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RSSNew Algorithms for Macromolecular Simulation | ||||||||||||||||||
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| Table of contents Part I. Macromolecular Models: From Theories to Effective Algorithms 1. Membrane Protein Simulations: Modelling a Complex Environment Peter J. Bond, Jonathan Cuthbertson, Sundeep S. Deol, Lucy R. Forrest, Jennifer Johnston, George Patargias, Mark S.P. Sansom 2. Modeling and Simulation Based Approaches for Investigating Allosteric Regulation in Enzymes Marc Q. Ma, Kentaro Sugino, Yu Wang, Narain Gehani, Annie V. Beuve 3. Exploring the Connection Between Synthetic and Natural RNAs in Genomes: A Novel Computational Approach Uri Laserson, Hin Hark Gan, Tamar Schlick 4. Learning to Align Sequences: A Maximum-Margin Approach Thorsten Joachims, Tamara Galor, Ron Elber Part II. Minimization of Complex Molecular Landscapes 5. Overcoming Energetic and Time Scale Barriers Using the Potential Energy Surface David J. Wales, Joanne M. Carr, Tim James 6. The Protein Folding Problem H. A. Scheraga, A. Liwo, S. Oldziej, C. Czaplewski, J. Pillardy, J. Lee, D.R. Ripoll, J.A. Vila, R. Kazmierkiewicz, J.A. Saunders, Y.A. Arnautova, K.D. Gibson, A. Jagielska, M. Khalili, M. Chinchio, M. Nanias, Y.K. Kang, H. Schafroth, A. Ghosh, R. Elber, M. Makowski Part III. Dynamical and Stochastic-Dynamical Foundations for Macromolecular Modelling 7. Biomolecular Sampling: Algorithms, Test Molecules, and Metrics Scott S. Hampton, Paul Brenner, Aaron Wenger, Santanu Chatterjee, Jesús A. Izaguirre 8. Approach to Thermal Equilibrium in Biomolecular Simulation Eric Barth, Ben Leimkuhler, Chris Sweet 9. The Targeted Shadowing Hybrid Monte Carlo (TSHMC) Method Elena Akhmatskaya, Sebastian Reich 10. The Langevin Equation for Generalized Coordinates Reinier L. C. Akkermans 11. Metastability and Dominant Eigenvalues of Transfer Operators Wilhelm Huisinga, Bernd Schmidt Part IV. Computation of the Free Energy 12. Free Energy Calculations in Biological Systems. How Useful Are They in Practice? Christophe Chipot 13. Numerical Methods for Calculating the Potential of Mean Force Eric Darve 14. Replica-Exchange-Based Free-Energy Methods Christopher J. Woods, Michael A. King, Jonathan W. Essex Part V. Fast Electrostatics and Enhanced Solvation Models 15. Implicit Solvent Electrostatics in Biomolecular Simulation Nathan A. Baker, Donald Bashford, David A. Case 16. New Distributed Multipole Metdhods for Accurate Electrostatics in Large-Scale Biomolecular Simulations Celeste Sagui, Christopher Roland, Lee G. Pedersen, Thomas A. Darden Part VI. Quantum-Chemical Models for Macromolecular Simulation 17. Towards Fast and Reliable Quantum Chemical Modelling of Macromolecules Yaoquan Tu, Aatto Laaksonen 18. Quantum Chemistry Simulations of Glycopeptide Antibiotics Jung-Goo Lee, Celeste Sagui, Christopher Roland 19. Panel Discussion DRM-restrictions Printing: not available Clipboard copying: not available | ||||||||||||||||||
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