Master Project
Peter Bolhuis

Incorporating experimental kinetic constraints in molecular dynamics simulations

In this project the student will apply a novel method to incorporate experimental kinetic rate constants in molecular dynamics simulation, using data generated with simple (toy) models, and existing molecular dynamics data on protein folding and conformational changes, together with existing experimental measurements. The project requires some programming skills, knowledge of python. Affinity with theory and mathematical modeling is recommended.

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Bachelor Project
Tristan Bereau

Structural investigation of drug-membrane selectivity by computational screening

The project will consist of determining the structural molecular features that lead to high selectivity. In the long run we aim at correlating these with changes in free energy, potentially leading to learning this structure-property relationship. The student will analyze a large, previously generated in-house database of 20k+ computer-simulation trajectories.

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Master Project
Jocelyne Vreede

Modeling protein-DNA assemblies

H-NS is a bacterial DNA organizing protein that forms large filaments on DNA. The structure of such filaments is unknown. In this project, we will develop an algorithm to construct such structures, using existing data from simulations and experiments.

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