Graph Transformation Method

Graph Transformation is an exact approach for calculating transition probabilities and waiting times in finite-state discrete-time Markov processes. It outperforms kinetic Monte Carlo, master equation and matrix multiplication methods for extraction of kinetic information from networks of rearrangement pathways.

This work was described in detail in: S. A. Trygubenko and D. J. Wales, 'Graph Transformation Method for Calculating Waiting Times in Markov Chains', J. Chem. Phys., 124, 234110 (2006) [JCP Online] [arXiv]

Fortran 95 implementations of the sparse- and dense-optimised graph transformation algorithms discussed in this article are distributed free of charge under the GPL. Source code for gt program is available for download.