Stochastic Models in Biology
Stochastic Models in Biology

Author: Narendra S. Goel

Publisher: Elsevier

Published: 2013-10-22

Total Pages: 282

ISBN-13: 1483278107

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Stochastic Models in Biology describes the usefulness of the theory of stochastic process in studying biological phenomena. The book describes analysis of biological systems and experiments though probabilistic models rather than deterministic methods. The text reviews the mathematical analyses for modeling different biological systems such as the random processes continuous in time and discrete in state space. The book also discusses population growth and extinction through Malthus' law and the work of MacArthur and Wilson. The text then explains the dynamics of a population of interacting species. The book also addresses population genetics under systematic evolutionary pressures known as deterministic equations and genetic changes in a finite population known as stochastic equations. The text then turns to stochastic modeling of biological systems at the molecular level, particularly the kinetics of biochemical reactions. The book also presents various useful equations such as the differential equation for generating functions for birth and death processes. The text can prove valuable for biochemists, cellular biologists, and researchers in the medical and chemical field who are tasked to perform data analysis.

Stochastic Modelling of Reaction–Diffusion Processes
Stochastic Modelling of Reaction–Diffusion Processes

Author: Radek Erban

Publisher: Cambridge University Press

Published: 2020-01-30

Total Pages: 322

ISBN-13: 1108572995

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This practical introduction to stochastic reaction-diffusion modelling is based on courses taught at the University of Oxford. The authors discuss the essence of mathematical methods which appear (under different names) in a number of interdisciplinary scientific fields bridging mathematics and computations with biology and chemistry. The book can be used both for self-study and as a supporting text for advanced undergraduate or beginning graduate-level courses in applied mathematics. New mathematical approaches are explained using simple examples of biological models, which range in size from simulations of small biomolecules to groups of animals. The book starts with stochastic modelling of chemical reactions, introducing stochastic simulation algorithms and mathematical methods for analysis of stochastic models. Different stochastic spatio-temporal models are then studied, including models of diffusion and stochastic reaction-diffusion modelling. The methods covered include molecular dynamics, Brownian dynamics, velocity jump processes and compartment-based (lattice-based) models.

Stochastic Modelling for Systems Biology
Stochastic Modelling for Systems Biology

Author: Darren J. Wilkinson

Publisher: CRC Press

Published: 2006-04-18

Total Pages: 296

ISBN-13: 9781584885405

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Although stochastic kinetic models are increasingly accepted as the best way to represent and simulate genetic and biochemical networks, most researchers in the field have limited knowledge of stochastic process theory. The stochastic processes formalism provides a beautiful, elegant, and coherent foundation for chemical kinetics and there is a wealth of associated theory every bit as powerful and elegant as that for conventional continuous deterministic models. The time is right for an introductory text written from this perspective. Stochastic Modelling for Systems Biology presents an accessible introduction to stochastic modelling using examples that are familiar to systems biology researchers. Focusing on computer simulation, the author examines the use of stochastic processes for modelling biological systems. He provides a comprehensive understanding of stochastic kinetic modelling of biological networks in the systems biology context. The text covers the latest simulation techniques and research material, such as parameter inference, and includes many examples and figures as well as software code in R for various applications. While emphasizing the necessary probabilistic and stochastic methods, the author takes a practical approach, rooting his theoretical development in discussions of the intended application. Written with self-study in mind, the book includes technical chapters that deal with the difficult problems of inference for stochastic kinetic models from experimental data. Providing enough background information to make the subject accessible to the non-specialist, the book integrates a fairly diverse literature into a single convenient and notationally consistent source.

An Introduction to Stochastic Modeling
An Introduction to Stochastic Modeling

Author: Howard M. Taylor

Publisher: Academic Press

Published: 2014-05-10

Total Pages: 410

ISBN-13: 1483269272

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An Introduction to Stochastic Modeling provides information pertinent to the standard concepts and methods of stochastic modeling. This book presents the rich diversity of applications of stochastic processes in the sciences. Organized into nine chapters, this book begins with an overview of diverse types of stochastic models, which predicts a set of possible outcomes weighed by their likelihoods or probabilities. This text then provides exercises in the applications of simple stochastic analysis to appropriate problems. Other chapters consider the study of general functions of independent, identically distributed, nonnegative random variables representing the successive intervals between renewals. This book discusses as well the numerous examples of Markov branching processes that arise naturally in various scientific disciplines. The final chapter deals with queueing models, which aid the design process by predicting system performance. This book is a valuable resource for students of engineering and management science. Engineers will also find this book useful.

