rates of each elementary step and (iii) a Frumkin type adsorption for the reaction intermediate. In order to verify the descriptive capability of the kinetic expressions derived, an experimental study of the HER was carried out on a rotating platinum disc electrode in acid solution. From the correlation of these results the elementary kinetic parameters were evaluated and several aspects related to the kinetic mechanism were discussed. Finally, the use of these kinetic expressions to interpret results obtained on microelectrodes is also analysed

  6. Hydrogen electrode reaction: A complete kinetic description

    Quaino, P.M. [Programa de Electroquimica Aplicada e Ingenieria Electroquimica (PRELINE), Facultad de Ingenieria Quimica, Universidad Nacional del Litoral, Santiago del Estero 2829, 3000 Santa Fe (Argentina); Gennero de Chialvo, M.R. [Programa de Electroquimica Aplicada e Ingenieria Electroquimica (PRELINE), Facultad de Ingenieria Quimica, Universidad Nacional del Litoral, Santiago del Estero 2829, 3000 Santa Fe (Argentina); Chialvo, A.C. [Programa de Electroquimica Aplicada e Ingenieria Electroquimica (PRELINE), Facultad de Ingenieria Quimica, Universidad Nacional del Litoral, Santiago del Estero 2829, 3000 Santa Fe (Argentina)]. E-mail:


    The kinetic description of the hydrogen electrode reaction (HER) in the whole range of overpotentials (-0.2 < {eta} (V) < 0.40) is presented. The Volmer-Heyrovsky-Tafel mechanism was solved considering simultaneously the following items: (i) the diffusional contribution of the molecular hydrogen from and towards the electrode surface, (ii) the forward and backward reaction rates of each elementary step and (iii) a Frumkin type adsorption for the reaction intermediate. In order to verify the descriptive capability of the kinetic expressions derived, an experimental study of the HER was carried out on a rotating platinum disc electrode in acid solution. From the correlation of these results the elementary kinetic parameters were evaluated and several aspects related to the kinetic mechanism were discussed. Finally, the use of these kinetic expressions to interpret results obtained on microelectrodes is also analysed.

  7. Chemical kinetics and reaction dynamics

    Houston, Paul L


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

  8. Mean field interaction in biochemical reaction networks

    Tembine, Hamidou


    In this paper we establish a relationship between chemical dynamics and mean field game dynamics. We show that chemical reaction networks can be studied using noisy mean field limits. We provide deterministic, noisy and switching mean field limits and illustrate them with numerical examples. © 2011 IEEE.

  9. SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

    Schröder Adrian


    Full Text Available Abstract Background The development of complex biochemical models has been facilitated through the standardization of machine-readable representations like SBML (Systems Biology Markup Language. This effort is accompanied by the ongoing development of the human-readable diagrammatic representation SBGN (Systems Biology Graphical Notation. The graphical SBML editor CellDesigner allows direct translation of SBGN into SBML, and vice versa. For the assignment of kinetic rate laws, however, this process is not straightforward, as it often requires manual assembly and specific knowledge of kinetic equations. Results SBMLsqueezer facilitates exactly this modeling step via automated equation generation, overcoming the highly error-prone and cumbersome process of manually assigning kinetic equations. For each reaction the kinetic equation is derived from the stoichiometry, the participating species (e.g., proteins, mRNA or simple molecules as well as the regulatory relations (activation, inhibition or other modulations of the SBGN diagram. Such information allows distinctions between, for example, translation, phosphorylation or state transitions. The types of kinetics considered are numerous, for instance generalized mass-action, Hill, convenience and several Michaelis-Menten-based kinetics, each including activation and inhibition. These kinetics allow SBMLsqueezer to cover metabolic, gene regulatory, signal transduction and mixed networks. Whenever multiple kinetics are applicable to one reaction, parameter settings allow for user-defined specifications. After invoking SBMLsqueezer, the kinetic formulas are generated and assigned to the model, which can then be simulated in CellDesigner or with external ODE solvers. Furthermore, the equations can be exported to SBML, LaTeX or plain text format. Conclusion SBMLsqueezer considers the annotation of all participating reactants, products and regulators when generating rate laws for reactions. Thus, for

  10. Kinetics of nitroxyl radical reactions

    Absolute rate-constants for the reaction of the nitroxyl free radicals TAN and TMPN with radiation-chemically-formed radicals and ions have been determined. k(TAN + X) (in M-1 sec-1) = 4.0 x 109 (for X =OH), 2.9 x 1010(esub(aq)-), 8.0 x 109 (H), 7.2 x 108 (CH2OH), 4.0 x 108 (CH3CHOH), 4.3 x 108 ((CH3)2COH), 2.8 x 108 (CH2(CH3)2COH), 5.9 x 107 (glucose radical), 4.0 x 108 (c-C5H9), and k(TMPN + X) = 3.4 x 109 (OH), 7.8 x 109 (esub(aq)-), 4.9 x 109 (H), 4.4 x 108 (CH2OH), 4.9 x 108 (CH3CHOH), 3.6 x 108 ((CH3)2COH), 1.5 x 108 (CH2(CH3)2COH), 4.9 x 107 (glucose radical), 4.3 x 108 (c-C5H9). Direct measurements by means of a pulse-radiolysis conductivity technique were based on the formation and destruction of charged species in these reactions within certain pH ranges. It is indicated that the radiosensitizing nitroxyles undergo both redox and addition reactions. (author)

  11. Modeling stochasticity in biochemical reaction networks

    Constantino, P. H.; Vlysidis, M.; Smadbeck, P.; Kaznessis, Y. N.


    Small biomolecular systems are inherently stochastic. Indeed, fluctuations of molecular species are substantial in living organisms and may result in significant variation in cellular phenotypes. The chemical master equation (CME) is the most detailed mathematical model that can describe stochastic behaviors. However, because of its complexity the CME has been solved for only few, very small reaction networks. As a result, the contribution of CME-based approaches to biology has been very limited. In this review we discuss the approach of solving CME by a set of differential equations of probability moments, called moment equations. We present different approaches to produce and to solve these equations, emphasizing the use of factorial moments and the zero information entropy closure scheme. We also provide information on the stability analysis of stochastic systems. Finally, we speculate on the utility of CME-based modeling formalisms, especially in the context of synthetic biology efforts.

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

    Laurie A Drozdowski; M Tom Clandinin; Alan BR Thomson


    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.

  13. Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems

    Goutsias John


    Full Text Available Abstract Background Estimating the rate constants of a biochemical reaction system with known stoichiometry from noisy time series measurements of molecular concentrations is an important step for building predictive models of cellular function. Inference techniques currently available in the literature may produce rate constant values that defy necessary constraints imposed by the fundamental laws of thermodynamics. As a result, these techniques may lead to biochemical reaction systems whose concentration dynamics could not possibly occur in nature. Therefore, development of a thermodynamically consistent approach for estimating the rate constants of a biochemical reaction system is highly desirable. Results We introduce a Bayesian analysis approach for computing thermodynamically consistent estimates of the rate constants of a closed biochemical reaction system with known stoichiometry given experimental data. Our method employs an appropriately designed prior probability density function that effectively integrates fundamental biophysical and thermodynamic knowledge into the inference problem. Moreover, it takes into account experimental strategies for collecting informative observations of molecular concentrations through perturbations. The proposed method employs a maximization-expectation-maximization algorithm that provides thermodynamically feasible estimates of the rate constant values and computes appropriate measures of estimation accuracy. We demonstrate various aspects of the proposed method on synthetic data obtained by simulating a subset of a well-known model of the EGF/ERK signaling pathway, and examine its robustness under conditions that violate key assumptions. Software, coded in MATLAB®, which implements all Bayesian analysis techniques discussed in this paper, is available free of charge at Conclusions Our approach provides an attractive statistical methodology for

  14. Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates

    Nielsen, Jens Bredal


    of the thermokinetic description of reaction rates to include the influence of effecters. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282......, 919-927] can be much more widely applied, although it was originally based on linearized kinetics. The methodology of determining elasticity coefficients directly from pool levels is illustrated with an analysis of the first two steps of the biosynthetic pathway of penicillin. The results compare well...

  15. Reaction kinetics of bond rotations in graphene

    Skowron, Stephen T.


    The formation and healing processes of the fundamental topological defect in graphitic materials, the Stone-Wales (SW) defect, are brought into a chemical context by considering the rotation of a carbon-carbon bond as chemical reaction. We investigate the rates and mechanisms of these SW transformations in graphene at the atomic scale using transmission electron microscopy. We develop a statistical atomic kinetics formalism, using direct observations obtained under different conditions to determine key kinetic parameters of the reactions. Based on the obtained statistics we quantify thermally and irradiation induced routes, identifying a thermal process of healing with an activation energy consistent with predicted adatom catalysed mechanisms. We discover exceptionally high rates for irradiation induced SW healing, incompatible with the previously assumed mechanism of direct knock-on damage and indicating the presence of an efficient nonadiabatic coupling healing mechanism involving beam induced electronic excitations of the SW defect.

  16. Kinetics of catalytic reactions-solutions manual

    Vannice, M Albert


    Including countless exercises and worked examples, this advanced reference work and textbook will be extremely useful for the work of many industrial scientists. It teaches readers to design kinetic experiments involving heterogeneous catalysts, to characterize these catalysts, to acquire rate data, to find heat and mass transfer limitations in these data, to select reaction models, to derive rate expressions based on these models, and to assess the consistency of these rate equations.

  17. Kinetics of rouleau formation. II. Reversible reactions.

    Samsel, R W; Perelson, A. S.


    Red blood cells aggregate face-to-face to form long, cylindrical, straight chains and sometimes branched structures called rouleaux. Here we extend a kinetic model developed by R. W. Samsel and A. S. Perelson (1982, Biophys. J. 37:493-514) to include both the formation and dissociation of rouleaux. We examine thermodynamic constraints on the rate constants of the model imposed by the principle of detailed balance. Incorporation of reverse reactions allows us to compute mean sizes of rouleaux ...

  18. Modelling biochemical reaction systems by stochastic differential equations with reflection.

    Niu, Yuanling; Burrage, Kevin; Chen, Luonan


    In this paper, we gave a new framework for modelling and simulating biochemical reaction systems by stochastic differential equations with reflection not in a heuristic way but in a mathematical way. The model is computationally efficient compared with the discrete-state Markov chain approach, and it ensures that both analytic and numerical solutions remain in a biologically plausible region. Specifically, our model mathematically ensures that species numbers lie in the domain D, which is a physical constraint for biochemical reactions, in contrast to the previous models. The domain D is actually obtained according to the structure of the corresponding chemical Langevin equations, i.e., the boundary is inherent in the biochemical reaction system. A variant of projection method was employed to solve the reflected stochastic differential equation model, and it includes three simple steps, i.e., Euler-Maruyama method was applied to the equations first, and then check whether or not the point lies within the domain D, and if not perform an orthogonal projection. It is found that the projection onto the closure D¯ is the solution to a convex quadratic programming problem. Thus, existing methods for the convex quadratic programming problem can be employed for the orthogonal projection map. Numerical tests on several important problems in biological systems confirmed the efficiency and accuracy of this approach. PMID:26920245

  19. Pozzolanic Reaction Kinetics of Coal Ashes

    ZHENG Hongwei; WANG Zhijuan; QIAN Jueshi; SONG Yuanming; WANG Zhi


    The pozzolanic reactivity was determined by the hydration kinetics of pozzolanic reaction based on the fact that the hydration products of active SiO_2 and Al_2O_3 with lime were soluble in dilute hydrochloric acid.The results show that the pozzolanic reaction of active SiO_2 and Al2O3 of coal ashes follows apparent first-order kinetics.The reaction rate constant of FBC ashes is greater than that of PC ashes,while the activation energy of the former is lower than that of the latter.It is confirmed that the pozzolanic activity of fluidized bed combustion(FBC)ashes is significantly higher than that of PC ashes,and the reaction barrier of the former is lower than that of the latter,because the microstructures of FBC ashes,such as mineralogical composition,morphology and polymerization degree of [SiO_4]and[AlO_6]are more favorable to the pozzolanic activity development than those of PC ashes.

  20. Spectroscopy and reaction kinetics of HCO

    The high-resolution infrared spectrum of the C-H stretching fundamental of HCO has been studied by means of infrared flash kinetic spectroscopy. HCO was generated by flash photolysis of acetaldehyde or formaldehyde using a 308 nm (XeCl) excimer laser. The transient absorption was probed with an infrared difference frequency laser system. The high resolution spectra obtained were assigned and fitted with rotational, spin-rotational, and centrifugal distortion constants. The ν1 band origin is 2434.48 cm/sup /minus/1/. New ground state constants have been derived from a least-squares fit combining the ν1 data with previous microwave and FIR LMR measurements. A new set of spectroscopic constants for the (1, 0, 0) state, the equilibrium rotational constants, and the orientation of the transition dipole moment are also reported. The kinetics and product branching ratios of the HCO + NO2 reaction have been studied using visible and infrared laser flash kinetic spectroscopy. The rate constant for the disappearance of HCO radical at 296 K is (5.7 +- 0.9) /times/ 10/sup /minus/11/ cm3 molec/sup /minus/1/ sec/sup /minus/1/, and it is independent of the pressure of SF6 buffer gas up to 700 torr. Less than 10% of the reaction goes through the most exothermic product channel, HNO + CO2. The product channel, H + CO2 + NO, is responsible for 52% of the reaction. HONO has been observed, though not quantitatively, as a reaction product corresponding to the HONO + CO channel. 51 refs., 21 figs., 8 tabs

  1. Kinetics of rouleau formation. II. Reversible reactions

    Samsel, R.W.; Perelson, A.S.


    Red blood cells aggregate face-to-face to form long, cylindrical, straight chains and sometimes branched structures called rouleaux. Here the authors extend a kinetic model developed by R.W. Samsel and A.S. Perelson to include both the formation and dissociation of rouleaux. Thermodynamic constraints on the rate constants of the model imposed by the principle of detailed balance were examined. Incorporation of reverse reactions allows computation of mean sizes of rouleaux and straight chain segments within rouleaux, as functions of time and at equilibrium. Using the Flory-Stockmayer method from polymer chemistry, a closed-form solution was obtained for the size distribution of straight chain segments within rouleaux at any point in the evolution of the reaction. The predictions of the theory compare favorably with data collected by D. Kernick, A.W.L. Jay, S. Rowlands, and L. Skibo on the kinetics of rouleaux formation. When rouleaux grow large, they may contain rings or loops and take on the appearance of a network. The importance of including the kinetics of ring closure in the development of realistic models of rouleaux formation was demonstrated.

  2. Bayesian inference of biochemical kinetic parameters using the linear noise approximation

    Finkenstädt Bärbel


    Full Text Available Abstract Background Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models requires the deveopment of effective statistical methods to calibrate such models against available data. Given the prevalence of stochasticity and noise in biochemical systems inference for stochastic models is of special interest. In this paper we present a simple and computationally efficient algorithm for the estimation of biochemical kinetic parameters from gene reporter data. Results We use the linear noise approximation to model biochemical reactions through a stochastic dynamic model which essentially approximates a diffusion model by an ordinary differential equation model with an appropriately defined noise process. An explicit formula for the likelihood function can be derived allowing for computationally efficient parameter estimation. The proposed algorithm is embedded in a Bayesian framework and inference is performed using Markov chain Monte Carlo. Conclusion The major advantage of the method is that in contrast to the more established diffusion approximation based methods the computationally costly methods of data augmentation are not necessary. Our approach also allows for unobserved variables and measurement error. The application of the method to both simulated and experimental data shows that the proposed methodology provides a useful alternative to diffusion approximation based methods.

  3. Kinetics of elementary atom and radical reactions

    During the past three years we have been working on four problems in the general area of gas phase kinetics and energy transfer of small molecules. These are: (1) measurements of the fine structure populations of ground state oxygen atoms produced in photodissociation reactions; (2) quenching of the Rydberg B (1Σ+) state of CO; (3) vibrational relaxation of highly excited molecules; and (4) kinetics of hydrogen molecules. The first two topics, which involve transitions between different electronic states of the parent molecule, are a departure from our previous research interests. In the accompanying renewal proposal we discuss plans to pursue these new topics vigorously during the coming year. The third topic is a continuation of our long interest in the energy dependence of the rates laws governing vibrational-to-translational energy transfer of molecules having large initial amounts of vibrational excitation. The final topic is a continuation of our studies of the reaction of O(3P) + H2. In this work we measured the rate constant for the reaction O(3P) with deuterium and also analyzed spectroscopically different sources of vibrationally excited hydrogen for possible future work. We discuss each of these four studies in the following sections

  4. Reaction kinetics of dolomite rim growth

    Helpa, V.; Rybacki, E.; Abart, R.; Morales, L. F. G.; Rhede, D.; Jeřábek, P.; Dresen, G.


    Reaction rims of dolomite (CaMg[CO3]2) were produced by solid-state reactions at the contacts of oriented calcite (CaCO3) and magnesite (MgCO3) single crystals at 400 MPa pressure, 750-850 °C temperature, and 3-146 h annealing time to determine the reaction kinetics. The dolomite reaction rims show two different microstructural domains. Elongated palisades of dolomite grew perpendicular into the MgCO3 interface with length ranging from about 6 to 41 µm. At the same time, a 5-71 µm wide rim of equiaxed granular dolomite grew at the contact with CaCO3. Platinum markers showed that the original interface is located at the boundary between the granular and palisade-forming dolomite. In addition to dolomite, a 12-80 µm thick magnesio-calcite layer formed between the dolomite reaction rims and the calcite single crystals. All reaction products show at least an axiotactic crystallographic relationship with respect to calcite reactant, while full topotaxy to calcite prevails within the granular dolomite and magnesio-calcite. Dolomite grains frequently exhibit growth twins characterized by a rotation of 180° around one of the equivalent axis. From mass balance considerations, it is inferred that the reaction rim of dolomite grew by counter diffusion of MgO and CaO. Assuming an Arrhenius-type temperature dependence, activation energies for diffusion of CaO and MgO are E a (CaO) = 192 ± 54 kJ/mol and E a (MgO) = 198 ± 44 kJ/mol, respectively.

  5. Kinetic modelling of the Maillard reaction between proteins and sugars

    Brands, C.M.J.


    Keywords: Maillard reaction, sugar isomerisation, kinetics, multiresponse modelling, brown colour formation, lysine damage, mutagenicity, casein, monosaccharides, disaccharides, aldoses, ketosesThe aim of this thesis was to determine the kinetics of the Maillard reaction between proteins and sugars, taking into account other simultaneously occurring sugar reactions. Model systems of foods, consisting of the protein casein and various sugars in a buffered solution, were studied. The reaction c...

  6. Understanding Chemical Reaction Kinetics and Equilibrium with Interlocking Building Blocks

    Cloonan, Carrie A.; Nichol, Carolyn A.; Hutchinson, John S.


    Chemical reaction kinetics and equilibrium are essential core concepts of chemistry but are challenging topics for many students, both at the high school and undergraduate university level. Visualization at the molecular level is valuable to aid understanding of reaction kinetics and equilibrium. This activity provides a discovery-based method to…

  7. Computational analysis of the roles of biochemical reactions in anomalous diffusion dynamics

    Naruemon, Rueangkham; Charin, Modchang


    Most biochemical processes in cells are usually modeled by reaction–diffusion (RD) equations. In these RD models, the diffusive process is assumed to be Gaussian. However, a growing number of studies have noted that intracellular diffusion is anomalous at some or all times, which may result from a crowded environment and chemical kinetics. This work aims to computationally study the effects of chemical reactions on the diffusive dynamics of RD systems by using both stochastic and deterministic algorithms. Numerical method to estimate the mean-square displacement (MSD) from a deterministic algorithm is also investigated. Our computational results show that anomalous diffusion can be solely due to chemical reactions. The chemical reactions alone can cause anomalous sub-diffusion in the RD system at some or all times. The time-dependent anomalous diffusion exponent is found to depend on many parameters, including chemical reaction rates, reaction orders, and chemical concentrations. Project supported by the Thailand Research Fund and Mahidol University (Grant No. TRG5880157), the Thailand Center of Excellence in Physics (ThEP), CHE, Thailand, and the Development Promotion of Science and Technology.

  8. A generalized kinetic model for heterogeneous gas-solid reactions

    Xu, Zhijie; Sun, Xin; Khaleel, Mohammad A.


    We present a generalized kinetic model for gas-solid heterogeneous reactions taking place at the interface between two phases. The model studies the reaction kinetics by taking into account the reactions at the interface, as well as the transport process within the product layer. The standard unreacted shrinking core model relies on the assumption of quasi-static diffusion that results in a steady-state concentration profile of gas reactant in the product layer. By relaxing this assumption and resolving the entire problem, general solutions can be obtained for reaction kinetics, including the reaction front velocity and the conversion (volume fraction of reacted solid). The unreacted shrinking core model is shown to be accurate and in agreement with the generalized model for slow reaction (or fast diffusion), low concentration of gas reactant, and small solid size. Otherwise, a generalized kinetic model should be used.

  9. Unravelling the Maillard reaction network by multiresponse kinetic modelling

    Martins, S.I.F.S.


    The Maillard reaction is an important reaction in food industry. It is responsible for the formation of colour and aroma, as well as toxic compounds as the recent discovered acrylamide. The knowledge of kinetic parameters, such as rate constants and activation energy, is necessary to predict its extent and, consequently, to optimise it. Each of the chapters presented in this thesis can be seen as a necessary step to succeed in applying multiresponse kinetic modelling in a complex reaction, su...

  10. Reaction schemes, escape times and geminate recombinations in particle-based spatial simulations of biochemical reactions

    Modeling the spatiotemporal dynamics of biochemical reaction systems at single-molecule resolution has become feasible with the increase of computing power and is applied especially to cellular signal transduction. For an association reaction the two molecules have to be in contact. Hence, a physically faithful model of the molecular interaction assumes non-overlapping molecules that interact at their surfaces (boundary scheme). For performance reasons, this model can be replaced by particles that can overlap and react when they are closer than a certain distance with a reaction probability (volume scheme). Here we present an analytical approximation for the reaction probability in the volume scheme and compare the volume- with the boundary scheme. A dissociation reaction, in contrast, creates two molecules next to each other. If the reaction is reversible, these two products can directly re-bind again, leading to an overestimation of the dimerized state in the simulation. We show how the correct recombination rate can be achieved if the products of the dissociation are placed at identical positions, but cannot react for a certain timespan. This refractory time corresponds to the completion of the diffusion-controlled dissociation of the two molecules to their contact distance ri + rj at t = τ-hat ×(ri+rj)2/(Di+Dj) with τ-hat = 1/10 for molecules with radii ri and rj and diffusion coefficients Di and Dj, respectively. (paper)

  11. Kinetics of the Exothermic Decomposition Reaction of s-Tripicryaminotrinitrobenzene

    ZHAO Feng-qi; HU Rong-zu; GAO Hong-xu; LUO Yang; GAO Sheng-li; SONG Ji-rong; SHI Qi-zhen


    The kinetic parameters of the exothermic decomposition reaction of s-Tripicryaminotrinitrobenzene under linear temperature rise condition are studied by means of DSC. The results show that the empirical kinetic model function in difs-1, respectively. The critical temperature of thermal explosion of the compound is 267.36 ℃.

  12. Kinetics of Acid Reactions: Making Sense of Associated Concepts

    Tan, Kim Chwee Daniel; Treagust, David F.; Chandrasegaran, A. L.; Mocerino, Mauro


    In chemical kinetics, in addition to the concepts related to kinetics, stoichiometry, chemical equilibrium and the characteristics of the reactants are often involved when comparing the rates of different reactions, making such comparisons very challenging for students at all levels, as well as for pre-service science teachers. Consequently, four…

  13. A moment-convergence method for stochastic analysis of biochemical reaction networks

    Zhang, Jiajun; Nie, Qing; Zhou, Tianshou


    Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

  14. A database of sources of information on mineral reaction kinetics

    Rochelle, C. A.; Turner, G


    The rate and magnitude of geochemical reactions can be described by two main processes; thermodynamics which determines the end point of reaction (i.e. approach to equilibrium conditions), and kinetics which determines how rapidly the reaction proceeds. There have been many studies that have investigated equilibrium conditions and have generated a wealth of data. However, for many systems the rate at which the end point of the reaction is reached is of equal, and possibly greater importance (...

