283998 Molecular Dynamics Study of Polymer Separation Using a Nanofluidic Staircase

Thursday, November 1, 2012: 10:59 AM
411 (Convention Center )
Frederick R. Phelan Jr., Materials Science and Engineering Division, NIST, Gaithersburg, MD and Christopher Forrey, Polymers Division, NIST, Gaithersburg, MD

The diffusive behavior of isolated polymer chains in a nanofluidic staircase has recently been studied experimentally [1–5] and by simulation [6]. Chains are observed to exhibit spontaneous 1-D biased diffusion from regions of high to low confinement, without the use of external forces, under conditions where the local confinement lies in either the Odijk or de Gennes regimes. The nanostaircase has potential for a number of applications in polymer measurement science and transport, an important one of which could be separations. In this work, we examine polymer separation in the nanofluidic staircase using the molecular dynamics simulation software LAMMPS [7], [8]. Length based separations of linear polymers as applicable to DNA separations are the main topic of the study, but the effect of more complex architectures such as branching and star-like polymers more common in commodity and specialty polymers are also examined.


[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,” Lab on a Chip, vol. 12, no. 6, pp. 1174–1182, 2012.

[3]   E. A. Strychalski, J. Geist, M. Gaitan, L. E. Locascio, and S. M. Stavis, “Quantitative measurements of the size scaling of linear and circular DNA in nanofluidic slitlike confinement,” Macromolecules, vol. 45, pp. 1602–1611, 2012.

[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 Chip, 2010.

[6]   Frederick R. Phelan Jr., Christopher Forrey, Lilian Johnson, Samuel M. Stavis, Jon Geist, and Elizabeth A. Strychalski, “The Nanofluidic Staircase: A Brownian Motor for Polymer Characterization and Transport,” in preparation, p. 2012.

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

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

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