Simulation of $\lambda$-phage DNA in microchannels using a coarse-grained MD method

In this work we present Dissipative Particle Dynamics (\textsc{dpd}) simulations of polymers subject to the Marko-Siggia wormlike chain (\textsc{wlc}) spring law. We demonstrate the advantages of Lowe's \textsc{dpd} method, which simulates high Schmidt numbers for the solvent, and contrast it with the velocity-Verlet scheme. Shear flow results for the wormlike chain (\textsc{wlc}) simulating single \textsc{dna} molecules compare well with average extensions from experiments, irrespective of the number of beads. However, coarse-graining with more than a few beads degrades the agreement of the autocorrelation of the extension.