  15. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

    Draeger, Andreas; Zielinski, Daniel C.; Keller, Roland;


    simplified the network reconstruction process, but building kinetic models for these systems is still a manually intensive task. Appropriate kinetic equations, based upon reaction rate laws, must be constructed and parameterized for each reaction. The complex test-and-evaluation cycles that can be involved...... during kinetic model construction would thus benefit from automated methods for rate law assignment. Results: We present a high-throughput algorithm to automatically suggest and create suitable rate laws based upon reaction type according to several criteria. The criteria for choices made by the...... algorithm can be influenced in order to assign the desired type of rate law to each reaction. This algorithm is implemented in the software package SBMLsqueezer 2. In addition, this program contains an integrated connection to the kinetics database SABIO-RK to obtain experimentally-derived rate laws when...

  16. Kinetics of Model Reactions for Interfacial Polymerization

    Henry Hall


    Full Text Available To model the rates of interfacial polycondensations, the rates of reaction of benzoyl chloride and methyl chloroformate with various aliphatic monoamines in acetonitrile were determined at 25 °C. Buffering with picric acid slowed these extremely fast reactions so the rate constants could be determined from the rate of disappearance of picrate ion. The rates of the amine reactions correlated linearly with their Swain-Scott nucleophilicities.

  17. Kinetics of Model Reactions for Interfacial Polymerization

    Henry Hall; Robert Bates; Jeffrey Robertson; Anne Padias; Trevor Centeno-Hall


    To model the rates of interfacial polycondensations, the rates of reaction of benzoyl chloride and methyl chloroformate with various aliphatic monoamines in acetonitrile were determined at 25 °C. Buffering with picric acid slowed these extremely fast reactions so the rate constants could be determined from the rate of disappearance of picrate ion. The rates of the amine reactions correlated linearly with their Swain-Scott nucleophilicities.

  18. Kinetics of photochromic reactions in condensed phases

    Sworakowski, J.; Janus, K.; Nešpůrek, Stanislav


    Roč. 116, 1-3 (2005), s. 97-110. ISSN 0001-8686 R&D Projects: GA MŠk 1P04OCD14.30 Grant ostatní: Polish Committee for Scientific Research(PL) 18/2004; Polish Committee for Scientific Research(PL) 50/2004 Keywords : photochromism * kinetics * rate constant Subject RIV: CH - Nuclear ; Quantum Chemistry Impact factor: 4.198, year: 2005

  19. Kinetic analysis of temperature-programmed reactions

    Kanervo, Jaana


    Temperature-programmed desorption (TPD), reduction (TPR) and oxidation (TPO) are thermoanalytical techniques for characterising chemical interactions between gaseous reactants and solid substances. The data collected by these techniques are commonly interpreted on a qualitative basis or by utilising simple, approximate kinetic methods. However, temperature-programmed techniques can also be regarded as transient response techniques and the experimental data can be utilised for dynamic modellin...

  20. Photocatalytic Water-Splitting Reaction from Catalytic and Kinetic Perspectives

    Hisatomi, Takashi


    Abstract: Some particulate semiconductors loaded with nanoparticulate catalysts exhibit photocatalytic activity for the water-splitting reaction. The photocatalysis is distinct from the thermal catalysis because photocatalysis involves photophysical processes in particulate semiconductors. This review article presents a brief introduction to photocatalysis, followed by kinetic aspects of the photocatalytic water-splitting reaction.Graphical Abstract: [Figure not available: see fulltext.

  1. Adsorption Isotherms and Surface Reaction Kinetics

    Lobo, L. S.; Bernardo, C. A.


    Explains an error that occurs in calculating the conditions for a maximum value of a rate expression for a bimolecular reaction. The rate expression is derived using the Langmuir adsorption isotherm to relate gas pressures and corresponding surface coverages. (GS)

  2. Kinetics of transuranium element oxidation-reduction reactions in solution

    A review of the kinetics of U, Np, Pu, Am oxidation-reduction reactions is proposed. The relations between the different activation thermodynamic functions (compensatory effect, formal entropy of the activated complex, magnitude of reactions velocities) are considered. The effects of acidity, ionic strength deuterium and mixed solvents polarity on reactions rates are described. The effect of different anions on reactions rates are explained by variations of the reaction standard free energy and variations of the activation free energy (coulombic interactions) resulting from the complexation of dissolved species by these anions. (author)

  3. Use of Competition Kinetics with Fast Reactions of Grignard Reagents

    Holm, Torkil


    Competition kinetics are useful for estimation of the reactivities of Grignard reagents if the reaction rates do not differ widely and if exact rates are not needed. If the rate of mixing is slower than the rate of reaction the ratios between the rates of fast and slow reagents are found to be too...... may account for almost all the product even when present as only 1 part in 100 parts of the competing agent. In this way allylmagnesium bromide is estimated to react with acetone, benzophenone, benzaldehyde, and diethylacetaldehyde ca. 1.5 x 105 times faster than does butylmagnesium bromide. The rates...... found for the four substrates do not differ significantly and it seems possible that there is a ceiling over the rate of reaction of this reagent, for example caused by diffusion control. This may explain that competition kinetics using allylmagnesium bromide have failed to show kinetic isotope effects...

  4. The influence of gas-kinetic evolution on plasma reactions

    Diver, D A; MacLachlan, C S; Potts, H E


    Plasmas in which there is a threshold for a dominant reaction to take place (such as recombination or attachment) will have particle distributions that evolve as the reaction progresses. The form of the Boltzmann collision term in such a context will cause the distribution to drift from its initial form, and so cause for example temperature fluctuations in the plasma if the distribution is originally Maxwellian. This behaviour will impact on the relevant reaction rates in a feedback loop that is missing from simple chemical kinetic descriptions since the plasma cannot be considered to be isothermal, as is the case in the latter approach. In this article we present a simple kinetic model that captures these essential features, showing how cumulative differences in the instantaneous species levels can arise over the purely chemical kinetic description, with implications for process yields and efficiencies.

  5. Antibiogram, Biochemical Reactions and Biotyping of Biofield Treated Providencia rettgeri

    Trivedi, Mahendra Kumar


    Providencia rettgeri (P. rettgeri) is the key organism for gastrointestinal tract infections due to its high virulence properties. The current study was designed to investigate the effect of Mr. Trivedi’s biofield energy treatment on P. rettgeri in lyophilized as well as revived state for antimicrobial susceptibility pattern, biochemical characteristics, and biotype number. The lyophilized strain of P. rettgeri (ATCC 9250) was divided into two parts, Group (Gr.)...

  6. Reduction of dynamical biochemical reactions networks in computational biology

    Radulescu, O.; Gorban, A.N.; Zinovyev, A.; Noel, V.


    Biochemical networks are used in computational biology, to model mechanistic details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multiscaleness, an important property of these networks, can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to...

  7. Stochastic Modeling and Simulation of Reaction-Diffusion Biochemical Systems

    LI Fei


    Reaction Diffusion Master Equation (RDME) framework, characterized by the discretization of the spatial domain, is one of the most widely used methods in the stochastic simulation of reaction-diffusion systems. Discretization sizes for RDME have to be appropriately chosen such that each discrete compartment is "well-stirred" and the computational cost is not too expensive. An efficient discretization size based on the reaction-diffusion dynamics of each species is derived in this disserta...

  8. Reaction kinetics of nanostructured silicon carbide

    Wallis, K. L.; Patyk, J. K.; Zerda, T. W.


    SiC nanowires were produced from carbon nanotubes and silicon by two different methods at high temperature. X-ray powder diffraction was used to determine SiC concentration. The reaction rate using the Avrami-Erofeev method was determined for samples sintered at temperatures ranging from 1313 to 1823 K. The activation energy was found to be (254 ± 36) kJ mol-1. The limiting factor in SiC formation is diffusion of silicon and carbon atoms through the produced layer of SiC.

  9. Reaction kinetics of nanostructured silicon carbide

    SiC nanowires were produced from carbon nanotubes and silicon by two different methods at high temperature. X-ray powder diffraction was used to determine SiC concentration. The reaction rate using the Avrami-Erofeev method was determined for samples sintered at temperatures ranging from 1313 to 1823 K. The activation energy was found to be (254 ± 36) kJ mol-1. The limiting factor in SiC formation is diffusion of silicon and carbon atoms through the produced layer of SiC

  10. Fast stochastic simulation of biochemical reaction systems by alternative formulations of the chemical Langevin equation

    Mélykúti, Bence


    The Chemical Langevin Equation (CLE), which is a stochastic differential equation driven by a multidimensional Wiener process, acts as a bridge between the discrete stochastic simulation algorithm and the deterministic reaction rate equation when simulating (bio)chemical kinetics. The CLE model is valid in the regime where molecular populations are abundant enough to assume their concentrations change continuously, but stochastic fluctuations still play a major role. The contribution of this work is that we observe and explore that the CLE is not a single equation, but a parametric family of equations, all of which give the same finite-dimensional distribution of the variables. On the theoretical side, we prove that as many Wiener processes are sufficient to formulate the CLE as there are independent variables in the equation, which is just the rank of the stoichiometric matrix. On the practical side, we show that in the case where there are m1 pairs of reversible reactions and m2 irreversible reactions there is another, simple formulation of the CLE with only m1 + m2 Wiener processes, whereas the standard approach uses 2 m1 + m2. We demonstrate that there are considerable computational savings when using this latter formulation. Such transformations of the CLE do not cause a loss of accuracy and are therefore distinct from model reduction techniques. We illustrate our findings by considering alternative formulations of the CLE for a human ether a-go-go related gene ion channel model and the Goldbeter-Koshland switch. © 2010 American Institute of Physics.

  11. Chemical kinetic reaction mechanism for the combustion of propane

    Jachimowski, C. J.


    A detailed chemical kinetic reaction mechanism for the combustion of propane is presented and discussed. The mechanism consists of 27 chemical species and 83 elementary chemical reactions. Ignition and combustion data as determined in shock tube studies were used to evaluate the mechanism. Numerical simulation of the shock tube experiments showed that the kinetic behavior predicted by the mechanism for stoichiometric mixtures is in good agrement with the experimental results over the entire temperature range examined (1150-2600K). Sensitivity and theoretical studies carried out using the mechanism revealed that hydrocarbon reactions which are involved in the formation of the HO2 radical and the H2O2 molecule are very important in the mechanism and that the observed nonlinear behavior of ignition delay time with decreasing temperature can be interpreted in terms of the increased importance of the HO2 and H2O2 reactions at the lower temperatures.

  12. Kinetic of the reaction between bitumen and sulphur

    The utilization of sulphur in bituminous binders has been tried for many years in a number of countries, mainly USA and Canada. The overall purpose of this study was to evaluate the kinetics of the reaction between elemental sulphur and bitumen, with the production of hydrogen sulfide. The work was carried out with the help of a thermo balance. It was shown that H2S evolution starts immediately after sulphur melting and that the rate of reaction is of second order

  13. Kinetics and Mechanisms of Calcite Reactions with Saline Waters

    Chapman, Piers; *Morse, John W. (*/deceased)


    1. Objective The general objective of this research was to determine the kinetics and mechanisms of calcite reactions with saline waters over a wide range of saline water composition, carbon dioxide partial pressure (pCO2), and modest ranges of T and P. This would be done by studying both reaction rates and solubility from changes in solution chemistry. Also, nanoscale observations of calcite surface morphology and composition would be made to provide an understanding of rate controlling mechanisms.

  14. Exact results for noise power spectra in linear biochemical reaction networks

    Warren, Patrick B.; Tanase-Nicola, Sorin; Wolde, Pieter Rein ten


    We present a simple method for determining the exact noise power spectra in linear chemical reaction networks. We apply the method to networks which are representative of biochemical processes such as gene expression and signal detection. Our results clarify how noise is transmitted by signal detection motifs, and indicate how to coarse-grain networks by the elimination of fast reactions.

  15. Penicillin Hydrolysis: A Kinetic Study of a Multistep, Multiproduct Reaction.

    McCarrick, Thomas A.; McLafferty, Fred W.


    Background, procedures used, and typical results are provided for an experiment in which students carry out the necessary measurements on the acid-catalysis of penicillin in two hours. By applying kinetic theory to the data obtained, the reaction pathways for the hydrolysis of potassium benzyl penicillin are elucidated. (JN)


    The kinetics of the reaction between CaO and HCl were investigated under conditions that minimize bulk mass transfer and pore diffusion limitations. Reactivity data from 0.2- to 1-s exposure to 5000 ppm HCl in a fixed bed reactor were analyzed by a shrinking core model of diffusi...

  17. Kinetics of interfacial reaction between uranium dioxide and zircaloy-2

    Solid state reaction between UO2 pellets and zircaloy-2 has been studied at temperature between 1270 and 1775 K. It has been observed that the reaction results in the formation of three layers. The kinetics of growth of these layers have been studied in depth and are found to obey parabolic relatjon with annealing time. The temperature dependence of the growth rate of these reaction layers obeys an Arrhenius type of relation. Micro cracks and longitudinal gaps were observed in some of the couples (towards UO2 pellet side) annealed for longer period. The presence of gaps and cracks suggests that the reaction is assisted by a process involving stress and strain in the reaction zone set up by differential contraction between uranium dioxide and reaction layers. (author)

  18. Intermediate-high energy nuclear reaction kinetics simulation and QMD

    The main features of the IHENRKS and its application in the study of thermalization for reaction of 830 MeV P + 56Fe are described. IHENRKS is the abbreviation of intermediate-high energy nuclear reaction kinetic simulation. It combines the idea and method of MCM, SSIENC and QMD. These kind of models treat the movement of each particle (nucleon and meson) and their collisions in time and space and concern with the new particle production. From calculations for 830 MeV proton bombarding reactions, it can be concluded that the nucleus is not wholly thermalized, but locally thermalized. (1 fig.)

  19. Evolutionary origin of power-laws in Biochemical Reaction Network; embedding abundance distribution into topology

    Furusawa, Chikara; Kaneko, Kunihiko


    The evolutionary origin of universal statistics in biochemical reaction network is studied, to explain the power-law distribution of reaction links and the power-law distributions of chemical abundances. Using cell models with catalytic reaction network, we find evidence that the power-law distribution in abundances of chemicals emerges by the selection of cells with higher growth speeds. Through the further evolution, this inhomogeneity in chemical abundances is shown to be embedded in the d...

  20. Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

    Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.


    Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

  1. Kinetics of fast reactions of excited species. Final report

    This report contains brief summaries of findings in the following areas: gamma radiation induced decomposition of chloroform; proton transfer and ion neutralization reactions in gaseous hydrocarbons; kinetics of thremal D-atom reactions with CH4 C2H6; the gamma radiation induced decomposition of liquid n-pentane; pulse radiolysis of rare gases and liquid n-pentane and n-pentane-O2 solutions; rate constants and activation energies for second order decay of pentyl and peroxypentyl radicals; pulse radiolysis fo aromatic solutes in halogenated solvents; the gamma radiation induced decomposition of nitromethane; the radiolysis of heavy water vapor; pulse radiolysis of solvated electrons in binary liquid solutions; collisional quenching of rare gas excimers by small foreign molecules; kinetics and mechanism for decay of Paschen-1s argon atoms; detection and monitoring of excited atoms in pulse irradiated rare gases



    The time integration method with four-order accuracy, self-starting and implicit for the diffuse chemical reaction kinetics equation or the transient instantaneous temperature filed equation was presented. The examples show that both accuracy and stability are better than Runge-Kutta method with four-order. The coefficients of the equation are stored with sparse matrix pattern, so an algorithm is presented which combines a compact storage scheme with reduced computation cost. The computation of the competitive and consecutive reaction in the rotating packed bed, taken as examples,shows that the method is effective.

  3. Some kinetics aspects of chlorine-solids reactions

    Kanari, N.; Mishra, D.; Mochón, J.; Verdeja, L. F.; Diot, F.; Allain, E.


    The present paper describes detailed kinetics investigations on some selected chlorine-solid reactions through thermogravimetric measurements. The solids studied in this article include chemical pure oxides and sulfides as well as their natural bearing materials. The chlorinating agents employed are gaseous mixtures of Cl2+N2 (chlorination), Cl2+O2 (oxychlorination), and Cl2+CO (...

  4. Variable elimination in chemical reaction networks with mass action kinetics

    Feliu, Elisenda; Wiuf, Carsten


    We consider chemical reaction networks taken with mass action kinetics. The steady states of such a system are solutions to a system of polynomial equations. Even for small systems the task of finding the solutions is daunting. We develop an algebraic framework and procedure for linear elimination of variables. The procedure reduces the variables in the system to a set of "core" variables by eliminating variables corresponding to a set of non-interacting species. The steady states are paramet...

  5. Characterization of hot hydrogen-atom reactions by kinetic spectrography.

    Tomalesky, R. E.; Sturm, J. E.


    The flash photolysis of hydrogen iodide in the presence of nitrous oxide, carbon dioxide, and water has been investigated by kinetic spectroscopy. Although the fraction of hydrogen iodide dissociated was very large, the only observable intermediate was imidogen. It was demonstrated that the rapid removal of imidogen and the apparent absence of hydroxyl radicals in each case is a result of the following two reactions, respectively: (1) NH + HI yields NH2 + I; and (2) OH + HI yields H2O + I.

  6. The reaction kinetics of amino radicals with sulfur dioxide

    Gao, Yide; Glarborg, Peter; Marshall, Paul


    Application of the laser photolysis-laser-induced fluorescence method to the reaction NH2+SO2 in argon bath gas yields pressure-dependent, third-order kinetics which may be summarized as k = (1.49 ± 0.15) × 10-31 (T/298 K)-0.83cm6 molecule-2 s-1 over 292-555K, where the uncertainty is the 95% con...

  7. Kinetics of the reversible reaction of struvite crystallisation.

    Crutchik, D; Garrido, J M


    The crystallisation of struvite could be a sustainable and economical alternative for recovering phosphorus from wastewater streams with high phosphate concentrations. Knowledge regarding the kinetics and thermodynamics that are involved in the crystallisation of struvite is the key to determine the optimal conditions for obtaining an efficient process. This study was conducted in a continuous stirred batch reactor. Different sets of experiments were performed in which struvite was either dissolved (undersaturated) or precipitated (oversaturated). These experiments were conducted at different temperatures (25, 30 and 35 °C) and pH values (8.2, 8.5 and 8.8) to determine the kinetics of struvite precipitation and dissolution. Struvite crystallisation was modelled as a reversible reaction. The kinetic rate parameters of struvite precipitation were 1.03·10(-4), 1.25·10(-4) and 1.54·10(-4) mol m(-2) min(-1) at 25, 30 and 35 °C, respectively. Similar kinetic rate parameters were determined for struvite dissolution. Struvite heterogeneous crystallisation can be represented by a first-order kinetic model that fitted well the experimental data. PMID:27085317

  8. Temperature Control System for Biochemical Reactions in Microchip-Based Devices

    荆高山; 张坚; 朱小山; 冯继宏; 谭智敏; 刘理天; 程京


    A silicon-glass chip based microreactor has been designed and fabricated for biochemical reactions such as polymerase chain reactions (PCR). The chip based microreactor has integrated resistive heating elements. The computer-controlled temperature control system is highly reliable with precise temperature control, excellent temperature uniformity, and rapid heating and cooling capabilities. The development of the microreaction system is an important step towards the construction of a lab-on-a-chip system.

  9. Radical-ion-pair reactions are the biochemical equivalent of the optical double slit experiment

    Kominis, I. K.


    Radical-ion-pair reactions were recently shown to represent a rich biophysical laboratory for the application of quantum measurement theory methods and concepts. We here show that radical-ion-pair reactions essentially form a non-linear biochemical double slit interferometer. Quantum coherence effects are visible when "which-path" information is limited, and the incoherent limit is approached when measurement-induced decoherence sets in. Based on this analogy with the optical double slit expe...


    Gökalp, Hüsnü Yusuf; Hüdayi ERCOŞKUN; Ahmet Hilmi ÇON


    Glycolysis, lipolysis and proteolysis are the main biochemical reactions which effect characteristic flavour, aroma, color and texture development of fermented meat products. These reactions are results of the microorganisms or endogenous meat enzymes. The products which are results of glycolysis are firstly responsible from decreasing of pH. Volatile compounds from glycolysis effect aroma. Compounds formed by lipolysis are the main reason that effect aroma. 60 % volatile compounds formed...

  11. Reaction Path Optimization with Holonomic Constraints and Kinetic Energy Potentials

    Two methods are developed to enhance the stability, efficiency, and robustness of reaction path optimization using a chain of replicas. First, distances between replicas are kept equal during path optimization via holonomic constraints. Finding a reaction path is, thus, transformed into a constrained optimization problem. This approach avoids force projections for finding minimum energy paths (MEPs), and fast-converging schemes such as quasi-Newton methods can be readily applied. Second, we define a new objective function - the total Hamiltonian - for reaction path optimization, by combining the kinetic energy potential of each replica with its potential energy function. Minimizing the total Hamiltonian of a chain determines a minimum Hamiltonian path (MHP). If the distances between replicas are kept equal and a consistent force constant is used, then the kinetic energy potentials of all replicas have the same value. The MHP in this case is the most probable isokinetic path. Our results indicate that low-temperature kinetic energy potentials (7eq-to-Cax isomerization of an alanine dipeptide, the 4C1-to-1C4 transition of an α-D-glucopyranose, and the helix-to-sheet transition of a GNNQQNY heptapeptide. By applying the methods developed in this work, convergence of reaction path optimization can be achieved for these complex transitions, involving full atomic details and a large number of replicas (>100). For the case of helix-to-sheet transition, we identify pathways whose energy barriers are consistent with experimental measurements. Further, we develop a method based on the work energy theorem to quantify the accuracy of reaction paths and to determine whether the atoms used to define a path are enough to provide quantitative estimation of energy barriers.

  12. A Note on the Kinetics of Diffusion-mediated Reactions

    Naqvi, K Razi


    The prevalent scheme of a diffusion-mediated bimolecular reaction $A+B\\rightarrow P$ is an adaptation of that proposed by Briggs and Haldane for enzyme action [{\\em Biochem J.\\/}, 19:338--339, 1925]. The purpose of this Note is to explain, {\\em by using an argument involving no mathematics\\/}, why the breakup of the encounter complex cannot be described, except in special circumstances, in terms of a first-order process $\\{AB\\}\\rightarrow A+B$. Briefly, such a description neglects the occurrence of re-encounters, which lie at the heart of Noyes's theory of diffusion-mediated reactions. The relation $k=\\alpha k_{\\mbox{\\scriptsize e}}$ becomes valid only when $\\alpha$ (the reaction probability per encounter) is very much smaller than unity (activation-controlled reactions), or when $\\beta$ (the re-encounter probability) is negligible (as happens in a gas-phase reaction). References to some works (by the author and his collaborators) which propound the correct approach for finding $k$ are also supplied.

  13. Reaction kinetics of resveratrol with thiyl and alkoxyl radicals

    Complete text of publication follows. Plant derived resveratrol (trans-3,5,4'-trihydroxystilbene) possesses a broad spectrum of biological activities, one of them are very well known its antioxidative properties. Our work aims to provide kinetic data with regard to the reactivity of resveratrol with uninvestigated short-lived bioradicals, identified as mediators in oxidative lipid degradation processes. Radicals of our interest are alkoxyl radicals, well known propagators of the chain free radical reactions in lipids, and thiyl radicals which protect lipids from their degradation pathway, but at the same time cause the isomerization of the double bonds. In order to investigate these reactions of resveratrol laser flash photolysis was used. On the basis of competitive kinetics the rate constants were determined under pseudo-first order conditions in acetonitrile solutions at room temperature. Thiyl radicals were generated indirectly in solution containing 1-octadecanthiol and photosensitive benzophenone in acetonitrile using the light pulses at 347 nm from ruby laser. Tert-butoxyl radicals were generated directly by peroxide bond cleavage from di-tert-butyl peroxide in acetonitrile by light pulses of Nd:YAG at 355 nm, and ruby at 347 nm. Obtained rate constants for the reactions of resveratrol and radicals generated by laser flash photolysis will be summarized and compared with rare literature data for the rate constants of investigated reactions of resveratrol and other radicals generated by pulse radiolysis.

