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Bacteria are ubiquitous microscopic, single-celled organisms. Many bacteria live on and inside animals and humans, but very few cause diseases. Bacterial infections are usually treated with antibiotics, but resistance to antibiotics is becoming a major challenge. To prevent resistance from emerging and find alternative ways of combatting infections, we must understand population dynamics of bacteria during an infection: how they invade host cells, how resistant mutations arise and spread, and how intracellular bacteria respond to antibiotics. This requires a concentrated interdisciplinary effort. In this project we take a physics-inspired approach and address these questions through a combination of laboratory experiments and mathematical modelling. We develop experimental model systems of bacterial infections together with advanced imaging methods to investigate the population dynamics of bacterial invasion. Mathematical models are used to interpret and direct experiments. The project fills an important gap between in vitro and animal models of infections. It enables quantitative research of bacterial ecology and evolution in an environment closer to the environment of the host than previous works, explore fascinating non-equilibrium physics of intracellular bacterial colonies, and the structure of within-host fitness landscapes.

Main responsibilities:
1. Planning and execution of specific elements of the research program under the guidance of the supervisor. This may involve but is not restricted to: developing algorithms for segmenting 2d and 3d images of intracellular bacterial colonies, obtaining abundances of different types bacteria from fluorescent images of biofilms, developing algorithms for tracking bacteria and animal cells in microscopic images, comparing experimental results with mathematical models of bacterial and cellular populations.
2. Communicating research results to team members and collaborators at IPC and other institutions through talks and discussions, as well as learning about others’ research through seminars and journal clubs.
4. Writing reports and scientific papers.
5. Attending and presenting at workshops and conferences.
6. Keeping up-to-date with relevant scientific developments through literature review.

We offer a full-time employment position in the Institute of Physical Chemistry PAS with a gross salary between 13 000-16 000 PLN per month financed from the NAWA POLSKIE POWROTY 2019 Project No. PPN/PPO/2019/1/ 00030.

The successful candidate will benefit from working in an international, interdisciplinary research group, a modern well equipped wet lab, office space, and access to computational/storage servers. The candidate will work closely with experimentalists and theorists from the Dioscuri Centre. The candidate will have the opportunity to visit collaborating research groups and to participate in international workshops and conferences.
Institute provides an opportunity to participate in ERASMUS+ programme.

Essential
• PhD in physics or physical chemistry, held or to be obtained before the job start date.
• Experience in image analysis and/or computer models of populations of bacteria or cells
• Very good programming skills in either Python, C++, Matlab, or Wolfram Mathematica
• Very good academic achievements as evidenced by peer-reviewed publications and talks/poster presentations at international conferences.
• Ability to draft (in English) scientific papers for academic journals.
• Ability to communicate (in English) complex information clearly, orally and in writing.
• Ability to think creatively, propose and develop new ideas.

• Capability of working without close supervision, exercising a high degree of initiative and demonstrating a pro-active approach to work.

Desirable
• Experience with Machine Learning applied to image analysis
• GitHub, Jupyter, Linux
• Ability to organise work so as to perform multiple tasks simultaneously.
• Ability to maintain a well-organised digital repository of software and data.
• Potential for career advancement as an independent researcher.
Candidates who possess these additional skills will be prioritized.

The selection panel will take into account the following criteria:
a) competencies of candidates for specific tasks in a research project,
b) previous scientific achievements of candidates,
c) awards and distinctions of the candidate resulting from the conducted research.