Stochastic Processes In Cell Biology

Author : Paul C. Bressloff
Publisher : Springer Nature
Page : 773 pages
File Size : 42,9 Mb
Release : 2022-01-04
Category : Mathematics
ISBN : 9783030725150

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Stochastic Processes in Cell Biology by Paul C. Bressloff Pdf

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.

Author : Paul C. Bressloff
Publisher : Unknown
Page : 700 pages
File Size : 42,6 Mb
Release : 2014-09-30
Category : Electronic
ISBN : 3319084895

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Stochastic Processes in Cell Biology by Paul C. Bressloff Pdf

Author : Paul C. Bressloff
Publisher : Springer Nature
Page : 724 pages
File Size : 42,9 Mb
Release : 2022-01-10
Category : Mathematics
ISBN : 9783030725198

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Stochastic Processes in Cell Biology by Paul C. Bressloff Pdf

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.

Author : David Holcman
Publisher : Springer
Page : 377 pages
File Size : 46,6 Mb
Release : 2017-10-04
Category : Mathematics
ISBN : 9783319626277

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Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology by David Holcman Pdf

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.

Author : Mukhtar Ullah,Olaf Wolkenhauer
Publisher : Springer Science & Business Media
Page : 290 pages
File Size : 40,5 Mb
Release : 2011-07-15
Category : Mathematics
ISBN : 9781461404781

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Stochastic Approaches for Systems Biology by Mukhtar Ullah,Olaf Wolkenhauer Pdf

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.

Author : Jan A. Freund,Thorsten Pöschel
Publisher : Springer
Page : 512 pages
File Size : 52,7 Mb
Release : 2008-01-11
Category : Science
ISBN : 9783540453963

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Stochastic Processes in Physics, Chemistry, and Biology by Jan A. Freund,Thorsten Pöschel Pdf

The theory of stochastic processes originally grew out of efforts to describe Brownian motion quantitatively. Today it provides a huge arsenal of methods suitable for analyzing the influence of noise on a wide range of systems. The credit for acquiring all the deep insights and powerful methods is due ma- ly to a handful of physicists and mathematicians: Einstein, Smoluchowski, Langevin, Wiener, Stratonovich, etc. Hence it is no surprise that until - cently the bulk of basic and applied stochastic research was devoted to purely mathematical and physical questions. However, in the last decade we have witnessed an enormous growth of results achieved in other sciences - especially chemistry and biology - based on applying methods of stochastic processes. One reason for this stochastics boom may be that the realization that noise plays a constructive rather than the expected deteriorating role has spread to communities beyond physics. Besides their aesthetic appeal these noise-induced, noise-supported or noise-enhanced effects sometimes offer an explanation for so far open pr- lems (information transmission in the nervous system and information p- cessing in the brain, processes at the cell level, enzymatic reactions, etc.). They may also pave the way to novel technological applications (noise-- hanced reaction rates, noise-induced transport and separation on the na- scale, etc.). Key words to be mentioned in this context are stochastic r- onance, Brownian motors or ratchets, and noise-supported phenomena in excitable systems.

Author : Tautu Petre
Publisher : #N/A
Page : 456 pages
File Size : 54,9 Mb
Release : 1990-12-05
Category : Electronic
ISBN : 9789814611923

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Stochastic Modelling In Biology: Relevant Mathematical Concepts And Recent Applications by Tautu Petre Pdf

These proceedings focus on future prospects as well as on the present status in some important areas of applied probability and mathematical biology. Some papers have educational intentions regarding the mathematical modelling of special biological situations. The workshop was the third one in Heidelberg dealing with stochastic modelling in biology, e.g., cell biology, embryology, oncology, epidemiology and genetics.

Author : David Holcman,Zeev Schuss
Publisher : Unknown
Page : 128 pages
File Size : 55,5 Mb
Release : 2015
Category : Electronic
ISBN : 1493931040

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Stochastic Narrow Escape in Molecular and Cellular Biology by David Holcman,Zeev Schuss Pdf

This book covers recent developments in the non-standard asymptotics of the mathematical narrow escape problem in stochastic theory, as well as applications of the narrow escape problem in cell biology. The first part of the book concentrates on mathematical methods, including advanced asymptotic methods in partial equations, and is aimed primarily at applied mathematicians and theoretical physicists who are interested in biological applications. The second part of the book is intended for computational biologists, theoretical chemists, biochemists, biophysicists, and physiologists. It includes a summary of output formulas from the mathematical portion of the book and concentrates on their applications in modeling specific problems in theoretical molecular and cellular biology. Critical biological processes, such as synaptic plasticity and transmission, activation of genes by transcription factors, or double-strained DNA break repair, are controlled by diffusion in structures that have both large and small spatial scales. These may be small binding sites inside or on the surface of the cell, or narrow passages between subcellular compartments. The great disparity in spatial scales is the key to controlling cell function by structure. This volume reports recent progress on resolving analytical and numerical difficulties in extracting properties from experimental data, biophysical models, and from Brownian dynamics simulations of diffusion in multi-scale structures.

Author : Christopher P. Fall,Eric S. Marland,John M. Wagner,John J. Tyson
Publisher : Springer Science & Business Media
Page : 468 pages
File Size : 50,5 Mb
Release : 2007-06-04
Category : Science
ISBN : 9780387224596

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Computational Cell Biology by Christopher P. Fall,Eric S. Marland,John M. Wagner,John J. Tyson Pdf

This textbook provides an introduction to dynamic modeling in molecular cell biology, taking a computational and intuitive approach. Detailed illustrations, examples, and exercises are included throughout the text. Appendices containing mathematical and computational techniques are provided as a reference tool.

