Dynamics of DNA Polymers in Post Arrays:  Comparison of Single Molecule Experiments and Simulations

Teclemariam, Nerayo P; Beck, Victor A.; Shaqfeh, Eric S. G.; Müller, Susan

doi:10.1021/ma062892e

Cited by 33 publications

(33 citation statements)

References 53 publications

(137 reference statements)

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“…Additionally, other Brownian dynamics simulation methods have had success reproducing the behavior of DNA being hydrodynamically driven through post arrays. 14 …”

Section: A Interactions With the Post Arraymentioning

confidence: 99%

“…10,11 Collisions with microfabricated obstacles have also been shown to linearize DNA. [12][13][14] But a very practical method for simple, inexpensive, high-throughput devices is using field gradients to deform the molecules. 15,16 In DLA devices, the molecules are typically stretched by field gradients in microcontractions.…”

Section: Introductionmentioning

confidence: 99%

“…[26][27][28] Several qualitatively different types of hooks have been identified, 25 and their stretching and unhooking dynamics have been investigated. 25,28 The effect of large arrays of posts has been considered as well, with studies focussed on the start-up behavior of the molecules as they enter the array 14 and their subsequent steady-state behavior. [29][30][31] Placing a post array just before the contraction to preconfigure the molecules is also advantageous because the resulting device is simple to fabricate, reusable, and easily scaled.…”

Section: Introductionmentioning

confidence: 99%

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Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning

Trahan

Doyle

2009

Biomicrofluidics

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Recently our group has reported experiments using an obstacle array to precondition the conformations of DNA molecules to facilitate their stretch in a microcontraction. Based upon previous successes simulating electrophoretic stretching in microcontractions without obstacles, we use our simulation model to study the deformation of DNA chains in a microcontraction preceded by an array of cylindrical obstacles. We compare our data to the experimental results and find good qualitative, and even quantitative, agreement concerning the behavior of the chains in the array; however, the simulations overpredict the mean stretch of the chains as they leave the contraction. We examine the amount of stretch gained between leaving the array and reaching the end of the contraction and speculate that the differences seen are caused by nonlinear electrokinetic effects that become important in the contraction due to a combination of field gradients and high field strengths.

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“…Additionally, other Brownian dynamics simulation methods have had success reproducing the behavior of DNA being hydrodynamically driven through post arrays. 14 …”

Section: A Interactions With the Post Arraymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning

Trahan

Doyle

2009

Biomicrofluidics

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“…Hence, in lab-on-a-chip systems, solutions of macromolecules may exhibit non-Newtonian behavior even at dilute concentrations due to the converging and diverging flow regions of canonical microfluidic components. A deeper understanding of the fundamental physics of macromolecular flow in the micro-regime will enable optimization of lab-on-a-chip device designs, such as advanced biosensors using single molecule identification [16,17].…”

Section: Introductionmentioning

confidence: 99%

Direct measurements of viscoelastic flows of DNA in a 2:1 abrupt planar micro-contraction

Gulati

Müller

Liepmann

2008

Journal of Non-Newtonian Fluid Mechanics

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“…They concluded that disordered arrays in strong electric fields are optimal conditions for separation [18]. Later, calculations of inhomogeneous electric field values used with post arrays were performed by a commercial FEM solver for more accurate calculations [94]. BEM was also applied to electric field calculations in post arrays [13] …”

Section: Arrays Of Postsmentioning

confidence: 99%

Computational Studies of DNA Separations in Micro-Fabricated Devices: Review of General Approaches and Recent Applications

Monjezi¹,

Behdani²,

Palaniappan³

et al. 2017

ACES

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DNA separation techniques have drawn attention because of their uses in applications such as gene analysis and manipulation. There have been many studies utilizing micro-fabricated devices for faster and more efficient separations than traditional methods using gel electrophoresis. Although many experimental studies have presented various new devices and methods, computational studies have played a pivotal role in this development by identifying separation mechanisms and by finding optimal designs for efficient separation conditions. The simulation of DNA separation methods in micro-fabricated devices requires the correct capture of the dynamics and the structure of a single polymer molecule that is being affected by an applied flow field or an electric field in complex geometries. In this work, we summarize the polymer models (the bead-spring model, the bead-rod model, the slender-body model, and the touching-bead model) and the methods, focusing on Brownian dynamics simulation, used to calculate inhomogeneous fields taking into consideration complex boundaries (the finite element method, the boundary element method, the lattice-Boltzmann method, and the dissipative particle dynamics simulation). The worm-like chain model (adapted from the bead-spring model) combined with the finite element method has been most commonly used but other models have shown more efficient and accurate results. We also review the applications of these simulation approaches in various separation methods and devices: gel electrophoresis, post arrays, capillary electrophoresis, microchannel flows, entropic traps, nanopores, and rotational flows. As more complicated geometries are involved in new devices, more rigorous models (such as incorporating the hydrodynamic interactions of DNA with solid boundaries) that can correctly capture the dynamic behaviors of DNA in such devices are needed.

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Dynamics of DNA Polymers in Post Arrays: Comparison of Single Molecule Experiments and Simulations

Cited by 33 publications

References 53 publications

Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning

Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning

Direct measurements of viscoelastic flows of DNA in a 2:1 abrupt planar micro-contraction

Computational Studies of DNA Separations in Micro-Fabricated Devices: Review of General Approaches and Recent Applications

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