Projects in summer semester 2025
Multi-scale biomolecular simulations - analysis of protein interaction patterns
Slots: 1, Hours per week: 4, Completion within: 9 monthsFor 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.
(more information)
Creating an analysis framework for Coarse-Grained LLPS-Simulations
Slots: 1, Hours per week: 6, Completion within: 6 monthsFor students inrolled in: Applied Physics B.Sc., BMC B.Sc., Chemestry B.Ed., Chemestry B.Sc., Environmental Sciences with a Focus in Atmosphere and Climate B.Sc., Geography B.Ed., Geography B.Sc., Geosciences B.Sc., Informatics B.Ed., Informatics B.Sc., Mathematics B.Ed., Mathematics B.Sc., Mathematics-Infomatics B.Sc., Meteorology B.Sc., Molecular Biology B.Sc., Molecular Biotechnology B.Sc., Physics B.Ed., Physics B.Sc.,
Discription
Complementary to the work of our experimentalists in biology, we investigate the liquid-liquid phase separation (LLPS) of different proteins using coarse-grained molecular dynamics (MD) simulations. To create a phase diagram, many simulations with varying starting parameters are carried out and evaluated according to the same scheme. Additional features are to be added to the existing framework for this purpose.
Role of the students
The students implement new analysis features and thus gain an insight into research using biophysical simulations, as well as the development of research software using test-driven development.
Qualifications
Basic knowledge of statistical physics, programming and willingness to familiarize yourself with an interdisciplinary field are required. Knowledge of MD simulations, the Julia programming language, good English skills, Git and statistics are advantageous.
(more information)
Reasons for no-show-ups in Physics for Chemistry
Slots: 1-4, Hours per week: 3-9, Completion within: 3-12 monthsFor students inrolled in: Applied Physics B.Sc., BMC B.Sc., Chemestry B.Ed., Chemestry B.Sc., Informatics B.Ed., Mathematics B.Ed., Meteorology B.Sc., Molecular Biotechnology B.Sc., Physics B.Ed., Physics B.Sc.,
Discription
The Physics for Chemistry course has low attendance in exercises and lectures. To investigate this, there has already been a semester-accompanying survey that asked questions every week about the basic attitude and perception of the lecture and exercise content. The next step is to identify reasons that motivate students to attend tutorials and lectures and to identify reasons that discourage them from doing so.
Role of the students
The students will use and adapt ready-made Python code to analyze the data from over 600 responses. In a second step, reasons and recommendations will be identified to give students more reasons to participate in the exercises and the lecture.
Qualifications
Basic Python skills are helpful but not necessary.
(more information)
Mathematical Pre-course in Biology, Chemestry, and Geosciences Guidelines
Slots: 1-3, Hours per week: 5, Completion within: 9 monthsFor students inrolled in: Applied Physics B.Sc., BMC B.Sc., Chemestry B.Ed., Chemestry B.Sc., Environmental Sciences with a Focus in Atmosphere and Climate B.Sc., Geography B.Ed., Geography B.Sc., Geosciences B.Sc., Informatics B.Ed., Informatics B.Sc., Mathematics B.Ed., Mathematics B.Sc., Meteorology B.Sc., Molecular Biotechnology B.Sc., Physics B.Ed., Physics B.Sc.,
Discription
The school mathematics pre-semester course for biology often receives criticism through the participants. The main criticism is, that the courses mostly do not start with mathematical basics which the students know. Goal of the project is to evaluate the current state of the course.
Role of the students
The role of the students is to mainly evaluate the worksheets the students work on during the course. Evaluate where the current problems are and how to change the worksheets for the needs of the students.
Qualifications
A good understanding of the mathematical courses in the first semester of biology is necessary. This includes analysis in more than one dimension, fundamental linear algebra, fundamental differential equations, complex-valued equations, and statistics of standard deviation and mean value
(more information)
Evaluating Tutorials in Experimental Physics 1 and 2
Slots: 1-3, Hours per week: 5, Completion within: 9 monthsFor students inrolled in: Applied Physics B.Sc., Chemestry B.Sc., Meteorology B.Sc., Physics B.Ed., Physics B.Sc.,
Discription
Tutorials in experimental physics 1 and 2 are currently changing due to the new law that prohibits forcing students to be present at every seminar day. These changes are currently being evaluated. The goal of the project is to write a handout for the tutorial lecturers.
Role of the students
Students have to prepare and analyze evaluations of different semesters of physics students. Evaluations of different semesters in the past have already been done but need to be considered, too. On the basis of this evaluation, the students write a short one-page handout for the lecturers.
Qualifications
Students need to have completed Experimental Physics 1 and 2 as well as the corresponding tutorials. Basic Python skills are helpful but not necessary.
(more information)
Choose your QUEST field:
