Main studies performed with PyRETIS¶
The Source Files link of each study below points to a folder with
ready-to-run inputs: a retis.rst for PyRETIS 3 and the equivalent
retis.toml for PyRETIS 4, together with a README describing the
case, its requirements and how to run it. Some studies are large solvated
or ab initio systems whose full convergence requires HPC resources.
Predicting the mechanism and rate of H-NS binding to AT-rich DNA.
The adsorption of H-NS on DNA is studied at atomistic resolution with GROMACS. Local minima have been located by metadynamics and the transition rates computed by RETIS.
Paper: E. Riccardi, E. C. van Mastbergen, W. W. Navarre and J. Vreede, Predicting the mechanism and rate of H-NS binding to AT-rich DNA, PLoS Comput. Biol. 15, e1006845 (2019).
Autoionization of water.
BO-DFT simulations, via the RETIS approach, were used to study water autoionization. The mechanism(s) have been highlighted and their rate(s) quantified. Machine learning was applied to test the quality of the order parameters.
Paper: M. Moqadam, A. Lervik, E. Riccardi, V. Venkatraman, B. K. Alsberg and T. S. van Erp, Local initiation conditions for water autoionization, Proc. Natl. Acad. Sci. U.S.A. 115, E4569-E4576 (2018).
Conformational study of Cyclophilin - A.
Full atomistic simulations with GROMACS have been performed to sample and quantify the rate of the structural rearrangements of CyP-A and its muted confomer.
Paper in preparation.
Proton transfer in a water trimer.
A study on the proton transfer reaction with a polarizable potential is included. The various features of PyVisA can be tested on the simulation outputs.
Paper: O. Aarøen, H. Kiær and E. Riccardi, PyVisA: Visualization and Analysis of path sampling trajectories, J. Comput. Chem. 42, 435-446 (2021).
Formic acid catalysed formation of sulfuric acid.
A study on the formic acid catalysed conversion of sulfur trioxide and water to sulfuric acid. The mechanism(s) have been highlighted and their rate(s) estimated as a function of the temperature.
Paper: C. D. Daub, E. Riccardi, V. Hänninen and L. Halonen, Path sampling for atmospheric reactions: formic acid catalysed conversion of SO3 + H2O to H2SO4, PeerJ Phys. Chem. 2, e7 (2020).
Enhanced path sampling using subtrajectory Monte Carlo moves.
A study on the effect of using the subtrajectory Wire Fencing move compared to the standard shooting move. Systems studied are the 1D potential double-well, thin film breaking and a ruthenium redox reaction.
Paper: D. T. Zhang, E. Riccardi and T. S. van Erp, Enhanced path sampling using subtrajectory Monte Carlo moves, J. Chem. Phys. 158, 024113 (2023).
Memory reduction using partial path ensembles.
A study on how the path ensemble definitions can be changed when long-lived metastable states are present in the reaction.
Paper: W. Vervust, D. T. Zhang, T. S. van Erp and A. Ghysels, Path sampling with memory reduction and replica exchange to reach long permeation timescales, Biophys. J. 122, 2960-2972 (2023).