Introduction to Practice of Molecular Simulation

Introduction to Practice of Molecular Simulation
Author: Akira Satoh
Publsiher: Elsevier
Total Pages: 330
Release: 2010-12-17
ISBN 10: 0123851491
ISBN 13: 9780123851499
Language: EN, FR, DE, ES & NL

Introduction to Practice of Molecular Simulation Book Review:

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 Simulations

Molecular Simulations
Author: Saman Alavi
Publsiher: VCH
Total Pages: 344
Release: 2020-06-03
ISBN 10: 3527341056
ISBN 13: 9783527341054
Language: EN, FR, DE, ES & NL

Molecular Simulations Book Review:

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.

Understanding Molecular Simulation

Understanding Molecular Simulation
Author: Daan Frenkel,Berend Smit
Publsiher: Elsevier
Total Pages: 664
Release: 2001-10-19
ISBN 10: 9780080519982
ISBN 13: 0080519989
Language: EN, FR, DE, ES & NL

Understanding Molecular Simulation Book Review:

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

The Art of Molecular Dynamics Simulation
Author: D. C. Rapaport,Rapaport, Dennis C. Rapaport
Publsiher: Cambridge University Press
Total Pages: 549
Release: 2004-04
ISBN 10: 9780521825689
ISBN 13: 0521825687
Language: EN, FR, DE, ES & NL

The Art of Molecular Dynamics Simulation Book Review:

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

Statistical Mechanics Theory and Molecular Simulation

Statistical Mechanics  Theory and Molecular Simulation
Author: Mark Tuckerman
Publsiher: OUP Oxford
Total Pages: 720
Release: 2010-02-11
ISBN 10: 9780191523465
ISBN 13: 0191523461
Language: EN, FR, DE, ES & NL

Statistical Mechanics Theory and Molecular Simulation Book Review:

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.

Molecular Modeling and Simulation

Molecular Modeling and Simulation
Author: Tamar Schlick
Publsiher: Springer Science & Business Media
Total Pages: 635
Release: 2013-04-18
ISBN 10: 0387224645
ISBN 13: 9780387224640
Language: EN, FR, DE, ES & NL

Molecular Modeling and Simulation Book Review:

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

Molecular Dynamics Simulation of Nanostructured Materials

Molecular Dynamics Simulation of Nanostructured Materials
Author: Snehanshu Pal,Bankim Chandra Ray
Publsiher: CRC Press
Total Pages: 314
Release: 2020-04-28
ISBN 10: 0429672454
ISBN 13: 9780429672453
Language: EN, FR, DE, ES & NL

Molecular Dynamics Simulation of Nanostructured Materials Book Review:

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.

An Introduction to Molecular Dynamics

An Introduction to Molecular Dynamics
Author: Mark S. Kemp
Publsiher: Nova Science Publishers
Total Pages: 184
Release: 2019
ISBN 10: 9781536160550
ISBN 13: 1536160555
Language: EN, FR, DE, ES & NL

An Introduction to Molecular Dynamics Book Review:

"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"--

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
Publsiher: Elsevier
Total Pages: 365
Release: 2019-08-09
ISBN 10: 0128169559
ISBN 13: 9780128169551
Language: EN, FR, DE, ES & NL

Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio Lammps and Gromacs Book Review:

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 Modeling Basics

Molecular Modeling Basics
Author: Jan H. Jensen
Publsiher: CRC Press
Total Pages: 189
Release: 2010-04-26
ISBN 10: 1420075276
ISBN 13: 9781420075274
Language: EN, FR, DE, ES & NL

Molecular Modeling Basics Book Review:

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

Computer Simulation of Liquids

Computer Simulation of Liquids
Author: M. P. Allen,M... P. Allen,D. J. Tildesley,D... J. Tildesley,TILDESLEY ALLEN
Publsiher: Oxford University Press
Total Pages: 385
Release: 1989
ISBN 10: 9780198556459
ISBN 13: 0198556454
Language: EN, FR, DE, ES & NL

Computer Simulation of Liquids Book Review:

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.

