We computationally investigate the transition from rigid to flowing states in dense assemblies of self-propelled particles. Such theoretical representations of biological assemblies have yielded tremendous insight into collective behaviour across many scales, from bird flocks, through bacterial colonies, tissue organisation and including sub-cellular assemblies such as the cytoskeleton. Of particular interest to us are observations of dramatic changes in the dynamics of chromatin within cell nuclei, understood to undelie changes in biological state and function. Dynamics in this context is controlled by the strength and temporal persistence of out-of-equilibrium mechanical perturbations, as well as the geometry of confinement. Evidence of a transition from rigid to flowing states across a critical perturbation strength, strongly reminiscent of yielding in externally deformed amorphous solids, motivates us to explore this analogy, and to investigate the role of persistence time and confinement geometry on the transition.
Collective behaviour in dense assemblies of self-propelled active particles occurs in a wide range of biological phenomena, including dynamical transitions of cellular and sub-cellular biological assemblies such as the cytoskeleton and the cell nucleus. Here, motivated by observations of mechanically induced changes in the dynamics of such systems and the apparent role of confinement geometry, we show that the fluidization transition broadly resembles yielding in amorphous solids, which is consistent with recent suggestions. More specifically, however, we find that a detailed analogy holds with the yielding transition under cyclic shear deformation, for large but finite persistence times. The fluidization transition is accompanied by driving induced annealing, strong dependence on the initial state of the system, a divergence of time scales to reach steady states, and a discontinuous onset of diffusive motion. We also observe a striking dependence of the transition on persistence times and on the nature of the confinement. Collectively, our results have implications for biological assemblies in confined geometries, including epigenetic cell state transitions.
Contact
Paul Scherrer Institut
Dr. Yagyik Goswami
Forschungsstrasse 111
5232 Villigen PSI