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Effects Of The Ewald Sum On The Free Energy Of Extended Simple Point Charge Modeled Water
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Book Synopsis Effects of the Ewald Sum on the Free Energy of Extended Simple Point Charge Modeled Water by : Brendan W. Arbuckle
Download or read book Effects of the Ewald Sum on the Free Energy of Extended Simple Point Charge Modeled Water written by Brendan W. Arbuckle and published by . This book was released on 2000 with total page 230 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Ewald Summation Approach to Potential Models of Aqueous Electrolytes Involving Gaussian Charges and Induced Dipoles by :
Download or read book Ewald Summation Approach to Potential Models of Aqueous Electrolytes Involving Gaussian Charges and Induced Dipoles written by and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: We present a detailed derivation of the complete set of expressions required for the implementation of an Ewald summation approach to handle the long-range electrostatic interactions of polar and ionic model systems involving Gaussian charges and induced dipole moments with a particular application to the isobaricisothermal molecular dynamics simulation of our Gaussian Charge Polarizable (GCP) water model and its extension to aqueous electrolytes solutions. The set comprises the individual components of the potential energy, electrostatic potential, electrostatic field and gradient, the electrostatic force and the corresponding virial. Moreover, we show how the derived expressions converge to known point-based electrostatic counterparts when the parameters, defining the Gaussian charge and induced-dipole distributions, are extrapolated to their limiting point values. Finally, we illustrate the Ewald implementation against the current reaction field approach by isothermal-isobaric molecular dynamics of ambient GCP water for which we compared the outcomes of the thermodynamic, microstructural, and polarization behavior.
Book Synopsis Specific Ion Effects by : Werner Kunz
Download or read book Specific Ion Effects written by Werner Kunz and published by World Scientific. This book was released on 2010 with total page 347 pages. Available in PDF, EPUB and Kindle. Book excerpt: Specific ion effects are important in numerous fields of science and technology. This book summarizes the main ideas that came up over the years. It presents the efforts of theoreticians and supports it by the experimental results stemming from various techniques.
Book Synopsis Comprehensive Medicinal Chemistry III by :
Download or read book Comprehensive Medicinal Chemistry III written by and published by Elsevier. This book was released on 2017-06-03 with total page 4609 pages. Available in PDF, EPUB and Kindle. Book excerpt: Comprehensive Medicinal Chemistry III, Eight Volume Set provides a contemporary and forward-looking critical analysis and summary of recent developments, emerging trends, and recently identified new areas where medicinal chemistry is having an impact. The discipline of medicinal chemistry continues to evolve as it adapts to new opportunities and strives to solve new challenges. These include drug targeting, biomolecular therapeutics, development of chemical biology tools, data collection and analysis, in silico models as predictors for biological properties, identification and validation of new targets, approaches to quantify target engagement, new methods for synthesis of drug candidates such as green chemistry, development of novel scaffolds for drug discovery, and the role of regulatory agencies in drug discovery. Reviews the strategies, technologies, principles, and applications of modern medicinal chemistry Provides a global and current perspective of today's drug discovery process and discusses the major therapeutic classes and targets Includes a unique collection of case studies and personal assays reviewing the discovery and development of key drugs
Download or read book Physics Briefs written by and published by . This book was released on 1993 with total page 1074 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Structure and Reactivity in Aqueous Solution by : Christopher J. Cramer
Download or read book Structure and Reactivity in Aqueous Solution written by Christopher J. Cramer and published by . This book was released on 1994 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides critical experimental studies and state-of-the-art theoretical analyses of organic reactions in which the role of the aqueous environment is particularly clear. Examines equilibrium and nonequilibrium solvent effects for a variety of chemical processes. Provides an overview of the scope and utility of the present broad array of modeling techniques for mimicking aqueous solution. Includes detailed studies of the hydrophobic effect as it influences protein folding and organic reactivity. Examines the effect of aqueous solvation on biological macromolecules and interfaces.
Book Synopsis Computer Simulation of Liquids by : M. P. Allen
Download or read book Computer Simulation of Liquids written by M. P. Allen and published by Oxford University Press. This book was released on 1989 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer simulation is an essential tool in studying the chemistry and physics of liquids. Simulations allow us to develop models and to test them against experimental data. This book is an introduction and practical guide to the molecular dynamics and Monte Carlo methods.
Book Synopsis The Monte Carlo Method in Condensed Matter Physics by : Kurt Binder
Download or read book The Monte Carlo Method in Condensed Matter Physics written by Kurt Binder and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Monte Carlo method is now widely used and commonly accepted as an important and useful tool in solid state physics and related fields. It is broadly recognized that the technique of "computer simulation" is complementary to both analytical theory and experiment, and can significantly contribute to ad vancing the understanding of various scientific problems. Widespread applications of the Monte Carlo method to various fields of the statistical mechanics of condensed matter physics have already been reviewed in two previously published books, namely Monte Carlo Methods in Statistical Physics (Topics Curro Phys. , Vol. 7, 1st edn. 1979, 2ndedn. 1986) and Applications of the Monte Carlo Method in Statistical Physics (Topics Curro Phys. , Vol. 36, 1st edn. 1984, 2nd edn. 1987). Meanwhile the field has continued its rapid growth and expansion, and applications to new fields have appeared that were not treated at all in the above two books (e. g. studies of irreversible growth phenomena, cellular automata, interfaces, and quantum problems on lattices). Also, new methodic aspects have emerged, such as aspects of efficient use of vector com puters or parallel computers, more efficient analysis of simulated systems con figurations, and methods to reduce critical slowing down at i>hase transitions. Taken together with the extensive activity in certain traditional areas of research (simulation of classical and quantum fluids, of macromolecular materials, of spin glasses and quadrupolar glasses, etc.
