Understanding Molecular Simulation

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Understanding Molecular Simulation

Daan Frenkel,Berend Smit
Understanding Molecular Simulation Book PDF

Author : Daan Frenkel,Berend Smit
Publisher : Elsevier
Page : 664 pages
File Size : 51,9 Mb
Release : 2001-10-19
Category : Science
ISBN : 0080519989

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Understanding Molecular Simulation by Daan Frenkel,Berend Smit Pdf

Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text. Since the first edition only five years ago, the simulation world has changed significantly -- current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on: · Transition path sampling and diffusive barrier crossing to simulaterare events · Dissipative particle dynamic as a course-grained simulation technique · Novel schemes to compute the long-ranged forces · Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations · Multiple-time step algorithms as an alternative for constraints · Defects in solids · The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules · Parallel tempering for glassy Hamiltonians Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.

Understanding Molecular Simulation

Daan Frenkel,Berend Smit
Understanding Molecular Simulation Book PDF

Author : Daan Frenkel,Berend Smit
Publisher : Unknown
Page : 443 pages
File Size : 42,9 Mb
Release : 1996
Category : Forces intermoléculaires - Simulation par ordinateur
ISBN : 0122673700

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Understanding Molecular Simulation by Daan Frenkel,Berend Smit Pdf

This book explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. Since a wide variety of computational tools exists, the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text. Examples are included that highlight current applications, and the codes of the case studies are available on the World Wide Web. No prior knowledge of computer simulation is assumed.

Understanding Molecular Simulation

Daan Frenkel,B. Smit
Understanding Molecular Simulation Book PDF

Author : Daan Frenkel,B. Smit
Publisher : Academic Press
Page : 664 pages
File Size : 49,8 Mb
Release : 2001-11-07
Category : Science
ISBN : 0122673514

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Understanding Molecular Simulation by Daan Frenkel,B. Smit Pdf

Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text. Since the first edition only five years ago, the simulation world has changed significantly -- current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on: Transition path sampling and diffusive barrier crossing to simulaterare events Dissipative particle dynamic as a course-grained simulation technique Novel schemes to compute the long-ranged forces Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations Multiple-time step algorithms as an alternative for constraints Defects in solids The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules Parallel tempering for glassy Hamiltonians Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.

Understanding Molecular Simulation

Daan Frenkel,Berend Smit
Understanding Molecular Simulation Book PDF

Author : Daan Frenkel,Berend Smit
Publisher : Elsevier
Page : 868 pages
File Size : 43,7 Mb
Release : 2023-07-13
Category : Science
ISBN : 9780323913188

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Understanding Molecular Simulation by Daan Frenkel,Berend Smit Pdf

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

Molecular Dynamics Simulation of Nanostructured Materials

Snehanshu Pal,Bankim Chandra Ray
Molecular Dynamics Simulation of Nanostructured Materials Book PDF

Author : Snehanshu Pal,Bankim Chandra Ray
Publisher : CRC Press
Page : 334 pages
File Size : 46,5 Mb
Release : 2020-04-28
Category : Mathematics
ISBN : 9780429672453

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Molecular Dynamics Simulation of Nanostructured Materials by Snehanshu Pal,Bankim Chandra Ray Pdf

Molecular dynamics simulation is a significant technique to gain insight into the mechanical behavior of nanostructured (NS) materials and associated underlying deformation mechanisms at the atomic scale. The purpose of this book is to detect and correlate critically current achievements and properly assess the state of the art in the mechanical behavior study of NS material in the perspective of the atomic scale simulation of the deformation process. More precisely, the book aims to provide representative examples of mechanical behavior studies carried out using molecular dynamics simulations, which provide contributory research findings toward progress in the field of NS material technology.

Statistical Mechanics: Theory and Molecular Simulation

Mark Tuckerman
Statistical Mechanics Theory and Molecular Simulation Book PDF

Author : Mark Tuckerman
Publisher : OUP Oxford
Page : 720 pages
File Size : 51,6 Mb
Release : 2010-02-11
Category : Science
ISBN : 0191523461

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Statistical Mechanics: Theory and Molecular Simulation by Mark Tuckerman Pdf

Complex systems that bridge the traditional disciplines of physics, chemistry, biology, and materials science can be studied at an unprecedented level of detail using increasingly sophisticated theoretical methodology and high-speed computers. The aim of this book is to prepare burgeoning users and developers to become active participants in this exciting and rapidly advancing research area by uniting for the first time, in one monograph, the basic concepts of equilibrium and time-dependent statistical mechanics with the modern techniques used to solve the complex problems that arise in real-world applications. The book contains a detailed review of classical and quantum mechanics, in-depth discussions of the most commonly used ensembles simultaneously with modern computational techniques such as molecular dynamics and Monte Carlo, and important topics including free-energy calculations, linear-response theory, harmonic baths and the generalized Langevin equation, critical phenomena, and advanced conformational sampling methods. Burgeoning users and developers are thus provided firm grounding to become active participants in this exciting and rapidly advancing research area, while experienced practitioners will find the book to be a useful reference tool for the field.

