Quantum Mechanical Simulation Methods for Studying Biological Systems PDF Download
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Author: Dominique Bicout
Publisher: Springer Science & Business Media
ISBN: 3662096382
Category : Science
Languages : en
Pages : 324
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Book Description
It is now generally agreed that a deeper understanding of biological processes requires a multi-disciplinary approach employing the tools of biology, chemistry, and physics. Such understanding involves study of biomacromolecules and their functions, which includes how they interact, their reactions, and how information is transmitted between them. This volume is devoted to quantum mechanical simulation techniques, which have developed rapidly in recent years. It covers quantum mechanical calculations of large systems, molecular dynamics combining quantum and classical algorithms, quantum dynamical simulations, and electron and proton transfer processes in proteins and in solutions.
Author: Dominique Bicout
Publisher: Springer Science & Business Media
ISBN: 3662096382
Category : Science
Languages : en
Pages : 324
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Book Description
It is now generally agreed that a deeper understanding of biological processes requires a multi-disciplinary approach employing the tools of biology, chemistry, and physics. Such understanding involves study of biomacromolecules and their functions, which includes how they interact, their reactions, and how information is transmitted between them. This volume is devoted to quantum mechanical simulation techniques, which have developed rapidly in recent years. It covers quantum mechanical calculations of large systems, molecular dynamics combining quantum and classical algorithms, quantum dynamical simulations, and electron and proton transfer processes in proteins and in solutions.
Author: Collectif
Publisher:
ISBN: 9782868832634
Category :
Languages : en
Pages :
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Book Description
Author: Perla Balbuena
Publisher: Elsevier
ISBN: 0080536840
Category : Science
Languages : en
Pages : 971
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Book Description
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: Bruce J Berne
Publisher: World Scientific
ISBN: 9814496057
Category : Science
Languages : en
Pages : 880
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Book Description
The school held at Villa Marigola, Lerici, Italy, in July 1997 was very much an educational experiment aimed not just at teaching a new generation of students the latest developments in computer simulation methods and theory, but also at bringing together researchers from the condensed matter computer simulation community, the biophysical chemistry community and the quantum dynamics community to confront the shared problem: the development of methods to treat the dynamics of quantum condensed phase systems. This volume collects the lectures delivered there. Due to the focus of the school, the contributions divide along natural lines into two broad groups: (1) the most sophisticated forms of the art of computer simulation, including biased phase space sampling schemes, methods which address the multiplicity of time scales in condensed phase problems, and static equilibrium methods for treating quantum systems; (2) the contributions on quantum dynamics, including methods for mixing quantum and classical dynamics in condensed phase simulations and methods capable of treating all degrees of freedom quantum-mechanically. Contents:Barrier Crossing: Classical Theory of Rare but Important Events (D Chandler)Monte Carlo Simulations (D Frenkel)Molecular Dynamics Methods for the Enhanced Sampling of Phase Space (B J Berne)Constrained and Nonequilibrium Molecular Dynamics (G Ciccotti & M Ferrario)From Erying to Kramers: Computation of Diffusive Barrier Crossing Rates (M J Ruiz-Montero)Monte Carlo Methods for Sampling of Rare Event States (W Janke)Proton Transfer in Ice (D Marx)Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions (H Jónsson et al.)RAW Quantum Transition State Theory (G Mills et al.)Dynamics of Peptide Folding (R Elber et al.)Theoretical Studies of Activated Processes in Biological Ion Channels (B Roux & S Crouzy)The Semiclassical Initial Value Representation for Including Quantum Effects in Molecular Dynamics Simulations (W H Miller)Tunneling in the Condensed Phase: Barrier Crossing and Dynamical Control (N Makri)Feynman Path Centroid Methods for Condensed Phase Quantum Dynamics (G A Voth)Quantum Molecular Dynamics Using Wigner Representation (V S Filinov et al.)Nonadiabatic Molecular Dynamics Methods for Diffusion (D Laria et al.)and other papers Readership: Computational and statistical physicists. Keywords:Quantum;Molecular Dynamics;DynamicsReviews: “… this volume is a useful introduction to currently popular, and widely-used techniques in chemical and statistical physics. The authors are well-respected researchers in the field and the level is appropriate to graduate students and researchers.” Journal of Statistical Physics
Author: John R. Hiller
Publisher:
ISBN:
Category : Science
Languages : en
Pages : 252
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Book Description
The Consortium for Upper Level Physics Software (CUPS) has developed a comprehensive series of Nine Book/Software packages that Wiley will publish in FY '95 and '96. CUPS is an international group of 27 physicists, all with extensive backgrounds in the research, teaching, and development of instructional software. The project is being supported by the National Science Foundation (PHY-9014548), and it has received other support from the IBM Corp., Apple Computer Corp., and George Mason University. The Simulations being developed are: Astrophysics, Classical Mechanics, Electricity & Magnetism, Modern Physics, Nuclear and Particle Physics, Quantum Mechanics, Solid State, Thermal and Statistical, and Waves and Optics.
Author: Edward Timoshenko
Publisher: Edward Timoshenko
ISBN:
Category : Computers
Languages : en
Pages : 32
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Book Description
We describe the important role of the in-silico methods in modern Chemistry and Physics of complex systems and overview the major techniques. The Born-Oppenheimer approximation for electronic configurations is introduced. Classical treatment of the motion of nuclei is then considered. Potential energy surfaces, force fields, geometry optimization and energy minimisation methods are discussed. The Newton’s equations of motion and their numerical integration methods are presented with the Euler and Verlet algorithms. Calculation of various observable averages is considered in Molecular Dynamics techniques in the NVE, NVT and NPT ensembles. Brownian stochastic Dynamics and the use of random numbers generators are introduced. Equilibrium simulations based on the Monte Carlo importance sampling methods and the Metropolis algorithm are discussed. The variational approach for the Schrödinger equation and various modern Quantum Chemistry methods for the electronic configurations of atomic and molecular systems are reviewed.
