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Interacting-Particle Reaction-Diffusion Simulations: Endocytosis

Presented by: 
Frank Noe Freie Universität Berlin
Tuesday 21st June 2016 - 11:00 to 11:45
INI Seminar Room 1
We have introduced interacting-particle reaction-diffusion (iPRD) simulations as a hybrid between molecular dynamics simulations and particle-based reaction-diffusion simulations. iPRD is a suitable modeling framework for many cellular signaling processes, especially such processes involving dense protein mixtures, supramolecular architectures or protein scaffolds at membranes. I will introduce to the theory behind iPRD and present computational algorithms.

One of our key application areas is clathrin-mediated endocytosis in neurons, and I will briefly elude to simulations of protein recruitment to clathrin-coated pits and the interplay between membrane-associated proteins and membrane deformation in endocytosis.

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