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Section: Research Program

Research axis 1: Computational cellular biochemistry

Biochemical kinetics developed as an extension of chemical kinetics in the early 20th century and inherited the main hypotheses underlying Van’t Hoff’s law of mass action : a perfectly-stirred homogeneous medium with deterministic kinetics. This classical view is however challenged by recent experimental results regarding both the movement and the metabolic fate of biomolecules. First, it is now known that the diffusive motion of many proteins in cellular media exhibits deviations from the ideal case of Brownian motion, in the form of position-dependent diffusion or anomalous diffusion, a hallmark of poorly mixing media. Second, several lines of evidence indicate that the metabolic fate of molecules in the organism not only depends on their chemical nature, but also on their spatial organisation – for example, the fate of dietary lipids depends on whether they are organized into many small or a few large droplets (see e.g. [28]). In this modern-day framework, cellular media appear as heterogeneous collections of contiguous spatial domains with different characteristics, thus providing spatial organization of the reactants. Moreover, the number of implicated reactants is often small enough that stochasticity cannot be ignored. To improve our understanding of intracellular biochemistry, we study spatiotemporal biochemical kinetics using computer simulations (particle-based spatially explicit stochastic simulations) and mathematical models (age-structured PDEs).