Active Nematic Hydrodynamics and Organization of Chromosomal Matter under Confinement

Chromatin organization and dynamics are affected by nonthermal active processes such as DNA repair, transcription and replication. Experimental observations from displacement correlation spectroscopy have revealed multiscale dynamics of chromatin motion that exhibit fast uncorrelated dynamics at short times, and slow correlated motion at longer timescales. We develop a continuum hydrodynamic theory of chromatin dynamics under confinement that considers extensile/contractile dipolar active forces, and an effective nematic liquid description of chromatin embedded in a passive viscous liquid. The phenomenology of this model is equivalent to a binary fluid mixture containing active and passive fluids inside a cavity. We first discuss the active hydrodynamics of a one component fluid in 2d to illustrate the effects of confinement. Additionally, the effects of anisotropic elastic constants (splay, bend and twist) on the elastic stresses are also demonstrated in 2d using a combination of lattice Boltzmann and finite element methods. Coupled dynamics in terms of a time-dependent velocity, evolution of nematic order parameter and dynamics of scalar concentration field reveal rich phase behavior and long-range correlations consistent with experimental observations.