Analysis and optimization of weighted ensemble sampling
ESAIM: Mathematical Modelling and Numerical Analysis , Tome 52 (2018) no. 4, pp. 1219-1238.

We give a mathematical framework for weighted ensemble (WE) sampling, a binning and resampling technique for efficiently computing probabilities in molecular dynamics. We prove that WE sampling is unbiased in a very general setting that includes adaptive binning. We show that when WE is used for stationary calculations in tandem with a coarse model, the coarse model can be used to optimize the allocation of replicas in the bins.

Reçu le :
Accepté le :
DOI : 10.1051/m2an/2017046
Classification : 65C05, 65C20, 65C40, 65Y05, 82C80
Mots-clés : Molecular dynamics, Markov chains, stationary distributions, long time dynamics, coarse graining, resampling, weighted ensemble
Aristoff, David 1

1 Colorado State University, Colorado 80523, USA
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Aristoff, David. Analysis and optimization of weighted ensemble sampling. ESAIM: Mathematical Modelling and Numerical Analysis , Tome 52 (2018) no. 4, pp. 1219-1238. doi : 10.1051/m2an/2017046. http://archive.numdam.org/articles/10.1051/m2an/2017046/

[1] R.J. Allen, D. Frenkel and P.R. Ten Wolde, Forward flux sampling-type schemes for simulating rare events: Efficiency analysis. J. Chem. Phys. 124 (2006) 463102. | DOI

[2] D. Aristoff, J.M. Bello-Rivas and R. Elber, A mathematical framework for exact milestoning. Multiscale Model. Simul. 14 (2016) 301–322. | DOI | MR | Zbl

[3] D. Bhatt and D. Zuckerman, Beyond Microscopic Reversibility: Are Observable Nonequilibrium Processes Precisely Reversible? J. Chem. Theory Comput. 7 (2011) 2520–2527. | DOI

[4] J.M. Bello-Rivas and R. Elber, Exact milestoning. J. Chem. Phys. 142 (2015) 094102.

[5] D. Bhatt and B.W. Zhang, and D.M. Zuckerman, Steady-state simulations using weighted ensemble path sampling. J. Chem. Phys. 133 (2010) 014110. | DOI

[6] F. Cérou and A. Guyader, Adaptive Multilevel Splitting for Rare Event Analysis. Stoch. Anal. Appl. 25 (2007) 417–443. | DOI | MR | Zbl

[7] F. Cérou, A. Guyader, T. Lelièvre and D. Pommier, A multiple replica approach to simulate reactive trajectories. J. Chem. Phys. 134 (2011) 054108. | DOI

[8] R. Costaouec, H. Feng, J. Izaguirre and E. Darve. Analysis of the accelerated weighted ensemble methodology, Supplement, Discrete and Continuous Dynamical Systems (2013). | MR

[9] E. Darve and E. Ryu, Computing reaction rates in bio-molecular systems using discrete macro-states, Innovations in Biomolecular Modeling and Simulations, RSC publishing (2012).

[10] P. Del Moral, Feynman-Kac Formulae: Genealogical and Interacting Particle Systems with Applications. Probability and Its Applications. Springer (2004). | MR | Zbl

[11] P. Del Moral and A. Doucet, Particle methods: an introduction with applications. ESAIM: Proc. 44 (2014) 1–46. | DOI | MR | Zbl

[12] P. Del Moral and J. Garnier, Genealogical particle analysis of rare events. Ann. Appl. Probab. 15 (2005) 2496–2534. | DOI | MR | Zbl

[13] A. Doucet, N.D. Freitas and N. Gordon, Sequential Monte Carlo Methods in Practice, Statistics for Engineering and Information Science, Springer (2001). | DOI | MR | Zbl

[14] R. Durrett, Probabiltiy: Theory and Examples. Duxbury Press, 3rd edn (2005). | Zbl

[15] A.K. Faradjian and R. Elber, Computing time scales from reaction coordinates by Milestoning. J. Chem. Phys. 120 (2004) 10880–10889. | DOI

[16] D.R. Glowacki, E. Paci and D.V. Shalashilin, Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation. J. Chem. Theory Comput. 7 (2011) 1244–1252. | DOI

[17] T.L. Hill, Free Energy Transduction and Biochemical Cycle Kinetics. Dover, New York (1989). | DOI

[18] G.A. Huber and S. Kim, Weighted-ensemble Brownian dynamics simulations for protein association reactions. Biophys. J. 70 (1996) 97–110. | DOI

[19] P. Metzner, C. Schütte and E. Vanden-Eijnden, Transition Path Theory for Markov jump processes. Multiscale Model. Simul. 7 (2009) 1192–1219. | DOI | MR | Zbl

[20] M. Sarich, F. Noé and C. Schütte, On the approximation quality of Markov State Models (2010). | MR | Zbl

[21] C. Schuütte and M. Sarich, Metastability and Markov State Models in Molecular Dynamics. Courant Lecture Notes. AMS (2013). | DOI | MR | Zbl

[22] T. Schlick, Molecular modeling and simulation: an interdisciplinary guide (2010). | DOI | MR | Zbl

[23] E. Suárez, S. Lettieri, M.C.Zwier, C.A. Stringer and S.R. Subramanian, L.T. Chong and D.M. Zuckerman, Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories. J. Chem. Theory Comput. 10 (2014) 2658–266. | DOI

[24] E. Suárez, A.J. Pratt, L.T. Chong and D.M. Zuckerman, Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses. Protein Sci. 25 (2016) 67–78. | DOI

[25] J.O.B. Tempkin, B. Van Koten, J.C. Mattingly, A.R Dinner and J. Weare, Trajectory Stratification of Stochastic Dynamics. Preprint, (2017). | arXiv | MR

[26] E. Vanden-Eijnden and M. Venturoli, Exact rate calculations by trajectory parallelization and tilting. J. Chem. Phys. 131 (2009) 1–7, 0904.3763 | DOI

[27] T.S. Van Erp, D. Moroni and P.G. Bolhuis, A novel path sampling method for the calculation of rate constants. J. Chemical Phys. 118 (2003) 7762–7774. | DOI

[28] A. Warmflash, P. Bhimalapuram and A.R. Dinner, Umbrella sampling for nonequilibrium processes. J. Chem. Phys. 127 (2007) 154112. | DOI

[29] B.W. Zhang, D. Jasnow and D.M. Zuckerman, The “weighted ensemble” path sampling method is exact for a broad class of stochastic processes and binning procedures. J. Chem. Phys. 132 (2010) 05417. | DOI

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