The effect of confinement on dynamics and rheology of dilute deoxyribose nucleic acid solutions. II. Effective rheology and single chain dynamics

In this study we use the correct entropic spring force in the gap as discussed in Part I including hydrodynamic interactions with the wall to study the effect of confinement on deoxyribose nucleic acid rheology and chain dynamics. We present results for the chain density, the velocity, and the force density of the chains, which change rapidly over the length scale of the chain size. We associate this size and dynamics in these near wall layers to the configurational dispersion layer thickness $δD$ found in polymer shear flow dynamics in the absence of the wall [Chopra and Larson (2002); Hur et al. (2000)]. Though such rapid variation in velocity and density profiles is localized near the wall, its effect on average mechanical properties is global and is felt even at large channel sizes beyond $20 Rg.$ We determine the effective viscosity of the dilute polymer solutions using self-consistent dynamics in these confined geometries and for large gap widths determine how the viscosity asymptotically approaches its bulk value. Finally, we also study the details of individual chain dynamics under confinement: This includes the tumbling motion of a chain in shear/Poiseuille flow, and relaxation from an extended state. We find that the confinement results in two different measures of the chain relaxation time: one shorter and the other longer than the longest relaxation time in the bulk. These two relaxation times are related to dynamics perpendicular and parallel to the walls, respectively. We show that different rheological experiments are sensitive to different specific relaxation times.