An Introduction To Molecular Dynamics

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An Introduction to Molecular Dynamics

Mark S. Kemp
An Introduction to Molecular Dynamics Book PDF

Author : Mark S. Kemp
Publisher : Nova Science Publishers
Page : 184 pages
File Size : 42,8 Mb
Release : 2019
Category : Science
ISBN : 1536160555

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An Introduction to Molecular Dynamics by Mark S. Kemp Pdf

"In the opening chapter of An Introduction to Molecular Dynamics, the method of statistical geometry, based on the construction of a Voronoi polyhedral, is applied to the pattern recognition of atomic environments and to the investigation of the local order in molecular dynamics-simulated materials. Next, the authors discuss the methodology of bimolecular simulations and their advancements, as well as their applications in the field of nanoparticle-biomolecular interactions. The theory of molecular dynamics simulation and some of the recent molecular dynamics methods such as steered molecular dynamics, umbrella sampling, and coarse-grained simulation are also discussed. The use of auxiliary programs in the cases of modified cyclodextrins is discussed. Additionally, results from molecular dynamics studies on cases of inclusion compounds of molecules of different sizes and shapes encapsulated in the same host cyclodextrin have been examined and compared. In closing, the authors discuss the methodology of molecular dynamics simulation with a non-constant force field. In the context of molecular simulations, the term "force field" refers to a set of equations and parameters for the calculation of forces acting on the particles of the system and its potential energy"--

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 : 41,6 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.

Understanding Molecular Simulation

Daan Frenkel,Berend Smit
Understanding Molecular Simulation Book PDF

Author : Daan Frenkel,Berend Smit
Publisher : Elsevier
Page : 664 pages
File Size : 54,9 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.

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 : 48,9 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.

An Introduction to Molecular Dynamics Simulation of Polymer Composites

Sumit Sharma
An Introduction to Molecular Dynamics Simulation of Polymer Composites Book PDF

Author : Sumit Sharma
Publisher : Nova Science Publishers
Page : 341 pages
File Size : 42,5 Mb
Release : 2020-03-03
Category : Molecular dynamics
ISBN : 1536174084

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An Introduction to Molecular Dynamics Simulation of Polymer Composites by Sumit Sharma Pdf

"This book will be beneficial for students, researchers and scientists working in the field of molecular dynamics simulation. In this book, Materials Studio software developed by Accelrys, a software company headquartered in the United States, has been used for performing the simulations and analysis. The source codes written in the book can be used by any one for modeling. The book starts with an introduction to molecular dynamics. Then various molecular dynamics methods will be discussed in detail. As the book progresses, various case studies related to modeling of composites at nano level will be discussed. The properties predicted are mechanical, thermal, optical and electrical. The concept of perl scripting has also been discussed in detail. Lastly the applications of molecular dynamics in various fields of engineering and technology will be discussed. The nanocomposite materials discussed in this book include polymer-matrix composites. The reinforcements used are carbon nanotubes, graphene, nanoparticles and nanofibers"--

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 : 43,6 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.

Introduction to Practice of Molecular Simulation

Akira Satoh
Introduction to Practice of Molecular Simulation Book PDF

Author : Akira Satoh
Publisher : Elsevier
Page : 0 pages
File Size : 53,9 Mb
Release : 2010-12-17
Category : Science
ISBN : 0323165192

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Introduction to Practice of Molecular Simulation by Akira Satoh Pdf

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.

Molecular Simulations

Saman Alavi
Molecular Simulations Book PDF

Author : Saman Alavi
Publisher : John Wiley & Sons
Page : 342 pages
File Size : 55,5 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.

