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Computational Molecular Dynamics: Challenges, Methods, Ideas

Proceeding of the 2nd International Symposium on Algorithms for Macromolecular Modelling, Berlin, May 21–24, 1997

  • Conference proceedings
  • © 1999

Overview

Editors:
  1. Peter Deuflhard

    1. Konrad-Zuse-Zentrum Berlin (ZIB), Berlin-Dahlem, Germany

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  2. Jan Hermans

    1. Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, USA

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  3. Benedict Leimkuhler

    1. Department of Mathematics, University of Kansas, Lawrence, USA

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  4. Alan E. Mark

    1. Laboratorium für Physikalische Chemie ETH Zentrum, Zürich, Switzerland

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  5. Sebastian Reich

    1. Department of Mathematics and Statistics, University of Surrey, Guildford, Surrey, UK

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  6. Robert D. Skeel

    1. Department of Computer Science, University of Illinois, Urbana, USA

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Part of the book series: Lecture Notes in Computational Science and Engineering (LNCSE, volume 4)

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Table of contents (29 papers)

  1. Front Matter

    Pages N1-XI
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  2. Introductory Survey

    1. Front Matter

      Pages 1-1
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    2. Molecular Dynamics Simulations: The Limits and Beyond

      • Herman J. C. Berendsen
      Pages 3-36

  3. Conformational Dynamics

    1. Front Matter

      Pages 37-37
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    2. Steered Molecular Dynamics

      • Sergei Izrailev, Sergey Stepaniants, Barry Isralewitz, Dorina Kosztin, Hui Lu, Ferenc Molnar et al.
      Pages 39-65

    3. Conformational Transitions of Proteins from Atomistic Simulations

      • Volkhard Helms, J. Andrew McCammon
      Pages 66-77

    4. Conformational Dynamics Simulations of Proteins

      • Markus Eichinger, Berthold Heymann, Helmut Heller, Helmut Grubmüller, Paul Tavan
      Pages 78-97

    5. Computation of Essential Molecular Dynamics by Subdivision Techniques

      • Peter Deuflhard, Michael Dellnitz, Oliver Junge, Christof Schütte
      Pages 98-115

    6. Mathematical Model of the Nucleic Acids Conformational Transitions with Hysteresis over Hydration—Dehydration Cycle

      • Michael Ye. Tolstorukov, Konstantin M. Virnik
      Pages 116-126

  4. Thermodynamic Modelling

    1. Front Matter

      Pages 127-127
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    2. Simulation Studies of Protein-Ligand Interactions

      • Jan Hermans, Geoffrey Mann, Lu Wang, Li Zhang
      Pages 129-148

    3. Estimating Relative Free Energies from a Single Simulation of the Initial State

      • Alan E. Mark, Heiko Schäfer, Haiyan Liu, Wilfred van Gunsteren
      Pages 149-162

    4. Exploration of Peptide Free Energy Surfaces

      • Krzysztof Kuczera
      Pages 163-175

    5. Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System

      • Jan Antosiewicz, Elzbieta Błachut-Okrasińska, Tomasz Grycuk, James M. Briggs, Stanisław T. Włodek, Bogdan Lesyng et al.
      Pages 176-196

    6. Exploiting Tsallis Statistics

      • John E. Straub, Ioan Andricioaei
      Pages 197-211

    7. New Techniques for the Construction of Residue Potentials for Protein Folding

      • Arnold Neumaier, Stefan Dallwig, Waltraud Huyer, Hermann Schichl
      Pages 212-224
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Keywords

About this book

On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics.
The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.

Editors and Affiliations

  • Konrad-Zuse-Zentrum Berlin (ZIB), Berlin-Dahlem, Germany

    Peter Deuflhard

  • Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, USA

    Jan Hermans

  • Department of Mathematics, University of Kansas, Lawrence, USA

    Benedict Leimkuhler

  • Laboratorium für Physikalische Chemie ETH Zentrum, Zürich, Switzerland

    Alan E. Mark

  • Department of Mathematics and Statistics, University of Surrey, Guildford, Surrey, UK

    Sebastian Reich

  • Department of Computer Science, University of Illinois, Urbana, USA

    Robert D. Skeel

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