T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
Abstract
▪ Abstract This article reviews the concepts and methods of transition path sampling. These methods allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction coordinates, and transition states. Based upon a statistical mechanics of trajectory space, they provide a perspective with which time dependent phenomena, even for systems driven far from equilibrium, can be examined with the same types of importance sampling tools that in the past have been applied so successfully to static equilibrium properties.
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In order to observe a rare (activated) event without developing dedicated hardware, one needs to selectively increase the speed at which the pathways related to the transition are traversed, to modify the probability distribution that is sampled during the simulation so that configurations close to the transition state occur more often, or to generate adaptively ensembles of trajectories that覆盖the
“In order to observe a rare (activated) event without developing dedicated hardware 1 one needs to selectively increase the speed at which the pathways related to the transition are traversed 51,87,88 , to modify the probability distribution that is sampled during the simulation so that configurations that are close to the transition state occur more often 15,89 , or to generate adaptively ens”
From Unsupervised machine learning in atomistic simulations, between predictions and understanding (2019) · cites this paper as [87]
Cites
Nonlinear Dimensionality Reduction by Locally Linear Embedding
Roweis, S. T., & Saul, L. K. (2000) · Science · doi:10.1126/science.290.5500.2323 · Cited by 14,965 · see citing works
A Global Geometric Framework for Nonlinear Dimensionality Reduction
Tenenbaum, J. B., Silva, V. D., & Langford, J. C. (2000) · Science · doi:10.1126/science.290.5500.2319 · Cited by 13,585 · see citing works
Unified Approach for Molecular Dynamics and Density-Functional Theory
Car, R., & Parrinello, M. (1985) · Physical Review Letters · doi:10.1103/physrevlett.55.2471 · Cited by 10,737 · see citing works
Understanding Molecular Simulation
Frenkel, D., Smit, B., Tobochnik, J., McKay, S. R., & Christian, W. (1997) · Computers in Physics · doi:10.1063/1.4822570 · Cited by 5,395 · see citing works
Understanding Molecular Simulation: From Algorithms to Applications
Ratner, M. A. (1997) · Physics Today · doi:10.1063/1.881812 · Cited by 5,114 · see citing works
Monte Carlo Methods in Statistical Physics
Newman, M. E. J., & Barkema, G. T. (1999) · doi:10.1093/oso/9780198517962.001.0001 · Cited by 3,191 · see citing works
Classical and Quantum Dynamics in Condensed Phase Simulations
(1998) · doi:10.1142/3816 · Cited by 2,284 · see citing works
Nonequilibrium Statistical Mechanics
Zwanzig, R. W. (2001) · doi:10.1093/oso/9780195140187.001.0001 · Cited by 2,075 · see citing works
Introduction to modern statistical mechanics.
Chandler, D. (1987) · Oxford University Press eBooks · Cited by 1,988 · see citing works
Self-citationIntroduction to Modern Statistical Mechanics
Chandler, D., & Percus, J. K. (1988) · Physics Today · doi:10.1063/1.2811680 · Cited by 1,977 · see citing works
Self-citationThe nature of the hydrated excess proton in water
Marx, D., Tuckerman, M. E., Hutter, J., & Parrinello, M. (1999) · Nature · doi:10.1038/17579 · Cited by 1,906 · see citing works
Proton Transfer, Acid‐Base Catalysis, and Enzymatic Hydrolysis. Part I: ELEMENTARY PROCESSES
Eigen, M. (1964) · Angewandte Chemie International Edition in English · doi:10.1002/anie.196400011 · Cited by 1,844 · see citing works
Multicanonical ensemble: A new approach to simulate first-order phase transitions
Berg, B. A., & Neuhaus, T. (1992) · Physical Review Letters · doi:10.1103/physrevlett.68.9 · Cited by 1,587 · see citing works
Statistical mechanics of isomerization dynamics in liquids and the transition state approximation
Chandler, D. (1978) · The Journal of Chemical Physics · doi:10.1063/1.436049 · Cited by 1,429 · see citing works
Self-citationNonequilibrium Statistical Mechanics
Zwanzig, R. W. (1990) · doi:10.1142/1009 · Cited by 1,339 · see citing works
Transition path sampling and the calculation of rate constants
Dellago, C., Bolhuis, P. G., Csajka, F. S., & Chandler, D. (1998) · The Journal of Chemical Physics · doi:10.1063/1.475562 · Cited by 1,066 · see citing works
Self-citationReal-Space Imaging of Nucleation and Growth in Colloidal Crystallization
Gasser, U., Weeks, E. R., Schofield, A. B., Pusey, P. N., & Weitz, D. A. (2001) · Science · doi:10.1126/science.1058457 · Cited by 1,052 · see citing works
Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events
Voter, A. F. (1997) · Physical Review Letters · doi:10.1103/physrevlett.78.3908 · Cited by 996 · see citing works
Tuckerman, M. E., Laasonen, K. E., Sprik, M., & Parrinello, M. (1995) · The Journal of Chemical Physics · doi:10.1063/1.469654 · Cited by 866 · see citing works
Autoionization in Liquid Water
Geissler, P. L., Dellago, C., Chandler, D., Hutter, J., & Parrinello, M. (2001) · Science · doi:10.1126/science.1056991 · Cited by 794 · see citing works
Self-citationCerjan, C., & Miller, W. H. (1981) · The Journal of Chemical Physics · doi:10.1063/1.442352 · Cited by 732 · see citing works
Predicting slow structural transitions in macromolecular systems: Conformational flooding
Grubmüller, H. (1995) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.52.2893 · Cited by 688 · see citing works
The Kinetics of the Recombination of Methyl Radicals and Iodine Atoms.
