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Simulation of single DNA molecule stretching and immobilization in a de-wetting two-phase flow over micropillar-patterned surface
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52.Our dimensionless relaxation will be 0.48 after transformed to the bead-spring model used in Ref. 3 where 19 beads were used for a 20.5 μm long DNA and their dimensionless relaxation time is 0.52. During the transformation, we use ξDNA = Nbξ where ξDNA the DNA drag coefficient in bulk solution and Nb the number of beads. The difference may result from the difference in contour length (19.8 μm in this study).
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We investigate single DNA stretching dynamics in a de-wetting flow over micropillars using Brownian dynamics simulation. The Brownian dynamics simulation is coupled with transient flow field computation through a numerical particle tracking algorithm. The droplet formation on the top of the micropillar during the de-wetting process creates a flow pattern that allows DNA to stretch across the micropillars. It is found that DNA nanowire forms if DNA molecules could extend across the stagnation point inside the connecting water filament before its breakup. It also shows that DNA locates closer to the top wall of the micropillar has higher chance to enter the flow pattern of droplet formation and thus has higher chance to be stretched across the micropillars. Our simulation tool has the potential to become a design tool for DNA manipulation in complex biomicrofluidic devices.
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