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Molecular Dynamics

Molecular Dynamics Author Ben Leimkuhler
ISBN-10 9783319163758
Release 2015-05-18
Pages 443
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This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications. Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method.

The Art of Molecular Dynamics Simulation

The Art of Molecular Dynamics Simulation Author D. C. Rapaport
ISBN-10 0521825687
Release 2004-04-01
Pages 549
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The extremely powerful technique of molecular dynamics simulation involves solving the classical many-body problem in contexts relevant to the study of matter at the atomistic level. Since there is no alternative approach capable of handling this extremely broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research. This book, first published in 2004, is a blend of tutorial and recipe collection, providing both an introduction to the subject for beginners and a reference manual for the more experienced practitioner. It is organized as a series of case studies that take the reader through each of the steps from formulating the problem, developing the necessary software, and then using the programs to make actual measurements. The second edition of the book includes a substantial amount of new material as well as completely rewritten software.

Molecular Modeling and Simulation

Molecular Modeling and Simulation Author Tamar Schlick
ISBN-10 9780387224640
Release 2013-04-18
Pages 635
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Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

An Introduction to Computational Stochastic PDEs

An Introduction to Computational Stochastic PDEs Author Gabriel J. Lord
ISBN-10 9780521899901
Release 2014-08-11
Pages 520
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This book gives a comprehensive introduction to numerical methods and analysis of stochastic processes, random fields and stochastic differential equations, and offers graduate students and researchers powerful tools for understanding uncertainty quantification for risk analysis. Coverage includes traditional stochastic ODEs with white noise forcing, strong and weak approximation, and the multi-level Monte Carlo method. Later chapters apply the theory of random fields to the numerical solution of elliptic PDEs with correlated random data, discuss the Monte Carlo method, and introduce stochastic Galerkin finite-element methods. Finally, stochastic parabolic PDEs are developed. Assuming little previous exposure to probability and statistics, theory is developed in tandem with state-of-the-art computational methods through worked examples, exercises, theorems and proofs. The set of MATLAB codes included (and downloadable) allows readers to perform computations themselves and solve the test problems discussed. Practical examples are drawn from finance, mathematical biology, neuroscience, fluid flow modelling and materials science.

Numerical Simulation in Molecular Dynamics

Numerical Simulation in Molecular Dynamics Author Michael Griebel
ISBN-10 9783540680956
Release 2007-08-16
Pages 476
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This book details the necessary numerical methods, the theoretical background and foundations and the techniques involved in creating computer particle models, including linked-cell method, SPME-method, tree codes, amd multipol technique. It illustrates modeling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. The text offers step-by-step explanations of numerical simulation, providing illustrative code examples. With the description of the algorithms and the presentation of the results of various simulations from fields such as material science, nanotechnology, biochemistry and astrophysics, the reader of this book will learn how to write programs capable of running successful experiments for molecular dynamics.

Numerical Methods for Unconstrained Optimization and Nonlinear Equations

Numerical Methods for Unconstrained Optimization and Nonlinear Equations Author J. E. Dennis, Jr.
ISBN-10 1611971209
Release 1996-12-01
Pages 378
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This book has become the standard for a complete, state-of-the-art description of the methods for unconstrained optimization and systems of nonlinear equations. Originally published in 1983, it provides information needed to understand both the theory and the practice of these methods and provides pseudocode for the problems. The algorithms covered are all based on Newton's method or "quasi-Newton" methods, and the heart of the book is the material on computational methods for multidimensional unconstrained optimization and nonlinear equation problems. The republication of this book by SIAM is driven by a continuing demand for specific and sound advice on how to solve real problems. The level of presentation is consistent throughout, with a good mix of examples and theory, making it a valuable text at both the graduate and undergraduate level. It has been praised as excellent for courses with approximately the same name as the book title and would also be useful as a supplemental text for a nonlinear programming or a numerical analysis course. Many exercises are provided to illustrate and develop the ideas in the text. A large appendix provides a mechanism for class projects and a reference for readers who want the details of the algorithms. Practitioners may use this book for self-study and reference. For complete understanding, readers should have a background in calculus and linear algebra. The book does contain background material in multivariable calculus and numerical linear algebra.

Computational Cell Biology

Computational Cell Biology Author Christopher P. Fall
ISBN-10 9780387224596
Release 2007-06-04
Pages 468
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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.

Stochastic Processes in Cell Biology

Stochastic Processes in Cell Biology Author Paul C. Bressloff
ISBN-10 9783319084886
Release 2014-08-22
Pages 679
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This book develops the theory of continuous and discrete stochastic processes within the context of cell biology. A wide range of biological topics are covered including normal and anomalous diffusion in complex cellular environments, stochastic ion channels and excitable systems, stochastic calcium signaling, molecular motors, intracellular transport, signal transduction, bacterial chemotaxis, robustness in gene networks, genetic switches and oscillators, cell polarization, polymerization, cellular length control, and branching processes. The book also provides a pedagogical introduction to the theory of stochastic process – Fokker Planck equations, stochastic differential equations, master equations and jump Markov processes, diffusion approximations and the system size expansion, first passage time problems, stochastic hybrid systems, reaction-diffusion equations, exclusion processes, WKB methods, martingales and branching processes, stochastic calculus, and numerical methods. This text is primarily aimed at graduate students and researchers working in mathematical biology and applied mathematicians interested in stochastic modeling. Applied probabilists and theoretical physicists should also find it of interest. It assumes no prior background in statistical physics and introduces concepts in stochastic 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.

Models of Calcium Signalling

Models of Calcium Signalling Author Geneviève Dupont
ISBN-10 9783319296470
Release 2016-06-07
Pages 436
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This book discusses the ways in which mathematical, computational, and modelling methods can be used to help understand the dynamics of intracellular calcium. The concentration of free intracellular calcium is vital for controlling a wide range of cellular processes, and is thus of great physiological importance. However, because of the complex ways in which the calcium concentration varies, it is also of great mathematical interest.This book presents the general modelling theory as well as a large number of specific case examples, to show how mathematical modelling can interact with experimental approaches, in an interdisciplinary and multifaceted approach to the study of an important physiological control mechanism. Geneviève Dupont is FNRS Research Director at the Unit of Theoretical Chronobiology of the Université Libre de Bruxelles; Martin Falcke is head of the Mathematical Cell Physiology group at the Max Delbrück Center for Molecular Medicine, Berlin; Vivien Kirk is an Associate Professor in the Department of Mathematics at the University of Auckland, New Zealand; James Sneyd is a Professor in the Department of Mathematics at The University of Auckland, New Zealand.

