Author: Dimitrios Vlachakis
Publisher: Lulu.com
ISBN: 0615176062
Category : Science
Languages : en
Pages : 160

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Book Description
A brief introduction to the basic knowledge underlying modern molecular modelling

Author: Daan Frenkel
Publisher: Elsevier
ISBN: 0080519989
Category : Science
Languages : en
Pages : 661

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Book Description
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: William B. Smith
Publisher: Wiley-VCH
ISBN:
Category : Science
Languages : en
Pages : 216

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Book Description
"Introduction to Theoretical Organic Chemistry" provides an introduction for chemists with a limited mathematical background, yet need a working understanding of quantum chemistry as applied to problems in organic chemistry. This book is unique in that it is written at the level of the advanced undergraduate or beginning graduate student in organic chemistry, whose exposure to theoretical chemistry is relatively recent. It fills a niche in that most books on theoretical organic chemistry are written by theoretical or computational chemists, whereas this book is written by an organic chemist. The book covers molecular modeling computer software, and offers a useful guide to the scope and limitations of each program, along with specific examples of input and output for several of the most popular software. Numerous examples and exercises are provided.

Author: Gregory R. Bowman
Publisher: Springer Science & Business Media
ISBN: 9400776063
Category : Science
Languages : en
Pages : 148

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Book Description
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: K. I. Ramachandran
Publisher: Springer Science & Business Media
ISBN: 3540773045
Category : Science
Languages : en
Pages : 405

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Book Description
The gap between introductory level textbooks and highly specialized monographs is filled by this modern textbook. It provides in one comprehensive volume the in-depth theoretical background for molecular modeling and detailed descriptions of the applications in chemistry and related fields like drug design, molecular sciences, biomedical, polymer and materials engineering. Special chapters on basic mathematics and the use of respective software tools are included. Numerous numerical examples, exercises and explanatory illustrations as well as a web site with application tools (http://www.amrita.edu/cen/ccmm) support the students and lecturers.

Author: Alan Hinchliffe
Publisher: John Wiley & Sons
ISBN: 0470030054
Category : Science
Languages : en
Pages : 428

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Book Description
Presenting a concise, basic introduction to modelling and computational chemistry this text includes relevant introductory material to ensure greater accessibility to the subject. Provides a comprehensive introduction to this evolving and developing field Focuses on MM, MC, and MD with an entire chapter devoted to QSAR and Discovery Chemistry. Includes many real chemical applications combined with worked problems and solutions provided in each chapter Ensures that up-to-date treatment of a variety of chemical modeling techniques are introduced.

Author: Martin J. Field
Publisher: Cambridge University Press
ISBN: 1139465813
Category : Science
Languages : en
Pages : 294

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Book Description
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: Jan H. Jensen
Publisher: CRC Press
ISBN: 1420075276
Category : Science
Languages : en
Pages : 192

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Book Description
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

Author: Errol G. Lewars
Publisher: Springer Science & Business Media
ISBN: 0306483912
Category : Science
Languages : en
Pages : 474

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Book Description
Computational chemistry has become extremely important in the last decade, being widely used in academic and industrial research. Yet there have been few books designed to teach the subject to nonspecialists. Computational Chemistry: Introduction to the Theory and Applications of Molecular and Quantum Mechanics is an invaluable tool for teaching and researchers alike. The book provides an overview of the field, explains the basic underlying theory at a meaningful level that is not beyond beginners, and it gives numerous comparisons of different methods with one another and with experiment. The following concepts are illustrated and their possibilities and limitations are given: - potential energy surfaces; - simple and extended Hückel methods; - ab initio, AM1 and related semiempirical methods; - density functional theory (DFT). Topics are placed in a historical context, adding interest to them and removing much of their apparently arbitrary aspect. The large number of references, to all significant topics mentioned, should make this book useful not only to undergraduates but also to graduate students and academic and industrial researchers.

Author: Mark Tuckerman
Publisher: OUP Oxford
ISBN: 0191523461
Category : Science
Languages : en
Pages : 719

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Book Description
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.