Theory Chemistry Seminars - Department of Chemistry
Theoretical Chemistry Seminars
Theoretical Chemistry Seminars
The plan is that Fridays at 15:00 a speaker will give a presentation about his/her research.
We have this time format
20 min + 10 min discussion for internal speakers
30 min + 10 min discussion for external speakers
Place: D3-114 (Onsager)
Schedule
We have to postpone the seminar series due to the current COVID situation. We hope to return soon!
26. November 2021
Speaker: Sander Roet
Title: ∞RETIS: hairy business
19. November 2021
Speaker: Regina Matveeva
Title: Grand Canonical Hartree-Fock
12. November 2021
Speaker: Jocelyne Vreede, University of Amsterdam, Zoom meeting
Title: Sampling rare events in biomolecular systems
5. November 2021
Speaker: Rosario Roberto Riso
Title: Fully consistent MO theory in QED environments
29. October 2021
Speaker: Prof. An Ghysels
IBiTech – BioMMeda research group, Ghent University, Belgium
https://www.ugent.be/ea/ibitech/en/research/biommeda
Title: Permeability of small molecules through membranes from computer simulations
Abstract:
Permeability is a key property of biological membranes. Several strategies have emerged to predict membrane permeability from molecular dynamics (MD) simulations. The counting method uses the number of membrane crossings in a long conventional unbiased molecular dynamics simulation, which might lack sufficient statistics when the membrane forms a large free energy well or barrier. Alternatively, the widespread inhomogeneous solubility-diffusion (ISD) model can be used, which assumes purely diffusive kinetics. A methodology based on the Smoluchowsky equation was derived to extract the dynamics of oxygen permeation from these trajectories using Bayesian analysis (BA). The results of the methodology are the free energy across the membrane, and the diffusion profiles normal and parallel to the membrane surface, from which the permeability and the characteristic entrance, transit, and escape times of permeants as well as characteristic lengths have been derived. The described BA methodology has the advantage that radial diffusion can be analyzed.
However, for a hydrophobic molecule like water, both the counting method and the BA methodology are confronted with convergence issues. Therefore we now present new methodologies for cases with poor statistics on the permeation events, such as a water molecule permeating through an lipid raft. One methodology is based on accelerated MD simulation but is limited to purely diffusive permeation. The other method is based on a divide-and-conquer strategy that can assess the exact kinetics of the permeation event, i.e. without assuming diffusive kinetics in the membrane, by extending the path sampling methodology to permeability calculations.
22. October 2021
Speaker: Alex Paul
Title: Efficient algorithms for coupled cluster with approximate triples for larger molecular systems
15. October 2021
Speaker: Daniel Zhang
Title: Path sampling and redox reactions