Stochastic Dynamics In Computational Biology
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Stochastic Dynamics For Systems Biology
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Author : Christian Mazza
language : en
Publisher: CRC Press
Release Date : 2016-04-19
Stochastic Dynamics For Systems Biology written by Christian Mazza and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-04-19 with Mathematics categories.
Stochastic Dynamics for Systems Biology is one of the first books to provide a systematic study of the many stochastic models used in systems biology. The book shows how the mathematical models are used as technical tools for simulating biological processes and how the models lead to conceptual insights on the functioning of the cellular processing
Stochastic Dynamics In Computational Biology
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Author : Stefanie Winkelmann
language : en
Publisher: Springer Nature
Release Date : 2021-01-04
Stochastic Dynamics In Computational Biology written by Stefanie Winkelmann and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-01-04 with Mathematics categories.
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.
Stochastic Modelling For Systems Biology Second Edition
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Author : Darren J. Wilkinson
language : en
Publisher: CRC Press
Release Date : 2011-11-09
Stochastic Modelling For Systems Biology Second Edition written by Darren J. Wilkinson and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-11-09 with Mathematics categories.
Since the first edition of Stochastic Modelling for Systems Biology, there have been many interesting developments in the use of "likelihood-free" methods of Bayesian inference for complex stochastic models. Re-written to reflect this modern perspective, this second edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. Keeping with the spirit of the first edition, all of the new theory is presented in a very informal and intuitive manner, keeping the text as accessible as possible to the widest possible readership. New in the Second Edition All examples have been updated to Systems Biology Markup Language Level 3 All code relating to simulation, analysis, and inference for stochastic kinetic models has been re-written and re-structured in a more modular way An ancillary website provides links, resources, errata, and up-to-date information on installation and use of the associated R package More background material on the theory of Markov processes and stochastic differential equations, providing more substance for mathematically inclined readers Discussion of some of the more advanced concepts relating to stochastic kinetic models, such as random time change representations, Kolmogorov equations, Fokker-Planck equations and the linear noise approximation Simple modelling of "extrinsic" and "intrinsic" noise An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional mathematical detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.
Stochastic Modelling For Systems Biology Third Edition
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Author : Darren J. Wilkinson
language : en
Publisher: CRC Press
Release Date : 2018-12-07
Stochastic Modelling For Systems Biology Third Edition written by Darren J. Wilkinson and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-12-07 with Mathematics categories.
Since the first edition of Stochastic Modelling for Systems Biology, there have been many interesting developments in the use of "likelihood-free" methods of Bayesian inference for complex stochastic models. Having been thoroughly updated to reflect this, this third edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. New methods and applications are included in the book, and the use of R for practical illustration of the algorithms has been greatly extended. There is a brand new chapter on spatially extended systems, and the statistical inference chapter has also been extended with new methods, including approximate Bayesian computation (ABC). Stochastic Modelling for Systems Biology, Third Edition is now supplemented by an additional software library, written in Scala, described in a new appendix to the book. New in the Third Edition New chapter on spatially extended systems, covering the spatial Gillespie algorithm for reaction diffusion master equation models in 1- and 2-d, along with fast approximations based on the spatial chemical Langevin equation Significantly expanded chapter on inference for stochastic kinetic models from data, covering ABC, including ABC-SMC Updated R package, including code relating to all of the new material New R package for parsing SBML models into simulatable stochastic Petri net models New open-source software library, written in Scala, replicating most of the functionality of the R packages in a fast, compiled, strongly typed, functional language Keeping with the spirit of earlier editions, all of the new theory is presented in a very informal and intuitive manner, keeping the text as accessible as possible to the widest possible readership. An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.
Stochastic Approaches For Systems Biology
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Author : Mukhtar Ullah
language : en
Publisher: Springer Science & Business Media
Release Date : 2011-07-12
Stochastic Approaches For Systems Biology written by Mukhtar Ullah and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-07-12 with Mathematics categories.
This textbook focuses on stochastic analysis in systems biology containing both the theory and application. While the authors provide a review of probability and random variables, subsequent notions of biochemical reaction systems and the relevant concepts of probability theory are introduced side by side. This leads to an intuitive and easy-to-follow presentation of stochastic framework for modeling subcellular biochemical systems. In particular, the authors make an effort to show how the notion of propensity, the chemical master equation and the stochastic simulation algorithm arise as consequences of the Markov property. The text contains many illustrations, examples and exercises to illustrate the ideas and methods that are introduced. Matlab code is also provided where appropriate. Additionally, the cell cycle is introduced as a more complex case study. Senior undergraduate and graduate students in mathematics and physics as well as researchers working in the area of systems biology, bioinformatics and related areas will find this text useful.
