New Algorithms for Macromolecular Simulation
New Algorithms for Macromolecular Simulation

Author: Benedict Leimkuhler

Publisher: Springer Science & Business Media

Published: 2006-03-22

Total Pages: 364

ISBN-13: 3540316183

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Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.

Computational Methods for Macromolecules: Challenges and Applications
Computational Methods for Macromolecules: Challenges and Applications

Author: Tamar Schlick

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 504

ISBN-13: 3642560806

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This special volume collects invited articles by participants of the Third International Workshop on Methods for Macromolecular Modeling, Courant Institute of Mathematical Sciences, Oct. 12-14, 2000. Leading developers of methods for biomolecular simulations review advances in Monte Carlo and molecular dynamics methods, free energy computational methods, fast electrostatics (particle-mesh Ewald and fast multipole methods), mathematics, and molecular neurobiology, nucleic acid simulations, enzyme reactions, and other essential applications in biomolecular simulations. A Perspectives article by the editors assesses the directions and impact of macromolecular modeling research, including genomics and proteomics. These reviews and original papers by applied mathematicians, theoretical chemists, biomedical researchers, and physicists are of interest to interdisciplinary research students, developers and users of biomolecular methods in academia and industry.

Computational Molecular Dynamics: Challenges, Methods, Ideas
Computational Molecular Dynamics: Challenges, Methods, Ideas

Author: Peter Deuflhard

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 500

ISBN-13: 3642583601

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On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics. The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.

Understanding Molecular Simulation
Understanding Molecular Simulation

Author: Daan Frenkel

Publisher: Elsevier

Published: 2023-07-13

Total Pages: 868

ISBN-13: 0323913180

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Understanding Molecular Simulation explains molecular simulation from a chemical-physics and statistical-mechanics perspective. It highlights how physical concepts are used to develop better algorithms and expand the range of applicability of simulations. Understanding Molecular Simulation is equally relevant for those who develop new code and those who use existing packages. Both groups are continuously confronted with the question of which computational technique best suits a given application. Understanding Molecular Simulation provides readers with the foundational knowledge they need to learn about, select and apply the most appropriate of these tools to their own work. The implementation of simulation methods is illustrated in pseudocodes, and their practical use is shown via case studies presented throughout the text. Since the second edition’s publication, the simulation world has expanded significantly: existing techniques have continued to develop, and new ones have emerged, opening up novel application areas. This new edition aims to describe these new developments without becoming exhaustive; examples are included that highlight current uses, and several new examples have been added to illustrate recent applications. Examples, case studies, questions, and downloadable algorithms are also included to support learning. No prior knowledge of computer simulation is assumed. Fully updated guide to both the current state and latest developments in the field of molecular simulation, including added and expanded information on such topics as molecular dynamics and statistical assessment of simulation results Gives a rounded overview by showing fundamental background information in practice via new examples in a range of key fields Provides online access to new data, algorithms and tutorial slides to support and encourage practice and learning

A New Parallel Method for Molecular Dynamics Simulation of Macromolecular Systems
A New Parallel Method for Molecular Dynamics Simulation of Macromolecular Systems

Author:

Publisher:

Published: 1994

Total Pages: 22

ISBN-13:

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Short-range molecular dynamics simulations of molecular systems are commonly parallelized by replicated-data methods, where each processor stores a copy of all atom positions. This enables computation of bonded 2-, 3-, and 4-body forces within the molecular topology to be partitioned among processors straightforwardly. A drawback to such methods is that the inter-processor communication scales as N, the number of atoms, independent of P, the number of processors. Thus, their parallel efficiency falls off rapidly when large numbers of processors are used. In this paper a new parallel method called force-decomposition for simulating macromolecular or small-molecule systems is presented. Its memory and communication costs scale as N/(square root)P, allowing larger problems to be run faster on greater numbers of processors. Like replicated-data techniques, and in contrast to spatial-decomposition approaches, the new method can be simply load-balanced and performs well even for irregular simulation geometries. The implementation of the algorithm in a prototypical macromolecular simulation code ParBond is also discussed. On a 1024-processor Intel Paragon, ParBond runs a standard benchmark simulation of solvated myoglobin with a parallel efficiency of 61% and at 40 times the speed of a vectorized version of CHARMM running on a single Cray Y-MP processor.

