Coarse-Graining of Condensed Phase and Biomolecular Systems

Gregory A. Voth

• Publisher: CRC Press
• Year: 2008
• eBook ISBN:
  9781040205518
• Topic: Physical Sciences
• Subtopic: Biophysics

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. Assembling some of the most influential, world-renowned researchers in the field, this book covers the latest developments in the coarse-grained molecular dynamics 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 discuss the minimalist, inversion, and multiscale approaches to coarse-graining, along with the emerging challenges of coarse-graining. They also connect atomic-level information with new coarse-grained representations of complex systems, such as lipid bilayers, proteins, peptides, and DNA.

Table of contents

• Cover
• Half Title
• Title Page
• Copyright Page
• Table of Contents
• Acknowledgments
• Editor
• Contributors
• 1: Introduction
• 2: The MARTINI Force Field
• 3: The Multiscale Coarse-Graining Method: A Systematic Approach to Coarse-Graining
• 4: A Model for Lipid Bilayers in Implicit Solvent
• 5: Coarse-Grained Dynamics of Anisotropic Systems
• 6: State-Point Dependence and Transferability of Potentials in Systematic Structural Coarse-Graining
• 7: Systematic Approach to Coarse-Graining of Molecular Descriptions and Interactions with Applications to Lipid Membranes
• 8: Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
• 9: Coarse-Grained Structure-Based Simulations of Proteins and RNA
• On the Development of Coarse-Grained Protein Models: Importance of Relative Side-Chain Orientations and Backbone Interactions
• 11: Characterization of Protein-Folding Landscapes by Coarse-Grained Models Incorporating Experimental Data
• 12: Principles and Practicalities of Canonical Mixed-Resolution Sampling of Biomolecules
• 13: Pathways of Conformational Transitions in Proteins
• 14: Insights into the Sequence-Dependent Macromolecular Properties of DNA from Base-Pair Level Modeling
• 15: Coarse-Grained Models for Nucleic Acids and Large Nucleoprotein Assemblies
• 16: Elastic Network Models of Coarse-Grained Proteins Are Effective for Studying the Structural Control Exerted over Their Dynamics
• 17: Coarse-Grained Elastic Normal Mode Analysis and Its Applications in X-Ray Crystallographic Refinement at Moderate Resolutions
• 18: Coarse-Grained Normal Mode Analysis to Explore Large-Scale Dynamics of Biological Molecules
• 19: One-Bead Coarse-Grained Models for Proteins
• 20: Application of Residue-Based and Shape-Based Coarse-Graining to Biomolecular Simulations
• 21: Coarse-Graining Protein Mechanics
• 22: Self-Assembly of Surfactants in Bulk Phases and at Interfaces Using Coarse-Grain Models
• 23: Coarse-Grained Simulations of Polyelectrolytes
• 24: Monte Carlo Simulations of a Coarse-Grain Model for Block Copolymer Systems
• 25: Structure-Based Coarse- and Fine-Graining in Soft Matter Simulations
• 26: From Atomistic Modeling of Macromolecules Toward Equations of State for Polymer Solutions and Melts: How Important Is the Accurate Description of the Local Structure?
• 27: Effective Interaction Potentials for Coarse-Grained Simulations of PolymerTethered Nanoparticle Self-Assembly in Solution
• 28: Coarse-Graining in Time: From Microscopics to Macroscopics
• Index