  14. Kinetics and Mechanisms of Calcite Reactions with Saline Waters

    Gorman, Brian P [Colorado School of Mines, Golden, CO (United States)


    Project Description: The general objective of the proposed research is to determine the kinetics and mechanisms of calcite reactions with saline waters over a wide range of saline water composition, pCO2, and modest ranges in T and P. This will be accomplished by studying both reaction rates and solubility from changes in solution chemistry, and making nanoscale observations of calcite precipitate surface morphology and composition at the micro-to-nano-scale to provide an understanding of controlling reaction mechanisms and pathways. The specific objectives necessary to reach the general objective are: a) determination of how pCO2, Ca2+, ionic strength and “foreign” ions influence reaction rates; and b) investigate the influence of these parameters on apparent kinetic solubility from dissolution and precipitation reactions. This information will clearly be central to the construction of reliable reaction-transport models to predict reservoir and formation response to increased CO2 in saline waters. This program was initially collaborative with John Morse at Texas A&M, however his passing shortly after the beginning of this program resulted in abbreviated research time and effort. Summary of Results: Early studies using electron microscopy and spectroscopy indicated that carbonate precipitation from natural seawater (NSW) conditions onto aragonite substrates was mediated by a surface amorphous calcium carbonate layer. It was hypothesized that this ACC layer (observed after < 5days reaction time) was responsible for the abnormal reaction kinetics and also served as a metastable seed layer for growth of epitaxial aragonite. Further studies of the ACC formation mechanism indicated a strong dependence on the Mg concentration in solution. Subsequent studies at shorter times (10 hrs) on calcite substrates and in a wide range of supersaturation conditions did not indicate any ACC layer. Instead, an epitaxial layer by layer

  15. An investigation of kinetic reaction and decomposition of sodium uranate

    For the management of severe accidents of sodium-cooled fast breeder reactor, the coolability of the fuel debris bed on a core support plate is a key concern during the post-accident heat removal phase. In an air ingress scenario, the reactions between the fuel and highly oxidized sodium are likely to form sodium uranoplutonate. This would negatively influence the coolability of the fuel debris bed due to a lowering of the thermal conductivity and density. This study has focused on the formation kinetics of sodium uranate from UO2 and liquid sodium including oxygen at a high concentration. In this paper, the experiments on reaction initiation temperatures, reaction rates, and the decomposition of sodium uranate are reported. (author)

  16. Variation of kinetic isotope effect in multiple proton transfer reactions

    B Saritha; M Durga Prasad


    Recently, we had suggested that the motion along the promoter mode in the first part of the IRC of proton transfer reaction enhances the delocalization of electrons on the acceptor atom into the * orbital of the donor-hydrogen covalent bond, and as a consequence weakens it. This leads to a reduction of the barrier to the proton transfer as well as the stretching frequency of donor-hydrogen bond. An extension of this to the concerted multiple proton transfer reactions implies that the kinetic isotope effect in such reaction depends exponentially on the number of protons that are being transferred. Computational evidence on three systems, (HF)3, formic acid dimer, and (H2O) clusters is provided to support this assertion.

  17. Biochemical features and kinetic properties of α-amylases from marine organisms.

    Homaei, Ahmad; Ghanbarzadeh, Mehri; Monsef, Ferial


    Marine organisms have the ability of producing enzymes with unique properties compared to those of the same enzymes from terrestrial organisms. α-Amylases are among the most important extracellular enzymes found in various groups of organisms such as plants, animals and microorganisms. They play important roles in their carbohydrates metabolism of each organism. Microbial production of α-amylases is more effective than other sources of the enzyme. Many microorganisms are known to produce α-amylase including bacteria, yeasts, fungi and actinomycetes. However, enzymes from fungal and bacterial sources have dominated applications in industrial sectors. This review deals with what is known about the kinetics, biochemical properties and applications of these enzymes that have only been found in them and not in other α-amylases, and discussing their mechanistic and regulatory implications. PMID:26657843

  18. Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm

    We address the problem of simulating biochemical reaction networks with time-dependent rates and propose a new algorithm based on our rejection-based stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)]. The computation for selecting next reaction firings by our time-dependent RSSA (tRSSA) is computationally efficient. Furthermore, the generated trajectory is exact by exploiting the rejection-based mechanism. We benchmark tRSSA on different biological systems with varying forms of reaction rates to demonstrate its applicability and efficiency. We reveal that for nontrivial cases, the selection of reaction firings in existing algorithms introduces approximations because the integration of reaction rates is very computationally demanding and simplifying assumptions are introduced. The selection of the next reaction firing by our approach is easier while preserving the exactness

  19. Radical-ion-pair reactions are the biochemical equivalent of the optical double-slit experiment.

    Kominis, Iannis K


    Radical-ion-pair reactions were recently shown to represent a rich biophysical laboratory for the application of quantum measurement theory methods and concepts. Here we show that radical-ion-pair reactions essentially form a nonlinear biochemical double-slit interferometer. Quantum coherence effects are visible when "which-path" information is limited, and the incoherent limit is approached when measurement-induced decoherence sets in. Based on this analogy with the optical double-slit experiment we derive and elaborate on the fundamental master equation of spin-selective radical-ion-pair reactions that covers the continuous range from complete incoherence to maximum singlet-triplet coherence. PMID:21728616

  20. Simulation of the kinetics of precipitation reactions in ferritic steels

    Computer simulations of diffusion-controlled phase transformations in model alloys of Fe-Cr-C, Fe-Cr-W-C, Fe-Cr-Si-C, and Fe-Cr-Co-V-C are presented. The compositions considered are typical for ferritic steels. The simulations are performed using the software DICTRA and the thermodynamic calculations of phase equilibria are performed using Thermo-Calc. The thermodynamic driving forces and the kinetics of diffusion-controlled precipitation reactions of M23C6, M7C3, cementite and Laves-phase (Fe, Cr)2W are discussed. The simultaneous growth of stable and metastable phases is treated in a multi-cell approach. The results show remarkable effects on the growth kinetics due to the competition during simultaneous growth

  1. Hybrid Differential Evolution for Estimation of Kinetic Parameters for Biochemical Systems

    ZHAO Chao; XU Qiaoling; LIN Siming; LI Xuelai


    Determination of the optimal model parameters for biochemical systems is a time consuming iterative process.In this study,a novel hybrid differential evolution(DE)algorithm based on the differential evolution technique and a local search strategy is developed for solving kinetic parameter estimation problems.By combining the merits of DE with Gauss-Newton method,the proposed hybrid approach employs a DE algorithm for identifying promising regions of the solution space followed by use of Gauss-Newton method to determine the optimum in the identified regions.Some well-known benchmark estimation problems are utilized to test the efficiency and the robustness of the proposed algorithm compared to other methods in literature.The comparison indicates that the present hybrid algorithm outperforms other estimation techniques in terms of the global searching ability and the convergence speed.Additionally,the estimation of kinetic model parameters for a feed batch fermentor is carried out to test the applicability of the proposed algorithm.The result suggests that the method can be used to estimate suitable values of model parameters for a complex mathematical model.

  2. Kinetics of the gas-phase tritium oxidation reaction

    Homogeneous gas-phase kinetics of tritium oxidation (2T2 + O2 →2T2O) have been studied with a model that accounts explicitly for radiolysis of the major species and the kinetics of the subsequent reactions of ionic, excited-state, and neutral species. Results from model calculations are given for 10-4 -1.0 mol% T2 in O2 (298 K, 1 atm). As the reaction evolves three different mechanisms control T2O production, each with a different overall rate expression and a different order with respect to the T2 concentration. The effects of self-radiolysis of pure T2 on the tritium oxidation reaction were calculated. Tritium atoms, the primary product of T2 self-radiolysis, altered the oxidation mechanism only during the first few seconds following the initiation of the T2-O2 reaction. Ozone, an important intermediate in T2 oxidation, was monitored in-situ by U.V. absorption spectroscopy for 0.01-1.0 mol% T2 an 1 atm O2. The shape of the experimental ozone time profile agreed with the model predictions. As predicted, the measured initial rate of ozone production varied linearly with initial T2 concentration ([T2]0.6o), but at an initial rate one-third the predicted value. The steady-state ozone concentration ([O3]ss) was predicted to be dependent on [T2]0.3o, but the measured value was [T2]0.6o, resulting in four times higher [O3]ss than predicted for a 1.0% T2-O2 mixture. Adding H2 to the T2-O2 mixture, to provide insight into the differences between the radiolytic and chemical behavior of the tritium, produced a greater decrease in [O3]ss than predicted. Adjusting the reaction cell surface-to-volume ratio showed implications of minor surface removal of ozone

  3. Kinetics and mechanisms of reactions involving small aromatic reactive intermediates

    Lin, M.C. [Emory Univ., Atlanta, GA (United States)


    Small aromatic radicals such as C{sub 6}H{sub 5}, C{sub 6}H{sub 5}O and C{sub 6}H{sub 4} are key prototype species of their homologs. C{sub 6}H{sub 5} and its oxidation product, C{sub 6}H{sub 5}O are believed to be important intermediates which play a pivotal role in hydrocarbon combustion, particularly with regard to soot formation. Despite their fundamental importance, experimental data on the reaction mechanisms and reactivities of these species are very limited. For C{sub 6}H{sub 5}, most kinetic data except its reactions with NO and NO{sub 2}, were obtained by relative rate measurements. For C{sub 6}H{sub 5}O, the authors have earlier measured its fragmentation reaction producing C{sub 5}H{sub 5} + CO in shock waves. For C{sub 6}H{sub 4}, the only rate constant measured in the gas phase is its recombination rate at room temperature. The authors have proposed to investigate systematically the kinetics and mechanisms of this important class of molecules using two parallel laser diagnostic techniques--laser resonance absorption (LRA) and resonance enhanced multiphoton ionization mass spectrometry (REMPI/MS). In the past two years, study has been focused on the development of a new multipass adsorption technique--the {open_quotes}cavity-ring-down{close_quotes} technique for kinetic applications. The preliminary results of this study appear to be quite good and the sensitivity of the technique is at least comparable to that of the laser-induced fluorescence method.

  4. Kinetics of the reactions of hydrated electrons with metal complexes

    The reactivity of the hydrated electron towards metal complexes is considered. Experiments are described involving metal EDTA and similar complexes. The metal ions studied are mainly Ni2+, Co2+ and Cu2+. Rates of the reactions of the complexes with e-(aq) were measured using the pulse radiolysis technique. It is shown that the reactions of e-(aq) with the copper complexes display unusually small kinetic salt effects. The results suggest long-range electron transfer by tunneling. A tunneling model is presented and the experimental results are discussed in terms of this model. Results of approximate molecular orbital calculations of some redox potentials are given, for EDTA chelates as well as for series of hexacyano and hexaquo complexes. Finally, equilibrium constants for the formation of ternary complexes are reported. (Auth./G.J.P.)

  5. Bayesian inference of chemical kinetic models from proposed reactions

    Galagali, Nikhil


    © 2014 Elsevier Ltd. Bayesian inference provides a natural framework for combining experimental data with prior knowledge to develop chemical kinetic models and quantify the associated uncertainties, not only in parameter values but also in model structure. Most existing applications of Bayesian model selection methods to chemical kinetics have been limited to comparisons among a small set of models, however. The significant computational cost of evaluating posterior model probabilities renders traditional Bayesian methods infeasible when the model space becomes large. We present a new framework for tractable Bayesian model inference and uncertainty quantification using a large number of systematically generated model hypotheses. The approach involves imposing point-mass mixture priors over rate constants and exploring the resulting posterior distribution using an adaptive Markov chain Monte Carlo method. The posterior samples are used to identify plausible models, to quantify rate constant uncertainties, and to extract key diagnostic information about model structure-such as the reactions and operating pathways most strongly supported by the data. We provide numerical demonstrations of the proposed framework by inferring kinetic models for catalytic steam and dry reforming of methane using available experimental data.

  6. Modified Step Variational Iteration Method for Solving Fractional Biochemical Reaction Model

    R. Yulita Molliq


    Full Text Available A new method called the modification of step variational iteration method (MoSVIM is introduced and used to solve the fractional biochemical reaction model. The MoSVIM uses general Lagrange multipliers for construction of the correction functional for the problems, and it runs by step approach, which is to divide the interval into subintervals with time step, and the solutions are obtained at each subinterval as well adopting a nonzero auxiliary parameter ℏ to control the convergence region of series' solutions. The MoSVIM yields an analytical solution of a rapidly convergent infinite power series with easily computable terms and produces a good approximate solution on enlarged intervals for solving the fractional biochemical reaction model. The accuracy of the results obtained is in a excellent agreement with the Adam Bashforth Moulton method (ABMM.

  7. Extension of a Kinetic-Theory Approach for Computing Chemical-Reaction Rates to Reactions with Charged Particles

    Liechty, Derek S.; Lewis, Mark J.


    Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties (i.e., no macroscopic reaction rate information) are extended to include reactions involving charged particles and electronic energy levels. The proposed extensions include ionization reactions, exothermic associative ionization reactions, endothermic and exothermic charge exchange reactions, and other exchange reactions involving ionized species. The extensions are shown to agree favorably with the measured Arrhenius rates for near-equilibrium conditions.

  8. HRSSA - Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

    Marchetti, Luca; Priami, Corrado; Thanh, Vo Hong


    This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.

  9. Some kinetics aspects of chlorine-solids reactions

    Kanari, N.; Mishra, D.; Mochon, J.; Verdeja, L. F.; Diot, F.; Allain, E.


    The present paper describes detailed kinetics investigations on some selected chlorine-solid reactions through thermogravimetric measurements. The solids studied in this article include chemical pure oxides and sulfides as well as their natural bearing materials. The chlorinating agents employed are gaseous mixtures of Cl{sub 2}+N{sub 2} (chlorination), Cl{sub 2}+O{sub 2} (oxy chlorination), and Cl{sub 2}+CO (carbochlorination). Results are presented as effects of various parameters on the reaction rate of these solids with these chlorinating agents. It was observed that the reactivity of these solids towards different chlorinating agents varied widely. Sulfides could be chlorinated at room temperature, while carbochlorination of chromium (III) oxide was possible only above 500 degree centigrade. The variation of the chlorination rate of these complex materials with respect to gas velocity, composition and temperature enabled us to focus some light on the plausible reaction mechanisms and stoichiometries. The obtained results were used for selective removal of iron from chromite concentrates, extraction of valuable metals from sulfide materials, purification of MgO samples, etc.. (Author) 12 refs.

  10. Kinetics of the Self Reaction of Cyclopentadienyl Radicals.

    Knyazev, Vadim D; Popov, Konstantin V


    The kinetics of the self-reaction of cyclopentadienyl radicals (c-C5H5) was studied by laser photolysis/photoionization mass spectroscopy. Overall rate constants were obtained in direct real-time experiments in the temperature region 304-600 K and at bath gas densities of (3.00-12.0) × 10(16) molecules cm(-3). The room-temperature value of the rate constant, (3.98 ± 0.41) × 10(-10) cm(3) molecule(-1) s(-1), is significantly higher than the rate constants for most hydrocarbon radical-radical reactions and coincides with the estimated collision rate. The observed overall c-C5H5 + c-C5H5 rate constant demonstrates an unprecedented strong negative temperature dependence: k1 = 2.9 × 10(-12) exp(+1489 K/T) cm(3) molecule(-1) s(-1), with estimated uncertainty increasing with temperature, from 13% at 304 to 32% at 600 K. Formation of C10H10 as the primary product of cyclopentadienyl self-reaction was observed. In additional experiments performed at the temperature of 800 K, formation of C10H10, C10H9, and C10H8 was observed. Final product analysis by gas chromatography/mass spectrometry detected two isomers of C10H8 at 800 K: naphthalene (major) and azulene (minor). PMID:25760686

  11. Biochemical Properties and Inhibition Kinetics of Phosphatase from Wheat Thylakoid Membranes


    A phosphatase that hydrolyses phosphate monoesters has been isolated from wheat thylakoid membranes.Biochemical properties and inhibition kinetics of the phosphatase were investigated using several ions, organic solvents, and inhibitors. Wheat (Triticum aestivum L. cv. PH82-2-2) thylakoid membrane phosphatase activity was activated by Mg2+, Ca2+, and Fe2+ and was inhibited by Mn2+ and Cu2+. For example, enzyme activity was activated 34.81% by 2 mmol/L Mg2+, but was inhibited 22.3% and 8.5% by 2 and 1 mmol/L Cu2+, respectively.Methanol, ethanol and glycol were all able to activate enzyme activity. Enzyme activity was activated 58.5%, 48.2%,and 8.7% by 40% ethanol, methanol and glycol, respectively. From these results, it can be seen that the degree of activation of the phosphatase was greatest for ethanol and the type of activation was uncompetitive. Moreover,the activity of the thylakoid membrane phosphatase was inhibited by molybdate, vanadate, phosphate, and fluoride and the type of inhibition produced by these elements was uncompetitive, non-competitive, competitive and mixed, respectively.

  12. Biochemical reactions in crowded environments: Revisiting the effects of volume exclusion with simulations

    David eGomez


    Full Text Available Molecular crowding is ubiquitous within cells and affects many biological processes including protein-protein binding, enzyme activities and gene regulation. Here we revisit some generic effects of crowding using a combination of lattice simulations and reaction-diffusion simulations with the program ReaDDy. Specifically, we implement three reactions, simple binding, a diffusion-limited reaction and a reaction with Michaelis-Menten kinetics. Histograms of binding and unbinding times provide a detailed picture how crowding affects these reactions and how the separate effects of crowding on binding equilibrium and on diffusion act together. In addition, we discuss how crowding affects processes related to gene expression such as RNA polymerase-promoter binding and translation elongation.

  13. Biochemical reactions in crowded environments: Revisiting the effects of volume exclusion with simulations

    Gomez, David; Klumpp, Stefan


    Molecular crowding is ubiquitous within cells and affects many biological processes including protein-protein binding, enzyme activities and gene regulation. Here we revisit some generic effects of crowding using a combination of lattice simulations and reaction-diffusion simulations with the program ReaDDy. Specifically, we implement three reactions, simple binding, a diffusion-limited reaction and a reaction with Michaelis-Menten kinetics. Histograms of binding and unbinding times provide a detailed picture how crowding affects these reactions and how the separate effects of crowding on binding equilibrium and on diffusion act together. In addition, we discuss how crowding affects processes related to gene expression such as RNA polymerase-promoter binding and translation elongation.

  14. Spectator Ions ARE Important! A Kinetic Study of the Copper-Aluminum Displacement Reaction

    Sobel, Sabrina G.; Cohen, Skyler


    Surprisingly, spectator ions are responsible for unexpected kinetics in the biphasic copper(II)-aluminum displacement reaction, with the rate of reaction dependent on the identity of the otherwise ignored spectator ions. Application of a published kinetic analysis developed for a reaction between a rotating Al disk and a Cu(II) ion solution to the…

  15. Reaction Kinetics of Meteoric Sodium Reservoirs in the Upper Atmosphere.

    Gómez Martín, J C; Garraway, S A; Plane, J M C


    The gas-phase reactions of a selection of sodium-containing species with atmospheric constituents, relevant to the chemistry of meteor-ablated Na in the upper atmosphere, were studied in a fast flow tube using multiphoton ionization time-of-flight mass spectrometry. For the first time, unambiguous observations of NaO and NaOH in the gas phase under atmospheric conditions have been achieved. This enabled the direct measurement of the rate constants for the reactions of NaO with H2, H2O, and CO, and of NaOH with CO2, which at 300-310 K were found to be (at 2σ confidence level): k(NaO + H2O) = (2.4 ± 0.6) × 10(-10) cm(3) molecule (-1) s(-1), k(NaO + H2) = (4.9 ± 1.2) × 10(-12) cm(3) molecule (-1) s(-1), k(NaO + CO) = (9 ± 4) × 10(-11) cm(3) molecule (-1) s(-1), and k(NaOH + CO2 + M) = (7.6 ± 1.6) × 10(-29) cm(6) molecule (-2) s(-1) (P = 1-4 Torr). The NaO + H2 reaction was found to make NaOH with a branching ratio ≥ 99%. A combination of quantum chemistry and statistical rate theory calculations are used to interpret the reaction kinetics and extrapolate the atmospherically relevant experimental results to mesospheric temperatures and pressures. The NaO + H2O and NaOH + CO2 reactions act sequentially to provide the major atmospheric sink of meteoric Na and therefore have a significant impact on the underside of the Na layer in the terrestrial mesosphere: the newly determined rate constants shift the modeled peak to about 93 km, i.e., 2 km higher than observed by ground-based lidars. This highlights further uncertainties in the Na chemistry cycle such as the unknown rate constant of the NaOH + H reaction. The fast Na-recycling reaction between NaO and CO and a re-evaluated rate constant of the NaO + CO2 sink should be now considered in chemical models of the Martian Na layer. PMID:25723735

  16. Variable elimination in chemical reaction networks with mass action kinetics

    Feliu, Elisenda


    We consider chemical reaction networks taken with mass action kinetics. The steady states of such a system are solutions to a system of polynomial equations. Even for small systems the task of finding the solutions is daunting. We develop an algebraic framework and procedure for linear elimination of variables. The procedure reduces the variables in the system to a set of "core" variables by eliminating variables corresponding to a set of non-interacting species. The steady states are parameterized algebraically by the core variables, and a graphical condition is given for when a steady state with positive core variables necessarily have all variables positive. Further, we characterize graphically the sets of eliminated variables that are constrained by a conservation law and show that this conservation law takes a specific form.

