Eye catcher

For any questions, do not hesitate to ask:
Dr. Michael Bussmann Tel.: +49 3581 37523 11,
+49 351 260 2616
Dr. Artur Yakimovich

Place of work:

Working hours:
19,5 h/week

31 December 2021

Online application
English / German
Job-Id: 2021/179 (1302)

The HZDR is committed to equal opportunity employment and we strongly encourage applications from qualified female candidates. We also carefully consider all applications from job candidates with severe disabilities.

Bautzner Landstraße 400
01328 Dresden

PhD (f/m/d) Data-driven Continuum Modelling of Infected Cell Dynamics on the Tissue Scale

As a member of the Helmholtz Association of German Research Centers, the HZDR employs about 1,400 people. The Center's focus is on interdisciplinary research in the areas energy, health and matter.

The Center for Advanced Systems Understanding (CASUS) is a German-Polish research center for data-intensive digital systems research. We combine innovative methods from mathematics, theoretical systems research, simulations, data science, and computer science to provide solutions for a range of disciplines – materials science under ambient and extreme conditions, earth system research, systems biology, and autonomous vehicles.

CASUS was jointly founded in August 2019 by the Helmholtz-Zentrum Dresden-Rossendorf, the Helmholtz Centre for Environmental Research, the Max Planck Institute of Molecular Cell Biology and Genetics, the Technical University of Dresden and the University of Wroclaw. The CASUS start-up phase is hosted by the Helmholtz-Zentrum Dresden-Rossendorf and is financed by the Federal Ministry of Education and Research and the Saxon State Ministry of Science and Art.

The Center for Advanced Systems Understanding (CASUS) invites applications as PhD (f/m/d) Data-driven Continuum Modelling of Infected Cell Dynamics on the Tissue Scale.

The position will be available from 1 April 2022. The employment contract is limited to three years.

The Scope of Your Job

If YOU are passionate about designing the next generation of mathematical models and algorithms in virology – we are looking for YOUR talent!

Viruses require host cells to procreate and spread their progeny. For this, they enter cells, replicate and egress in a stepwise process occurring through interactions between molecules of the host cell and the pathogen molecules. These are known as host-pathogen interactions, they include various host mechanisms exploitations by the pathogen. Synchronized with virus entry, uncoating, and replication through a virus genetic program, virus induce dramatic changes of cell morphology. However, connecting the dynamics of host-pathogens interactions at cellular and tissue levels requires advanced simulations.

Using Physic-informed Neural Networks in differential equation discovery mode, as well as data-driven discriminative and generative approaches developed in our group, YOU will propose novel continuum models of infected cell dynamics on the scale of a tissue.


  • Engage with our international collaborators (Dresden, London, Zurich, Taipei etc.) to understand existing approaches and datasets

  • Develop novel mathematical models and data-efficient algorithms for continuum modelling of host-pathogen interactions

  • Design novel physics-informed deep learning architectures suitable for time-lapse microscopy data

  • Publish high-impact peer-reviewed research


  • Master’s degree in Physics, Computer science, Bioinformatics, Computational biology, Data science, Machine learning or relevant discipline

  • A solid background in physics, mathematics, software engineering, machine learning, or in a related subject

  • Excellent programming skills in languages such as python, or Julia

  • Familiarity with modern deep learning frameworks like Tensorflow 2.x.x, PyTorch

  • Previous experience or interest in Computer Vision, Deep Learning and cluster environments is a plus

  • Strong motivation to work in a collaborative environment

  • Excellent communication skills in English in a professional context (presentation of research results at scientific meetings, colloquial discussions, writing of manuscripts)

We offer:

  • A vibrant research community in an open, diverse and international work environment
  • Scientific excellence and extensive professional networking opportunities
  • The employment contract is limited to three years
  • Salary and social benefits in conformity with the provisions of the Collective Agreement TVöD-Bund
  • 30 days of paid holiday leave
  • Company pension scheme (VBL)
  • A good work/life balance for which we offer assistance in the form of:
    • Possibility to work part-time

    • Flexible working hours

    • In-house health management

Kindly submit your completed application (including cover letter, CV, diplomas/transcripts, etc.) only via our Online-application-system.