Numerical Simulation in Molecular Dynamics
Numerical Simulation in Molecular Dynamics

Author: Michael Griebel

Publisher: Springer Science & Business Media

Published: 2007-08-16

Total Pages: 472

ISBN-13: 3540680950

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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.

Molecular Modeling and Simulation
Molecular Modeling and Simulation

Author: Tamar Schlick

Publisher: Springer Science & Business Media

Published: 2013-04-18

Total Pages: 669

ISBN-13: 0387224645

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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

Scientific Computing with MATLAB and Octave
Scientific Computing with MATLAB and Octave

Author: Alfio Quarteroni

Publisher: Springer Science & Business Media

Published: 2010-05-30

Total Pages: 379

ISBN-13: 3642124305

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Preface to the First Edition This textbook is an introduction to Scienti?c Computing. We will illustrate several numerical methods for the computer solution of c- tain classes of mathematical problems that cannot be faced by paper and pencil. We will show how to compute the zeros or the integrals of continuous functions, solve linear systems, approximate functions by polynomials and construct accurate approximations for the solution of di?erential equations. With this aim, in Chapter 1 we will illustrate the rules of the game thatcomputersadoptwhenstoringandoperatingwith realandcomplex numbers, vectors and matrices. In order to make our presentation concrete and appealing we will 1 adopt the programming environment MATLAB as a faithful c- panion. We will gradually discover its principal commands, statements and constructs. We will show how to execute all the algorithms that we introduce throughout the book. This will enable us to furnish an - mediate quantitative assessment of their theoretical properties such as stability, accuracy and complexity. We will solve several problems that will be raisedthrough exercises and examples, often stemming from s- ci?c applications.

Molecular Dynamics Simulations in Statistical Physics: Theory and Applications
Molecular Dynamics Simulations in Statistical Physics: Theory and Applications

Author: Hiqmet Kamberaj

Publisher: Springer Nature

Published: 2020-03-20

Total Pages: 463

ISBN-13: 3030357023

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This book presents computer simulations using molecular dynamics techniques in statistical physics, with a focus on macromolecular systems. The numerical methods are introduced in the form of computer algorithms and can be implemented in computers using any desired computer programming language, such as Fortran 90, C/C++, and others. The book also explains how some of these numerical methods and their algorithms can be implemented in the existing computer programming software of macromolecular systems, such as the CHARMM program. In addition, it examines a number of advanced concepts of computer simulation techniques used in statistical physics as well as biological and physical systems. Discussing the molecular dynamics approach in detail to enhance readers understanding of the use of this method in statistical physics problems, it also describes the equations of motion in various statistical ensembles to mimic real-world experimental conditions. Intended for graduate students and research scientists working in the field of theoretical and computational biophysics, physics and chemistry, the book can also be used by postgraduate students of other disciplines, such as applied mathematics, computer sciences, and bioinformatics. Further, offering insights into fundamental theory, it as a valuable resource for expert practitioners and programmers and those new to the field.

Elements of Scientific Computing
Elements of Scientific Computing

Author: Aslak Tveito

Publisher: Springer Science & Business Media

Published: 2010-09-27

Total Pages: 470

ISBN-13: 3642112986

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Science used to be experiments and theory, now it is experiments, theory and computations. The computational approach to understanding nature and technology is currently flowering in many fields such as physics, geophysics, astrophysics, chemistry, biology, and most engineering disciplines. This book is a gentle introduction to such computational methods where the techniques are explained through examples. It is our goal to teach principles and ideas that carry over from field to field. You will learn basic methods and how to implement them. In order to gain the most from this text, you will need prior knowledge of calculus, basic linear algebra and elementary programming.