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Long time dynamics of complex systems.

Ron Elber1, Avijit Ghosh, Alfredo Cárdenas

  • 1Department of Computer Science, Upson Hall 4130, Cornell University, Ithaca, New York 14853, USA. ron@cs.cornell.edu

Accounts of Chemical Research
|June 19, 2002
PubMed
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We developed a computational method to significantly extend molecular dynamics simulations. This allows for the study of large biological molecules over much longer timescales, revealing new insights into their behavior.

Area of Science:

  • Computational Chemistry
  • Biophysics
  • Molecular Modeling

Background:

  • Molecular dynamics (MD) simulations are crucial for understanding biological molecules.
  • Current MD methods are limited to nanosecond timescales for large biomolecules.
  • Extending simulation times is essential for capturing slow biological processes.

Purpose of the Study:

  • To present a novel computational method for extending molecular simulation timescales.
  • To enable the computation of microsecond and millisecond trajectories for large biomolecules.
  • To provide a feasible approach for atomically detailed approximate molecular trajectories.

Main Methods:

  • Optimization of a specific functional to enhance simulation step size.
  • Development of a computational technique to overcome timescale limitations in MD.

Related Experiment Videos

  • Application of the method to model peptide conformational changes and helix formation.

    • Main Results:

    • The method successfully extends molecular simulation times by orders of magnitude.
    • Achieved microsecond and millisecond timescales in simulation trajectories.
    • Demonstrated feasibility through numerical examples of peptide dynamics.

    Conclusions:

    • The developed computational method significantly advances the timescale accessible in molecular dynamics.
    • This technique offers a powerful tool for investigating slow conformational changes and processes in large biomolecules.
    • Enables more comprehensive and biologically relevant simulations of molecular behavior.