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Cellular tissue behavior is a multiscale problem. At the cell level, out of equilibrium, biochemical reactions drive physical cell-cell interactions in a typical active matter process. Cell modeling computer simulations are a robust tool to explore the countless possibilities and test hypotheses. Here, we introduce a two dimensional, extended active matter model for biological cells. A ring of interconnected self-propelled particles represents the cell. Translational modes, rotational modes, and mixtures of these appear as collective states. Using analytic results derived from active Brownian particles, we identify effective characteristic time scales for ballistic and diffusive movements. Finite-size scale investigation shows that the ring diffusion increases linearly with its size when in collective movement. A study on the ring shape reveals that all collective states are present even when bending forces are weak. In that case, when in translational mode, the collective velocity aligns with the largest rings direction in a spontaneous polarization emergence.
We present a generic framework for modelling three-dimensional deformable shells of active matter that captures the orientational dynamics of the active particles and hydrodynamic interactions on the shell and with the surrounding environment. We fin
We present a Brownian dynamics model of driven polymer translocation, in which non-equilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a time-dependent friction. To solve the effective fric
The flagellated bacterium Escherichia coli is increasingly used experimentally as a self-propelled swimmer. To obtain meaningful, quantitative results that are comparable between different laboratories, reproducible protocols are needed to control, `
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to liquid-liqui
Epithelial cell monolayers show remarkable displacement and velocity correlations over distances of ten or more cell sizes that are reminiscent of supercooled liquids and active nematics. We show that many observed features can be described within th