Publications

The WESTPA Papers:

  1. MC Zwier, JL Adelman, JW Kaus, AJ Pratt, KF Wong, NB Rego, E Suárez, S Lettieri, DW Wang, M Grabe, DM Zuckerman, and LT Chong. “WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis”. J. Chem. Theory Comput., 11: 800-809 (2015).
  2. JD Russo*, S Zhang*, JMG Leung*, AT Bogetti*, JP Thompson, AJ DeGrave, PA Torrillo, AJ Pratt, KF Wong, J Xia, J Copperman, JL Adelman, MC Zwier, DN LeBard, DM Zuckerman, and LT Chong. "WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications". J. Chem. Theory Comput, 18 (2), 638–649 (2022) *equal authorship.

A Review of the WE Strategy:

  1. DM Zuckerman and LT Chong. “Weighted ensemble simulation: Review of methodology, applications, and software”. Annu. Rev. Biophys. 2017, 46: 43–57 (2017).

WESTPA Tutorials:

  1. AT Bogetti*, B Mostofian*, A Dickson*, AJ Pratt*, AS Saglam*, PO Harrison*, JL Adelman, M Dudek, PA Torrillo, AJ DeGrave, U Adhikari, MC Zwier, DM Zuckerman, and LT Chong. "A suite of tutorials for the WESTPA rare-events sampling software." Living Journal of Computational Molecular Science, 1: 10607 (2019) *equal authorship.

Made with WESTPA:

  1. MC Zwier, JW Kaus, and LT Chong. “Efficient explicit-solvent molecular dynamics simulations of molecular associations: Methane/methane, Na+/Cl-, methane/benzene, and K+/18-crown-6 ether.” J. Chem. Theory Comput., 7: 1189-1197 (2011).
  2. JL Adelman, A Scarbrough, MC Zwier, D Bhatt, LT Chong, DM Zuckerman, and M Grabe. “Simulations of the alternating access mechanism of the sodium symporter Mhp1.” Biophys. J., 101: 2399-2407 (2011).
  3. JL Adelman and M Grabe. “Simulating rare events using a weighted ensemble-based string method.” J. Chem. Phys., 138: 044105 (2013).
  4. RM Donovan, AJ Sedgewick, JR Faeder and DM Zuckerman. “Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories.” J. Chem. Phys., 139: 115105 (2013).
  5. E Suarez, S Lettieri, MC Zwier, CA Stringer, SR Subramanian, LT Chong and DM Zuckerman. “Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories.” J. Chem. Theory Comput. 10: 2658-2667 (2014).
  6. JL Adelman and M Grabe. “Simulating current–voltage relationships for a narrow ion channel using the weighted ensemble method” J. Chem. Theory Comput., 11: 1907-1918 (2015).
  7. AS Saglam and LT Chong. “Highly efficient computation of the basal kon using direct simulation of protein-protein association with flexible molecular models” J. Phys. Chem. B (2015).
  8. J Spiriti and DM Zuckerman. “Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits” J. Chem. Phys., 143: 243159 (2015).
  9. E Suarez, AJ Pratt, and LT Chong. “Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses” Prot. Sci., 1: 67-78 (2016).
