Download or read book Quantum Mechanical Simulation Methods for Studying Biological Systems written by Dominique Bicout and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book QUANTUM MECHANICAL SIMULATION METHODS written by Collectif and published by . This book was released on 1996-02 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Classical And Quantum Dynamics In Condensed Phase Simulations Proceedings Of The International School Of Physics written by Bruce J Berne and published by World Scientific. This book was released on 1998-06-17 with total page 881 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Molecular Dynamics written by Perla Balbuena and published by Elsevier. This book was released on 1999-04-22 with total page 971 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Computational Chemistry Computer Simulation Techniques written by Edward Timoshenko and published by Edward Timoshenko. This book was released on 2021-05-06 with total page 32 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Quantum Mechanical Molecular Mechanical Approaches for the Investigation of Chemical Systems Recent Developments and Advanced Applications written by Thomas S. Hofer and published by Frontiers Media SA. This book was released on 2018-11-28 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Quantum Mechanics Simulations written by John R. Hiller and published by . This book was released on 1995-03-03 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Computer Simulations Of Molecules And Condensed Matter From Electronic Structures To Molecular Dynamics written by Wang Enge and published by World Scientific. This book was released on 2018-01-17 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Semiclassical Molecular Dynamics Simulation Method written by Hiroki Nakamura and published by World Scientific Publishing Company. This book was released on 2024-11-30 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Atomistic Simulation Methods in Solid Mechanics written by Zhiping Xu and published by Academic Press. This book was released on 2018-07-01 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many exciting problems in mechanics are multiscale in nature. For example, the failure of materials involves breaking of chemical bonds at the atomic scale and crack spreading at larger scales. Mechanics of the cell as a material is defined by the cytoskeleton networks and membrane, as built up from proteins and lipids at the molecular level. To solve these problems, one must be equipped with techniques that are able to address the multiphysics nature at different space and time scales and successfully bridging them. Recently, rapid progresses in micro-, nanomechanics and mechanics of biological materials urges the development of theoretical models and numerical techniques within this scenario. The goal of this book is to bring a pedestrian introduction and in-depth discussion on the key ideas and challenges. In this book, we aim to present the developing field of atomistic simulation methods and their applications in solid mechanics, in a self-contained way. The first part (the algorithm) will cover basics in quantum, classical and statistical mechanics knowledge, also basic concepts and physics of solid mechanics. With this background, the algorithm of molecular dynamics and relative methods such as Monte-Carlo methods are introduced as well. The second part of the book focuses on a number of hot topics in the current mechanics community, from failure of materials, nanomechanics, to mechanics of biological materials. In the third part, extended discussion on novel methods for solving multiscale solid mechanics problems are introduced. Some of them are fresh and still under development at the time the manuscript is prepared and are believed by the authors to be the future direction in this field. The book addresses theoretical issues, and detailed numeric algorithms as well. The readers are assumed to have basic knowledge in engineering mechanics and college physics. Some experience with physical chemistry or solid-state physics will be helpful. Illustrative examples and problems are prepared after many chapters for self-study purposes.

Download or read book Computational Electronics written by Dragica Vasileska and published by CRC Press. This book was released on 2017-12-19 with total page 708 pages. Available in PDF, EPUB and Kindle. Book excerpt: Starting with the simplest semiclassical approaches and ending with the description of complex fully quantum-mechanical methods for quantum transport analysis of state-of-the-art devices, Computational Electronics: Semiclassical and Quantum Device Modeling and Simulation provides a comprehensive overview of the essential techniques and methods for effectively analyzing transport in semiconductor devices. With the transistor reaching its limits and new device designs and paradigms of operation being explored, this timely resource delivers the simulation methods needed to properly model state-of-the-art nanoscale devices. The first part examines semiclassical transport methods, including drift-diffusion, hydrodynamic, and Monte Carlo methods for solving the Boltzmann transport equation. Details regarding numerical implementation and sample codes are provided as templates for sophisticated simulation software. The second part introduces the density gradient method, quantum hydrodynamics, and the concept of effective potentials used to account for quantum-mechanical space quantization effects in particle-based simulators. Highlighting the need for quantum transport approaches, it describes various quantum effects that appear in current and future devices being mass-produced or fabricated as a proof of concept. In this context, it introduces the concept of effective potential used to approximately include quantum-mechanical space-quantization effects within the semiclassical particle-based device simulation scheme. Addressing the practical aspects of computational electronics, this authoritative resource concludes by addressing some of the open questions related to quantum transport not covered in most books. Complete with self-study problems and numerous examples throughout, this book supplies readers with the practical understanding required to create their own simulators.

Download or read book Molecular Quantum Dynamics written by Fabien Gatti and published by Springer Science & Business Media. This book was released on 2014-04-09 with total page 281 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book "Molecular Quantum Dynamics" offers them an accessible introduction. Although the calculation of large systems still presents a challenge - despite the considerable power of modern computers - new strategies have been developed to extend the studies to systems of increasing size. Such strategies are presented after a brief overview of the historical background. Strong emphasis is put on an educational presentation of the fundamental concepts, so that the reader can inform himself about the most important concepts, like eigenstates, wave packets, quantum mechanical resonances, entanglement, etc. The chosen examples highlight that high-level experiments and theory need to work closely together. This book thus is a must-read both for researchers working experimentally or theoretically in the concerned fields, and generally for anyone interested in the exciting world of molecular quantum dynamics.

