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Molecular Dynamics Simulation

Molecular Dynamics Simulation
A Book

by Giovanni Ciccotti,Mauro Ferrario,Christof Schuette

  • Publisher : MDPI
  • Release : 2018-10-08
  • Pages : 636
  • ISBN : 3906980650
  • Language : En, Es, Fr & De
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Printed Edition of the Special Issue Published in Entropy

The Art of Molecular Dynamics Simulation

The Art of Molecular Dynamics Simulation
A Book

by D. C. Rapaport,Rapaport, Dennis C. Rapaport

  • Publisher : Cambridge University Press
  • Release : 2004-04
  • Pages : 549
  • ISBN : 9780521825689
  • Language : En, Es, Fr & De
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First time paperback of successful physics monograph. Copyright © Libri GmbH. All rights reserved.

Molecular Dynamics Simulation

Molecular Dynamics Simulation
Elementary Methods

by J. M. Haile

  • Publisher : Wiley-Interscience
  • Release : 1992-06-05
  • Pages : 489
  • ISBN : 9780471819660
  • Language : En, Es, Fr & De
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"Provides a lot of reading pleasure and many new insights." -Journal of Molecular Structure "This is the most entertaining, stimulating and useful book which can be thoroughly recommended to anyone with an interest in computer simulation." -Contemporary Physics "A very useful introduction . . . more interesting to read than the often dry equation-based texts." -Journal of the American Chemical Society Written especially for the novice, Molecular Dynamics Simulation demonstrates how molecular dynamics simulations work and how to perform them, focusing on how to devise a model for specific molecules and then how to simulate their movements using a computer. This book provides a collection of methods that until now have been scattered through the literature of the last 25 years. It reviews elements of sampling theory and discusses how modern notions of chaos and nonlinear dynamics explain the workings of molecular dynamics. Stresses easy-to-use molecules * Provides sample calculations and figures * Includes four complete FORTRAN codes

Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs

Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs
A Book

by Sumit Sharma

  • Publisher : Elsevier
  • Release : 2019-08-09
  • Pages : 365
  • ISBN : 0128169559
  • Language : En, Es, Fr & De
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Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs presents the three major software packages used for the molecular dynamics simulation of nanocomposites. The book explains, in detail, how to use each of these packages, also providing real-world examples that show when each should be used. The latter two of these are open-source codes which can be used for modeling at no cost. Several case studies how each software package is used to predict various properties of nanocomposites, including metal-matrix, polymer-matrix and ceramic-matrix based nanocomposites. Properties explored include mechanical, thermal, optical and electrical properties. This is the first book that explores methodologies for using Materials Studio, Lammps and Gromacs in the same place. It will be beneficial for students, researchers and scientists working in the field of molecular dynamics simulation. Gives a detailed explanation of basic commands and modules of Materials Studio, Lammps and Gromacs Shows how Materials Studio, Lammps and Gromacs predict mechanical, thermal, electrical and optical properties of nanocomposites Uses case studies to show which software should be used to solve a variety of nanoscale modeling problems

Understanding Molecular Simulation

Understanding Molecular Simulation
From Algorithms to Applications

by Daan Frenkel,Berend Smit

  • Publisher : Elsevier
  • Release : 2001-10-19
  • Pages : 664
  • ISBN : 9780080519982
  • Language : En, Es, Fr & De
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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.

Computer Simulations of Surfaces and Interfaces

Computer Simulations of Surfaces and Interfaces
A Book

by Burkhard Dünweg,David P. Landau,Andrey I. Milchev

  • Publisher : Springer Science & Business Media
  • Release : 2003-12-31
  • Pages : 451
  • ISBN : 9781402014642
  • Language : En, Es, Fr & De
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Proceedings of the NATO Advanced Study Institute, Albena, Bulgaria, from 9 to 20 September 2002

Molecular Dynamics Simulation of Nanostructured Materials

Molecular Dynamics Simulation of Nanostructured Materials
An Understanding of Mechanical Behavior

by Snehanshu Pal,Bankim Chandra Ray

  • Publisher : CRC Press
  • Release : 2020-04-28
  • Pages : 314
  • ISBN : 0429672454
  • Language : En, Es, Fr & De
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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.

