Computer Simulation In Biology

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Computer Simulation and Data Analysis in Molecular Biology and Biophysics

Author : Victor Bloomfield
Publisher : Springer Science & Business Media
ISBN 13 : 1441900837
Total Pages : 325 pages
Book Rating : 4.4/5 (419 download)

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Book Synopsis Computer Simulation and Data Analysis in Molecular Biology and Biophysics by : Victor Bloomfield

Download or read book Computer Simulation and Data Analysis in Molecular Biology and Biophysics written by Victor Bloomfield and published by Springer Science & Business Media. This book was released on 2009-06-05 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Computer Simulation in Biology

Author : Robert E. Keen
Publisher : Wiley-Liss
ISBN 13 :
Total Pages : 524 pages
Book Rating : 4.E/5 ( download)

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Book Synopsis Computer Simulation in Biology by : Robert E. Keen

Download or read book Computer Simulation in Biology written by Robert E. Keen and published by Wiley-Liss. This book was released on 1992 with total page 524 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Simulation Algorithms for Computational Systems Biology

Author : Luca Marchetti
Publisher : Springer
ISBN 13 : 3319631136
Total Pages : 245 pages
Book Rating : 4.3/5 (196 download)

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Book Synopsis Simulation Algorithms for Computational Systems Biology by : Luca Marchetti

Download or read book Simulation Algorithms for Computational Systems Biology written by Luca Marchetti and published by Springer. This book was released on 2017-09-27 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Biological Modeling and Simulation

Author : Russell Schwartz
Publisher : MIT Press
ISBN 13 : 0262303396
Total Pages : 403 pages
Book Rating : 4.2/5 (623 download)

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Book Synopsis Biological Modeling and Simulation by : Russell Schwartz

Download or read book Biological Modeling and Simulation written by Russell Schwartz and published by MIT Press. This book was released on 2008-07-25 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Computer Simulations with Mathematica

Author : Richard J. Gaylord
Publisher :
ISBN 13 :
Total Pages : 330 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Computer Simulations with Mathematica by : Richard J. Gaylord

Download or read book Computer Simulations with Mathematica written by Richard J. Gaylord and published by . This book was released on 1995 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Computational Modeling of Biological Systems

Author : Nikolay V Dokholyan
Publisher : Springer Science & Business Media
ISBN 13 : 1461421454
Total Pages : 360 pages
Book Rating : 4.4/5 (614 download)

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Book Synopsis Computational Modeling of Biological Systems by : Nikolay V Dokholyan

Download or read book Computational Modeling of Biological Systems written by Nikolay V Dokholyan and published by Springer Science & Business Media. This book was released on 2012-02-12 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Computer Simulation of Biomolecular Systems

Author : W.F. van Gunsteren
Publisher : Springer Science & Business Media
ISBN 13 : 9789072199256
Total Pages : 664 pages
Book Rating : 4.1/5 (992 download)

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Book Synopsis Computer Simulation of Biomolecular Systems by : W.F. van Gunsteren

Download or read book Computer Simulation of Biomolecular Systems written by W.F. van Gunsteren and published by Springer Science & Business Media. This book was released on 1997-11-30 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Introduction to Computational Science

Author : Angela B. Shiflet
Publisher : Princeton University Press
ISBN 13 : 140085055X
Total Pages : 857 pages
Book Rating : 4.4/5 (8 download)

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Book Synopsis Introduction to Computational Science by : Angela B. Shiflet

Download or read book Introduction to Computational Science written by Angela B. Shiflet and published by Princeton University Press. This book was released on 2014-03-30 with total page 857 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Calculated Surprises

Author : Johannes Lenhard
Publisher : Oxford University Press
ISBN 13 : 0190873299
Total Pages : 273 pages
Book Rating : 4.1/5 (98 download)

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Book Synopsis Calculated Surprises by : Johannes Lenhard

Download or read book Calculated Surprises written by Johannes Lenhard and published by Oxford University Press. This book was released on 2019-02-18 with total page 273 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Computer Simulation in Human Population Studies

Author : Bennett Dyke
Publisher : Academic Press
ISBN 13 : 1483264556
Total Pages : 541 pages
Book Rating : 4.4/5 (832 download)

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Book Synopsis Computer Simulation in Human Population Studies by : Bennett Dyke

Download or read book Computer Simulation in Human Population Studies written by Bennett Dyke and published by Academic Press. This book was released on 2014-05-12 with total page 541 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer Simulation in Human Population Studies contains the proceedings of a conference held at Pennsylvania State University on June 12-14, 1972, under the sponsorship of the Social Science Research Council. The conference provided a forum for discussing the application of computer simulation techniques to human population studies and organized topics around four themes: anthropology and social systems; genetics and adaptive systems; demography; and simulation methodology. Comprised of 23 chapters, this volume begins with an analysis of two tests of computer microsimulation: the effect of an incest taboo on population viability, and the effect of age differences between spouses on the skewing of their consanguineal relationships. The reader is then introduced to computer simulation of incest prohibition and clan proscription rules in closed, finite population; an empirical perspective on simulation models of human population; and models applicable to geographic variation in humans. Subsequent chapters deal with the role of co-adapted sets in the process of adaptation; simulation of human reproduction; and the mathematics of population simulation models. This book will be of interest to anthropologists, geneticists, biologists, computer scientists, mathematicians, and social scientists.

Modeling in Systems Biology

Author : Ina Koch
Publisher : Springer Science & Business Media
ISBN 13 : 1849964742
Total Pages : 378 pages
Book Rating : 4.8/5 (499 download)

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Book Synopsis Modeling in Systems Biology by : Ina Koch

Download or read book Modeling in Systems Biology written by Ina Koch and published by Springer Science & Business Media. This book was released on 2010-10-21 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt: The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification. Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin. This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.

