Department Bionanoscience
Principal investigator Jos Zwanikken
E-mail address j.w.zwanikken@tudelft.nl
Stochastic simulations of phase separation in the polarisation network of budding yeast
Although the relevant proteins in the polarisation network of budding yeast have been clearly identified, including their mutual interactions, there is increasing experimental evidence that some of the components can form characteristic structures and aggregates under special conditions. The origin of these structures, and their potential function in the network is unclear, and currently under experimental and computational investigation. This project uses stochastic computational methods to simulate the reaction-diffusion system of the polarisation network, and explore potential scenarios, to interrogate the potential function of these liquid-like structures of proteins. (This project is largely inspired by the experiments of the Laan Lab).
Techniques
- Stochastic simulations (Gillespie algorithm)
- Theory of phase separation
- Statistical mechanics in general
- c++ programming (not essential)
- Data analysis using python
Collective swimming behaviour of C. Reinhardtii and the influence on their environment
Swimming algae and bacteria show a very different, and much more complex dynamic behaviour than ‘passive’ diffusing solutes. While the swimming behaviour of bacteria like Pseudomonas A. are rather well described by a ‘run-and-tumble motion’, the individual swimming behaviour and decision making of single algae is still under investigation, and is much more complex, let alone their flocking behaviour and the influence on the environment such as other diffusing particles and swimmers. This project uses simulation methods to find relations between the individual swimming behaviour of algae and their collective properties. In particular how flocks of swimmers can influence diffusing particles and the medium they are suspended in. (This project is largely inspired by the experiments in the group of Marie-Eve Aubin).
Techniques
- Molecular Dynamics-like simulation of swimmers
- MD-like simulations of passive particles