DNA Molecules in Microfluidic Oscillatory Flow

Chen, Yeng-Long; Graham, Michael D.; Pablo, Juan J. de; Jo, Kyubong; Schwartz, David C.

doi:10.1021/ma050238d

Cited by 62 publications

(89 citation statements)

References 43 publications

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“…We speculate that the depletion of DNA near the wall is the manifestation of the "shear-induced migration" phenomenon. 31,32 It is well known that DNA (or long chain polymer) molecules in strong pressure driven flow will migrate away from the solid boundary and form a depletion layer 33,34 due to the hydrodynamic interaction between extended DNA and the boundary. 31,35,36 The thickness of the depletion layer in bulk condition was shown to grow with the shear rate 31,33,37 and can be much larger than the radius of gyration of DNA.…”

Section: Resultsmentioning

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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Section: Resultsmentioning

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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“…58 More interestingly, the simulations predict that during pressure-driven flow in a channel, the molecules will tend to migrate toward the centerline, forming depletion layers that are much larger than the radius of gyration of the molecules. 11,12,59 The goal of the present work is to complement those detailed simulations with theoretical results that provide a more fundamental understanding of the migration phenomenon.…”

Section: Introductionmentioning

confidence: 99%

Theory of shear-induced migration in dilute polymer solutions near solid boundaries

2005

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In this work, a continuum theory is developed for the behavior of flowing dilute polymer solutions near solid surfaces, using a bead-spring dumbbell model of the dissolved polymer chains. Hydrodynamic interactions between the chains and the wall lead to migration away from the wall in shear flow. At steady state, this hydrodynamic effect is balanced by molecular diffusion; an analytical expression for the resulting concentration profile is derived. It is shown that the depletion layer thickness is determined by the normal stresses that develop in flow and can be much larger than the size of the polymer molecule. The transient development of this depletion layer is also studied, as well as the spatial development downstream from an entrance. Numerical and similarity solutions in these cases show that the developing concentration profile generally displays a maximum at an intermediate distance from the wall.

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“…As a computationally efficient explicitsolvent method, CGH-MD is potentially useful for simulating systems of large number of water particles to complement more rigorous methods. It may also be applied to the study of polar and hydrophobic effects, 13 nonuniformly distributed electrostatic interactions, and the effects associated with bound and sequestered water molecules 12,13 in various bio-macromolecular and nanofluidic systems such as the electrophoresis of DNA, 36 proteins, 60 viral particles, and complexes 61 in nanofluidic, 34,58,59,62 microfluidic, 63,64 and microstructure array 16,65 systems. …”

Section: Ion Distribution Patternmentioning

confidence: 99%

Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse‐grained hybrid molecular dynamics approach

Wang

Liu

et al. 2008

J Comput Chem

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Simulation of DNA electrophoresis facilitates the design of DNA separation devices. Various methods have been explored for simulating DNA electrophoresis and other processes using implicit and explicit solvent models. Explicit solvent models are highly desired but their applications may be limited by high computing cost in simulating large number of solvent particles. In this work, a coarse-grained hybrid molecular dynamics (CGH-MD) approach was introduced for simulating DNA electrophoresis in explicit solvent of large number of solvent particles. CGH-MD was tested in the simulation of a polymer solution and computation of nonuniform charge distribution in a cylindrical nanotube, which shows good agreement with observations and those of more rigorous computational methods at a significantly lower computing cost than other explicit-solvent methods. CGH-MD was further applied to the simulation of DNA electrophoresis in a polymer solution and in a well-studied nanofluidic device. Simulation results are consistent with observations and reported simulation results, suggesting that CGH-MD is potentially useful for studying electrophoresis of macromolecules and assemblies in nanofluidic, microfluidic, and microstructure array systems that involve extremely large number of solvent particles, nonuniformly distributed electrostatic interactions, bound and sequestered water molecules.

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DNA Molecules in Microfluidic Oscillatory Flow

Cited by 62 publications

References 43 publications

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

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

Theory of shear-induced migration in dilute polymer solutions near solid boundaries

Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse‐grained hybrid molecular dynamics approach

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