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Ph.D. position (f/m) in molecular dynamics and Markov modeling of protein-protein binding processes
Published(356 days ago)
Max Planck Institute of Colloids and InterfacesBerlin, Potsdam
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. In this project, 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.
Diploma/MSc in Physics, Mathematics, or Theoretical Chemistry
good knowledge of statistical mechanics or physical chemistry