Introduction to Practice of Molecular Simulation

Introduction to Practice of Molecular Simulation
Molecular Dynamics, Monte Carlo, Brownian Dynamics, Lattice Boltzmann and Dissipative Particle Dynamics

by Akira Satoh

  • Publisher : Elsevier
  • Release : 2010-12-17
  • Pages : 330
  • ISBN : 0123851491
  • Language : En, Es, Fr & De
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This book presents the most important and main concepts of the molecular and microsimulation techniques. It enables readers to improve their skills in developing simulation programs by providing physical problems and sample simulation programs for them to use. Provides tools to develop skills in developing simulations programs Includes sample simulation programs for the reader to use Appendix explains Fortran and C languages in simple terms to allow the non-expert to use them

Numerical Simulation in Molecular Dynamics

Numerical Simulation in Molecular Dynamics
Numerics, Algorithms, Parallelization, Applications

by Michael Griebel,Stephan Knapek,Gerhard Zumbusch

  • Publisher : Springer Science & Business Media
  • Release : 2007-08-16
  • Pages : 476
  • ISBN : 3540680950
  • Language : En, Es, Fr & De
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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 Dynamics

Molecular Dynamics
From Classical to Quantum Methods

by Perla Balbuena,Jorge M. Seminario

  • Publisher : Elsevier
  • Release : 1999-04-22
  • Pages : 945
  • ISBN : 9780080536842
  • Language : En, Es, Fr & De
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The latest developments in quantum and classical molecular dynamics, related techniques, and their applications to several fields of science and engineering. Molecular simulations include a broad range of methodologies such as Monte Carlo, Brownian dynamics, lattice dynamics, and molecular dynamics (MD). Features of this book: • Presents advances in methodologies, introduces quantum methods and lists new techniques for classical MD • Deals with complex systems: biomolecules, aqueous solutions, ice and clathrates, liquid crystals, polymers • Provides chemical reactions, interfaces, catalysis, surface phenomena and solids Although the book is not formally divided into methods and applications, the chapters are arranged starting with those that discuss new algorithms, methods and techniques, followed by several important applications.

Molecular Dynamics Simulations of Disordered Materials

Molecular Dynamics Simulations of Disordered Materials
From Network Glasses to Phase-Change Memory Alloys

by Carlo Massobrio,Jincheng Du,Marco Bernasconi,Philip S. Salmon

  • Publisher : Springer
  • Release : 2015-04-22
  • Pages : 529
  • ISBN : 3319156756
  • Language : En, Es, Fr & De
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This book is a unique reference work in the area of atomic-scale simulation of glasses. For the first time, a highly selected panel of about 20 researchers provides, in a single book, their views, methodologies and applications on the use of molecular dynamics as a tool to describe glassy materials. The book covers a wide range of systems covering "traditional" network glasses, such as chalcogenides and oxides, as well as glasses for applications in the area of phase change materials. The novelty of this work is the interplay between molecular dynamics methods (both at the classical and first-principles level) and the structure of materials for which, quite often, direct experimental structural information is rather scarce or absent. The book features specific examples of how quite subtle features of the structure of glasses can be unraveled by relying on the predictive power of molecular dynamics, used in connection with a realistic description of forces.

Molecular Dynamics Simulations in Statistical Physics: Theory and Applications

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

by Hiqmet Kamberaj

  • Publisher : Springer Nature
  • Release : 2020-03-20
  • Pages : 463
  • ISBN : 3030357023
  • Language : En, Es, Fr & De
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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.

Protein Simulations

Protein Simulations
A Book

by Valerie Daggett

  • Publisher : Elsevier
  • Release : 2003-11-26
  • Pages : 459
  • ISBN : 0080493785
  • Language : En, Es, Fr & De
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Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function. * Force Fields * Ligand Binding * Protein Membrane Simulation * Enzyme Dynamics * Protein Folding and unfolding simulations

Industrial Applications of Molecular Simulations

Industrial Applications of Molecular Simulations
A Book

by Marc Meunier

  • Publisher : CRC Press
  • Release : 2016-04-19
  • Pages : 421
  • ISBN : 1439861021
  • Language : En, Es, Fr & De
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The field of quantum and molecular simulations has experienced strong growth since the time of the early software packages. A recent study, showed a large increase in the number of people publishing papers based on ab initio methods from about 3,000 in 1991 to roughly 20,000 in 2009, with particularly strong growth in East Asia. Looking to the future, the question remains as to how these methods can be further integrated into the R&D value chain, bridging the gap from engineering to manufacturing. Using successful case studies as a framework, Industrial Applications of Molecular Simulations demonstrates the capability of molecular modeling to tackle problems of industrial relevance. This book presents a wide range of various modeling techniques, including methods based on quantum or classical mechanics, molecular dynamics, Monte Carlo simulations, etc. It also explores a wide range of materials, from soft materials such as polymeric blends widely used in the chemical industry to hard or inorganic materials such as glasses and alumina. Features Demonstrates how modeling can solve everyday problems for scientists in industry Provides a broad overview of theoretical approaches Presents a wide range of applications in areas such as materials research, catalysis, pharmaceutical development and electronics Emphasizes the relationship between theory and experiments

