Fragmentation Toward Accurate Calculations On Complex Molecular Systems

Author : Mark S. Gordon
Publisher : John Wiley & Sons
Page : 376 pages
File Size : 41,7 Mb
Release : 2017-08-04
Category : Science
ISBN : 9781119129264

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Fragmentation: Toward Accurate Calculations on Complex Molecular Systems by Mark S. Gordon Pdf

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems introduces the reader to the broad array of fragmentation and embedding methods that are currently available or under development to facilitate accurate calculations on large, complex systems such as proteins, polymers, liquids and nanoparticles. These methods work by subdividing a system into subunits, called fragments or subsystems or domains. Calculations are performed on each fragment and then the results are combined to predict properties for the whole system. Topics covered include: Fragmentation methods Embedding methods Explicitly correlated local electron correlation methods Fragment molecular orbital method Methods for treating large molecules This book is aimed at academic researchers who are interested in computational chemistry, computational biology, computational materials science and related fields, as well as graduate students in these fields.

Author : Mark S. Gordon
Publisher : John Wiley & Sons
Page : 376 pages
File Size : 40,5 Mb
Release : 2017-10-23
Category : Science
ISBN : 9781119129240

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Fragmentation: Toward Accurate Calculations on Complex Molecular Systems by Mark S. Gordon Pdf

Fragmentation: Toward Accurate Calculations on Complex Molecular Systems introduces the reader to the broad array of fragmentation and embedding methods that are currently available or under development to facilitate accurate calculations on large, complex systems such as proteins, polymers, liquids and nanoparticles. These methods work by subdividing a system into subunits, called fragments or subsystems or domains. Calculations are performed on each fragment and then the results are combined to predict properties for the whole system. Topics covered include: Fragmentation methods Embedding methods Explicitly correlated local electron correlation methods Fragment molecular orbital method Methods for treating large molecules This book is aimed at academic researchers who are interested in computational chemistry, computational biology, computational materials science and related fields, as well as graduate students in these fields.

Author : Yuji Mochizuki,Shigenori Tanaka,Kaori Fukuzawa
Publisher : Springer Nature
Page : 606 pages
File Size : 47,6 Mb
Release : 2021-01-04
Category : Science
ISBN : 9789811592355

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Recent Advances of the Fragment Molecular Orbital Method by Yuji Mochizuki,Shigenori Tanaka,Kaori Fukuzawa Pdf

This book covers recent advances of the fragment molecular orbital (FMO) method, consisting of 5 parts and a total of 30 chapters written by FMO experts. The FMO method is a promising way to calculate large-scale molecular systems such as proteins in a quantum mechanical framework. The highly efficient parallelism deserves being considered the principal advantage of FMO calculations. Additionally, the FMO method can be employed as an analysis tool by using the inter-fragment (pairwise) interaction energies, among others, and this feature has been utilized well in biophysical and pharmaceutical chemistry. In recent years, the methodological developments of FMO have been remarkable, and both reliability and applicability have been enhanced, in particular, for non-bio problems. The current trend of the parallel computing facility is of the many-core type, and adaptation to modern computer environments has been explored as well. In this book, a historical review of FMO and comparison to other methods are provided in Part I (two chapters) and major FMO programs (GAMESS-US, ABINIT-MP, PAICS and OpenFMO) are described in Part II (four chapters). dedicated to pharmaceutical activities (twelve chapters). A variety of new applications with methodological breakthroughs are introduced in Part IV (six chapters). Finally, computer and information science-oriented topics including massively parallel computation and machine learning are addressed in Part V (six chapters). Many color figures and illustrations are included. Readers can refer to this book in its entirety as a practical textbook of the FMO method or read only the chapters of greatest interest to them.

Author : Dmitri Fedorov,Kazuo Kitaura
Publisher : CRC Press
Page : 304 pages
File Size : 44,6 Mb
Release : 2009-05-14
Category : Science
ISBN : 9781420078497

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The Fragment Molecular Orbital Method by Dmitri Fedorov,Kazuo Kitaura Pdf

Answering the need to facilitate quantum-chemical calculations of systems with thousands of atoms, Kazuo Kitaura and his coworkers developed the Fragment Molecular Orbital (FMO) method in 1999. Today, the FMO method can be applied to the study of whole proteins and protein-ligand interactions, and is extremely effective in calculating the propertie

Author : János Ángyán,John Dobson,Georg Jansen,Tim Gould
Publisher : Royal Society of Chemistry
Page : 380 pages
File Size : 55,5 Mb
Release : 2020-04-03
Category : Science
ISBN : 9781839160189

