Transition path sampling methods

Lecture Notes in Physics

Volumn 703, Issue , 2006, Pages 349-391

  Dellago, Christoph ^a   Bolhuis, Peter G ^b   Geissler, P L ^c  

^a UNIVERSITY OF VIENNA   (Austria)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33947271977     PISSN: 00758450     EISSN: None     Source Type: Book Series    
DOI: 10.1007/3-540-35273-2_10     Document Type: Article

References (58)

1. H.-X. Zhou and R. Zwanzig (1991) A rate process with an entropy barrier. J. Chem. Phys., 94, pp. 6147-6152
2. J. B. Anderson (1973) Statistical theories of chemical reactions: Distributions in the transition region. J. Chem. Phys., 58, pp. 4684-4692
3. C.H. Bennett (1977) Molecular Dynamics and Transition State Theory: the Simulation of Infrequent Events. In Algorithms for Chemical Computations, ed. R. E. Christoffersen, pp. 63-97; Washington, D.C.: Amer. Chem. Soc.
4. D. Chandler (1978) Statistical mechanics of isomerization dynamics in liquids and the transition state approximation. J. Chem. Phys., 68, pp. 2959-2970
5. L.R. Pratt (1986) A statistical method for identifying transition states in high dimensional problems. J. Chem. Phys., 85, pp. 5045-5048
6. C. Dellago, P.G. Bolhuis, F.S. Csajka, and D. Chandler (1998) Transition Path Sampling and the Calculation of Rate Constants. J. Chem. Phys., 108, pp. 1964-1977
7. C. Dellago, P.G. Bolhuis, and D. Chandler (1998) Efficient Transition Path Sampling: Applications to Lennard-Jones cluster rearrangements. J. Chem. Phys., 108, pp. 9236-9245
8. P.G. Bolhuis, C. Dellago, and D. Chandler (1998) Sampling ensembles of deterministic transition pathways. Faraday Discuss., 110, pp. 421-436
9. W. E, W. Ren, and E. Vanden-Eijnden (2002) String method for the study of rare events. Phys. Rev. B, 66, 052301/1-4
10. W. E, W. Ren, and E. Vanden-Eijnden (2005) Finite Temperature String Method for the Study of Rare Events. J. Phys. Chem. B, 109, pp. 6688-6693
11. R. Elber, A. Ghosh, A. Cardenas, and H. Stern (2004) Bridging the gap between reaction pathways, long time dynamics and calculation of rates. Adv. Chem. Phys., 126, pp. 93-129
12. D. Passerone, M. Ceccarelli, and M. Parrinello (2003) A concerted variational strategy for investigating rare events. J. Chem. Phys., 118, pp. 2025-2032
13. P. G. Bolhuis, D. Chandler, C. Dellago, and P.L. Geissler (2002) Transition Path Sampling: Throwing Ropes over Mountain Passes in the Dark. Ann. Rev. Phys. Chem., 53, pp. 291-318
14. C. Dellago, P.G. Bolhuis, and P.L. Geissler (2002) Transition Path Sampling. Adv. Chem. Phys., 123, pp. 1-78
15. C. Dellago and D. Chandler (2002) Bridging the time scale gap with transition path sampling, in Molecular Simulation for the Next Decade, ed. by P. Nielaba, M. Mareschal, and G. Ciccotti, Springer, Berlin. pp. 321-333
16. C. Dellago (2005) Transition Path Sampling, in Handbook of Materials Modeling, ed. by S. Yip, Springer, Berlin. pp. 1585-1596
17. C. Dellago (2006) Transition Path Sampling and the Calculation of Free Energies, in Free energy calculations: Theory and applications in chemistry and biology, ed. by A. Pohorille and C. Chipot, Springer, Berlin, pp. 265-294
18. G.E. Crooks and D. Chandler (2001) Efficient transition path sampling for nonequilibrium stochastic dynamics. Phys. Rev. E, E 64, 026109/1-4
19. R. Car and M. Parrinello (1985) Unified Approach for Molecular Dynamics and Density-Functional Theory. Phys. Rev. Lett., 55, pp. 2471-2474
20. S. Nose (1984) A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys, 81, pp. 511-519
21. W.G. Hoover (1985) Canonical dynamics: Equilibrium phase-space distributions", Phys. Rev. A, 31, pp. 1695-1697
22. D.J. Evans, W.G. Hoover, B.H. Failor, B. Moran, and A.J.C. Ladd (1983) Nonequilibrium molecular dynamics via Gauss's principle of least constraint. Phys. Rev. A, 28, pp. 1016-2021
23. R. Zwanzig (2001) Nonequilibrium Statistical Mechanics, Oxford University Press, Oxford
24. M.P. Allen and D.J. Tildesley (1987) Computer Simulation of Liquids, Clarendon Press, Oxford
25. S. Chandrasekhar (1943) Stochastic Problems in Physics and Astronomy. Rev. Mod. Phys., 15, pp. 1-89
26. P.L. Geissler, C. Dellago, D. Chandler, J. Hutter, and M. Parrinello (2001) Autoionization in liquid water. Science, 291, pp. 2121-2124
