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Stochastic Chemical Kinetics
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Book Synopsis Stochastic Chemical Kinetics by : Péter Érdi
Download or read book Stochastic Chemical Kinetics written by Péter Érdi and published by Springer. This book was released on 2014-05-06 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume reviews the theory and simulation methods of stochastic kinetics by integrating historical and recent perspectives, presents applications, mostly in the context of systems biology and also in combustion theory. In recent years, due to the development in experimental techniques, such as optical imaging, single cell analysis, and fluorescence spectroscopy, biochemical kinetic data inside single living cells have increasingly been available. The emergence of systems biology brought renaissance in the application of stochastic kinetic methods.
Book Synopsis Stochastic Chemical Reaction Systems in Biology by : Hong Qian
Download or read book Stochastic Chemical Reaction Systems in Biology written by Hong Qian and published by Springer Nature. This book was released on 2021-10-18 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an introduction to the analysis of stochastic dynamic models in biology and medicine. The main aim is to offer a coherent set of probabilistic techniques and mathematical tools which can be used for the simulation and analysis of various biological phenomena. These tools are illustrated on a number of examples. For each example, the biological background is described, and mathematical models are developed following a unified set of principles. These models are then analyzed and, finally, the biological implications of the mathematical results are interpreted. The biological topics covered include gene expression, biochemistry, cellular regulation, and cancer biology. The book will be accessible to graduate students who have a strong background in differential equations, the theory of nonlinear dynamical systems, Markovian stochastic processes, and both discrete and continuous state spaces, and who are familiar with the basic concepts of probability theory.
Book Synopsis Mathematical Models of Chemical Reactions by : Péter Érdi
Download or read book Mathematical Models of Chemical Reactions written by Péter Érdi and published by Manchester University Press. This book was released on 1989 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Reaction Kinetics: Exercises, Programs and Theorems by : János Tóth
Download or read book Reaction Kinetics: Exercises, Programs and Theorems written by János Tóth and published by Springer. This book was released on 2018-09-18 with total page 476 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fifty years ago, a new approach to reaction kinetics began to emerge: one based on mathematical models of reaction kinetics, or formal reaction kinetics. Since then, there has been a rapid and accelerated development in both deterministic and stochastic kinetics, primarily because mathematicians studying differential equations and algebraic geometry have taken an interest in the nonlinear differential equations of kinetics, which are relatively simple, yet capable of depicting complex behavior such as oscillation, chaos, and pattern formation. The development of stochastic models was triggered by the fact that novel methods made it possible to measure molecules individually. Now it is high time to make the results of the last half-century available to a larger audience: students of chemistry, chemical engineering and biochemistry, not to mention applied mathematics. Based on recent papers, this book presents the most important concepts and results, together with a wealth of solved exercises. The book is accompanied by the authors’ Mathematica package, ReactionKinetics, which helps both students and scholars in their everyday work, and which can be downloaded from http://extras.springer.com/ and also from the authors’ websites. Further, the large set of unsolved problems provided may serve as a springboard for individual research.
Book Synopsis Simulation Algorithms for Computational Systems Biology by : Luca Marchetti
Download or read book Simulation Algorithms for Computational Systems Biology written by Luca Marchetti and published by Springer. This book was released on 2017-09-27 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explains the state-of-the-art algorithms used to simulate biological dynamics. Each technique is theoretically introduced and applied to a set of modeling cases. Starting from basic simulation algorithms, the book also introduces more advanced techniques that support delays, diffusion in space, or that are based on hybrid simulation strategies. This is a valuable self-contained resource for graduate students and practitioners in computer science, biology and bioinformatics. An appendix covers the mathematical background, and the authors include further reading sections in each chapter.
Book Synopsis Stochastic Approach to Chemical Kinetics by : Donald Allan McQuarrie
Download or read book Stochastic Approach to Chemical Kinetics written by Donald Allan McQuarrie and published by . This book was released on 1968 with total page 82 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Chemical Kinetics, Stochastic Processes, and Irreversible Thermodynamics by : Moises Santillan
Download or read book Chemical Kinetics, Stochastic Processes, and Irreversible Thermodynamics written by Moises Santillan and published by . This book was released on 2014-07-31 with total page 142 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Statistical Thermodynamics and Stochastic Kinetics by : Yiannis N. Kaznessis
Download or read book Statistical Thermodynamics and Stochastic Kinetics written by Yiannis N. Kaznessis and published by Cambridge University Press. This book was released on 2012 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides engineers with the knowledge they need to apply thermodynamics and solve engineering challenges at the molecular level.
