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Advertising division: JSC - Jülich Supercomputing Centre
Reference number: 2020D-011

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The Jülich Supercomputing Centre (JSC) operates supercomputers of the highest performance class, enabling scientists and engineers in Germany and Europe to tackle some of the most complex and challenging problems of our time.

The Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) provides an interdisciplinary environment for educating the next generation of data scientists in close contact to domain-specific knowledge and research. All three domains – life & medical sciences, earth sciences, and energy systems/materials – are characterized by the generation of huge heterogeneously structured data sets, which have to be evaluated in order to obtain a holistic understanding of very complex systems. Visit HDS-LEE at: https://www.hds-lee.de/

We are offering a

PhD position - Modelling ions interaction with intrinsically disordered proteins

Your Job:

Intrinsically disordered proteins (IDPs) are characterized by a lack of stable tertiary structure under physiological conditions. 79% of cancer associated proteins, 57% of the cardiovascular disease associated proteins, 55% of neurodegenerative disease associated proteins are predicted to contain 30 or more consecutive disordered residues. Therefore, it is key to understand their behaviours. IDPs structural ensembles are particularly susceptible to changes in solution conditions. For instance, IDPs binding affinities with ligands and cellular partners, can be ion-specific already at physiological concentrations. Here we aim to the development of a transferable model for ion placement around IDPs in implicit or continuum solvent. We plan to implement a data driven model based on training data obtained from both MD simulations in explicit solvent and experimental data.

  • Generate training data from state-of-the-art MD simulations (testing latest ffs including polarizable ffs)
  • Inclusion of experimental data on ion positions where available
  • Developing learnable representations from simulated and experimental ion positions
  • Development of different inference methods for ion positions and interactions (structure + sequence based, sequence based)
  • Validation: reproducibility tests on experimental structures and implicit solvent simulations using a MCMC simulator developed at JSC


Your Profile:

  • A master in physics, chemistry, molecular biology, applied mathematics or computer science,
  • Experience with UNIX-like operating systems
  • Mathematical and programming skills (Python, Machine Learning)
  • Basic understanding of molecular forces and structures
  • Excellent knowledge of written and oral English: TOEFL or equivalent evidence of English-speaking skills
  • Interactive person with good communication skills
  • Used to work in international teams
  • Ideal prior knowledge on MD simulations
  • A high level of scholarship as indicated, for example, by bachelor and master study transcripts and two reference letters


Our Offer:

  • This HDS-LEE PhD position will be located at the Institute for Advanced Simulations at the Forschungszentrum Jülich. The candidate will be supervised by Jun.-Prof. Dr. Giulia Rossetti.
  • The PhD title will be awarded by the University of Aachen.
  • Outstanding scientific and technical infrastructure – ideal conditions for successfully completing a doctoral degree
  • A highly motivated group as well as an international and interdisciplinary working environment at one of Europe’s largest research establishments
  • Unique HDS-LEE graduate school program
  • Continuous scientific mentoring by your scientific advisor
  • Further development of your personal strengths, e.g. via a comprehensive further training program
  • Chance of participating in (international) conferences
  • Pay in line with 100 % of pay group 13 of the Collective Agreement for the Public Service (TVöD-Bund)
  • A contract for the duration of 3 years
  • Information on employment as a PhD student at Forschungszentrum Jülich can be found here http://www.fz-juelich.de/gp/Careers_Docs


Forschungszentrum Jülich promotes equal opportunities and diversity in its employment relations.

We also welcome applications from disabled persons.