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Applications of parallel computing to biological problems

B Ostrovsky1, M A Smith, Y Bar-Yam

  • 1Electrical, Computer and Systems Engineering Department, Boston University, Massachusetts 02215, USA.

Annual Review of Biophysics and Biomolecular Structure
|January 1, 1995
PubMed
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This review explores parallel computing strategies for polymer simulations. Efficient algorithms like the two-space algorithm and cellular automata are highlighted for simulating polymer melts, gel electrophoresis, and collapse.

Area of Science:

  • Computational physics
  • Materials science
  • Biophysics

Background:

  • Parallel computing offers significant processing power for complex scientific simulations.
  • Simulating biological and artificial polymers requires efficient algorithms and architectures.
  • Existing methods face challenges in handling large-scale polymer systems.

Purpose of the Study:

  • To review general strategies and specific algorithms for parallel polymer simulations.
  • To discuss the application of these methods to polymer melts, gel electrophoresis, and polymer collapse.
  • To highlight efficient algorithms suitable for both parallel and serial computation.

Main Methods:

  • Space partitioning (domain decomposition, cell methods) and distributed independent simulations.

Related Experiment Videos

  • Cellular automata and the two-space algorithm for abstract polymer simulation.
  • Application of these methods to simulate 2D polymer melts, gel electrophoresis, and polymer collapse.

    • Main Results:

    • High-density 2D polymer melts show significant interpenetration, contrary to segregation expectations.
    • Preliminary gel electrophoresis simulations demonstrate diffusive behavior and Cellular Automaton Machine (CAM) utility.
    • Polymer collapse simulations reveal kinetics' importance and nucleation by chain end migration.

    Conclusions:

    • Parallel computing strategies and algorithms like cellular automata are crucial for advancing polymer simulations.
    • The two-space algorithm offers efficiency for both parallel and serial polymer computations.
    • Simulations provide insights into polymer behavior in melts, electrophoresis, and collapse regimes.