Algorithmic Challenges in Computational Molecular Biophysics

Tamar Schlick, Robert D. Skeel, Axel T. Brunger, Laxmikant V. Kalé, John A. Board, Jan Hermans, Klaus Schulten

Research output: Contribution to journalArticlepeer-review

Abstract

A perspective of biomolecular simulations today is given, with illustrative applications and an emphasis on algorithmic challenges, as reflected by the work of a multidisciplinary team of investigators from five institutions. Included are overviews and recent descriptions of algorithmic work in long-time integration for molecular dynamics; fast electrostatic evaluation; crystallographic refinement approaches; and implementation of large, computation-intensive programs on modern architectures. Expected future developments of the field are also discussed.

Original languageEnglish (US)
Pages (from-to)9-48
Number of pages40
JournalJournal of Computational Physics
Volume151
Issue number1
DOIs
StatePublished - May 1 1999

Keywords

  • Biomolecular simulations
  • Crystallographic refinement
  • Fast electrostatics
  • High-performance platforms
  • Long-time integration
  • Molecular dynamics

ASJC Scopus subject areas

  • Numerical Analysis
  • Modeling and Simulation
  • Physics and Astronomy (miscellaneous)
  • Physics and Astronomy(all)
  • Computer Science Applications
  • Computational Mathematics
  • Applied Mathematics

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