(142bc) On the Persistence Length Dependence of Single Molecule Dynamics in Shear Flow

The dynamics of single-molecules in shear flow has been an active area of research due to the advancements in the field of fluorescence microscopy, which provides a means to directly visualize polymer configurations. Several researchers have studied the dynamics of free and tethered polymers in shear flow using theory, experiments, and numerical simulations (Smith et al (1999), Hur et al. (2000), Schroeder et al (2005), Doyle et al. (2000)). Most of these studies were performed for flexible polymers with a large number of degrees of freedom—i.e. lambda-DNA with approximately 150 Kuhn lengths—and, all studies displayed complex dynamic conformational behavior. For example, the tumbling of a lambda-DNA in free shear flow shows rather complicated dynamics in which different parts of the DNA can undergo independent tumbling events simultaneously. On the other end of the spectrum, a stiff rod in free shear flow goes through a distinguishable tumbling motion, allowing one to precisely measure the mean tumbling times which can be directly compared to theory or simulations. Although considerable research has been devoted to understanding the dynamics of a flexible polymer in shear flow, rather few studies have considered how the shear dynamics of a polymer is affected as one changes the flexibility moving from the rod-like to the flexible limit.

Recently, Guihua et al. (2011) examined the extensional behavior of a series of tethered DNA chains with different lengths (17.3 μm, 7.8 μm, and 4.2 μm) under shear flow. Although even the smallest of these DNA chains lies in the flexible range with 40 Kuhn-lengths, the fractional extensional data for three chain lengths was found to depend intrinsically on the number of Kuhn steps as an independent parameter. More recently, Harasim et al. (personal communication) have visualized the dynamics of semiflexible actin filaments having persistence length 320 times that of lambda-DNA. They reported the tumbling times for different lengths of actin filaments with varying flow strengths, and also proposed an analytical model. In this talk, we use Brownian dynamics to simulate the experimental data from both Guihua et al. (2011) and Harasim et al., spanning the flexible to the stiff polymer regime. We use these simulations to examine the stochastic nature of tumbling dynamics and relate it to the mean fractional extension in free shear flow. In addition, we also study tethered single molecules in shear flow and analyze the effect of stiffness on the scaling behavior of this different dynamical system. We ultimately compare the physical mechanisms of tumbling and length fluctuations between the free and tethered polymers systems over the broad range of stiffness.