Effective two-dimensional model does not account for geometry sensing by self-organized proteins patterns - Supplementary document

Here we provide a thorough discussion of the model for Min protein dynamics proposed by Schweizer et al. [11]. The manuscript serves as supplementary document for our letter to the editor to appear in PNAS. Our analysis is based on the original COMSOL simulation files that were used for the publication. We show that all computational data in Schweizer et al. rely on exploitation of simulation artifacts and various unmentioned modifications of model parameters that strikingly contradict the experimental setup and experimental data. We find that the model neither accounts for MinE membrane interactions nor for any observed MinDE protein patterns. All conclusions drawn from the computational model are void. There is no evidence at all that persistent MinE membrane binding has any role in geometry sensing.

Spontaneous Unknotting of a Polymer Confined in a Nanochannel

We study the dynamics of a knot in a semiflexible polymer confined to a narrow channel of width comparable to the polymers persistence length. Using a combination of Brownian dynamics simulations and a coarse-grained stochastic model, we characterize the coupled dynamics of knot size variation and knot diffusion along the polymer, which ultimately leads to spontaneous unknotting. We find that the knot grows to macroscopic size before disappearing. Interestingly, an external force applied to the ends of the confined polymer speeds up spontaneous unknotting.