Modeling of dynamical phenomena in biology
The goal of this topic is to study physical/mathematical models derived for various biological processes. The emphasis is put on understanding the underlying mechanisms at work in a broad spectrum of biological phenomena and on studying the fascinating dynamical behavior that results.
As possible topics, we propose the following biological systems
- Population dynamics of one or more species in competition. E.g. think of the competition between a predator and its prey. As the predators feed on the prey, the superior species (predators) can't survive if there is a shortage of the weaker species (prey). This mutual dependence can lead to interesting population dynamics. Interesting applications include modeling the dynamics of microbial communities that populate our bodies.
- Small networks related to gene transcription. Proteins are synthesized via the creation of mRNA from the DNA. These proteins themselves can stimulate or repress their own creation (or the creation of other proteins). Such feedback-networks in the cell can e.g. lead to biological oscillators that are crucial to the survival of organisms.
- In collaboration with the lab of Prof. E. Peeters (VUB), we aim at designing simple gene regulatory networks to build a toolbox for synthetic biology with Arcaea. Among the three domains of life, the Archaea are the least studied organisms but they could potentially be very useful in synthetic biology because they can survive extreme environmental conditions that are sometimes met in the industrial processes.
In the study of the topics above, we will go through the following steps:
- Understanding the biological process/problem.
- Writing down a realistic mathematical representation of the most important biological processes.
- Searching for solutions to the problem, numerically and/or analytically, where we pay special attention to techniques from nonlinear dynamics.
- Interpreting the solutions found in the context of the original biological problem.