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http://dx.doi.org/10.1201/9781420059564
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Front MatterAbstract - Hi-Res PDF (279 KB) - PDF w/links (279 KB)
Chapter 1. IntroductionAbstract - Hi-Res PDF (453 KB) - PDF w/links (454 KB)
Chapter 2. The MARTINI Force FieldH. Jelger Risselada, Marc Fuhrmans, Xavier Periole, Siewert J. MarrinkAbstract - Hi-Res PDF (1706 KB) - PDF w/links (1620 KB)
Chapter 3. The Multiscale Coarse- Graining MethodW. G. Noid, Gary S. Ayton, Sergei IzvekovAbstract - Hi-Res PDF (2579 KB) - PDF w/links (2188 KB)
Chapter 4. A Model for Lipid Bilayers in Implicit SolventFrank L.H. Brown, Grace BranniganAbstract - Hi-Res PDF (2318 KB) - PDF w/links (1914 KB)
Chapter 5. Coarse-Grained Dynamics of Anisotropic SystemsS. N. Yaliraki, M. G. Burke, L. ParamonovAbstract - Hi-Res PDF (1274 KB) - PDF w/links (1154 KB)
Chapter 6. State-Point Dependence and Transferability of Potentials in Systematic Structural Coarse-GrainingRoland Faller, Qi Sun, Jayeeta GhoshAbstract - Hi-Res PDF (1806 KB) - PDF w/links (1727 KB)
Chapter 7. Systematic Approach to Coarse-Graining of Molecular Descriptions and Interactions with Applications to Lipid MembranesMikko Karttunen, Teemu Murtola, Ilpo VattulainenAbstract - Hi-Res PDF (3452 KB) - PDF w/links (2283 KB)
Chapter 8. Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force FieldAna V. Rojas, Cezary Czaplewski, Adam Liwo, Mariusz Makowski, Stanisław Ołdziej, Rajmund Kaz´mierkiewicz, Harold A. Scheraga, Rajesh K. MurarkaAbstract - Hi-Res PDF (1816 KB) - PDF w/links (1739 KB)
Chapter 9. Coarse-Grained Structure-Based Simulations of Proteins and RNAJosé N. Onuchic, Alexander Schug, Changbong HyeonAbstract - Hi-Res PDF (2764 KB) - PDF w/links (1930 KB)
Chapter 10. On the Development of Coarse-Grained Protein ModelsD. Thirumalai, N.-V. Buchete, J. E. StraubAbstract - Hi-Res PDF (1713 KB) - PDF w/links (1719 KB)
Chapter 11. Characterization of Protein-Folding Landscapes by Coarse-Grained Models Incorporating Experimental DataCecilia Clementi, Silvina MatysiakAbstract - Hi-Res PDF (2029 KB) - PDF w/links (1591 KB)
Chapter 12. Principles and Practicalities of Canonical Mixed-Resolution Sampling of BiomoleculesDaniel M. ZuckermanAbstract - Hi-Res PDF (1574 KB) - PDF w/links (1541 KB)
Chapter 13. Pathways of Conformational Transitions in ProteinsHarel Weinstein, Ron Elber, Peter MájekAbstract - Hi-Res PDF (3320 KB) - PDF w/links (2202 KB)
Chapter 14. Insights into the Sequence-Dependent Macromolecular Properties of DNA from Base-Pair Level ModelingAndrew V. Colasanti, Luke Czapla, Guohui Zheng, Wilma K. OlsonAbstract - Hi-Res PDF (2383 KB) - PDF w/links (2233 KB)
Chapter 15. Coarse-Grained Models for Nucleic Acids and Large Nucleoprotein AssembliesAnton S. Petrov, Stephen C. Harvey, Batsal Devkota, Robert K.-Z. TanAbstract - Hi-Res PDF (1001 KB) - PDF w/links (983 KB)
Chapter 16. Elastic Network Models of Coarse-Grained Proteins Are Effective for Studying the Structural Control Exerted over Their DynamicsGuang Song, Pemra Doruker, Robert L. Jernigan, Ozge Kurkcuoglu, Lei YangAbstract - Hi-Res PDF (20643 KB) - PDF w/links (3245 KB)
Chapter 17. Coarse-Grained Elastic Normal Mode Analysis and Its Applications in X-Ray at Moderate Resolutions Crystallographic RefinementJianpeng MaAbstract - Hi-Res PDF (1811 KB) - PDF w/links (1568 KB)
Chapter 18. Coarse-Grained Normal Mode Analysis to Explore Large-Scale Dynamics of Biological MoleculesFlorence Tama, Osamu MiyashitaAbstract - Hi-Res PDF (2767 KB) - PDF w/links (1970 KB)
Chapter 19. One-Bead Coarse-Grained Models for ProteinsJ. Andrew McCammon, Valentina TozziniAbstract - Hi-Res PDF (2020 KB) - PDF w/links (1737 KB)
Chapter 20. Application of Residue-Based and Shape-Based Coarse-Graining to Biomolecular SimulationsAnton Arkhipov, Klaus Schulten, Peter L. Freddolino, Ying Ying, Amy Y. Shih, Zhongzhou ChenAbstract - Hi-Res PDF (2715 KB) - PDF w/links (1878 KB)
Chapter 21. Coarse-Graining Protein MechanicsRichard Lavery, Sophie Sacquin-MoraAbstract - Hi-Res PDF (1773 KB) - PDF w/links (1258 KB)
Chapter 22. Self-Assembly of Surfactants in Bulk Phases and at Interfaces Using Coarse-Grain ModelsMichael L. Klein, Wataru Shinoda, Russell DeVaneAbstract - Hi-Res PDF (3054 KB) - PDF w/links (1903 KB)
Chapter 23. Coarse-Grained Simulations of PolyelectrolytesMark J. StevensAbstract - Hi-Res PDF (1998 KB) - PDF w/links (1806 KB)
Chapter 24. Monte Carlo Simulations of a Coarse-Grain Model for Block Copolymer SystemsJ. J. de Pablo, K. Ch.Daoulas, P. F. Nealey, M. Müller, F. A. DetcheverryAbstract - Hi-Res PDF (4197 KB) - PDF w/links (2141 KB)
Chapter 25. Structure-Based Coarse- and Fine-Graining in Soft Matter SimulationsNico F.A. van der Vegt, Christine Peter, Kurt KremerAbstract - Hi-Res PDF (2457 KB) - PDF w/links (2018 KB)
Chapter 26. From Atomistic Modeling of Macromolecules Toward Equations of State for Polymer Solutions and MeltsMarcus Müller, Leonid Yelash, Peter Virnau, Wolfgang Paul, Luis González MacDowell, Kurt BinderAbstract - Hi-Res PDF (1706 KB) - PDF w/links (1757 KB)
Chapter 27. Effective Interaction Potentials for Coarse-Grained Simulations of Polymer-Tethered Nanoparticle Self-Assembly in SolutionElaine R. Chan, Sharon C. Glotzer, Peter T. Cummings, Clare McCabe, Alberto StrioloAbstract - Hi-Res PDF (2299 KB) - PDF w/links (1838 KB)
Chapter 28. Coarse-Graining in TimeAngela VioliAbstract - Hi-Res PDF (1820 KB) - PDF w/links (1671 KB)
