Coarse-Graining of Condensed Phase and Biomolecular Systems

Coarse-Graining of Condensed Phase and Biomolecular Systems

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ISBN 9781420059557
Cat# 59556
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Features

  • Covers the latest developments in the coarse-grained molecular dynamics simulation and modeling of condensed phase and biomolecular systems
  • Presents the main approaches to coarse-graining, including minimalist, inversion, and multiscale
  • Connects atomic-level information with new coarse-grained representations of complex systems, such as lipid bilayers, proteins, peptides, and DNA
  • Describes the emerging challenges of coarse-graining, including the degree of “believable” predictive power of coarse-grained models and their transferability between dissimilar systems

Summary

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

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