Marcus, R. A., & Rice, O. K. (1951) · The Journal of Physical Chemistry · doi:10.1021/j150489a013 · Cited by 671 · see citing works
The computer simulation of proton transport in water
Schmitt, U. W., & Voth, G. A. (1999) · The Journal of Chemical Physics · doi:10.1063/1.480032 · Cited by 618 · see citing works
Wales, D. J., Miller, M. A., & Walsh, T. R. (1998) · Nature · doi:10.1038/29487 · Cited by 598 · see citing works
On the transition coordinate for protein folding
Du, R., Pande, V. S., Grosberg, A. Y., Tanaka, T., & Shakhnovich, E. I. (1998) · The Journal of Chemical Physics · doi:10.1063/1.475393 · Cited by 486 · see citing works
THEORIES OF UNIMOLECULAR GAS REACTIONS AT LOW PRESSURES
Rice, O. K., & Ramsperger, H. C. (1927) · Journal of the American Chemical Society · doi:10.1021/ja01406a001 · Cited by 448 · see citing works
Studies in Homogeneous Gas Reactions. I
Kassel, L. S. (1928) · The Journal of Physical Chemistry · doi:10.1021/j150284a007 · Cited by 436 · see citing works
Reaction coordinates of biomolecular isomerization
Bolhuis, P. G., Dellago, C., & Chandler, D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.100127697 · Cited by 426 · see citing works
Self-citationTheory of the time development of the stokes shift in polar media
Bagchi, B., Oxtoby, D. W., & Fleming, G. R. (1984) · Chemical Physics · doi:10.1016/0301-0104(84)80014-2 · Cited by 397 · see citing works
A method for determining reaction paths in large molecules: application to myoglobin
Elber, R., & Karplus, M. (1987) · Chemical Physics Letters · doi:10.1016/0009-2614(87)80576-6 · Cited by 391 · see citing works
Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements
Christoph Dellago, A., Bolhuis, P. G., & Chandler, D. (1998) · The Journal of Chemical Physics · doi:10.1063/1.476378 · Cited by 364 · see citing works
Self-citationKinetic Pathways of Ion Pair Dissociation in Water
Geissler, P. L., Dellago, C., & Chandler, D. (1999) · The Journal of Physical Chemistry B · doi:10.1021/jp984837g · Cited by 351 · see citing works
Self-citationOn the calculation of reaction rate constants in the transition path ensemble
Dellago, C., Bolhuis, P. G., & Chandler, D. (1999) · The Journal of Chemical Physics · doi:10.1063/1.478569 · Cited by 322 · see citing works
Self-citationAspects of Protein Reaction Dynamics: Deviations from Simple Behavior
Karplus, M. (1999) · The Journal of Physical Chemistry B · doi:10.1021/jp993555t · Cited by 306 · see citing works
Frantz, D. D., Freeman, D. L., & Doll, J. D. (1990) · The Journal of Chemical Physics · doi:10.1063/1.458863 · Cited by 305 · see citing works
Sampling ensembles of deterministic transition pathways
Bolhuis, P. G., Christoph Dellago, A., & Chandler, D. (1998) · Faraday Discussions · doi:10.1039/a801266k · Cited by 304 · see citing works
Self-citationSpiers Memorial Lecture Quantum and semiclassical theory of chemical reaction rates
Miller, W. H. (1998) · Faraday Discussions · doi:10.1039/a805196h · Cited by 282 · see citing works
A statistical method for identifying transition states in high dimensional problems
Pratt, L. R. (1986) · The Journal of Chemical Physics · doi:10.1063/1.451695 · Cited by 280 · see citing works
Pathways for protein folding: is a new view needed?
