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Transition path sampling (TPS), which involves finding probable paths connecting two points on an energy landscape, remains a challenge due to the complexity of real-world atomistic systems.
Fluctuations and irreversible process. ii. systems with kinetic energy
Machlup, S. and Onsager, L · 1953
Earlier work this paper cites.
Fluctuations and irreversible processes
Onsager, L. and Machlup, S · 1953
Earlier work this paper cites.
Integration in functional spaces and its applications in quantum physics
Gel’fand, I. M. and Yaglom, A. M · 1960
Earlier work this paper cites.
Protein data bank
Bank, P. D · 1971
Earlier work this paper cites.
Nonphysical sampling distributions in monte carlo free-energy estimation: Umbrella sampling
Torrie, G. M. and Valleau, J. P · 1977
Earlier work this paper cites.
Location of saddle points and minimum energy paths by a constrained simplex optimization procedure
Müller, K. and Brown, L. D · 1979
Earlier work this paper cites.
Replica monte carlo simulation of spin-glasses
Swendsen, R. H. and Wang, J.-S · 1986
Earlier work this paper cites.
A stochastic estimator of the trace of the influence matrix for laplacian smoothing splines
Hutchinson, M. F · 1989
Earlier work this paper cites.
The weighted histogram analysis method for free-energy calculations on biomolecules. i. the method
Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H., and Kollman, P. A · 1992
Earlier work this paper cites.
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Kabsch, W · 1993
Earlier work this paper cites.
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Dellago, C., Bolhuis, P. G., Csajka, F. S., and Chandler, D · 1998
Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
Onsager–Machlup action-based path sampling and its combination with replica exchange for diffusive and multiple pathways
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Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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a Beccara, S., Škrbić, T., Covino, R., and Faccioli, P · 2012
Earlier work this paper cites.
Non-Equilibrium Thermodynamics in Multiphase Flows
Mauri, R · 2012
Earlier work this paper cites.
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Kingma, D. P. and Welling, M · 2013
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Earlier work this paper cites.
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Earlier work this paper cites.
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Goodfellow, I., Pouget-Abadie, J., Mirza, M., Xu, B., Warde-Farley, D., Ozair, S., Courville, A., and Bengio, Y · 2014
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Easy transition path sampling methods: Flexible-length aimless shooting and permutation shooting
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Frenkel, D. and Smit, B · 2023
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Doob’s lagrangian: A sample-efficient variational approach to transition path sampling
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