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Behavior of individual DNA molecules in free-surface flows


Top: Visualization of individual DNA molecules in a small-scale coating flow: DNA molecule undergoing oscillations from extended to coiled conformation (yoyo motion) for local Wi = 361. The snapshots are at intervals of 1/30 s. Bottom: Multiscale simulation of dilute DNA in a roll-knife coating flow: Images of a single chain of 11 beads moving along a streamline through x = 0, y = - 3.3 μm. Tracking the end beads shows the change in the orientation of the molecule as the chain flows.

By using techniques developed by Chu and co-workers, we have been able to visualize individual DNA molecules in a scaled-down roll-knife coating flow, offering insight for the first time on how polymer molecules behave in complex free surface flows. We modeled the flow with a combination of finite element, Brownian dynamics (BD) along streamlines, and successive-fine-graining (to extract information on polymer configuration that is independent of the number of beads used in the simulations). Both in experiments and simulations, we observed that DNA molecules stretch to their full contour length in certain regions of the flow. This observation led to the counter-intuitive realization that coating flows often introduce interference of length scales between the macroscopic, process length scales (e.g., the coating gap or film thickness) and molecular length scales (the molecule contour length), which can be comparable.