  10. RM Donovan, JJ Tapia, DP Sullivan, JR Faeder, RF Murphy, M Dittrich, and DM Zuckerman. “Unbiased rare event sampling in spatial stochastic systems biology models using a weighted ensemble of trajectories” PLoS Comput. Biol., 12: e1004611 (2016).
  11. MC Zwier, AJ Pratt, JL Adelman, JW Kaus, DM Zuckerman and LT Chong. “Efficient atomistic simulation of pathways and calculation of rate constants for protein-peptide binding process: Application to the MDM2 protein and an intrinsically disordered p53 peptide” J. Chem. Phys. Lett., 17: 3440-3445 (2016).
  12. AS Saglam, DW Wang, MC Zwier, and LT Chong. “Flexibility vs preorganization: Direct comparison of binding kinetics for a disordered peptide and its exact preorganized analogues” J. Phys. Chem. B, 121: 10046-10054 (2017).
  13. AJ DeGrave, JH Ha, SN Loh, and LT Chong. “Large enhancements of response times of a protein conformational switch by computational design” Nat. Commun., 9: 1013 (2018).
  14. A Nunes-Alves, DM Zuckerman, and GM Arantes. “Escape of a small molecule from inside T4 lysozyme by multiple pathways” Biophys. J., 114: 1058-1066 (2018).
  15. AS Saglam and LT Chong. "Protein-protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations." Chem. Sci., (2019).
  16. U Adhikari, B Mostofian, J Copperman, SR Subramanian, AA Petersen, and DM Zuckerman. "Computational estimation of microsecond to second atomistic folding times." J. Am. Chem. Soc., 141: 6519-6526 (2019).
  17. B Mostofian and DM Zuckerman. "Statistical uncertainty analysis for small-sample, high log-variance data: cautions for bootstrapping and Bayesian bootstrapping." J. Chem. Theory. Comput., 15: 3499-3509 (2019).
  18. D Aristoff and DM Zuckerman. "Optimizing weighted ensemble sampling of steady states." Multiscale Model. Sim. (2020).
  19. J Copperman and DM Zuckerman. "Accelerated estimation of long-timescale kinetics from weighted ensemble simulation via non-Markovian “microbin” analysis." J. Chem. Theory Comput., 16: 6763–6775 (2020).
  20. DM Zuckerman and JD Russo. "A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications." arXiv (2020).
  21. T Sztain, S Ahn, AT Bogetti, L Casalino, JA Goldsmith, E Seitz, RS McCool, FL Kearns, F Acosta-Reyes, S Maji, G Mashayekhi, JA McCammon, A Ourmazd, J Frankm, JS McLellan, LT Chong, and RE Amaro. "A glycan gate controls opening of the SARS-CoV-2 spike protein." Nat. Chem. (2021).
  22. S Choe. "Free Energy Analyses of Cell-Penetrating Peptides Using the Weighted Ensemble Method." Membranes (2021).
  23. M Beasley, N Frazee, S Groover, SJ Valentine, B Mertz, and J Legleiter "Physicochemical Properties Altered by the Tail Group of Lipid Membranes Influence Huntingtin Aggregation and Lipid Binding." J. Phys. Chem. B (2022).
  24. S Sur and A Grossfield "Effects of cholesterol on the mechanism of fengycin, a biofungicide." Biophys. J. (2022).