Book Synopsis Free Energy Calculations by : Christophe Chipot
Download or read book Free Energy Calculations written by Christophe Chipot and published by Springer Science & Business Media. This book was released on 2007-01-08 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.
Book Synopsis The Physics and Physical Chemistry of Water by : Felix Franks
Download or read book The Physics and Physical Chemistry of Water written by Felix Franks and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 610 pages. Available in PDF, EPUB and Kindle. Book excerpt: to arrive at some temporary consensus model or models; and to present reliable physical data pertaining to water under a range of conditions, i.e., "Dorsey revisited," albeit on a less ambitious scale. I should like to acknowledge a debt of gratitude to several of my col leagues, to Prof. D. J. G. Ives and Prof. Robert L. Kay for valuable guidance and active encouragement, to the contributors to this volume for their willing cooperation, and to my wife and daughters for the understanding shown to a husband and father who hid in his study for many an evening. My very special thanks go to Mrs. Joyce Johnson, who did all the cor respondence and much of the arduous editorial work with her usual cheerful efficiency. F. FRANKS Biophysics Division Unilever Research Laboratory ColworthjWelwyn Colworth House, Sharnbrook, Bedford March 1972 Contents Chapter 1 Introduction-Water, the Unique Chemical F. Franks I. lntroduction ........................................ . 2. The Occurrence and Distribution of Water on the Earth 2 3. Water and Life ...................................... 4 4. The Scientific Study of Water-A Short History ........ 8 5. The Place of Water among Liquids . . . . . . . . . . . . . . . 13 . . . . . Chapter 2 The Water Moleeule C. W. Kern and M. Karplus 1. Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 . . . . . . . . . . 2. Principles of Structure and Spectra: The Born-Oppenheimer Separation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 . . . . . . . . . . . . 3. The Electronic Motion ............................... 26 3.1. The Ground Electronic State of Water ............ 31 3.2. The Excited Electronic States of Water ........... 50 4. The Nuclear Motion ................................. 52 5. External-Field Effects ................................. 70 5.1. Perturbed Hartree-Fock Method . . . . . . . . . . . . . . . 74 . . .
Book Synopsis Numerical Simulation in Molecular Dynamics by : Michael Griebel
Download or read book Numerical Simulation in Molecular Dynamics written by Michael Griebel and published by Springer Science & Business Media. This book was released on 2007-08-16 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Amber 2021 written by David A. Case and published by University of California, San Francisco. This book was released on 2021-06-13 with total page 959 pages. Available in PDF, EPUB and Kindle. Book excerpt: Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term Amber is also used to refer to the empirical force fields that are implemented here. It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools21, a collection of freely available programs mostly under the GPL license, and Amber20, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber20 represents a significant change from the most recent previous version, Amber18. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.
Book Synopsis Physics of Surfaces and Interfaces by : Harald Ibach
Download or read book Physics of Surfaces and Interfaces written by Harald Ibach and published by Springer Science & Business Media. This book was released on 2006-11-18 with total page 653 pages. Available in PDF, EPUB and Kindle. Book excerpt: This graduate-level textbook covers the major developments in surface sciences of recent decades, from experimental tricks and basic techniques to the latest experimental methods and theoretical understanding. It is unique in its attempt to treat the physics of surfaces, thin films and interfaces, surface chemistry, thermodynamics, statistical physics and the physics of the solid/electrolyte interface in an integral manner, rather than in separate compartments. It is designed as a handbook for the researcher as well as a study-text for graduate students. Written explanations are supported by 350 graphs and illustrations.
Book Synopsis Ab Initio Molecular Dynamics by : Dominik Marx
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.
Book Synopsis Simulation Methods for Polymers by : Michael Kotelyanskii
Download or read book Simulation Methods for Polymers written by Michael Kotelyanskii and published by CRC Press. This book was released on 2004-03-01 with total page 572 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mathematical Models in Biology by : Leah Edelstein-Keshet
Download or read book Mathematical Models in Biology written by Leah Edelstein-Keshet and published by SIAM. This book was released on 1988-01-01 with total page 629 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical Models in Biology is an introductory book for readers interested in biological applications of mathematics and modeling in biology. A favorite in the mathematical biology community, it shows how relatively simple mathematics can be applied to a variety of models to draw interesting conclusions. Connections are made between diverse biological examples linked by common mathematical themes. A variety of discrete and continuous ordinary and partial differential equation models are explored. Although great advances have taken place in many of the topics covered, the simple lessons contained in this book are still important and informative. Audience: the book does not assume too much background knowledge--essentially some calculus and high-school algebra. It was originally written with third- and fourth-year undergraduate mathematical-biology majors in mind; however, it was picked up by beginning graduate students as well as researchers in math (and some in biology) who wanted to learn about this field.
Book Synopsis Electrical Properties of Ice by : Victor F. Petrenko
Download or read book Electrical Properties of Ice written by Victor F. Petrenko and published by . This book was released on 1993 with total page 86 pages. Available in PDF, EPUB and Kindle. Book excerpt:
