PhD position in Biomolecular Simulation
The computational chemistry and physics group at the Van ‘t Hoff Institute for Molecular Sciences in the Faculty of Science of …
- Science Park, Amsterdam, Noord-Holland
- Vast contract
- Uren per week:
- 38 - 38 uur
- € 2325 - € 2972 per maand
The computational chemistry and physics group at the Van ‘t Hoff Institute for Molecular Sciences in the Faculty of Science of the University of Amsterdam (UvA) is looking for a highly motivated and creative PhD to join a challenging and interdisciplinary project to study the next level of transcription regulation. Transcription is the process by which a gene segment on DNA is copied into messenger RNA, involving several proteins. These proteins bind, though weakly, to other sequences of DNA and thus, the total amount of DNA available for these proteins to bind to, competes with the binding to promoter regions. Surprisingly, this ‘next level’ of transcription regulation has not been systematically addressed yet. By using computational and theoretical approaches, we aim to provide quantitative and detailed insights into how the size of the accessible DNA regulates transcription. This project is in collaboration with Utrecht University, where this topic will be studied experimentally.
What are you going to do?
You will develop a computational approach to predict the number of accessible DNA in various conditions, using molecular simulation methods such as all-atom molecular dynamics simulations in combination with rare event techniques and a coarse-grained description of proteins binding to DNA; you will analyze and interpret the results; you will report your results in peer-reviewed journals and at international conferences; you will be a member of a dynamic and interdisciplinary research group.
- An MSc degree in chemistry, life sciences, physics or computational science;
- good communication skills in oral and written English;
- experience in programming and/or molecular simulation is an advantage.
A temporary contract for 38 hours per week for the duration of 4 years (initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years) and should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.
The salary, depending on relevant experience before the beginning of the employment contract, will be €2,325 to €2,972 (scale P) gross per month, based on a full-time contract (38 hours a week), exclusive 8 % holiday allowance and 8,3% end-of-year bonus. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Dutch Universities is applicable.
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