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Free Energy Computations
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Book Synopsis Free Energy Computations by : Tony Lelivre
Download or read book Free Energy Computations written by Tony Lelivre and published by World Scientific. This book was released on 2010 with total page 471 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph provides a general introduction to advanced computational methods for free energy calculations, from the systematic and rigorous point of view of applied mathematics. Free energy calculations in molecular dynamics have become an outstanding and increasingly broad computational field in physics, chemistry and molecular biology within the past few years, by making possible the analysis of complex molecular systems. This work proposes a new, general and rigorous presentation, intended both for practitioners interested in a mathematical treatment, and for applied mathematicians interested in molecular dynamics.
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 Reviews in Computational Chemistry, Volume 28 by : Abby L. Parrill
Download or read book Reviews in Computational Chemistry, Volume 28 written by Abby L. Parrill and published by John Wiley & Sons. This book was released on 2015-04-27 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered around molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics in Volume 28 include: Free-energy Calculations with Metadynamics Polarizable Force Fields for Biomolecular Modeling Modeling Protein Folding Pathways Assessing Structural Predictions of Protein-Protein Recognition Kinetic Monte Carlo Simulation of Electrochemical Systems Reactivity and Dynamics at Liquid Interfaces
Book Synopsis Simple Solutions to Energy Calculations by : Richard Vaillencourt
Download or read book Simple Solutions to Energy Calculations written by Richard Vaillencourt and published by The Fairmont Press, Inc.. This book was released on 2001 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Rugged Free Energy Landscapes by : Wolfhard Janke
Download or read book Rugged Free Energy Landscapes written by Wolfhard Janke and published by Springer Science & Business Media. This book was released on 2007-11-22 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: This collection of lectures and tutorial reviews focuses on the common computational approaches in use to unravel the static and dynamical behaviour of complex physical systems at the interface of physics, chemistry and biology. Prominent consideration is given to rugged free-energy landscapes. The authors aim to provide a common basis and technical language for the (computational) technology transfer between the fields and systems considered.
Book Synopsis Thermodynamics and the Free Energy of Chemical Substances by : Gilbert Newton Lewis
Download or read book Thermodynamics and the Free Energy of Chemical Substances written by Gilbert Newton Lewis and published by . This book was released on 1923 with total page 690 pages. Available in PDF, EPUB and Kindle. Book excerpt: The scope of thermodynamics. Definitions; the concept of equilibrium. Conventions and mathematical methods. Solutions. The first law of thermodynamics and the concept of energy. The fugacity. Application of the second law to solutions. The perfect solution. The laws of the dilute solution. Systems involving variables other than pressure, temperature and composition. A useful function, called the activity, and its application to solutions. Change of activity with the temperature, and the calculation of activity from freezing points. The standard change of free energy; the equilibrium constant. Solutions of electrolytes. The activity of strong electrolytes. The activity of electrolytes from freezing point data, and tables of activity coefficients. Activity coefficient in mixed electrolytes; the principle of the ionic strength; the activity of individual ions. The galvanic cell. Single potentials; standard electrode potentials of the elements. The third law of thermodynamics. The entropy of monatomic gases and a table of atomic entropies. Introduction to systematic free energy calculations: the free energy of elementary hydrogen and metallic hydrides. Oxygen and its compouns with hydrogen and with some metals. Chlorine and its compouns. Bromine and its compounds. Iodine and its compounds. Nitrogen compounds. Carbon and some of its compounds. Compounds of carbon and nitrogen. Table of free energies; and examples illustrating its use. Conversion table for mol fractions, mol ratios and molities. Some useful numerical factors. Coefficients employed in converting activity, equilibrium constant and free energy from one temperature to another. Publications by the authrs, pertaining to thermodynamics.
Book Synopsis Entropy and Free Energy in Structural Biology by : Hagai Meirovitch
Download or read book Entropy and Free Energy in Structural Biology written by Hagai Meirovitch and published by CRC Press. This book was released on 2020-08-14 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nuclear Structure Physics connects to some of our fundamental questions about the creation of the universe and its basic constituents. At the same time, precise knowledge on the subject has led to the development of many important tools for humankind such as proton therapy and radioactive dating, among others. This book has chapters on some of the crucial and trending research topics in nuclear structure, including the nuclei lying on the extremes of spin, isospin and mass. A better theoretical understanding of these topics is important beyond the confines of the nuclear structure community. Additionally, the book will showcase the applicability and success of the different nuclear effective interaction parameters near the drip line, where hints for level reordering have already been seen, and where one can test the isospin-dependence of the interaction. The book offers comprehensive coverage of the most essential topics, including: • Nuclear Structure of Nuclei at or Near Drip-Lines • Synthesis challenges and properties of Superheavy nuclei • Nuclear Structure and Nuclear models - Ab-initio calculations, cluster models, Shell-model/DSM, RMF, Skyrme • Shell Closure, Magicity and other novel features of nuclei at extremes • Structure of Toroidal, Bubble Nuclei, halo and other exotic nuclei These topics are not only very interesting from a theoretical nuclear physics perspective but are also quite complimentary for ongoing nuclear physics experimental programs worldwide. The book chapters, written by experienced and well-known researchers/experts, will be helpful for master students, graduate students and researchers and serve as a standard and up-to-date research reference book on the topics covered.
