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The Art of Molecular Dynamics Simulation

The Art of Molecular Dynamics Simulation
  • Author : D. C. Rapaport,Rapaport, Dennis C. Rapaport
  • Publisher :Unknown
  • Release Date :2004-04
  • Total pages :549
  • ISBN : 0521825687
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Summary : First time paperback of successful physics monograph. Copyright © Libri GmbH. All rights reserved.

Molecular Dynamics Simulation

Molecular Dynamics Simulation
  • Author : Giovanni Ciccotti,Mauro Ferrario,Christof Schuette
  • Publisher :Unknown
  • Release Date :2018-10-08
  • Total pages :636
  • ISBN : 9783906980652
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Summary : Printed Edition of the Special Issue Published in Entropy

Supercomputing for Molecular Dynamics Simulations

Supercomputing for Molecular Dynamics Simulations
  • Author : Alexander Heinecke,Wolfgang Eckhardt,Martin Horsch,Hans-Joachim Bungartz
  • Publisher :Unknown
  • Release Date :2015-04-09
  • Total pages :76
  • ISBN : 331917147X
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Summary : This work presents modern implementations of relevant molecular dynamics algorithms using ls1 mardyn, a simulation program for engineering applications. The text focuses strictly on HPC-related aspects, covering implementation on HPC architectures, taking Intel Xeon and Intel Xeon Phi clusters as representatives of current platforms. The work describes distributed and shared-memory parallelization on these platforms, including load balancing, with a particular focus on the efficient implementation of the compute kernels. The text also discusses the software-architecture of the resulting code.

Molecular Dynamics Simulation

Molecular Dynamics Simulation
  • Author : J. M. Haile
  • Publisher :Unknown
  • Release Date :1997-03-14
  • Total pages :512
  • ISBN : 047118439X
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Summary : "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

Molecular Dynamics Simulation
  • Author : Kun Zhou,Bo Liu
  • Publisher :Unknown
  • Release Date :2020-09
  • Total pages :400
  • ISBN : 0128164190
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Summary : Molecular Dynamic Simulation for Engineering and Materials explains the fundamentals of MD simulation and explores recent developments in advanced modeling approaches based on the MD method. The improvements in efficiency and accuracy delivered by this new research are explained to help readers apply them to a wide range of tasks. Details of the implementation of MD simulation are illustrated by presenting the applications of MD simulation in various aspects of materials study including mechanical, thermal, mass transportation, and absorption/desorption problems. Innovative methods of using MD to explore the mechanics of nano/micromaterials, and for the characterization of crystalline, amorphous and liquid materials are also presented. The rich research experience of the authors in molecular dynamic simulation will ensure that readers are provided with both an in-depth understanding of this method and clear technical guidance.

Molecular Dynamics Simulation of Nanostructured Materials

Molecular Dynamics Simulation of Nanostructured Materials
  • Author : Snehanshu Pal,Bankim Chandra Ray
  • Publisher :Unknown
  • Release Date :2020-04-28
  • Total pages :314
  • ISBN : 9780429672453
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Summary : 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.

Numerical Simulation in Molecular Dynamics

Numerical Simulation in Molecular Dynamics
  • Author : Michael Griebel,Stephan Knapek,Gerhard Zumbusch
  • Publisher :Unknown
  • Release Date :2007-08-16
  • Total pages :476
  • ISBN : 9783540680956
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Summary : 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.

Understanding Molecular Simulation

Understanding Molecular Simulation
  • Author : Daan Frenkel,Berend Smit
  • Publisher :Unknown
  • Release Date :2001-10-19
  • Total pages :664
  • ISBN : 0080519989
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Summary : 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.

