Author: Victor Bloomfield Publisher: Springer Science & Business Media ISBN: 1441900837 Category : Science Languages : en Pages : 325
Book Description
This book provides an introduction to two important aspects of modern bioch- istry, molecular biology, and biophysics: computer simulation and data analysis. My aim is to introduce the tools that will enable students to learn and use some f- damental methods to construct quantitative models of biological mechanisms, both deterministicandwithsomeelementsofrandomness;tolearnhowconceptsofpr- ability can help to understand important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data. The availability of very capable but inexpensive personal computers and software makes it possible to do such work at a much higher level, but in a much easier way, than ever before. TheExecutiveSummaryofthein?uential2003reportfromtheNationalAcademy of Sciences, “BIO 2010: Transforming Undergraduate Education for Future - search Biologists” [12], begins The interplay of the recombinant DNA, instrumentation, and digital revolutions has p- foundly transformed biological research. The con?uence of these three innovations has led to important discoveries, such as the mapping of the human genome. How biologists design, perform, and analyze experiments is changing swiftly. Biological concepts and models are becoming more quantitative, and biological research has become critically dependent on concepts and methods drawn from other scienti?c disciplines. The connections between the biological sciences and the physical sciences, mathematics, and computer science are rapidly becoming deeper and more extensive.
Author: Robert E. Keen Publisher: Wiley-Liss ISBN: Category : Science Languages : en Pages : 524
Book Description
Role of modeling and computer simulation in biology; Simple model equations; Analytical models based on differential equations; Analytical models based on stable states; Estimating model coefficients from experimental data; Planning and problems of programming; Numerical solution of rate equations; Models with multiple components; Kinetics of biochemical reactions; Models of homogeneous populations of organisms; Simple models of microbial growth; Population models based on age-specific events; Simulations of population genetics; Models of light and photosynthesis; Temperature and biological activity; Compartmental models of biogeochemical cycling; Diffusion models; Compartmental models in Physiology; Application of matrix methods to simulations; Physiological control systems; Probabilistic models; Monte Carlo modeling of simple stochastic processes; Modeling of sampling processes; Random walks and related stochastic processes; Markov chain simulations in biology; Supplementary models; Models of cellular function; Models of development and morphogenesis; Models of epidemics; Appendixes; Literature cited; Index.
Author: Luca Marchetti Publisher: Springer ISBN: 3319631136 Category : Computers Languages : en Pages : 245
Book Description
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.
Author: Richard J. Gaylord Publisher: ISBN: Category : Computers Languages : en Pages : 330
Book Description
The study of natural phenomena using computer simulation is a major new research tool in the physical, chemical, biological and social sciences. It is useful for studying simple systems, and it is essential for the study of complex systems. Using Mathematica, an integrated software environment for scientific programming, numerical analysis and visualization, this book describes computer simulations applicable to a wide range of phenomena.
Author: Russell Schwartz Publisher: MIT Press ISBN: 0262303396 Category : Science Languages : en Pages : 403
Book Description
A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.
Author: Joseph DiStefano III Publisher: Academic Press ISBN: 0124104932 Category : Science Languages : en Pages : 886
Book Description
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 - 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]
Author: W.F. van Gunsteren Publisher: Springer Science & Business Media ISBN: 9789072199256 Category : Science Languages : en Pages : 664
Book Description
This book is the third volume in this highly successful series. Since the first volume in 1989 and the second in 1993, many exciting developments have occurred in the development of simulation techniques and their application to key biological problems such as protein folding, protein structure prediction and structure-based design, and in how, by combining experimental and theoretical approaches, very large biological systems can be studied at the molecular level. This series attempts to capture that progress. Volume 3 includes contributions that highlight developments in methodology which enable longer and more realistic simulations (e.g. multiple time steps and variable reduction techniques), a study of force fields for proteins and new force field development, a novel approach to the description of molecular shape and the use of molecular shape descriptors, the study of condensed phase chemical reactions, the use of electrostatic techniques in the study of protonation, equilibria and flexible docking studies, structure refinement using experimental data (X-ray, NMR, neutron, infrared) and theoretical methods (solvation models, normal mode analysis, MD simulations, MC lattice dynamics, and knowledge-based potentials). There are several chapters that show progress in the development of methodologies for the study of folding processes, binding affinities, and the prediction of ligand-protein complexes. The chapters, contributed by experienced researchers, many of whom are leaders in their field of study, are organised to cover developments in: simulation methodology the treatment of electrostatics protein structure refinement the combined experimental and theoretical approaches to the study of very large biological systems applications and methodology involved in the study of protein folding applications and methodology associated with structure-based design.
Author: Nikolay V Dokholyan Publisher: Springer Science & Business Media ISBN: 1461421454 Category : Science Languages : en Pages : 360
Book Description
Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.
Author: Angela B. Shiflet Publisher: Princeton University Press ISBN: 140085055X Category : Computers Languages : en Pages : 857
Book Description
The essential introduction to computational science—now fully updated and expanded Computational science is an exciting new field at the intersection of the sciences, computer science, and mathematics because much scientific investigation now involves computing as well as theory and experiment. This textbook provides students with a versatile and accessible introduction to the subject. It assumes only a background in high school algebra, enables instructors to follow tailored pathways through the material, and is the only textbook of its kind designed specifically for an introductory course in the computational science and engineering curriculum. While the text itself is generic, an accompanying website offers tutorials and files in a variety of software packages. This fully updated and expanded edition features two new chapters on agent-based simulations and modeling with matrices, ten new project modules, and an additional module on diffusion. Besides increased treatment of high-performance computing and its applications, the book also includes additional quick review questions with answers, exercises, and individual and team projects. The only introductory textbook of its kind—now fully updated and expanded Features two new chapters on agent-based simulations and modeling with matrices Increased coverage of high-performance computing and its applications Includes additional modules, review questions, exercises, and projects An online instructor's manual with exercise answers, selected project solutions, and a test bank and solutions (available only to professors) An online illustration package is available to professors
Author: Johannes Lenhard Publisher: Oxford University Press ISBN: 0190873299 Category : Science Languages : en Pages : 273
Book Description
If all philosophy starts with wondering, then Calculated Surprises starts with wondering about how computers are changing the face and inner workings of science. In this book, Lenhard concentrates on the ways in which computers and simulation are transforming the established conception of mathematical modeling. His core thesis is that simulation modeling constitutes a new mode of mathematical modeling that rearranges and inverts key features of the established conception. Although most of these new key features--such as experimentation, exploration, or epistemic opacity--have their precursors, the new ways in which they are being combined is generating a distinctive style of scientific reasoning. Lenhard also documents how simulation is affecting fundamental concepts of solution, understanding, and validation. He feeds these transformations back into philosophy of science, thereby opening up new perspectives on longstanding oppositions. By combining historical investigations with practical aspects, Calculated Surprises is accessible for a broad audience of readers. Numerous case studies covering a wide range of simulation techniques are balanced with broad reflections on science and technology. Initially, what computers are good at is calculating with a speed and accuracy far beyond human capabilities. Lenhard goes further and investigates the emerging characteristics of computer-based modeling, showing how this simple observation is creating a number of surprising challenges for the methodology and epistemology of science. These calculated surprises will attract both philosophers and scientific practitioners who are interested in reflecting on recent developments in science and technology.
Author: Victor Bloomfield
Author: Robert E. Keen
Author: Luca Marchetti
Author: Richard J. Gaylord
Author: Russell Schwartz
Author: Joseph DiStefano III
Author: W.F. van Gunsteren
Author: Nikolay V Dokholyan
Author: Angela B. Shiflet
Author: Johannes Lenhard