Methods In Molecular Modelling Methods Algorithms And Implementation

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Methods in Molecular Modelling: Methods, Algorithms and Implementation

David O. Scanlon
Methods in Molecular Modelling Methods Algorithms and Implementation Book PDF

Author : David O. Scanlon
Publisher : Elsevier
Page : 0 pages
File Size : 47,6 Mb
Release : 2023-08-01
Category : Science
ISBN : 0443187630

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Methods in Molecular Modelling: Methods, Algorithms and Implementation by David O. Scanlon Pdf

Methods in Molecular Modelling: Methods, Algorithms and Implementation offers a brief, concise and functional overview of methods available for materials modeling, enabling readers to identify the right level of theory for their calculations. It explains the pros and cons of each method, giving the reader an understanding for which method and which level of theory to apply to get trustable results for the minimum computational cost. It serves as the foundation volume for a series which will explore different application areas in detail.The theoretical foundations of methods for modeling molecules and materials are complex, and in addition to physics and chemistry, they also require a solid understanding of mathematics and programming. Beginners in this area will appreciate helpful case studies and examples of application in this book, rather than the derivation of complicated equations. Through a balanced ratio of theoretical background of methods and practical application of these methods to representative problems from physics, chemistry, and materials science, this book teaches how to perform calculations that enable them to design new materials. More experienced researchers will also appreciate the practical applications described that can be used to prepare lectures.

New Algorithms for Macromolecular Simulation

Benedict Leimkuhler,Christophe Chipot,Ron Elber,Aatto Laaksonen,Alan Mark,Tamar Schlick,Christoph Schütte,Robert Skeel
New Algorithms for Macromolecular Simulation Book PDF

Author : Benedict Leimkuhler,Christophe Chipot,Ron Elber,Aatto Laaksonen,Alan Mark,Tamar Schlick,Christoph Schütte,Robert Skeel
Publisher : Springer Science & Business Media
Page : 364 pages
File Size : 43,5 Mb
Release : 2006-03-22
Category : Computers
ISBN : 9783540316183

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New Algorithms for Macromolecular Simulation by Benedict Leimkuhler,Christophe Chipot,Ron Elber,Aatto Laaksonen,Alan Mark,Tamar Schlick,Christoph Schütte,Robert Skeel Pdf

Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.

Understanding Molecular Simulation

Daan Frenkel,Berend Smit
Understanding Molecular Simulation Book PDF

Author : Daan Frenkel,Berend Smit
Publisher : Elsevier
Page : 664 pages
File Size : 42,9 Mb
Release : 2001-10-19
Category : Science
ISBN : 0080519989

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Understanding Molecular Simulation by Daan Frenkel,Berend Smit Pdf

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.

Molecular Modeling at the Atomic Scale

Ruhong Zhou
Molecular Modeling at the Atomic Scale Book PDF

Author : Ruhong Zhou
Publisher : CRC Press
Page : 392 pages
File Size : 41,6 Mb
Release : 2014-08-21
Category : Science
ISBN : 9781466562950

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Molecular Modeling at the Atomic Scale by Ruhong Zhou Pdf

Although molecular modeling has been around for a while, the groundbreaking advancement of massively parallel supercomputers and novel algorithms for parallelization is shaping this field into an exciting new area. Developments in molecular modeling from experimental and computational techniques have enabled a wide range of biological applications. Responding to this renaissance, Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology includes discussions of advanced techniques of molecular modeling and the latest research advancements in biomolecular applications from leading experts. The book begins with a brief introduction of major methods and applications, then covers the development of cutting-edge methods/algorithms, new polarizable force fields, and massively parallel computing techniques, followed by descriptions of how these novel techniques can be applied in various research areas in molecular biology. It also examines the self-assembly of biomacromolecules, including protein folding, RNA folding, amyloid peptide aggregation, and membrane lipid bilayer formation. Additional topics highlight biomolecular interactions, including protein interactions with DNA/RNA, membrane, ligands, and nanoparticles. Discussion of emerging topics in biomolecular modeling such as DNA sequencing with solid-state nanopores and biological water under nanoconfinement round out the coverage. This timely summary contains the perspectives of leading experts on this transformation in molecular biology and includes state-of-the-art examples of how molecular modeling approaches are being applied to critical questions in modern quantitative biology. It pulls together the latest research and applications of molecular modeling and real-world expertise that can boost your research and development of applications in this rapidly changing field.