Download or read book Drug Design written by Kenneth M. Merz and published by Cambridge University Press. This book was released on 2010-05-31 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a complete snapshot of various experimental approaches to structure-based and ligand-based drug design and is illustrated with more than 200 images.
Book Synopsis Reviews in Computational Chemistry by : Kenny B. Lipkowitz
Download or read book Reviews in Computational Chemistry written by Kenny B. Lipkowitz and published by Wiley-VCH Verlag GmbH. This book was released on 1995 with total page 414 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume in computational chemistry includes aspects of: theoretical chemistry, physical chemistry, computer graphics in chemistry, molecular structure, and pharmaceutical chemistry.
Book Synopsis Molecular Modeling of Proteins by : Andreas Kukol
Download or read book Molecular Modeling of Proteins written by Andreas Kukol and published by Humana Press. This book was released on 2017-04-30 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls. Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.
Book Synopsis Free Energy Computations by : Tony Lelivre
Download or read book Free Energy Computations written by Tony Lelivre and published by World Scientific. This book was released on 2010 with total page 471 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph provides a general introduction to advanced computational methods for free energy calculations, from the systematic and rigorous point of view of applied mathematics. Free energy calculations in molecular dynamics have become an outstanding and increasingly broad computational field in physics, chemistry and molecular biology within the past few years, by making possible the analysis of complex molecular systems. This work proposes a new, general and rigorous presentation, intended both for practitioners interested in a mathematical treatment, and for applied mathematicians interested in molecular dynamics.
Book Synopsis Free Energy Methods in Drug Discovery by : Kira A. Armacost
Download or read book Free Energy Methods in Drug Discovery written by Kira A. Armacost and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book is about Free Energy Methods in Drug Discovery: Current State and Future Directions"--
Book Synopsis Understanding Molecular Simulation by : Daan Frenkel
Download or read book Understanding Molecular Simulation written by Daan Frenkel and published by Elsevier. This book was released on 2001-10-19 with total page 661 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Proteins written by David M. Leitner and published by CRC Press. This book was released on 2009-09-28 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational modeling can provide a wealth of insight into how energy flow in proteins mediates protein function. Computational methods can also address fundamental questions related to molecular signaling and energy flow in proteins. Proteins: Energy, Heat and Signal Flow presents state-of-the-art computational strategies for studying energy redi
Book Synopsis Computational Thermodynamics of Materials by : Zi-Kui Liu
Download or read book Computational Thermodynamics of Materials written by Zi-Kui Liu and published by Cambridge University Press. This book was released on 2016-06-30 with total page 261 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integrates fundamental concepts with experimental data and practical applications, including worked examples and end-of-chapter problems.
Book Synopsis Essentials of Computational Chemistry by : Christopher J. Cramer
Download or read book Essentials of Computational Chemistry written by Christopher J. Cramer and published by John Wiley & Sons. This book was released on 2013-04-29 with total page 624 pages. Available in PDF, EPUB and Kindle. Book excerpt: Essentials of Computational Chemistry provides a balanced introduction to this dynamic subject. Suitable for both experimentalists and theorists, a wide range of samples and applications are included drawn from all key areas. The book carefully leads the reader thorough the necessary equations providing information explanations and reasoning where necessary and firmly placing each equation in context.
Book Synopsis Potential Energy Surfaces and Dynamics Calculations by : Donald Truhlar
Download or read book Potential Energy Surfaces and Dynamics Calculations written by Donald Truhlar and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 859 pages. Available in PDF, EPUB and Kindle. Book excerpt: The present volume is concerned with two of the central questions of chemical dynamics. What do we know about the energies of interaction of atoms and molecules with each other and with solid surfaces? How can such interaction energies be used to understand and make quantitative predictions about dynamical processes like scattering, energy transfer, and chemical reactions? It is becoming clearly recognized that the computer is leading to rapid progress in answering these questions. The computer allows probing dynamical mechanisms in fine detail and often allows us to answer questions that cannot be addressed with current experimental techniques. As we enter the 1980's, not only are more powerful and faster computers being used, but techniques and methods have been honed to a state where exciting and reliable data are being generated on a variety of systems at an unprecedented pace. The present volume presents a collection of work that illustrates the capabilities and some of the successes of this kind of computer-assisted research. In a 1978 Chemical Society Report, Frey and Walsh pointed out that "it is extremely doubtful if a calculated energy of activation for any unimolecular decomposition can replace an experimental deter mination. " However they also recorded that they "believe[d] that some of the elaborate calculations being performed at present do suggest that we may be approaching a time when a choice between reaction mechanisms will be helped by such [computational] work.