  17. Reaction kinetics of annealing of high energy implantation by XRD

    The annealing of structural defects caused by high energy implantation is studied using X-ray diffraction. The implanted sample (dose: 1 x 1014 ions/cm2) was isochronally annealed in flowing nitrogen in steps of 50 K up to 823 K for 10 min each, using a RTA system developed in Mumbai University. XRD patterns were recorded after each annealing and analyzed for strain and curvature. Also, the screw dislocation density was estimated at each stage of annealing using the FWHM of w scans in high resolution mode. The XRD profiles were simulated using the dynamical theory of X-ray diffraction for layer damage i.e. thickness, mismatch with respect to substrate, Debye Waller factor and sample curvature. The activation energy and characteristic temperature of annealing were estimated through reaction kinetics, utilizing the experimental XRD for progressive changes with temperature, of strain and dislocation density

  18. Kinetic Deuterium Isotope Effects in Cytochrome P450 Oxidation Reactions

    Guengerich, F. Peter


    Cytochrome P450 (P450) enzymes account for ~ 75% of the metabolism of drugs. Most of the reactions catalyzed by P450s are mixed-function oxidations, and a C-H bond is (usually) broken. The rate-limiting nature of this step can be analyzed using the kinetic isotope effect (KIE) approach. The most relevant type of KIE is one termed intermolecular non-competitive, indicative of rate-limiting C-H bond breaking. A KIE vs. kcat for several P450s showed a correlation coefficient (r2) of 0.62. Deuterium substitution has been considered as a potential means of slowing drug metabolism or redirecting sites of metabolism in some cases, and several general points can be made regarding the potential for application of deuterium in drug design/development based on what is known about P450 KIEs. PMID:24285515

  19. The mechanism and kinetics of epoxy-amine reactions

    Full text.Silane coupling agents have an important role at the interface for improving the performance of composite materials based on polymer matrices reinforced with glass fibers or mineral fillers. The silanes are also used in some adhesive formulations or as substrate primers, giving higher strength of adhesives joints. In these interface or interphase problems, most of the data in the literature concerns the final properties of the composite materials, such as strength or young's modulus; there is very little information about the chemical properties of the interphase. The aim of this study is to try to provide some of this basic data. The coupling agent studied here is the γ-aminopropyltriethoxysilane (γ-APS) or A1100. It is the most commonly used coupling agents. During composite processing, it is frequently reacted with an epoxy prepolymer based on diglycidylether of bisphenol A. We have studied these reactions from a fundamental point of view and not in industrial conditions. First we compared the kinetics results of different analytical techniques. Secondly, we compared the reactivities of the epoxy in DGEBA and the amino-hydrogen functions in coupling agent to those of model reagents like phenylglycidylether and hexylamine. the third part consists of validating a kinetic mechanism and calculating the rate constants, activation energy and reactivity ratios

  20. Nuclear quantum effects and kinetic isotope effects in enzyme reactions.

    Vardi-Kilshtain, Alexandra; Nitoker, Neta; Major, Dan Thomas


    Enzymes are extraordinarily effective catalysts evolved to perform well-defined and highly specific chemical transformations. Studying the nature of rate enhancements and the mechanistic strategies in enzymes is very important, both from a basic scientific point of view, as well as in order to improve rational design of biomimetics. Kinetic isotope effect (KIE) is a very important tool in the study of chemical reactions and has been used extensively in the field of enzymology. Theoretically, the prediction of KIEs in condensed phase environments such as enzymes is challenging due to the need to include nuclear quantum effects (NQEs). Herein we describe recent progress in our group in the development of multi-scale simulation methods for the calculation of NQEs and accurate computation of KIEs. We also describe their application to several enzyme systems. In particular we describe the use of combined quantum mechanics/molecular mechanics (QM/MM) methods in classical and quantum simulations. The development of various novel path-integral methods is reviewed. These methods are tailor suited to enzyme systems, where only a few degrees of freedom involved in the chemistry need to be quantized. The application of the hybrid QM/MM quantum-classical simulation approach to three case studies is presented. The first case involves the proton transfer in alanine racemase. The second case presented involves orotidine 5'-monophosphate decarboxylase where multidimensional free energy simulations together with kinetic isotope effects are combined in the study of the reaction mechanism. Finally, we discuss the proton transfer in nitroalkane oxidase, where the enzyme employs tunneling as a catalytic fine-tuning tool. PMID:25769515

  1. Kinetic study of hydrated lime reaction with HCl.

    Yan, Rong; Chin, Terence; Liang, David Tee; Laursen, Karin; Ong, Wan Yean; Yao, Kaiwen; Tay, Joo Hwa


    Hydrochloride (HCl) is an acidic pollutant present in the flue gas of most municipal or hazardous waste incinerators. Hydrated lime (Ca(OH)2) is often used as a dry sorbent for injection in a spray reactor to remove HCI. However, due to the short residence time encountered, this control method has generally been found to have low conversion efficiencies which results in the high lime usage and generates large amount of fly ash as solid wastes. A fundamental study was carried outto investigate the kinetics of HCl-lime reaction under simulated flue gas conditions in order to better understand the process thereby providing a basis for an optimized lime usage and reduced fly ash production. The initial reaction rate and conversion of three limes were studied using a thermogravimetric analyzer by varying the gas flow rate, temperature (170-400 degrees C), and HCI concentrations (600-1200 mg/m3) as well as the associated particle size and surface area of the limes. The initial lime conversions were found to rely mostly on the residence time, while the ultimate lime conversions were strongly influenced by temperature and the reaction products. CaOHCI was found to be the primary product in most cases, while for one specific lime, CaCl2 was the ultimate conversion product after an extended time period. The true utilization of lime in flue gas cleanup is thus higher when CaOHCl is considered as the final product than those based on CaCl2 as the final product, which has been commonly used in previous studies. The initial reaction was controlled by diffusion of HCl in gas phase and the subsequent reaction by gaseous diffusion through the developing product layer. Increasing the HCI concentration raised the initial rate as well as conversion. However, overloading the lime with excessive HCI caused clogging at its surface and a drop in the ultimate conversion. Limes with smaller particle diameters and higher surface areas were found to be more reactive. The effect of gas

  2. Thin film reaction kinetics of niobium/aluminum multilayers

    Phase formation kinetics in Nb/Al multilayered thin films having overall compositions of 25, 33, 50, and 75 at. % Al have been investigated using scanning calorimetry, x-ray diffraction, and cross-sectional transmission electron microscopy. The first phase to form upon annealing the Nb/Al layered structure of all samples is the NbAl3 intermetallic. Calorimetry clearly identifies the NbAl3 formation to be a two-stage process. The first stage is the formation of a planar layer by nucleation and growth to coalescence while the second stage is the thickening of the planar layer. The large amount of heat released (and hence large volume fraction of NbAl3 formed) during the first reaction stage is consistent with heterogeneous nucleation at well-isolated sites in the Nb/Al interface. This is surprising in light of the large thermodynamic driving force expected for nucleation and suggests that the local nonequilibrium nature of the Nb/Al interface greatly reduces the driving force for nucleation. The next phase observed in samples of 25 and 33 at. % Al is the A15 superconducting phase, Nb3Al. The Nb3Al growth completes a first reaction stage similar to the NbAl3, but the subsequent thickening reaction stage is not observed without simultaneous Nb2Al growth. The high interface velocities derived from the calorimetry for formation of both NbAl3 and the A15 Nb3Al indicate that atomic transport must be by grain boundary diffusion

  3. Effects of temperature on biochemical reactions and drug resistance of virulent and avirulent Aeromonas salmonicida

    Hahnel, G.B.; Gould, R.W.


    Incubation temperatures of 11°, 18° and 28° did not substantially affect biochemical reactions of either virulent or avirulent forms of Aeromonas salmonicida subspecies salmonicida. The only change observed, amygdalin fermentation, was positive at 11° and 18° but negative at 28°C. Several isolates utilized sucrose, a characteristic not normally recognized for A. salmonicida subspecies salmonicida.Antimicrobial susceptibility screening indicated resistance to novobiocin increased at the higher incubation temperatures. Standardized drug sensitivity testing procedures and precise zone diameter interpretive standards for bacterial fish pathogens are needed.

  4. Introduction to dynamic spin chemistry magnetic field effects on chemical and biochemical reactions

    Hayashi, Hisaharu


    This book presents a detailed account of one of the most mysterious problems in science - whether ordinary magnetic fields can exert an appreciable influence on chemical and biochemical reactions. The first aim of the book is to introduce this research, through theoretical and dynamic spin chemistry, to graduate students and researchers, by means of detailed theoretical and experimental descriptions. The second aim is to review typical recent investigations, which will stimulate new interest and applications in the 21st century. Because dynamic spin chemistry is based on established science, i

  5. Reaction kinetics of dual setting α-tricalcium phosphate cements.

    Hurle, Katrin; Christel, Theresa; Gbureck, Uwe; Moseke, Claus; Neubauer, Juergen; Goetz-Neunhoeffer, Friedlinde


    Addition of ductile polymers to calcium-deficient hydroxyapatite (CDHA)-forming bone cements based on α-tricalcium phosphate (α-TCP) is a promising approach to improve the mechanical performance of α-TCP cements and extend their application to load-bearing defects, which is else impeded by the brittleness of the hardened cement. One suitable polymer is poly-(2-hydroxyethylmethacrylate) (p-HEMA), which forms during cement setting by radical polymerisation of the monomer. In this study the hydration kinetics and the mechanical performance of α-TCP cements modified with addition of different HEMA concentrations (0-50 wt% in the cement liquid) was investigated by quantitative in situ XRD and four-point bending tests. Morphology of CDHA crystals was monitored by scanning electron microscopy. The hydration of α-TCP to CDHA was increasingly impeded and the visible crystal size of CDHA increasingly reduced with increasing HEMA concentration. Modification of the cements by adding 50 wt% HEMA to the cement liquid changed the brittle performance of the hardened cement to a pseudoplastic behaviour, reduced the flexural modulus and increased the work of fracture, while lower HEMA concentrations had no significant effect on these parameters. In such a composite, the extent of CDHA formation was considerably reduced (34.0 ± 1.8 wt% CDHA with 50 % HEMA compared to 54.1 ± 2.4 wt% CDHA in the reference formed after 48 h), while the general reaction kinetics were not changed. In conclusion, while the extent of CDHA formation was decreased, the mechanical properties were noticeably improved by addition of HEMA. Hence, α-TCP/HEMA composites might be suitable for application in some load-bearing defects and have adequate properties for mechanical treatment after implantation, like insertion of screws. PMID:26610924

  6. Proton mediated control of biochemical reactions with bioelectronic pH modulation

    Deng, Yingxin; Miyake, Takeo; Keene, Scott; Josberger, Erik E.; Rolandi, Marco


    In Nature, protons (H+) can mediate metabolic process through enzymatic reactions. Examples include glucose oxidation with glucose dehydrogenase to regulate blood glucose level, alcohol dissolution into carboxylic acid through alcohol dehydrogenase, and voltage-regulated H+ channels activating bioluminescence in firefly and jellyfish. Artificial devices that control H+ currents and H+ concentration (pH) are able to actively influence biochemical processes. Here, we demonstrate a biotransducer that monitors and actively regulates pH-responsive enzymatic reactions by monitoring and controlling the flow of H+ between PdHx contacts and solution. The present transducer records bistable pH modulation from an “enzymatic flip-flop” circuit that comprises glucose dehydrogenase and alcohol dehydrogenase. The transducer also controls bioluminescence from firefly luciferase by affecting solution pH.

  7. Proton mediated control of biochemical reactions with bioelectronic pH modulation

    Deng, Yingxin; Miyake, Takeo; Keene, Scott; Josberger, Erik E.; Rolandi, Marco


    In Nature, protons (H+) can mediate metabolic process through enzymatic reactions. Examples include glucose oxidation with glucose dehydrogenase to regulate blood glucose level, alcohol dissolution into carboxylic acid through alcohol dehydrogenase, and voltage-regulated H+ channels activating bioluminescence in firefly and jellyfish. Artificial devices that control H+ currents and H+ concentration (pH) are able to actively influence biochemical processes. Here, we demonstrate a biotransducer that monitors and actively regulates pH-responsive enzymatic reactions by monitoring and controlling the flow of H+ between PdHx contacts and solution. The present transducer records bistable pH modulation from an “enzymatic flip-flop” circuit that comprises glucose dehydrogenase and alcohol dehydrogenase. The transducer also controls bioluminescence from firefly luciferase by affecting solution pH. PMID:27052724

  8. Kinetics of the self reaction of cyclohexyl radicals.

    Loginova, Ksenia A; Knyazev, Vadim D


    The kinetics of the self-reaction of cyclohexyl radicals was studied by laser photolysis/photoionization mass spectroscopy. Overall rate constants were obtained in direct real-time experiments in the temperature region 303-520 K and at bath gas (helium with up to 5% of radical precursors) densities (3.00-12.0) × 10(16) molecules cm(-3). Cyclohexyl radicals were produced by a combination of the 193 nm photolysis of oxalyl chloride ((CClO)(2)) with the subsequent fast reaction of Cl atoms with cyclohexane, and their initial concentrations were determined from real-time profiles of HCl. The observed overall c-C(6)H(11) + c-C(6)H(11) rate constants demonstrate negative temperature dependence, which can be described by the following expressions: k(1) = 4.8 × 10(-12) exp(+542 K/T) cm(3) molecule(-1) s(-1), with estimated uncertainty of 16% over the 303-520 K temperature range. The fraction of disproportionation equal to 41 ± 7% was determined at 305 K; analysis of earlier experimental determinations of the disproportionation-to-recombination branching ratio leads to recommending this room-temperature value for other temperatures. The corresponding temperature dependences of the recombination (1a, bicyclohexyl product) and the disproportionation (1b, cyclohexene and cyclohexane products) channels are k(1a) = 2.8 × 10(-12) exp(+542 K/T) and k(1b) = 2.0 × 10(-12) exp(+542 K/T) cm(3) molecule(-1) s(-1), with estimated uncertainties of 20% and 29%, respectively. PMID:21702489

  9. Constraining kinetic rates of mineral reactions using reactive transport models

    Bolton, E. W.; Wang, Z.; Ague, J.; Bercovici, D.; Cai, Z.; Karato, S.; Oristaglio, M. L.; Qiu, L.


    We use a reactive transport model to better understand results of experiments to obtain kinetic rates of mineral reactions in closed systems. Closed system experiments pose special challenges in that secondary minerals may form that modify the fluid composition evolution and may grow on the dissolving minerals thus armoring the surface. Even so, such closed system experiments provide critical data for what minerals would actually form in field applications and how coupled dissolution and precipitation mineral reactions are strongly linked. Comparing to experimental observations can test the reactive transport model, and the experimental observations can be better understood by comparing the results to the modeling. We apply a 0D end member of the model to understand the dissolution of single crystals of forsterite in a variety of settings (low pH, high pH, or NaHCO3 initial fluids, at 100 C and 1 bar, or 200 C and 150 bar). Depending on the initial conditions, we observe the precipitation of talc, brucite, amorphous silica, chrysotile, or magnesite, in various combinations. We compare simulation results to fluid compositions and the presence of secondary minerals experimentally sampled at various times. Insight from the simulations helped create an inverse model to extract the rates of forsterite dissolution and to create a simple forward model useful for exploring the influence of system size, secondary mineral surface areas, etc. Our reactive transport model allows secondary minerals to armor the forsterite surface, which can strongly decrease the dissolution rate as the system evolves. Tuning our model with experimentally derived rates and assuring relevant processes are included so as to reproduce experimental observations is necessary before upscaling to heterogeneous field conditions. The reactive transport model will be used for field-scale sequestration simulations and coupled with a geomechanical model that includes the influence of deformation.

  10. Kinetics and Mechanism of Iodide Oxidation by Iron(III): A Clock Reaction Approach

    Bauer, Jurica; Tomisic, Vladislav; Vrkljan, Petar B. A.


    A simple method for studying the kinetics of a chemical reaction is described and the significance of reaction orders in deducing reaction mechanisms is demonstrated. In this student laboratory experiment, oxidation of iodide by iron(III) ions in an acidic medium is transformed into a clock reaction. By means of the initial rates method, it is…

  11. Theory of Square-wave Voltammetry of Kinetically Controlled Two-step Electrode Reactions

    Lovrić, Milivoj; Komorsky-Lovrić, Šebojka


    An influence of electron transfer kinetics on square-wave voltammograms of two-step electrode reaction is investigated theoretically. A phenomenon of “kinetic burden” of potential inversion is described for the case of equal kinetic parameters. A linear relationship between standard rate constant and the difference between standard potentials of the second and the first charge transfers is demonstrated for the reactions with thermodynamically unstable intermediate. (doi: 10.5562/cca2126)

  12. Kinetics of the Uninhibited Reaction of 2-Chloropropene-Part II: Comparison with Inhibited Reaction

    The kinetics of the uninhibited reaction of 2-chloropropene in the gas-phase has been studied between 662 and 747 K at pressures ranging from 11 to 76 Torr with the object of determining the overall mechanism using static system. The reaction was found to be accurately of the first order at the high pressures and the observed rate coefficient is expressed by the following Arrhenius equation:K sub total (uninhibited) = 10 super 7.98 ± 0.6 (s super -1) exp super -167 ± 7.8 (kJ/mole)/RT The activation energy was calculated at 167 ± 7.98kJ/mol and identified with the dissociation of C-Cl bond. The reaction is pressured to be unimolecular at lower temperature with formation of propyne and elimination of hydrogen chloride. However, at high temperature C-Cl bond fission takes place and this changes the mechanism of the reaction. Two mechanisms dehydrohalogenation molecular elimination and C-Cl bond fission are discussed. (author)

  13. Reaction of Phenyl Radical with O2: Thermodynamic Properties, Important Reaction Paths and Kinetics

    Bozzelli, J; Sebbar, N; Pitz, W; Bockhorn, H


    The Phenyl + O{sub 2} association results in a chemically activated phenyl-peroxy radical which can dissociate to phenoxy radical + O, undergo intramolecular addition of the peroxy radical to several unsaturated carbon sites or react back to phenyl + O{sub 2}. The intramolecular addition channels further react through several paths to ring opening (unsaturated + carbonyl moieties) as well as cyclopentadieny radical + CO{sub 2}. Enthalpy ({Delta}H{sub f(298)}{sup o}), Entropy (S{sub 298}), and heat capacities Cp(T) for species in the decomposition of the ring are evaluated using density functional and ab initio calculations and by comparisons to vinyl + O{sub 2} data of Mebel et al, and phenyl + O{sub 2} data of Hadad et al. Isodesmic reaction analysis is used to estimate enthalpy values of the intermediates and well depths of the adducts. High Pressure limit kinetic parameters are obtained from the calculation results using canonical Transition State Theory. Quantum RRK analysis is utilized to obtain k(E) and modified strong collision or master equation analysis is used for evaluation of pressure fall-off in this complex bimolecular, chemical activation, reaction system. Uncertainty in key barriers is discussed, resulting variations in important reaction product ratios are illustrated, and changes in these branching ratios are evaluated with a detailed reaction mechanism.

  14. Kinetic analysis of complex solid-state reactions. A new deconvolution procedure

    Perejón, Antonio; Sánchez-Jiménez, P.E.; Criado, J. M.; Pérez-Maqueda, Luis A


    The kinetic analysis of complex solid-state reactions that involve simultaneous overlapping processes is challenging. A method that involves the deconvolution of the individual processes from the overall differential kinetic curves obtained under linear heating rate conditions, followed by the kinetic analysis of the discrete processes using combined kinetic analysis, is proposed. Different conventional mathematical fitting functions have been tested for deconvolution, paying special attentio...

  15. Chemical Reactions and Kinetics of the Carbon Monoxide Coupling in the Presence of Hydrogen

    Fandong Meng; Genhui Xu; Zhenhua Li; Pa Du


    The chemical reactions and kinetics of the catalytic coupling reaction of carbon monoxide to diethyl oxalate were studied in the presence of hydrogen over a supported palladium catalyst in the gaseous phase at the typical coupling reaction conditions. The experiments were performed in a continuous flow fixed-bed reactor. The results indicated that hydrogen only reacts with ethyl nitrite to form ethanol, and kinetic studies revealed that the rate-determining step is the surface reaction of adsorbed hydrogen and the ethoxy radical (EtO-). A kinetic model is proposed and a comparison of the observed and calculated conversions showed that the rate expressions are of rather high confidence.

  16. Soil solid materials affect the kinetics of extracellular enzymatic reactions

    Lammirato, C.; Miltner, A.; Kästner, M.


    INTRODUCTION Soil solid materials affect the degradation processes of many organic compounds by decreasing the bioavailability of substrates and by interacting with degraders. The magnitude of this effect in the environment is shown by the fact that xenobiotics which are readily metabolized in aquatic environments can have long residence times in soil. Extracellular enzymatic hydrolysis of cellobiose (enzyme: beta-glucosidase from Aspergillus niger) was chosen as model degradation process since it is easier to control and more reproducible than a whole cell processes. Furthermore extracellular enzymes play an important role in the environment since they are responsible for the first steps in the degradation of organic macromolecules; beta-glucosidase is key enzyme in the degradation of cellulose and therefore it is fundamental in the carbon cycle and for soil in general. The aims of the project are: 1) quantification of solid material effect on degradation, 2) separation of the effects of minerals on enzyme (adsorption →change in activity) and substrate (adsorption →change in bioavailability). Our hypothesis is that a rate reduction in the enzymatic reaction in the presence of a solid phase results from the sum of decreased bioavailability of the substrate and decreased activity of enzyme molecules. The relative contribution of the two terms to the overall effect can vary widely depending on the chemical nature of the substrate, the properties of the enzyme and on the surface properties of the solid materials. Furthermore we hypothesize that by immobilizing the enzyme in an appropriate carrier the adsorption of enzymes to soil materials can be eliminated and that therefore immobilization can increase the overall reaction rate (activity loss caused by immobilization activity loss caused by adsorption to soil minerals). MATERIALS AND METHODS Enzymatic kinetic experiments are carried out in homogeneous liquid systems and in heterogeneous systems where solid

  17. Evaluating the effect of potassium on cellulose pyrolysis reaction kinetics

    This paper proposes modifications to an existing cellulose pyrolysis mechanism in order to include the effect of potassium on product yields and composition. The changes in activation energies and pre-exponential factors due to potassium were evaluated based on the experimental data collected from pyrolysis of cellulose samples treated with different levels of potassium (0–1% mass fraction). The experiments were performed in a pyrolysis reactor coupled to a molecular beam mass spectrometer (MBMS). Principal component analysis (PCA) performed on the collected data revealed that cellulose pyrolysis products could be divided into two groups: anhydrosugars and other fragmentation products (hydroxyacetaldehyde, 5-hydroxymethylfurfural, acetyl compounds). Multivariate curve resolution (MCR) was used to extract the time resolved concentration score profiles of principal components. Kinetic tests revealed that potassium apparently inhibits the formation of anhydrosugars and catalyzes char formation. Therefore, the oil yield predicted at 500 °C decreased from 87.9% from cellulose to 54.0% from cellulose with 0.5% mass fraction potassium treatment. The decrease in oil yield was accompanied by increased yield of char and gases produced via a catalyzed dehydration reaction. The predicted char and gas yield from cellulose were 3.7% and 8.4%, respectively. Introducing 0.5% mass fraction potassium treatment resulted in an increase of char yield to 12.1% and gas yield to 33.9%. The validation of the cellulose pyrolysis mechanism with experimental data from a fluidized-bed reactor, after this correction for potassium, showed good agreement with our results, with differences in product yields of up to 5%

  18. Growth kinetics of forsterite reaction rims at high-pressure

    Nishihara, Yu; Maruyama, Genta; Nishi, Masayuki


    Growth kinetics of forsterite (Fo) reaction rims between periclase (Per) and enstatite (En) were studied experimentally at pressure (P) and temperature (T) conditions of 3.0-11.1 GPa and 1473-1873 K, respectively. Pt markers originally placed at the Per-En interface were always observed at the Per-Fo interface, which indicates that Mg and O are the diffusing species in Fo rim growth (Mg-O coupled diffusion). The presence of some En inclusions in Fo grains and the growth rate of the Fo rim suggests that grain boundary diffusion is dominant rather than lattice diffusion. Considering the very fast grain boundary diffusion of O in olivine, the Mg-O coupled grain boundary diffusion in Fo is deduced to be rate-limited by the diffusivity of Mg. Based on an analysis of data collected under dry conditions, the product of the Mg grain boundary diffusion coefficient (Dgb) and the effective grain boundary width (δ) was determined to be δDgb = δDgb,0exp[-(E∗ + PV∗)/RT] with δDgb,0 = 10-9.68 ± 1.51 m3/s, E∗ = 379 ± 44 kJ/mol and V∗ = -1.9 ± 1.4 cm3/mol. Our results, combined with previously reported data on Mg lattice diffusion in Fo, suggest that for Mg, the significance of grain boundary diffusion increases with depth in the Earth's upper mantle, although lattice diffusion is still dominant for typical mantle grain sizes of 1-10 mm.

  19. Kinetics of exciplex formation/dissipation in reaction following Weller Scheme II

    Fedorenko, S. G. [Voevodsky Institute of Chemical Kinetics and Combustion, Novosibirsk (Russian Federation); Burshtein, A. I. [Weizmann Institute of Science, 76100, Rehovot (Israel)


    Creation of exciplexes from the charged products of photoionization is considered by means of Integral Encounter Theory. The general kinetic equations of such a reaction following the Weller scheme II are developed. The special attention is given to the particular case of irreversible remote ionization of primary excited electron donor. Kinetics of exciplex formation is considered at fast biexponential geminate transformation of exciplexes in cage that gives way to subsequent bulk reaction of equilibrated reaction products controlled by power law recombination of ions. It is shown that the initial geminate stage of exciplex kinetics is observed only in diffusion controlled regime of the reaction and disappears with increasing mobility of ions in passing to kinetic regime. The quantum yield of exciplexes is studied along with their kinetics.

