Coarse-Graining of Condensed Phase and Biomolecular Systems: 1st Edition (Hardback) book cover

Coarse-Graining of Condensed Phase and Biomolecular Systems

1st Edition

Edited by Gregory A. Voth

CRC Press

456 pages | 24 Color Illus. | 144 B/W Illus.

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pub: 2008-09-22
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Description

Exploring recent developments in the field, Coarse-Graining of Condensed Phase and Biomolecular Systems examines systematic ways of constructing coarse-grained representations for complex systems. It explains how this approach can be used in the simulation and modeling of condensed phase and biomolecular systems.

Each chapter focuses on specific examples of evolving coarse-graining methodologies and presents results for a variety of complex systems. The contributors carefully detail their own coarse-graining approach, exploring its motivation, strengths, weaknesses, and important application examples. They discuss two of the most successful coarse-graining schemes for soft matter: inverse and multiscale coarse-graining. The book also describes current coarse-grained model development for peptides and proteins at the amino acid level and larger length scales.

Assembling the work of some of the most influential, world-renowned researchers in the field, this book provides a unified, in-depth overview of all the coarse-grained schemes developed for condensed phase and biomolecular systems. It shows the promise of coarse-graining as a revolutionary advancement in the scientific community.

Table of Contents

Introduction

Gregory A. Voth

The MARTINI Force Field

Siewert J. Marrink, Marc Fuhrmans, H. Jelger Risselada, and Xavier Periole

               

The Multiscale Coarse-Graining Method: A Systematic Approach to Coarse Graining

W.G. Noid, Gary S. Ayton, Sergei Izvekov, and Gregory A. Voth

A Model for Lipid Bilayers in Implicit Solvent

Grace Brannigan, and Frank L.H. Brown

Coarse-Grained Dynamics of Anisotropic Systems

L. Paramonov, M.G. Burke, and S.N. Yaliraki

State-Point Dependence and Transferability of Potentials in Systematic Structural Coarse-Graining

Qi Sun, Jayeeta Ghosh, and Roland Faller

Systematic Approach to Coarse-Graining of Molecular Descriptions and Interactions with Applications to Lipid Membranes

Teema Murtola, Ilpo Vattulainen, and Mikko Karttunen

Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field

Adam Liwo, Cezary Czaplewski, Stanisław Ołdziej, Ana V. Rojas,

Rajmund Kaźmierkiewicz, Mariusz Makowski, Rajesh K. Murarka, and Harold A. Scheraga

Coarse-Grained Structure-Based Simulations of Proteins and RNA

Alexander Schug, Changbong Hyeon, and José N. Onuchic

On the Development of Coarse-Grained Protein Models: Importance of Relative Side-Chain Orientations and Backbone Interactions

N.-V. Buchete, J.E. Straub, and D. Thirumalai

Characterization of Protein-Folding Landscapes by Coarse-Grain Models Incorporating Experimental Data

Silvina Matysiak and Cecilia Clementi

Principles and Practicalities of Canonical Mixed-Resolution Sampling of Biomolecules

Daniel M. Zuckerman

Pathways of Conformational Transitions in Proteins

Peter Májek, Ron Elber, and Harel Weinstein

Insights into the Sequence-Dependent Macromolecular Properties of DNA from Base-Pair Level Modeling

Wilma K. Olson, Andrew V. Colasanti, Luke Czapla, and Guohui Zheng

Coarse-Grain Models for Nucleic Acids and Large Nucleoprotein Assemblies

Robert K.-Z. Tan, Anton S. Petrov, Batsal Devkota, and Stephen C. Harvey

Elastic Network Models of Coarse-Grained Proteins Are Effective for Studying the Structural Control Exerted over Their Dynamics

Robert L. Jernigan, Lei Yang, Ozge Kurkcuoglu, Guang Song, and Pemra Doruker

Coarse-Grained Elastic Normal Mode Analysis and Its Applications in X-Ray Crystallographic Refinement at Moderate Resolutions

Jianpeng Ma

Coarse-Grained Normal Mode Analysis to Explore Large-Scale Dynamics of Biological Molecules

Osamu Miyashita and Florence Tama

One-Bead Coarse-Grained Models for Proteins

Valentina Tozzini and J. Andrew McCammon

Application of Residue-Based and Shape-Based Coarse-Graining to Biomolecular Simulations

Peter L. Freddolino, Anton Arkhipov, Amy Y. Shih, Ying Ying, Zhongzhou Chen, and Klaus Schulten

Coarse-Graining Protein Mechanics

Richard Lavery and Sophie Sacquin-Mora

Self-Assembly of Surfactants in Bulk Phases and at Interfaces Using Coarse-Grain Models

Wataru Shindoa, Russell DeVane, and Michael L. Klein

Coarse-Grained Simulations of Polyelectrolytes

Mark J. Stevens

Monte Carlo Simulations of a Coarse-Grain Model for Block Copolymer Systems

F.A. Detcheverry, K.Ch. Daoulas, P.F. Nealey, M. Müller, and J.J. de Pablo

Structure-Based Coarse- and Fine-Graining in Soft Matter Simulations

Nico F.A. van der Vegt, Christine Peter, and Kurt Kremer

From Atomistic Modeling of Macromolecules toward Equations of State for Polymer Solutions and Melts: How Important Is the Accurate Description of the Local Structure?

Kurt Binder, Wolfgang Paul, Peter Virnau, Leonid Yelash,

Marcus Müller, and Luis González MacDowell

Effective Interaction Potentials for Coarse-Grained Simulations of Polymer-Tethered Nanoparticle Self-Assembly in Solution

Elaine R. Chan, Alberto Striolo, Clare McCabe, Peter T. Cummings, and Sharon C. Glotzer

Coarse-Graining in Time: From Microscopics to Macroscopics

Angela Violi

Index

Subject Categories

BISAC Subject Codes/Headings:
SCI013050
SCIENCE / Chemistry / Physical & Theoretical
SCI055000
SCIENCE / Physics
SCI077000
SCIENCE / Solid State Physics