The concept of exploiting molecular propulsion mechanisms for the DNA separation technology is relatively new. Some work already exists in the area of utilizing micron or submicron fluidic devices to enhance DNA separation techniques. Most of these techniques utilize electric fields or electroosmotic flow to induce movement in these macromolecules, but rely on differences in molecular potential energy to induce separation.

The traditional approach to modeling macromolecular behavior has been molecular dynamic simulations. However these techniques are computationally time intensive, and therefore limited to relatively small molecular lengths. Essentially molecular dynamic simulations compute the attraction and repulsion forces between atoms as a function of distance. However, this complex and time consuming step can actually be eliminated by simulating the interactions between simple beams. Additionally, because the molecules of interest (i.e. DNA) are large, but fundamentally composed of subunits (e.g., nucleotide), the molecule can be treated as small units bonded into long chains. This kind of chain network can be modeled as an equivalent beam system possessing either elastic or hyperelastic material properties. The work presented here uses a model molecule: Carbonic Anhydrase (CA) that is considerably smaller than DNA, but is well characterized. The molecule was computationally reconstructed by bonding its backbone carbon atoms to demonstrate the ability of this technique to capture the impact of conformation on stored energy and relate this to the well understood phenomena of molecular motion through a converging nozzle throat, as shown in the figure below.

Reference

Yi, Y. B. and Lengsfeld, C. S., 2006, Mechanical Modeling of Carbonic Anhydrase Motion in Simple Channels, Journal of Applied Physics, Vol. 100, No.014701.

Lentz, Y., Worden, L., Anchordoquy, T.A. and Lengsfeld, C.S., 2005, Impact of jet nebulization of plasmid DNA: degradation mechanism and mitigation methods. J. of Aerosol Science, Vol. 36, pp. 973-990.

Turner, S.W.P., Cabodi, M. and Craighead, H.G., 2002, Confinement-induced entropic recoil of single DNA molecules in nanofluidic structure. Phys. Rev. Let., 88(12), No. 128103.