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Author : Martin J. Field
Publisher : Unknown
Page : 339 pages
File Size : 55,6 Mb
Release : 2007
Category : Electronic
ISBN : OCLC:613155351
Author : Martin J. Field
Publisher : Cambridge University Press
Page : 294 pages
File Size : 51,7 Mb
Release : 2007-07-19
Category : Science
ISBN : 9781139465816
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.
Author : Tamar Schlick
Publisher : Springer Science & Business Media
Page : 757 pages
File Size : 47,7 Mb
Release : 2010-08-03
Category : Mathematics
ISBN : 9781441963512
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
Author : Daan Frenkel,Berend Smit
Publisher : Elsevier
Page : 664 pages
File Size : 54,6 Mb
Release : 2001-10-19
Category : Science
ISBN : 0080519989
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.
Author : Saman Alavi
Publisher : John Wiley & Sons
Page : 414 pages
File Size : 44,5 Mb
Release : 2020-05-11
Category : Technology & Engineering
ISBN : 9783527699469
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.
Author : T. Grant Glover,Bin Mu
Publisher : CRC Press
Page : 523 pages
File Size : 53,5 Mb
Release : 2018-09-03
Category : Technology & Engineering
ISBN : 9780429891762
This text discusses the synthesis, characterization, and application of metal-organic frameworks (MOFs) for the purpose of adsorbing gases. It provides details on the fundamentals of thermodynamics, mass transfer, and diffusion that are commonly required when evaluating MOF materials for gas separation and storage applications and includes a discussion of molecular simulation tools needed to examine gas adsorption in MOFs. Additionally, the work presents techniques that can be used to characterize MOFs after gas adsorption has occurred and provides guidance on the water stability of these materials. Lastly, applications of MOFs are considered with a discussion of how to measure the gas storage capacity of MOFs, a discussion of how to screen MOFs to for filtration applications, and a discussion of the use of MOFs to perform industrial separations, such as olefin/paraffin separations. Throughout the work, fundamental information, such as a discussion on the calculation of MOF surface area and description of adsorption phenomena in packed-beds, is balanced with a discussion of the results from research literature.
Author : Akira Satoh
Publisher : Elsevier
Page : 333 pages
File Size : 54,7 Mb
Release : 2010-12-17
Category : Technology & Engineering
ISBN : 9780123851499
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
Author : Jerzy Leszczynski
Publisher : World Scientific
Page : 260 pages
File Size : 45,9 Mb
Release : 2005
Category : Computers
ISBN : 9789812560971
"Vast progress in the area of computational chemistry has been achieved in the last decade. Theoretical methods such as quantum mechanics, molecular dynamics and statistical mechanics have been successfully used to characterize chemical systems and to design new materials, drugs and chemicals. The reviews presented in this volume discuss the current advances in computational methodologies and their applications. The areas covered include materials science, nanotechnology, inorganic and biological systems. The major thrust of the book is to bring timely overviews of new findings and methods applied in the rapidly changing field of computational chemistry."--BOOK JACKET.
