Polymer stretch in two-phase microfluidics: Effect of wall wettability

Hu, Ssu Wei; Sheng, Yu Jane; Tsao, Heng Kwong

doi:10.1063/1.4729129

Cited by 12 publications

(9 citation statements)

References 22 publications

(23 reference statements)

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“…The DNA has to migrate into the shrinking water filament and extend across the stagnation point of the water filament before the breakup in order to form the stretched nanostrands across the micropillars. Our simulation technique can be used to investigate the DNA dynamics in not only two-phase flows [52][53][54] but also other complex transient flows [55][56][57] in microfluidic systems. The computational time in this approach could be further reduced when being integrated with high performance parallel computing.…”

Section: Discussionmentioning

confidence: 99%

Simulation of single DNA molecule stretching and immobilization in a de-wetting two-phase flow over micropillar-patterned surface

Liao

Hu²,

Wang³

et al. 2013

Biomicrofluidics

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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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Section: Discussionmentioning

confidence: 99%

Simulation of single DNA molecule stretching and immobilization in a de-wetting two-phase flow over micropillar-patterned surface

Liao

Hu²,

Wang³

et al. 2013

Biomicrofluidics

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“…To implement this DNA barcode system, finding an efficient and reliable method to stretch DNA is crucial. Although different approaches are available, [8][9][10][11][12][13] the most popular choice is to stretch DNA by either flow or electric field in a microfluidic device with a microcontraction. [5][6][7]14,15 Such a device can stretch DNA in a continuous process, and therefore it is capable of providing a very high throughput.…”

Section: Introductionmentioning

confidence: 99%

Stretching DNA by electric field and flow field in microfluidic devices: An experimental validation to the devices designed with computer simulations

Lee

Hsieh

2013

Biomicrofluidics

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We examined the performance of three microfluidic devices for stretching DNA. The first device is a microchannel with a contraction, and the remaining two are the modifications to the first. The modified designs were made with the help of computer simulations [C. C. Hsieh and T. H. Lin, Biomicrofluidics 5(4), 044106 (2011) and C. C. Hsieh, T. H. Lin, and C. D. Huang, Biomicrofluidics 6, 044105 (2012)] and they were optimized for operating with electric field. In our experiments, we first used DC electric field to stretch DNA. However, the experimental results were not even in qualitative agreement with our simulations. More detailed investigation revealed that DNA molecules adopt a globular conformation in high DC field and therefore become more difficult to stretch. Owing to the similarity between flow field and electric field, we turned to use flow field to stretch DNA with the same devices. The evolution patterns of DNA conformation in flow field were found qualitatively the same as our prediction based on electric field. We analyzed the maximum values, the evolution and the distributions of DNA extension at different Deborah number in each device. We found that the shear and the hydrodynamic interaction have significant influence on the performance of the devices. V C 2013 American Institute of Physics.

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“…14 that use coarse-grained molecular models to treat both solvents and biomolecules. For example, DNA as biomolecules are usually modeled by a bead-spring model 15 or a beadrod model 16,17 while the solvents are modeled by mesoscale models such as lattice Boltzmann method, 18 dissipative particles dynamics, 19 and stochastic rotational dynamics. 20 However, the mesoscale simulations are still expensive in computer time, especially when one is more interested in the behavior of biomolecules.…”

Section: Introductionmentioning

confidence: 99%

Simulation guided design of a microfluidic device for electrophoretic stretching of DNA

2012

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We have used Brownian dynamics-finite element method (BD-FEM) to guide the optimization of a microfluidic device designed to stretch DNA for gene mapping. The original design was proposed in our previous study [C. C. Hsieh and T. H. Lin, Biomicrofluidics 5(4), 044106 (2011)] for demonstrating a new pre-conditioning strategy to facilitate DNA stretching through a microcontraction using electrophoresis. In this study, we examine the efficiency of the original device for stretching DNA with different sizes ranging from 48.5 kbp (k-DNA) to 166 kbp (T4-DNA). The efficiency of the device is found to deteriorate with increasing DNA molecular weight. The cause of the efficiency loss is determined by BD-FEM, and a modified design is proposed by drawing an analogy between an electric field and a potential flow. The modified device does not only regain the efficiency for stretching large DNA but also outperforms the original device for stretching small DNA. V C 2012 American Institute of Physics. [http://dx

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Polymer stretch in two-phase microfluidics: Effect of wall wettability

Cited by 12 publications

References 22 publications

Simulation of single DNA molecule stretching and immobilization in a de-wetting two-phase flow over micropillar-patterned surface

Simulation of single DNA molecule stretching and immobilization in a de-wetting two-phase flow over micropillar-patterned surface

Stretching DNA by electric field and flow field in microfluidic devices: An experimental validation to the devices designed with computer simulations

Simulation guided design of a microfluidic device for electrophoretic stretching of DNA

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