PhD in Computational Methods for Biomolecular Structure and Dynamics

2 PhD positions are available (from October 2015) in the newly established lab of Integrative Structural Biology at the Department of Chemistry, Technische Universität München (TUM).
Please directly contact Carlo Camilloni (carlo.camilloni@gmail.com) for enquiries.

Our research is focused on the development of computational techniques to combine experimental data, molecular dynamics simulations and enhanced sampling, in order to study and rationalize complex bio-molecular processes, from the determination of individual structures to full equilibrium ensemble of conformations.

The approach of the lab is interdisciplinary and combines together mathematical, physical, chemical and bioinformatics approaches with a strong link to specific biochemical applications. A background in chemistry or physics and previous experience in molecular simulations and statistical mechanics is preferable. Programming experience is highly desirable.

Projects include:
-       The application of restrained simulations to the study of the dynamics of intrinsically disordered proteins,
         membrane proteins, protein-protein and protein-nucleic acid complexes;
-       The development of implicit solvent force-fields tailored to the study of intrinsically disordered proteins;
-       The development of experimental restraints (SAXS, Cryo-EM, Chemical Shifts) in the PLUMED package to study large macromolecular complexes;
-       The development and application of scoring functions for structure determination and assessment (with a particular attention to Bayesian Inference based methods);
-       The development of coarse-grained models, based on experimental data and the maximum entropy principle, to study protein oligomerisation and aggregation.

List of representative publications:
·      Brewer K.D., et al. (2015) Dynamic Binding Mode of a Synaptotagmin-1-SNARE Complex in Solution. Nat. Struct. Mol. Biol. 22, 555
·      Camilloni C., et al. (2014) Cyclophilin A catalyses proline isomerization by an electrostatic handle mechanism. Proc. Natl. Acad. Sci. U.S.A. 111, 10203
·      Camilloni C. & Vendruscolo M. (2014) Statistical mechanics of the denatured state of a protein using replica-averaged metadynamics. J. Am. Chem. Soc. 136, 8982
·      Krieger J.R., et al. (2014) Conformational Recognition of an Intrinsically Disordered Protein. Biophys. J. 106, 1771
·      Tribello G.A., et al. (2014) PLUMED2: New feathers for an old bird. Comp. Phys. Comm. 185, 604
·      Cavalli A., et al. (2013) Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles that satisfy the maximum entropy principle. J. Chem. Phys. 138, 094112