Synopses & Reviews
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.
Review
From the reviews: "This is a welcome book for computational chemists. ... the book assumes an advanced knowledge of graduate and research-level statistical mechanics. ... The book can be highly recommended to serious practitioners who carry out or plan to carry out, proper liquid-phase simulations of free energy changes or equilibrium constants by the molecular dynamics method." (Donald G. Truhlar, Theoretical Chemistry Accounts, Vol. 121, 2008)
Synopsis
This volume offers a coherent account of the concepts that underlie different approaches devised for the determination of free energies. It provides insight into the theoretical and computational foundations of the subject and presents relevant applications from molecular-level modeling and simulations of chemical and biological systems. The book is aimed at a broad readership of graduate students and researchers.
Table of Contents
Introduction: C. Chipot, M.S. Shell and A. Pohorille.- Calculating Free Energy Differences Using Perturbation Theory: C. Chipot and A. Pohorille.- Methods Based on Probability Distributions and Histograms: M.S. Shell and A. Panagiotopoulos.- Thermodynamic Integration Using Constrained and Unconstrained Dynmaics: E. Darve.- Nonequilibrium Methods for Equilibrium Free Energy Calculations: G. Hummer.- Understanding and Improving Free Energy Calculations in Molecular Simulations: Error Analysis and Reduction Methods: N. Lu and Th.B. Woolf.- Transition Path Sampling and the Calculation of Free Energies: C. Dellago.- Specialized Methods For Improving Ergodic Sampling Using Molecular Dynamics and Monte Carlo Simulations: I Andricioaei.- Potential Distribution Methods and Free Energy Models of Molecular Solutions: L.R. Pratt and D. Asthagiri.- Methods for Examining Phase Equilibria: A.Z. Panagiotopoulos and M. Scott Shell.- Quantum Contributions to Free Energy Changes in Fluids: Th.L. Beck.- Free Energy Calculations: Approximate Methos for Biological Macromolecules: T. Simonson.- Significant Applications of Free Energy Calculations to Chemistry and Biology: C. Chipot, V.S. Pande, A.E. Mark and T. Simonson.- Summary and Outlook: A. Pohorille and C. Chipot.