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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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Figures

Image of FIG. 1.

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FIG. 1.

(a) The geometrical setup of the CFD computation with meshed boundaries. (b) The schematic diagram defining the micropillar dipping depth . (c) The SEM picture of stretched DNA over micropillars and salt crystals on micropillars.

Image of FIG. 2.

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FIG. 2.

Illustration of the particle tracking algorithm. (a) is the reference point located in the control volume and is the tracking point located in the control volume . (b) and are possible interaction points of the tracking vector with the boundaries of . to are normal vectors on the boundaries.

Image of FIG. 3.

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FIG. 3.

The formed droplet volume on the top of the first micropillar after the retreat of water under different initial micropillar dipping depths in the simulation at m/s.

Image of FIG. 4.

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FIG. 4.

Time series of free surface profile of (a) proper-dipping ( m) and (b) over-dipping ( m) at m/s.

Image of FIG. 5.

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FIG. 5.

The time series of the flow field for m and m/s. The velocity vectors and dynamic pressure contours at the de-wetting free surface are plotted.

Image of FIG. 6.

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FIG. 6.

The time series of DNA dynamics in the de-wetting flow ( m and m/s). (a)-(f) Five instantaneous DNA conformations in yellow (Y), blue (B), red (R), green (G), and purple (P). (g) Instantaneous DNA conformations after the formation of the second droplet along with DNA center-of-mass trajectories starting from (a).

Image of FIG. 7.

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FIG. 7.

Temporal profiles of chain extension for five DNAs shown in Fig. 6 .

Image of FIG. 8.

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FIG. 8.

The interplay between the flow and the stretching DNA ( m and m/s). (a) Free surface profiles and DNA instantaneous configurations at four specific moments. DNA conformations are marked by square (□), circle (○), diamond (⋄), and delta (Δ). (b) Extracted -component flow velocities at DNA beads versus bead -coordinates. (c) Extracted -component velocity gradients in the -direction versus bead -coordinates.

Image of FIG. 9.

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FIG. 9.

Time series of simulated DNA configurations ( m and m/s). Five layers of DNAs initially locate over the first pillar from the left that are plotted in gray scale. From bottom to top, each layer is named as black-1 (B-1), gray-2 (G-2), white-3 (W-3), black-4 (B-4), and gray-5 (G-5), respectively. In each layer, there are 36 DNA chains with a constant -coordinate. From the pillar top wall, each layer of DNA is assigned every 0.5 m.

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/content/aip/journal/bmf/7/3/10.1063/1.4807462
2013-05-21
2014-04-19

Abstract

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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Scitation: Simulation of single DNA molecule stretching and immobilization in a de-wetting two-phase flow over micropillar-patterned surface
http://aip.metastore.ingenta.com/content/aip/journal/bmf/7/3/10.1063/1.4807462
10.1063/1.4807462
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