Book Synopsis Stochastic and Dynamic Views of Chemical Reaction Kinetics in Solutions by : A. M. Kuznet︠s︡ov (dokt. fiz.-mat. nauk.)
Download or read book Stochastic and Dynamic Views of Chemical Reaction Kinetics in Solutions written by A. M. Kuznet︠s︡ov (dokt. fiz.-mat. nauk.) and published by EPFL Press. This book was released on 1999-01-01 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Deterministic Versus Stochastic Modelling in Biochemistry and Systems Biology by : Paola Lecca
Download or read book Deterministic Versus Stochastic Modelling in Biochemistry and Systems Biology written by Paola Lecca and published by Elsevier. This book was released on 2013-04-09 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: Stochastic kinetic methods are currently considered to be the most realistic and elegant means of representing and simulating the dynamics of biochemical and biological networks. Deterministic versus stochastic modelling in biochemistry and systems biology introduces and critically reviews the deterministic and stochastic foundations of biochemical kinetics, covering applied stochastic process theory for application in the field of modelling and simulation of biological processes at the molecular scale. Following an overview of deterministic chemical kinetics and the stochastic approach to biochemical kinetics, the book goes onto discuss the specifics of stochastic simulation algorithms, modelling in systems biology and the structure of biochemical models. Later chapters cover reaction-diffusion systems, and provide an analysis of the Kinfer and BlenX software systems. The final chapter looks at simulation of ecodynamics and food web dynamics. Introduces mathematical concepts and formalisms of deterministic and stochastic modelling through clear and simple examples Presents recently developed discrete stochastic formalisms for modelling biological systems and processes Describes and applies stochastic simulation algorithms to implement a stochastic formulation of biochemical and biological kinetics
Book Synopsis Space in Discrete Stochastic Simulation of Chemical Kinetics by : Sotiria Lampoudi
Download or read book Space in Discrete Stochastic Simulation of Chemical Kinetics written by Sotiria Lampoudi and published by ProQuest. This book was released on 2008 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis is concerned with studying what happens when space must be taken into account in discrete stochastic simulation of chemical kinetics. The Stochastic Simulation Algorithm of Gillespie, which is the simulation technique of choice for mesoscopic stochastic chemical kinetics, is rigorously applicable to systems of point molecules which are well-stirred. The former condition means that the molecules must occupy volume negligible compared to the total volume of the system. The latter condition means that the distribution of the molecules' positions in space must be uniformly random.
Book Synopsis Stochasticity in Processes by : Peter Schuster
Download or read book Stochasticity in Processes written by Peter Schuster and published by Springer. This book was released on 2016-10-14 with total page 728 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book has developed over the past fifteen years from a modern course on stochastic chemical kinetics for graduate students in physics, chemistry and biology. The first part presents a systematic collection of the mathematical background material needed to understand probability, statistics, and stochastic processes as a prerequisite for the increasingly challenging practical applications in chemistry and the life sciences examined in the second part. Recent advances in the development of new techniques and in the resolution of conventional experiments at nano-scales have been tremendous: today molecular spectroscopy can provide insights into processes down to scales at which current theories at the interface of physics, chemistry and the life sciences cannot be successful without a firm grasp of randomness and its sources. Routinely measured data is now sufficiently accurate to allow the direct recording of fluctuations. As a result, the sampling of data and the modeling of relevant processes are doomed to produce artifacts in interpretation unless the observer has a solid background in the mathematics of limited reproducibility. The material covered is presented in a modular approach, allowing more advanced sections to be skipped if the reader is primarily interested in applications. At the same time, most derivations of analytical solutions for the selected examples are provided in full length to guide more advanced readers in their attempts to derive solutions on their own. The book employs uniform notation throughout, and a glossary has been added to define the most important notions discussed.
Book Synopsis Molecular Kinetics in Condensed Phases by : Ron Elber
Download or read book Molecular Kinetics in Condensed Phases written by Ron Elber and published by John Wiley & Sons. This book was released on 2020-02-10 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: A guide to the theoretical and computational toolkits for the modern study of molecular kinetics in condensed phases Molecular Kinetics in Condensed Phases: Theory, Simulation and Analysis puts the focus on the theory, algorithms, simulations methods and analysis of molecular kinetics in condensed phases. The authors – noted experts on the topic – offer a detailed and thorough description of modern theories and simulation methods to model molecular events. They highlight the rigorous stochastic modelling of molecular processes and the use of mathematical models to reproduce experimental observations, such as rate coefficients, mean first passage times and transition path times. The book’s exploration of simulations examines atomically detailed modelling of molecules in action and the connections of these simulations to theory and experiment. The authors also explore the applications that range from simple intuitive examples of one- and two-dimensional systems to complex solvated macromolecules. This important book: Offers an introduction to the topic that combines theory, simulation and analysis Presents a guide written by authors that are well-known and highly regarded leaders in their fields Contains detailed examples and explanation of how to conduct computer simulations of kinetics. A detailed study of a two-dimensional system and of a solvated peptide are discussed. Discusses modern developments in the field and explains their connection to the more traditional concepts in chemical dynamics Written for students and academic researchers in the fields of chemical kinetics, chemistry, computational statistical mechanics, biophysics and computational biology, Molecular Kinetics in Condensed Phases is the authoritative guide to the theoretical and computational toolkits for the study of molecular kinetics in condensed phases.
