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pcCell Report Summary

Project ID: 307494
Funded under: FP7-IDEAS-ERC
Country: Germany

Final Report Summary - PCCELL (Physicochemical principles of efficient information processing in biological cells)

The ERC starting grant "pcCell" grant has made fundamental contribution to our ability to understand complex, biological processes by means of computer simulations. Biological function, such as metabolism, oxygen transport through the blood or muscle contraction rely on the ability of biomolecules, such as proteins, to dynamically change their shape, associate and dissociate. These processes "implement" the computational logic of biology which leads to these functions of the body, and likewise dysfunction of these processes may lead to diseases that could be influence by drug treatment. Unfortunately, these processes are fundamentally difficult to observe, as they are too small and too fast for experimental techniques such as microscopy and spectroscopy, but they are on the other hand too complex and require too many simulation timesteps for computer simulations. Even when running the largest supercomputer on earth for an entire year, we could not simulate one second of a single protein molecule with atomic resolution. The ERC project "pcCell" has made methodological groundwork in order to resolve these limitations. On the theoretical side, we have combined ideas from machine learning and quantum physics in order to derive a so-called variational theory that describes how optimal models of molecular dynamics can be extracted from simulation data that may be produced in many short parallel trajectories. We have then developed so-called multi-ensemble methods which use such data in order to reconstruct the dynamics of processes beyond the seconds timescale without surrendering the atomistic resolution. As a highlight, the process of association of two proteins and the dissociation of their long-lived complex on the timescale of hours was simulated in all-atom resolution, revealing all the details and intermediate steps of this process that cannot be directly observed in an experiment. On the biological side, we have teamed up with experts in structural biology, cell biology and super-resolution microscopy in order to reconstruct the spatiotemporal evolution of highly complex processes, such as endocytosis - the process by which a cell uptakes cargo from its outside and transports it into the inside.

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