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

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