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Author : Martin J. Field
Publisher :
ISBN 13 :
Total Pages : 339 pages
Book Rating : 4.:/5 (613 download)
Download or read book A Practical Introduction to the Simulation of Molecular Systems written by Martin J. Field and published by . This book was released on 2007 with total page 339 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Martin J. Field
Publisher : Cambridge University Press
ISBN 13 : 1139465813
Total Pages : 294 pages
Book Rating : 4.1/5 (394 download)
Download or read book A Practical Introduction to the Simulation of Molecular Systems written by Martin J. Field and published by Cambridge University Press. This book was released on 2007-07-19 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Daan Frenkel
Publisher : Elsevier
ISBN 13 : 9780080519982
Total Pages : 664 pages
Book Rating : 4.5/5 (199 download)
Download or read book Understanding Molecular Simulation written by Daan Frenkel and published by Elsevier. This book was released on 2001-10-19 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Tamar Schlick
Publisher : Springer Science & Business Media
ISBN 13 : 1441963510
Total Pages : 757 pages
Book Rating : 4.4/5 (419 download)
Download or read book Molecular Modeling and Simulation: An Interdisciplinary Guide written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2010-08-03 with total page 757 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Saman Alavi
Publisher : John Wiley & Sons
ISBN 13 : 3527699465
Total Pages : 414 pages
Book Rating : 4.5/5 (276 download)
Download or read book Molecular Simulations written by Saman Alavi and published by John Wiley & Sons. This book was released on 2020-05-11 with total page 414 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Gregory R. Bowman
Publisher : Springer Science & Business Media
ISBN 13 : 9400776063
Total Pages : 139 pages
Book Rating : 4.4/5 (7 download)
Download or read book An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation written by Gregory R. Bowman and published by Springer Science & Business Media. This book was released on 2013-12-02 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : T. Grant Glover
Publisher : CRC Press
ISBN 13 : 0429891768
Total Pages : 523 pages
Book Rating : 4.4/5 (298 download)
Download or read book Gas Adsorption in Metal-Organic Frameworks written by T. Grant Glover and published by CRC Press. This book was released on 2018-09-03 with total page 523 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Philippe G. Ciarlet
Publisher : Elsevier
ISBN 13 : 9780444537614
Total Pages : 400 pages
Book Rating : 4.5/5 (376 download)
Download or read book Essential Computational Modeling in Chemistry written by Philippe G. Ciarlet and published by Elsevier. This book was released on 2010-12-07 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Akira Satoh
Publisher : Elsevier
ISBN 13 : 0123851491
Total Pages : 333 pages
Book Rating : 4.1/5 (238 download)
Download or read book Introduction to Practice of Molecular Simulation written by Akira Satoh and published by Elsevier. This book was released on 2010-12-17 with total page 333 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
ISBN 13 : 9812560971
Total Pages : 260 pages
Book Rating : 4.8/5 (125 download)
Download or read book Computational Chemistry written by Jerzy Leszczynski and published by World Scientific. This book was released on 2005 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: "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
ISBN 13 : 1439835063
Total Pages : 562 pages
Book Rating : 4.4/5 (398 download)
Download or read book Simulations in Nanobiotechnology written by Kilho Eom and published by CRC Press. This book was released on 2011-10-19 with total page 562 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Jerzy Leszczynski
Publisher : World Scientific
ISBN 13 : 9814481394
Total Pages : 258 pages
Book Rating : 4.8/5 (144 download)
Download or read book Computational Chemistry: Reviews Of Current Trends, Vol. 9 written by Jerzy Leszczynski and published by World Scientific. This book was released on 2005-05-30 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Jean-Louis Rivail
Publisher : Springer
ISBN 13 : 3319216260
Total Pages : 523 pages
Book Rating : 4.3/5 (192 download)
Download or read book Quantum Modeling of Complex Molecular Systems written by Jean-Louis Rivail and published by Springer. This book was released on 2015-10-13 with total page 523 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Philippe G. Ciarlet
Publisher : Gulf Professional Publishing
ISBN 13 : 9780444512482
Total Pages : 928 pages
Book Rating : 4.5/5 (124 download)
Download or read book Computational Chemistry written by Philippe G. Ciarlet and published by Gulf Professional Publishing. This book was released on 1990 with total page 928 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 :
Publisher : Academic Press
ISBN 13 : 0128118776
Total Pages : 366 pages
Book Rating : 4.1/5 (281 download)
Download or read book Structural and Mechanistic Enzymology written by and published by Academic Press. This book was released on 2017-07-17 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 : Lemont B. Kier
Publisher : Springer Science & Business Media
ISBN 13 : 1402036906
Total Pages : 175 pages
Book Rating : 4.4/5 (2 download)
Download or read book Modeling Chemical Systems using Cellular Automata written by Lemont B. Kier and published by Springer Science & Business Media. This book was released on 2006-02-23 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modeling Chemical Systems using Cellular Automata provides a practical introduction to an exciting modeling paradigm for complex systems. The book first discusses the nature of scientific inquiry using models and simulations, and then describes the nature of cellular automata models. It then gives detailed descriptions, with examples and exercises, of how cellular automata models can be used in the study of a wide variety chemical, physical, and biochemical phenomena. Topics covered include models of water itself, solution phenomena, solution interactions with stationary systems, first- and second-order kinetic phenomena, enzyme kinetics, vapor-liquid equilibrium, and atomic and molecular excited-state kinetics. The student experiences these systems through hands-on examples and guided studies. This book is the first of its kind: a textbook and a laboratory manual about cellular automata modeling of common systems in chemistry. The book is designed to be used as a text in undergraduate courses dealing with complex systems and/or as a computational supplement to laboratory courses taught at the undergraduate level. The book includes: - Compact descriptions of a large variety of physical and chemical phenomena - Illustrative examples of simulations, with exercises for further study - An instructor's manual for use of the program The book will be of great value in undergraduate courses in chemistry, physics, biology, applied mathematics, and bioinformatics, and as a supplement for laboratory courses in introductory chemistry, organic chemistry, physical chemistry, medicinal chemistry, chemical engineering and other courses dealing with statistical and dynamic systems. It allows the exploration of a wide range of dynamic phenomena, many of which are not normally accessible within conventional laboratory settings due to limitations of time, cost, and experimental equipment. The book is both a textbook on applied Cellular Automata and a lab manual for chemistry (physics, engineering) courses with lab activity. It would supplement other lab work and be an additonal book the students would use in the course. The authors have assessed the emerging need for this kind of activity in science labs because of the cost of the practical activitites and the frequent failure of some exercises leading to lost didactic value of some experiments. This book is pioneering an alternative that will grow in use. There are no course directors who would use Cellular Automata exclusively. The authors see an emerging interest in this kind of work in courses that contain lab exercises. One such course is the graduate course that Lemont Kier gives in Life Sciences about complexity. He uses many examples and studies from Cellular Automata in the latter part of this course.
Author : Mark Tuckerman
Publisher : OUP Oxford
ISBN 13 : 9780191523465
Total Pages : 720 pages
Book Rating : 4.5/5 (234 download)
Download or read book Statistical Mechanics: Theory and Molecular Simulation written by Mark Tuckerman and published by OUP Oxford. This book was released on 2010-02-11 with total page 720 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
