| Promoting transparency and reproducibility in enhanced molecular simulations M Bonomi, G Bussi, C Camilloni, GA Tribello, P Banáš, A Barducci, ... Nature methods 16 (8), 670-673, 2019 | 634 | 2019 |
| OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics DWH Swenson, JH Prinz, F Noe, JD Chodera, PG Bolhuis Journal of chemical theory and computation 15 (2), 813-836, 2018 | 57 | 2018 |
| Application of a semiclassical model for the second-quantized many-electron Hamiltonian to nonequilibrium quantum transport: The resonant level model DWH Swenson, T Levy, G Cohen, E Rabani, WH Miller The Journal of chemical physics 134 (16), 2011 | 45 | 2011 |
| Transition path sampling as Markov chain Monte Carlo of trajectories: Recent algorithms, software, applications, and future outlook PG Bolhuis, DWH Swenson Advanced Theory and Simulations 4 (4), 2000237, 2021 | 43 | 2021 |
| OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes DWH Swenson, JH Prinz, F Noe, JD Chodera, PG Bolhuis Journal of chemical theory and computation 15 (2), 837-856, 2018 | 42 | 2018 |
| A replica exchange transition interface sampling method with multiple interface sets for investigating networks of rare events DWH Swenson, PG Bolhuis The Journal of chemical physics 141 (4), 2014 | 34 | 2014 |
| A Cartesian quasi-classical model to nonequilibrium quantum transport: The Anderson impurity model B Li, TJ Levy, DWH Swenson, E Rabani, WH Miller The Journal of Chemical Physics 138 (10), 2013 | 17 | 2013 |
| A semiclassical model for the non-equilibrium quantum transport of a many-electron Hamiltonian coupled to phonons DWH Swenson, G Cohen, E Rabani Molecular Physics 110 (9-10), 743-750, 2012 | 14 | 2012 |
| Atomistic insight into the kinetic pathways for Watson–Crick to Hoogsteen transitions in DNA J Vreede, A Pérez de Alba Ortíz, PG Bolhuis, DWH Swenson Nucleic acids research 47 (21), 11069-11076, 2019 | 13 | 2019 |
| The opposing effects of isotropic and anisotropic attraction on association kinetics of proteins and colloids AC Newton, R Kools, DWH Swenson, PG Bolhuis The Journal of Chemical Physics 147 (15), 2017 | 11 | 2017 |
| Remarkable features in the interactions of quadrupolar molecules HM Jaeger, DWH Swenson, CE Dykstra The Journal of Physical Chemistry A 110 (20), 6399-6407, 2006 | 9 | 2006 |
| choderalab/openmmtools: 0.14. 0: exact treatment of alchemical PME electrostatics, water cluster test system, optimizations. http s J Chodera, A Rizzi, L Naden, K Beauchamp, P Grinaway, J Fass, ... doi. org/10.5281/zenod o 11611, 49, 2018 | 7 | 2018 |
| Clustering of molecular hydrogen around benzene DWH Swenson, HM Jaeger, CE Dykstra Chemical physics 326 (2-3), 329-334, 2006 | 4 | 2006 |
| Quantum effects from classical trajectories: New methodologies and applications for semiclassical dynamics DWH Swenson University of California, Berkeley, 2011 | 2 | 2011 |
| Path sampling simulations reveal how the Q61L mutation restricts the dynamics of KRas S Roet, F Hooft, PG Bolhuis, DWH Swenson, J Vreede bioRxiv, 2020.02. 28.969451, 2020 | 1 | 2020 |
| Path sampling simulations of the mechanisms and rates of transitions between Watson-Crick and Hoogsteen base pairing in DNA J Vreede, PG Bolhuis, DWH Swenson Biophysical Journal 112 (3), 214a, 2017 | 1 | 2017 |
| Predicting the mechanism and kinetics of the Watson-Crick to Hoogsteen base pairing transition J Vreede, PG Bolhuis, DWH Swenson Biophysical Journal 110 (3), 563a-564a, 2016 | 1 | 2016 |
| Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations B Ries, I Alibay, DWH Swenson, HM Baumann, MM Henry, JRB Eastwood, ... Journal of Chemical Theory and Computation, 2024 | | 2024 |
| Kartograf: An Accurate Geometry-Based Atom Mapper for Hybrid Topology Relative Free Energy Calculations B Ries, I Alibay, DWH Swenson, HM Baumann, MM Henry, JRB Eastwood, ... | | 2023 |
| Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas S Roet, F Hooft, PG Bolhuis, DWH Swenson, J Vreede The Journal of Physical Chemistry B 126 (48), 10034-10044, 2022 | | 2022 |
