Chipot, Christophe
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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Nyckelord: COMPUTERS / Computer Science COM014000
- Författare
- Chipot, Christophe
- Elber, Ron
- Laaksonen, Aatto
- Leimkuhler, Benedict
- Mark, Alan
- Schlick, Tamar
- Schütte, Christoph
- Skeel, Robert
- Utgivare
- Springer
- Utgivningsår
- 2006
- Språk
- en
- Utgåva
- 1
- Kategori
- Datateknik, Datakommunikation
- Format
- E-bok
- eISBN (PDF)
- 9783540316183