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BP: Fachverband Biologische Physik
BP 4: Computational Biophysics II
BP 4.5: Vortrag
Montag, 9. März 2026, 16:15–16:30, BAR/SCHÖ
Grand canonical simulations of micellization in intrinsically disordered proteins — •Rodrigo F. Dillenburg1, 2, Martin Girard1, 5, Friederike Schmid2, and Edward A. Lemke3, 4 — 1Max Planck Institute for Polymer Research, Mainz, Germany — 2Institute of Physics, Johannes Gutenberg University, Mainz, Germany — 3Biocenter, Johannes Gutenberg University, Mainz, Germany — 4Institute of Molecular Biology, Mainz, Germany — 5Institute for quantitative and computational biosciences, Mainz, Germany
Molecular dynamics (MD) simulations with coarse-grained force fields have been the gold standard in the computational modeling of liquid-liquid phase separation (LLPS) and biomolecular condensates. While much attention has been focused on large droplets, very little is known about the formation of microphases, such as micelles, in such systems. There is evidence that such assemblies arise from intrinsically disordered proteins (IDPs) with a block co-polymer architecture. However, due to their finite size they are highly sensitive to the periodic boundary conditions of the simulation box. The commonly implemented slab geometry is thus unfit to tackle such systems. To overcome this we have implemented a semi-grand canonical monte carlo (SGCMC) algorithm that significantly speeds-up MD simulations. Our implementation is compatible with implicit solvent 1-bead-per-amino acid force fields such as Calvados and HPS. We show that such approach allows one to run simulations efficiently in a cubic box, at very low densities typical of biological systems. We also highlight the advantages of SGCMC in simulating micelles compared to regular MD.
Keywords: biomolecular condensates; intrinsically disordered proteins; monte carlo; molecular dynamics