Ph.D. position in molecular dynamics and Markov modeling of protein-protein binding processes
The binding of proteins often involves changes between different three-dimensional conformations. A central question is how these conformational changes are coupled to the binding events during which they occur. Because experiments cannot resolve the conformational dynamics of proteins in both space and time, molecular dynamics (MD) simulations with atomistic models play an important role in understanding protein binding and function. A current challenge for MD simulations of protein binding is that the typical timescales of the conformational transitions and binding events are in the millisecond and second range, while individual simulation trajectories are limited to typical timescales of microseconds.
In this project, you will address this challenge with state-of-the-art methods in Markov modelling to obtain a detailed atomistic perspective of protein-protein binding from hundreds of MD simulation trajectories. You will simulate protein-protein binding on a large computational cluster of graphics processing units (GPUs), and will systematically analyze the trajectories obtained from these MD simulations with Markov modelling. You will be jointly supervised by Dr. Thomas Weikl at the Max Planck Institute of Colloids and Interfaces in Potsdam and Prof. Frank Noe at the Free University Berlin.
The Ph.D. position is part of Collaborative Research Centre 1114 “Scaling Cascades in Complex Systems” of the German Research Foundation.
Diploma/MSc in Physics, 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