Coarse-Graining of Condensed Phase and Biomolecular Systems

Front Cover
Gregory A. Voth
CRC Press, Sep 22, 2008 - Science - 456 pages
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.

 

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Contents

Chapter 1 Introduction
1
Chapter 2 The MARTINI Force Field
5
A Systematic Approach to CoarseGraining
21
Chapter 4 A Model for Lipid Bilayers in Implicit Solvent
41
Chapter 5 CoarseGrained Dynamics of Anisotropic Systems
59
Chapter 6 StatePoint Dependence and Transferability of Potentials in Systematic Structural CoarseGraining
69
Chapter 7 Systematic Approach to CoarseGraining of Molecular Descriptions and Interactions with Applications to Lipid Membranes
83
Chapter 8 Simulation of Protein Structure and Dynamics with the CoarseGrained UNRES Force Field
107
Chapter 17 CoarseGrained Elastic Normal Mode Analysis and Its Applications in XRay Crystallographic Refinement at Moderate Resolutions
255
Chapter 18 CoarseGrained Normal Mode Analysis to Explore LargeScale Dynamics of Biological Molecules
267
Chapter 19 OneBead CoarseGrained Models for Proteins
285
Chapter 20 Application of ResidueBased and ShapeBased Coarse Graining to Biomolecular Simulations
299
Chapter 21 CoarseGraining Protein Mechanics
317
Chapter 22 SelfAssembly of Surfactants in Bulk Phases and at Interfaces Using CoarseGrain Models
329
Chapter 23 CoarseGrained Simulations of Polyelectrolytes
343
Chapter 24 Monte Carlo Simulations of a CoarseGrain Model for Block Copolymer Systems
361

Chapter 9 CoarseGrained StructureBased Simulations of Proteins and RNA
123
Importance of Relative SideChain Orientations and Backbone Interactions
141
Chapter 11 Characterization of ProteinFolding Landscapes by CoarseGrained Models Incorporating Experimental Data
157
Chapter 12 Principles and Practicalities of Canonical MixedResolution Sampling of Biomolecules
171
Chapter 13 Pathways of Conformational Transitions in Proteins
185
Chapter 14 Insights into the Sequence Dependent Macromolecular Properties of DNA from BasePair Level Modeling
205
Chapter 15 CoarseGrained Models for Nucleic Acids and Large Nucleoprotein Assemblies
225
Chapter 16 Elastic Network Models of CoarseGrained Proteins Are Effective for Studying the Structural Control Exerted over Their Dynamics
237
Chapter 25 StructureBased Coarse and FineGraining in Soft Matter Simulations
379
How Important Is the Accurate Description of the Local Structure?
399
Chapter 27 Effective Interaction Potentials for CoarseGrained Simulations of Polymer Tethered Nanoparticle SelfAssembly in Solution
415
From Microscopics to Macroscopics
433
Index
449
Back cover
473
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