Department Bionanoscience
Principal investigator Marianne Bauer
E-mail address m.s.bauer@tudelft.nl
Control aster positioning in droplets
This project will explore the regulatory precision and sensing in published plant datasets. Depending on interest, we will use either published data from sequencing in seedling data sets or responsed to stimuli from sunflower seedlings. Using either simple Bayesian inference or a delayed-embedding framework for data analysis, we will infer how variable the seedlings are, and whether and with how much data we can infer the stimulus. This project will be the first in a series targeted at understanding plant adaptation.
Techniques
- Numerics/computation
- Data analysis
- Probability distribution
- Some information theory
Further reading
Greenwood, M., et al. (2022). Molecular Systems Biology, 18, e10140. DOI: 10.15252/msb.202010140.
Rivière, M. & Meroz, Y. (2023). Biophysics and Computational Biology, 120(42), e2306655120. DOI: 10.1073/pnas.2306655120.
Control aster positioning in droplets
We are proposing a theoretical Masters project to analyse traces of neuronal activity of a system of connected neurons in culture in comparison to mouse cortex. The aim of this project is to identify information- theoretical or statistical quantifiers that could serve as indicators for different experimental conditions. The long-term goal is to investigate if particular cells within the same culture, between different cultures or compared to the cortex are uniquely recognizable, and if they can be assigned correctly to their environment. (This project is together with the Daan Brinks Lab.)
Techniques
- Numerics/computation
- Statistical physics (Ising models)
- Entropy calculations (no previous knowledge required)
Further reading
Tian, H., et al. (2021). BioRxiv. DOI: 10.1101/2021.11.22.469481.
Palmer, S.E., et al. (2015). PNAS, 112, 6911. DOI: 10.1073/pnas.1506855112.
Control aster positioning in droplets
This project will involve polymer simulations (Brownian dynamics) with clustering molecules, to investigate how molecules can affect contact statistics of different parts of a polymer (corresponding to enhancers and promoters) in various synthetic and natural contexts. Using simulations as well as simple analytical calculations, we will try to see how these contacts affect the noise in the enhancer. The project will further involve stochastic simulations of the enhancer in order to investigate how an enhancer should optimally respond to different stimuli.
Techniques
- Brownian motion simulations
- Stochastic simulations
- Data analysis
Further reading
Bintu, L., et al. (2005). Current Opinion in Genetics & Development, 15(2), 116-124. DOI: 10.1016/j.gde.2005.02.007.
Bauer, M. (2022). Biochemical Society Transactions, 50(5), 1365-1376. DOI: 10.1042/BST20220333.