Job offer for a researcher from Ukraine

Requirements:

• PhD degree (known as the Candidate of Sciences under the Ukrainian system) in Chemistry, Biology, Biotechnology or related disciplines.
• Employment at a Ukrainian university or other research centre directly before the outbreak of the war.
• Arrival in Poland related to the Russian invasion of Ukraine on February 24, 2022.
• Command of English sufficient to read scientific papers and for communication.
• Knowledge of molecular dynamics and experience in running MD simulations and analyzing and interpreting the results of simulations. The knowledge of MD extensions (replica exchange nad Hamiltonian replica exchange) is desirable.
• Knowledge of experimental methods for protein-structure determination, in particular those based on nuclear magnetic resonance, at least regarding the quantities available from experiments and using them in data-assisted structure modeling. Experience in modeling MD-based data-assisted modeling of protein structures is desirable.
• Ability to work with UNIX-operated workstations at least at the medium-advanced level, including the ability to write UNIX scripts. Literacy in programming languages (Fortran, C/C++) is desirable.

Project information and task description:

The goal of the project is to develop the Ensemble Oriented Data Assisted Molecular Dynamics (EODAMD) approach to determine the dynamic structure of the Intrinsically Disordered Proteins (IDPs) and other flexible multistate proteins (such as, e.g., molecular chaperones). The method will be based on MD simulations with Hamiltonian replica exchange with the coarse-grained UNRES force field (www.unres.pl), designed in the laboratory of the project leader. The experimental restraints will be imposed on the whole conformational ensemble by their averaging over replicas and simulation windows. The researcher will be engaged in performing the following tasks:

• Development of a method for the computation of backbone proton, ¹³C and ¹⁵N chemical shifts, and the RDCs for a given coarse-grained geometry.
• Implementation of the cross-link pseudopotentials into the UNRES package and testing these potentials in crosslinking assisted UNRES simulations of known protein structures.
• Development of the extended replica-exchange molecular dynamics algorithm, with time- and replica averaged restraints to take into account conformationally-averaged experimental restraints, and testing the methodology with multistate proteins for which the experimental data are already available.

Conditions of employment:

• 6 month employment period, starting immeditely after acceptance.
• Gross-gross salary 8333 PLN/month.
• Employment based on ``Contract of Mandate'' (umowa zlecenia in Polish) or ``Contract work'' (umowa o dzieło in Polish). Job contract (umowa o pracę in Polish) possible if a researcher has the Ph.D. diploma recongized in Poland without nostrification procedures or a nostrified diploma.

Required documents:

• Cover letter (can constitute the body of the email).
• CV with a description of scientific interests.
• A scan of Ph.D. diploma.

How to apply:

Please email the documents specified above to Prof. Józef Adam Liwo at adam.liwo@ug.edu.pl or adam.liwo@gmail.com. Please include the phrase SHENG-2: researcher from Ukraine in the subject line.

Please contact Prof. Józef Adam Liwo at adam.liwo@ug.edu.pl or adam.liwo@gmail.com if you need more detailed information.