Free Energy Calculations

Free Energy Calculations

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  • Author: Christophe Chipot
  • Publisher: Springer Science & Business Media
  • ISBN: 3540384472
  • Category : Science
  • Languages : en
  • Pages : 528

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.


Free Energy Computations

Free Energy Computations

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  • Author: Tony LeliŠvre
  • Publisher: World Scientific
  • ISBN: 1848162480
  • Category : Science
  • Languages : en
  • Pages : 471

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.


Free Energy Calculations in Rational Drug Design

Free Energy Calculations in Rational Drug Design

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  • Author: M. Rami Reddy
  • Publisher: Springer Science & Business Media
  • ISBN: 9780306466762
  • Category : Medical
  • Languages : en
  • Pages : 420

Free energy calculations represent the most accurate computational method available for predicting enzyme inhibitor binding affinities. Advances in computer power in the 1990s enabled the practical application of these calculations in rationale drug design. This book represents the first comprehensive review of this growing area of research and covers the basic theory underlying the method, numerous state of the art strategies designed to improve throughput and dozen examples wherein free energy calculations were used to design and evaluate potential drug candidates.


Simulation Based Free Energy Calculations and Drug Design

Simulation Based Free Energy Calculations and Drug Design

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  • Author: Randall J. Radmer
  • Publisher:
  • ISBN:
  • Category : Drugs
  • Languages : en
  • Pages : 316


Computational Biophysics of Membrane Proteins

Computational Biophysics of Membrane Proteins

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  • Author: Carmen Domene
  • Publisher: Royal Society of Chemistry
  • ISBN: 1782626697
  • Category : Science
  • Languages : en
  • Pages : 264

Exploring current themes in modern computational and membrane protein biophysics, this book presents a comprehensive account of the fundamental principles underlying different methods and techniques used to describe the intriguing mechanisms by which membrane proteins function. The book discusses the experimental approaches employed to study these proteins, with chapters reviewing recent crucial structural advances that have allowed computational biophysicists to discern how these molecular machines work. The book then explores what computational methods are available to researchers and what these have taught us about three key families of membrane proteins: ion channels, transporters and receptors. The book is ideal for researchers in computational chemistry and computational biophysics.


Mass and Energy Balancing

Mass and Energy Balancing

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  • Author: David Pritchard
  • Publisher: CRC Press
  • ISBN: 1000392317
  • Category : Technology & Engineering
  • Languages : en
  • Pages : 147

The aim of this text is to provide a comprehensive set of calculations relating to mass and energy balances for an entire process plant. An ammonia synthesis plant will be taken as a calculation model to develop the relevant mass and energy balances necessary for the design and subsequent production, as the production of ammonia synthesis gas is an internationally used process. Instead of teaching the basics of mass and energy balances, the text aims to give a detailed series of process integrated and illustrated calculations to help readers develop and design a process plant. • Details complete mass and energy calculations related to a manufacturing plant and includes stepwise procedures for mass and energy balances • Demonstrates how the series of integrated calculations will lead to the production of a specified amount of final product • Features “teaching” appendices that lay out applications of prior-assumed knowledge, which can be used in conjunction with the main text where more detailed explanation may be needed • Contains problems linked to various manufacturing sections covered in the text to help readers consolidate their knowledge This book will serve undergraduate Chemical Engineering students as a teaching aid in capstone design and related courses and gives useful insights to advanced students, researchers, and industry personnel within the Chemical Engineering field.


On Free Energy Calculations Using Fluctuation Theorems of Work

On Free Energy Calculations Using Fluctuation Theorems of Work

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  • Author: Aljoscha M. Hahn
  • Publisher:
  • ISBN:
  • Category :
  • Languages : en
  • Pages : 0

Subject of the present thesis is the problem of free energy calculations of systems which hardly can be treated analytically. Former stochastic methods like R. Zwanzig's free energy perturbation and Ch. Bennett's acceptance ratio method have recently been generalized using the Jarzynski Equation and Crooks' Fluctuation Theorem, such that they connect the statistics of work done in nonequilibrium processes with the associated free energy difference. We have studied the acceptance ratio method (bridge sampling) in detail, depicted its effectiveness, proven some characteristics, showed how to enhance its performance, worked out its convergence properties, and proposed and tested a measure of convergence for that method. In addition, we established a fluctuation theorem for a generalized notion of work and applied it to the calculation of the chemical potential of a Lennard-Jones fluid at high density. engl.


New Algorithms for Macromolecular Simulation

New Algorithms for Macromolecular Simulation

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  • Author: Benedict Leimkuhler
  • Publisher: Springer Science & Business Media
  • ISBN: 3540316183
  • Category : Computers
  • Languages : en
  • Pages : 367

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.


Thermodynamics and Kinetics of Drug Binding

Thermodynamics and Kinetics of Drug Binding

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  • Author: György Keserü
  • Publisher: John Wiley & Sons
  • ISBN: 352733582X
  • Category : Medical
  • Languages : en
  • Pages : 360

This practical reference for medicinal and pharmaceutical chemists combines the theoretical background with modern methods as well as applications from recent lead finding and optimization projects. Divided into two parts on the thermodynamics and kinetics of drug-receptor interaction, the text provides the conceptual and methodological basis for characterizing binding mechanisms for drugs and other bioactive molecules. It covers all currently used methods, from experimental approaches, such as ITC or SPR, right up to the latest computational methods. Case studies of real-life lead or drug development projects are also included so readers can apply the methods learned to their own projects. Finally, the benefits of a thorough binding mode analysis for any drug development project are summarized in an outlook chapter written by the editors.


Statistical Mechanics: Theory and Molecular Simulation

Statistical Mechanics: Theory and Molecular Simulation

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  • Author: Mark Tuckerman
  • Publisher: OUP Oxford
  • ISBN: 9780191523465
  • Category : Science
  • Languages : en
  • Pages : 720

Complex systems that bridge the traditional disciplines of physics, chemistry, biology, and materials science can be studied at an unprecedented level of detail using increasingly sophisticated theoretical methodology and high-speed computers. The aim of this book is to prepare burgeoning users and developers to become active participants in this exciting and rapidly advancing research area by uniting for the first time, in one monograph, the basic concepts of equilibrium and time-dependent statistical mechanics with the modern techniques used to solve the complex problems that arise in real-world applications. The book contains a detailed review of classical and quantum mechanics, in-depth discussions of the most commonly used ensembles simultaneously with modern computational techniques such as molecular dynamics and Monte Carlo, and important topics including free-energy calculations, linear-response theory, harmonic baths and the generalized Langevin equation, critical phenomena, and advanced conformational sampling methods. Burgeoning users and developers are thus provided firm grounding to become active participants in this exciting and rapidly advancing research area, while experienced practitioners will find the book to be a useful reference tool for the field.