A mean-field theory for predicting single polymer collapse induced by neutral crowders

Q Chaboche and G Campos-Villalobos and G Giunta and M Dijkstra and MC Lagomarsino and VF Scolari, SOFT MATTER, 20, 3271-3282 (2024).

DOI: 10.1039/d3sm01522j

Macromolecular crowding can induce the collapse of a single long polymer into a globular form due to depletion forces of entropic nature. This phenomenon has been shown to play a significant role in compacting the genome within the bacterium Escherichia coli into a well-defined region of the cell known as the nucleoid. Motivated by the biological significance of this process, numerous theoretical and computational studies have searched for the primary determinants of the behavior of polymer-crowder phases. However, our understanding of this process remains incomplete and there is debate on a quantitatively unified description. In particular, different simulation studies with explicit crowders have proposed different order parameters as potential predictors for the collapse transition. In this work, we present a comprehensive analysis of published simulation data obtained from different sources. Based on the common behavior we find in this data, we develop a unified phenomenological model that we show to be predictive. Finally, to further validate the accuracy of the model, we conduct new simulations on polymers of various sizes, and investigate the role of jamming of the crowders. Depletion forces arising from molecular crowding compact single polymers. Simulations lead to a unified description. Collapse is governed by the packing fraction of crowders and the ratio of crowder to monomer size, and can be hindered by jamming.

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