Author: Wang Enge
Publisher: World Scientific
ISBN: 9813230460
Category : Science
Languages : en
Pages : 280
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Book Description
This book provides a relatively complete introduction to the methods used in computational condensed matter. A wide range of electronic structure theories are introduced, including traditional quantum chemistry methods, density functional theory, many-body perturbation theory, and more. Molecular dynamics simulations are also discussed, with extensions to enhanced sampling and free-energy calculation techniques including umbrella sampling, meta-dynamics, integrated tempering sampling, etc. As a further extension beyond the standard Born-Oppenheimer molecular dynamics, some simulation techniques for the description of quantum nuclear effects are also covered, based on Feynman's path-integral representation of quantum mechanics. The book aims to help beginning graduate students to set up a framework of the concepts they should know before tackling the physical/chemical problems they will face in their research. Contents: Introduction to Computer Simulations of Molecules and Condensed MatterQuantum Chemistry Methods and Density-Functional TheoryPseudopotentials, Full Potential, and Basis SetsMany-Body Green's Function Theory and the GW ApproximationMolecular DynamicsExtension of Molecular Dynamics, Enhanced Sampling and the Free-Energy CalculationsQuantum Nuclear EffectsAppendices: Useful Mathematical RelationsExpansion of a Non-Local FunctionThe Brillouin-Zone IntegrationThe Frequency IntegrationReferencesAcknowledgements Readership: Researchers in computational condensed matter physics. Keywords: Electronic Structures;First-Principle;Molecular Dynamics;Path-IntegralReview: Key Features: Elaboration on a framework of concepts based on the authors' research experiencesIllustrations of methods ranging from electronic structures to molecular dynamicsDetailed explanation of the path-integral method
Author: Hiroki Nakamura
Publisher: World Scientific Publishing Company
ISBN: 9789811266348
Category : Science
Languages : en
Pages : 0
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Book Description
Various quantum mechanical effects such as nonadiabatic transition, tunneling, and interference phenomena play crucial roles in chemical and biological systems. Semiclassical molecular dynamics is an attempt to properly treat these effects in computational simulations, and this book presents and explains how this may be achieved with the use of new methods and theoretical frameworks developed by the authors. This semiclassical approach could provide a powerful step forward to tackle and clarify the quantum dynamics in large chemical and biological systems, which is currently not feasible by the full quantum mechanical methods.
Author: Thomas S. Hofer
Publisher: Frontiers Media SA
ISBN: 2889456269
Category :
Languages : en
Pages : 188
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Book Description
The QM/MM method, short for quantum mechanical/molecular mechanical, is a highly versatile approach for the study of chemical phenomena, combining the accuracy of quantum chemistry to describe the region of interest with the efficiency of molecular mechanical potentials to represent the remaining part of the system. Originally conceived in the 1970s by the influential work of the the Nobel laureates Martin Karplus, Michael Levitt and Arieh Warshel, QM/MM techniques have evolved into one of the most accurate and general approaches to investigate the properties of chemical systems via computational methods. Whereas the first applications have been focused on studies of organic and biomolecular systems, a large variety of QM/MM implementations have been developed over the last decades, extending the range of applicability to address research questions relevant for both solution and solid-state chemistry as well. Despite approaching their 50th anniversary in 2022, the formulation of improved QM/MM methods is still an active field of research, with the aim to (i) extend the applicability to address an even broader range of research questions in chemistry and related disciplines, and (ii) further push the accuracy achieved in the QM/MM description beyond that of established formulations. While being a highly successful approach on its own, the combination of the QM/MM strategy with other established theoretical techniques greatly extends the capabilities of the computational approaches. For instance the integration of a suitable QM/MM technique into the highly successful Monte-Carlo and molecular dynamics simulation protocols enables the description of the chemical systems on the basis of an ensemble that is in part constructed on a quantum-mechanical basis. This eBook presents the contributions of a recent Research Topic published in Frontiers in Chemistry, that highlight novel approaches as well as advanced applications of QM/MM method to a broad variety of targets. In total 2 review articles and 10 original research contributions from 48 authors are presented, covering 12 different countries on four continents. The range of research questions addressed by the individual contributions provide a lucid overview on the versatility of the QM/MM method, and demonstrate the general applicability and accuracy that can be achieved for different problems in chemical sciences. Together with the development of improved algorithms to enhance the capabilities of quantum chemical methods and the continuous advancement in the capacities of computational resources, it can be expected that the impact of QM/MM methods in chemical sciences will be further increased already in the near future.
Author: National Academy of Engineering
Publisher: National Academies Press
ISBN: 0309487501
Category : Technology & Engineering
Languages : en
Pages : 125
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Book Description
This volume presents papers on the topics covered at the National Academy of Engineering's 2018 US Frontiers of Engineering Symposium. Every year the symposium brings together 100 outstanding young leaders in engineering to share their cutting-edge research and innovations in selected areas. The 2018 symposium was held September 5-7 and hosted by MIT Lincoln Laboratory in Lexington, Massachusetts. The intent of this book is to convey the excitement of this unique meeting and to highlight innovative developments in engineering research and technical work.
