Regensburg 2025 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 32: Computational Biophysics II

BP 32.1: Vortrag

Freitag, 21. März 2025, 09:30–09:45, H46

From slabs to cubes: finite size effects in biomolecular simulations — •Rodrigo F. Dillenburg and Martin Girard — Max Planck Institute for Polymer Research, Mainz, Germany

Coarse-grained simulations of intrinsically disordered proteins have become essential to the study of biomolecular condensates. Multiple choices of force fields, simulations techniques and box geometries have been employed in such studies, assuming that results will converge due to the law of large numbers. This assumption is, however, not automatically valid for all systems and needs to be carefully examined to assure the validity of the results. In our work we focused on the choice of box geometry (cubic or slab) and statistical ensemble (canonical or grand-canonical) and its effect on the phase behavior of systems undergoing liquid-liquid phase separation. Our results allow us to estimate if a system can be approximated by the thermodynamic limit or if finite size effects have to be taken into consideration. We are able to derive expressions for these corrections depending on the choice of system and are also able to relate it to condensate properties such as surface tension. Our results provide a rational approach to selecting the most appropriate simulation methods for a given system.

Keywords: Biomolecular Simulations; Liquid-liquid phase separation; Intrinsically disordered proteins; Molecular dynamics; Monte Carlo