Numerical simulation of tethered DNA in shear flow

The behavior of tethered DNA in shear flow is investigated numerically by the smoothed dissipative particle dynamics (SDPD) method. Unlike numerical methods used in previous studies, SDPD models the solvent explicitly, takes into account the fully coupled hydrodynamic interactions and is free of the numerical artifact of wall sticking. Based on numerical simulations the static and dynamic properties of a tethered DNA is studied both qualitatively and quantitatively. The observed properties are in general agreement with previous experimental, numerical and theoretical work. Furthermore, the cyclic-motion phenomenon is studied by power spectrum density and cross-correlation function analysis, which suggest that there is only a very weak coherent motion of tethered DNA for a characteristic timescale larger than the relaxation time. Cyclic motion is more likely relevant as an isolated event than a typical mode of DNA motion.