Coarse-Graining of Condensed Phase and Biomolecular Systems

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, Stanislaw Oldziej, Ana V. Rojas, Rajmund Kazmierkiewicz, Mariusz Makowski, Rajesh K. Murarka, and Harold A. Scheraga Coarse-Grained Structure-Based Simulations of Proteins and RNA Alexander Schug, Changbong Hyeon, and Jose 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 Majek, 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. Muller, 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 Muller, and Luis Gonzalez 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