Department Bionanoscience
Principal investigator Timon Idema
E-mail address t.idema@tudelft.nl
Website www.idemalab.tudelft.nl
Mechanics of tissue development
During development, tissues undergo large conformational changes. As part of such changes, tissues sometimes behave as a solid, and sometimes as a fluid. In this project, we’ll study the mechanics of a developing tissue, built from cells that we describe with a ‘sticks and balls’ model (representing the nucleus and cytoskeleton of each cell). We already know that this model can correctly predict the geometric pattern of the cells in an actual tissue, and that non-adhering cells flow like soap bubbles when we shear them. In this project, we will study the effect of cell division on tissue. As always, we will aim to predict the outcome of similar tests in experiments.
Techniques
- Simulations
- Data analysis
Further reading
Van Drongelen, R., et al. (2018). Journal of Theoretical Biology, 454, 182-189. DOI: 10.1016/j.jtbi.2018.06.002.
Interactions between crawling cells
The ‘sticks and balls’ model of project 1 allows us to create not only growing but also crawling cells. In this project, we will study the interaction between such crawling cells, and see if and how excluded volume and transient adhesion interactions cause the cells to exhibit nontrivial collective dynamics. While we will initially do our simulations in an empty environment, the next step will be to include patterns, resembling extracellular material and ultimately other tissue that the cells are moving through.
Techniques
- Simulations
- Data analysis
Further reading
Van Drongelen, R., et al. (2018). Journal of Theoretical Biology, 454, 182-189. DOI: 10.1016/j.jtbi.2018.06.002.
Bacterial colony growth and shape
Bacterial colonies grow through repeated growt h-and-division cycles. Rod-shaped bacteria do so by elongating along their long axis, defining a clear local orientation. However, after a couple of division rounds, the global orientation is lost, and orientational defects appear. In this project, we’ll study how the properties of the colony, like the defect density, correlation length, and colony shape, are affected by the bacterial properties, such as their growth protocol (‘adder’ and ‘sizer’ models) and their interactions, to figure out which of these we can induce directly from experimental observations of growing colonies.
Techniques
- Simulations
- Data analysis
Further reading
Los, R., et al. (2022). arXiv. DOI: 10.48550/arXiv.2003.10509.
Oscillation-induced phase separation in bacterial colonies
Some species of swimming bacteria can oscillate: they repeatedly flip the direction in which they are moving by 180°. While this behaviour may appear counterproductive for colony spreading, earlier work has shown that it can actually help a colony boundary move faster, by better aligning the bacteria inside. In this project, we’ll study what happens when we mix two species of oscillating bacteria together. We expect that under the right conditions, these bacteria can phase-separate, much like the motility-induced phase separation observed in self-propelling systems.
Techniques
- Simulations
- Data analysis