Industrial Applications of Molecular Simulations

Industrial Applications of Molecular Simulations
Author: Marc Meunier
Publsiher: CRC Press
Total Pages: 421
Release: 2011-11-28
ISBN 10: 1439861013
ISBN 13: 9781439861011
Language: EN, FR, DE, ES & NL

Industrial Applications of Molecular Simulations Book Review:

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

Molecular Pathology and the Dynamics of Disease

Molecular Pathology and the Dynamics of Disease
Author: Maika G. Mitchell
Publsiher: Academic Press
Total Pages: 178
Release: 2018-04-16
ISBN 10: 0128146117
ISBN 13: 9780128146118
Language: EN, FR, DE, ES & NL

Molecular Pathology and the Dynamics of Disease Book Review:

Molecular Pathology and the Dynamics of Disease bridges the basic science of, and primary clinical literature on, human disease. Topics covered include several major disease areas, such as inflammation and host response, vascular disease, obesity, weight regulation and appetite, cancer biology, drug development, and gene- and cell-based therapeutics that are all presented in a way that emphasizes the interplay between clinical care and investigation. As new technologies and techniques are constantly changing and laboratory scientists plays a critical role in validating data used by clinicians in diagnosing patients, this book provides a timely guide that includes a clinical, research and theory perspective. Assimilates theoretical knowledge with practical lab work Provides a needed clinical perspective, along with research and theory Highlights the impact of basic science on the practice of medicine

Computational Materials Science

Computational Materials Science
Author: June Gunn Lee
Publsiher: CRC Press
Total Pages: 375
Release: 2016-11-25
ISBN 10: 1498749755
ISBN 13: 9781498749756
Language: EN, FR, DE, ES & NL

Computational Materials Science Book Review:

This book covers the essentials of Computational Science and gives tools and techniques to solve materials science problems using molecular dynamics (MD) and first-principles methods. The new edition expands upon the density functional theory (DFT) and how the original DFT has advanced to a more accurate level by GGA+U and hybrid-functional methods. It offers 14 new worked examples in the LAMMPS, Quantum Espresso, VASP and MedeA-VASP programs, including computation of stress-strain behavior of Si-CNT composite, mean-squared displacement (MSD) of ZrO2-Y2O3, band structure and phonon spectra of silicon, and Mo-S battery system. It discusses methods once considered too expensive but that are now cost-effective. New examples also include various post-processed results using VESTA, VMD, VTST, and MedeA.

The Chemistry and Physics of Engineering Materials

The Chemistry and Physics of Engineering Materials
Author: Alexandr A. Berlin,Roman Joswik,Nikolai I. Vatin
Publsiher: CRC Press
Total Pages: 392
Release: 2018-07-17
ISBN 10: 0429843143
ISBN 13: 9780429843143
Language: EN, FR, DE, ES & NL

The Chemistry and Physics of Engineering Materials Book Review:

This new volume focuses on the limitations, properties, and models in the chemistry and physics of engineering materials that have potential for applications in several disciplines of engineering and science. Contributions range from new methods to novel applications of existing methods. The collection of topics in this volume reflects the diversity of recent advances in chemistry and physics of engineering materials with a broad perspective that will be useful for scientists as well as for graduate students and engineers. This new book presents leading-edge research from around the world. Topics in the book include: • aerogels materials and technology • diffusion dynamics in nanomaterials • entropic nomograms • structural analyses of particulate-filled polymer nanocomposites mechanical properties • protection of rubbers against aging • structure-property correlation and forecast of corrosion This volume is also sold as part of a two-volume set. Volume 1 focuses on modern analytic methodologies in the chemistry and physics of engineering materials.

