Slip-Link Simulations and Comparison to Single Molecule Studies of Entangled DNA In Shear Flow
Eric S. G. Shaqfeh, Stanford University, 381 North South Mall, Stanford, CA 94305 and Ajey Dambal, Chemical Engineering, Stanford University, 381 North South Mall, Stanford, CA 94305.
The dynamics of entangled polymeric systems is most often inferred from the changes in macroscopic properties such as viscosity, birefringence, etc. Such observations may be inadequate to distinguish different models of entangled polymer dynamics in the “fast flow” regime where convective constraint release (CCR) and chain stretch within the ‘tube' are important. Recently Teixeira et al. 2007 presented a complete single molecule examination of DNA in the shear flow of an entangled solution including examining various aspects of the length fluctuations and length distribution as well as the mechanical properties all within the CCR regime. In order to understand the physical principles behind these measurements, a molecular scale simulation using the slip-link method (Masubuchi et al. 2001) has been implemented. The method includes examining nonlinear, worm-like chains for different levels of entanglement and Kuhn step numbers (i.e. polymer molecular weights). We demonstrate that, in parameter regimes comparable to the experiments, the simulations a) demonstrate molecular individualism and broadening of the polymer conformation length distribution, b) they reproduce the shear stress plateau, and c) they demonstrate chain tumbling with a PSD signature comparable to that of the experiments. In short, they demonstrate all the salient features of the single molecule experiments. In light of this, we then analyze in detail how CCR in the simulations increases the stress and creates a nonlinear stress plateau, in contrast to the original Doi Edwards model.