  20. A computational approach to persistence, permanence, and endotacticity of biochemical reaction systems.

    Johnston, Matthew D; Pantea, Casian; Donnell, Pete


    We introduce a mixed-integer linear programming (MILP) framework capable of determining whether a chemical reaction network possesses the property of being endotactic or strongly endotactic. The network property of being strongly endotactic is known to lead to persistence and permanence of chemical species under genetic kinetic assumptions, while the same result is conjectured but as yet unproved for general endotactic networks. The algorithms we present are the first capable of verifying endotacticity of chemical reaction networks for systems with greater than two constituent species. We implement the algorithms in the open-source online package CoNtRol and apply them to a large sample of networks from the European Bioinformatics Institute's BioModels Database. We use strong endotacticity to establish for the first time the permanence of a well-studied circadian clock mechanism. PMID:25986743

  1. Kinetic Modelling of the Maillard Browning Reaction in Pekmez (Grape Molasses)

    Bozkurt, Hüseyin; Göğüş, Fahrettin; Eren, Sami


    The effects of pH, temperature and total solube solids on the Maillard reactions which occurred during the storage of Pekmez were determined using accelerated storage test. The reaction was followed measurement of by the amount of 5-Hydroxymethyl furfural, an intermediate product of the Maillard reaction. The change in the reaction rate was defined with a kinetic model as a function of pH, temperature and the total soluble solids. The reaction rate was correlated with the independen...

  2. Reaction kinetics of the iron-catalysed decomposition of SO3 / Abraham Frederik van der Merwe

    Van der Merwe, Abraham Frederik


    In this study the performance of pure, very fine iron (III) oxide powder was investigated as catalyst for the decomposition of sulphur trioxide into sulphur dioxide and oxygen. This highly endothermic reaction requires a catalyst to lower the reaction temperature. This reaction forms part of the HyS (Hybrid Sulphur) cycle, a proposed thermochemical process for the industrial scale production of hydrogen and oxygen from water. The study aimed at obtaining reaction kinetics for this reaction...

  3. Some kinetics aspects of chlorine-solids reactions

    Kanari, N.


    Full Text Available The present paper describes detailed kinetics investigations on some selected chlorine-solid reactions through thermogravimetric measurements. The solids studied in this article include chemical pure oxides and sulfides as well as their natural bearing materials. The chlorinating agents employed are gaseous mixtures of Cl2+N2 (chlorination, Cl2+O2 (oxychlorination, and Cl2+CO (carbochlorination. Results are presented as effects of various parameters on the reaction rate of these solids with these chlorinating agents. It was observed that the reactivity of these solids towards different chlorinating agents varied widely. Sulfides could be chlorinated at room temperature, while carbochlorination of chromium (III oxide was possible only above 500 °C. The variation of the chlorination rate of these complex materials with respect to gas velocity, composition and temperature enabled us to focus some light on the plausible reaction mechanisms and stoichiometries. The obtained results were used for selective removal of iron from chromite concentrates, extraction of valuable metals from sulfide materials, purification of MgO samples, etc.

    Este trabajo describe detalladas investigaciones cinéticas en algunas reacciones seleccionadas de cloro-sólido a través de medidas termogravimétricas. Los sólidos estudiados en este artículo incluyen óxidos químicos puros y sulfuros, así como sus materiales naturales de soporte. Los agentes de cloración empleados son mezclas de gases de Cl2+N2 (cloración, Cl2+O2 (oxicloración y Cl2+O2 (carbocloración. Los resultados se presentan como efecto de varios parámetros en el porcentaje de reacción de estos sólidos con los agentes de cloración. Se ha observado que la reactividad de estos sólidos a través de diferentes agentes de cloración varía ampliamente. Los sulfuros se pudieron

  4. Reaction kinetics of oxygen on single-phase alloys, oxidation of nickel and niobium alloys

    This research thesis first addresses the reaction kinetics of oxygen on alloys. It presents some generalities on heterogeneous reactions (conventional theory, theory of jumps), discusses the core reaction (with the influence of pressure), discusses the influence of metal self-diffusion on metal oxidation kinetics (equilibrium conditions at the interface, hybrid diffusion regime), reports the application of the hybrid diffusion model to the study of selective oxidation of alloys (Wagner model, hybrid diffusion model) and the study of the oxidation kinetics of an alloy forming a solid solution of two oxides. The second part reports the investigation of the oxidation of single phase nickel and niobium alloys (phase α, β and γ)

  5. Kinetics of the γ-radiation-initiated reaction of 2-propanol with tri- and hexafluoropropylene

    The initiation of telomerization reactions by ionizing radiation provides good opportunities for studying the kinetics of free radical reactions. The fluoroalcohols and their derivatives prepared using fluoroolefins and aliphatic alcohols find wide practical application. The object of this exercise was to study the reactivity of trifluoropropylene and hexafluoropropylene with 2-propanol. The reaction products were analyzed gas chromatographically

  6. Influence of hydrogen fluoride on kinetics of thermal reaction of hydrogen with chlorine monofluoride

    Zhitneva, G.P.


    The influence of HF on the kinetics of the thermal reaction of H/sub 2/ with ClF in a fused quartz vessel was studied. It was shown that HF inbibits the reaction by blocking the reaction centers on the vessel surface, which lowers the rate of the heterogeneous generation of chains.

  7. Stochastic focusing coupled with negative feedback enables robust regulation in biochemical reaction networks.

    Milias-Argeitis, Andreas; Engblom, Stefan; Bauer, Pavol; Khammash, Mustafa


    Nature presents multiple intriguing examples of processes that proceed with high precision and regularity. This remarkable stability is frequently counter to modellers' experience with the inherent stochasticity of chemical reactions in the regime of low-copy numbers. Moreover, the effects of noise and nonlinearities can lead to 'counterintuitive' behaviour, as demonstrated for a basic enzymatic reaction scheme that can display stochastic focusing (SF). Under the assumption of rapid signal fluctuations, SF has been shown to convert a graded response into a threshold mechanism, thus attenuating the detrimental effects of signal noise. However, when the rapid fluctuation assumption is violated, this gain in sensitivity is generally obtained at the cost of very large product variance, and this unpredictable behaviour may be one possible explanation of why, more than a decade after its introduction, SF has still not been observed in real biochemical systems. In this work, we explore the noise properties of a simple enzymatic reaction mechanism with a small and fluctuating number of active enzymes that behaves as a high-gain, noisy amplifier due to SF caused by slow enzyme fluctuations. We then show that the inclusion of a plausible negative feedback mechanism turns the system from a noisy signal detector to a strong homeostatic mechanism by exchanging high gain with strong attenuation in output noise and robustness to parameter variations. Moreover, we observe that the discrepancy between deterministic and stochastic descriptions of stochastically focused systems in the evolution of the means almost completely disappears, despite very low molecule counts and the additional nonlinearity due to feedback. The reaction mechanism considered here can provide a possible resolution to the apparent conflict between intrinsic noise and high precision in critical intracellular processes. PMID:26609065

  8. Removal of triclosan via peroxidases-mediated reactions in water: Reaction kinetics, products and detoxification.

    Li, Jianhua; Peng, Jianbiao; Zhang, Ya; Ji, Yuefei; Shi, Huanhuan; Mao, Liang; Gao, Shixiang


    This study investigated and compared reaction kinetics, product characterization, and toxicity variation of triclosan (TCS) removal mediated by soybean peroxidase (SBP), a recognized potential peroxidase for removing phenolic pollutants, and the commonly used horseradish peroxidase (HRP) with the goal of assessing the technical feasibility of SBP-catalyzed removal of TCS. Reaction conditions such as pH, H2O2 concentration and enzyme dosage were found to have a strong influence on the removal efficiency of TCS. SBP can retain its catalytic ability to remove TCS over broad ranges of pH and H2O2 concentration, while the optimal pH and H2O2 concentration were 7.0 and 8μM, respectively. 98% TCS was removed with only 0.1UmL(-1) SBP in 30min reaction time, while an HRP dose of 0.3UmL(-1) was required to achieve the similar conversion. The catalytic performance of SBP towards TCS was more efficient than that of HRP, which can be explained by catalytic rate constant (KCAT) and catalytic efficiency (KCAT/KM) for the two enzymes. MS analysis in combination with quantum chemistry computation showed that the polymerization products were generated via CC and CO coupling pathways. The polymers were proved to be nontoxic through growth inhibition of green alga (Scenedesmus obliquus). Taking into consideration of the enzymatic treatment cost, SBP may be a better alternative to HRP upon the removal and detoxification of TCS in water/wastewater treatment. PMID:26921508

  9. Kinetic determination of iodide by the oxidation reaction of benzidine with chloramine B

    Iodide catalyzed oxidation of benzidine with Chloramine B is studied for its possible application to kinetic determination of iodides. Based on the results of kinetic studies performed, optimal conditions for the catalytic reaction are revealed and a kinetic method for iodide determination is developed. The determination limit of iodide is 2x10-4 μg/ml. It was demonstrated that the proposed method can be used for the determination of iodides in water, soil, and kelp

  10. Study of the kinetics of the steam-zirconium reaction using a one rod assembly model

    The results of the investigation of steam-zirconium reaction kinetics at the HPE simulator surface are presented in the paper. The dynamic characteristics of the hydrogen production resulted from the heated surface dryout are determined. (author)

  11. Kinetics and thermodynamics of chemical reactions in Li/SOCl2 cells

    Hansen, Lee D.; Frank, Harvey


    Work is described that was designed to determine the kinetic constants necessary to extrapolate kinetic data on Li/SOCl2 cells over the temperature range from 25 to 75 C. A second objective was to characterize as far as possible the chemical reactions that occur in the cells since these reactions may be important in understanding the potential hazards of these cells. The kinetics of the corrosion processes in undischarged Li/SOCl2 cells were determined and separated according to their occurrence at the anode and cathode; the effects that switching the current on and off has on the corrosion reactions was determined; and the effects of discharge state on the kinetics of the corrosion process were found. A thermodynamic analysis of the current-producing reactions in the cell was done and is included.

  12. A Model of Hydrogen Desorption Kinetics Controlled both by Interface and Surface Reactions for Metal Hydrides

    Drozdov, I


    The desorption kinetics was modelled with the both interface- and surface reactions as rate-controlling steps. It has been shown analytically, that in the model of 'shrinking core' desorption, the finite hydride-decomposition-rate causes a modified slope of kinetics. The dependence of desorption time on the powder particle size has the same power of order as for the surface controlled desorption.

  13. Physico-Geometrical Kinetics of Solid-State Reactions in an Undergraduate Thermal Analysis Laboratory

    Koga, Nobuyoshi; Goshi, Yuri; Yoshikawa, Masahiro; Tatsuoka, Tomoyuki


    An undergraduate kinetic experiment of the thermal decomposition of solids by microscopic observation and thermal analysis was developed by investigating a suitable reaction, applicable techniques of thermal analysis and microscopic observation, and a reliable kinetic calculation method. The thermal decomposition of sodium hydrogen carbonate is…

  14. The Mechanisms, Products, and Kinetics of Triclosan-Free Chlorine Reactions

    Rule, Krista Lynn


    The kinetics, products, and reaction pathways of triclosan/free chlorine reactions were investigated for the pH range 3.5-11. Although pH dependent speciation occurs in both triclosan and free chlorine, only the reaction between HOCl and the phenolate-triclosan was found to play a significant role in the kinetics. The second order rate constant for the reaction between phenolate-triclosan and HOCl was found to be 5.40 (±1.82) à 103 M-1s-1. Three chlorinated triclosan intermediates were t...

  15. Kinetics of Nonenzymatic Browning Reaction in Citrus Juice Concentrates during Storage

    KOCA, Nuray; BURDURLU, Hande Selen; KARADENİZ, Feryal


    The kinetics of nonenzymatic browning in citrus juice concentrates (orange, lemon, grapefruit and tangerine) during 8 weeks of storage at 28, 37 and 45 ºC were investigated. Browning development was followed by measuring absorbance at 420 nm (A420) and using CIE-Lab color system. Analysis of kinetic data from A420 values suggested a zero-order reaction for nonenzymatic browning, while changes in L* and b* parameters followed a first-order reaction. Activation energy for nonenzymatic browning...

  16. Reaction Mechanism and Kinetics of Aqueous Solutions of Primary and Secondary Alkanolamines and Carbon Dioxide

    BAVBEK, Olgac; ALPER, Erdoğan


    The mechanism and kinetics of the reaction between aqueous solutions of CO2 and the alkanolamines 1-amino-2-propanol, 3-amino-1-propanol,2-methyl aminoethanol and 2-ethyl aminoethanol were investigated using a stopped flow technique. It was found that the reaction orders according to power law kinetics were between 1.1 and 2.0, depending on the alkanolamine and the concentration ranges investigated. This fractional order was therefore considered to be further evidence that carbamate ...

  17. The renneting of milk. A kinetic study of the enzymic and aggregation reactions.

    Hooydonk, van, V.E.


    The rennet-induced clotting of milk was studied under various conditions. The kinetics of the enzymic and aggregation reactions was analysed separately and, where possible, related to the physico-chemical properties of the casein micelle and its environment.The effects of important variables, such as temperature, pH, divalent cations, ionic strength, casein concentration and pre-heat treatment of milk, are given and discussed in relation to the reaction kinetics and to the implications for th...

  18. Stochastic reaction-diffusion kinetics in the microscopic limit

    Fange, David; Berg, Otto G.; Sjöberg, Paul; Elf, Johan


    Quantitative analysis of biochemical networks often requires consideration of both spatial and stochastic aspects of chemical processes. Despite significant progress in the field, it is still computationally prohibitive to simulate systems involving many reactants or complex geometries using a microscopic framework that includes the finest length and time scales of diffusion-limited molecular interactions. For this reason, spatially or temporally discretized simulations schemes are commonly u...

  19. Probing Aluminum Reactions in Combustion and Explosion Via the Kinetic Isotope Effect

    Tappan, Bryce


    The mechanism that controls the reaction speed of aluminum in explosion and combustion is poorly understood, and experimentally difficult to measure. Recently, work in our laboratory has demonstrated that during the combustion of nanoparticulate aluminum with H2O or D2O, different reaction rates due to the kinetic isotope effect are observed. This result is the first-ever observed kinetic isotope effect in a metal combustion reaction and verifies that chemical reaction kinetics play a major role in determining the global burning rate. During or shortly after a detonation, however, the reaction rates are dramatically faster and the physical mechanism controlling Al reaction is likely different than during combustion events. To utilize the kinetic isotope effect to probe Al reactions in detonation, formulations were produced that contain powdered Al in deuterated high explosives and high-fidelity detonation velocity were determined along with PDV measurements to observe early wall velocity expansion measurements. The JWL equation of state was solved to determine temperature, pressure and energies at specific time periods, in addition of Gurney energies, which enables the elucidation of Al reaction extent. By comparison of the Al oxidation with LiF, data indicate that Al oxidation occurs on an extremely fast time scale and isotope effects in both the HE detonation and post-detonation Al reactions are discussed.

  20. Ion-neutral gas reactions in a collision/reaction cell in inductively coupled plasma mass spectrometry: Correlation of ion signal decrease to kinetic rate constants

    Reaction gas flow rate dependent Ar2+ and Ar+ signals are correlated to fundamental kinetic rate coefficients. A simple calculation, assuming that gas exits the reaction cell due only to effusion, is described to estimate the gas pressure in the reaction cell. The value of the product of the kinetic rate constant and the ion residence time in the reaction cell can be determined from experimental measurement of the decrease in an ion signal as a function of reaction gas flow rate. New kinetic rate constants are determined for the reaction of CH3F with Ar+ and Ar2+. - Highlights: • How to determine pressure and the product of the kinetic rate constant times the ion residence time in reaction cell • Relate measured ICP-DRC-MS signals versus gas flow rate to kinetic rate constants measured previously using SIFT-MS • Describe how to determine previously unmeasured kinetic rate constants using ICP-DRC-MS

  1. Kinetics of the reaction between carbon dioxide and tertiary amines

    Crooks, J.E.; Donnellan, J.P. (King' s Coll., London (England))


    The reaction between carbon dioxide and amines is of great technical importance and has been the subject of many investigations. The authors have shown that the reaction for secondary amines in anhydrous ethanol and in aqueous solution is exclusively second-order in amine and that the zwitterion intermediate postulated by Danckwerts is probably of negligible significance in the mechanism. The reaction with tertiary amines has also been studied, but the data are less controversial. In order to complete their studies of the reactions of carbon dioxide with amines, using their conductimetric stopped-flow apparatus, they have studied this reaction for MDEA (methyldiethanolamine, IUPAC name N-methyl-2,2{prime}-iminodiethanol) and TEA (triethanolamine, IUPAC name 2,2{prime},2{double prime}-nitrilotris(ethanol)).

  2. Kinetic Monte Carlo studies of the reaction kinetics of crystal defects that diffuse one-dimensionally with occasional transverse migration

    Heinisch, H.L.; Trinkaus, H.; Singh, Bachu Narain


    The reaction kinetics of the various species of mobile defects in irradiated materials are crucially dependent on the dimensionality of their migration. Sink strengths for one-dimensionally (1D) gliding interstitial loops undergoing occasional direction changes have been described analytically and...... transverse to their 1D glide direction. Their transition from 1D to 3D kinetics is significantly different from that due to direction changes. The KMC results are compared to an analytical description of this diffusion mode in the form of a master curve relating the 1D normalized sink strength to the...

  3. Comparison of four commercialized biochemical systems for clinical yeast identification by colour-producing reactions.

    Paugam, A; Benchetrit, M; Fiacre, A; Tourte-Schaefer, C; Dupouy-Camet, J


    We compared the ability of four commercially available yeast identification systems for routine laboratory hospital use: Auxacolor (AUX) (Sanofi Diagnostics Pasteur, Marne-la-Coquette), Fungichrom I (FUC) and Fungifast I Twin (FUF) (International Microbio, Toulon), Api Candida (API) (bioMérieux, Lyon). These systems are based on obtaining a biochemical profile easily defined by colorimetric reactions. We tested 202 yeasts belonging to 19 species which were included or were not included in the manufacturer's data base of the identification systems. Without extra tests, for all the organisms tested, after 24 h of incubation, the percentage of organisms correctly identified was 48% for AUX, 75% for FUC, 77% for FUF and 81% for API. However, if we consider the ratio of the number of correct identifications without extra tests with the number of yeasts included in the manufacturers' data bases (sensitivity) the results increased to 61% for AUX, 81% for FUC, 91% for FUF and 83% for API. These systems are particularly well adapted to medical use, they are simple to set up, interpret, and have very good efficiency for the yeasts most commonly isolated in clinical specimens. The findings reported here indicate that the most favourable results were obtained with FUF and API systems. PMID:10200929

  4. Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems—an analytical theory

    The nonlinear dynamics of biochemical reactions in a small-sized system on the order of a cell are stochastic. Assuming spatial homogeneity, the populations of n molecular species follow a multi-dimensional birth-and-death process on Zn. We introduce the Delbrück–Gillespie process, a continuous-time Markov jump process, whose Kolmogorov forward equation has been known as the chemical master equation, and whose stochastic trajectories can be computed via the Gillespie algorithm. Using simple models, we illustrate that a system of nonlinear ordinary differential equations on Rn emerges in the infinite system size limit. For finite system size, transitions among multiple attractors of the nonlinear dynamical system are rare events with exponentially long transit times. There is a separation of time scales between the deterministic ODEs and the stochastic Markov jumps between attractors. No diffusion process can provide a global representation that is accurate on both short and long time scales for the nonlinear, stochastic population dynamics. On the short time scale and near deterministic stable fixed points, Ornstein–Uhlenbeck Gaussian processes give linear stochastic dynamics that exhibit time-irreversible circular motion for open, driven chemical systems. Extending this individual stochastic behaviour-based nonlinear population theory of molecular species to other biological systems is discussed. (invited article)

  5. Biological and within-subject variability of calcium kinetics and biochemical markers of bone turnover

    Bone loss is a critical issue during space flight. Evaluating changes in bone and calcium metabolism in astronauts often requires multiple preflight data collection points. Bone turnover and calcium kinetics were measured in 4 healthy subjects, and the day-to-day and between-subject variations were ...

  6. Nitrite-Driven Nitrous Oxide Production Under Aerobic Soil Conditions: Kinetics and Biochemical Controls

    Nitrite (NO2-) can accumulate during nitrification in soil following fertilizer application. While the role of NO2- as a substrate regulating nitrous oxide (N2O) production is recognized, kinetic data are not available that allow for estimating N2O production or soil-to-atmosphere fluxes as a functi...

  7. Kinetics of liquid-solid reactions in naphthenic acid conversion and Kraft pulping

    Yang, Ling

    Two liquid-solid reactions, in which the morphology of the solid changes as the reactions proceeds, were examined. One is the NA conversion in oil by decarboxylation on metal oxides and carbonates, and the other is the Kraft pulping in which lignin removal by delignification reaction. In the study of the NA conversion, CaO was chosen as the catalyst for the kinetic study from the tested catalysts based on NA conversion. Two reaction mixtures, carrier oil plus commercial naphthenic acids and heavy vacuum gas oil (HVGO) from Athabasca bitumen, were applied in the kinetic study. The influence of TAN, temperature, and catalyst loading on the NA conversion and decarboxylation were studied systematically. The results showed that the removal rate of TAN and the decarboxylation of NA were both independent of the concentration of NA over the range studied, and significantly dependent on reaction temperature. The data from analyzing the spent catalyst demonstrated that calcium naphthenate was an intermediate of the decarboxylation reaction of NA, and the decomposition of calcium naphthenate was a rate-determining step. In the study on the delignification of the Kraft pulping, a new mechanism was proposed for the heterogeneous delignification reaction during the Kraft pulping process. In particular, the chemical reaction mechanism took into account the heterogeneous nature of Kraft pulping. Lignin reacted in parallel with sodium hydroxide and sodium sulfide. The mechanism consists of three key kinetic steps: (1) adsorption of hydroxide and hydrosulfide ions on lignin; (2) surface reaction on the solid surface to produce degraded lignin products; and (3) desorption of degradation products from the solid surface. The most important step for the delignification process is the surface reaction, rather than the reactions occurring in the liquid phase. A kinetic model has, thus, been developed based on the proposed mechanism. The derived kinetic model showed that the mechanism

  8. A simultaneous one pot synthesis of two fractal structures via swapping two fractal reaction kinetic states.

    Ghosh, Subrata; Dutta, Mrinal; Ray, Kanad; Fujita, Daisuke; Bandyopadhyay, Anirban


    We introduce a new class of fractal reaction kinetics wherein two or more distinct fractal structures are synthesized as parts of a singular cascade reaction in a single chemical beaker. Two examples: sphere ↔ spiral & triangle ↔ square fractals, grow 10(6) orders from a single dendrimer (8 nm) to the visible scale. PMID:27166589

  9. Kinetics of the reaction between dissolved sodium sulfide and biologically produced sulfur

    Kleinjan, W.E.; Keizer, de A.; Janssen, A.J.H.


    The kinetics of the heterogeneous reaction between dissolved sodium sulfide and biologically produced sulfur particles has been studied by measuring the formation of polysulfide ions, Sx2-, in time (pH = 8.0, T = 30-50 °C). Detailed knowledge of this reaction is essential to understand its effect on

  10. Mechanistic interpretation of glass reaction: Input to kinetic model development

    Actinide-doped SRL 165 type glass was reacted in J-13 groundwater at 90 degree C for times up to 278 days. The reaction was characterized by both solution and solid analyses. The glass was seen to react nonstoichiometrically with preferred leaching of alkali metals and boron. High resolution electron microscopy revealed the formation of a complex layer structure which became separated from the underlying glass as the reaction progressed. The formation of the layer and its effect on continued glass reaction are discussed with respect to the current model for glass reaction used in the EQ3/6 computer simulation. It is concluded that the layer formed after 278 days is not protective and may eventually become fractured and generate particulates that may be transported by liquid water. 5 refs., 5 figs. , 3 tabs

  11. Ab Initio Calculations of Hydrocarbon Thermochemistry and Reaction Kinetics

    Aguilera Iparraguirre, Jorge


    In the framework of the SFB 551 "Carbon from the Gas Phase: Elementary Reactions, Structures, Materials" several areas of carbon related chemistry have been studied with help of computational tools. They include the exploration of different ways of building PAHs, the attempt to check the limits of quantum chemistry methods in hydrocarbon chemistry using explicitly-correlated methods and the calculation of accurate reaction rates.

