1st Edition

Coarse-Graining of Condensed Phase and Biomolecular Systems

Edited By Gregory A. Voth Copyright 2009
    490 Pages 24 Color & 144 B/W Illustrations
    by CRC Press

    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.

    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

    Biography

    Gregory A. Voth