Reviews in Computational Chemistry

Reviews in Computational Chemistry
Author: Abby L. Parrill,Kenny B. Lipkowitz
Publsiher: John Wiley & Sons
Total Pages: 560
Release: 2015-04-27
ISBN 10: 1118407776
ISBN 13: 9781118407776
Language: EN, FR, DE, ES & NL

Reviews in Computational Chemistry Book Review:

REVIEWS IN COMPUTATIONAL CHEMISTRY The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered on molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics in Volume 28 include: Free-energy Calculations with Metadynamics Polarizable Force Fields for Biomolecular Modeling Modeling Protein Folding Pathways Assessing Structural Predictions of Protein-Protein Recognition Kinetic Monte Carlo Simulation of Electrochemical Systems Reactivity and Dynamics at Liquid InterfacesFrom Reviews Of The Series FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."—JOURNAL OF MOLECULAR GRAPHICS AND MODELLING "One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."—JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Numerical Simulation in Molecular Dynamics

Numerical Simulation in Molecular Dynamics
Author: Michael Griebel,Stephan Knapek,Gerhard Zumbusch
Publsiher: Springer Science & Business Media
Total Pages: 476
Release: 2007-08-16
ISBN 10: 3540680950
ISBN 13: 9783540680956
Language: EN, FR, DE, ES & NL

Numerical Simulation in Molecular Dynamics Book Review:

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.

Mechanics of Particle and Fiber Reinforced Polymer Nanocomposites

Mechanics of Particle  and Fiber Reinforced Polymer Nanocomposites
Author: Sumit Sharma
Publsiher: John Wiley & Sons
Total Pages: 320
Release: 2021-03-03
ISBN 10: 1119653622
ISBN 13: 9781119653622
Language: EN, FR, DE, ES & NL

Mechanics of Particle and Fiber Reinforced Polymer Nanocomposites Book Review:

Learn to model your own problems for predicting the properties of polymer-based composites Mechanics of Particle- and Fiber-Reinforced Polymer Nanocomposites: Nanoscale to Continuum Simulations provides readers with a thorough and up-to-date overview of nano, micro, and continuum approaches for the multiscale modeling of polymer-based composites. Covering nanocomposite development, theoretical models, and common simulation methods, the text includes a variety of case studies and scripting tutorials that enable readers to apply and further develop the supplied simulations. The book describes the foundations of molecular dynamics and continuum mechanics methods, guides readers through the basic steps required for multiscale modeling of any material, and correlates the results between the experimental and theoretical work performed. Focused primarily on nanocomposites, the methods covered in the book are applicable to various other materials such as carbon nanotubes, polymers, metals, and ceramics. Throughout the book, readers are introduced to key topics of relevance to nanocomposite materials and structures—supported by journal articles that discuss recent developments in modeling techniques and in the prediction of mechanical and thermal properties. This timely, highly practical resource: Explains the molecular dynamics (MD) simulation procedure for nanofiber and nanoparticle reinforced polymer composites Compares results of experimental and theoretical results from mechanical models at different length scales Covers different types of fibers and matrix materials that constitute composite materials, including glass, boron, carbon, and Kevlar Reviews models that predict the stiffness of short-fiber composites, including the self-consistent model for finite-length fibers, bounding models, and the Halpin-Tsai equation Describes various molecular modeling methods such as Monte Carlo, Brownian dynamics, dissipative particle dynamics, and lattice Boltzmann methods Highlights the potential of nanocomposites for defense and space applications Perfect for materials scientists, materials engineers, polymer scientists, and mechanical engineers, Mechanics of Particle- and Fiber-Reinforced Polymer Nanocomposites is also a must-have reference for computer simulation scientists seeking to improve their understanding of reinforced polymer nanocomposites.