Deterministic, Stochastic and Thermodynamic Modelling of some Interacting Species
Deterministic, Stochastic and Thermodynamic Modelling of some Interacting Species

Author: Guruprasad Samanta

Publisher: Springer Nature

Published: 2021-11-24

Total Pages: 188

ISBN-13: 9811663122

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This book presents the understanding of how the different forms of regulatory mechanisms, like birth and death, competition, consumption and the like, result in changes in the stability and dynamics of ecological systems. It deals with a profound and unique insight into the mathematical richness of basic ecological models. Organised into eight chapters, the book discusses the models of mathematical ecology, the dynamical models of single-species system in a polluted environment, the dynamical behaviour of different nonautonomous two species systems in a polluted environment, the influence of environmental noise in Gompertzian and logistic growth models, stability behaviour in randomly fluctuating versus deterministic environments of two interacting species, stochastic analysis of a demographic model of urbanization and stability behaviour of a social group by means of loop analysis, thermodynamic criteria of stability and stochastic criteria of stability. The book will be useful to the researchers and graduate students who wish to pursue research in mathematical ecology.

Deterministic Versus Stochastic Modelling in Biochemistry and Systems Biology
Deterministic Versus Stochastic Modelling in Biochemistry and Systems Biology

Author: Paola Lecca

Publisher: Elsevier

Published: 2013-04-09

Total Pages: 411

ISBN-13: 1908818212

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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

Stochastic Interacting Systems in Life and Social Sciences
Stochastic Interacting Systems in Life and Social Sciences

Author: Nicolas Lanchier

Publisher: Walter de Gruyter GmbH & Co KG

Published: 2024-07-01

Total Pages: 486

ISBN-13: 3110791889

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This volume provides an overview of two of the most important examples of interacting particle systems, the contact process, and the voter model, as well as their many variants introduced in the past 50 years. These stochastic processes are organized by domains of application (epidemiology, population dynamics, ecology, genetics, sociology, econophysics, game theory) along with a flavor of the mathematical techniques developed for their analysis.

Mathematical Modeling in Systems Biology
Mathematical Modeling in Systems Biology

Author: Brian P. Ingalls

Publisher: MIT Press

Published: 2022-06-07

Total Pages: 423

ISBN-13: 0262545829

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An introduction to the mathematical concepts and techniques needed for the construction and analysis of models in molecular systems biology. Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology. It is accessible to upper-level undergraduate or graduate students in life science or engineering who have some familiarity with calculus, and will be a useful reference for researchers at all levels. The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials. Chapters 3–8 end with optional sections that address more specialized modeling topics. Exercises, solvable with pen-and-paper calculations, appear throughout the text to encourage interaction with the mathematical techniques. More involved end-of-chapter problem sets require computational software. Appendixes provide a review of basic concepts of molecular biology, additional mathematical background material, and tutorials for two computational software packages (XPPAUT and MATLAB) that can be used for model simulation and analysis.

Stochastic Processes and Functional Analysis
Stochastic Processes and Functional Analysis

Author: Randall J. Swift

Publisher: American Mathematical Society

Published: 2021-11-22

Total Pages: 248

ISBN-13: 1470459825

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This volume contains the proceedings of the AMS Special Session on Celebrating M. M. Rao's Many Mathematical Contributions as he Turns 90 Years Old, held from November 9–10, 2019, at the University of California, Riverside, California. The articles show the effectiveness of abstract analysis for solving fundamental problems of stochastic theory, specifically the use of functional analytic methods for elucidating stochastic processes and their applications. The volume also includes a biography of M. M. Rao and the list of his publications.