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London Dispersion Forces in Molecules, Solids and Nano-structures by János Ángyán,John Dobson,Georg Jansen,Tim Gould Pdf

London dispersion interactions are responsible for numerous phenomena in physics, chemistry and biology. Recent years have seen the development of new, physically well-founded models, and dispersion-corrected density functional theory (DFT) is now a hot topic of research. This book is an overview of current understanding of the physical origin and modelling of London dispersion forces manifested at an atomic level. It covers a wide range of system, from small intermolecular complexes, to organic molecules and crystalline solids, through to biological macromolecules and nanostructures. In presenting a broad overview of the of the physical foundations of dispersion forces, the book provides theoretical, physical and synthetic chemists, as well as solid-state physicists, with a systematic understanding of the origins and consequences of these ubiquitous interactions. The presentation is designed to be accessible to anyone with intermediate undergraduate mathematics, physics and chemistry.

Author : Yuji Mochizuki,Shigenori Tanaka,Kaori Fukuzawa
Publisher : Unknown
Page : 0 pages
File Size : 53,6 Mb
Release : 2021
Category : Electronic
ISBN : 9811592365

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Recent Advances of the Fragment Molecular Orbital Method by Yuji Mochizuki,Shigenori Tanaka,Kaori Fukuzawa Pdf

This book covers recent advances of the fragment molecular orbital (FMO) method, consisting of 5 parts and a total of 30 chapters written by FMO experts. The FMO method is a promising way to calculate large-scale molecular systems such as proteins in a quantum mechanical framework. The highly efficient parallelism deserves being considered the principal advantage of FMO calculations. Additionally, the FMO method can be employed as an analysis tool by using the inter-fragment (pairwise) interaction energies, among others, and this feature has been utilized well in biophysical and pharmaceutical chemistry. In recent years, the methodological developments of FMO have been remarkable, and both reliability and applicability have been enhanced, in particular, for non-bio problems. The current trend of the parallel computing facility is of the many-core type, and adaptation to modern computer environments has been explored as well. In this book, a historical review of FMO and comparison to other methods are provided in Part I (two chapters) and major FMO programs (GAMESS-US, ABINIT-MP, PAICS and OpenFMO) are described in Part II (four chapters). dedicated to pharmaceutical activities (twelve chapters). A variety of new applications with methodological breakthroughs are introduced in Part IV (six chapters). Finally, computer and information science-oriented topics including massively parallel computation and machine learning are addressed in Part V (six chapters). Many color figures and illustrations are included. Readers can refer to this book in its entirety as a practical textbook of the FMO method or read only the chapters of greatest interest to them.

Author : Anonim
Publisher : Unknown
Page : 128 pages
File Size : 40,6 Mb
Release : 2020
Category : Electronic
ISBN : 0815394756

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FRAGMENT MOLECULAR ORBITAL METHOD by Anonim Pdf

Author : David S. Sholl,Janice A. Steckel
Publisher : John Wiley & Sons
Page : 252 pages
File Size : 50,7 Mb
Release : 2011-09-20
Category : Science
ISBN : 9781118211045

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Density Functional Theory by David S. Sholl,Janice A. Steckel Pdf

Demonstrates how anyone in math, science, and engineering can master DFT calculations Density functional theory (DFT) is one of the most frequently used computational tools for studying and predicting the properties of isolated molecules, bulk solids, and material interfaces, including surfaces. Although the theoretical underpinnings of DFT are quite complicated, this book demonstrates that the basic concepts underlying the calculations are simple enough to be understood by anyone with a background in chemistry, physics, engineering, or mathematics. The authors show how the widespread availability of powerful DFT codes makes it possible for students and researchers to apply this important computational technique to a broad range of fundamental and applied problems. Density Functional Theory: A Practical Introduction offers a concise, easy-to-follow introduction to the key concepts and practical applications of DFT, focusing on plane-wave DFT. The authors have many years of experience introducing DFT to students from a variety of backgrounds. The book therefore offers several features that have proven to be helpful in enabling students to master the subject, including: Problem sets in each chapter that give readers the opportunity to test their knowledge by performing their own calculations Worked examples that demonstrate how DFT calculations are used to solve real-world problems Further readings listed in each chapter enabling readers to investigate specific topics in greater depth This text is written at a level suitable for individuals from a variety of scientific, mathematical, and engineering backgrounds. No previous experience working with DFT calculations is needed.

Author : Dominik Marx,Jürg Hutter
Publisher : Cambridge University Press
Page : 503 pages
File Size : 49,5 Mb
Release : 2009-04-30
Category : Science
ISBN : 9781139477192

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Ab Initio Molecular Dynamics by Dominik Marx,Jürg Hutter Pdf

Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.

