PhD Student in Biomolecular Modellig Group

Field: theoretical biophysics


Title of the position: PhD Student in Biomolecular Modelling Group
Scientific discipline: theoretical biophysics
Job type: initial period: civil law agreement, after extension: NCN stipend
Number of job offers: 1
Remuneration/Stipend amount/month: 4000
Position starts on: 01.06.2019
Maximum period of contract/stipend agreement: 6 + possible extension for the next 24
Institution: Biomolecular Modelling Group
Project leader: Piotr Setny
Project title: Interaction of influenza virus fusion peptides with lipid bilayers
Project Description: Influenza is one of the five most lethal infectious diseases faced by humans. One of viable therapeutic strategies is targeting virus entry into host cells, in particular its stage involving the fusion of viral and cellular membranes. In the case of influenza virus, membrane fusion is mediated by a hemagglutinin (HA) protein. It inserts its N-terminal fragments, known as fusion peptides (HAfp), into the target membrane and initiates lipid mixing. Intriguingly, HAfps in the form of synthetic 20 – 23 amino acid long peptides are already able to fuse liposomes without the aid of the entire HA structure. Atomistic details of this process, while crucial for understanding HA-mediated fusion, remain elusive. In this project we will conduct extensive computer simulations of HAfp-membrane systems in fully atomistic resolution coupled to experimental studies. We will characterise HAfp behaviour within lipid bilayers and will attempt to capture early stages of the fusion process. Aside from giving the opportunity to tackle fascinating scientific problems, the project will allow mastering state of the art simulation approaches, including enhanced sampling techniques and free energy methods, providing as well ample room for creative work on novel analysis.

Key responsibilities include:
Initial period:
Mastering simulation techniques and analysis methods
After extension:
Conducting and analysing computer simulations of peptide-membrane systems
Presenting the results on seminars & conferences

Profile of candidates/requirements:
1. MSc degree (or equivalent) in physics, chemistry, biology, computer science, or related discipline
2. Good oral and written command of English
3. Basic knowledge of Linux operating system and scripting language (e.g. Python, Perl)
4. Previous experience with molecular modelling would be welcome, although it is not strictly necessary

Required documents:
1. Motivation letter
2. CV with the list of scientific activities undertaken to date
3. Contact details of the former supervisor or a recommendation letter send directly to the project leader (email below)

We offer:
1. Work in a friendly atmosphere, in a modern and well equipped institute
2. Extensive training in computational modelling of complex biomolecular systems
3. Opportunity to participate in courses and conferences
4. Access to state of the art computing equipment

Please submit the following documents to:


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Deadline: 15/05/2019

Tags: computer simulations, lipid membranes, membrane fusion, influenza virus