Deterministic Versus Stochastic Modelling In Biochemistry And Systems Biology
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Author : Paola Lecca
language : en
Publisher: Elsevier
Release Date : 2013-04-09
Deterministic Versus Stochastic Modelling In Biochemistry And Systems Biology written by Paola Lecca and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-04-09 with Mathematics categories.
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 Processes Multiscale Modeling And Numerical Methods For Computational Cellular Biology
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Author : David Holcman
language : en
Publisher: Springer
Release Date : 2017-10-04
Stochastic Processes Multiscale Modeling And Numerical Methods For Computational Cellular Biology written by David Holcman and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-10-04 with Mathematics categories.
This book focuses on the modeling and mathematical analysis of stochastic dynamical systems along with their simulations. The collected chapters will review fundamental and current topics and approaches to dynamical systems in cellular biology. This text aims to develop improved mathematical and computational methods with which to study biological processes. At the scale of a single cell, stochasticity becomes important due to low copy numbers of biological molecules, such as mRNA and proteins that take part in biochemical reactions driving cellular processes. When trying to describe such biological processes, the traditional deterministic models are often inadequate, precisely because of these low copy numbers. This book presents stochastic models, which are necessary to account for small particle numbers and extrinsic noise sources. The complexity of these models depend upon whether the biochemical reactions are diffusion-limited or reaction-limited. In the former case, one needs to adopt the framework of stochastic reaction-diffusion models, while in the latter, one can describe the processes by adopting the framework of Markov jump processes and stochastic differential equations. Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology will appeal to graduate students and researchers in the fields of applied mathematics, biophysics, and cellular biology.
Stochastic Chemical Reaction Systems In Biology
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Author : Hong Qian
language : en
Publisher: Springer Nature
Release Date : 2021-10-18
Stochastic Chemical Reaction Systems In Biology written by Hong Qian and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-10-18 with Mathematics categories.
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 Of Reacting Biomolecules
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Author : Werner Ebeling
language : en
Publisher: World Scientific
Release Date : 2003-01-29
Stochastic Dynamics Of Reacting Biomolecules written by Werner Ebeling and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003-01-29 with Science categories.
This is a book about the physical processes in reacting complex molecules, particularly biomolecules. In the past decade scientists from different fields such as medicine, biology, chemistry and physics have collected a huge amount of data about the structure, dynamics and functioning of biomolecules. Great progress has been achieved in exploring the structure of complex molecules. However, there is still a lack of understanding of the dynamics and functioning of biological macromolecules. In particular this refers to enzymes, which are the basic molecular machines working in living systems. This book contributes to the exploration of the physical mechanisms of these processes, focusing on critical aspects such as the role of nonlinear excitations and of stochastic effects. An extensive range of original results has been obtained in the last few years by the authors, and these results are presented together with a comprehensive survey of the state of the art in the field. Contents:Introduction to the Reaction Theory and Cluster Dynamics of Enzymes (W Ebeling, A Netrebko & Yu Romanovsky)Tools of Stochastic Dynamics (L Schimansky-Geier & P Talkner)Motion of Test Particles in a 2-D Potential Landscape (O A Chichigina, A V Netrebko & N V Netrebko)Microscopic Simulations of Activation and Dissociation (W Ebeling, V Yu Podlipchuk, M G Sapeshinsky & A A Valuev)Excitations on Rings of Molecules (A Chetverikov, W Ebeling, M Jenssen & Yu Romanovsky)Fermi Resonance and Kramers Problem in 2-D Force Field (S V Kroo, A V Netrebko, Yu M Romanovsky & L Schimansky-Geier)Molecular Scissors. Cluster Model of Acetylcholinesterase (A Yu Chikishev, S V Kroo, A V Netrebko, N V Netrebko & Yu Romanovsky)Dynamics of Proton Transfer in the Active Site of Chymotrypsin (A Yu Chikishev, B A Grishanin & E V Shuvalova)On the Damping of Cluster Oscillations in Protein Molecules (A Yu Chikishev, A V Netrebko & Yu M Romanovsky)Protein Dynamics and New Approaches to the Molecular Mechanisms of Protein Functioning (K V Shaitan) Readership: Researchers and graduate students in physics, biophysics, molecular biology and the life sciences; experts on nonlinear dynamics and the stochastic process in molecular systems and biomolecules. Keywords:Stochastic Dynamics;Reacting Complex Molecules;Biomolecules;Enzymatic Reactions;Molecular Dynamics;Nonlinear Excitations;Resonances
Simulation Algorithms For Computational Systems Biology
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Author : Luca Marchetti
language : en
Publisher: Springer
Release Date : 2017-09-27
Simulation Algorithms For Computational Systems Biology written by Luca Marchetti and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-09-27 with Computers categories.
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.