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Efficient calculation of rate constants: downhill versus uphill sampling.

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  • 1Steinbuch Centre for Computing, Karlsruhe Institute of Technology, P.O. Box 3640, D-76021 Karlsruhe, Germany.

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|August 24, 2014
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We developed downhill sampling, a modified transition interface sampling (TIS) and forward flux sampling (FFS) method, for calculating transmission coefficients in complex biomolecular reactions. This approach improves efficiency, even with poor reaction coordinates, outperforming traditional uphill sampling methods.

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Area of Science:

  • Computational Chemistry
  • Biomolecular Dynamics
  • Statistical Mechanics

Background:

  • Classical transition state theory (TST) is valuable for rare event rate calculations.
  • Defining transition states is challenging in complex systems like protein folding.
  • Transition Interface Sampling (TIS) and Forward Flux Sampling (FFS) are alternative methods.

Purpose of the Study:

  • To adapt TIS and FFS algorithms for calculating transmission coefficients.
  • To introduce a more efficient "downhill sampling" procedure.
  • To combine the strengths of TST, TIS, and FFS in a novel computational scheme.

Main Methods:

  • Modification of existing TIS and FFS algorithms.
  • Implementation of a "downhill sampling" approach.
  • Development of a hybrid TST-TIS-FFS computational strategy.

Main Results:

  • Demonstrated successful application of modified TIS/FFS for transmission coefficient calculation.
  • Showcased superior efficiency of downhill sampling over uphill sampling, even with ill-defined reaction coordinates.
  • Validated the effectiveness of the new computational scheme.

Conclusions:

  • Downhill sampling offers an efficient method for calculating transmission coefficients in complex biomolecular systems.
  • The proposed hybrid approach integrates the benefits of TST, TIS, and FFS.
  • This work provides a more robust computational tool for studying rare events in chemistry and biology.