Fracture of DNA in transient extensional flow. A numerical simulation study

Abstract

Using the Brownian dynamics simulation technique, we studied the fracture process of DNA chains subjected to transient extensional flow, letting the solution with DNA molecules pass through a very small orifice (radius = 0.0065 cm), thus experiencing extensional flow of the convergent (sink) type. The DNA molecules were modeled as FENE bead-spring chains with the springs obeying a modified Warner force law, as proposed by Reese and Zimm. The fracture yield was strongly dependent on flow rate and molecular weight, reaching, in our setup, a level of 100% at a flow rate of around 0.001 cm3/s for DNA with molecular weight 26 × 106 (T7 DNA). There was found to exist a critical flow rate (Qcrit) below which fracture did not occur, in accordance with what was observed in studies on polystyrene in transient extensional flow. We found that for DNA, the critical flow rate depended on the molecular weight as Qcrit ∼ M−14 when the hydrodynamic interaction effect (HI) was not included in the simulations. When HI was accounted for, the relation was found to be Qcrit ∼ M−1.1, close to the theoretical prediction for fracture of partly extended chains in transient extensional flow. © 1996 John Wiley & Sons, Inc.