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We review the mechanism and consequences of the bridging-induced attraction, a generic biophysical principle which underpins some existing models for chromosome organisation in 3-D. This attraction, which was revealed in polymer physics-inspired computer simulations, is a generic clustering tendency arising in multivalent chromatin-binding proteins, and it provides an explanation for the biogenesis of nuclear bodies and transcription factories via microphase separation. Including post-translational modification reactions involving these multivalent proteins can account for the fast dynamics of the ensuing clusters, as is observed via microscopy and photobleaching experiments. The clusters found in simulations also give rise to chromatin domains which conform well with the observation of A/B compartments in HiC experiments.
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
Non-equilibrium phase separating systems with reactions can break time-reversal symmetry (TRS) in two distinct ways. Firstly, the conservative and non-conservative sectors of the dynamics can be governed by incompatible free energies; when both secto
We study the liquid-liquid phase separation (LLPS) of a cell-free transcription-translation (TXTL) system. When the TXTL reaction, composed of a large amount of proteins, is concentrated, the uniformly mixed state becomes unstable and membrane-less d
As a result of nonequilibrium forces, purely repulsive self-propelled particles undergo macrophase separation between a dense and a dilute phase. We present a thorough study of the ordering kinetics of such motility-induced phase separation (MIPS) in
The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and simulations