Extending and Modifying LAMMPS Writing Your Own Source Code

Extending and Modifying LAMMPS Writing Your Own Source Code
Author: Dr. Shafat Mubin,Jichen Li,Dr. Steven Plimpton
Publsiher: Packt Publishing Ltd
Total Pages: 394
Release: 2021-02-19
ISBN 10: 1800567235
ISBN 13: 9781800567238
Language: EN, FR, DE, ES & NL

Extending and Modifying LAMMPS Writing Your Own Source Code Book Review:

Understand the LAMMPS source code and modify it to meet your research needs, and run simulations for bespoke applications involving forces, thermostats, pair potentials and more with ease Key Features Understand the structure of the LAMMPS source code Implement custom features in the LAMMPS source code to meet your research needs Run example simulations involving forces, thermostats, and pair potentials based on implemented features Book Description LAMMPS is one of the most widely used tools for running simulations for research in molecular dynamics. While the tool itself is fairly easy to use, more often than not you'll need to customize it to meet your specific simulation requirements. Extending and Modifying LAMMPS bridges this learning gap and helps you achieve this by writing custom code to add new features to LAMMPS source code. Written by ardent supporters of LAMMPS, this practical guide will enable you to extend the capabilities of LAMMPS with the help of step-by-step explanations of essential concepts, practical examples, and self-assessment questions. This LAMMPS book provides a hands-on approach to implementing associated methodologies that will get you up and running and productive in no time. You'll begin with a short introduction to the internal mechanisms of LAMMPS, and gradually transition to an overview of the source code along with a tutorial on modifying it. As you advance, you'll understand the structure, syntax, and organization of LAMMPS source code, and be able to write your own source code extensions to LAMMPS that implement features beyond the ones available in standard downloadable versions. By the end of this book, you'll have learned how to add your own extensions and modifications to the LAMMPS source code that can implement features that suit your simulation requirements. What you will learn Identify how LAMMPS input script commands are parsed within the source code Understand the architecture of the source code Relate source code elements to simulated quantities Learn how stored quantities are accessed within the source code Explore the mechanisms controlling pair styles, computes, and fixes Modify the source code to implement custom features in LAMMPS Who this book is for This book is for students, faculty members, and researchers who are currently using LAMMPS or considering switching to LAMMPS, have a basic knowledge of how to use LAMMPS, and are looking to extend LAMMPS source code for research purposes. This book is not a tutorial on using LAMMPS or writing LAMMPS scripts, and it is assumed that the reader is comfortable with the basic LAMMPS syntax. The book is geared toward users with little to no experience in source code editing. Familiarity with C++ programming is helpful but not necessary.

Molecular Modeling at the Atomic Scale

Molecular Modeling at the Atomic Scale
Author: Ruhong Zhou
Publsiher: CRC Press
Total Pages: 388
Release: 2014-08-21
ISBN 10: 146656296X
ISBN 13: 9781466562967
Language: EN, FR, DE, ES & NL

Molecular Modeling at the Atomic Scale Book Review:

Although molecular modeling has been around for a while, the groundbreaking advancement of massively parallel supercomputers and novel algorithms for parallelization is shaping this field into an exciting new area. Developments in molecular modeling from experimental and computational techniques have enabled a wide range of biological applications. Responding to this renaissance, Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology includes discussions of advanced techniques of molecular modeling and the latest research advancements in biomolecular applications from leading experts. The book begins with a brief introduction of major methods and applications, then covers the development of cutting-edge methods/algorithms, new polarizable force fields, and massively parallel computing techniques, followed by descriptions of how these novel techniques can be applied in various research areas in molecular biology. It also examines the self-assembly of biomacromolecules, including protein folding, RNA folding, amyloid peptide aggregation, and membrane lipid bilayer formation. Additional topics highlight biomolecular interactions, including protein interactions with DNA/RNA, membrane, ligands, and nanoparticles. Discussion of emerging topics in biomolecular modeling such as DNA sequencing with solid-state nanopores and biological water under nanoconfinement round out the coverage. This timely summary contains the perspectives of leading experts on this transformation in molecular biology and includes state-of-the-art examples of how molecular modeling approaches are being applied to critical questions in modern quantitative biology. It pulls together the latest research and applications of molecular modeling and real-world expertise that can boost your research and development of applications in this rapidly changing field.