Pande, V. S., Grosberg, A. Y., Tanaka, T., & Rokhsar, D. S. (1998) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(98)80012-2 · Cited by 252 · see citing works
Statistical theories of chemical reactions. Distributions in the transition region
Anderson, J. B. (1973) · The Journal of Chemical Physics · doi:10.1063/1.1679032 · Cited by 247 · see citing works
Annealing Markov Chain Monte Carlo with Applications to Ancestral Inference
Geyer, C. J., & Thompson, E. A. (1995) · Journal of the American Statistical Association · doi:10.2307/2291325 · Cited by 229 · see citing works
Molecular Dynamics and Transition State Theory: The Simulation of Infrequent Events
Bennett, C. H. (1977) · ACS symposium series · doi:10.1021/bk-1977-0046.ch004 · Cited by 223 · see citing works
Potential of mean force by constrained molecular dynamics: A sodium chloride ion-pair in water
Guàrdia, E., Rey, R., & Padró, J. À. (1991) · Chemical Physics · doi:10.1016/0301-0104(91)87019-r · Cited by 219 · see citing works
Algorithms for Chemical Computations
Christoffersen, R. E. (1977) · ACS symposium series · doi:10.1021/bk-1977-0046 · Cited by 212 · see citing works
Calculation of classical trajectories with a very large time step: Formalism and numerical examples
Olender, R., & Elber, R. (1996) · The Journal of Chemical Physics · doi:10.1063/1.472727 · Cited by 210 · see citing works
The Mechanism of Hydrated Proton Transport in Water
Day, T., Schmitt, U. W., & Voth, G. A. (2000) · Journal of the American Chemical Society · doi:10.1021/ja002506n · Cited by 185 · see citing works
From silicon to RNA: The coming of age of ab initio molecular dynamics
Parrinello, M. (1997) · Solid State Communications · doi:10.1016/s0038-1098(96)00723-5 · Cited by 173 · see citing works
THEORIES OF UNIMOLECULAR GAS REACTIONS AT LOW PRESSURES. II
Rice, O. K., & Ramsperger, H. C. (1928) · Journal of the American Chemical Society · doi:10.1021/ja01390a002 · Cited by 171 · see citing works
Sahu, P. K. (2013) · Springer eBooks · doi:10.1007/978-81-322-1020-7_12 · Cited by 170 · see citing works
Toda, M., Kubo, R., & Saitô, N. (1983) · Springer series in solid-state sciences · doi:10.1007/978-3-642-58134-2 · Cited by 168 · see citing works
Solvation structure of a sodium chloride ion pair in water
Belch, A. C., Berkowitz, M. L., & McCammon, J. A. (1986) · Journal of the American Chemical Society · doi:10.1021/ja00268a007 · Cited by 122 · see citing works
Transition path sampling of cavitation between molecular scale solvophobic surfaces
Bolhuis, P. G., & Chandler, D. (2000) · The Journal of Chemical Physics · doi:10.1063/1.1315997 · Cited by 121 · see citing works
Self-citationDynamical aspects of the sodium(1+)-chloride ion pair association in water
Rey, R., & Guàrdia, E. (1992) · The Journal of Physical Chemistry · doi:10.1021/j100190a104 · Cited by 103 · see citing works
Elber, R., Meller, J., & Olender, R. (1999) · The Journal of Physical Chemistry B · doi:10.1021/jp983774z · Cited by 103 · see citing works
Proton Solvation and Proton Mobility
Agmon, N. (1999) · Israel Journal of Chemistry · doi:10.1002/ijch.199900054 · Cited by 103 · see citing works
Shadowing, rare events, and rubber bands. A variational Verlet algorithm for molecular dynamics
Gillilan, R. E., & Wilson, K. R. (1992) · The Journal of Chemical Physics · doi:10.1063/1.463163 · Cited by 99 · see citing works
Simulation of protein folding by reaction path annealing
Eastman, P. K., Grønbech‐Jensen, N., & Doniach, S. (2001) · The Journal of Chemical Physics · doi:10.1063/1.1342162 · Cited by 95 · see citing works
Importance sampling and theory of nonequilibrium solvation dynamics in water
Geissler, P. L., & Chandler, D. (2000) · The Journal of Chemical Physics · doi:10.1063/1.1290136 · Cited by 95 · see citing works
Self-citationEfficient transition path sampling for nonequilibrium stochastic dynamics
Crooks, G. E., & Chandler, D. (2001) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.64.026109 · Cited by 92 · see citing works
Self-citationDynamic reaction paths and rates through importance-sampled stochastic dynamics
Zuckerman, D. M., & Woolf, T. B. (1999) · The Journal of Chemical Physics · doi:10.1063/1.480278 · Cited by 88 · see citing works
Sevick, E. M., Bell, A. T., & Theodorou, D. N. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464093 · Cited by 82 · see citing works
Dynamics of a sodium chloride ion pair in water
Karim, O. A., & McCammon, J. A. (1986) · Journal of the American Chemical Society · doi:10.1021/ja00268a008 · Cited by 81 · see citing works
Predicting Rare Events in Molecular Dynamics
