Coarse-Graining of Condensed Phase and Biomolecular Systems

University of Utah, Salt Lake City, USA

Introduction. The MARTINI Force Field. The Multiscale Coarse-Graining Method. A Model for Lipid Bilayers in Implicit Solvent. Coarse-Grained Dynamics of Anisotropic Systems. State-Point Dependence and Transferability of Potentials in Systematic Structural Coarse-Graining. Systematic Approach to Coarse-Graining of Molecular Descriptions and Interactions with Applications to Lipid Membranes. Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field. Coarse-Grained Structure-Based Simulations of Proteins and RNA. On the Development of Coarse-Grained Protein Models. Characterization of Protein-Folding Landscapes by Coarse-Grain Models Incorporating Experimental Data. Principles and Practicalities of Canonical Mixed-Resolution Sampling of Biomolecules. Pathways of Conformational Transitions in Proteins. Insights into the Sequence-Dependent Macromolecular Properties of DNA from Base-Pair Level Modeling. Coarse-Grain Models for Nucleic Acids and Large Nucleoprotein Assemblies. Elastic Network Models of Coarse-Grained Proteins Are Effective for Studying the Structural Control Exerted over Their Dynamics. Coarse-Grained Elastic Normal Mode Analysis and Its Applications in X-Ray Crystallographic Refinement at Moderate Resolutions. Coarse-Grained Normal Mode Analysis to Explore Large-Scale Dynamics of Biological Molecules. One-Bead Coarse-Grained Models for Proteins. Application of Residue-Based and Shape-Based Coarse-Graining to Biomolecular Simulations. Coarse-Graining Protein Mechanics. Self-Assembly of Surfactants in Bulk Phases and at Interfaces Using Coarse-Grain Models. Coarse-Grained Simulations of Polyelectrolytes. Monte Carlo Simulations of a Coarse-Grain Model for Block Copolymer Systems. Structure-Based Coarse- and Fine-Graining in Soft Matter Simulations. From Atomistic Modeling of Macromolecules toward Equations of State for Polymer Solutions and Melts. Effective Interaction Potentials for Coarse-Grained Simulations of Polymer-Tethered Nanoparticle Self-Assembly in Solution. Coarse-Graining in Time. Index.