The Art of Molecular Dynamics Simulation

D. C. Rapaport
The Art of Molecular Dynamics Simulation Book PDF

Author : D. C. Rapaport
Publisher : Cambridge University Press
Page : 568 pages
File Size : 49,7 Mb
Release : 2004-04
Category : Science
ISBN : 0521825687

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The Art of Molecular Dynamics Simulation by D. C. Rapaport Pdf

First time paperback of successful physics monograph. Copyright © Libri GmbH. All rights reserved.

Molecular Dynamics Simulation

Kun Zhou,Bo Liu
Molecular Dynamics Simulation Book PDF

Author : Kun Zhou,Bo Liu
Publisher : Academic Press
Page : 375 pages
File Size : 52,9 Mb
Release : 2022-02-10
Category : Technology & Engineering
ISBN : 9780128166161

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Molecular Dynamics Simulation by Kun Zhou,Bo Liu Pdf

Molecular Dynamic Simulation: Fundamentals and Applications explains the basic principles of MD simulation and explores its recent developments and roles in advanced modeling approaches. The implementation of MD simulation and its application to various aspects of materials science and engineering including mechanical, thermal, mass transportation, and physical/chemical reaction problems are illustrated. Innovative modeling techniques that apply MD to explore the mechanics of typical nanomaterials and nanostructures and to characterize crystalline, amorphous, and liquid systems are also presented. The rich research experience of the authors in MD simulation will ensure that the readers are provided with both an in-depth understanding of MD simulation and clear technical guidance. Provides a comprehensive overview of the underlying theories of molecular dynamics (MD) simulation Presents application-based examples pertaining to a broad range of mechanical, thermal, and mass transport problems Explores innovative modeling techniques for simulating typical nanomaterials and nanostructures and for characterizing crystalline, amorphous, and liquid systems

A Practical Introduction to the Simulation of Molecular Systems

Martin J. Field
A Practical Introduction to the Simulation of Molecular Systems Book PDF

Author : Martin J. Field
Publisher : Cambridge University Press
Page : 294 pages
File Size : 50,5 Mb
Release : 2007-07-19
Category : Science
ISBN : 9781139465816

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A Practical Introduction to the Simulation of Molecular Systems by Martin J. Field Pdf

Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through www.cambridge.org/9780521852524.

Molecular Simulations

Saman Alavi
Molecular Simulations Book PDF

Author : Saman Alavi
Publisher : John Wiley & Sons
Page : 342 pages
File Size : 40,5 Mb
Release : 2020-06-29
Category : Technology & Engineering
ISBN : 9783527341054

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Molecular Simulations by Saman Alavi Pdf

Provides hands-on knowledge enabling students of and researchers in chemistry, biology, and engineering to perform molecular simulations This book introduces the fundamentals of molecular simulations for a broad, practice-oriented audience and presents a thorough overview of the underlying concepts. It covers classical mechanics for many-molecule systems as well as force-field models in classical molecular dynamics; introduces probability concepts and statistical mechanics; and analyzes numerous simulation methods, techniques, and applications. Molecular Simulations: Fundamentals and Practice starts by covering Newton's equations, which form the basis of classical mechanics, then continues on to force-field methods for modelling potential energy surfaces. It gives an account of probability concepts before subsequently introducing readers to statistical and quantum mechanics. In addition to Monte-Carlo methods, which are based on random sampling, the core of the book covers molecular dynamics simulations in detail and shows how to derive critical physical parameters. It finishes by presenting advanced techniques, and gives invaluable advice on how to set up simulations for a diverse range of applications. -Addresses the current need of students of and researchers in chemistry, biology, and engineering to understand and perform their own molecular simulations -Covers the nitty-gritty ? from Newton's equations and classical mechanics over force-field methods, potential energy surfaces, and probability concepts to statistical and quantum mechanics -Introduces physical, chemical, and mathematical background knowledge in direct relation with simulation practice -Highlights deterministic approaches and random sampling (eg: molecular dynamics versus Monte-Carlo methods) -Contains advanced techniques and practical advice for setting up different simulations to prepare readers entering this exciting field Molecular Simulations: Fundamentals and Practice is an excellent book benefitting chemist, biologists, engineers as well as materials scientists and those involved in biotechnology.