Dynamics of Cancer

Dynamics of Cancer Author Dominik Wodarz
ISBN-10 9789814566384
Release 2014-04-24
Pages 532
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The book aims to provide an introduction to mathematical models that describe the dynamics of tumor growth and the evolution of tumor cells. It can be used as a textbook for advanced undergraduate or graduate courses, and also serves as a reference book for researchers. The book has a strong evolutionary component and reflects the viewpoint that cancer can be understood rationally through a combination of mathematical and biological tools. It can be used both by mathematicians and biologists. Mathematically, the book starts with relatively simple ordinary differential equation models, and subsequently explores more complex stochastic and spatial models. Biologically, the book starts with explorations of the basic dynamics of tumor growth, including competitive interactions among cells, and subsequently moves on to the evolutionary dynamics of cancer cells, including scenarios of cancer initiation, progression, and treatment. The book finishes with a discussion of advanced topics, which describe how some of the mathematical concepts can be used to gain insights into a variety of questions, such as epigenetics, telomeres, gene therapy, and social interactions of cancer cells. Contents:Teaching GuideCancer and Somatic EvolutionMathematical Modeling of TumorigenesisBasic Growth Dynamics and Deterministic Models:Single Species GrowthTwo-Species Competition DynamicsCompetition Between Genetically Stable and Unstable CellsChromosomal Instability and Tumor GrowthAngiogenesis Inhibitors, Promoters, and Spatial GrowthEvolutionary Dynamics and Stochastic Models:Evolutionary Dynamics of Tumor Initiation Through Oncogenes: The Gain-of-Function ModelEvolutionary Dynamics of Tumor Initiation Through Tumor-Suppressor Genes: The Loss-of-Function Model and Stochastic TunnelingMicrosatellite and Chromosomal Instability in Sporadic and Familial Colorectal CancersEvolutionary Dynamics in Hierarchical PopulationsSpatial Evolutionary Dynamics of Tumor InitiationComplex Tumor Dynamics in SpaceStochastic Modeling of Cellular Growth, Treatment, and Resistance GenerationEvolutionary Dynamics of Drug Resistance in Chronic Myeloid LeukemiaAdvanced Topics:Evolutionary Dynamics of Stem-Cell Driven Tumor GrowthTumor Growth Kinetics and Disease ProgressionEpigenetic Changes and the Rate of DNA MethylationTelomeres and Cancer ProtectionGene Therapy and Oncolytic Virus TherapyImmune Responses, Tumor Growth, and TherapiesTowards Higher Complexities: Social Interactions Readership: Researchers in mathematical biology, mathematical modeling, biology, mathematical oncology. Keywords:Mathematical Oncology;Dynamics;Evolution;Evolutionary Dynamics;Cancer;Mathematical Models;Somatic Evolution;TeachingKey Features:Both a reference book for the topic, and provides material for undergraduate and graduate coursesTries to bridge the divide between mathematicians and biologists, which is also reflected in the backgrounds of the two authorsShows how mathematical concepts can be translated into experimentally and clinically useful insightsRooted in evolutionary biology, the book handles this very complex phenomenon in an intuitive and mathematically elegant wayContains problems and research projects for each topic10 pages of figures in color

Semigroups of Operators Theory and Applications

Semigroups of Operators  Theory and Applications Author Jacek Banasiak
ISBN-10 9783319121451
Release 2014-11-20
Pages 337
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Many results, both from semi group theory itself and from the applied sciences, are phrased in discipline-specific languages and hence are hardly known to a broader community. This volume contains a selection of lectures presented at a conference that was organised as a forum for all mathematicians using semi group theory to learn what is happening outside their own field of research. The collection will help to establish a number of new links between various sub-disciplines of semigroup theory, stochastic processes, differential equations and the applied fields. The theory of semigroups of operators is a well-developed branch of functional analysis. Its foundations were laid at the beginning of the 20th century, while the fundamental generation theorem of Hille and Yosida dates back to the forties. The theory was, from the very beginning, designed as a universal language for partial differential equations and stochastic processes, but at the same time it started to live as an independent branch of operator theory. Nowadays, it still has the same distinctive flavour: it develops rapidly by posing new ‘internal’ questions and in answering them, discovering new methods that can be used in applications. On the other hand, it is influenced by questions from PDEs and stochastic processes as well as from applied sciences such as mathematical biology and optimal control, and thus it continually gathers a new momentum. Researchers and postgraduate students working in operator theory, partial differential equations, probability and stochastic processes, analytical methods in biology and other natural sciences, optimization and optimal control will find this volume useful.

Molecular Modelling Principles And Applications 2 E

Molecular Modelling  Principles And Applications  2 E Author Leach
ISBN-10 8131728609
Release 2009-09-01
Pages 768
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Molecular Modelling Principles And Applications 2 E has been writing in one form or another for most of life. You can find so many inspiration from Molecular Modelling Principles And Applications 2 E also informative, and entertaining. Click DOWNLOAD or Read Online button to get full Molecular Modelling Principles And Applications 2 E book for free.

Algorithms in Structural Molecular Biology

Algorithms in Structural Molecular Biology Author Bruce R. Donald
ISBN-10 9780262297844
Release 2011-06-01
Pages 464
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Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules.Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility.The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.

Computational Systems Biology

Computational Systems Biology Author Andres Kriete
ISBN-10 9780124059382
Release 2013-11-26
Pages 548
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This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.

