Author: Alexander N. Gorban
Publisher: Springer Science & Business Media
ISBN: 3540358889
Category : Science
Languages : en
Pages : 554
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Book Description
Model reduction and coarse-graining are important in many areas of science and engineering. How does a system with many degrees of freedom become one with fewer? How can a reversible micro-description be adapted to the dissipative macroscopic model? These crucial questions, as well as many other related problems, are discussed in this book. All contributions are by experts whose specialities span a wide range of fields within science and engineering.
Author: Stephan Dahlke
Publisher: Springer
ISBN: 3319081594
Category : Mathematics
Languages : en
Pages : 446
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Book Description
In April 2007, the Deutsche Forschungsgemeinschaft (DFG) approved the Priority Program 1324 “Mathematical Methods for Extracting Quantifiable Information from Complex Systems.” This volume presents a comprehensive overview of the most important results obtained over the course of the program. Mathematical models of complex systems provide the foundation for further technological developments in science, engineering and computational finance. Motivated by the trend toward steadily increasing computer power, ever more realistic models have been developed in recent years. These models have also become increasingly complex, and their numerical treatment poses serious challenges. Recent developments in mathematics suggest that, in the long run, much more powerful numerical solution strategies could be derived if the interconnections between the different fields of research were systematically exploited at a conceptual level. Accordingly, a deeper understanding of the mathematical foundations as well as the development of new and efficient numerical algorithms were among the main goals of this Priority Program. The treatment of high-dimensional systems is clearly one of the most challenging tasks in applied mathematics today. Since the problem of high-dimensionality appears in many fields of application, the above-mentioned synergy and cross-fertilization effects were expected to make a great impact. To be truly successful, the following issues had to be kept in mind: theoretical research and practical applications had to be developed hand in hand; moreover, it has proven necessary to combine different fields of mathematics, such as numerical analysis and computational stochastics. To keep the whole program sufficiently focused, we concentrated on specific but related fields of application that share common characteristics and as such, they allowed us to use closely related approaches.
Author: David Holcman
Publisher: Springer
ISBN: 3319626272
Category : Mathematics
Languages : en
Pages : 377
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Book Description
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: Peter Benner
Publisher: SIAM
ISBN: 161197481X
Category : Science
Languages : en
Pages : 421
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Book Description
Many physical, chemical, biomedical, and technical processes can be described by partial differential equations or dynamical systems. In spite of increasing computational capacities, many problems are of such high complexity that they are solvable only with severe simplifications, and the design of efficient numerical schemes remains a central research challenge. This book presents a tutorial introduction to recent developments in mathematical methods for model reduction and approximation of complex systems. Model Reduction and Approximation: Theory and Algorithms contains three parts that cover (I) sampling-based methods, such as the reduced basis method and proper orthogonal decomposition, (II) approximation of high-dimensional problems by low-rank tensor techniques, and (III) system-theoretic methods, such as balanced truncation, interpolatory methods, and the Loewner framework. It is tutorial in nature, giving an accessible introduction to state-of-the-art model reduction and approximation methods. It also covers a wide range of methods drawn from typically distinct communities (sampling based, tensor based, system-theoretic).?? This book is intended for researchers interested in model reduction and approximation, particularly graduate students and young researchers.
Author: Radek Erban
Publisher: Cambridge University Press
ISBN: 1108572995
Category : Mathematics
Languages : en
Pages : 322
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Book Description
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.
Author: Joel Keizer
Publisher: Springer Science & Business Media
ISBN: 1461210542
Category : Science
Languages : en
Pages : 517
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Book Description
The structure of the theory ofthermodynamics has changed enormously since its inception in the middle of the nineteenth century. Shortly after Thomson and Clausius enunciated their versions of the Second Law, Clausius, Maxwell, and Boltzmann began actively pursuing the molecular basis of thermo dynamics, work that culminated in the Boltzmann equation and the theory of transport processes in dilute gases. Much later, Onsager undertook the elucidation of the symmetry oftransport coefficients and, thereby, established himself as the father of the theory of nonequilibrium thermodynamics. Com bining the statistical ideas of Gibbs and Langevin with the phenomenological transport equations, Onsager and others went on to develop a consistent statistical theory of irreversible processes. The power of that theory is in its ability to relate measurable quantities, such as transport coefficients and thermodynamic derivatives, to the results of experimental measurements. As powerful as that theory is, it is linear and limited in validity to a neighborhood of equilibrium. In recent years it has been possible to extend the statistical theory of nonequilibrium processes to include nonlinear effects. The modern theory, as expounded in this book, is applicable to a wide variety of systems both close to and far from equilibrium. The theory is based on the notion of elementary molecular processes, which manifest themselves as random changes in the extensive variables characterizing a system. The theory has a hierarchical character and, thus, can be applied at various levels of molecular detail.
