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Technical Briefs

Modeling the Electrophoretic Separation of Short Biological Molecules in Nanofluidic Devices

[+] Author and Article Information
Ghassan N. Fayad

e-mail: gfayad@alum.mit.edu

Nicolas G. Hadjiconstantinou

e-mail: ngh@mit.edu
Department of Mechanical Engineering,
Massachusetts Institute of Technology,
Cambridge, MA 02139

1Corresponding author.

Manuscript received May 5, 2012; final manuscript received October 22, 2012; published online March 19, 2013. Assoc. Editor: Prof. Ali Beskok.

J. Fluids Eng 135(2), 024501 (Mar 19, 2013) (4 pages) Paper No: FE-12-1227; doi: 10.1115/1.4023445 History: Received May 05, 2012; Revised October 22, 2012

Via comparisons with rigid-rod and wormlike-chain Brownian dynamics (BD) simulations and the experimental results of Fu et al. (2006, “Molecular Sieving in Periodic Free-Energy Landscapes Created by Patterned Nanofilter Arrays,” Phys. Rev. Lett., 97(1), p. 018103), we demonstrate that, for the purposes of low-to-medium field electrophoretic separation, sufficiently short biomolecules can be modeled as point particles, with their orientational degrees of freedom accounted for using partition coefficients. This observation is used in the present work to build an efficient BD simulation method. Particular attention is paid to the model's ability to quantitatively capture experimental results using realistic values of all physical parameters.

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Figures

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Fig. 1

Schematic of one period of the nanofilter array

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Fig. 2

Free energy landscape of a charged DNA molecule along the nanofilter channel

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Fig. 4

Comparison between experimental data and the partition-coefficient-based model

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Fig. 3

Comparison between the rigid-rod, WLC and partition-coefficient-based models

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