Biochemical reaction systems in living cells constantly exchange material and energy with their environment; they operate in an open non-equilibrium setting. It is thus fundamental
T4 lysozyme is an enzyme is used by enterobacteria phage T4 to destroy bacterial cell walls by catalyzing the cleavage of glycosidic bonds. The interaction of
Continuous injection of energy into many-body systems can lead to formation of novel non-equilibrium structures which are inaccessible in equilibrium assembly. From the statistical physics
Recently, the structure of a membrane bound protein involved in the onset of sporulation in Bacillus subtilis was elucidated, see the publication in J. Intl. Mol. Sci. . With this structural investigation as a starting point, the aim of this project is to investigate the mechanisms of triggering sporulation, using molecular simulation.
Investigate inhibitor unbinding transitions in the main protease from SARS-CoV-2 using path sampling.
BSc project on linking peptide conformation to experimental observations in analytical chemistry.
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.
The student will conduct large scale simulations of patchy particles, using transition path sampling, in order to understand rare transitions in active colloidal systems.
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.