Related Weighted Ensemble Publications:

  1. GA Huber and S Kim. "Weighted-ensemble Brownian dynamics simulations for protein association reactions." Biophys. J., 70: 97–110 (1996).
  2. A Rojnuckarin, S Kim, and S Subramaniam. "Brownian dynamics simulations of protein folding: Access to milliseconds time scale and beyond." Proc. Nat. Acad. Sci. USA, 95: 4288–4292 (1998).
  3. A Rojnuckarin, DR Livesay, and S Subramaniam. "Bimolecular reaction simulation using weighted ensemble Brownian dynamics and the University of Houston Brownian dynamics program." Biophys. J., 79: 686-693 (2000).
  4. BW Zhang, D Jasnow, and DM Zuckerman. "Efficient and verified simulation of a path-ensemble for conformational change in a united-residue model of calmodulin." Proc. Nat. Acad. Sci. USA, 104: 18043-18048 (2007).
  5. BW Zhang, D Jasnow, and DM Zuckerman. "The ”weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures." J. Chem. Phys., 132: 054107 (2010).
  6. D Bhatt, BW Zhang, and DM Zuckerman. "Steady state via weighted ensemble path sampling" J. Chem. Phys., 133: 014110 (2010).
  7. D Bhatt and DM Zuckerman. "Heterogeneous path ensembles for conformational transitions in semiatomistic models of adenylate kinase." J. Chem. Theory Comput., 6: 3527–3539 (2010).
  8. MC Zwier and LT Chong. “Reaching biological timescales with all-atom molecular dynamics simulations.” Curr. Opin. Pharmacol., 10: 745-752 (2010).
  9. D Bhatt and DM Zuckerman. "Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible?" J. Chem. Theory Comput., 7: 2520-2527 (2011).
  10. D Bhatt and I Bahar. "An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates." J. Chem. Phys., 137: 104101 (2012). 
  11. E Darve and E Ryu. "Computing reaction rates in bio-molecular systems using discrete macro-states." Innovations in Biomolecular Modeling and Simulations. Royal Society of Chemistry, 1: 138-206 (2012).
  12. BW Zhang, D Jasnow, and DM Zuckerman. "Weighted ensemble path sampling for multiple reaction channels." arXiv:0902.2772
  13. A Dickson and CL Brooks, III. "WExplore: Hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm." J. Phys. Chem. B, 138: 3532-3542 (2014). 
  14. B Abdul-Wahid, H Feng, D Rajan, R Costaouec, E Darve, D Thain, and JA Izaguirre. "AWE-WQ: Fast-forwarding molecular dynamics using the accelerated weighted ensemble." J. Chem. Inf. Model., 54: 3033-3043 (2014). 
  15. H Feng, R Costaouec, E Darve and JA Izaguirre. "A comparison of weighted ensemble and Markov state model methodologies." J. Chem. Phys., 142: 214113 (2015). 
  16. A Dickson, AM Mustoe, L Salmon and CL Brooks, III. "Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore." Nucl. Acids Res., 42: 12126-12137 (2014).
  17. MJ Tse, BK Chu, M Roy and EL Read. "DNA-binding kinetics determines the mechanism of noise-induced switching in gene networks." Biophy. J., 109: 1746-1757 (2015).
  18. E Suarez, JL Adelman and DM Zuckerman. "Accurate estimation of protein folding and unfolding times: Beyond Markov state models." J. Chem. Theory Comput., 12: 3473-3481 (2016).
  19. LT Chong, AS Saglam and DM Zuckerman. "Path-sampling strategies for simulating rare events in biomolecular systems.." Curr. Opin. Struc. Biol., 43: 88-94 (2017).
  20. A Dickson and SD Lotz. "Multiple ligand unbinding pathways and ligand-induced destabilization revealed by WExplore.." Biophys. J., 112: 620-629 (2017).
  21. A Dickson and SD Lotz. "Ligand release pathways obtained with WExplore: Residence times and mechanisms.." J. Phys. Chem. B, 120: 5377-5385 (2017).
  22. SD Lotz and A Dickson. "Unbiased molecular dynamics of 11 min timescale drug unbinding reveals transition state stabilizing interactions.." J. Am. Chem. Soc., 140: 618-628 (2018).
  23. D Aristoff. "Analysis and optimization of weighted ensemble sampling." ESAIM:M2AN., 52: 1219-1238 (2018).
  24. N Donyapour, NM Rousey and A Dickson. "REVO: Resampling of ensembles byvariation optimization." J. Chem. Phys., 150: 244112 (2019).
  25. K Liu, B Chu, J Newby, EL Read, J Lowengrub and J Allard. "Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length." PLOS Comput. Biol., 15: e1006352 (2019).
  26. D Ray and I Andricioaei. "Weighted ensemble milestoning (WEM): A combined approach for rare event simulations." J. Chem. Phys., 152, 234114 (2020).
  27. S Lotz and A Dickson. "Wepy: A flexible software framework for simulating rare events with weighted ensemble resampling." ChemRXiv (2020).
  28. NM Roussey and A Dickson. "Enhanced Jarzynski free energy calculations using weighted ensemble." J. Chem. Phys. 153, 134116 (2020).
  29. K Moritsugu, N Yamamoto, Y Yonezawa, S Tate, and H Fujisaki. "Path ensembles for pin1-catalyzed cis–trans isomerization of a substrate calculated by weighted ensemble simulations." J. Chem. Theory Comput. 17, 2522-2529 (2021).
  30. R Taylor, J Allard, and EL Read. "Simulation of receptor triggering by kinetic segregation shows role of oligomers and close contacts." Biophys. J. 121, 1660-1675 (2022).