Quantum Mechanical Simulation Methods for Studying Biological Systems

1. Front Matter

   Pages I-XIV

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2. Density Functional Theory

   • N. C. Handy

   Pages 1-35

3. Practical Density Functional Approaches in Chemistry and Biochemistry

   • A. St-Amant

   Pages 37-60

4. A Quantum Chemical View of the Initial Photochemical Event in Photosynthesis

   • M. C. Zerner

   Pages 61-84

5. Curve Crossing in a Protein: Coupling of the Elementary Quantum Process to Motions of the Protein

   • K. Schulten

   Pages 85-118

6. Quantum-Classical Molecular Dynamics. Models and Applications

   • P. Bała, P. Grochowski, B. Lesyng, J. A. McCammon

   Pages 119-156

7. Quantum Dynamics Simulation of a Small Quantum System Embedded in a Classical Environment

   • H. J. C. Berendsen, J. Mavri

   Pages 157-179

8. A Tubular View of Electron Transfer in Azurin

   • J. J. Regan, J. N. Onuchic

   Pages 181-200

9. Biological Electron Transfer: Measurement, Mechanism, Engineering Requirements

   • C. C. Moser, P. L. Dutton

   Pages 201-214

10. The Photodetachment of an Electron from a Chloride Ion in Water Studied by Quantum Molecular Dynamics Simulation

    • A. Staib, D. Borgis

    Pages 215-234

11. Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

    • I. Logunov, K. Schulten

    Pages 235-256

12. Towards an Understanding of Quantum Factors in Small Ligand Geminate Recombination to Heme Proteins

    • W. Nowak, J.-L. Martin

    Pages 257-270

13. A Parallel Direct SCF Method for Large Molecular Systems

    • T. R. Furlani, H. F. King

    Pages 271-284

14. Multigrid Electrostatic Computations in Density Functional Theory

    • M. P. Merrick, K. A. Iyer, T. L. Beck

    Pages 285-294

15. Symmetry-Oriented Research of Polymers PC Program POLSym and DNA

    • I. Milošević, A. Damjanović, M. Damnjanović

    Pages 295-311

16. Back Matter

    Pages 313-313

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It is now generally agreed that a deeper understanding of biological processes requires a multi-disciplinary approach employing the tools of biology, chemistry, and physics. Such understanding involves study of biomacromolecules and their functions, which includes how they interact, their reactions, and how information is transmitted between them. This volume is devoted to quantum mechanical simulation techniques, which have developed rapidly in recent years. It covers quantum mechanical calculations of large systems, molecular dynamics combining quantum and classical algorithms, quantum dynamical simulations, and electron and proton transfer processes in proteins and in solutions.

• Electron Transfer
• Molecular Dynamics
• Photochemistry
• algorithms
• density functional theory
• molecule
• photosynthesis
• proteins
• quantum chemistry
• quantum dynamics
• solution

• Institut de Biologie Structurale, Laboratoire de Dynamique Molculaire, Grenoble Cedex 1, France

  Dominique Bicout, Martin Field

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