On mesoscale modelling of dsDNA molecules in fluid flow

The paper presents a new mesoscale modelling approach to investigation of dsDNA molecules motion in fluid flow. The proposed method includes the effects of inertia and is capable of capturing accurately dsDNA relaxation and stretching phenomena. The accuracy of the proposed method is explored through comparisons with published experimental data. For the simulation of disengaged dsDNA molecules, a novel correction to the elastic force formulation is suggested. The proposed adjustment offers a significant improvement in the prediction of dsDNA length for both relaxation in resting buffer and extension using hydrodynamic focusing. Analysis of the individual contributions to the force acting on the dsDNA molecules demonstrates that the dynamics of dsDNA extension observed experimentally is dominated by the hydrodynamic drag force.