[PDF] Polarizable Potential Energy Functions For Molecular Simulation eBook

Author : Perla Balbuena
Publisher : Elsevier
Page : 971 pages
File Size : 31,15 MB
Release : 1999-04-22
Category : Science
ISBN : 0080536840

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The latest developments in quantum and classical molecular dynamics, related techniques, and their applications to several fields of science and engineering. Molecular simulations include a broad range of methodologies such as Monte Carlo, Brownian dynamics, lattice dynamics, and molecular dynamics (MD). Features of this book: • Presents advances in methodologies, introduces quantum methods and lists new techniques for classical MD • Deals with complex systems: biomolecules, aqueous solutions, ice and clathrates, liquid crystals, polymers • Provides chemical reactions, interfaces, catalysis, surface phenomena and solids Although the book is not formally divided into methods and applications, the chapters are arranged starting with those that discuss new algorithms, methods and techniques, followed by several important applications.

Author : Jean-Louis Rivail
Publisher : Springer
Page : 524 pages
File Size : 15,67 MB
Release : 2015-10-13
Category : Science
ISBN : 3319216260

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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 : Alan Hinchliffe
Publisher : John Wiley & Sons
Page : 369 pages
File Size : 15,44 MB
Release : 2011-08-17
Category : Science
ISBN : 1119964814

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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.

Author : Joshua A. Rackers
Publisher :
Page : 289 pages
File Size : 23,19 MB
Release : 2019
Category : Electronic dissertations
ISBN :

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The grand challenge of biophysics is to use the fundamental laws of physics to predict how biological molecules will move and interact. The atomistic HIPPO (Hydrogen-like Intermolecular Polarizable Potential) force field is meant to address this challenge. It does so by breaking down the intermolecular potential energy function of biomolecular interactions into physically meaningful components (electrostatics, polarization, dispersion, and exchange-repulsion) and using this function to drive molecular dynamics simulations. This force field is able to achieve accuracy within 1 kcal/mol for each component when compared with ab initio Symmetry Adapted Perturbation Theory calculations. HIPPO is capable of this accuracy because it introduces a model electron density on every atom in the molecular system. Since the model is built on first-principles physics, it is transferable from small model systems to bulk phase. In the first test case, the HIPPO force field for water was able to reproduce the experimental density, heat of vaporization and dielectric constant to within 1%. Importantly, HIPPO has been shown to be only 10% more computationally expensive than the widely-used AMOEBA force field, meaning that more accurate simulations of larger biological molecules are well within reach.

Author : Kun Zhou
Publisher : Academic Press
Page : 375 pages
File Size : 30,83 MB
Release : 2022-02-10
Category : Technology & Engineering
ISBN : 0128166169

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Molecular Dynamic Simulation: Fundamentals and Applications explains the basic principles of MD simulation and explores its recent developments and roles in advanced modeling approaches. The implementation of MD simulation and its application to various aspects of materials science and engineering including mechanical, thermal, mass transportation, and physical/chemical reaction problems are illustrated. Innovative modeling techniques that apply MD to explore the mechanics of typical nanomaterials and nanostructures and to characterize crystalline, amorphous, and liquid systems are also presented. The rich research experience of the authors in MD simulation will ensure that the readers are provided with both an in-depth understanding of MD simulation and clear technical guidance. Provides a comprehensive overview of the underlying theories of molecular dynamics (MD) simulation Presents application-based examples pertaining to a broad range of mechanical, thermal, and mass transport problems Explores innovative modeling techniques for simulating typical nanomaterials and nanostructures and for characterizing crystalline, amorphous, and liquid systems

Author : Donald Truhlar
Publisher : Springer
Page : 878 pages
File Size : 29,77 MB
Release : 1981-08
Category : Science
ISBN :

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The present volume is concerned with two of the central questions of chemical dynamics. What do we know about the energies of interaction of atoms and molecules with each other and with solid surfaces? How can such interaction energies be used to understand and make quantitative predictions about dynamical processes like scattering, energy transfer, and chemical reactions? It is becoming clearly recognized that the computer is leading to rapid progress in answering these questions. The computer allows probing dynamical mechanisms in fine detail and often allows us to answer questions that cannot be addressed with current experimental techniques. As we enter the 1980's, not only are more powerful and faster computers being used, but techniques and methods have been honed to a state where exciting and reliable data are being generated on a variety of systems at an unprecedented pace. The present volume presents a collection of work that illustrates the capabilities and some of the successes of this kind of computer-assisted research. In a 1978 Chemical Society Report, Frey and Walsh pointed out that "it is extremely doubtful if a calculated energy of activation for any unimolecular decomposition can replace an experimental deter mination. " However they also recorded that they "believe[d] that some of the elaborate calculations being performed at present do suggest that we may be approaching a time when a choice between reaction mechanisms will be helped by such [computational] work.

Author : Saman Alavi
Publisher : John Wiley & Sons
Page : 342 pages
File Size : 23,53 MB
Release : 2020-06-29
Category : Technology & Engineering
ISBN : 3527341056

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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.