Computational Systems Biology

Author : Andres Kriete
Publisher : Academic Press
ISBN 13 : 0124059384
Total Pages : 549 pages
Book Rating : 4.1/5 (24 download)

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Book Synopsis Computational Systems Biology by : Andres Kriete

Download or read book Computational Systems Biology written by Andres Kriete and published by Academic Press. This book was released on 2013-11-26 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Would-Be Worlds

Author : John Casti
Publisher : Perseus Books Group
ISBN 13 :
Total Pages : 272 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Would-Be Worlds by : John Casti

Download or read book Would-Be Worlds written by John Casti and published by Perseus Books Group. This book was released on 1997 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: There is a new breed of computer simulations, known as 'artificial worlds' or 'would-be worlds', that allows scientists to create artificial versions of real-life phenomena inside their computers. Casti explores how these are being used.

Modeling and Simulation in Medicine and the Life Sciences

Author : Frank C. Hoppensteadt
Publisher : Springer Science & Business Media
ISBN 13 : 0387215719
Total Pages : 362 pages
Book Rating : 4.3/5 (872 download)

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Book Synopsis Modeling and Simulation in Medicine and the Life Sciences by : Frank C. Hoppensteadt

Download or read book Modeling and Simulation in Medicine and the Life Sciences written by Frank C. Hoppensteadt and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: The result of lectures given by the authors at New York University, the University of Utah, and Michigan State University, the material is written for students who have had only one term of calculus, but it contains material that can be used in modeling courses in applied mathematics at all levels through early graduate courses. Numerous exercises are given as well as solutions to selected exercises, so as to lead readers to discover interesting extensions of that material. Throughout, illustrations depict physiological processes, population biology phenomena, corresponding models, and the results of computer simulations. Topics covered range from population phenomena to demographics, genetics, epidemics and dispersal; in physiological processes, including the circulation, gas exchange in the lungs, control of cell volume, the renal counter-current multiplier mechanism, and muscle mechanics; to mechanisms of neural control. Each chapter is graded in difficulty, so a reading of the first parts of each provides an elementary introduction to the processes and their models.

Modeling Dynamic Biological Systems

Author : Bruce Hannon
Publisher : Springer Science & Business Media
ISBN 13 : 1461206510
Total Pages : 399 pages
Book Rating : 4.4/5 (612 download)

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Book Synopsis Modeling Dynamic Biological Systems by : Bruce Hannon

Download or read book Modeling Dynamic Biological Systems written by Bruce Hannon and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: Models help us understand the dynamics of real-world processes by using the computer to mimic the actual forces that are known or assumed to result in a system's behavior. This book does not require a substantial background in mathematics or computer science.

Computational Modeling And Simulations Of Biomolecular Systems

Author : Benoit Roux
Publisher : World Scientific
ISBN 13 : 9811232776
Total Pages : 209 pages
Book Rating : 4.8/5 (112 download)

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Book Synopsis Computational Modeling And Simulations Of Biomolecular Systems by : Benoit Roux

Download or read book Computational Modeling And Simulations Of Biomolecular Systems written by Benoit Roux and published by World Scientific. This book was released on 2021-08-23 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook originated from the course 'Simulation, Modeling, and Computations in Biophysics' that I have taught at the University of Chicago since 2011. The students typically came from a wide range of backgrounds, including biology, physics, chemistry, biochemistry, and mathematics, and the course was intentionally adapted for senior undergraduate students and graduate students. This is not a highly technical book dedicated to specialists. The objective is to provide a broad survey from the physical description of a complex molecular system at the most fundamental level, to the type of phenomenological models commonly used to represent the function of large biological macromolecular machines.The key conceptual elements serving as building blocks in the formulation of different levels of approximations are introduced along the way, aiming to clarify as much as possible how they are interrelated. The only assumption is a basic familiarity with simple mathematics (calculus and integrals, ordinary differential equations, matrix linear algebra, and Fourier-Laplace transforms).

Learning Science Through Computer Games and Simulations

Author : National Research Council
Publisher : National Academies Press
ISBN 13 : 0309212669
Total Pages : 174 pages
Book Rating : 4.3/5 (92 download)

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Book Synopsis Learning Science Through Computer Games and Simulations by : National Research Council

Download or read book Learning Science Through Computer Games and Simulations written by National Research Council and published by National Academies Press. This book was released on 2011-04-12 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt: At a time when scientific and technological competence is vital to the nation's future, the weak performance of U.S. students in science reflects the uneven quality of current science education. Although young children come to school with innate curiosity and intuitive ideas about the world around them, science classes rarely tap this potential. Many experts have called for a new approach to science education, based on recent and ongoing research on teaching and learning. In this approach, simulations and games could play a significant role by addressing many goals and mechanisms for learning science: the motivation to learn science, conceptual understanding, science process skills, understanding of the nature of science, scientific discourse and argumentation, and identification with science and science learning. To explore this potential, Learning Science: Computer Games, Simulations, and Education, reviews the available research on learning science through interaction with digital simulations and games. It considers the potential of digital games and simulations to contribute to learning science in schools, in informal out-of-school settings, and everyday life. The book also identifies the areas in which more research and research-based development is needed to fully capitalize on this potential. Learning Science will guide academic researchers; developers, publishers, and entrepreneurs from the digital simulation and gaming community; and education practitioners and policy makers toward the formation of research and development partnerships that will facilitate rich intellectual collaboration. Industry, government agencies and foundations will play a significant role through start-up and ongoing support to ensure that digital games and simulations will not only excite and entertain, but also motivate and educate.