(650h) Molecular Dynamics Study of Polymer Separation Using a Nanofluidic Staircase

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.

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,? 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].