Biomolecular and Bioanalytical Techniques

Biomolecular and Bioanalytical Techniques
Theory, Methodology and Applications

by Vasudevan Ramesh

  • Publisher : Wiley
  • Release : 2019-05-13
  • Pages : 576
  • ISBN : 1119483964
  • Language : En, Es, Fr & De
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An essential guide to biomolecular and bioanalytical techniques and their applications Biomolecular and Bioanalytical Techniques offers an introduction to, and a basic understanding of, a wide range of biophysical techniques. The text takes an interdisciplinary approach with contributions from a panel of distinguished experts. With a focus on research, the text comprehensively covers a broad selection of topics drawn from contemporary research in the fields of chemistry and biology. Each of the internationally reputed authors has contributed a single chapter on a specific technique. The chapters cover the specific technique’s background, theory, principles, technique, methodology, protocol and applications. The text explores the use of a variety of analytical tools to characterise biological samples. The contributors explain how to identify and quantify biochemically important molecules, including small molecules as well as biological macromolecules such as enzymes, antibodies, proteins, peptides and nucleic acids. This book is filled with essential knowledge and explores the skills needed to carry out the research and development roles in academic and industrial laboratories. A technique-focused book that bridges the gap between an introductory text and a book on advanced research methods Provides the necessary background and skills needed to advance the research methods Features a structured approach within each chapter Demonstrates an interdisciplinary approach that serves to develop independent thinking Written for students in chemistry, biological, medical, pharmaceutical, forensic and biophysical sciences, Biomolecular and Bioanalytical Techniques is an in-depth review of the most current biomolecular and bioanalytical techniques in the field.

Molecular Simulations

Molecular Simulations
Fundamentals and Practice

by Saman Alavi

  • Publisher : VCH
  • Release : 2020-06-03
  • Pages : 344
  • ISBN : 3527341056
  • Language : En, Es, Fr & De
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Addressing the need of chemistry, biology and engineering students to understand and perform their own molecular simulations, the author introduces the fundamentals of molecular modeling for a broad, practice-oriented audience and presents versatile practical applications. The book presents a thorough overview of the underlying concepts.

Computational Molecular Dynamics: Challenges, Methods, Ideas

Computational Molecular Dynamics: Challenges, Methods, Ideas
Proceeding of the 2nd International Symposium on Algorithms for Macromolecular Modelling, Berlin, May 21–24, 1997

by Peter Deuflhard,Jan Hermans,Benedict Leimkuhler,Alan E. Mark,Sebastian Reich,Robert D. Skeel

  • Publisher : Springer Science & Business Media
  • Release : 2012-12-06
  • Pages : 494
  • ISBN : 3642583601
  • Language : En, Es, Fr & De
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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.

Molecular Dynamics of Nanostructures and Nanoionics

Molecular Dynamics of Nanostructures and Nanoionics
Simulations in Complex Systems

by Junko Habasaki

  • Publisher : CRC Press
  • Release : 2020-12-01
  • Pages : 318
  • ISBN : 1000066800
  • Language : En, Es, Fr & De
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Nanostructured materials with multiple components and complex structures are the current focus of research and are expected to develop further for material designs in many applications in electrochemical, colloidal, medical, pharmaceutical, and several other fields. This book discusses complex nanostructured systems exemplified by nanoporous silicates, spontaneously formed gels from silica-nanocolloidal solutions, and related systems, and examines them using molecular dynamics simulations. Nanoporous materials, nanocolloidal systems, and gels are useful in many applications and can be used in electric devices and storage, and for gas, ion, and drug delivery. The book gives an overview of the history, current status, and frontiers of the field. It also discusses the fundamental aspects related to the common behaviors of some of these systems and common analytical methods to treat them.

Molecular Dynamics

Molecular Dynamics
With Deterministic and Stochastic Numerical Methods

by Ben Leimkuhler,Charles Matthews

  • Publisher : Springer
  • Release : 2015-05-18
  • Pages : 443
  • ISBN : 3319163752
  • Language : En, Es, Fr & De
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This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications. Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method.

Molecular Modeling and Simulation: An Interdisciplinary Guide

Molecular Modeling and Simulation: An Interdisciplinary Guide
An Interdisciplinary Guide

by Tamar Schlick

  • Publisher : Springer Science & Business Media
  • Release : 2010-08-03
  • Pages : 723
  • ISBN : 9781441963512
  • Language : En, Es, Fr & De
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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