New Algorithms for Macromolecular Simulation

Peter J. Bond, Jonathan Cuthbertson, Sundeep S. Deol, Lucy R. Forrest (auth.), Benedict Leimkuhler, Christophe Chipot, Ron Elber, Aatto Laaksonen, Alan Mark, Tamar Schlick, Christoph Schütte, Robert Skeel (eds.)9783540255420, 9783540316183, 3540255427

Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.

Table of contents :
Front Matter….Pages 1-1
Membrane Protein Simulations: Modelling a Complex Environment….Pages 3-20
Modeling and Simulation Based Approaches for Investigating Allosteric Regulation in Enzymes….Pages 21-34
Exploring the Connection Between Synthetic and Natural RNAs in Genomes: A Novel Computational Approach….Pages 35-56
Learning to Align Sequences: A Maximum-Margin Approach….Pages 57-69
Front Matter….Pages 71-71
Overcoming Energetic and Time Scale Barriers Using the Potential Energy Surface….Pages 73-87
The Protein Folding Problem….Pages 89-100
Front Matter….Pages 101-101
Biomolecular Sampling: Algorithms, Test Molecules, and Metrics….Pages 103-123
Approach to Thermal Equilibrium in Biomolecular Simulation….Pages 125-140
The Targeted Shadowing Hybrid Monte Carlo (TSHMC) Method….Pages 141-153
The Langevin Equation for Generalized Coordinates….Pages 155-165
Metastability and Dominant Eigenvalues of Transfer Operators….Pages 167-182
Front Matter….Pages 183-183
Free Energy Calculations in Biological Systems. How Useful Are They in Practice?….Pages 185-211
Numerical Methods for Calculating the Potential of Mean Force….Pages 213-249
Replica-Exchange-Based Free-Energy Methods….Pages 251-259
Front Matter….Pages 261-261
Implicit Solvent Electrostatics in Biomolecular Simulation….Pages 263-295
New Distributed Multipole Metdhods for Accurate Electrostatics in Large-Scale Biomolecular Simulations….Pages 297-312
Front Matter….Pages 313-313
Towards Fast and Reliable Quantum Chemical Modelling of Macromolecules….Pages 315-341
Quantum Chemistry Simulations of Glycopeptide Antibiotics….Pages 343-351
Panel Discussion….Pages 353-362