References

TPS:

1. Bolhuis, P.G., D. Chandler, C. Dellago, and P.L. Geissler, Transition path sampling: Throwing ropes over rough mountain passes, in the dark. Annual Review of Physical Chemistry, 2002. 53: p. 291-318.
2. Dellago, C., P.G. Bolhuis and P.L. Geissler, Transition Path Sampling, Adv. Chem. Phys. 123, 1-78, 2002.
3. Crooks, G. E. and D. Chandler, "Efficient transition path sampling for nonequilibirum stochastic dynamics," Phys. Rev. E 64, 026109. 1- 026109. 4 (2001).
4. Dellago, C., P.G. Bolhuis, F.S. Csajka, and D. Chandler, Transition path sampling and the calculation of rate constants. J. Chem. Phys., 1998. 108(5): p. 1964-1977.
5. Bolhuis, P.G., C. Dellago, and D. Chandler, Sampling ensembles of deterministic transition pathways. Faraday Discussions, 1998(110): p. 421-436.

TIS:

1. Van Erp, T.S. and Bolhuis, P.G., “Elaborating Transition Interface Sampling Methods.” J. Computational Phys. 205 (2005) 157-181.

FFS:

1. Allen, R.J., Warren, P.B., and ten Wolde, P.R., “Sampling Rare Events in Biochemical Networks.” PRL 94, 018104 (2005).

Aimless Shooting:

1. Peters, B., Trout B.L., Obtaining reaction coordinates by likelihood maximization, J. Chem. Phys. 125, 054108 (2006)
2. Peters, B., Beckham G.T., Trout B.L., Extensions to the likelihood maximization approach for finding reaction coordinates, J. Chem. Phys. 127, 034109 (2007)

Some example applications:

1. M.F. Hagen and D. Chandler, Dynamic pathways for viral capsid assembly, cond-mat: arXiv:q-bio.BM/0511006v1 7 Nov 2005.
2. P.G. Bolhuis, “Transition-path sampling of beta hairpin folding” Proc. Nat. Acad. Sci. USA 100: 12129-12134 (2003).
3. Geissler, P. L., C. Dellago, D. Chandler, J. Hutter and M. Parrinello, "Autoionization in liquid water," Science 291, 2121-2124 (2001).
4. D. Zahn “Atomistic Mechanism of NaCl Nucleation From an Aqueous Solution”Phys. Rev. Lett. 92, 040801 (2004)
5. R.A. Kuharski, J.S. Bader, D. Chandler, M. Sprik, M.L. Klein and R.W. Impey, "Molecular model for aqueous Ferrous-Ferric electron transfer," J. Chem. Phys. 89, 3248-3257 (1988).
6. M. Marchi, J.N. Gehlen, D. Chandler and M. Newton, "Diabatic surfaces and the pathway for primary electron transfer in a photosynthetic reaction center," J. Am. Chem. Soc. 115, 4178-4190 (1993).

Useful links:

1. TPS reference 1: http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.physchem.53.082301.113146
2. TPS reference 2: http://www.science.uva.nl/~bolhuis/tps/pdf/article.pdf
3. TIS reference 1: http://arxiv.org/abs/cond-mat/0405116
4. FFS reference 1: http://arxiv.org/abs/cond-mat/0602269

Link to Chandler group website: http://gold.cchem.berkeley.edu/research_path.html

Notes: Unless otherwise indicated, the images shown on this site are from TPS reference #1 below, by Pieter Bolhuis, et al.