Author : Volkhard Helms
Publisher : John Wiley & Sons
Page : 458 pages
File Size : 41,7 Mb
Release : 2019-04-29
Category : Medical
ISBN : 9783527333585

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Principles of Computational Cell Biology by Volkhard Helms Pdf

Computational cell biology courses are increasingly obligatory for biology students around the world but of course also a must for mathematics and informatics students specializing in bioinformatics. This book, now in its second edition is geared towards both audiences. The author, Volkhard Helms, has, in addition to extensive teaching experience, a strong background in biology and informatics and knows exactly what the key points are in making the book accessible for students while still conveying in depth knowledge of the subject.About 50% of new content has been added for the new edition. Much more room is now given to statistical methods, and several new chapters address protein-DNA interactions, epigenetic modifications, and microRNAs.

Author : Oliver Ibe
Publisher : Newnes
Page : 514 pages
File Size : 55,5 Mb
Release : 2013-05-22
Category : Mathematics
ISBN : 9780124078390

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Markov Processes for Stochastic Modeling by Oliver Ibe Pdf

Markov processes are processes that have limited memory. In particular, their dependence on the past is only through the previous state. They are used to model the behavior of many systems including communications systems, transportation networks, image segmentation and analysis, biological systems and DNA sequence analysis, random atomic motion and diffusion in physics, social mobility, population studies, epidemiology, animal and insect migration, queueing systems, resource management, dams, financial engineering, actuarial science, and decision systems. Covering a wide range of areas of application of Markov processes, this second edition is revised to highlight the most important aspects as well as the most recent trends and applications of Markov processes. The author spent over 16 years in the industry before returning to academia, and he has applied many of the principles covered in this book in multiple research projects. Therefore, this is an applications-oriented book that also includes enough theory to provide a solid ground in the subject for the reader. Presents both the theory and applications of the different aspects of Markov processes Includes numerous solved examples as well as detailed diagrams that make it easier to understand the principle being presented Discusses different applications of hidden Markov models, such as DNA sequence analysis and speech analysis.

Author : Marek Kimmel,David E. Axelrod
Publisher : Springer Science & Business Media
Page : 242 pages
File Size : 50,9 Mb
Release : 2006-05-26
Category : Mathematics
ISBN : 9780387216393

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Branching Processes in Biology by Marek Kimmel,David E. Axelrod Pdf

This book introduces biological examples of Branching Processes from molecular and cellular biology as well as from the fields of human evolution and medicine and discusses them in the context of the relevant mathematics. It provides a useful introduction to how the modeling can be done and for what types of problems branching processes can be used.

Author : Mark M. Meerschaert,Alla Sikorskii
Publisher : Walter de Gruyter GmbH & Co KG
Page : 337 pages
File Size : 53,6 Mb
Release : 2019-10-21
Category : Mathematics
ISBN : 9783110560244

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Stochastic Models for Fractional Calculus by Mark M. Meerschaert,Alla Sikorskii Pdf

Fractional calculus is a rapidly growing field of research, at the interface between probability, differential equations, and mathematical physics. It is used to model anomalous diffusion, in which a cloud of particles spreads in a different manner than traditional diffusion. This monograph develops the basic theory of fractional calculus and anomalous diffusion, from the point of view of probability. In this book, we will see how fractional calculus and anomalous diffusion can be understood at a deep and intuitive level, using ideas from probability. It covers basic limit theorems for random variables and random vectors with heavy tails. This includes regular variation, triangular arrays, infinitely divisible laws, random walks, and stochastic process convergence in the Skorokhod topology. The basic ideas of fractional calculus and anomalous diffusion are closely connected with heavy tail limit theorems. Heavy tails are applied in finance, insurance, physics, geophysics, cell biology, ecology, medicine, and computer engineering. The goal of this book is to prepare graduate students in probability for research in the area of fractional calculus, anomalous diffusion, and heavy tails. Many interesting problems in this area remain open. This book will guide the motivated reader to understand the essential background needed to read and unerstand current research papers, and to gain the insights and techniques needed to begin making their own contributions to this rapidly growing field.

Author : Michael Kraus,Bernhard Wolf
Publisher : CRC Press
Page : 250 pages
File Size : 55,8 Mb
Release : 1995-07-31
Category : Science
ISBN : 0849347726

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Structured Biological Modelling by Michael Kraus,Bernhard Wolf Pdf

Structured Biological Modelling presents a straightforward introduction for computer-aided analysis, mathematical modelling, and simulation of cell biological systems. This unique guide brings together the physiological, structural, molecular biological, and theoretical aspects of the signal transduction network that regulates growth and proliferation in normal and tumor cells. It provides comprehensive survey of functional and theoretical features of intracellular signal processing and introduces the concept of cellular self-organization. Exemplified by oscillatory calcium waves, strategies for the design of computer experiments are presented that can assist or even substitute for time-consuming biological experiments. The presented minimal model for proliferation-associated signal transduction clearly shows the alterations of the cellular signal network involved in neoplastic growth. This book will be useful to cell and molecular biologists, oncologists, physiologists, theoretical biologists, computer scientists, and all other researchers and students studying functional aspects of cellular signaling.

Author : Jinzhi Lei
Publisher : Springer Nature
Page : 308 pages
File Size : 50,5 Mb
Release : 2021-05-13
Category : Mathematics
ISBN : 9783030730338

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Systems Biology by Jinzhi Lei Pdf

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.