(284c) Trapping Rate and Conformation of DNA at a Converging Stagnation Point

Surface stagnation point flow has been suggested as a means to stretch and trap long polymers in microfluidic devices. We numerically investigate the trapping of DNA at a convergent stagnation point created by counter- rotating vortices using a lattice Boltzmann based simulation with a bead-spring model for the polymer. A uniform attractive potential which models DNA-surface affinity or an external field pulls the polymer towards the wall. The trapping rate and the conformation and fluctuation of the trapped DNAs are not sensitive to the attraction potential at a sufficiently high Peclet numbers Pe, where the Peclet number is based on the monomer diffusivity and the vortex size. The trapping rate scales as Pe^(1/3), which is consistent with the mean-field continuum theory for convective surface flux at high Peclet numbers. A well-mixed region is detected at the center of the vortex but a clear diffusion layer exists near the surface with a thickness that obeys the classical scaling of Pe^(-1/3) with respect to the vortex size.

In contrast to earlier studies with DNAs at a stagnation point, we find that the conformation of the DNA is determined during their transport and adsorption onto the stagnation line, rather than hydrodynamic stretching after they have been immobilized. The flow effect and surface affinity determine how many points along the DNA will attach to the surface to produce a particular conformation. Because of this new physics, we find the counter-intuitive result that the coiled state is favored at high flow rates (high Peclet numbers and Weissenberg numbers), which is in direct contrast to the classical theory of De Gennes on coil-stretch transition. Hence the trapping, stretching and conformation of DNAs by a high-Pe converging flow is determined by the competition between the non-specific attractive force and the hydrodynamic forces exerted on the polymers.