Author: Stefanie Winkelmann
Publisher: Springer Nature
ISBN: 3030623874
Category : Mathematics
Languages : en
Pages : 284
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Book Description
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.
Author: Ivanov, Ivan V.
Publisher: IGI Global
ISBN: 1522503544
Category : Medical
Languages : en
Pages : 437
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Book Description
While technological advancements have been critical in allowing researchers to obtain more and better quality data about cellular processes and signals, the design and practical application of computational models of genomic regulation continues to be a challenge. Emerging Research in the Analysis and Modeling of Gene Regulatory Networks presents a compilation of recent and emerging research topics addressing the design and use of technology in the study and simulation of genomic regulation. Exploring both theoretical and practical topics, this publication is an essential reference source for students, professionals, and researchers working in the fields of genomics, molecular biology, bioinformatics, and drug development.
Author: Donald Allan McQuarrie
Publisher:
ISBN:
Category : Chemical kinetics
Languages : en
Pages : 82
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Book Description
Author: Brian Munsky
Publisher: MIT Press
ISBN: 0262038080
Category : Science
Languages : en
Pages : 729
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Book Description
An introduction to the quantitative modeling of biological processes, presenting modeling approaches, methodology, practical algorithms, software tools, and examples of current research. The quantitative modeling of biological processes promises to expand biological research from a science of observation and discovery to one of rigorous prediction and quantitative analysis. The rapidly growing field of quantitative biology seeks to use biology's emerging technological and computational capabilities to model biological processes. This textbook offers an introduction to the theory, methods, and tools of quantitative biology. The book first introduces the foundations of biological modeling, focusing on some of the most widely used formalisms. It then presents essential methodology for model-guided analyses of biological data, covering such methods as network reconstruction, uncertainty quantification, and experimental design; practical algorithms and software packages for modeling biological systems; and specific examples of current quantitative biology research and related specialized methods. Most chapters offer problems, progressing from simple to complex, that test the reader's mastery of such key techniques as deterministic and stochastic simulations and data analysis. Many chapters include snippets of code that can be used to recreate analyses and generate figures related to the text. Examples are presented in the three popular computing languages: Matlab, R, and Python. A variety of online resources supplement the the text. The editors are long-time organizers of the Annual q-bio Summer School, which was founded in 2007. Through the school, the editors have helped to train more than 400 visiting students in Los Alamos, NM, Santa Fe, NM, San Diego, CA, Albuquerque, NM, and Fort Collins, CO. This book is inspired by the school's curricula, and most of the contributors have participated in the school as students, lecturers, or both. Contributors John H. Abel, Roberto Bertolusso, Daniela Besozzi, Michael L. Blinov, Clive G. Bowsher, Fiona A. Chandra, Paolo Cazzaniga, Bryan C. Daniels, Bernie J. Daigle, Jr., Maciej Dobrzynski, Jonathan P. Doye, Brian Drawert, Sean Fancer, Gareth W. Fearnley, Dirk Fey, Zachary Fox, Ramon Grima, Andreas Hellander, Stefan Hellander, David Hofmann, Damian Hernandez, William S. Hlavacek, Jianjun Huang, Tomasz Jetka, Dongya Jia, Mohit Kumar Jolly, Boris N. Kholodenko, Markek Kimmel, Michał Komorowski, Ganhui Lan, Heeseob Lee, Herbert Levine, Leslie M Loew, Jason G. Lomnitz, Ard A. Louis, Grant Lythe, Carmen Molina-París, Ion I. Moraru, Andrew Mugler, Brian Munsky, Joe Natale, Ilya Nemenman, Karol Nienałtowski, Marco S. Nobile, Maria Nowicka, Sarah Olson, Alan S. Perelson, Linda R. Petzold, Sreenivasan Ponnambalam, Arya Pourzanjani, Ruy M. Ribeiro, William Raymond, William Raymond, Herbert M. Sauro, Michael A. Savageau, Abhyudai Singh, James C. Schaff, Boris M. Slepchenko, Thomas R. Sokolowski, Petr Šulc, Andrea Tangherloni, Pieter Rein ten Wolde, Philipp Thomas, Karen Tkach Tuzman, Lev S. Tsimring, Dan Vasilescu, Margaritis Voliotis, Lisa Weber
