Stochastic Dynamics For Systems 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.
This 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 system. Examples cover the phage lambda genetic switch, eukaryotic gene expression, noise propagation in gene networks, and more. Most of the text should be accessible to scientists with basic knowledge in calculus and probability theory.
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.
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 Dynamics Of Reacting Biomolecules
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Author : Werner Ebeling
language : en
Publisher: World Scientific
Release Date : 2002
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 2002 with Mathematics 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.
Stochastic Models In Biology
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Author : Narendra S. Goel
language : en
Publisher: Elsevier
Release Date : 2013-10-22
Stochastic Models In Biology written by Narendra S. Goel and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-10-22 with Science categories.
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 Dynamics Of Complex Systems From Glasses To Evolution
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Author : Henrik Jeldtoft Jensen
language : en
Publisher: World Scientific Publishing Company
Release Date : 2013-02-20
Stochastic Dynamics Of Complex Systems From Glasses To Evolution written by Henrik Jeldtoft Jensen and has been published by World Scientific Publishing Company this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-02-20 with Science categories.
Dynamical evolution over long time scales is a prominent feature of all the systems we intuitively think of as complex — for example, ecosystems, the brain or the economy. In physics, the term ageing is used for this type of slow change, occurring over time scales much longer than the patience, or indeed the lifetime, of the observer. The main focus of this book is on the stochastic processes which cause ageing, and the surprising fact that the ageing dynamics of systems which are very different at the microscopic level can be treated in similar ways.The first part of this book provides the necessary mathematical and computational tools and the second part describes the intuition needed to deal with these systems. Some of the first few chapters have been covered in several other books, but the emphasis and selection of the topics reflect both the authors' interests and the overall theme of the book. The second part contains an introduction to the scientific literature and deals in some detail with the description of complex phenomena of a physical and biological nature, for example, disordered magnetic materials, superconductors and glasses, models of co-evolution in ecosystems and even of ant behaviour. These heterogeneous topics are all dealt with in detail using similar analytical techniques.This book emphasizes the unity of complex dynamics and provides the tools needed to treat a large number of complex systems of current interest. The ideas and the approach to complex dynamics it presents have not appeared in book form until now./a
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.
Recent Development In Stochastic Dynamics And Stochastic Analysis
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Author : Jinqiao Duan
language : en
Publisher: World Scientific
Release Date : 2010
Recent Development In Stochastic Dynamics And Stochastic Analysis written by Jinqiao Duan and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with Mathematics categories.
1. Hyperbolic equations with random boundary conditions / Zdzisław Brzeźniak and Szymon Peszat -- 2. Decoherent information of quantum operations / Xuelian Cao, Nan Li and Shunlong Luo -- 3. Stabilization of evolution equations by noise / Tomás Caraballo and Peter E. Kloeden -- 4. Stochastic quantification of missing mechanisms in dynamical systems / Baohua Chen and Jinqiao Duan -- 5. Banach space-valued functionals of white noise / Yin Chen and Caishi Wang -- 6. Hurst index estimation for self-similar processes with long-memory / Alexandra Chronopoulou and Frederi G. Viens -- 7. Modeling colored noise by fractional Brownian motion / Jinqiao Duan, Chujin Li and Xiangjun Wang -- 8. A sufficient condition for non-explosion for a class of stochastic partial differential equations / Hongbo Fu, Daomin Cao and Jinqiao Duan -- 9. The influence of transaction costs on optimal control for an insurance company with a new value function / Lin He, Zongxia Liang and Fei Xing -- 10. Limit theorems for p-variations of solutions of SDEs driven by additive stable Lévy noise and model selection for paleo-climatic data / Claudia Hein, Peter Imkeller and Ilya Pavlyukevich -- 11. Class II semi-subgroups of the infinite dimensional rotation group and associated Lie algebra / Takeyuki Hida and Si Si -- 12. Stopping Weyl processes / Robin L. Hudson -- 13. Karhunen-Loéve expansion for stochastic convolution of cylindrical fractional Brownian motions / Zongxia Liang -- 14. Stein's method meets Malliavin calculus : a short survey with new estimates / Ivan Nourdin and Giovanni Peccati -- 15. On stochastic integrals with respect to an infinite number of Poisson point process and its applications / Guanglin Rang, Qing Li and Sheng You -- 16. Lévy white noise, elliptic SPDEs and Euclidean random fields / Jiang-Lun Wu -- 17. A short presentation of Choquet integral / Jia-An Yan
Stochastic Processes In Cell Biology
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Author : Paul C. Bressloff
language : en
Publisher: Springer Nature
Release Date : 2022-01-04
Stochastic Processes In Cell Biology written by Paul C. Bressloff and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-01-04 with Mathematics categories.
This book develops the theory of continuous and discrete stochastic processes within the context of cell biology. In the second edition the material has been significantly expanded, particularly within the context of nonequilibrium and self-organizing systems. Given the amount of additional material, the book has been divided into two volumes, with volume I mainly covering molecular processes and volume II focusing on cellular processes. A wide range of biological topics are covered in the new edition, including stochastic ion channels and excitable systems, molecular motors, stochastic gene networks, genetic switches and oscillators, epigenetics, normal and anomalous diffusion in complex cellular environments, stochastically-gated diffusion, active intracellular transport, signal transduction, cell sensing, bacterial chemotaxis, intracellular pattern formation, cell polarization, cell mechanics, biological polymers and membranes, nuclear structure and dynamics, biological condensates, molecular aggregation and nucleation, cellular length control, cell mitosis, cell motility, cell adhesion, cytoneme-based morphogenesis, bacterial growth, and quorum sensing. The book also provides a pedagogical introduction to the theory of stochastic and nonequilibrium processes – Fokker Planck equations, stochastic differential equations, stochastic calculus, master equations and jump Markov processes, birth-death processes, Poisson processes, first passage time problems, stochastic hybrid systems, queuing and renewal theory, narrow capture and escape, extreme statistics, search processes and stochastic resetting, exclusion processes, WKB methods, large deviation theory, path integrals, martingales and branching processes, numerical methods, linear response theory, phase separation, fluctuation-dissipation theorems, age-structured models, and statistical field theory. This text is primarily aimed at graduate students and researchers working in mathematical biology, statistical and biological physicists, and applied mathematicians interested in stochastic modeling. Applied probabilists should also find it of interest. It provides significant background material in applied mathematics and statistical physics, and introduces concepts in stochastic and nonequilibrium processes via motivating biological applications. The book is highly illustrated and contains a large number of examples and exercises that further develop the models and ideas in the body of the text. It is based on a course that the author has taught at the University of Utah for many years.
Systems Biology
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Author : Jinzhi Lei
language : en
Publisher: Springer Nature
Release Date : 2021-05-13
Systems Biology written by Jinzhi Lei and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-05-13 with Mathematics categories.
This book discusses the mathematical simulation of biological systems, with a focus on the modeling of gene expression, gene regulatory networks and stem cell regeneration. The diffusion of morphogens is addressed by introducing various reaction-diffusion equations based on different hypotheses concerning the process of morphogen gradient formation. The robustness of steady-state gradients is also covered through boundary value problems. The introduction gives an overview of the relevant biological concepts (cells, DNA, organism development) and provides the requisite mathematical preliminaries on continuous dynamics and stochastic modeling. A basic understanding of calculus is assumed. The techniques described in this book encompass a wide range of mechanisms, from molecular behavior to population dynamics, and the inclusion of recent developments in the literature together with first-hand results make it an ideal reference for both new students and experienced researchers in the field of systems biology and applied mathematics.