Brownian dynamics simulations of a DNA molecule in an extensional flow field

The unraveling dynamics of long, isolated, molecules of DNA subjected to an extensional flow in a crossed-slot device [T. T. Perkins, D. E. Smith, and S. Chu, "Single polymer dynamics in an elongational flow," Science 276, 20 16-2021 (1997); D. E. Smith and S. Chu, "Response of Flexible Polymers to a Sudden Elongational Flow," Science 281, 1335-1340 (1998)] are predicted by Brownian dynamics simulations using measured elastic and viscous propertie s of the DNA as the only inputs. Quantitative agreement is obtained both in the percentages of various unraveling states, such as "folds," "kinks," "d umbbells," half-dumbbells," and "coils," and in the ensemble-averaged stret ch and rate of stretch. Under fast flows (De greater than or similar to 10) , unraveling is initially nearly affine, but for fractional stretch greater than approximate to 1/3, stretching is delayed to an extent that varies wi dely from molecule to molecule by flow-induced folded states, which are far -from-equilibrium kinetic hindrances not predicted by dumbbell models. From the computer simulations, the source of the high molecule-to-molecule hete rogeneity in the experiments is traced to variability in the initial polyme r configuration, which sets the unraveling path the molecule must take at D e greater than or similar to 10. Formation of folds and kinks during unrave ling can be predicted fairly reliably just by examining the initial state. The high-De unraveling behavior is consistent with the predictions of one-d imensional "kink dynamics" simulations. (C) 1999 The Society of Rheology. [ S0148-6055(99)00502-7].