Introduction to Practice of Molecular Simulation

Introduction to Practice of Molecular Simulation
  • Author : Akira Satoh
  • Publisher :Unknown
  • Release Date :2010-12-17
  • Total pages :330
  • ISBN : 9780123851499
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Summary : 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

Molecular Dynamics

Molecular Dynamics
  • Author : Perla Balbuena,Jorge M. Seminario
  • Publisher :Unknown
  • Release Date :1999-04-22
  • Total pages :945
  • ISBN : 0080536840
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Summary : 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 Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs

Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs
  • Author : Sumit Sharma
  • Publisher :Unknown
  • Release Date :2019-08-09
  • Total pages :365
  • ISBN : 9780128169551
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Summary : 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

Molecular Dynamics Simulation of Nanostructured Materials

Molecular Dynamics Simulation of Nanostructured Materials
  • Author : Snehanshu Pal,Bankim Chandra Ray
  • Publisher :Unknown
  • Release Date :2020-05-12
  • Total pages :314
  • ISBN : 0367029820
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Summary : 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.

Carbon-Based Smart Materials

Carbon-Based Smart Materials
  • Author : Constantinos A. Charitidis,Elias P. Koumoulos,Dimitrios A. Dragatogiannis
  • Publisher :Unknown
  • Release Date :2020-04-20
  • Total pages :194
  • ISBN : 9783110479133
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Summary : Presents technologies and key concepts to produce suitable smart materials and intelligent structures for sensing, information and communication technology, biomedical applications (drug delivery, hyperthermia therapy), self-healing, flexible memories and construction technologies. Novel developments of environmental friendly, cost-effective and scalable production processes are discussed by experts in the field.

Molecular Dynamics Simulations of Disordered Materials

Molecular Dynamics Simulations of Disordered Materials
  • Author : Carlo Massobrio,Jincheng Du,Marco Bernasconi,Philip S. Salmon
  • Publisher :Unknown
  • Release Date :2015-04-22
  • Total pages :529
  • ISBN : 9783319156750
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Summary : 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 Simulations

Molecular Simulations
  • Author : Saman Alavi
  • Publisher :Unknown
  • Release Date :2020-06-03
  • Total pages :344
  • ISBN : 9783527341054
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Summary : 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.

A Practical Introduction to the Simulation of Molecular Systems

A Practical Introduction to the Simulation of Molecular Systems
  • Author : Martin J. Field
  • Publisher :Unknown
  • Release Date :2007-07-19
  • Total pages :229
  • ISBN : 9781139465816
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Summary : 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.

Computer Simulation of Liquids

Computer Simulation of Liquids
  • Author : M. P. Allen,M... P. Allen,D. J. Tildesley,D... J. Tildesley,TILDESLEY ALLEN
  • Publisher :Unknown
  • Release Date :1989
  • Total pages :385
  • ISBN : 0198556454
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Summary : Computer simulation is an essential tool in studying the chemistry and physics of liquids. Simulations allow us to develop models and to test them against experimental data. This book is an introduction and practical guide to the molecular dynamics and Monte Carlo methods.

Molecular Dynamics Simulations in Statistical Physics: Theory and Applications

Molecular Dynamics Simulations in Statistical Physics: Theory and Applications
  • Author : Hiqmet Kamberaj
  • Publisher :Unknown
  • Release Date :2020-03-20
  • Total pages :463
  • ISBN : 9783030357023
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Summary : 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.

Biomolecular and Bioanalytical Techniques

Biomolecular and Bioanalytical Techniques
  • Author : Vasudevan Ramesh
  • Publisher :Unknown
  • Release Date :2019-05-13
  • Total pages :576
  • ISBN : 9781119483960
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Summary : 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 Dynamics

Molecular Dynamics
  • Author : Ben Leimkuhler,Charles Matthews
  • Publisher :Unknown
  • Release Date :2015-05-18
  • Total pages :443
  • ISBN : 9783319163758
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Summary : 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.

An Introduction to Molecular Dynamics

An Introduction to Molecular Dynamics
  • Author : Mark S. Kemp
  • Publisher :Unknown
  • Release Date :2019
  • Total pages :184
  • ISBN : 1536160555
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Summary : "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"--