27. D.P. Landau and K. Binder (2000) A Guide to Monte Carlo Simulations in Statistical Physics, Cambridge University Press, Cambridge
28. N. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, A.H. Teller, and E. Teller (1953) Equation of State Calculations by Fast Computing Machines. J. Chem. Phys., 21, pp. 1087-1092
29. T.J.H. Vlugt, C. Dellago, and B. Smit (2000) Diffusion of Isobutane in Silicalite studied by Transition Path Sampling. J. Chem. Phys., 113, p. 8791
30. P.G. de Gennes (1971) Reptation of a Polymer Chain in the Presence of Fixed Obstacles. J. Chem. Phys., 55, pp. 572-579
31. R.B. Best and G. Hummer (2005) Reaction coordinates and rates from transition paths. Proc. Nat. Acad. Sci. USA, 102, pp. 6732-6737
32. L. Onsager (1938) Initial Recombination of Ions. Phys. Rev., 54, pp. 554-557
33. V. Pande, A.Y. Grosberg, T. Tanaka, and E.I. Shakhnovich (1998) On the transition coordinate for protein folding. J. Chem. Phys., 108, pp. 334-350
34. S. Auer and D. Frenkel (2001) Prediction of absolute crystal-nucleation rate in hard-sphere colloids. Nature, 409, pp. 1020-1023
35. E.A. Carter, G. Ciccotti, J.T. Hynes, and R. Kapral (1989) Constrained reaction coordinate dynamics for the simulation of rare events. Chem. Phys. Lett., 156, pp. 472-477
36. D. Moroni, P.R. tenWolde, and P.G. Bolhuis (2005) Interplay between Structure and Size in a Critical Crystal Nucleus. Phys. Rev. Lett., 94, 235703/1-4
37. D. Chandler (1987) Introduction to Modern Statistical Mechanics, Oxford University Press, New York
38. G.M. Torrie and J.P. Valleau (1974) Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid. Chem. Phys. Lett., 28, pp. 578-581
39. C. Dellago, P.G. Bolhuis and D. Chandler (1999) On the calculation of rate constants in the transition path ensemble. J. Chem. Phys., 110, pp. 6617-6625
40. T.S. van Erp, D. Moroni, and P.G. Bolhuis (2003) A novel path sampling method for the calculation of rate constants. J. Chem. Phys., 118, pp. 7762-7774
41. T.S. van Erp and P.G. Bolhuis (2005) Elaborating transition interface sampling methods. J. Comp. Phys., 205, pp. 157-181
42. D. Moroni, P.G. Bolhuis, and T.S. van Erp (2004) Rate constants for diffusive processes by partial path sampling. J. Chem. Phys., 120, pp. 4055-4065
43. A.K. Faradjian and R. Elber (2004) Computing time scales from reaction coordinates by milestoning. J. Chem. Phys., 120, pp. 10880-10889
44. R. J. Allen, P. B. Warren, and P. R. ten Wolde (2005) Sampling Rare Switching Events in Biochemical Networks. Phys. Rev. Lett., 94, 018104/ 1-4
45. P.W. Atkins (2001) Physical Chemistry, 7th edition, Oxford University Press, Oxford
46. C. Dellago and P.G. Bolhuis (2004) Activation energies from transition path sampling simulations. Mol. Sim., 30, pp. 795-799
47. H.B. Callen (1985) Thermodynamics and an Introduction to Thermostatistics, 2nd edition, John Wiley and Sons, New York
48. C. Jarzynski (1997) Nonequilibrium Equality for Free Energy Differences. Phys. Rev. Lett., 78, pp. 2690-2693
49. G.E. Crooks (1998) Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems. J. Stat. Phys., 90, pp. 1481-1487
50. F. Ritort (2003) Work fluctuations and transient violations of the second law: Perspectives in theory and experiments. Sem. Poincare 2, pp. 193-226
51. G. Hummer (2001) Fast-growth thermodynamic integration: Error and efficiency analysis. J. Chem. Phys., 114, pp. 7330-7337
52. H. Oberhofer, C. Dellago and P.L. Geissler (2005) Biased sampling of nonequilibrium trajectories: Can fast switching simulations outperform conventional free energy calculation methods? J. Phys. Chem. B, 69, pp. 6902-6915
53. R. Zwanzig (1954) High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases. J. Chem. Phys., 22, pp. 1420-1426
54. B. Widom (1963) Some Topics in the Theory of Fluids. J. Chem. Phys., 39, pp. 2808-2812
55. S.X. Sun (2003) Equilibrium free energies from path sampling of nonequilibrium trajectories. J. Chem. Phys., 118, pp. 5769-5775
56. F.M. Ytreberg and D.M. Zuckerman (2004) Single-ensemble nonequilibrium path-sampling estimates of free energy differences. J. Chem. Phys., 120, pp. 10876-10879
57. M. Athènes (2004) A path-sampling scheme for computing thermodynamic properties of a many-body system in a generalized ensemble. Eur. Phys. J. B, 38, pp. 651-663
58. D. Frenkel and B. Smit (2002) Understanding Molecular Simulation, Academic Press, San Diego