Transition Path Sampling

Contents

List of References

Up to this date, the most comprehensive paper on the fundamentals and implementation of Transition path sampling is the review article in the Advances of Chemical Physics

C.Dellago, P.G.Bolhuis and P.L. Geissler, "Transition Path Sampling", Adv. Chem. Phys. 123 (2002) [PDF]

P.G. Bolhuis, C.Dellago, P.L. Geissler, and D. Chandler "Transition Path Sampling: throwing ropes over dark mountain passes", Ann. Rev. Phys. Chem. 54 , 20(2002) [PDF]

Rate constants for diffusive processes by partial path sampling
D. Moroni, P.G. Bolhuis, T.S. van Erp TS, J. Chem. Phys. 120 (9): 4055-4065 (2004)

A novel path sampling method for the calculation of rate constants
T.S. van Erp, D. Moroni and P.G. Bolhuis, J. Chem Phys. 118, pp 7762-7774, (2003)

Transtion Path Sampling on diffusive barriers
P.G. Bolhuis, J. Phys. Cond. Matt., 15 pp S113-S120, (2003)

Monte Carlo sampling in path space: Calculating time correlation functions by transforming ensembles of trajectories
C. Dellago and P. L. Geissler, in Proceedings of "The Monte Carlo Method in the Physical Sciences: Celebrating the 50th anniversary of the Metropolis algorithm", AIP Conference Proceedings, vol. 690 (2003).

Bridging the time scale gap with transition path sampling
C. Dellago and D. Chandler, in "Molecular Simulation for the Next Decade", ed. by P. Nielaba, M. Mareschal, and G. Ciccotti, Springer, Berlin (2002).

G.E. Crooks and D. Chandler, Efficient transition path sampling for nonequilibrium stochastic dynamics, Phys Rev E 64 (2): Art. No. 026109 Part 2( 2001)

T.J.H. Vlugt and B. Smit, On the efficient sampling of pathways in the transition path ensemble Phys. Chem. Comm. (2): Art. No. 2 (2001 )

C. Dellago, P. Bolhuis, F. S. Csajka, and D. Chandler, "Transition Path Sampling and the Calculation of Rate Constants", J. Chem. Phys., 108, 1964 (1998).

P. Bolhuis, C. Dellago and D. Chandler, "Sampling ensembles of deterministic transition pathways", Faraday Discussion, 110 (1998).

C. Dellago, P. Bolhuis, and D. Chandler, "Efficient Transition Path Sampling: Applications to Lennard-Jones cluster rearrangements", J. Chem. Phys., 108, 9236 (1998).

C. Dellago, P. G. Bolhuis and D. Chandler, "On the calculation of rate constants in the transition path ensemble," J. Chem. Phys. 110, 6617 (1999). [PDF]

are referenced here for completeness but are not recommended as reading material for novices

Application of transition path sampling is described in:

M.F. Hagan, A.R. Dinner, D. Chandler, and A.K. Chakraborty, Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA Proc. Natl Acad Sci USA 100 (24): 13922-13927 (2003 )

P.G. Bolhuis, Transition-path sampling of beta hairpin folding, Proc. Nat. Acad. Sci. USA 100: 12129-12134 (2003)

J. Marti and F.S. Csajka, Flip-flop dynamics in a model lipid bilayer membrane Europhys Lett 61 (3): 409-414 (2003)

D. Ensing and E.J. Baerends, Reaction path sampling of the reaction between iron(II) and hydrogen peroxide in aqueous solution J. Phys. Chem. A 106 (34): 7902-7910 (2002)

P.R. ten Wolde and D. Chandler, Drying-induced hydrophobic polymer collapse Proc. Natl. Acad. SCI USA 99 (10): 6539-6543 (2002 )

J. Rodriguez, G. Moriena and Laria D Dynamical pathways for isomerization processes in the water nonamer, Chem Phys Lett 356 (1-2): 147-152 (2002)

J. Ramirez and M. Laso, Conformational kinetics in liquid n-butane by transition path sampling J CHEM PHYS 115 (15): 7285-7292 (2001)

J.Marti, Transition path sampling study of the local molecular structure in the aqueous solvation of sodium chloride, Mol. Simulation 27 (3): 169-+ (2001)

D. Laria, J. Rodriguez J and C. Dellago C, Dynamical aspects of isomerization and melting transitions in [H2O](8), J. Phys Chem A 105 (12): 2646-2651 (2001)

P. L. Geissler, C. Dellago, D. Chandler, J. Hutter, and M. Parrinello, "Autodissociation of a water molecule in liquid water",Science 291, 2121 (2001). Supplementary Web Material.

P. L. Geissler, T. van Voorhis, and C. Dellago, "Potential energy landscape for proton transfer in (H2O)3H+: Comparison of density functional theory and wavefunction based methods", Chem. Phys. Lett. 324, 149 (2000).:

P.L. Geissler amd D. Chandler, Importance sampling and theory of nonequilibrium solvation dynamics in water, J. Chem Phys 113 (21): 9759-9765 (2000)

P.G. Bolhuis and D. Chandler, Transition path sampling of cavitation between molecular scale solvophobic surfaces, J. Chem. Phys. 113 (18): 8154-8160 (2000)

J. Marti, F.S. Csajka and D. Chandler, Stochastic transition pathways in the aqueous sodium chloride dissociation process, Chem. Phys. Lett. 328 (1-2): 169-176 (2000)

J. Marti and F.S. Csajka, The aqueous solvation of sodium chloride: A Monte Carlo transition path sampling study, J. Chem. Phys. 113 (3): 1154-1161 (2000)

P.L. Geissler, C. Dellago and D. Chandler D, Ab initio analysis of proton transfer dynamics in (H2O)(3)H+, Chem. Phys. Lett. 321 (3-4): 225-230 APR 28 2000

P. G. Bolhuis, C. Dellago, P. L. Geissler, and D. Chandler, "Transition path sampling: throwing ropes over mountains in the dark", J. Phys. C12, A147 (2000). :

P. G. Bolhuis, C. Dellago and D. Chandler, "Reaction Coordinates of Biomolecular Isomerization", Proc. Nat. Acad. Sci. USA 97, 5877 (2000). :

P. L. Geissler, C. Dellago, D. Chandler, J. Hutter, and M. Parrinello, "Ab initio analysis of proton transfer dynamics in (H2O)3H+", Chem. Phys. Lett. 321, 225 (2000).:

T. J. H. Vlugt, C. Dellago, and B. Smit, "Diffusion of Isobutane in Silicalite studied by Transition Path Sampling", J. Chem. Phys. 113, 8791 (2000). :

P. Geissler, C. Dellago, and D. Chandler, "Kinetic Pathways of Ion Dissociation in Water", J. Phys. Chem. B103, 3706 (1999).:

P.L. Geissler, C. Dellago and D. Chandler, Chemical dynamics of the protonated water trimer analyzed by transition path sampling, Phys Chem Chem Phys 1 (6): 1317-1322 (1999)