understanding molecular simulation from algorithms to applications computational science

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Understanding Molecular Simulation

Author : Daan Frenkel
ISBN : 0080519989
Genre : Science
File Size : 35. 24 MB
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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.

Molecular Modelling For Beginners

Author : Alan Hinchliffe
ISBN : 9781119964810
Genre : Science
File Size : 65. 14 MB
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A concise, basic introduction to modelling and computational chemistry which focuses on the essentials, including MM, MC, and MD, along with a chapter devoted to QSAR and Discovery Chemistry. Includes supporting website featuring background information, full colour illustrations, questions and answers tied into the text,Visual Basic packages and many realistic examples with solutions Takes a hands-on approach, using state of the art software packages G03/W and/or Hyperchem, Gaussian .gjf files and sample outputs. Revised with changes in emphasis and presentation to appeal to the modern student.

Statistical Mechanics Theory And Molecular Simulation

Author : Mark Tuckerman
ISBN : 0191523461
Genre : Science
File Size : 61. 53 MB
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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

Author : Tamar Schlick
ISBN : 9780387224640
Genre : Science
File Size : 44. 52 MB
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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

Computational Materials Science

Author : June Gunn Lee
ISBN : 9781498749763
Genre : Science
File Size : 88. 37 MB
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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.

Essentials Of Computational Chemistry

Author : Christopher J. Cramer
ISBN : 9781118712276
Genre : Science
File Size : 88. 18 MB
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Essentials of Computational Chemistry provides a balanced introduction to this dynamic subject. Suitable for both experimentalists and theorists, a wide range of samples and applications are included drawn from all key areas. The book carefully leads the reader thorough the necessary equations providing information explanations and reasoning where necessary and firmly placing each equation in context.

Theory And Applications Of Computational Chemistry

Author : Clifford Dykstra
ISBN : 9780080456249
Genre : Science
File Size : 66. 70 MB
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Computational chemistry is a means of applying theoretical ideas using computers and a set of techniques for investigating chemical problems within which common questions vary from molecular geometry to the physical properties of substances. Theory and Applications of Computational Chemistry: The First Forty Years is a collection of articles on the emergence of computational chemistry. It shows the enormous breadth of theoretical and computational chemistry today and establishes how theory and computation have become increasingly linked as methodologies and technologies have advanced. Written by the pioneers in the field, the book presents historical perspectives and insights into the subject, and addresses new and current methods, as well as problems and applications in theoretical and computational chemistry. Easy to read and packed with personal insights, technical and classical information, this book provides the perfect introduction for graduate students beginning research in this area. It also provides very readable and useful reviews for theoretical chemists. * Written by well-known leading experts * Combines history, personal accounts, and theory to explain much of the field of theoretical and compuational chemistry * Is the perfect introduction to the field

The Art Of Molecular Dynamics Simulation

Author : D. C. Rapaport
ISBN : 0521825687
Genre : Science
File Size : 82. 79 MB
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The extremely powerful technique of molecular dynamics simulation involves solving the classical many-body problem in contexts relevant to the study of matter at the atomistic level. Since there is no alternative approach capable of handling this extremely broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research. This book, first published in 2004, is a blend of tutorial and recipe collection, providing both an introduction to the subject for beginners and a reference manual for the more experienced practitioner. It is organized as a series of case studies that take the reader through each of the steps from formulating the problem, developing the necessary software, and then using the programs to make actual measurements. The second edition of the book includes a substantial amount of new material as well as completely rewritten software.

Molecular Modelling Principles And Applications 2 E

Author : Leach
ISBN : 8131728609
Genre :
File Size : 43. 56 MB
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Metastable Liquids

Author : Pablo G. Debenedetti
ISBN : 0691085951
Genre : Science
File Size : 30. 35 MB
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Metastable Liquids provides a comprehensive treatment of the properties of liquids under conditions where the stable state is a vapor, a solid, or a liquid mixture of different composition. It examines the fundamental principles that govern the equilibrium properties, stability, relaxation mechanisms, and relaxation rates of metastable liquids. Building on the interplay of kinetics and thermodynamics that determines the thermophysical properties and structural relaxation of metastable liquids, it offers an in-depth treatment of thermodynamic stability theory, the statistical mechanics of metastability, nucleation, spinodal decomposition, supercooled liquids, and the glass transition. Both traditional topics--such as stability theory--and modern developments--including modern theories of nucleation and the properties of supercooled and glassy water--are treated in detail. An introductory chapter illustrates, with numerous examples, the importance and ubiquity of metastable liquids. Examples include the ascent of sap in plants, the strategies adopted by many living organisms to survive prolonged exposure to sub-freezing conditions, the behavior of proteins at low temperatures, metastability in mineral inclusions, ozone depletion, the preservation and storage of labile biochemicals, and the prevention of natural gas clathrate hydrate formation. All mathematical symbols are defined in the text and key equations are clearly explained. More complex mathematical explanations are available in the appendixes.

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