PhD position at the Department of Physics, University of Duisburg-Essen, Germany

Molecular dynamics simulations using classical atomistic force fields have yielded unprecedented insight into biomolecular systems. In typical simulation setups, the systems are simple and with low concentration: one or a few proteins in a simulation box with water and ~0.1 M of a monovalent salt. This setup is a crude approximation of the cytoplasm or of the extra cellular matrix, which have a high total concentration of non- water molecules: biopolymers, sugars, nucleotides, other proteins, small molecules, and salt. Despite this crudeness, this remains the recommended setup in most cases because available force fields have not been developed to handle systems with complex composition and high concentrations of non-aqueous components.

In this project we aim to develop next-generation, classical, atomistic force fields that can adequately capture the structure and the energetics of interactions of biomolecular systems with complex composition. The focus will be on force fields for inorganic salts in water, from the dilute to the solubility limit, and for their interactions with biomolecules.

We will use the force fields to investigate the mechanisms governing the stability of halophilic proteins in multimolar salt concentrations. Halophilic proteins are natural proteins that exist in the cytoplasm of halophilic organisms, which thrive in places like the Dead Sea. To counteract the high osmotic pressure of the external medium, some halophilic organisms accumulate KCl in their cytoplasm in multi-molar concentrations. Halophilic proteins are thus able to remain folded and functional under conditions where most other proteins would cease to function, by mechanisms that are not yet understood.

The project will be done in close collaboration with experimental partners, who will perform NMR and solvation shell spectroscopy of proteins in electrolyte solutions, and who will provide thermodynamic data used to develop the force fields.

Funding: The position has guaranteed funding for 36 months. Salary will be paid at the TVL-13 75% level: this corresponds to a regular work contract with healthcare, social security, paid parental leave and paid vacation.

Teaching duties amount to a maximum of 22% of the work time. Guaranteed funds are available to attend yearly conferences, for a 2-3 months visit to an international research group, and to participate in soft skill courses.

Requirements:
1- Bachelor and Master degrees with grade A (in the German system this corresponds to a grade of 1.5 or better) in Physics, Physical-Chemistry, Chemistry, or related Engineering areas.
2- Grade A in the following subjects, taken at Bachelor or MSc. level: calculus (2 semesters), intro statistical mechanics, intro quantum mechanics, physical-chemistry.
3- Prior experience with at least ONE of the following techniques: i) energy decomposition calculations from first principles; ii) molecular dynamics simulations with classical force fields; iii) force field development.
4-Excellent oral and written communication skills in English.

Contact: The position is based in the group of Dr. Ana Vila Verde (https://wiki.uni-due.de/vilaverde/) at the Physics department of the University of Duisburg-Essen (UDE), in Duisburg, Germany. To apply, send a short (0.25-0.5 page) motivation letter, a CV with contact information of referees, and university transcripts as pdfs to ana.araujo-vila-verde@uni-due.de. All application materials must be in English and must be legible.

Research environment: The successful candidate will be a part of the Excellence cluster RESOLV (https://www.solvation.de/about), which is a research initiative involving 200 scientists from 6 institutions in the German Ruhr area. The UDE is a full-fledged university, with 40000 undergraduates and 5000 graduates in all areas of knowledge; 25% of our doctoral students are international. Duisburg is 7 minutes away from the Dusseldorf airport.

The University of Duisburg-Essen aims to promote the diversity of its members (see http://www.uni- due.de/diversity) It is seeking to increase the number of women on its scientific staff and therefore strongly encourages suitably qualified women to apply. In case of equal qualification, women will be given preference in accordance with state equal opportunity legislation. Applications from suitable handicapped persons and equivalent applicants according to Article 2, Paragraph 3 of the social code (SGB IX) are also welcome.