Numerical Simulation in Molecular Dynamics

Michael Griebel,Stephan Knapek,Gerhard Zumbusch
Numerical Simulation in Molecular Dynamics Book PDF

Author : Michael Griebel,Stephan Knapek,Gerhard Zumbusch
Publisher : Springer Science & Business Media
Page : 472 pages
File Size : 47,6 Mb
Release : 2007-08-16
Category : Science
ISBN : 9783540680956

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Numerical Simulation in Molecular Dynamics by Michael Griebel,Stephan Knapek,Gerhard Zumbusch Pdf

This book details the necessary numerical methods, the theoretical background and foundations and the techniques involved in creating computer particle models, including linked-cell method, SPME-method, tree codes, amd multipol technique. It illustrates modeling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. The text offers step-by-step explanations of numerical simulation, providing illustrative code examples. With the description of the algorithms and the presentation of the results of various simulations from fields such as material science, nanotechnology, biochemistry and astrophysics, the reader of this book will learn how to write programs capable of running successful experiments for molecular dynamics.

Molecular Modelling

Peter Bladon,John E. Gorton,Robert B. Hammond
Molecular Modelling Book PDF

Author : Peter Bladon,John E. Gorton,Robert B. Hammond
Publisher : Royal Society of Chemistry
Page : 311 pages
File Size : 55,5 Mb
Release : 2012
Category : Science
ISBN : 9781849733526

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Molecular Modelling by Peter Bladon,John E. Gorton,Robert B. Hammond Pdf

This book is a practical, easy-to-use guide for readers with limited experience of molecular modelling. Unlike many other textbooks in this field, the authors avoid extensive discussion around complex mathematical foundations behind the methods, choosing instead to provide the reader with the choice of methods themselves.

Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery

Dastmalchi, Siavoush
Methods and Algorithms for Molecular Docking Based Drug Design and Discovery Book PDF

Author : Dastmalchi, Siavoush
Publisher : IGI Global
Page : 456 pages
File Size : 47,8 Mb
Release : 2016-05-03
Category : Medical
ISBN : 9781522501169

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Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery by Dastmalchi, Siavoush Pdf

The role of technology in the medical field has resulted in significant developments within the pharmaceutical industry. Computational approaches have emerged as a crucial method in further advancing drug design and development. Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery presents emerging research on the application of computer-assisted design methods for drugs, emphasizing the benefits and improvements that molecular docking has caused within the pharmaceutical industry. Focusing on validation methods, search algorithms, and scoring functions, this book is a pivotal resource for professionals, researchers, students, and practitioners in the field of theoretical and computational chemistry.

Molecular Modelling: The Chemistry Of The 21st Century

Marco Antonio Chaer Nascimento
Molecular Modelling The Chemistry Of The 21st Century Book PDF

Author : Marco Antonio Chaer Nascimento
Publisher : World Scientific
Page : 174 pages
File Size : 42,9 Mb
Release : 1994-03-28
Category : Electronic
ISBN : 9789814552110

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Molecular Modelling: The Chemistry Of The 21st Century by Marco Antonio Chaer Nascimento Pdf

This volume attempts to show molecular modeling as a new multidisciplinary area of research that transcends the boundaries traditionally separating biology, chemistry and physics. To this purpose, leading scientists present applications of molecular modeling to a variety of important problems such as: drug design, protein modeling, catalyst modeling, properties of glass, mechanical properties of materials and materials design. The emphasis here is on the atomistic approach.

Computational Molecular Dynamics: Challenges, Methods, Ideas

Peter Deuflhard,Jan Hermans,Benedict Leimkuhler,Alan E. Mark,Sebastian Reich,Robert D. Skeel
Computational Molecular Dynamics Challenges Methods Ideas Book PDF

Author : Peter Deuflhard,Jan Hermans,Benedict Leimkuhler,Alan E. Mark,Sebastian Reich,Robert D. Skeel
Publisher : Springer Science & Business Media
Page : 500 pages
File Size : 49,7 Mb
Release : 2012-12-06
Category : Mathematics
ISBN : 9783642583605

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Computational Molecular Dynamics: Challenges, Methods, Ideas by Peter Deuflhard,Jan Hermans,Benedict Leimkuhler,Alan E. Mark,Sebastian Reich,Robert D. Skeel Pdf

On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics. The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.

Molecular Modeling and Simulation

Tamar Schlick
Molecular Modeling and Simulation Book PDF

Author : Tamar Schlick
Publisher : Springer Science & Business Media
Page : 669 pages
File Size : 49,7 Mb
Release : 2013-04-18
Category : Science
ISBN : 9780387224640

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Molecular Modeling and Simulation by Tamar Schlick Pdf

Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

Molecular Modelling and Synthesis of Nanomaterials

Ihsan Boustani
Molecular Modelling and Synthesis of Nanomaterials Book PDF

Author : Ihsan Boustani
Publisher : Springer Nature
Page : 598 pages
File Size : 55,7 Mb
Release : 2020-07-14
Category : Technology & Engineering
ISBN : 9783030327262

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Molecular Modelling and Synthesis of Nanomaterials by Ihsan Boustani Pdf

This book presents nanomaterials as predicted by computational modelling and numerical simulation tools, and confirmed by modern experimental techniques. It begins by summarizing basic theoretical methods, then giving both a theoretical and experimental treatment of how alkali metal clusters develop into nanostructures, as influenced by the cluster's "magic number" of atoms. The book continues with a discussion of atomic clusters and nanostructures, focusing primarily on boron and carbon, exploring, in detail, the one-, two-, and three-dimensional structures of boron and carbon, and describing their myriad potential applications in nanotechnology, from nanocoating and nanosensing to nanobatteries with high borophene capacity. The broad discussion of computational modelling as well as the specific applications to boron and carbon, make this book an essential reference resource for materials scientists in this field of research.