Author : Errol G. Lewars
Publisher : Springer Science & Business Media
Page : 471 pages
File Size : 45,9 Mb
Release : 2007-05-08
Category : Science
ISBN : 9780306483912

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Computational Chemistry by Errol G. Lewars Pdf

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 : Saman Alavi
Publisher : John Wiley & Sons
Page : 342 pages
File Size : 41,8 Mb
Release : 2020-06-29
Category : Technology & Engineering
ISBN : 9783527341054

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Molecular Simulations by Saman Alavi Pdf

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 : Rajarshi Guha,Andreas Bender
Publisher : John Wiley & Sons
Page : 281 pages
File Size : 53,6 Mb
Release : 2011-11-30
Category : Science
ISBN : 9781118131428

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Computational Approaches in Cheminformatics and Bioinformatics by Rajarshi Guha,Andreas Bender Pdf

A breakthrough guide employing knowledge that unites cheminformatics and bioinformatics as innovation for the future Bridging the gap between cheminformatics and bioinformatics for the first time, Computational Approaches in Cheminformatics and Bioinformatics provides insight on how to blend these two sciences for progressive research benefits. It describes the development and evolution of these fields, how chemical information may be used for biological relations and vice versa, the implications of these new connections, and foreseeable developments in the future. Using algorithms and domains as workflow tools, this revolutionary text drives bioinformaticians to consider chemical structure, and similarly, encourages cheminformaticians to consider large biological systems such as protein targets and networks. Computational Approaches in Cheminformatics and Bioinformatics covers: Data sources available for modelling and prediction purposes Developments of conventional Quantitative Structure-Activity Relationships (QSAR) Computational tools for manipulating chemical and biological data Novel ways of probing the interactions between small molecules and proteins Also including insight from public (NIH), academic, and industrial sources (Novartis, Pfizer), this book offers expert knowledge to aid scientists through industry and academic study. The invaluable applications for drug discovery, cellular and molecular biology, enzymology, and metabolism make Computational Approaches in Cheminformatics and Bioinformatics the essential guidebook for evolving drug discovery research and alleviating the issue of chemical control and manipulation of various systems.

Author : Ron Elber,Dmitrii E. Makarov,Henri Orland
Publisher : John Wiley & Sons
Page : 268 pages
File Size : 45,8 Mb
Release : 2019-12-06
Category : Science
ISBN : 9781119176794

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Molecular Kinetics in Condensed Phases by Ron Elber,Dmitrii E. Makarov,Henri Orland Pdf

A guide to the theoretical and computational toolkits for the modern study of molecular kinetics in condensed phases Molecular Kinetics in Condensed Phases: Theory, Simulation and Analysis puts the focus on the theory, algorithms, simulations methods and analysis of molecular kinetics in condensed phases. The authors – noted experts on the topic – offer a detailed and thorough description of modern theories and simulation methods to model molecular events. They highlight the rigorous stochastic modelling of molecular processes and the use of mathematical models to reproduce experimental observations, such as rate coefficients, mean first passage times and transition path times. The book’s exploration of simulations examines atomically detailed modelling of molecules in action and the connections of these simulations to theory and experiment. The authors also explore the applications that range from simple intuitive examples of one- and two-dimensional systems to complex solvated macromolecules. This important book: Offers an introduction to the topic that combines theory, simulation and analysis Presents a guide written by authors that are well-known and highly regarded leaders in their fields Contains detailed examples and explanation of how to conduct computer simulations of kinetics. A detailed study of a two-dimensional system and of a solvated peptide are discussed. Discusses modern developments in the field and explains their connection to the more traditional concepts in chemical dynamics Written for students and academic researchers in the fields of chemical kinetics, chemistry, computational statistical mechanics, biophysics and computational biology, Molecular Kinetics in Condensed Phases is the authoritative guide to the theoretical and computational toolkits for the study of molecular kinetics in condensed phases.

Author : Bruce Alberts
Publisher : Unknown
Page : 0 pages
File Size : 52,8 Mb
Release : 2002
Category : Cytology
ISBN : 0815332181

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Molecular Biology of The Cell by Bruce Alberts Pdf

Author : Anonim
Publisher : Academic Press
Page : 457 pages
File Size : 40,8 Mb
Release : 2009-08-04
Category : Science
ISBN : 9780080951010

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Advances in Atomic, Molecular, and Optical Physics by Anonim Pdf

This volume continues the tradition of the Advances series. It contains contributions from experts in the field of atomic, molecular, and optical (AMO) physics. The articles contain some review material, but are intended to provide a comprehensive picture of recent important developments in AMO physics. Both theoretical and experimental articles are included in the volume. International experts Comprehensive articles New developments