Entropophoresis of a Polymer Chain Confined In a Nanofluidic Staircase

Entropophoresis of a Polymer Chain Confined in a Nanofluidic Staircase[*]

Frederick R. Phelan Jr.[†] ¹, Christopher Forrey², Samuel M. Stavis³, Jon Geist³, and Elizabeth A. Strychalski⁴

¹Polymers Division, NIST, Gaithersburg, MD 20899

²Center for Devices and Radiological Health, FDA, Silver Spring, MD 20993

³Semiconductor Electronics Division, NIST, Gaithersburg, MD 20899

⁴Biochemical Sciences Division, Division, NIST, Gaithersburg, MD 20899

  Abstract

Mass transfer by diffusion can be alternatively thought of as net molecular transport driven along an entropy gradient, known as entropophoresis. Entropophoresis has recently been observed experimentally as a transport mechanism for single chain -phage DNA confined in a nanofluidic staircase [1-5], a device which consists of a collection of nanoslits of increasing depth arranged in step-like fashion along the length of a channel. A DNA molecule placed in the highly confined region of the geometry and allowed to freely diffuse exhibits a net 1-D drift velocity down the staircase direction, using only changes in entropy due to confinement (i.e., not external forces) to generate the motion.

In this work, we examine the diffusive motion of a coarse-grained polymer chain confined in the nanofluidic staircase using the molecular dynamics simulation software LAMMPS [6-7] for the regime , where is the local gap thickness quantifying the degree of confinement at each step position (i.e., step depth), is the Kuhn length, and  is the polymer radius of gyration. Simulation results show that a net 1-D drift velocity is spontaneously generated under conditions where the differential change in entropic free energy of the chain from step to step [8] is greater than the thermal energy available for diffusion. The steps thus effectively function as a Brownian ratchet by retarding the diffusive motion of the polymer in the direction of greater confinement. The drift velocity down the staircase direction is independent of step height at high confinement, but slows as the local gap thickness approaches. The effect of chain stiffness and the polymer contour length/step size ratio are also considered.

References

[1]  E. A. Strychalski, S. M. Stavis, M. Gaitan, and L. E. Locascio, “Nanoslinky: DNA Entropophoresis Down A Nanofluidic Staircase,” presented at the The 14th International Conference on Miniaturized Systems for Chemistry and Life Sciences, Groningen, The Netherlands, 2010, pp. 2071-2073.

[2]  S. M. Stavis, J. Geist, M. Gaitan, L. E. Locascio, and E. A. Strychalski, “DNA molecules descending a nanofluidic staircase by entropophoresis,” Submitted, 2011.

[3]  E. A. Strychalski, J. Geist, M. Gaitan, L. E. Locascio, and S. M. Stavis, “Multiplexed size measurements of confined DNA molecules by entropophoresis down a nanofluidic staircase,” Submitted, 2011.

[4]  S. M. Stavis, E. A. Strychalski, and M. Gaitan, “Nanofluidic structures with complex three-dimensional surfaces,” Nanotechnology, vol. 20, no. 16, p. 165302, Apr. 2009.

[5]  S. M. Stavis, J. Geist, and M. Gaitan, “Separation and metrology of nanoparticles by nanofluidic size exclusion,” Lab on a Chip, 2010.

[6]  S. Plimpton, “Fast Parallel Algorithms for Short-Range Molecular Dynamics,” Journal of Computational Physics, vol. 117, no. 1, pp. 1-19, Mar. 1995.

[7]  “LAMMPS Molecular Dynamics Simulator.” [Online]. Available: http://lammps.sandia.gov/. [Accessed: 02-May-2011].

[8]  P. G. de Gennes, Scaling Concepts in Polymer Physics. Ithaca: Cornell University Press, 1979.

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[*] Official contribution of the National Institute of Standards and Technology; not subject to copyright in the United States.

[†] Corresponding author: NIST, 100 Bureau Dr., STOP 8542, Gaithersburg, MD 20899; (301) 975-6761; Fax: (301) 975-4924; frederick.phelan@nist.gov