Implications of different membrane compartmentalization models in particle-based in silico studies

Studying membrane dynamics is important to understand the cellular response to environmental stimuli. A decisive spatial characteristic of the plasma membrane is its compartmental structure created by the actin-based membrane-skeleton (fences) and anchored transmembrane proteins (pickets). Particle-based reaction-diffusion simulation of the membrane offers a suitable temporal and spatial resolution to analyse its spatially heterogeneous and stochastic dynamics. Fences have been modelled via hop probabilities, potentials or explicit picket fences. Our study analyses the different approaches' constraints and their impact on simulation results and performance. Each of the methods comes with its own constraints; the picket fences require small timesteps, potential fences might induce a bias in diffusion in crowded systems, and probabilistic fences, in addition to carefully scaling the probability with the timesteps, induce higher computational costs for each propagation step.

Automated summary

Studying membrane dynamics is crucial for understanding cellular response to environmental stimuli. The plasma membrane's compartmental structure, created by actin-based membrane-skeleton and anchored transmembrane proteins, plays an important role in this process. Particle-based reaction-diffusion simulation offers a suitable approach for analyzing the membrane's stochastic and spatially heterogeneous dynamics. However, different methods for modeling the compartmental structure have their own constraints and impact on simulation results and performance.