Review articles

• B.G. Keller, P.G. Bolhuis "Dynamical reweighting for biased rare event simulations" Annu. Rev. Phys. Chem. (2024), 75, 137-162, https://doi.org/10.1146/annurev-physchem-083122-124538

• L. Donati, M. Weber, B. G. Keller "A review of Girsanov Reweighting and of Square Root Approximation for building molecular Markov State Models" J. Math. Phys. (2022) 63, 123306. https://doi.org/10.1063/5.0127227

• S. Kieninger, L. Donati, B. G. Keller, “Dynamical reweighting methods for Markov models,” Curr. Opin. Struct. Biol., 61, 124–131 (2020), https://doi.org/10.1016/j.sbi.2019.12.018

Girsanov reweighting

• J.-L. Schäfer, B. G. Keller "Implementation of Girsanov reweighting in OpenMM and Deeptime" J. Phys. Chem. B (2024), 128, 6014-6027, https://doi.org/10.1021/acs.jpcb.4c01702

• P.G. Bolhuis, Z.F. Brotzakis, B.G. Keller "Optimizing molecular potential models by imposing kinetic constraints with path reweighting" J. Chem. Phys. (2023), 159, 074102 (Special issue: Machine Learning Hits Molecular Simulations), https://doi.org/10.1063/5.0151166

• S. Kieninger, S. Ghysbrecht, B. G. Keller "Girsanov reweighting for simulations of underdamped Langevin dynamics. Theory" arXiv (2023) https://arxiv.org/abs/2303.14696

• S. Kieninger, B.G. Keller "GROMACS Stochastic Dynamics and BAOAB are equivalent configurational sampling algorithms" J. Chem. Theory Comput. 18 (2022), p. 5792-5798. https://doi.org/10.1021/acs.jctc.2c00585

• S. Kieninger, B.G. Keller “Path probability ratios for Langevin dynamics - exact and approximate” J. Chem. Phys. 154 (2021), p. 094102. https://doi.org/10.1063/5.0038408

• L. Donati  B. G. Keller, “Girsanov reweighting for metadynamics simulations,” J. Chem. Phys.,  149, 072335 (2018) https://doi.org/10.1063/1.5027728
• J. Quer, L. Donati, B. G. Keller,  M. Weber, “An Automatic Adaptive Importance Sampling Algorithm for Molecular Dynamics in Reaction Coordinates,” SIAM Journal on Scientific Computing,  40, A653–A670, (2018) https://doi.org/10.1137/17M1124772
• L. Donati, C. Hartmann,  B. G. Keller, “Girsanov reweighting for path ensembles and Markov state models,” J. Chem.  Phys.,  146, 244112 (2017) https://doi.org/10.1063/1.4989474

Square-root approximation for the Fokker-Planck equation

• H. Zupan, F. Heinz, B. G. Keller "Grid-based state space exploration for molecular binding" arXiv DOI: 10.48550/arXiv.2211.00566, Can. J. Chem. (2023) 101, 710-724. https://doi.org/10.1139/cjc-2022-0282
• L. Donati, M. Weber, B.G. Keller “Markov models from the Square Root Approximation of the Fokker- Planck equation: calculating the grid-dependent flux” J. Phys.: Condens. Matter 33 (2021), p. 115902 https://doi.org/10.1088/1361-648X/abd5f7
• L. Donati, M. Heida, B. G. Keller,  M. Weber, “Estimation of the infinitesimal generator by square-root approximation,” J. Phys.: Condens. Matter,  30, 425201 (2018). https://doi.org/10.1088/1361-648X/aadfc8