Conformational dynamics of a flexible polymer in a confined active fluid

Chromatin, the functional form of DNA inside cells, has a form of a complex biopolymer immersed in the nucleoplasmic fluid and confined in the cell nucleus. Recent in vivo experiments have shown that ATP-powered activity drives coherent motions of chromatin inside the nucleus, which persist for several seconds and extend over a few microns. Motivated by these observations, here we consider a long flexible polymeric chain immersed in a suspension of active force dipoles as a simplified model for a chromatin fiber in an active fluid, the nucleoplasm. Using multiscale continuum modeling and immersed boundary simulations, we study how the dynamics and conformations of these confined, densely packed chains are affected by active nucleoplasmic flows and by the details of their microstructure. Our simulations show that extensile activity can increase correlations of coherent motions in time, and these correlations are closely tied to alignment interactions between the chain and the suspension. This work demonstrates how interactions between active and passive structures can lead to large-scale organization in a general setting.