6 papers
A Machine-Learned Symbolic Committor for a Chemical Reaction: Retinal Isomerization
Kai Töpfer, Gianmarco Lazzeri, Vittoria Ossanna +4
The thermal cis-trans isomerization around the C=C double bond of retinal is a prototypical high-barrier reaction whose mechanism hinges on subtle out-of-plane bendin…
-Girsanov: A Generalized Method to Construct Markov State Models from Non-Equilibrium and Multiensemble Biased Simulations
Mingyuan Zhang, Yong Wang, Bettina G. Keller +1
We introduce -Girsanov, a new method for constructing Markov state models from biased enhanced-sampling molecular dynamics simulations based on Girsanov reweighting. The key ide…
Internal Trajectories and Observation Effects in Langevin Splitting Schemes
Bettina G. Keller
Langevin integrators based on operator splitting are widely used in molecular dynamics. This work examines Langevin splitting schemes from the perspective of their internal traject…
Estimating Solvation Free Energies with Boltzmann Generators
Maximilian Schebek, Nikolas M. Froböse, Bettina G. Keller +1
Accurate calculations of solvation free energies remain a central challenge in molecular simulations, often requiring extensive sampling and numerous alchemical intermediates to en…
Thermal Isomerization Rates in Retinal Analogues using Ab-Initio Molecular Dynamics
Simon Ghysbrecht, Bettina G. Keller
For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theo…
Accuracy of reaction coordinate based rate theories for modelling chemical reactions: insights from the thermal isomerization in retinal
Simon Ghysbrecht, Luca Donati, Bettina G. Keller
Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transit…