  12. A study on reaction kinetics of the radicals produced in the laser-induced silane plasma

    The reaction kinetic processes of species produced in a pulsed TEA CO2 laser induced silane plasma were studied with the time-resolved OES. It is showed that the time position of main peaks for different fragments' characteristic lines are appreciably different. The reaction kinetic processes are discussed based on the results. By comparing the time evolution of the lines of the fragments and considering the other results of OES, the authors infer that the final reaction channel of the laser-induced silane plasma is a Si producing channel

  13. Kinetics of the Bray-Liebhafsky oscillatory reaction perturbed by polymer supported cobalt catalyst

    Maksimović J.P.; Čupić Ž.D.; Lončarević D.; Pejić N.; Vasiljević-Radović D.; Anić S.


    The Bray-Liebhafsky (BL) oscillatory reaction generated in the batch reactor at 62- 68 oC was perturbed by cobalt(II)-nitrate, supported on the macroreticular copolymer of poly-4-vinylpyridine with divinylbenzene (Co-PVPDVB). The kinetic data was analyzed of the complex pathways of the hydrogen peroxide decomposition in the examined BL reaction. The obtained results confirm that the kinetics of the BL reaction in the presence Co-PVPDVB comes partially from the Co-catalyst and partially ...

  14. Kinetics of the Bray-Liebhafsky oscillatory reaction perturbed by polymer supported cobalt catalyst

    Maksimović J.P.


    Full Text Available The Bray-Liebhafsky (BL oscillatory reaction generated in the batch reactor at 62- 68 oC was perturbed by cobalt(II-nitrate, supported on the macroreticular copolymer of poly-4-vinylpyridine with divinylbenzene (Co-PVPDVB. The kinetic data was analyzed of the complex pathways of the hydrogen peroxide decomposition in the examined BL reaction. The obtained results confirm that the kinetics of the BL reaction in the presence Co-PVPDVB comes partially from the Co-catalyst and partially from the macroreticular copolymer support.

  15. Kinetic and mechanistic studies of free-radical reactions in combustion

    Tully, F.P. [Sandia National Laboratories, Livermore, CA (United States)


    Combustion is driven by energy-releasing chemical reactions. Free radicals that participate in chain reactions carry the combustion process from reactants to products. Research in chemical kinetics enables us to understand the microscopic mechanisms involved in individual chemical reactions as well as to determine the rates at which they proceed. Both types of information are required for an understanding of how flames burn, why engines knock, how to minimize the production of pollutants, and many other important questions in combustion. In this program the authors emphasize accurate measurements over wide temperature ranges of the rates at which ubiquitous free radicals react with stable molecules. The authors investigate a variety of OH, CN, and CH + stable molecule reactions important to fuel conversion, emphasizing application of the extraordinarily precise technique of laser photolysis/continuous-wave laser-induced fluorescence (LP/cwLIF). This precision enables kinetic measurements to serve as mechanistic probes. Since considerable effort is required to study each individual reaction, prudent selection is critical. Two factors encourage selection of a specific reaction: (1) the rates and mechanisms of the subject reaction are required input to a combustion model; and (2) the reaction is a chemical prototype which, upon characterization, will provide fundamental insight into chemical reactivity, facilitate estimation of kinetic parameters for similar reactions, and constrain and test the computational limits of reaction-rate theory. Most studies performed in this project satisfy both conditions.


    J.H. Liu; J. Y. Zhang; S.K. Wei


    The present paper presents the structure, features and functions of a computerized system on kinetic analysis and evaluation of gas/solid reactions, KinPreGSR. KinPreGSR is a menu driven system, can be operated with MS Windows as workbench in a PC computer. It has been developed using visual C++ with FoxPro hybrid coding technique.KinPreGSR combines the characteristics of gas/solid reactions with the kinetic models as well as mass and heat transfer equations. The database files were established for the apparent activation energies of some reduction and decomposition reactions to allow the prediction of the reaction kinetics to some extents. Outputs can be displayed using graphical or numerical forms. Examples regarding the oxide reduction and carbonate decomposition under isothermal conditions are given to show those functions.

  17. Kinetics and optimization on discoloration of dyeing wastewater by schorl-catalyzed fenton-like reaction

    Xu Huan-Yan


    Full Text Available Kinetics and optimization on the discoloration of an active commercial dye, Argazol Blue BFBR (ABB by heterogeneous Fenton-like reaction catalyzed by natural schorl were investigated in this study. Kinetic investigations revealed that the first-order kinetic model was more favorable to describe the discoloration of ABB at different reaction conditions than the second-order and Behnajady-Modirshahla-Ghanbery models. The relationship between the reaction rate constant k and reaction temperature T followed the Arrhenius equation, with the apparent activation energy Ea of 51.31kJ•mol-1. The central composite design under the response surface methodology was employed for the experimental design and optimization of the ABB discoloration process. The significance of a second order polynomial model for predicting the optimal values of ABB discoloration was evaluated by the analysis of variance and 3D response surface plots for the interactions between two variables were constructed. Then, the optimum conditions were determined.

  18. Explaining the atypical reaction profiles of heme enzymes with a novel mechanistic hypothesis and kinetic treatment.

    Kelath Murali Manoj

    Full Text Available Many heme enzymes show remarkable versatility and atypical kinetics. The fungal extracellular enzyme chloroperoxidase (CPO characterizes a variety of one and two electron redox reactions in the presence of hydroperoxides. A structural counterpart, found in mammalian microsomal cytochrome P450 (CYP, uses molecular oxygen plus NADPH for the oxidative metabolism (predominantly hydroxylation of substrate in conjunction with a redox partner enzyme, cytochrome P450 reductase. In this study, we employ the two above-mentioned heme-thiolate proteins to probe the reaction kinetics and mechanism of heme enzymes. Hitherto, a substrate inhibition model based upon non-productive binding of substrate (two-site model was used to account for the inhibition of reaction at higher substrate concentrations for the CYP reaction systems. Herein, the observation of substrate inhibition is shown for both peroxide and final substrate in CPO catalyzed peroxidations. Further, analogy is drawn in the "steady state kinetics" of CPO and CYP reaction systems. New experimental observations and analyses indicate that a scheme of competing reactions (involving primary product with enzyme or other reaction components/intermediates is relevant in such complex reaction mixtures. The presence of non-selective reactive intermediate(s affords alternate reaction routes at various substrate/product concentrations, thereby leading to a lowered detectable concentration of "the product of interest" in the reaction milieu. Occam's razor favors the new hypothesis. With the new hypothesis as foundation, a new biphasic treatment to analyze the kinetics is put forth. We also introduce a key concept of "substrate concentration at maximum observed rate". The new treatment affords a more acceptable fit for observable experimental kinetic data of heme redox enzymes.

  19. Intramolecular Lactonization of Poly(α-hydroxyacrylic acid: Kinetics and Reaction Mechanism

    Heli Virkki


    Full Text Available Poly(α-hydroxyacrylic acid, PHA, is one of the few polymers with biodegradable properties used in mechanical pulp bleaching to stabilize hydrogen peroxide. A new method for the in situ follow-up of the lactone ring formation of PHA has been developed. The results have further been applied to describe the reaction kinetics of the lactonization and hydrolysis reactions through parameter estimation. In addition, the reaction mechanism is elucidated by multivariate data analysis. Satisfactory identification and semiquantitative separation of the lactone ring as well as the acyclic (carboxyl and hydroxyl groups forms have been established by 1H NMR in the pH range of 1–9. The lactonization reaction approaching equilibrium can be described by pseudo-first-order kinetics in the pH range of 1–6. The rate constants of the pseudo-first-order kinetic model have been estimated by nonlinear regression. Due to the very low rates of lactonization as well as the weak pH dependency of the reaction, an addition-elimination mechanism is proposed. Additionally, the presence of a transient reaction intermediate during lactonization reaction could be identified by subjecting the measurement data to multivariate data analysis (PCA, principal component analysis. A good correlation was found between the kinetic and the PCA models in terms of model validity.

  20. Kinetics and Mechanism of the Chlorate-Bromide Reaction.

    Sant'Anna, Rafaela T P; Faria, Roberto B


    The chlorate-bromide reaction, ClO3(-) + 6Br(-) + 6H(+) → 3Br2 + Cl(-) + 3H2O, was followed at the Br3(-)/Br2 isosbestic point (446 nm). A fifth-order rate law was found: (1)/3 d[Br2]/dt = k[ClO3(-)][Br(-)][H(+)](3) (k = 5.10 × 10(-6) s(-1) L(4) mol(-4)) at 25 °C and I = 2.4 mol L(-1). At high bromide concentrations, the bromide order becomes close to zero, indicating a saturation profile on bromide concentration, similar to the chloride saturation profile observed in the chlorate-chloride reaction. A mechanism is proposed that considers the formation of the intermediate BrOClO2(2-), similar to the intermediate ClOClO2(2-) proposed in the mechanism of the chlorate-chloride reaction. PMID:26467822

  1. Mechanism of prooxidant reaction of vitamin E. Kinetic, spectroscopic, and ab initio study of proton-transfer reaction

    Nagoaka, Shin-ichi; Sawada, Kouhei; Fukumoto, Youji [Ehime Univ., Matsuyama (Japan)] [and others


    This paper discusses using kinetic, spectroscopic, and ab initio studies of the prooxidant reaction of vitamin E derivatives to determine second-order rate constants for the reaction of six tocopheroxyl radicals with five alkyl hydroperoxides in benzene along with the first adiabatic ionization potentials of the alkyl hydroperoxides. These results suggest that charge transfer and proton tunneling play important roles in this prooxidant reaction, with proton tunneling taking place below the transition state and allowing the proton to cut a corner on the potential energy surface. 31 refs., 10 figs., 2 tabs.

  2. Kinetics of the decomposition reaction of phosphorite concentrate

    Huang Run


    Full Text Available Apatite is the raw material, which is mainly used in phosphate fertilizer, and part are used in yellow phosphorus, red phosphorus, and phosphoric acid in the industry. With the decrease of the high grade phosphorite lump, the agglomeration process is necessary for the phosphorite concentrate after beneficiation process. The decomposition behavior and the phase transformation are of vital importance for the agglomeration process of phosphorite. In this study, the thermal kinetic analysis method was used to study the kinetics of the decomposition of phosphorite concentrate. The phosphorite concentrate was heated under various heating rate, and the phases in the sample heated were examined by the X-ray diffraction method. It was found that the main phases in the phosphorite are fluorapatiteCa5(PO43F, quartz SiO2,and dolomite CaMg(CO32.The endothermic DSC peak corresponding to the mass loss caused by the decomposition of dolomite covers from 600°C to 850°C. The activation energy of the decomposition of dolomite, which increases with the increase in the extent of conversion, is about 71.6~123.6kJ/mol. The mechanism equation for the decomposition of dolomite agrees with the Valensi equation and G-B equation.

  3. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space

    Ruess, Jakob


    Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space.

  4. Kinetics of thermal decomposition and kinetics of substitution reaction of nano uranyl Schiff base complexes

    Asadi, Z.; Zeinali, A.; Dušek, Michal; Eigner, Václav


    Roč. 46, č. 12 (2014), s. 718-729. ISSN 0538-8066 R&D Projects: GA ČR(CZ) GAP204/11/0809 Institutional support: RVO:68378271 Keywords : uranyl * Schiff base * kinetics * anticancer activity Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.517, year: 2014

  5. Oxygen Diffusion and Reaction Kinetics in Continuous Fiber Ceramic Matrix Composites

    Halbig, Michael C.; Eckel, Andrew J.; Cawley, James D.


    Previous stressed oxidation tests of C/SiC composites at elevated temperatures (350 C to 1500 C) and sustained stresses (69 MPa and 172 MPa) have led to the development of a finite difference cracked matrix model. The times to failure in the samples suggest oxidation occurred in two kinetic regimes defined by the rate controlling mechanisms (i.e. diffusion controlled and reaction controlled kinetics). Microstructural analysis revealed preferential oxidation along as-fabricated, matrix microcracks and also suggested two regimes of oxidation kinetics dependent on the oxidation temperature. Based on experimental results, observation, and theory, a finite difference model was developed. The model simulates the diffusion of oxygen into a matrix crack bridged by carbon fibers. The model facilitates the study of the relative importance of temperature, the reaction rate constant, and the diffusion coefficient on the overall oxidation kinetics.

  6. Kinetic characterization of the photosynthetic reaction centres in microalgae by means of fluorescence methodology.

    Gargano, Immacolata; Olivieri, Giuseppe; Spasiano, Danilo; Andreozzi, Roberto; Pollio, Antonino; Marotta, Raffaele; D'Ambrosio, Nicola; Marzocchella, Antonio


    The kinetic characterization of the photosynthetic activity in autotrophic microalgae plays a key role in the design of optimized photobioreactors. This paper presents a procedure to assess kinetic parameters of a three-state photosynthetic reaction centres model. Four kinetic parameters of the model were assessed by processing the time-series measurements of pulse-amplitude modulation fluorimetry. The kinetic parameters were assessed for several microalgal strains (Stichococcus bacillaris, Scenedesmus vacuolatus, Chlamydomonas reinhardtii, Chlorella vulgaris) growth in vertical and inclined bubble columns and irradiated by white-light or red/blue light. The procedure was successfully applied to the investigated strains. The assessed parameters allow identifying the irradiance range under which: the photochemical process is controlled by the photons capture; the photoinhibition competes with the photochemical quenching. The analysis of the time-scale of the photosynthetic reaction centres as a function of the irradiance allows interpreting the performances of photobioreactors characterized by non-homogeneous irradiance. PMID:26216180

  7. Film forming kinetics and reaction mechanism of γ-glycidoxypropyltrimethoxysilane on low carbon steel surfaces

    The film forming kinetics and reaction mechanism of γ-GPS on low carbon steel surfaces was investigated by FTIR-ATR, AFM, NSS and theoretical calculation method. The results from experimental section indicated that the reaction of γ-GPS on low carbon steel surfaces followed the conventional reaction mechanism, which can be described as reaction (I) (Me (Metal)-OH + HO-Si → Me-O-Si + H2O) and reaction (II) (Si-OH + Si-OH → Si-O-Si + H2O). During film forming process, the formation of Si-O-Fe bond (reaction (I)) exhibited oscillatory phenomenon, the condensation degree of silanol monomers (reaction (II)) increased continuously. The metal hydroxyl density had significant influence on the growth mechanisms and corrosion resisting property of γ-GPS films. The results from theoretical calculation section indicated that the patterns of reaction (I) and reaction (II) were similar, involving a nucleophilic attack on the silicon center. The formation of Si-O-Fe bond (reaction (I)) was kinetically and thermodynamically preferred, which had catalytic effect on its condensation with neighboring silanol monomers (reaction (II)). Our DFT calculations were good consistent with the experimental measurements.

  8. LSENS, a general chemical kinetics and sensitivity analysis code for gas-phase reactions: User's guide

    Radhakrishnan, Krishnan; Bittker, David A.


    A general chemical kinetics and sensitivity analysis code for complex, homogeneous, gas-phase reactions is described. The main features of the code, LSENS, are its flexibility, efficiency and convenience in treating many different chemical reaction models. The models include static system, steady, one-dimensional, inviscid flow, shock initiated reaction, and a perfectly stirred reactor. In addition, equilibrium computations can be performed for several assigned states. An implicit numerical integration method, which works efficiently for the extremes of very fast and very slow reaction, is used for solving the 'stiff' differential equation systems that arise in chemical kinetics. For static reactions, sensitivity coefficients of all dependent variables and their temporal derivatives with respect to the initial values of dependent variables and/or the rate coefficient parameters can be computed. This paper presents descriptions of the code and its usage, and includes several illustrative example problems.

  9. Determination of a global kinetics for the sodium-water reaction using heat transfer statuses

    The aim of this study is the determination of a global kinetics for the sodium (solid) - water (vapor) reaction in diffusional regime. One of the methods used consists in implementing a temperature evolution measurement. Because of the exo-thermal property of the reaction, the use of the heat transfer status of a small reactor allows to evaluate the kinetics of the reaction. The heat dissipated by the reaction is shared among the sodium support and the gas. The main component is the flux inside the support. In order to evaluate this flux, an inverse method is used. A flux estimation inside the support is performed using a minimization algorithm applied to the differences between the temperatures measured on different points of the support and the calculated temperatures. This non-intrusive measurement technique allows to follow up the evolution of temperatures with time, and thus the heat flux of the reaction. (J.S.)


    Qui Tran-Cong-Miyata; Dan-Thuy Van-Pham; Kei Noma; Tomohisa Norisuye; Hideyuki Nakanishi


    The roles of reaction inhomogeneity in phase separation of polymer mixtures were described and summarized via two examples:photocross-link of polymer mixtures in the bulk state and photopolymerization of monomer in the liquid state.The reaction kinetics,the reaction-induced elastic strain and the phase separation kinetics were monitored respectively by UV-Vis spectroscopy,Mach-Zehnder interferometry and laser-scanning confocal microscopy.It was found that phase separation in the bulk state was strongly influenced by the elastic strain associated with the intrinsic inhomogeneity of the reaction,whereas the autocatalytic behavior of the polymerization plays an important role in the resulting morphology in the liquid state.These experimental results are discussed in conjunction with the morphology control of polymer mixtures by using chemical reactions.

  11. Effect of temperature on kinetic parameters of decomposition reaction of calcium carbonate

    CHEN Hongwei; CHEN Jiangtao; WEI Riguang; SUO Xinliang


    In order to investigate the influence of temperature on behavior of calcium carbonate decomposition,especially on kinetic parameters of the decomposition reaction,the analytically pure calcium carbonate was calcined on a self-built large dose thermogravimetric analyzer.The results indicated that,with an increase in the reaction temperature,the reactivity index of calcium carbonate decomposition increased at stage state while the kinetic parameters decreased at stage state.Moreover,both the reaction indices and the kinetic parameters can be divided into three stages and the temperature turning points in different stages were the same.The phase boundary reaction (cylindrical symmetry) theory was more suitable for calcium carbonate calcination under N2 atmosphere.The change trend of the logarithm of reaction activation with temperature was similar as that of the pre-exponential factor.There existed good liner relationship and kinetic compensation effect between them.The isokinetic temperature of the CaCO3 calcination was 842 ℃ and the reaction rate constant was 0.104 9 min-1 derived by the compensation coefficients.

  12. An investigation of the general regularity of size dependence of reaction kinetics of nanoparticles

    In the processes of preparation and application of nanomaterials, the chemical reactions of nanoparticles are often involved, and the size of nanoparticles has dramatic influence on the reaction kinetics. Nevertheless, there are many conflicts on regularities of size dependence of reaction kinetic parameters, and these conflicts have not been explained so far. In this paper, taking the reaction of nano-ZnO (average diameter is from 20.96 to 53.31 nm) with acrylic acid solution as a system, the influence regularities of the particle size on the kinetic parameters were researched. The regularities were consistent with that in most literatures, but inconsistent with that in a few of literatures, the reasons for the conflicts were interpreted. The reasons can be attributed to two factors: one is improper data processing for fewer data points, and the other is the difference between solid particles and porous particles. A general regularity of the size dependence of reaction kinetics for solid particles was obtained. The regularity shows that with the size of nanoparticles decreasing, the rate constant and the reaction order increase, while the apparent activation energy and the pre-exponential factor decrease; and the relationships of the logarithm of rate constant, the logarithm of pre-exponential factor, and the apparent activation energy to the reciprocal of the particle size are linear, respectively

  13. Investigation of the kinetics of the reactions of oxidation, nitration, and hydrogenation of uranium

    Various physico-chemical methods have been used to investigate the kinetics of the oxidation hydridation and nitridation of uranium. The experimental results show that the kinetics of these reactions are influenced by many factors also the Pilling and Bedworth rule is valid only under very limited conditions. The disagreement between this rule and the experimental results could be explained by the existence of numerous mechanical faults in the compounds obtained by the dry corrosion of the metal. (author)

  14. Measuring the Electrode Kinetics of Surface Confined Electrode Reactions at a Constant Scan Rate

    Guziejewski, Dariusz; Mirceski, Valentin; Jadresko, Dijana


    Abstract: The kinetics of surface confined electrode reactions of alizarin, vitamin B12, and vitamin K2 is measured with square-wave voltammetry over a wide pH interval, by applying the recent methodology for kinetic analysis at a constant scan rate [V. Mirceski, D. Guziejewski, K. Lisichkov, Electrochim. Acta 2013, 114, 667–673]. The reliability and the simplicity of the recent methodology is confirmed. The methodology requires analysis of the peak potential separation o...

  15. Ab initio studies of the kinetic isotope effect of the CH4 + OH atmospheric reaction

    Lasaga, Antonio C.; Gibbs, G. V.


    High level ab initio calculations have been carried out on the C-13 - C-12 kinetic isotope effect of the CH4 + OH reaction in the atmosphere. The results agree quite well with both the absolute value of the isotope effect and the temperature dependence of the effect, based on new experimental data. The calculated kinetic isotope effect supports a bigger effect of biomass burning on the methane global budget.

  16. Optimization and kinetic studies of sea mango (Cerbera odollam) oil for biodiesel production via supercritical reaction

    Highlights: • Sea mango oil as feedstock for biodiesel via non-catalytic supercritical reaction. • Extracted sea mango oil with high FFA could produce high yield of FAME. • Employment of Response Surface Methodology for optimization of FAME. • Kinetic study for reversible transesterification and esterification reactions. - Abstract: Sea mango (Cerbera odollam) oil, which is rich in free fatty acids, was utilized to produce fatty acid methyl esters (FAME) via supercritical transesterification reaction. Sea mango oil was extracted from seeds and was subsequently reacted with methanol in a batch-type supercritical reactor. Response surface methodology (RSM) analysis was used to optimize important parameters, including reaction temperature, reaction time and the molar ratio of methanol to oil. The optimum conditions were found as 380 °C, 40 min and 45:1 mol/mol, respectively, to achieve 78% biodiesel content. The first kinetic modelling of FAME production from sea mango oil incorporating reversible transesterification and reversible esterification was verified simultaneously. The kinetic parameters, including reaction rate constants, k, the pre-exponential constant, A, and the activation energy, Ea, for transesterification and esterification were determined using an ordinary differential equation (ODE45) solver. The highest activation energy of 40 kJ/mol and the lowest reaction rate constant of 2.50 × 10−5 dm3/mol s verified that the first stepwise reaction of TG to produce DG was the rate-limiting step

  17. Complex Cure Kinetics of the Hydroxyl-Epoxide Reaction in DGEBA Epoxy Hardened with Diethanolamine

    Ancipink, Windy; McCoy, John; Kropka, Jamie; Celina, Mathias

    The curing of a diglycidyl ether of bisphenol-A Epoxy (Epon 828) with diethanolamine (DEA) involves a fast amine-epoxide reaction followed by a slower hydroxyl-epoxide reaction. At curing temperatures below 100°C, the time scales of these two reactions are well separated, and the hydroxyl addition can be studied as an ''isolated'' reaction. The hydroxyl-epoxide reaction is of great interest due to the complex kinetics involved, which are brought about by competing reactions. The reaction kinetics are believed to be tertiary amine catalyzed and are well fit to a modified form of the Kamal-type equation. Here we study the complex long term reaction kinetics at various temperatures, by using isothermal modulated differential scanning calorimetry, micro calorimetry, and infrared spectroscopy. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

  18. Reaction Kinetics and Mechanism of Magnetic Field Effects in Cryptochrome

    Ilia A Solov'yov; Schulten, Klaus


    Creatures as varied as mammals, fish, insects, reptiles, and birds have an intriguing ‘sixth’ sense that allows them to orient themselves in the Earth's magnetic field. Despite decades of study, the physical basis of this magnetic sense remains elusive. A likely mechanism is furnished by magnetically sensitive radical pair reactions occurring in the retina, the light-sensitive part of animal eyes. A photoreceptor, cryptochrome, has been suggested to endow birds with magnetoreceptive abilities...

