Computational Modeling And Simulations Of Biomolecular Systems
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Computational Modeling And Simulations Of Biomolecular Systems
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Author : Benoit Roux
language : en
Publisher: World Scientific
Release Date : 2021-08-23
Computational Modeling And Simulations Of Biomolecular Systems written by Benoit Roux and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-08-23 with Computers categories.
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).
Computational Modeling And Simulations Of Biomolecular Systems
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Author : Benoît Roux
language : en
Publisher:
Release Date : 2021
Computational Modeling And Simulations Of Biomolecular Systems written by Benoît Roux and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with Electronic books categories.
Computer Simulation Of Biomolecular Systems
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Author : W.F. van Gunsteren
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-11-27
Computer Simulation Of Biomolecular Systems written by W.F. van Gunsteren and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-11-27 with Technology & Engineering categories.
The third volume in the series on Computer Simulation of Biomolecular Systems continues with the format introduced in the first volume [1] and elaborated in the second volume [2]. The primary emphasis is on the methodological aspects of simulations, although there are some chapters that present the results obtained for specific systems of biological interest. The focus of this volume has changed somewhat since there are several chapters devoted to structure-based ligand design, which had only a single chapter in the second volume. It seems useful to set the stage for this volume by quoting from my preface to Volume 2 [2]. "The long-range 'goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last fifty years great progress has been made in applying the equations representing the underlying physical laws to chemical problems involv ing the structures and reactions of small molecules. Corresponding studies of mesoscopic systems have been undertaken much more recently. Molecular dynamics simulations, which are the primary focus of this volume, represent the most important theoretical approach to macromolecules of biological interest." ...
Computational Modeling Of Biological Systems
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Author : Nikolay V Dokholyan
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-02-12
Computational Modeling Of Biological Systems written by Nikolay V Dokholyan and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-02-12 with Science categories.
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
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Author : Alliant Computer Systems Corporation
language : en
Publisher: Springer
Release Date : 1989-02-28
Computer Simulation Of Biomolecular Systems written by Alliant Computer Systems Corporation and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 1989-02-28 with Computers categories.
Innovations In Biomolecular Modeling And Simulations
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Author : Tamar Schlick
language : en
Publisher: Royal Society of Chemistry
Release Date : 2012-05-24
Innovations In Biomolecular Modeling And Simulations written by Tamar Schlick and has been published by Royal Society of Chemistry this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-05-24 with Science categories.
The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.
Biological Modeling And Simulation
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Author : Russell Schwartz
language : en
Publisher: MIT Press
Release Date : 2008-07-25
Biological Modeling And Simulation written by Russell Schwartz and has been published by MIT Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-07-25 with Science categories.
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 Simulation Of Biomolecular Systems
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Author : W.F. van Gunsteren
language : en
Publisher: Springer
Release Date : 1994-01-31
Computer Simulation Of Biomolecular Systems written by W.F. van Gunsteren and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 1994-01-31 with Computers categories.
The long-range goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last fifty years great progress has been made in applying the equations representing the underlying physical laws to chemical problems involving the structures and reactions of small molecules. Corresponding studies of mesoscopic systems have been undertaken much more recently. Molecular dynamics simulations, which are the primary focus of this volume, represent the most important theoretical approach to macromolecules of biological interest. Now that molecular dynamics of macromolecules is a flourishing field, serious questions have to be asked concerning what more can be done with the methodology. What is the present and the future role of molecular dynamics in the development of our knowledge of macromolecules of biological interest? How does the methodology need to be improved to make it applicable to important problems? The present volume is concerned with providing some answers with its primary focus on the methodology and its recent developments.
Innovations In Biomolecular Modeling And Simulations
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Author : Tamar Schlick
language : en
Publisher: Royal Society of Chemistry
Release Date : 2012
Innovations In Biomolecular Modeling And Simulations written by Tamar Schlick and has been published by Royal Society of Chemistry this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with Biomolecules categories.
This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts.
Coarse Grained Modeling Of Biomolecules
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Author : Garegin A. Papoian
language : en
Publisher: CRC Press
Release Date : 2017-10-30
Coarse Grained Modeling Of Biomolecules written by Garegin A. Papoian and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-10-30 with Science categories.
"The chapters in this book survey the progress in simulating biomolecular dynamics.... The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling. Introduces coarse-grained models of proteins and nucleic acids. Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics Gives the physical foundations of coarse-graining Demonstrates use of models for large-scale assemblies in modern studies Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.