Author : Kilho Eom
Publisher : CRC Press
Page : 562 pages
File Size : 53,6 Mb
Release : 2011-10-19
Category : Science
ISBN : 9781439835067
Until the late 20th century, computational studies of biomolecules and nanomaterials had considered the two subjects separately. A thorough presentation of state-of-the-art simulations for studying the nanoscale behavior of materials, Simulations in Nanobiotechnology discusses computational simulations of biomolecules and nanomaterials together. Th
Author : Philippe G. Ciarlet
Publisher : Elsevier
Page : 400 pages
File Size : 52,7 Mb
Release : 2010-12-07
Category : Science
ISBN : 0444537619
Essential Computational Modeling in Chemistry presents key contributions selected from the volume in the Handbook of Numerical Analysis: Computational Modeling in Chemistry Vol. 10(2005). Computational Modeling is an active field of scientific computing at the crossroads between Physics, Chemistry, Applied Mathematics and Computer Science. Sophisticated mathematical models are increasingly complex and extensive computer simulations are on the rise. Numerical Analysis and scientific software have emerged as essential steps for validating mathematical models and simulations based on these models. This guide provides a quick reference of computational methods for use in understanding chemical reactions and how to control them. By demonstrating various computational methods in research, scientists can predict such things as molecular properties. The reference offers a number of techniques and the numerical analysis needed to perform rigorously founded computations. Various viewpoints of methods and applications are available for researchers to chose and experiment with; Numerical analysis and open problems is useful for experimentation; Most commonly used models and techniques for the molecular case is quickly accessible
Author : Jerzy Leszczynski
Publisher : World Scientific
Page : 258 pages
File Size : 51,5 Mb
Release : 2005-05-30
Category : Science
ISBN : 9789814481397
Vast progress in the area of computational chemistry has been achieved in the last decade. Theoretical methods such as quantum mechanics, molecular dynamics and statistical mechanics have been successfully used to characterize chemical systems and to design new materials, drugs and chemicals. The reviews presented in this volume discuss the current advances in computational methodologies and their applications. The areas covered include materials science, nanotechnology, inorganic and biological systems. The major thrust of the book is to bring timely overviews of new findings and methods applied in the rapidly changing field of computational chemistry.
Author : Philippe G. Ciarlet,Jacques-Louis Lions
Publisher : Gulf Professional Publishing
Page : 928 pages
File Size : 47,8 Mb
Release : 1990
Category : Mathematics
ISBN : 0444512489
Aiming to provide the reader with a general overview of the mathematical and numerical techniques used for the simulation of matter at the microscopic scale, this book lays the emphasis on the numerics, but modelling aspects are also addressed. The contributors come from different scientific communities: physics, theoretical chemistry, mathematical analysis, stochastic analysis, numerical analysis, and the text should be suitable for graduate students in mathematics, sciences and engineering and technology.
Author : Anonim
Publisher : Academic Press
Page : 366 pages
File Size : 43,5 Mb
Release : 2017-07-17
Category : Medical
ISBN : 9780128118771
Structural and Mechanistic Enzymology, Volume 109, the latest release in the Advances in Protein Chemistry and Structural Biology series, is an essential resource for protein chemists. Chapters in this new volume include Collagenolytic Matrix Metalloproteinase Structure–Function Relationships: Insights from Molecular Dynamics Studies, Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design, Computational Biochemistry─Enzyme Mechanisms Explored, and A Paradigm for C─H Bond Cleavage: Structural and Functional Aspects of Transition State Stabilization by Mandelate Racemase. This series presents new information on protocols and analysis of proteins, with each volume guest edited by leading experts in a broad range of protein-related topics. This volume presents state-of-the-art contributions, providing insights into the relationship between enzyme structure, catalysis, and function. Provides cutting-edge developments in protein chemistry and structural biology Features new information about protocols and analysis of proteins Contains chapters written by authorities in their respective fields Targeted to a wide audience of researchers, specialists and students
Author : Jean-Louis Rivail,Manuel Ruiz-Lopez,Xavier Assfeld
Publisher : Springer
Page : 523 pages
File Size : 42,6 Mb
Release : 2015-10-13
Category : Science
ISBN : 9783319216263
This multi-author contributed volume includes methodological advances and original applications to actual chemical or biochemical phenomena which were not possible before the increased sophistication of modern computers. The chapters contain detailed reviews of the developments of various computational techniques, used to study complex molecular systems such as molecular liquids and solutions (particularly aqueous solutions), liquid-gas, solid-gas interphase and biomacromolecular systems. Quantum modeling of complex molecular systems is a useful resource for graduate students and fledgling researchers and is also an excellent companion for research professionals engaged in computational chemistry, material science, nanotechnology, physics, drug design, and molecular biochemistry.
Author : Gregory R. Bowman,Vijay S. Pande,Frank Noé
Publisher : Springer Science & Business Media
Page : 139 pages
File Size : 53,8 Mb
Release : 2013-12-02
Category : Science
ISBN : 9789400776067
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.