Computational Many-Particle Physics

Holger Fehske,Ralf Schneider,Alexander Weiße
Computational Many Particle Physics Book PDF

Author : Holger Fehske,Ralf Schneider,Alexander Weiße
Publisher : Springer
Page : 780 pages
File Size : 50,5 Mb
Release : 2007-12-10
Category : Science
ISBN : 9783540746867

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Computational Many-Particle Physics by Holger Fehske,Ralf Schneider,Alexander Weiße Pdf

Looking for the real state of play in computational many-particle physics? Look no further. This book presents an overview of state-of-the-art numerical methods for studying interacting classical and quantum many-particle systems. A broad range of techniques and algorithms are covered, and emphasis is placed on their implementation on modern high-performance computers. This excellent book comes complete with online files and updates allowing readers to stay right up to date.

Numerical Simulation in Molecular Dynamics

Michael Griebel,Stephan Knapek,Gerhard Zumbusch
Numerical Simulation in Molecular Dynamics Book PDF

Author : Michael Griebel,Stephan Knapek,Gerhard Zumbusch
Publisher : Springer Science & Business Media
Page : 472 pages
File Size : 48,5 Mb
Release : 2007-08-16
Category : Science
ISBN : 9783540680956

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Numerical Simulation in Molecular Dynamics by Michael Griebel,Stephan Knapek,Gerhard Zumbusch Pdf

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

Lichang Wang
Molecular Dynamics Book PDF

Author : Lichang Wang
Publisher : BoD – Books on Demand
Page : 448 pages
File Size : 42,9 Mb
Release : 2012-04-11
Category : Computers
ISBN : 9789535104445

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Molecular Dynamics by Lichang Wang Pdf

Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This second book begins with an introduction of molecular dynamics simulations to macromolecules and then illustrates the computer experiments using molecular dynamics simulations in the studies of synthetic and biological macromolecules, plasmas, and nanomachines. Coverage of this book includes: Complex formation and dynamics of polymers Dynamics of lipid bilayers, peptides, DNA, RNA, and proteins Complex liquids and plasmas Dynamics of molecules on surfaces Nanofluidics and nanomachines

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 : 49,8 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

Molecular Quantum Dynamics

Fabien Gatti
Molecular Quantum Dynamics Book PDF

Author : Fabien Gatti
Publisher : Springer Science & Business Media
Page : 281 pages
File Size : 40,6 Mb
Release : 2014-04-09
Category : Science
ISBN : 9783642452901

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Molecular Quantum Dynamics by Fabien Gatti Pdf

This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book "Molecular Quantum Dynamics" offers them an accessible introduction. Although the calculation of large systems still presents a challenge - despite the considerable power of modern computers - new strategies have been developed to extend the studies to systems of increasing size. Such strategies are presented after a brief overview of the historical background. Strong emphasis is put on an educational presentation of the fundamental concepts, so that the reader can inform himself about the most important concepts, like eigenstates, wave packets, quantum mechanical resonances, entanglement, etc. The chosen examples highlight that high-level experiments and theory need to work closely together. This book thus is a must-read both for researchers working experimentally or theoretically in the concerned fields, and generally for anyone interested in the exciting world of molecular quantum dynamics.

Computer Simulations of Surfaces and Interfaces

Burkhard Dünweg,David P. Landau,Andrey I. Milchev
Computer Simulations of Surfaces and Interfaces Book PDF

Author : Burkhard Dünweg,David P. Landau,Andrey I. Milchev
Publisher : Springer Science & Business Media
Page : 480 pages
File Size : 44,5 Mb
Release : 2003-12-31
Category : Computers
ISBN : 1402014643

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Computer Simulations of Surfaces and Interfaces by Burkhard Dünweg,David P. Landau,Andrey I. Milchev Pdf

Proceedings of the NATO Advanced Study Institute, Albena, Bulgaria, from 9 to 20 September 2002

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

Sumit Sharma
Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio Lammps and Gromacs Book PDF

Author : Sumit Sharma
Publisher : Elsevier
Page : 365 pages
File Size : 54,7 Mb
Release : 2019-08-09
Category : Technology & Engineering
ISBN : 9780128169551

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Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs by Sumit Sharma Pdf

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