To model the dynamics of highly confined biopolymers, we consider semi-flexible polymer dynamics in the bulk and in micro and nanochannels. In this model, the bending energy between polymer segments is accounted for, giving the polymer a finite persistence length. On a length scale smaller than the persistence length, the polymer conformation and dynamics are rod-like. On a length scale much larger than the persistence length, the polymer conformation and dynamics are coil-like.
1. In bulk solution, we investigate how DNA topology and connectivity affects its dynamics. We investigated the dynamics of polymer chains that are closed at the chain end (circular polymer), near mid-chain, and at the quarter chain position. Of these different chain topology, we found that the partially-looped chain molecules have the fastest diffusivity and the smallest average size. This is due to the fact that the chain tails are able to fold into the chain loops in partially-looped chains, allowing these molecules to have smaller average size than even the circular chains. [1]
2. In microchannels, we investigate how to control the location and conformation of DNA using different flow and channel designs. DNA molecules migrate away from the channel walls during flow due to near wall hydrodynamic interactions. This effect causes the DNA molecules to have a faster average velocity than the average fluid flow velocity. In addition, longer DNA molecules exhibit stronger migration effect, allowing for the possiblity of DNA separation by flow. [2,3]
3. In nanochannels, DNA dynamics and conformation are strongly affected by the confinement as they are confined in sub-Kuhn length channels. The competition between bending and conformational entropy leads to channel size-dependent modes of DNA dynamics to become dominant. [4]
[1] J.F. Chang and Y.-L. Chen, manuscript in preparation.
[2] R.M. Jendrejack, M.D. Graham, and J.J. de Pablo, Physical Review Letters, 91, 038201 (2003).
[3] Y.-L. Chen, K. Jo, D.C. Schwartz, M.D. Graham, and J.J. de Pablo, Macromolecules, 38, 6680 (2005).
[4] A. Grigoryan, J.F. Chang, and Y.-L. Chen, manuscript in preparation.