New Algorithms for Macromolecular Simulation

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

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Keywords: COMPUTERS / Computer Science COM014000