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Doctoral Researcher Position: Virtual infection model for Aspergillus fumigatus in human alveoli

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The Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute – in cooperation with the Friedrich Schiller University and the Max Planck Institute for Chemical Ecology are offering an international graduate training program.
The International Leibniz Research School (ILRS Jena) gives doctoral researchers the possibility to prepare for their PhD exam in an ambitious program providing excellent research conditions.
We invite applications for a Doctoral Researcher Position (Ref.No. ILRS_07/2015)

Virtual infection model for Aspergillus fumigatus in human alveoli

Aspergillus fumigatus is one of the most dangerous human fungal pathogens that can cause life-threatening diseases. Since humans inhale hundreds to thousands of fungal conidia every day, the lower respiratory tract is the primary site of infection. In a previous doctoral study, we implemented a spatio-temporal agent-based model of a human alveolus and performed in silico experiments of a virtual infection scenario under physiological conditions. However, our investigations were so far limited to study the detection of pathogens by alveolar macrophages (AM) in a single alveolus. We compared the time duration of first pathogen-encounter for different migration modes of the phagocytic cells and deciphered properties of a chemokine that directs AM to the invaded pathogen. The objective of this project is to exploit the flexibility and extensibility of the agent-based modeling framework by including more complex aspects of host-pathogen interactions to enable simulations of the immune response at a substantially higher level of realism. In particular, it will be investigated how the concurrent buildup in the dynamic interplay between infection and inflammation might be regulated and affected, for example, by the dose of infection. In order to achieve this challenging goal within a spatio-temporal modeling approach, the whole time course of the innate immune network will be simulated on the computer, including the impact of the complement system, phagocytosis by resident AM as well as by recruited neutrophils (PMN) and dendritic cells (DC). This will be realized within a multi-scale approach comprising cytokine dynamics at the molecular level up to inter-alveolar communication within alveolar sacs. Since the peculiar physiology of the lung generally complicates in vivo imaging of cell dynamics, predictive computer simulations are a convenient and adequate option to decipher the dynamics of the immune network and to direct future experimental investigations.

We expect:
  • a Master’s degree (or equivalent allowing you to pursue a PhD degree) in Natural or Life Sciences. Research at ILRS is centred around “Microbial and Biomolecular Interactions”. Candidates about to earn their degree are welcome to apply.
  • high motivation and interest to join one of the research areas of ILRS
  • mathematical skills and programming skills in C++ are required for this thesis project
  • an integrative and cooperative personality with enthusiasm for actively participating in our lively community
  • very good communication skills in English
We offer:
  • a top-level research environment
  • efficient supervision by a team of advisors
  • a comprehensive mentoring program (cf. Program of Study)
  • courses in state-of-the-art technologies and soft skills
  • strong communication and interaction between the involved institutions
  • Jena – City of Science: innovative business activities, successful scientific centres and a vibrant cultural scene around the famous Friedrich Schiller University
The three-year Doctoral Researcher position is available starting from February 2016. Salary will be paid according to TV-L (salary agreement for public service employees). HKI is an equal opportunity employer.

Further information:
Prof. Dr. Thilo Figge, PI,
Dr. Christine Vogler, ILRS Coordinator,

The application process is handled exclusively online. Please acquaint yourself with the scientific projects offered on our website and thoroughly follow the instructions for the online application process:

Deadline for application: November 17, 2015.
Successful applicants will be invited to attend a recruitment meeting in Jena (envisaged date: Jan 13-15, 2016).


Art des Bewerbungszugangs
Online Application at
Kontakt f├╝r Bewerbungen
Dr. Christine Vogler,

Details der Stellenanzeige

Befristete Anstellung
Berufserfahrung nicht vorausgesetzt
Deutschland (Th├╝ringen)
07745 Jena
Biologie & Life Sciences, Informatik