Open Positions 1
Time Span 01 Oct 2021 for 42 months
Application Deadline 03 Aug 2021
Type of Position
PhD - Doctoral Programme
Field of Research
Mathematics / Natural Sciences
Subjects Physics, Biophysics, Bioengineering, Mathematics, Computer
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-
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
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.
• 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
• 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.
• 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
• A highly communicative atmosphere within an energetic scientific network
• A comprehensive mentoring program and soft skill courses for early career
• Jena – City of Science: a young and lively town with a vibrant local
• 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
• 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.
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 (www. microverse-cluster.de) 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:
https: // apply.jsmc.uni-jena.de/
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 www4.uni-
jena.de/stellenmarkthinweis.html (in German)
Please also note the information on the collection of personal data at
Language of Dissertation
Letter of Motivation
List of Publication
More Information https: // www. jsmc-phd.de/vacant-positions.html