  19. Reaction Kinetic Parameters and Surface Thermodynamic Properties of Cu2O Nanocubes

    Xingxing Li


    Full Text Available Cuprous oxide (Cu2O nanocubes were synthesized by reducing Cu(OH2 in the presence of sodium citrate at room temperature. The samples were characterized in detail by field-emission scanning electron microscopy, transmission electron microscopy, high-resolution transmission electron microscopy, X-ray powder diffraction, and N2 absorption (BET specific surface area. The equations for acquiring reaction kinetic parameters and surface thermodynamic properties of Cu2O nanocubes were deduced by establishment of the relations between thermodynamic functions of Cu2O nanocubes and these of the bulk Cu2O. Combined with thermochemical cycle, transition state theory, basic theory of chemical thermodynamics, and in situ microcalorimetry, reaction kinetic parameters, specific surface enthalpy, specific surface Gibbs free energy, and specific surface entropy of Cu2O nanocubes were successfully determined. We also introduced a universal route for gaining reaction kinetic parameters and surface thermodynamic properties of nanomaterials.

  20. Multiresponse kinetic modelling of Maillard reaction and caramelisation in a heated glucose/wheat flour system.

    Kocadağlı, Tolgahan; Gökmen, Vural


    The study describes the kinetics of the formation and degradation of α-dicarbonyl compounds in glucose/wheat flour system heated under low moisture conditions. Changes in the concentrations of glucose, fructose, individual free amino acids, lysine and arginine residues, glucosone, 1-deoxyglucosone, 3-deoxyglucosone, 3,4-dideoxyglucosone, 5-hydroxymethyl-2-furfural, glyoxal, methylglyoxal and diacetyl concentrations were determined to form a multiresponse kinetic model for isomerisation and degradation reactions of glucose. Degradation of Amadori product mainly produced 1-deoxyglucosone. Formation of 3-deoxyglucosone proceeded directly from glucose and also Amadori product degradation. Glyoxal formation was predominant from glucosone while methylglyoxal and diacetyl originated from 1-deoxyglucosone. Formation of 5-hydroxymethyl-2-furfural from fructose was found to be a key step. Multi-response kinetic modelling of Maillard reaction and caramelisation simultaneously indicated quantitatively predominant parallel and consecutive pathways and rate limiting steps by estimating the reaction rate constants. PMID:27283710

  1. Reaction kinetics of solid fuels during entrained flow gasification

    Tremel, Alexander


    Despite the application of entrained flow gasification on larger scales, the reaction rates in the hot conversion zone are almost unknown. But the knowledge of the rates of the gasification reactions at high temperature and high pressure is crucial for the detailed design and optimisation of these gasifiers. This dissertation provides measurements of fuel conversion under operation conditions relevant to industrial gasifiers and aims at the transfer of the data to larger scale applications. A novel pilot-scale research reactor is developed that enables the study of gasification reactions at high temperature, high pressure and under entrained flow conditions. The Pressurised High Temperature Entrained Flow Reactor (PiTER) is operated at up to 1600 C and 4.0 MPa in pyrolysis and gasification experiments. The data set is extended by measurements in an atmospheric entrained flow reactor and a pressurised wire mesh reactor. Devolatilisation and gasification behaviour of a wide range of fuels is analysed including anthracite, bituminous coal, lignite, biocoal (from hydrothermal carbonisation), and biomass; however, Rhenish lignite is used in most of the experiments. The pyrolysis data enable the validation of a simple first order reaction model that describes the influence of pressure, temperature, and residence time on volatile yield. Char samples collected from the three reactors are analysed using laboratory procedures and bench-scale setups. Specific char surface area is measured by CO{sub 2} adsorption at 273 K, and is found to be significantly influenced by char conversion, reaction temperature, and devolatilisation pressure. The surface data are described by an extension of the Random Pore Model. Intrinsic char reactivity is measured in a pressurised thermogravimetric analyser and the influence of reactant partial pressure and temperature on the char-CO{sub 2} and char-H{sub 2}O reaction is studied. The intrinsic reaction rate is described by nth order and

  2. Reaction diffusion and solid state chemical kinetics handbook

    Dybkov, V I


    This monograph deals with a physico-chemical approach to the problem of the solid-state growth of chemical compound layers and reaction-diffusion in binary heterogeneous systems formed by two solids; as well as a solid with a liquid or a gas. It is explained why the number of compound layers growing at the interface between the original phases is usually much lower than the number of chemical compounds in the phase diagram of a given binary system. For example, of the eight intermetallic compounds which exist in the aluminium-zirconium binary system, only ZrAl3 was found to grow as a separate

  3. Self-triggering reaction kinetics between nitrates and aluminium powder

    During the night between the 19 and 20 September 2003, a loud explosion occurred at about 3 km from the town of Carignano that was clearly heard at a distance of some tens of kilometres. The explosion almost completely destroyed most of the laboratories of the Panzera Company that were used for the production of fireworks. The results of the research activities that were carried out using a differential scanning calorimeter (DSC) on the same raw materials that made up the pyrotechnical mixture that exploded are reported in this paper. This activity was carried out to identify the dynamics of the accident. It proved possible to verify how the event was produced because of a slow exothermic reaction which, after about 8 h, caused the self-triggering of 120 kg of finished product. The detonation can therefore be put down to a runaway reaction in the solid phase, whose primogenial causes can be attributed to a still craftsman type production system, not conformed to the rigorous controls and inspections as those required by a safety management system for major risk plants, as the Panzera Company was

  4. Glycerol acetals, kinetic study of the reaction between glycerol and formaldehyde

    The acetalization reaction between glycerol and formaldehyde using Amberlyst 47 acidic ion exchange resin was studied. These acetals can be obtained from renewable sources (bioalcohols and bioalcohol derived aldehydes) and seem to be good candidates for different applications such as oxygenated diesel additives. A preliminary kinetic study was performed in a batch stirred tank reactor studying the influence of different process parameters like temperature, feed composition and the stirring speed. A pseudo homogenous kinetic model able to explain the reaction mechanism was adjusted. Thus, the corresponding order of reaction was determined. Amberlyst 47 acidic ion exchange resin showed a fairly good behavior allowing 100% of selectivity towards acetals formation. However, the studied acetalization reaction showed high thermodynamic limitations achieving glycerol conversions around 50% using a stoichiometric feed ratio at 353 K. The product is a mixture of two isomers (1,3-Dioxan-5-ol and 1,3-dioxolane-4-methanol) and the conversion of 1,3-dioxolane-4-methanol into 1,3-Dioxan-5-ol was also observed. -- Highlights: → The reaction between glycerol and acetaldehyde shows thermodynamic limitations. → Amberlyst 47 ion exchange resins show 100% of selectivity. → A pseudo-homogeneous kinetic model is able to predict the reaction progress. → Isomerization reactions were observed from dioxalanes to dioxanes.

  5. Kinetics of pozzolanic reaction for preparation of flue gas desulfurizer from fly ash and Ca(OH)2

    WANG Jingang; HU Jinbang; WANG Daobin; DUAN Zhenya


    A kinetic model of the pozzolanic reaction for the preparation of flue gas desulfurizers from fly ash and Ca(OH)2 was deduced on the basis of solid phase reaction kinetic theory.Kinetic expressions and parameters were obtained and verified by experiment.A comparison of calculated results with experimental results showed that precision in kinetic expressions was good.The apparent reaction rate constants of the pozzolanic reaction could be raised by increasing the specific surface area of fly ash and the hydration temperature,and by using a suitable additive.

  6. DME Dissociation Reaction on Platinum Electrode Surface : A Quantitative Kinetic Analysis by In Situ IR Spectroscopy

    Zhang, Yi; Tong, Yujin; Lu, Leilei; Osawa, Masatoshi; Ye, Shen


    The kinetics of electrocatalytic dissociation reaction of dimethyl ether (DME) on a platinum (Pt) polycrystalline electrode in an acidic solution yielding carbon monoxide (CO) has been quantitatively analyzed by in situ IR spectroscopy in the potential region between 100 and 500 mV (vs reversible hydrogen electrode). A two-step consecutive reaction model, an initial dehydrogenation step followed by a CO formation step, is proposed for the dissociation process of the DME molecule. The mechanis...

  7. A kinetic model for chemical reactions without barriers : transport coefficients and eigenmodes

    Alves, Giselle M.; Marques Júnior, Wilson; Soares, A. J.; Kremer, Gilberto M.


    The kinetic model of the Boltzmann equation proposed in the work of Kremer and Soares 2009 for a binary mixture undergoing chemical reactions of symmetric type which occur without activation energy is revisited here, with the aim of investigating in detail the transport properties of the reactive mixture and the influence of the reaction process on the transport coefficients. Accordingly, the non-equilibrium solution of the Boltzmann equation is determined through an expansion in Sonine polyn...

  8. On the Mathematical Structure of Balanced Chemical Reaction Networks Governed by Mass Action Kinetics

    der Schaft, Arjan van; Rao, Shodhan; Jayawardhana, Bayu


    Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic equilibrium we derive a compact formulation exhibiting at the same time the structure of the complex graph and the stoichiometry of the network, and which admits a direct thermodynamical interpretation. This formulation allows us to easily characterize the set ...

  9. Excluded volume effects on the intrachain reaction kinetics.

    Kim, Ji-Hyun; Lee, Woojin; Sung, Jaeyoung; Lee, Sangyoub


    On the basis of the recently developed optimized Rouse-Zimm theory of chain polymers with excluded volume interactions, we calculate the long-time first-order rate constant k(1) for end-to-end cyclization of linear chain polymers. We first find that the optimized Rouse-Zimm theory provides the longest chain relaxation times tau(1) of excluded volume chains that are in excellent agreement with the available Brownian dynamics simulation results. In the free-draining limit, the cyclization rate is diffusion-controlled and k(1) is inversely proportional to tau(1), and the k(1) values calculated using the Wilemski-Fixman rate theory are in good agreement with Brownian dynamics simulation results. However, when hydrodynamic interactions are included, noticeable deviations are found. The main sources of errors are fluctuating hydrodynamic interaction and correlation hole effects as well as the non-Markovian reaction dynamic effect. The physical natures of these factors are discussed, and estimates for the magnitudes of required corrections are given. When the corrections are included, the present theory allows the prediction of accurate k(1) values for the cyclization of finite-length chains in good solvents as well as the correct scaling exponent in the long-chain limit. PMID:18419166

  10. Approximation and inference methods for stochastic biochemical kinetics - a tutorial review

    Schnoerr, David; Grima, Ramon


    Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose dynamics are governed by the Chemical Master Equation. Despite its simple structure, no analytic solutions to the Chemical Master Equation are known for most systems. Moreover, stochastic simulations are computationally expensive, making systematic analysis and statistical inference a challenging task. Consequently, significant effort has been spent in recent decades on the development of efficient approximation and inference methods. This article gives an introduction to basic modelling concepts as well as an overview of state of the art methods. First, we motivate and introduce deterministic and stochastic models for chemical networks, and give an overview of simulation and exact solution methods. Next, we discuss several approximation methods, including the chemical Langev...

  11. Variable elimination in chemical reaction networks with mass-action kinetics

    Feliu, Elisenda; Wiuf, C.


    We consider chemical reaction networks taken with mass-action kinetics. The steady states of such a system are solutions to a system of polynomial equations. Even for small systems the task of finding the solutions is daunting. We develop an algebraic framework and procedure for linear elimination...

  12. Kinetic Study of the Reaction between Tert-butyl Hydrazine and Nitrous Acid


    The kinetic study of the reaction between tert-butyl hydrazine(TBH)and nitrous acid in nitric acid system is performed by spectrophotometry. The effect of some factors such as the concentration of TBH, the concentration of nitric acid, ionic strength, temperature and the

  13. Interfacial reaction kinetics of coated SiC fibers with various titanium alloys

    Gundel, D. B.; Wawner, F. E.


    The kinetics of the reaction between the silicon carbide fibers and the titanium-based alloy matrix was investigated at temperatures from 800 to 1000 C for several titanium-based alloys (including Ti-1100 alloy and BETA 21S) and unalloyed Ti, reinforced with coated silicon carbide fiber SCS-6. The reaction zone growth kinetics was studied by exposing vacuum encapsulated samples to temperatures from 700 to 1000 C for times up to 150 hrs, followed by SAM observations of samples which were polished perpendicular to the fiber axis and etched. It was found that the reaction zone growth kinetics of the alpha (hcp) and beta (bcc) phases of unalloyed titanium reacting with SCS-6 fibers exhibited different values of the apparent activation energy and of the preexponential factor. Additions of other metals to Ti was found to slow down the reaction kinetics. Among the alloys studied, the Ti-1100 was the slowest reacting conventional alloy and the Ti-14Al-21Nb (in wt pct) was the slowest overall.

  14. On the graph and systems analysis of reversible chemical reaction networks with mass action kinetics

    Rao, Shodhan; Jayawardhana, Bayu; Schaft, Arjan van der


    Motivated by the recent progresses on the interplay between the graph theory and systems theory, we revisit the analysis of reversible chemical reaction networks described by mass action kinetics by reformulating it using the graph knowledge of the underlying networks. Based on this formulation, we

  15. Employing Magnetic Levitation to Monitor Reaction Kinetics and Measure Activation Energy

    Benz, Lauren; Cesafsky, Karen E.; Le, Tran; Park, Aileen; Malicky, David


    This article describes a simple and inexpensive undergraduate-level kinetics experiment that uses magnetic levitation to monitor the progress and determine the activation energy of a condensation reaction on a polymeric solid support. The method employs a cuvette filled with a paramagnetic solution positioned between two strong magnets. The…

  16. Marcus Theory: Thermodynamics CAN Control the Kinetics of Electron Transfer Reactions

    Silverstein, Todd P.


    Although it is generally true that thermodynamics do not influence kinetics, this is NOT the case for electron transfer reactions in solution. Marcus Theory explains why this is so, using straightforward physical chemical principles such as transition state theory, Arrhenius' Law, and the Franck-Condon Principle. Here the background and…

  17. A Gas-Kinetic Scheme for Multimaterial Flows and Its Application in Chemical Reaction

    Lian, Yongsheng; Xu, Kun


    This paper concerns the extension of the multicomponent gas-kinetic BGK-type scheme to multidimensional chemical reactive flow calculations. In the kinetic model, each component satisfies its individual gas-kinetic BGK equation and the equilibrium states of both components are coupled in space and time due to the momentum and energy exchange in the course of particle collisions. At the same time, according to the chemical reaction rule one component can be changed into another component with the release of energy, where the reactant and product could have different gamma. Many numerical test cases are included in this paper, which show the robustness and accuracy of kinetic approach in the description of multicomponent reactive flows.

  18. Kinetics of deso/sub x/ reaction on copper and cerium-based sorbent-catalysts

    Kinetics of SO/sub 2/ removal using a copper-based sorbent CuO/gamma-AI/sub 2/O/sub 3/ and a cerium modified copper sorbent CuO-CeO/sub 2/gamma-AI/sub 2/O, were measured on a TGA and their kinetics behaviors were simulated with a proposed empirical rate model (ERM). The purpose of cerium addition to the copper sorbent was to study the difference of sorbent's kinetics. The cerium modified copper sorbent showed a higher reaction rate on initial sulfation than the regular copper sorbent. Both sorbents however had similar calculated activation energy. The proposed ERM model appeared to describe the SO/sub 2/ removal kinetics well in the temperature range 250-400 degree C. (author)

  19. 生化反应的五行归属%Anfive elements classification of bio-chemical reactions



    五行学说提供了对事物进行系统分类的合理方法。人类体内充满了复杂的生物化学反应体系,能否用五行学说的基本规律归纳生物化学反应体系值得探讨。在以往相关研究的基础上,本文利用五行思想对生化反应的物质和反应类型进行分类,用简洁的中医学规律研究复杂的生化反应过程,这种新思路对药物研究、中西医结合学科的发展等具有挖掘价值。%Thefive elements theory provides us a system classification of all things so we can do the research in a much reasonable way. Further more, our bodies are full of complicated bio-chemical reactions and thefive elements theory should also be applicable to those reaction systems. This paper will try to make use of thefive elements theory to carry on an innovative classification of different types of bio-chemical reactions with the help of the former foundation of related researches, to make the complicated bio-chemical reactions easy to understand, and point out that this kind of lately academic thought is of great significance to the medicine researches as well as the integrated traditional Chinese and western medicine.

  20. Prediction of Reaction Kinetic of Al- Doura Heavy Naphtha Reforming Process Using Genetic Algorithm

    Ramzy H. Saihod


    Full Text Available In this study, genetic algorithm was used to predict the reaction kinetics of Iraqi heavy naphtha catalytic reforming process located in Al-Doura refinery in Baghdad. One-dimensional steady state model was derived to describe commercial catalytic reforming unit consisting of four catalytic reforming reactors in series process. The experimental information (Reformate composition and output temperature for each four reactors collected at different operating conditions was used to predict the parameters of the proposed kinetic model. The kinetic model involving 24 components, 1 to 11 carbon atoms for paraffins and 6 to 11 carbon atom for naphthenes and aromatics with 71 reactions. The pre-exponential Arrhenius constants and activation energies were determined after fine tuning of the model results with experimental data. The input to the optimization is the compositions for 21 components and the temperature for the effluent stream for each one of the four reactors within the reforming process while the output of optimization is 142 predicted kinetic parameters for 71 reactions within reforming process. The differential optimization technique using genetic algorithm to predict the parameters of the kinetic model. To validate the kinetic model, the simulation results of the model based on proposed kinetic model was compared with the experimental results. The comparison between the predicted and commercially results shows a good agreement, while the percentage of absolute error for aromatics compositions are (7.5, 2, 8.3, and 6.1% and the temperature absolute percentage error are (0.49, 0.5, 0.01, and 0.3% for four reactors respectively.

  1. Biochemical and morphological changes during the growth kinetics of Araucaria angustifolia suspension cultures

    André Luis Wendt dos Santos


    Full Text Available Embryogenic cultures of Araucaria angustifolia were established in a BM liquid medium supplemented with 2 µM 2,4-dichlorophenoxyacetic acid, 1 µM 6-benzylaminopurine and 1 µM kinetin (BM2 and in a BM medium free of growth regulators (BM0. During 42 days in culture, the cell growth pattern of both cultures was similar. The pH of the culture medium of both BM0 and BM2 underwent progressive reduction during culture time. For both the embryogenic cultures a preferential uptake of glucose in the late stages of cell growth kinetics was observed. The extracellular protein content was similar for both the embryogenic cultures. Acetocarmine and Evan's blue double stain showed major differences for early somatic embryo organisation, in which only the embryogenic culture grown in a liquid culture medium free of plant growth regulators showed the presence of bipolar somatic pro-embryos.Culturas embriogênicas de Araucaria angustifolia foram estabelecidas em meio de cultura líquido BM suplementado com 2 µM Ácido 2,4 Diclorofenoxiacético, 1 µM 6-Benzilaminopurina e 1 µM Cinetina (BM2 e em meio BM isento de reguladores de crescimento (BM0. Durante 42 dias de cultivo, o padrão de crescimento celular em ambas as culturas foi similar. O pH do meio de cultura BM0 e BM2 sofreu uma progressiva redução durante o período de cultivo. Em ambas as culturas embriogênicas foram observadas um consumo preferencial de glicose no período final da curva de crescimento celular. O nível de proteínas extracelulares foi similar para ambas as culturas embriogênicas. A dupla coloração com carmin acético e azul de Evans revelou diferenças na organização das linhagens celulares embriogênicas, sendo que a presença de proembriões somáticos bipolares foi apenas evidenciada nas culturas embriogênicas mantidas em meio de cultura líquido sem reguladores de crescimento.

  2. Thermodynamic and Kinetic Studies on the SiH + XH3 (X=N, P) Reactions

    Wei Jiang SI; hu Ping ZHUO; Guan Zhi JU


    Based on the quantum chemical study of the silylidyne insertion reaction with NH3 or PH3, the general statistical thermodynamics and Eyring transition state theory with Wigner correction are used to compute the changes of thermodynamic functions, equilibrium constants, A factors and rate constants of the two reactions in the temperature range 200-2000K. The results show that both of these reactions are thermodynamically dominant at low temperatures and kinetically favored at higher temperatures. The comparison between these two reactions shows that the SiH reaction with NH3 is more exothermic than SiH with PH3, while the rate constant of SiH reaction with NH3 is lower than that of SiH with PH3 at the same temperature.

  3. SurfKin: an ab initio kinetic code for modeling surface reactions.

    Le, Thong Nguyen-Minh; Liu, Bin; Huynh, Lam K


    In this article, we describe a C/C++ program called SurfKin (Surface Kinetics) to construct microkinetic mechanisms for modeling gas-surface reactions. Thermodynamic properties of reaction species are estimated based on density functional theory calculations and statistical mechanics. Rate constants for elementary steps (including adsorption, desorption, and chemical reactions on surfaces) are calculated using the classical collision theory and transition state theory. Methane decomposition and water-gas shift reaction on Ni(111) surface were chosen as test cases to validate the code implementations. The good agreement with literature data suggests this is a powerful tool to facilitate the analysis of complex reactions on surfaces, and thus it helps to effectively construct detailed microkinetic mechanisms for such surface reactions. SurfKin also opens a possibility for designing nanoscale model catalysts. PMID:25111729

  4. Bench-scale Kinetics Study of Mercury Reactions in FGD Liquors

    Gary Blythe; John Currie; David DeBerry


    This document is the final report for Cooperative Agreement DE-FC26-04NT42314, 'Kinetics Study of Mercury Reactions in FGD Liquors'. The project was co-funded by the U.S. DOE National Energy Technology Laboratory and EPRI. The objective of the project has been to determine the mechanisms and kinetics of the aqueous reactions of mercury absorbed by wet flue gas desulfurization (FGD) systems, and develop a kinetics model to predict mercury reactions in wet FGD systems. The model may be used to determine optimum wet FGD design and operating conditions to maximize mercury capture in wet FGD systems. Initially, a series of bench-top, liquid-phase reactor tests were conducted and mercury species concentrations were measured by UV/visible light spectroscopy to determine reactant and byproduct concentrations over time. Other measurement methods, such as atomic absorption, were used to measure concentrations of vapor-phase elemental mercury, that cannot be measured by UV/visible light spectroscopy. Next, a series of bench-scale wet FGD simulation tests were conducted. Because of the significant effects of sulfite concentration on mercury re-emission rates, new methods were developed for operating and controlling the bench-scale FGD experiments. Approximately 140 bench-scale wet FGD tests were conducted and several unusual and pertinent effects of process chemistry on mercury re-emissions were identified and characterized. These data have been used to develop an empirically adjusted, theoretically based kinetics model to predict mercury species reactions in wet FGD systems. The model has been verified in tests conducted with the bench-scale wet FGD system, where both gas-phase and liquid-phase mercury concentrations were measured to determine if the model accurately predicts the tendency for mercury re-emissions. This report presents and discusses results from the initial laboratory kinetics measurements, the bench-scale wet FGD tests, and the kinetics modeling

  5. Oxygen exchange reaction kinetics for cerium(IV) oxide at 1000 °C

    Bulk oxygen exchange rate kinetics on CeO2 at 1000 °C were observed to have a first order dependence on the fraction of reaction remaining and to be independent of oxygen partial pressure, total pressure, particle size, and specific surface area. This suggests that the exchange reaction is dominated by an internal chemical reaction that is occurring throughout the bulk of the material, and not at the material surface. Oxygen exchange rates were limited by this internal chemical reaction for all CeO2 powders studied (15 nm to −325 mesh), and had a rate constant of 1.19×10−2 s−1 with a time to completion of 617 s. These results are similar to the exchange rates observed previously on PuO2, suggesting that oxygen exchange on PuO2 may also be dominated by an internal chemical reaction under similar conditions. This work will help guide future experiments on 238PuO2 oxygen exchange reactions. - Graphical abstract: Oxygen exchange kinetics on CeO2 at 1000 °C are independent of a wide range of experimental conditions and exhibit first-order chemical reaction kinetics. - Highlights: • Stable oxygen exchange rates obtained on a variety of CeO2 powders at 1000 °C. • Exchange rates are independent of atmospheric composition and specific surface area. • Exchange rates are limited by an internal chemical reaction, not a surface reaction. • CeO2 exchange rates appear similar to the rates observed on PuO2 at 1000 °C

  6. Coherent chemical kinetics as quantum walks. I. Reaction operators for radical pairs

    Chia, A.; Tan, K. C.; Pawela, Ł.; Kurzyński, P.; Paterek, T.; Kaszlikowski, D.