Application of Optimization Algorithms in Chemistry

Jorge M. C. Marques,Emilio Martinez-Nunez,William L. Hase
Application of Optimization Algorithms in Chemistry Book PDF

Author : Jorge M. C. Marques,Emilio Martinez-Nunez,William L. Hase
Publisher : Frontiers Media SA
Page : 145 pages
File Size : 46,9 Mb
Release : 2020-06-08
Category : Electronic
ISBN : 9782889637102

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Application of Optimization Algorithms in Chemistry by Jorge M. C. Marques,Emilio Martinez-Nunez,William L. Hase Pdf

This eBook is dedicated to Prof. William L. Hase, who passed away on Monday, March 23, 2020.

Methods in Membrane Lipids

Alex M. Dopico
Methods in Membrane Lipids Book PDF

Author : Alex M. Dopico
Publisher : Springer Science & Business Media
Page : 1265 pages
File Size : 41,9 Mb
Release : 2007-08-30
Category : Medical
ISBN : 9781588296627

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Methods in Membrane Lipids by Alex M. Dopico Pdf

This book presents a compendium of methodologies for the study of membrane lipids, varying from traditional lab bench experimentation to computer simulation and theoretical models. The volume provides a comprehensive set of techniques for studying membrane lipids with a strong biophysical emphasis. It compares the various available techniques including the pros and cons as seen by the experts.

Understanding Molecular Simulation

Daan Frenkel,Berend Smit
Understanding Molecular Simulation Book PDF

Author : Daan Frenkel,Berend Smit
Publisher : Elsevier
Page : 868 pages
File Size : 42,8 Mb
Release : 2023-07-13
Category : Science
ISBN : 9780323913188

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Understanding Molecular Simulation by Daan Frenkel,Berend Smit Pdf

Understanding Molecular Simulation explains molecular simulation from a chemical-physics and statistical-mechanics perspective. It highlights how physical concepts are used to develop better algorithms and expand the range of applicability of simulations. Understanding Molecular Simulation is equally relevant for those who develop new code and those who use existing packages. Both groups are continuously confronted with the question of which computational technique best suits a given application. Understanding Molecular Simulation provides readers with the foundational knowledge they need to learn about, select and apply the most appropriate of these tools to their own work. The implementation of simulation methods is illustrated in pseudocodes, and their practical use is shown via case studies presented throughout the text. Since the second edition’s publication, the simulation world has expanded significantly: existing techniques have continued to develop, and new ones have emerged, opening up novel application areas. This new edition aims to describe these new developments without becoming exhaustive; examples are included that highlight current uses, and several new examples have been added to illustrate recent applications. Examples, case studies, questions, and downloadable algorithms are also included to support learning. No prior knowledge of computer simulation is assumed. Fully updated guide to both the current state and latest developments in the field of molecular simulation, including added and expanded information on such topics as molecular dynamics and statistical assessment of simulation results Gives a rounded overview by showing fundamental background information in practice via new examples in a range of key fields Provides online access to new data, algorithms and tutorial slides to support and encourage practice and learning

Nature-inspired Methods in Chemometrics: Genetic Algorithms and Artificial Neural Networks

Riccardo Leardi
Nature inspired Methods in Chemometrics Genetic Algorithms and Artificial Neural Networks Book PDF

Author : Riccardo Leardi
Publisher : Elsevier
Page : 402 pages
File Size : 45,5 Mb
Release : 2003-12-03
Category : Science
ISBN : 0080522629

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Nature-inspired Methods in Chemometrics: Genetic Algorithms and Artificial Neural Networks by Riccardo Leardi Pdf

In recent years Genetic Algorithms (GA) and Artificial Neural Networks (ANN) have progressively increased in importance amongst the techniques routinely used in chemometrics. This book contains contributions from experts in the field is divided in two sections (GA and ANN). In each part, tutorial chapters are included in which the theoretical bases of each technique are expertly (but simply) described. These are followed by application chapters in which special emphasis will be given to the advantages of the application of GA or ANN to that specific problem, compared to classical techniques, and to the risks connected with its misuse. This book is of use to all those who are using or are interested in GA and ANN. Beginners can focus their attentions on the tutorials, whilst the most advanced readers will be more interested in looking at the applications of the techniques. It is also suitable as a reference book for students. Subject matter is steadily increasing in importance Comparison of Genetic Algorithms (GA) and Artificial Neural Networks (ANN) with the classical techniques Suitable for both beginners and advanced researchers