Van 't Hoff Institute for Molecular Sciences University of Amsterdam
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
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.
Derivation of analytical second derivatives with respect to position and strain for the out-of-plane and Wilson potential. First and second derivatives of angle-dependent potentials are very tedious to derive (using application of chain-rules for derivatives), but very useful in molecular simulations.