Deterministic Kinetics In Chemistry And Systems Biology
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Deterministic Kinetics in Chemistry and Systems Biology by Gábor Lente Pdf
This book gives a concise overview of the mathematical foundations of kinetics used in chemistry and systems biology. The analytical and numerical methods used to solve complex rate equations with the widely used deterministic approach will be described, with primary focus on practical aspects important in designing experimental studies and the evaluation of data. The introduction of personal computers transformed scientific attitudes in the last two decades considerably as computational power ceased to be a limiting factor. Despite this improvement, certain time-honored approximations in solving rate equations such as the pre-equilibrium or the steady-state approach are still valid and necessary as they concern the information content of measured kinetic traces. The book shows the role of these approximations in modern kinetics and will also describe some common misconceptions in this field.
Deterministic Kinetics in Chemistry and Systems Biology by Gábor Lente Pdf
This book gives a concise overview of the mathematical foundations of kinetics used in chemistry and systems biology. The analytical and numerical methods used to solve complex rate equations with the widely used deterministic approach will be described, with primary focus on practical aspects important in designing experimental studies and the evaluation of data. The introduction of personal computers transformed scientific attitudes in the last two decades considerably as computational power ceased to be a limiting factor. Despite this improvement, certain time-honored approximations in solving rate equations such as the pre-equilibrium or the steady-state approach are still valid and necessary as they concern the information content of measured kinetic traces. The book shows the role of these approximations in modern kinetics and will also describe some common misconceptions in this field.
Stochastic Chemical Kinetics by Péter Érdi,Gábor Lente Pdf
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.
Deterministic Versus Stochastic Modelling in Biochemistry and Systems Biology by Paola Lecca,Ian Laurenzi,Ferenc Jordan Pdf
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
Enzyme Kinetics for Systems Biology by Ambrosius Publishing Pdf
This book introduces fundamental concepts in kinetics that relate to system biology. The text is suitable for junior/senior undergraduates and graduates who need access to information relevant to modeling biochemical pathways.
Reaction Kinetics: Exercises, Programs and Theorems by János Tóth,Attila László Nagy,Dávid Papp Pdf
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.
Analysis of Kinetic Reaction Mechanisms by Tamás Turányi,Alison S. Tomlin Pdf
Chemical processes in many fields of science and technology, including combustion, atmospheric chemistry, environmental modelling, process engineering, and systems biology, can be described by detailed reaction mechanisms consisting of numerous reaction steps. This book describes methods for the analysis of reaction mechanisms that are applicable in all these fields. Topics addressed include: how sensitivity and uncertainty analyses allow the calculation of the overall uncertainty of simulation results and the identification of the most important input parameters, the ways in which mechanisms can be reduced without losing important kinetic and dynamic detail, and the application of reduced models for more accurate engineering optimizations. This monograph is invaluable for researchers and engineers dealing with detailed reaction mechanisms, but is also useful for graduate students of related courses in chemistry, mechanical engineering, energy and environmental science and biology.
Asymmetric Autocatalysis by Kenso Soai,Tsuneomi Kawasaki,Arimasa Matsumoto Pdf
Asymmetric autocatalysis is a reaction in which chiral compound acts as a chiral catalyst for its own production. The process is a catalytic automultiplication of the chiral compound leading to an end product with a high enantiomeric excess. It has advantages over non-autocatalytic reactions because the amount of catalyst increases and no loss or deterioration of the catalyst is observed. Additionally, because the catalyst and product have the same structure, the separation of product from the catalyst is not necessary. Asymmetric Autocatalysis provides a comprehensive introduction to the topic of autocatalysis and an in-depth review of the current state of the research. Edited by a team including Professor Kenso Soai, who first described these types of reaction, and written by experts from around the world this book is a great resource for anyone with an interest in organic synthesis, catalysis and chirality.
Stochastic Chemical Reaction Systems in Biology by Hong Qian,Hao Ge Pdf
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.
Stochastic Dynamics in Computational Biology by Stefanie Winkelmann,Christof Schütte Pdf
The aim of this book is to provide a well-structured and coherent overview of existing mathematical modeling approaches for biochemical reaction systems, investigating relations between both the conventional models and several types of deterministic-stochastic hybrid model recombinations. Another main objective is to illustrate and compare diverse numerical simulation schemes and their computational effort. Unlike related works, this book presents a broad scope in its applications, from offering a detailed introduction to hybrid approaches for the case of multiple population scales to discussing the setting of time-scale separation resulting from widely varying firing rates of reaction channels. Additionally, it also addresses modeling approaches for non well-mixed reaction-diffusion dynamics, including deterministic and stochastic PDEs and spatiotemporal master equations. Finally, by translating and incorporating complex theory to a level accessible to non-mathematicians, this book effectively bridges the gap between mathematical research in computational biology and its practical use in biological, biochemical, and biomedical systems.