Book Synopsis Reaction Rate Theory and Rare Events by : Baron Peters
Download or read book Reaction Rate Theory and Rare Events written by Baron Peters and published by Elsevier. This book was released on 2017-03-22 with total page 636 pages. Available in PDF, EPUB and Kindle. Book excerpt: Reaction Rate Theory and Rare Events bridges the historical gap between these subjects because the increasingly multidisciplinary nature of scientific research often requires an understanding of both reaction rate theory and the theory of other rare events. The book discusses collision theory, transition state theory, RRKM theory, catalysis, diffusion limited kinetics, mean first passage times, Kramers theory, Grote-Hynes theory, transition path theory, non-adiabatic reactions, electron transfer, and topics from reaction network analysis. It is an essential reference for students, professors and scientists who use reaction rate theory or the theory of rare events. In addition, the book discusses transition state search algorithms, tunneling corrections, transmission coefficients, microkinetic models, kinetic Monte Carlo, transition path sampling, and importance sampling methods. The unified treatment in this book explains why chemical reactions and other rare events, while having many common theoretical foundations, often require very different computational modeling strategies. Offers an integrated approach to all simulation theories and reaction network analysis, a unique approach not found elsewhere Gives algorithms in pseudocode for using molecular simulation and computational chemistry methods in studies of rare events Uses graphics and explicit examples to explain concepts Includes problem sets developed and tested in a course range from pen-and-paper theoretical problems, to computational exercises
Book Synopsis Chemical Kinetics: Beyond The Textbook by : Lindenberg Katja
Download or read book Chemical Kinetics: Beyond The Textbook written by Lindenberg Katja and published by World Scientific. This book was released on 2019-08-27 with total page 620 pages. Available in PDF, EPUB and Kindle. Book excerpt: Processes involving randomly moving particles, which react either upon encounter or via distance-dependent reaction rates, are ubiquitous in nature. A few stray examples are recombination of ions or holes and electrons, excitation energy migration and quenching, trapping of particles by other species, coagulation, binding of ligands and proteins to specific sites, chemotaxis, catalytically-induced self-propulsion, polymerization, growth of dendrites or aggregates, or nuclei of a new phase.Several decades ago, it was recognized that the kinetic behavior in some systems with reactions and random transport is strongly affected by many factors, which were not taken into account in previous studies. These are, to name but a few, fluctuations in the spatial distributions of the reactants and fluctuations of the reactivity, some essentially many-particle phenomena, effects of anomalous diffusion, molecular crowding, as well as the internal geometry of the reaction bath. Within recent years, along with a growing interest in chemical processes ocurring in biological systems or cellular environments, numerous advances have been made and considerable knowledge has been acquired. These seminal contributions are, however, scattered among many journals and no attempt has been made so far to present a unified picture.This book presents a general overview of different contemporary facets of chemical kinetics in a variety of different environments. It includes 23 seminal works and reviews on different aspects of reaction processes in chemical, physical and biophysical systems, both theoretical and experimental.
Book Synopsis Kinetics of Chemical Reactions by : Guy B. Marin
Download or read book Kinetics of Chemical Reactions written by Guy B. Marin and published by John Wiley & Sons. This book was released on 2018-12-07 with total page 446 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second, extended and updated edition presents the current state of kinetics of chemical reactions, combining basic knowledge with results recently obtained at the frontier of science. Special attention is paid to the problem of the chemical reaction complexity with theoretical and methodological concepts illustrated throughout by numerous examples taken from heterogeneous catalysis combustion and enzyme processes. Of great interest to graduate students in both chemistry and chemical engineering.
Book Synopsis Model Reconstruction for Moment-based Stochastic Chemical Kinetics by : Alexander Andreychenko
Download or read book Model Reconstruction for Moment-based Stochastic Chemical Kinetics written by Alexander Andreychenko and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
