Multi-scale biomolecular simulations - analysis of protein interaction patterns

Slots: 1
Hours per week: 4
Completion within: 9 months

For students inrolled in:
Applied Physics B.Sc., BMC B.Sc., Chemestry B.Sc., Informatics B.Ed., Informatics B.Sc., Mathematics B.Ed., Mathematics B.Sc., Mathematics-Infomatics B.Sc., Physics B.Ed., Physics B.Sc.,

Discription
In collaboration with our experimental partner at IMB, we study protein granules, a molecular condensate involved in epigenetic inheritance. To study their formation, we use molecular dynamics simulations and analyze protein interaction patterns. These help us investigate the underlying biophysical mechanism.

Role of the students
This QUEST project offers a first perspective on biophysical research on proteins that play a role in epigenetic inheritance. We perform molecular dynamics (MD) simulations on MOGON2, extracting insights by analyzing contact patterns. You can choose your focus to work with us on advancing our Python workflow: (a) pattern analysis through frequent item set mining or simple ML/generative models, (b) performance optimization via benchmarking and test development, or (c) molecular system exploration through sequence mutations.

Qualifications
Curiosity to support protein research through simulations and method development is helpful. You should be interested in collaborating with a PhD student in an interdisciplinary lab. A first experience with Python is helpful or at least you should bring high motivation to develop programming skills. Some interest in gaining experience with High-Performance Computing (HPC) systems is recommended.


Supervisor: Lucia Baltz
Location: Campus Mainz
Primary Language: English


If you have any further questions you can always write a mail to quest@uni-mainz.de.

 

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