Ph.D. position in molecular dynamics and Markov modeling of protein-ligand binding processes.
Jointly between:
- Thomas Weikl at the Max Planck Institute of Colloids and Interfaces, Potsdam (Germany)
- Frank Noe at the Freie Universitaet, Berlin (Germany)
The function of proteins often involves changes between different three-dimensional conformations. A central question is how these changes are coupled to the binding processes or catalytic processes of the proteins during which they occur. In this project, we will investigate the conformational changes of proteins during binding to ligand molecules with molecular dynamics (MD) simulations and Markov state modeling. A challenge for MD simulations of protein binding is that the typical timescales of the conformational transitions and binding events are in the microsecond and millisecond range, while the timesteps of these simulations are in the femtosecond range. This challenge is addressed by a combination of enhanced sampling and Markov state modeling techniques that allows the key molecular processes occurring on slow timescales to be characterized.
Requirements:
- MSc in Physics, Bioinformatics, Mathematics, or Theoretical Chemistry
- good knowledge of statistical mechanics or physical chemistry
- excellent computing skills (Linux, Latex, scripting).
- programming skills in python and ideally a higher programming language (C, C++, Java).
- experience with biomolecules, in particular protein structures.
Contact:
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