PhD position
Efficient numerical methods for the simulation of protein-ligand unbinding
ERC MSMath
The simulation of the kinetics of protein-ligand unbinding is a crucial
ingredient for in silico analysis of drug efficacy. In particular, the
efficient calculation of the unbinding rate remains a challenge. In
collaboration with researchers from the pharmaceutical company
SANOFI and with researchers from the Theoretical and Computational
Biophysics Group of the Beckman Institute, we would like to investigate
the interest of new numerical methods on practical test cases. We will
investigate in particular the use of multilevel splitting techniques,
as well as accelerated dynamics algorithms. The PhD will consist in (i)
understanding the algorithms and their mathematical foundations, (ii)
developing expertise on the biological systems of interest and (iii)
programming and testing the algorithms in the framework of the well
distributed NAMD software. New methodological developments will be
necessary in view of the intended applications (biological models,
constraints related to the hardware and software).
The basic requirement for applying is a relevant and sufficient
scientific background in Monte Carlo methods and stochastic algorithms
(implementation and understanding of the mathematical foundations). Good programming skills in C++ and Tcl are required. The
project is very interdisciplinary in nature, and candidates with a
master in applied mathematics, theoretical biology or theoretical
chemistry will be considered. The PhD will be supervised by T. Lelièvre
with the help of other members of the MSMath ERC project (in particular
M. Rousset and G. Stoltz). The PhD is funded by the MSMath ERC project.
Back to homepage.