An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation

Gregory R. Bowman,Vijay S. Pande,Frank Noé
An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation Book PDF

Author : Gregory R. Bowman,Vijay S. Pande,Frank Noé
Publisher : Springer Science & Business Media
Page : 148 pages
File Size : 41,5 Mb
Release : 2013-12-02
Category : Science
ISBN : 9789400776067

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An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation by Gregory R. Bowman,Vijay S. Pande,Frank Noé Pdf

The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range of problems. The Markov state model (MSM) approach aims to address two key challenges of molecular simulation: 1) How to reach long timescales using short simulations of detailed molecular models. 2) How to systematically gain insight from the resulting sea of data. MSMs do this by providing a compact representation of the vast conformational space available to biomolecules by decomposing it into states sets of rapidly interconverting conformations and the rates of transitioning between states. This kinetic definition allows one to easily vary the temporal and spatial resolution of an MSM from high-resolution models capable of quantitative agreement with (or prediction of) experiment to low-resolution models that facilitate understanding. Additionally, MSMs facilitate the calculation of quantities that are difficult to obtain from more direct MD analyses, such as the ensemble of transition pathways. This book introduces the mathematical foundations of Markov models, how they can be used to analyze simulations and drive efficient simulations, and some of the insights these models have yielded in a variety of applications of molecular simulation.

Molecular Modeling Basics

Jan H. Jensen
Molecular Modeling Basics Book PDF

Author : Jan H. Jensen
Publisher : CRC Press
Page : 192 pages
File Size : 55,9 Mb
Release : 2010-04-26
Category : Science
ISBN : 9781420075274

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Molecular Modeling Basics by Jan H. Jensen Pdf

Molecular modeling is becoming an increasingly important part of chemical research and education as computers become faster and programs become easier to use. The results, however, have not become easier to understand. Addressing the need for a "workshop-oriented" book, Molecular Modeling Basics provides the fundamental theory needed to understand

Molecular Simulation on Cement-Based Materials

Dongshuai Hou
Molecular Simulation on Cement Based Materials Book PDF

Author : Dongshuai Hou
Publisher : Springer Nature
Page : 197 pages
File Size : 50,8 Mb
Release : 2019-09-26
Category : Technology & Engineering
ISBN : 9789811387111

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Molecular Simulation on Cement-Based Materials by Dongshuai Hou Pdf

This book presents a number of studies on the molecular dynamics of cement-based materials. It introduces a practical molecular model of cement-hydrate, delineates the relationship between molecular structure and nanoscale properties, reveals the transport mechanism of cement-hydrate, and provides useful methods for material design. Based on the molecular model presented here, the book subsequently sheds light on nanotechnology applications in the design of construction and building materials. As such, it offers a valuable asset for researchers, scientists, and engineers in the field of construction and building materials.

Computer Meets Theoretical Physics

Giovanni Battimelli,Giovanni Ciccotti,Pietro Greco
Computer Meets Theoretical Physics Book PDF

Author : Giovanni Battimelli,Giovanni Ciccotti,Pietro Greco
Publisher : Springer Nature
Page : 214 pages
File Size : 51,9 Mb
Release : 2020-06-17
Category : Science
ISBN : 9783030393991

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Computer Meets Theoretical Physics by Giovanni Battimelli,Giovanni Ciccotti,Pietro Greco Pdf

This book provides a vivid account of the early history of molecular simulation, a new frontier for our understanding of matter that was opened when the demands of theoretical physicists were met by the availability of the modern computers. Since their inception, electronic computers have enormously increased their performance, thus making possible the unprecedented technological revolution that characterizes our present times. This obvious technological advancement has brought with it a silent scientific revolution in the practice of theoretical physics. In particular, in the physics of matter it has opened up a direct route from the microscopic physical laws to observable phenomena. One can now study the time evolution of systems composed of millions of molecules, and simulate the behaviour of macroscopic materials and actually predict their properties. Molecular simulation has provided a new theoretical and conceptual tool that physicists could only dream of when the foundations of statistical mechanics were laid. Molecular simulation has undergone impressive development, both in the size of the scientific community involved and in the range and scope of its applications. It has become the ubiquitous workhorse for investigating the nature of complex condensed matter systems in physics, chemistry, materials and the life sciences. Yet these developments remain largely unknown outside the inner circles of practitioners, and they have so far never been described for a wider public. The main objective of this book is therefore to offer a reasonably comprehensive reconstruction of the early history of molecular simulation addressed to an audience of both scientists and interested non-scientists, describing the scientific and personal trajectories of the main protagonists and discussing the deep conceptual innovations that their work produced.

Molecular Dynamics Simulations in Statistical Physics: Theory and Applications

Hiqmet Kamberaj
Molecular Dynamics Simulations in Statistical Physics Theory and Applications Book PDF

Author : Hiqmet Kamberaj
Publisher : Springer Nature
Page : 463 pages
File Size : 41,5 Mb
Release : 2020-03-20
Category : Science
ISBN : 9783030357023

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Molecular Dynamics Simulations in Statistical Physics: Theory and Applications by Hiqmet Kamberaj Pdf

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.