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.
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.
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.
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.
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.
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.