Research

My interests lie at the interface between physics and biology.  I began my scientific adventure with a focus on DNA replication – the most critical process for every living organism. More recently, I have also become interested in cellular mechanics during tissue formation as well as how cellular differences arise on the chromatin level of early embryonic cells, and technical  applications to engineered systems.

DNA Replication

So far, my research on DNA replication contributes to the elucidation of the physical principles which govern faithful and on-time DNA duplication each time a cell divides. This is done using stochastic modelling of protein-DNA interaction and DNA replication replication kinetics, combining theoretical techniques from statistical physics with numerical approaches, for example Monte-Carlo simulations.

DNA Damage, Damage Response, and Repair in E. coli

DNA damage is a hazard all cells must face, and evolution has created a number of mechanisms to repair damaged bases in the chromosome. Paradoxically, many of these repair mechanisms can create double-strand breaks in the DNA molecule which are fatal to the cell. This indicates that the connection between DNA repair and death is far from straightforward, and suggests that the repair mechanisms can be a double-edged sword.

Early Embryonic Genome Activation

 I continue working on physical problems in  biology, aiming to further the understanding of stochastic processes involved in the macromolecular building blocks of life, and identify the constraints for living organisms. Specifically, I look at a theoretical investigation of  what causes the genome activation of the early zebrafish embryo to become activated during its early development.

Self-organization of robust liver transport networks

The liver represents a “chemical factory” that is characterized by intertwined transport networks for toxins and metabolites. Each hepatocyte cell interacts with two space-filling networks which either transport bile or blood through bile canaliculi or sinusoids. How these networks grow and establish their distinct geometry to supply all cells whilst providing robustness with respect to perturbations remains elusive.In this project, I elucidate design principles of liver architecture and network self-organization to ultimately understand bile and blood transport in the liver — pursuing a two-fold approach: (i) we analyse high-resolution imaging data of cell membrane compartmentalisation in mouse liver tissue. For this, we propose a nematic tensor formalism to characterise an unconventional type of hepatic cell polarity. Our analysis reveals global patterns of aligned cell polarity on the scale of the liver lobule, the functional unit of the liver, thereby characterizing the three-dimensional liver tissue as a biaxial nematic liquid crystal. We quantify co-alignment of hepatocyte cell polarity and transport network anisotropy. (ii) We then ascertain the functional relevance of this network geometry for robust transport, seeking to elucidate the relationship between local network properties and global transport properties. For that aim, we perform flow simulations in reconstructed bile canaliculi networks as well as in synthetic networks simulated by sets of simple local rules. With this approach that bridges physics and biology, we seek to link structure and function of transport networks in liver tissue.

Renormalisation Group Theory for Time-Varying Networks

I apply statistical physics to understand resilience properties of multi-hop routing in wireless communication networks with unreliable links. This leads to intriguing predictions for the design of network reliability in accordance to single link measure that can be extrapolated to the large whole network scale.

 

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