Geometric and topological potentials driving self-assembly

Date

Jan 22, 2026

Time

3:00 PM - 4:00 PM

Speaker

Ivan Spirandelli

Affiliation

University of Potsdam

Language

en

Main Topic

Biologie

Host

Local Organisers: Nikola Sadovek, Maximilian Wiesmann, Giulio Zucal

Description

The assembly of molecular building blocks into functional complexes is central to biology and materials science. We investigate the generative and predictive capabilities of a geometric model, the morphometric approach to solvation free energy, in a simulation setting. We show that biologically relevant structural motifs appear for generic building blocks under geometric optimization. Applying the same method to the self-assembly of protein subunits, we show that geometric fit alone predicts the native nucleation states of various systems. To overcome limitations in efficiency of the geometric model caused by its short-range nature, we introduce a novel energetic bias based on persistent homology. By combining these shape-based potentials we obtain an efficient simulation strategy increasing success rates by an order of magnitude, or enabling assembly in the first place, when compared to the geometric model alone. Integrating topological descriptions into energy functions offers a general strategy for overcoming kinetic barriers in molecular simulations, with potential applications in drug design, material development, and the study of complex self-assembly processes.

Last modified: Jan 22, 2026, 7:38:59 AM