PhD and post-doc positions available
- Created: Thursday, 09 July 2020 17:02
- Last Updated: Wednesday, 19 August 2020 15:53
We currently have two positions open in our group:
(1) A PhD position (4yr) on resolving the molecular driving forces behind the switching behavior of light harvesting complexes. Together with experimental colleagues, we would like to unravel the role of PsbS, an important protein that is involved in the switching (which occurs under high light conditions). If you are not afraid of teaming up with experimentalists (these are nice ones, I promise) and running large scale simulations, this is your chance. We might even end up modeling a whole chloroplast !
(2) A post-doc position (2yr) on development of titratable Martini, aimed at improving the model and extending the application range. Our recently introduced method to enable constant pH Martini simulations opens the way to extend Martini into unknown territories, including reactive-Martini. If you would like to be the main explorer, then consider applying.
More background on the positions from the funded proposals:
PhD position. (responsible for the computational aspects). Photosynthetic efficiency is tightly coupled to the fitness of plants in fluctuating environmental conditions. In excess light, the balance between light excitation and substrate availability is disturbed, causing the formation of lethal reactive species. As a photo-protective response, the photosynthetic antenna switches into a ‘safety mode’ where excitations are non-photochemically quenched. The switches are triggered by particular proteins that can detect the overflow of the electron transport chain by sensing the pH of the lumenal side of the thylakoid membrane and/or altered local electric fields. This switching occurs on various time scales, ranging from seconds to minutes. When light intensity decreases again, photoprotection switches off, again on various time scales, which can take many minutes, meanwhile causing unwanted losses of excitation energy. Despite the central role of the photoprotective mechanisms in regulating energy conversion in photosynthetic cells and leaves, the underlying molecular mechanisms remain a mystery. We aim to reveal the nanoscale mechanisms of light-stress regulation and understand how the pH sensing protein PsbS operates from atom to organism level. To undertake this challenge, we have assembled a team of experts in the fields of molecular biology and biochemistry, advanced solid-state NMR, time- resolved infrared, 2-dimensional infrared (2D-IR) spectroscopy and ultrafast fluorescence (micro)spectroscopy, complemented by 2D-IR quantum chemical spectral simulation, as well as all-atom and coarse-grain (CG) molecular dynamics. We will integrate our state-of-the-art experimental, computational and theoretical approaches from the field of physics, chemistry and biology and push the limit for analyzing molecular structure and dynamics and nanoscale processes in truly native biological environments. The results will open smart ways for targeted engineering of plants and re-wiring the excitation pathways to combine optimal photosynthetic yields with high stress tolerance as adaptation to changing environmental conditions.
Post-doc position. The MARTINI force field, developed by the PI, is widely used to simulate large scale (bio)molecular processes. However, like most force fields, it is not capable of modeling pH dependent effects in an efficient and realistic way. Here we propose a pragmatic approach to allow MARTINI based simulations to be run at constant pH, with tititratable groups that can become (de)protonated on the fly. Our method enables coarse-grained molecular dynamics simulations of complex systems with pH as external variable, and can be used to study pH-dependent processes as varied as the permeation of charged drugs across lipid membranes or the swelling of charged polymers. In addition, the proposed constant pH approach opens the way to include generic chemical reactions into the MARTINI model.