Lezing 'Meet the PhD Jury: Enhanced sampling strategies for molecular simulation of DNA'
- Voor wie
- Medewerkers , Privépersonen , Studenten
- Wanneer
- 25-09-2024 van 11:00 tot 12:00
- Waar
- UZ campus, building B3, room 3.1 (3rd floor), entrance 46 C, Corneel Heymanslaan 10, 9000 Gent
- Voertaal
- Engels
- Door wie
- BioMMedA Research Group - Faculty of Engineering and Architecture
- Contact
- an.ghysels@ugent.be
Prof Vreede (University of Amsterdam) will explain how molecular dynamics (MD) simulations can provide detailed insights into complex molecular systems, such as DNA, at high resolution in space and time.
Using current computer architectures, time scales of tens of microseconds are feasible, but are insufficient to accurately characharacterize large conformational transitions in DNA and compare calculations to experimental data.
The lecture will discuss various strategies to model molecular systems containing DNA, and how to link them to experiments. Starting from procedures to generate starting structures, two enhanced sampling approaches will be discussed. One approach adds biasing potentials to the system to drive transitions and the other strategy focuses MD simulations on the transitions. Applications are the Watson–Crick–Franklin to Hoogsteen transition in adenine–thymine base pairs and the formation of protein-DNA complexes.
Talk 45' Q&A 15' (optional) in-person discussions 60'