(316v) Dynamics of DNA Tumbling in Shear and Rotational Flows

DNA dynamics in extensional flows have been carefully studied by many researchers, and a universal relationship between mean fractional extension and the effective Weissenberg number (Wi_eff) defined as the product of Weissenberg number (Wi) and square root of flow type parameter (α), has been found. More recently, Shaqfeh and Chu and co-workers [1] have investigated DNA tumbling dynamics in pure shear flow (α=0). Motivated by these results, the tumbling dynamics of single DNA molecules have been investigated in a range of shear and rotational flows of varying Wi and α. Through Brownian dynamics simulations, we find the tumbling motion obeys a universal scaling law with Wi_eff for strong flows when the Wi_eff is greater than 1.0. However, it was impossible to make a master curve for weak flow using Wi_eff, due to the increasingly strong effects of Brownian motion relative to flow. We propose a new scaling law for this weak flow region, and demonstrate its success in describing the tumbling period. Moreover, there are two kinds of pathway (i.e., folded shape and coiled state) when the molecule tumbles. In shear flow the probability via the folded shape increased with the flow strength as in experiments [2], and vanished when the flow type approaches rotational flow since the chance to stretch diminishes in rotational flow.

1. Teixeira, R.E., H.P. Babcock, E.S.G. Shaqfeh, and S. Chu, 2005. Shear thinning and tumbling dynamics of single polymers in the flow-gradient plane. Macromol. 38: 581-592.

2. Smith, D.E., H.P. Babcock, and S. Chu, 1999. Single-polymer dynamics in steady shear flow. Science 283: 1724-1727.