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  • © 2006

New Algorithms for Macromolecular Simulation

Part of the book series: Lecture Notes in Computational Science and Engineering (LNCSE, volume 49)

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Table of contents (19 chapters)

  1. Front Matter

    Pages I-XVI
  2. Macromolecular Models: From Theories to Effective Algorithms

    1. Front Matter

      Pages 1-1
    2. Membrane Protein Simulations: Modelling a Complex Environment

      • Peter J. Bond, Jonathan Cuthbertson, Sundeep S. Deol, Lucy R. Forrest, Jennifer Johnston, George Patargias et al.
      Pages 3-20
    3. Modeling and Simulation Based Approaches for Investigating Allosteric Regulation in Enzymes

      • Marc Q. Ma, Kentaro Sugino, Yu Wang, Narain Gehani, Annie V. Beuve
      Pages 21-34
    4. Learning to Align Sequences: A Maximum-Margin Approach

      • Thorsten Joachims, Tamara Galor, Ron Elber
      Pages 57-69
  3. Minimization of Complex Molecular Landscapes

    1. Front Matter

      Pages 71-71
    2. Overcoming Energetic and Time Scale Barriers Using the Potential Energy Surface

      • David J. Wales, Joanne M. Carr, Tim James
      Pages 73-87
    3. The Protein Folding Problem

      • H. A. Scheraga, A. Liwo, S. Oldziej, C. Czaplewski, J. Pillardy, J. Lee et al.
      Pages 89-100
  4. Dynamical and Stochastic-Dynamical Foundations for Macromolecular Modelling

    1. Front Matter

      Pages 101-101
    2. Biomolecular Sampling: Algorithms, Test Molecules, and Metrics

      • Scott S. Hampton, Paul Brenner, Aaron Wenger, Santanu Chatterjee, Jesús A. Izaguirre
      Pages 103-123
    3. Approach to Thermal Equilibrium in Biomolecular Simulation

      • Eric Barth, Ben Leimkuhler, Chris Sweet
      Pages 125-140
    4. The Targeted Shadowing Hybrid Monte Carlo (TSHMC) Method

      • Elena Akhmatskaya, Sebastian Reich
      Pages 141-153
    5. The Langevin Equation for Generalized Coordinates

      • Reinier L. C. Akkermans
      Pages 155-165
    6. Metastability and Dominant Eigenvalues of Transfer Operators

      • Wilhelm Huisinga, Bernd Schmidt
      Pages 167-182
  5. Computation of the Free Energy

    1. Front Matter

      Pages 183-183
    2. Replica-Exchange-Based Free-Energy Methods

      • Christopher J. Woods, Michael A. King, Jonathan W. Essex
      Pages 251-259
  6. Fast Electrostatics and Enhanced Solvation Models

    1. Front Matter

      Pages 261-261

About this book

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.

Editors and Affiliations

  • Department of Mathematics, University of Leicester, Leicester, UK

    Benedict Leimkuhler

  • Institut nancéien de chimie moléculaire, Université Henri Poincaré - Nancy I, Vandoeuvre-lès-Nancy, France

    Christophe Chipot

  • Department of Computer Science, Cornell University, Ithaca, USA

    Ron Elber

  • Arrhenius Laboratory Division of Physical Chemistry, Stockholm University, Stockholm, Sweden

    Aatto Laaksonen

  • Laboratory of Biophysical Chemistry, University of Groningen, Groningen, The Netherlands

    Alan Mark

  • Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, New York, USA

    Tamar Schlick

  • FB Mathematik und Informatik, Freie Universität Berlin, Berlin, Germany

    Christoph Schütte

  • Department of Computer Science, Purdue University, West Lafayette, USA

    Robert Skeel

Bibliographic Information

Buy it now

Buying options

eBook USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access