Dynamic Systems Biology Modeling and Simulation

Dynamic Systems Biology Modeling and Simulation Author Joseph DiStefano III
ISBN-10 9780124104938
Release 2015-01-10
Pages 884
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Dynamic Systems Biology Modeling and Simuation consolidates and unifies classical and contemporary multiscale methodologies for mathematical modeling and computer simulation of dynamic biological systems – from molecular/cellular, organ-system, on up to population levels. The book pedagogy is developed as a well-annotated, systematic tutorial – with clearly spelled-out and unified nomenclature – derived from the author’s own modeling efforts, publications and teaching over half a century. Ambiguities in some concepts and tools are clarified and others are rendered more accessible and practical. The latter include novel qualitative theory and methodologies for recognizing dynamical signatures in data using structural (multicompartmental and network) models and graph theory; and analyzing structural and measurement (data) models for quantification feasibility. The level is basic-to-intermediate, with much emphasis on biomodeling from real biodata, for use in real applications. Introductory coverage of core mathematical concepts such as linear and nonlinear differential and difference equations, Laplace transforms, linear algebra, probability, statistics and stochastics topics; PLUS ....... The pertinent biology, biochemistry, biophysics or pharmacology for modeling are provided, to support understanding the amalgam of “math modeling” with life sciences. Strong emphasis on quantifying as well as building and analyzing biomodels: includes methodology and computational tools for parameter identifiability and sensitivity analysis; parameter estimation from real data; model distinguishability and simplification; and practical bioexperiment design and optimization. Companion website provides solutions and program code for examples and exercises using Matlab, Simulink, VisSim, SimBiology, SAAMII, AMIGO, Copasi and SBML-coded models. A full set of PowerPoint slides are available from the author for teaching from his textbook. He uses them to teach a 10 week quarter upper division course at UCLA, which meets twice a week, so there are 20 lectures. They can easily be augmented or stretched for a 15 week semester course. Importantly, the slides are editable, so they can be readily adapted to a lecturer’s personal style and course content needs. The lectures are based on excerpts from 12 of the first 13 chapters of DSBMS. They are designed to highlight the key course material, as a study guide and structure for students following the full text content. The complete PowerPoint slide package (~25 MB) can be obtained by instructors (or prospective instructors) by emailing the author directly, at: [email protected]

Introduction to Turbulent Dynamical Systems in Complex Systems

Introduction to Turbulent Dynamical Systems in Complex Systems Author Andrew Majda
ISBN-10 9783319322179
Release 2016-09-14
Pages 91
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This volume is a research expository article on the applied mathematics of turbulent dynamical systems through the paradigm of modern applied mathematics. It involves the blending of rigorous mathematical theory, qualitative and quantitative modeling, and novel numerical procedures driven by the goal of understanding physical phenomena which are of central importance to the field. The contents cover general framework, concrete examples, and instructive qualitative models. Accessible open problems are mentioned throughout. Topics covered include: · Geophysical flows with rotation, topography, deterministic and random forcing · New statistical energy principles for general turbulent dynamical systems, with applications · Linear statistical response theory combined with information theory to cope with model errors · Reduced low order models · Recent mathematical strategies for online data assimilation of turbulent dynamical systems as well as rigorous results for finite ensemble Kalman filters The volume will appeal to graduate students and researchers working mathematics, physics and engineering and particularly those in the climate, atmospheric and ocean sciences interested in turbulent dynamical as well as other complex systems.

Monte Carlo Strategies in Scientific Computing

Monte Carlo Strategies in Scientific Computing Author Jun S. Liu
ISBN-10 9780387763712
Release 2013-11-11
Pages 344
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This book provides a self-contained and up-to-date treatment of the Monte Carlo method and develops a common framework under which various Monte Carlo techniques can be "standardized" and compared. Given the interdisciplinary nature of the topics and a moderate prerequisite for the reader, this book should be of interest to a broad audience of quantitative researchers such as computational biologists, computer scientists, econometricians, engineers, probabilists, and statisticians. It can also be used as a textbook for a graduate-level course on Monte Carlo methods.