Download or read book Novel Approaches to the Structure and Dynamics of Liquids Experiments Theories and Simulations written by Vladimir A. Durov and published by Springer Science & Business Media. This book was released on 2004 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Quantum Monte Carlo Methods in Condensed Matter Physics written by Masuo Suzuki and published by World Scientific. This book was released on 1993 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews recent developments of quantum Monte Carlo methods and some remarkable applications to interacting quantum spin systems and strongly correlated electron systems. It contains twenty-two papers by thirty authors. Some of the features are as follows. The first paper gives the foundations of the standard quantum Monte Carlo method, including some recent results on higher-order decompositions of exponential operators and ordered exponentials. The second paper presents a general review of quantum Monte Carlo methods used in the present book. One of the most challenging problems in the field of quantum Monte Carlo techniques, the negative-sign problem, is also discussed and new methods proposed to partially overcome it. In addition, low-dimensional quantum spin systems are studied. Some interesting applications of quantum Monte Carlo methods to fermion systems are also presented to investigate the role of strong correlations and fluctuations of electrons and to clarify the mechanism of high-c superconductivity. Not only thermal properties but also quantum-mechanical ground-state properties have been studied by the projection technique using auxiliary fields. Further, the Haldane gap is confirmed by numerical calculations. Active researchers in the forefront of condensed matter physics as well as young graduate students who want to start learning the quantum Monte Carlo methods will find this book useful.

Download or read book New Methods in Computational Quantum Mechanics written by Ilya Prigogine and published by John Wiley & Sons. This book was released on 2009-09-09 with total page 812 pages. Available in PDF, EPUB and Kindle. Book excerpt: The use of quantum chemistry for the quantitative prediction of molecular properties has long been frustrated by the technical difficulty of carrying out the needed computations. In the last decade there have been substantial advances in the formalism and computer hardware needed to carry out accurate calculations of molecular properties efficiently. These advances have been sufficient to make quantum chemical calculations a reliable tool for the quantitative interpretation of chemical phenomena and a guide to laboratory experiments. However, the success of these recent developments in computational quantum chemistry is not well known outside the community of practitioners. In order to make the larger community of chemical physicists aware of the current state of the subject, this self-contained volume of Advances in Chemical Physics surveys a number of the recent accomplishments in computational quantum chemistry. This stand-alone work presents the cutting edge of research in computational quantum mechanics. Supplemented with more than 150 illustrations, it provides evaluations of a broad range of methods, including: * Quantum Monte Carlo methods in chemistry * Monte Carlo methods for real-time path integration * The Redfield equation in condensed-phase quantum dynamics * Path-integral centroid methods in quantum statistical mechanics and dynamics * Multiconfigurational perturbation theory-applications in electronic spectroscopy * Electronic structure calculations for molecules containing transition metals * And more Contributors to New Methods in Computational Quantum Mechanics KERSTIN ANDERSSON, Department of Theoretical Chemistry, Chemical Center, Sweden DAVID M. CEPERLEY, National Center for Supercomputing Applications and Department of Physics, University of Illinois at Urbana-Champaign, Illinois MICHAEL A. COLLINS, Research School of Chemistry, Australian National University, Canberra, Australia REINHOLD EGGER, Fakultät für Physik, Universität Freiburg, Freiburg, Germany ANTHONY K. FELTS, Department of Chemistry, Columbia University, New York RICHARD A. FRIESNER, Department of Chemistry, Columbia University, New York MARKUS P. FÜLSCHER, Department of Theoretical Chemistry, Chemical Center, Sweden K. M. HO, Ames Laboratory and Department of Physics, Iowa State University, Ames, Iowa C. H. MAK, Department of Chemistry, University of Southern California, Los Angeles, California PER-ÅKE Malmqvist, Department of Theoretical Chemistry, Chemical Center, Sweden MANUELA MERCHán, Departamento de Química Física, Universitat de Valéncia, Spain LUBOS MITAS, National Center for Supercomputing Applications and Materials Research Laboratory, University of Illinois at Urbana-Champaign, Illinois STEFANO OSS, Dipartimento di Fisica, Università di Trento and Istituto Nazionale di Fisica della Materia, Unità di Trento, Italy KRISTINE PIERLOOT, Department of Chemistry, University of Leuven, Belgium W. THOMAS POLLARD, Department of Chemistry, Columbia University, New York BJÖRN O. ROOS, Department of Theoretical Chemistry, Chemical Center, Sweden LUIS SERRANO-ANDRÉS, Department of Theoretical Chemistry, Chemical Center, Sweden PER E. M. SIEGBAHN, Department of Physics, University of Stockholm, Stockholm, Sweden WALTER THIEL, Institut für Organische Chemie, Universität Zürich, Zürich, Switzerland GREGORY A. VOTH, Department of Chemistry, University of Pennsylvania, Pennsylvania C. Z. Wang, Ames Laboratory and Department of Physi

Download or read book Ab Initio Molecular Dynamics written by Dominik Marx and published by Cambridge University Press. This book was released on 2009-04-30 with total page 503 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Computer Simulation in Chemical Physics written by M. P. Allen and published by Springer Science & Business Media. This book was released on 1993 with total page 538 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proceedings of a NATO ASI held near Alghero, Italy in September 1992. The school focused on recent progress in applying the methods of computer simulation to problems in chemical physics. The 14 lectures address topics including the molecular dynamics method, advanced Monte Carlo techniques, thermodynamic constraints, computer simulations in the Gibbs ensemble, effective pair potentials and beyond, first principles molecular dynamics, computer simulation methods for nonadiabatic dynamics in condensed systems, long length- scale aspects of self organization phenomena, computer simulation of polymers, computer simulation of surfactants, parallel computing and molecular dynamics simulations, and scientific visualization--a user view. Annotation copyright by Book News, Inc., Portland, OR