Advances in Asymmetric Autocatalysis and Related Topics by Gyula Palyi,Robert Kurdi,Claudia Zucchi Pdf
Advances in Asymmetric Autocatalysis and Related Topics provides various viewpoints on the important developments in asymmetric autocatalysis that have occurred in the past few years, also including brand new information in the field. Asymmetric autocatalysis is a chemical reaction which leads from achiral starting materials to chiral products, and in which the product accelerates its own formation reaction (conventional catalysis) and promotes the prevalence of its own chiral configuration (asymmetric induction). The combination of these two effects in the same reaction was unprecedented before 1995 when it was first described by Kenso SOAI at the Tokyo University of Science. Since then, several new combinations of this effect have been found, most intriguingly the possibility of absolute asymmetric synthesis, which is the spontaneous formation of the excess of one of the enantiomers of the product, a dream of organic chemists for more than a century. The book contains expert-contributed chapters that describe the most exciting recent developments in the field of the Soai reaction and in related topics, ranging from mechanistic studies and theoretical research, to very practical problems in chiral syntheses and products. Features contributions from global experts, including several chapters from Kenso Soai and expert colleagues Focuses on recent developments in the field of asymmetric autocatalysis and newly reported findings Explores the Soai reaction, new developments, and the light it sheds on homochirality in certain biomolecules
Dynamic Systems Biology Modeling and Simulation by Joseph DiStefano III Pdf
Dynamic Systems Biology Modeling and Simuation consolidates and unifies classical and contemporary multiscale methodologies for mathematical modeling and computer simulation of dynamic biological systems – from molecular/cellular, organ-system, on up to population levels. The book pedagogy is developed as a well-annotated, systematic tutorial – with clearly spelled-out and unified nomenclature – derived from the author’s own modeling efforts, publications and teaching over half a century. Ambiguities in some concepts and tools are clarified and others are rendered more accessible and practical. The latter include novel qualitative theory and methodologies for recognizing dynamical signatures in data using structural (multicompartmental and network) models and graph theory; and analyzing structural and measurement (data) models for quantification feasibility. The level is basic-to-intermediate, with much emphasis on biomodeling from real biodata, for use in real applications. Introductory coverage of core mathematical concepts such as linear and nonlinear differential and difference equations, Laplace transforms, linear algebra, probability, statistics and stochastics topics; PLUS ....... The pertinent biology, biochemistry, biophysics or pharmacology for modeling are provided, to support understanding the amalgam of “math modeling” with life sciences. Strong emphasis on quantifying as well as building and analyzing biomodels: includes methodology and computational tools for parameter identifiability and sensitivity analysis; parameter estimation from real data; model distinguishability and simplification; and practical bioexperiment design and optimization. Companion website provides solutions and program code for examples and exercises using Matlab, Simulink, VisSim, SimBiology, SAAMII, AMIGO, Copasi and SBML-coded models. A full set of PowerPoint slides are available from the author for teaching from his textbook. He uses them to teach a 10 week quarter upper division course at UCLA, which meets twice a week, so there are 20 lectures. They can easily be augmented or stretched for a 15 week semester course. Importantly, the slides are editable, so they can be readily adapted to a lecturer’s personal style and course content needs. The lectures are based on excerpts from 12 of the first 13 chapters of DSBMS. They are designed to highlight the key course material, as a study guide and structure for students following the full text content. The complete PowerPoint slide package (~25 MB) can be obtained by instructors (or prospective instructors) by emailing the author directly, at: joed@cs.ucla.edu
Mathematical Models of Chemical Reactions by Peter Erdi,Péter Érdi,Janos Toth,János Tóth,J. Tóth Pdf
Chemical kinetics may be considered as a prototype of nonlinear science, since the velocities of a reaction are generally nonlinear functions of the quantities of reactants. Although an actual chemical process is spatially extensive and involves very large numbers of constituent particles and a considerable number of intermediate transition compounds, the behavior--equilibria, periodicity, or chaos--may be described by the stoichiometric equations for a relatively small number of reactants. The macroscopic description of the kinetics can be deterministic, by a low-order system of nonlinear ordinary differential equations with polynomial right-hand sides, or stochastic, in terms of Markov jump processes. This volume surveys the mathematical models of chemical kinetics--their algebraic structure, mass action deterministic models, continuous time, discrete state stochastic models, and spatial effects mediated by diffusion. Further, the metalanguage of chemical kinetics is used to describe behavior in systems of interacting components, in neurochemistry, population biology, and ecology.
Numerical Methods and Applications by Ivan Georgiev,Maria Datcheva,Krassimir Georgiev,Geno Nikolov Pdf
This book constitutes the thoroughly refereed post-conference proceedings of the 10th International Conference on Numerical Methods and Applications, NMA 2022, held in Borovets, Bulgaria, in August 2022.The 30 revised regular papers presented were carefully reviewed and selected from 38 submissions for inclusion in this book. The papers are organized in the following topical sections: numerical search and optimization; problem-driven numerical method: motivation and application, numerical methods for fractional diffusion problems; orthogonal polynomials and numerical quadratures; and Monte Carlo and Quasi-Monte Carlo methods.