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Understanding Molecular Simulation: From Algorithms to Applications
Daan Frenkel,Berend Smit +1 more
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TLDR
In this paper, the physics behind molecular simulation for materials science is explained, and the implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text.Abstract:
From the Publisher:
This book 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. Since a wide variety of computational tools exists, 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. Examples are included that highlight current applications, and the codes of the case studies are available on the World Wide Web. No prior knowledge of computer simulation is assumed.read more
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The Amber biomolecular simulation programs
David A. Case,Thomas E. Cheatham,Tom Darden,Holger Gohlke,Ray Luo,Kenneth M. Merz,Alexey V. Onufriev,Carlos Simmerling,Bing Wang,Robert J. Woods +9 more
TL;DR: The development, current features, and some directions for future development of the Amber package of computer programs, which contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
Journal ArticleDOI
Hydrogen storage in metal–organic frameworks
TL;DR: This critical review of the current status of hydrogen storage within microporous metal-organic frameworks provides an overview of the relationships between structural features and the enthalpy of hydrogen adsorption, spectroscopic methods for probing framework-H(2) interactions, and strategies for improving storage capacity.
Journal ArticleDOI
Carbon Dioxide Capture: Prospects for New Materials
TL;DR: The most recent developments and emerging concepts in CO(2) separations by solvent absorption, chemical and physical adsorption, and membranes, amongst others, will be discussed, with particular attention on progress in the burgeoning field of metal-organic frameworks.
BookDOI
MCMC using Hamiltonian dynamics
TL;DR: In this paper, the authors discuss theoretical and practical aspects of Hamiltonian Monte Carlo, and present some of its variations, including using windows of states for deciding on acceptance or rejection, computing trajectories using fast approximations, tempering during the course of a trajectory to handle isolated modes, and short-cut methods that prevent useless trajectories from taking much computation time.