Date Posted
5 Jul 2021

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PhD Project
Cluster Balance of the Microverse

Doctoral Researcher Position “Biophysical modelling of the bacterial cell wall” (m/f/d)

5 Jul 2021

Position Description

Friedrich Schiller University is a traditional university with a strong research profile rooted in the heart of Germany. As a university covering all disciplines, it offers a wide range of subjects. Its research is focused on the areas Light—Life—Liberty. It is closely networked with non-research institutions, research companies and renowned cultural institutions. With around 18,000 students and more than 8,600 employees, the university plays a major role in shaping Jena’s character as a cosmopolitan and future-oriented city.

The Cluster of Excellence “Balance of the Microverse” at the Friedrich Schiller University Jena, Germany, combines expertise in life, material, optical and computational sciences to elevate microbiome studies from descriptive to hypothesis-driven and functional analyses. Our core mission is to elucidate fundamental principles of the interactions and functions in microbial communities in diverse habitats ranging from oceans and groundwater to plant and human hosts. We aim to identify the shared characteristics of disturbed or polluted ecosystems as well as infectious diseases on the microbiome level, and develop strategies for their remediation by targeted interventions. Our full spectrum of expertise in the physical and life sciences will be leveraged to address these important issues in natural habitats as well as synthetic arenas in a collaborative manner. The affiliated early career program of the Jena School for Microbial Communication (JSMC) offers an ambitious, structured and interdisciplinary post-graduate training based on top-level fundamental research.

The new professorship Theoretical Microbial Ecology, Prof. Rosalind Allen, at the Faculty of Biological Sciences invites applications for a

Doctoral Researcher Position
“Biophysical modelling of the bacterial cell wall” (m/f/d)

commencing on 01.10.2021. A later start may be possible if desired. The position is initially limited to 3 and a half years. We offer a part-time position 65%.

Our research group seeks to understand how bacteria grow, how they are inhibited by antibiotics, and how they evolve resistance to antibiotics. To do this, we combine computational and theoretical models with lab experiments, to gain insights that could not be obtained from experiments alone. Many of the most clinically relevant antibiotics target the bacterial cell wall, which consists of an interlinked mesh of glycan and peptide molecules, known as peptidoglycan. Yet much remains to be understood about the cell wall, including the biophysical properties of the peptidoglycan mesh, the details of how it is synthesized, and how it becomes compromised by antibiotic action, leading to bacterial death. The objectives of this doctoral research project are to address these questions using computational modelling. You will use and extend a computer simulation model that has been developed in our group, in which the peptidoglycan mesh is represented as a collection of beads and springs. You will perform Langevin dynamics simulations of this model in different scenarios, to address important microbiological questions. The work will be performed in close collaboration with biochemists at the University of Newcastle (UK) and biophysicists at the Universities of Sheffield and Cambridge (UK) who will provide experimental data.

Your responsibilities:
• Conduct research on the biophysical properties of the bacterial cell envelope, specifically peptidoglycan, using computer simulations.
• Develop and modify code in languages such as python, c++, matlab etc.
• Produce and analyse results, and interact productively with international and local collaborators who may not have a physical science background.
• Contribute to the development of project direction, as the project evolves.
• Produce high-quality written reports and draft papers.
• Present your results at local meetings and national and international conferences.
• Assist with training other researchers, including Masters’ and undergraduate project students, where required.
• Assist with the teaching activities of the group where required.
• Contribute to maintaining the friendly, welcoming and collaborative environment within the group.

Your profile
• An MSc (or equivalent) in Physics, Biophysics, Bioengineering, Mathematics, Computer Science or related discipline. Candidates in the final stages of obtaining their degree are also eligible to apply.
• Required methodological skills: computer programming (e.g. python, C, C++, matlab or other languages), computer simulation, knowledge of mechanics, linear and non-linear dynamics and related topics.
• Desired methodological skills: Experience in biophysical modelling, systems biology, computational biology or related topic. Prior microbiological knowledge is not required but a keen interest in the topic is essential.
• Interest in performing experimental work as well as theory/simulations is welcome but is not required.
• You should be a highly motivated individual with an interest in joining an interdisciplinary research group within the Cluster of Excellence.
• You should have an integrative and cooperative personality with enthusiasm for actively participating in the dynamic Microverse community, and for interacting with individuals from many different scientific backgrounds.
• Excellent skills at writing and oral communication, in English, are essential.

We offer:
• A highly communicative atmosphere within an energetic scientific network
• A comprehensive mentoring program and soft skill courses for early career researchers
• Jena – City of Science: a young and lively town with a vibrant local cultural agenda
• A family-friendly working environment with a variety of offers for families: University Family Office ‘JUniFamilie’ and flexible childcare (‘JUniKinder);
• University health promotion and a wide range of university sports activities;
• Attractive fringe benefits, e.g. capital formation benefits (VL), Job Ticket (benefits for public transport), and an occupational pension (VBL)
• Remuneration based on the provisions of the Collective Agreement for the Public Sector of the Federal States (TV-L) at salary scale E 13 — depending on the candidate’s personal qualifications—, including a special annual payment in accordance with the collective agreement.
The Friedrich Schiller University Jena is an equal opportunity employer and part-time contracts can be discussed.
To promote gender equality in science, applications by woman are especially welcome. Candidates with severe disabilities will be given preference in the case of equal qualifications and suitability.

How to Apply

Applications in English should comprise a cover letter, a detailed curriculum vitae and copies of academic certificates. Please familiarize yourself with the currently available doctoral projects ( and the application process as described in the Online Application Portal. Please submit your application via the JSMC Online Application Portal, under the vacancy ID 227/2021 by 3rd August 2021: Since all application documents will be duly destroyed after the recruitment process, we ask you to submit only copies of your documents. For further information for applicants, please also refer to (in German) Please also note the information on the collection of personal data at

Position Category: Medical & Biological Sciences. Position Type: PhD Project.