Computational Systems Biochemistry Group

Our research group is located at the Institute of Biochemistry of the Charité – Universitätsmedizin Berlin. Our research focus is the development of mathematical models of complex molecular reaction systems with emphasis on (A) metabolic regulation (liver, CNS, heart), (B) proteolysis and antigen presentation, and (C) self-organization of membranes and cellular organelles.

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Field of Interest

Metabolic Regulation

We are developing and using large-scale, molecular resolved, kinetic models for liver, brain and heart metabolism by modeling each enzyme with a kinetic rate equation. By including the regulatory properties of all enzymes these network models integrate the knowledge from decades of biochemical research and enable quantitative predictions of systems’ behavior. With these models, we are able to functionally interpret multi-omics data (proteomics, metabolomics) obtained by high-throughput methods and predict the cellular phenotype from its genotype.

Self-Organization of Membranes and Cellular Organelles

Biological membranes consist of a multitude of interacting lipids and proteins, which segregate into membrane domains with different composition and functionality. We are developing agent-based models to describe the formation of these membrane domains. One application of these models is the simulation of bile formation in the liver.

Steatosis hepatis is a potentially harmful condition characterized by excessive intrahepatic lipid accumulation. Lipid droplets are the intracellular organelles that regulate the storage and availability of lipids in the liver. We are developing and using kinetic models to investigate the lipid droplet metabolism to better understand pathological changes underlying hepatic fat accumulation.

Formation, degradation and renewal of cellular organelles are dynamic processes based on permanent budding, fusion and inter-organelle traffic of vesicles. Vesicles play key roles in the intracellular communication and intracellular transport of substances and are important for the self-organization of cellular structures. To better understand cellular self-organization we are developing and using agent-based models of intracellular vesicle dynamics.