    Classical chemical kinetics uses rate-equation models to describe how a reaction proceeds in time. Such models are sufficient for describing state transitions in a reaction where coherences between different states do not arise, in other words, a reaction that contains only incoherent transitions. A prominent example of a reaction containing coherent transitions is the radical-pair model. The kinetics of such reactions is defined by the so-called reaction operator that determines the radical-pair state as a function of intermediate transition rates. We argue that the well-known concept of quantum walks from quantum information theory is a natural and apt framework for describing multisite chemical reactions. By composing Kraus maps that act only on two sites at a time, we show how the quantum-walk formalism can be applied to derive a reaction operator for the standard avian radical-pair reaction. Our reaction operator predicts the same recombination dephasing rate as the conventional Haberkorn model, which is consistent with recent experiments [K. Maeda et al., J. Chem. Phys. 139, 234309 (2013), 10.1063/1.4844355], in contrast to previous work by Jones and Hore [J. A. Jones and P. J. Hore, Chem. Phys. Lett. 488, 90 (2010), 10.1016/j.cplett.2010.01.063]. The standard radical-pair reaction has conventionally been described by either a normalized density operator incorporating both the radical pair and reaction products or a trace-decreasing density operator that considers only the radical pair. We demonstrate a density operator that is both normalized and refers only to radical-pair states. Generalizations to include additional dephasing processes and an arbitrary number of sites are also discussed.

  7. The analysis of Al-based alloys by calorimetry: quantitative analysis of reactions and reaction kinetics

    Starink, M.J.


    Differential scanning calorimetry (DSC) and isothermal calorimetry have been applied extensively to the analysis of light metals, especially Al based alloys. Isothermal calorimetry and differential scanning calorimetry are used for analysis of solid state reactions, such as precipitation, homogenisation, devitrivication and recrystallisation; and solid–liquid reactions, such as incipient melting and solidification, are studied by differential scanning calorimetry. In producing repeatable calo...

  8. A small-scale, inexpensive method for detecting formaldehyde or methanol in biochemical reactions containing interfering substances.

    Jiang, Wen Zhi; Adamec, Jiri; Weeks, Donald P


    A simple, inexpensive microdistillation device is described for capturing methanol or formaldehyde as end products of biochemical reactions or in environmental samples. We demonstrate that the microdistillation protocol, coupled with the use of alcohol oxidase and the formaldehyde-sensitive reagent Purpald (4-amino-3-hydrazino-5-mercapto-1,2,4-triazole), serves as a quick and inexpensive alternative to chromatographic and mass spectrometer analyses for determining if formaldehyde or methanol is a product of reactions that contain substances that interfere with the Purpald reaction. These techniques were used to affirm formaldehyde as the end product of the dicamba monooxygenase-catalyzed O-demethylation of the herbicide dicamba (2-methoxy-3,6-dichlorobenzoic acid). PMID:23938775

  9. A Kinetic Study of the Gas-Phase Reaction of OH with Br2

    Bryukov, Mikhail G.; Dellinger, Barry; Knyazev, Vadim D.


    An experimental, temperature-dependent kinetic study of the gas-phase reaction of the hydroxyl radical with molecular bromine (reaction 1) has been performed using a pulsed laser photolysis/pulsed-laser-induced fluorescence technique over a wide temperature range of 297 – 766 K, and at pressures between 6.68 and 40.29 kPa of helium. The experimental rate coefficients for reaction 1 demonstrate no correlation with pressure and exhibit a negative temperature dependence with a slight negative cu...

  10. A kinetic study of the reaction of water vapor and carbon dioxide on uranium

    The kinetic study of the reaction of water vapour and carbon dioxide with uranium has been performed by thermogravimetric methods at temperatures between 160 and 410 deg G in the first case, 350 and 1050 deg C in the second: Three sorts of uranium specimens were used: uranium powder, thin evaporated films, and small spheres obtained from a plasma furnace. The experimental results led in the case of water vapour, to a linear rate of reaction controlled by diffusion at the lower temperatures, and by a surface reaction at the upper ones. In the case of carbon dioxide, a parabolic law has been found, controlled by diffusional processes. (author)

  11. Kinetics and Mechanism of the Exothermic First-stage Decomposition Reaction of Dinitroglycoluril

    ZHAO,Feng-Qi(赵凤起); HU,Rong-Zu(胡荣祖); CHEN,Pei(陈沛); LUO,Yang(罗阳); GAO,Sheng-Li(高胜利); SONG,Ji-Rong(宋纪蓉); SHI,Qi-Zhen(史启祯)


    Under linear temperature increase condition, the thermal behavior, mechanism and kinetic parameters of the exothermic decomposition reaction of the title compound have been studied by means of DSC and IR. The initial stage of the mechanism was proposed. The empirical kinetic model function in differential form, apparent activation energy and pre-exponential constant of the exothermic decomposition reaction are α 0.526, 207.0 kJ·mol-1 and 1018.49 s-1, respectively. The critical temperature of thermal explosion of the compound is 252.87 ℃. The values of △S≠, △H≠ and △G≠ of the reaction are 128.4 J·mol-1·K-1, 218.9 kJ·mol-1 and 152.7 kJ·mol-1, respectively.

  12. A hydrodynamics-reaction kinetics coupled model for evaluating bioreactors derived from CFD simulation.

    Wang, Xu; Ding, Jie; Guo, Wan-Qian; Ren, Nan-Qi


    Investigating how a bioreactor functions is a necessary precursor for successful reactor design and operation. Traditional methods used to investigate flow-field cannot meet this challenge accurately and economically. Hydrodynamics model can solve this problem, but to understand a bioreactor in sufficient depth, it is often insufficient. In this paper, a coupled hydrodynamics-reaction kinetics model was formulated from computational fluid dynamics (CFD) code to simulate a gas-liquid-solid three-phase biotreatment system for the first time. The hydrodynamics model is used to formulate prediction of the flow field and the reaction kinetics model then portrays the reaction conversion process. The coupled model is verified and used to simulate the behavior of an expanded granular sludge bed (EGSB) reactor for biohydrogen production. The flow patterns were visualized and analyzed. The coupled model also demonstrates a qualitative relationship between hydrodynamics and biohydrogen production. The advantages and limitations of applying this coupled model are discussed. PMID:20727741

  13. New method for spectrophotometric determination of quinones and barbituric acid through their reaction. A kinetic study

    Medien, H. A. A.


    A new and sensitive spectrophotometric method is described for the determination of p-benzoquinone, p-chloranil and 1.4-naphthoquinone. The method is based on the reaction between quinones and barbituric acid, by which a color is developed with maximum absorption between 485 and 555 nm in 50% methyl alcohol-water mixture. The absorption of the product obeys Beer's law within the concentration range 0.025-05 mM of orginal quinone. The kinetics of the reaction between p-benzoquinone and barbituric acid was studied in a range of methyl alcohol-water mixtures. The reaction follows overall second order kinetics, first order in each of the reactants. The rate increases with increasing dielectric constant. The method was applied for determination of barbituric acid with p-benzoquinone in the concentration range of 0.025-0.345 mM. Other barbiturates do not interfere.

  14. Kinetics of phyllosemiquinone oxidation in the Photosystem I reaction centre of Acaryochloris marina.

    Santabarbara, Stefano; Bailleul, Benjamin; Redding, Kevin; Barber, James; Rappaport, Fabrice; Telfer, Alison


    Light-induced electron transfer reactions in the chlorophyll a/d-binding Photosystem I reaction centre of Acaryochloris marina were investigated in whole cells by pump-probe optical spectroscopy with a temporal resolution of ~5ns at room temperature. It is shown that phyllosemiquinone, the secondary electron transfer acceptor anion, is oxidised with bi-phasic kinetics characterised by lifetimes of 88±6ns and 345±10ns. These lifetimes, particularly the former, are significantly slower than those reported for chlorophyll a-binding Photosystem I, which typically range in the 5-30ns and 200-300ns intervals. The possible mechanism of electron transfer reactions in the chlorophyll a/d-binding Photosystem I and the slower oxidation kinetics of the secondary acceptors are discussed. PMID:22037394

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

    Lundberg, Dan; Stjerndahl, Maria


    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…

  16. The kinetic model for slow photoinduced electron transport in the reaction centers of purple bacteria.

    Serdenko, T V; Barabash, Y M; Knox, P P; Seifullina, N Kh


    The present work is related to the investigation of slow kinetics of electron transport in the reaction centers (RCs) of Rhodobacter sphaeroides. Experimental data on the absorption kinetics of aqueous solutions of reaction centers at different modes of photoexcitation are given. It is shown that the kinetics of oxidation and reduction of RCs are well described by the sum of three exponential functions. This allows to suggest a two-level kinetic model for electron transport in the RC as a system of four electron-conformational states which correspond to three balance differential equations combined with state equation. The solution of inverse problem made it possible to obtain the rate constant values in kinetic equations for different times and intensities of exciting light. Analysis of rate constant values in different modes of RC excitation allowed to suggest that two mechanisms of structural changes are involved in RC photo-oxidation. One mechanism leads to the increment of the rate of electron return, another one-to its drop. Structural changes were found out to occur in the RCs under incident light. After light was turned off, the reduction of RCs was determined by the second mechanism. PMID:27271854

  17. Determination of Carbohydrazide and Kinetics of Condensation reaction of Carbohydrazide with Malachite Green by Spectrophotometry

    伍涛; 张同来; 陈红艳; 张建国


    The kinetics of the condensation reaction of malachite green and carbohydrazide was studied by spectrophotometry in aqueous solution in the temperature range of 15.0-22.0℃. The reaction was found to be second-order overall, first-order with respect to each reactant. The effect of ionic strength on the reaction has negative salt effect in the range of 0.2-1.0 mol·L-1. A mechanism of the reaction between malachite green and carbohydrazide was proposed, and the rate equation derived from the mechanism can explain all experimental observations properly. Based on this reaction, a method of determining the content of carbohydrazide in the concentration range of (0.02-0.5) )<10-3 mol·L-1 was proposed.

  18. Kinetic analysis of the reactions of hypobromous acid with protein components

    Pattison, David I; Davies, Michael Jonathan


    proteins isolated from patients with atherosclerosis, asthma, and cystic fibrosis, implicating the production of HOX in these diseases. The quantitative significance of these findings requires knowledge of the kinetics of reaction of HOX with protein targets, and such data have not been previously...... more, and Cys and Met much less, important targets for HOBr than HOCl. Kinetic models have been developed to predict the targets of HOX attack on proteins and free amino acids. Overall, these results shed light on the mechanisms of cell damage induced by HOX and indicate, for example, that the 3-chloro...

  19. Thermal decomposition of sugarcane straw, kinetics and heat of reaction in synthetic air.

    Rueda-Ordóñez, Yesid Javier; Tannous, Katia


    The aim of this work was to analyze the thermal decomposition, kinetics and heat of reaction of sugarcane straw in synthetic air by thermogravimetry (TG) and differential scanning calorimetry (DSC). The TG and DSC experiments were carried out using heating rates of 2.5°C/min, 5°C/min, and 10°C/min, and particle diameter of 0.250mm. In the study of the smoldering reaction were identified three consecutive stages, drying, oxidative pyrolysis, and combustion. Thus, the kinetic pathway was composed by six independent parallel reactions, three for each stage after drying, in which the activation energies were 176, 313, 150, 80, 150, and 100kJ/mol. The heat of reaction in synthetic air was completely exothermic releasing 8MJ/kg. The modeled curves of thermal decomposition of sugarcane straw presented good agreement with experimental data. Then, the kinetic parameters obtained could be used to analyze different processes involving smoldering. PMID:27019126

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

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


    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.

  1. Chemical kinetic analysis of hydrogen-air ignition and reaction times

    Rogers, R. C.; Schexnayder, C. J., Jr.


    An anaytical study of hydrogen air kinetics was performed. Calculations were made over a range of pressure from 0.2 to 4.0 atm, temperatures from 850 to 2000 K, and mixture equivalence ratios from 0.2 to 2.0. The finite rate chemistry model included 60 reactions in 20 species of the H2-O2-N2 system. The calculations also included an assessment of how small amounts of the chemicals H2O, NOx, H2O2, and O3 in the initial mixture affect ignition and reaction times, and how the variation of the third body efficiency of H2O relative of N2 in certain key reactions may affect reaction time. The results indicate that for mixture equivalence ratios between 0.5 and 1.7, ignition times are nearly constant; however, the presence of H2O and NO can have significant effects on ignition times, depending on the mixture temperature. Reaction time is dominantly influenced by pressure but is nearly independent of initial temperature, equivalence ratio, and the addition of chemicals. Effects of kinetics on reaction at supersonic combustor conditions are discussed.

  2. Kinetic method for enzymatic analysis by predicting background with uricase reaction as model

    LIAO Fei; ZHAO Yun-sheng; ZHAO Li-na; TAO Jia; ZHU Xiao-yun; WANG Yong-mei; ZUO Yu-ping


    Objective:To investigate the reliability for kinetic assay of substance with background predicted by the integrated method using uricase reaction as model. Methods: Absorbance before uricase action (A0) was estimated by extrapolation with given lag time of steady-state reaction. With Km fixed at12.5 μmol/L, background absorbance (Ab) was predicted by nonlinearly fitting integrated MichaelisMenten equation to Candida utilis uricase reaction curve. Uric acid in reaction solution was determined by the difference (ΔA) between A0 and Ab. Results :Ab usually showed deviation <3% from direct assay with residual substrate <one-fifth of initial substrate for analysis. ΔA showed CV <5% with resistance to common interferences except xanthine, and it linearly responded to uric acid with slope consistent to the absorptivity of uric acid. The lower limit was 2.0 μmol/L and upper limit reached 30 μmol/L in reaction solution with data monitored within 8 min reaction at 0. 015 U/ml uricase. Preliminary application to serum and urine gave better precision than the direct equilibrium method without the removal of proteins before analysis. Conclusion:This kinetic method with background predicted by the integrated method was reliable for enzymatic analysis, and it showed resistance to common interferences and enhanced efficiency at much lower cost.


    Weese, R K; Burnham, A K; Fontes, A T


    The properties of pentaamine (5-cyano-2H-tetrazolato-N2) cobalt (III) perchlorate (CP), which was first synthesized in 1968, continues to be of interest for predicting behavior in handling, shipping, aging, and thermal cook-off situations. We report coefficient of thermal expansion (CTE) values over four specific temperature ranges, decomposition kinetics using linear heating rates, and the reaction to three different types of stimuli: impact, spark, and friction. The CTE was measured using a Thermal Mechanical Analyzer (TMA) for samples that were uniaxially compressed at 10,000 psi and analyzed over a dynamic temperature range of -20 C to 70 C. Using differential scanning calorimetry, DSC, CP was decomposed at linear heating rates of 1, 3, and 7 C/min and the kinetic triplet calculated using the LLNL code Kinetics05. Values are also reported for spark, friction, and impact sensitivity.

  4. Kinetics of free radical decay reactions in lactic acid homo and copolymers irradiated to sterilization dose

    The kinetics of free radical decay reactions of poly(L-Lactic acid), poly(DL-Lactic acid) and random copolymer of lactic and glycolic acid have been investigated for decays taking place in air and in vacuum. The change in ESR lines of γ-irradiated polymers have been followed over a long time period. The decay has been found to follow neither simple first-order nor second-order kinetics. Various kinetic approaches including composite first or second-order mechanisms and diffusion-controlled first or second-order equations were determined to be also unsatisfactory. The decay of radicals in bulk irradiated lactic acid homo and copolymers was found to be best described when the second-order non-classical equation with time dependent rate constant approach was used. (Author)

  5. Stochastic modeling of biochemical systems with multistep reactions using state-dependent time delay.

    Wu, Qianqian; Tian, Tianhai


    To deal with the growing scale of molecular systems, sophisticated modelling techniques have been designed in recent years to reduce the complexity of mathematical models. Among them, a widely used approach is delayed reaction for simplifying multistep reactions. However, recent research results suggest that a delayed reaction with constant time delay is unable to describe multistep reactions accurately. To address this issue, we propose a novel approach using state-dependent time delay to approximate multistep reactions. We first use stochastic simulations to calculate time delay arising from multistep reactions exactly. Then we design algorithms to calculate time delay based on system dynamics precisely. To demonstrate the power of proposed method, two processes of mRNA degradation are used to investigate the function of time delay in determining system dynamics. In addition, a multistep pathway of metabolic synthesis is used to explore the potential of the proposed method to simplify multistep reactions with nonlinear reaction rates. Simulation results suggest that the state-dependent time delay is a promising and accurate approach to reduce model complexity and decrease the number of unknown parameters in the models. PMID:27553753

  6. On the ultrafast kinetics of the energy and electron transfer reactions in photosystem I

    Slavov, Chavdar Lyubomirov


    The subject of the current work is one of the main participants in the light-dependent phase of oxygenic photosynthesis, Photosystem I (PS I). This complex carries an immense number of cofactors: chlorophylls (Chl), carotenoids, quinones, etc, which together with the protein entity exhibit several exceptional properties. First, PS I has an ultrafast light energy trapping kinetics with a nearly 100% quantum efficiency. Secondly, both of the electron transfer branches in the reaction center are suggested to be active. Thirdly, there are some so called 'red' Chls in the antenna system of PS I, absorbing light with longer wavelengths than the reaction center. These 'red' Chls significantly modify the trapping kinetics of PS I. The purpose of this thesis is to obtain better understanding of the above-mentioned, specific features of PS I. This will not merely cast more light on the mechanisms of energy and electron transfer in the complex, but also will contribute to the future developments of optimized artificial light-harvesting systems. In the current work, a number of PS I complexes isolated from different organisms (Thermosynechococcus elongatus, Chlamydomonas reinhardtii, Arabidopsis thaliana) and possessing distinctive features (different macroorganisation, monomers, trimers, monomers with a semibelt of peripheral antenna attached; presence of 'red' Chls) is investigated. The studies are primarily focused on the electron transfer kinetics in each of the cofactor branches in the PS I reaction center, as well as on the effect of the antenna size and the presence of 'red' Chls on the trapping kinetics of PS I. These aspects are explored with the help of several ultrafast optical spectroscopy methods: (i) time-resolved fluorescence ? single photon counting and synchroscan streak camera; and (ii) ultrafast transient absorption. Physically meaningful information about the molecular mechanisms of the energy trapping in PS I is

  7. Role of reaction kinetics and mass transport in glucose sensing with nanopillar array electrodes

    Rao Yeswanth L


    Full Text Available Abstract The use of nanopillar array electrodes (NAEs for biosensor applications was explored using a combined experimental and simulation approach to characterize the role of reaction kinetics and mass transport in glucose detection with NAEs. Thin gold electrodes with arrays of vertically standing gold nanopillars were fabricated and their amperometric current responses were measured under bare and functionalized conditions. Results show that the sensing performances of both the bare and functionalized NAEs were affected not only by the presence and variation of the nanoscale structures on the electrodes but also by the reaction kinetics and mass transport of the analyte species involved. These results will shed new light for enhancing the performance of nanostructure based biosensors.

  8. Constrained reaction volume approach for studying chemical kinetics behind reflected shock waves

    Hanson, Ronald K.


    We report a constrained-reaction-volume strategy for conducting kinetics experiments behind reflected shock waves, achieved in the present work by staged filling in a shock tube. Using hydrogen-oxygen ignition experiments as an example, we demonstrate that this strategy eliminates the possibility of non-localized (remote) ignition in shock tubes. Furthermore, we show that this same strategy can also effectively eliminate or minimize pressure changes due to combustion heat release, thereby enabling quantitative modeling of the kinetics throughout the combustion event using a simple assumption of specified pressure and enthalpy. We measure temperature and OH radical time-histories during ethylene-oxygen combustion behind reflected shock waves in a constrained reaction volume and verify that the results can be accurately modeled using a detailed mechanism and a specified pressure and enthalpy constraint. © 2013 The Combustion Institute.

  9. Reaction kinetics and modeling of photoinitiated cationic polymerization of an alicyclic based diglycidyl ether

    Harikrishna, R., E-mail: [Polymer Science and Engineering Division, National Chemical Laboratory, Pune 411008 (India); Ponrathnam, S. [Polymer Science and Engineering Division, National Chemical Laboratory, Pune 411008 (India); Tambe, S.S. [Chemical Engineering and Process Development Division, National Chemical Laboratory, Pune 411008 (India)


    Highlights: • Photocationic polymerization of alicyclic based diglycidyl ether was carried out. • Kinetic parameters were influenced by gelation and diffusional restrictions. • Applicability of autocatalytic model was established by nonlinear regression. • System showed higher activation energy than cycloaliphatic and aromatic diepoxides. -- Abstract: Photoinitiated cationic polymerization of cycloaliphatic diepoxides had received tremendous attention, while studies with lesser polymerizable diglycidyl ethers are comparatively less reported. The present work deals with the photoinitiated cationic polymerization of cyclohexane dimethanol diglycidyl ether followed by estimation of kinetic parameters. The effects of concentration of photoinitiator and temperature on curing performance were studied using photo differential scanning calorimeter or photo DSC with polychromatic radiation. It was observed that the rate of polymerization as well as ultimate conversion increased with increasing concentration of photoinitiator and temperature. The influences of gelation as well as diffusional restrictions have remarkable effect on cure performance. The kinetic parameters as per autocatalytic kinetic model were studied by Levenberg–Marquardt nonlinear regression method instead of conventional linear method for obtaining more accurate values of apparent rate constant. It was observed that the model fits with data from initial stages to almost towards the end of the reaction. The activation energy was found to be higher than the values reported for more reactive cycloaliphatic diepoxides. The value of pre-exponential factor increased with increase in activation energy showing influence of gelation at early stages of reaction.

  10. Purification and characterization of Fab fragments with rapid reaction kinetics against myoglobin.

    Song, Hyung-Nam; Kim, Dong-Hyung; Park, Sung-Goo; Lee, Myung Kyu; Paek, Se-Hwan; Woo, Eui-Jeon


    Myoglobin is an early biomarker for acute myocardial infarction. Recently, we isolated the antibody IgG-Myo2-7ds, which exhibits unique rapid reaction kinetics toward human myoglobin antigen. Antibodies with rapid dissociation kinetics are thought to be premature IgG forms that are produced during the early stage of in vivo immunization. In the present study, we identified the epitope region of the IgG-Myo2-7ds antibody to be the C-terminal region of myoglobin, which corresponds to 144-154 aa. The Fab fragment was directly purified by papain cleavage and protein G affinity chromatography and demonstrated kinetics of an association constant of 4.02 × 10(4) M(-1) s(-1) and a dissociation constant of 2.28 × 10(-2) s(-1), which retained the unique reaction kinetics of intact IgG-Myo2-7ds antibodies. Because a rapid dissociation antibody can be utilized for antibody recycling, the results from this study would provide a platform for the development of antibody engineering in potential diagnostic areas such as a continuous monitoring system for heart disease. PMID:25561012