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Finding pathways between distant local minima.

Joanne M Carr¹, Semen A Trygubenko, David J Wales

¹University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

The Journal of Chemical Physics

|July 13, 2005

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This study introduces an efficient algorithm for mapping complex molecular pathways, significantly improving computational speed for analyzing transition states in chemical reactions and biomolecular folding.

Area of Science:

Computational Chemistry
Biophysics
Materials Science

Background:

Mapping reaction pathways and conformational changes is crucial for understanding chemical reactions and biomolecular function.
Traditional methods struggle with complex potential energy surfaces featuring numerous transition states.

Purpose of the Study:

To develop a novel, efficient algorithm for constructing pathways between local minima on potential energy surfaces.
To improve the computational efficiency of exploring complex molecular transformations.

Main Methods:

The study employs Dijkstra's algorithm to identify shortest paths between local minima.
A new strategy for selecting endpoint pairs enhances search efficiency.
Path length is determined using a metric based on minimized Euclidean distance.

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Main Results:

The algorithm successfully constructs pathways involving a large number of transition states.
Applications demonstrated include buckminsterfullerene formation and the folding of diverse biomolecules (Protein G B1 domain, tryptophan zippers, villin headpiece).
Pathways with up to 163 transition states were generated.

Conclusions:

The new algorithm offers a significant improvement in efficiency for pathway construction.
This method provides a robust framework for future discrete path sampling calculations.
The approach is applicable to complex systems in chemistry and biology.