Anderson, J. B. (1995) · Advances in chemical physics · doi:10.1002/9780470141502.ch5 · Cited by 77 · see citing works
The Kramers Problem in the Turnover Regime: The Role of the Stochastic Separatrix
Kłosek, M. M., Matkowsky, B. J., & Schuss, Z. (1991) · Berichte der Bunsengesellschaft für physikalische Chemie · doi:10.1002/bbpc.19910950318 · Cited by 76 · see citing works
Mechanical Unfolding of a β-Hairpin Using Molecular Dynamics
Bryant, Z. D., Pande, V. S., & Rokhsar, D. S. (2000) · Biophysical Journal · doi:10.1016/s0006-3495(00)76618-5 · Cited by 66 · see citing works
Multidimensional Transition State Theory and the Validity of Grote−Hynes Theory
Truhlar, D. G., & Garrett, B. C. (2000) · The Journal of Physical Chemistry B · doi:10.1021/jp992430l · Cited by 65 · see citing works
Chemical dynamics of the protonated water trimer analyzed by transition path sampling
Geissler, P. L., Dellago, C., & Chandler, D. (1999) · Physical Chemistry Chemical Physics · doi:10.1039/a808871c · Cited by 64 · see citing works
Self-citationAb initio analysis of proton transfer dynamics in (H2O)3H+
Geissler, P. L., Dellago, C., Chandler, D., et al. (2000) · Chemical Physics Letters · doi:10.1016/s0009-2614(00)00381-x · Cited by 55 · see citing works
Self-citationDiffusion of isobutane in silicalite studied by transition path sampling
Vlugt, T. J. H., Dellago, C., & Smit, B. (2000) · The Journal of Chemical Physics · doi:10.1063/1.1318771 · Cited by 53 · see citing works
Self-citationDynamical Aspects of Isomerization and Melting Transitions in [H2O]8
Laría, D., Rodríguez, J., Dellago, C., et al. (2001) · The Journal of Physical Chemistry A · doi:10.1021/jp003955c · Cited by 38 · see citing works
Self-citationGeissler, P. L., Voorhis, T. V., & Dellago, C. (2000) · Chemical Physics Letters · doi:10.1016/s0009-2614(00)00479-6 · Cited by 24 · see citing works
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Laio, A., & Parrinello, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202427399 · Cited by 5,626 · see citing works
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Noé, F., Schütte, C., Vanden-Eijnden, E., Reich, L., & Weikl, T. R. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0905466106 · Cited by 820 · see citing works
Tiwary, P., & Parrinello, M. (2013) · Physical Review Letters · doi:10.1103/physrevlett.111.230602 · Cited by 494 · see citing works
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Buchete, N.-V., & Hummer, G. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp0761665 · Cited by 477 · see citing works
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Peters, B., & Trout, B. L. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2234477 · Cited by 417 · see citing works
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Ma, A., & Dinner, A. R. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp045546c · Cited by 400 · see citing works
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Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., et al. (2019) · Structure · doi:10.1016/j.str.2019.01.003 · Cited by 404 · see citing works
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- Authors
- Bolhuis, P. G., Chandler, D., Dellago, C., & Geissler, P. L.
- Affiliations
- Department of Chemical Engineering, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands;
- University of California, Berkeley (US)
- Department of Chemistry, University of Rochester, Rochester, New York 14627;
- Harvard University (US)
- Venue
- Annual Review of Physical Chemistry
- Publisher
- Annual Reviews
- Published
- 2002-10
- Volume
- 53
- Issue
- 1
- Pages
- 291-318
- ISSN
- 0066-426X (ISSN-L)
- 1545-1593
- OpenAlex
- W2099490136
- Cited by
- 1,972
- References
- 72
- Citations by year
- 2026: 65 · 2025: 93 · 2024: 91 · 2023: 73 · 2022: 101 · 2021: 81 · 2020: 107 · 2019: 94 · 2018: 99 · 2017: 99 · 2016: 119 · 2015: 107 · 2014: 93 · 2013: 74 · 2012: 91
- FWCI
- 4.48
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Annual Review of Physical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- UvA-DARE (University of Amsterdam) (publishedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Topics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Physical Sciences › Physics and Astronomy › Condensed Matter Physics › Theoretical and Computational Physics
- Physical Sciences › Mathematics › Statistics and Probability › Markov Chains and Monte Carlo Methods
- Keywords
- transition path sampling, rare events, importance sampling, reaction coordinate, transition state, nonequilibrium dynamics, molecular dynamics simulation
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