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Team:Alberta/References/Publications/Stochastic simulations of DNA in flow: dynamics and the effects of hydrodynamic interactions
From 2009.igem.org
Richard M. Jendrejack, Juan J. de Pablo and Michael D. Graham
JOURNAL OF CHEMICAL PHYSICS VOLUME 116, NUMBER 17
Abstract: We present a fully parametrized bead–spring chain model for stained l-phage DNA. The model
accounts for the finite extensibility of the molecule, excluded volume effects, and fluctuating
hydrodynamic interactions ~HI!. Parameters are determined from equilibrium experimental data
for 21 mm stained l-phage DNA, and are shown to quantitatively predict the non-equilibrium
behavior of the molecule. The model is then used to predict the equilibrium and nonequilibrium
behavior of DNA molecules up to 126 mm. In particular, the HI model gives results that are in
quantitative agreement with experimental diffusivity data over a wide range of molecular weights.
When the bead friction coefficient is fit to the experimental relaxation time at a particular molecular
weight, the stretch in shear and extensional flows is adequately predicted by either a free-draining
or HI model at that molecular weight, although the fitted bead friction coefficients for the two
models differ significantly. In shear flow, we find two regimes at high shear rate ( g ˙ ) that follow
different scaling behavior. In the first, the viscosity and first normal stress coefficient scale roughly
as g ˙ 26/11 and g ˙ 214/11, respectively. At higher shear rates, these become g ˙ 22/3 and g ˙ 24/3. These
regimes are found for both free-draining and HI models and can be understood based on scaling
arguments for the diffusion of chain ends.
Link: University of Wisconsin
