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Helm­holtz-Zen­trum Dres­den-Ros­sen­dorf e.V.

Through cut­ting-edge research in the fields of ENERGY, HEALTH and MAT­TER, Helm­holtz-Zen­trum Dresden-Rossen­dorf (HZDR) solves some of the press­ing soci­etal and indus­trial chal­lenges of our time. Join our 1.400 employ­ees from more than 50 nations at one of our six research sites and help us mov­ing research to the next level!

The Cen­ter for Advanced Sys­tems Under­stand­ing (CASUS) is a Ger­man-Pol­ish research cen­ter for data-intens­ive digital sys­tems research. CASUS was foun­ded in 2019 in Görl­itz and con­ducts digital inter­dis­cip­lin­ary sys­tems research in vari­ous fields such as earth sys­tems research, sys­tems bio­logy and mater­i­als research.

CASUS invites applic­a­tions as

PhD Stu­dent (f/m/d) Machine-learn­ing-driven Digital Twin of Virus Infec­ted Cell Dynam­ics

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

The Scope of Your Job:

The global SARS-CoV2 Pan­demic has demon­strated the urgency to develop new tools for our arsenal against patho­gens. If YOU are pas­sion­ate about design­ing the next gen­er­a­tion of math­em­at­ical mod­els and machine learn­ing 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. These may be observed in cell cul­ture using light micro­scopy tech­niques at a mod­er­ate mag­ni­fic­a­tion. 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 develop a Digital Twin model of infec­ted cell dynam­ics on the scale of a tis­sue, which will help us under­stand how vir­uses spread across the tis­sue.

Working field:

  • 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 Com­puter Sci­ence, Data Sci­ence, Machine Learn­ing, or Phys­ics, Bioin­form­at­ics, Com­pu­ta­tional Bio­logy, 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 Mat­lab and Python
  • Famili­ar­ity with mod­ern deep learn­ing frame­works like Numpy, Tensor­flow 2.x.x, PyT­orch
  • Pre­vi­ous exper­i­ence or interest in Mat­lab to Python code­base con­ver­sion, Com­puter Vis­ion, Deep Learn­ing and Slurm 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)

What we offer:

  • A vibrant research com­munity in an open, diverse and inter­na­tional work envir­on­ment
  • Sci­entific excel­lence and extens­ive pro­fes­sional net­work­ing oppor­tun­it­ies
  • A struc­tured PhD pro­gram with a com­pre­hens­ive range of con­tinu­ing edu­ca­tion and net­work­ing oppor­tun­it­ies - more inform­a­tion about the PhD pro­gram at the HZDR can be found here
  • The employ­ment con­tract is lim­ited to three years
  • Salary and social bene­fits in accord­ance with the col­lect­ive agree­ment for the pub­lic sec­tor (TVöD-Bund) includ­ing 30 days of paid hol­i­day leave, com­pany pen­sion scheme (VBL)
  • Numer­ous com­pany health man­age­ment offer­ings
  • An employer sub­sidy for the VVO job ticket

How to apply:

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