Multiscale modelling of actin filaments

We are currently seeking a highly motivated postdoctoral fellow who will be mentored by Dr. Matthieu Chavent (IPBS, Toulouse, http://matthieuchavent.com ) and Prof Jean-Philip Piquemal (Sorbonne University, Paris, https://piquemalresearch.com ). The researcher will be hosted in Dr Chavent’s lab in Toulouse and will regularly visit Prof Piquemal in Paris. The postdoc is funded for 2 years with a possibility of extension. It will start beginning of 2021. The deadline to send an application is the 1st of December 2020.

Project:

The goal of this project is to investigate, at the atomistic level, the mechanics of actin filaments and understand how external forces can modulate them. To do that, the candidate will perform high performance computing of polarizable forcefield using Tinker-HP [1], atomistic simulations, and up to coarse-grain models [2]. The results will then be combined to numerical and analytical models developed by our collaborator Dr Dmitrieff to design new mesoscale models [3]. The models will be validated at different scales by our collaborator experimentalists (see bellow).

[1]  L. Lagardère, L.-H. Jolly, F. Lipparini, F. Aviat, B. Stamm, Z. F. Jing, M. Harger, H. Torabifard, G. A. Cisneros, M. J. Schnieders, N. Gresh, Y. Maday, P. Y. Ren, J. W. Ponder, and J.-P. Piquemal, “Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields” Chem. Sci., vol. 9, no. 4, pp. 956–972, Jan. 2018.

[2]  M. Chavent, E. Seiradake, E. Y. Jones, and M. Sansom, “Structures of the EphA2 Receptor at the Membrane: Role of Lipid Interactions” Structure (London, England : 1993), 2016.

[3]  M. Mund, J. A. van der Beek, J. Deschamps, S. Dmitrieff, P. Hoess, J. L. Monster, A. Picco, F. Nédélec, M. Kaksonen, and J. Ries, “Systematic Nanoscale Analysis of Endocytosis Links Efficient Vesicle Formation to Patterned Actin Nucleation” Cell, vol. 174, no. 4, pp. 884–896.e17, Aug. 2018.

Eligibility

• Ph.D. in Computational Structural Biology, Biophysics or closely related disciplines.

• Familiarity of Linux operating systems.

• Experience with at least one of the following programming languages: python, tcl, C++.

• Experience with molecular dynamics simulations.

• Experience with high-performance computing environments.

• Record of published peer-reviewed research articles.

• Ability to work independently and communicate effectively.

Required Application Materials to send to M. Chavent and J.P. Piquemal by email

• Curriculum vitae

• List of two references

• List of peer-reviewed publications

   

Dr. Matthieu Chavent (matthieu.chavent@ipbs.fr) and Prof. Jean-Philip Piquemal (jean-philip.piquemal@sorbonne-universite.fr)