(269h) Simulating the Behavior of Confined DNA in Slit-like Geometry Using Stochastic Rotation Dynamics

With the advance of nanotechnology, many novel devices have been created for manipulating biomolecules. The working principles of these devices often rely on the direct or indirect confinement-induced change in molecular properties. This inspires the needs for more fundamental and quantitative understanding on the behavior of biomolecules in confinement. In this study, we have used stochastic rotation dynamics (SRD) and molecular dynamics hybrid method to simulate DNA confined in slit-like geometry. The height of the slit was set between the persistence length and the radius of gyration of DNA. The scalings of static and dynamic properties of DNA were examined as functions of the slit height and DNA contour length. The simulation results were found in quantitative agreement with recent experimental data. Moreover, two different DNA relaxation regimes were also observed in our simulations, again consistent with recent experimental findings. We also compared our results with predictions derived from blob theory and confirmed that blobs in confinement are partial draining, not fully non-draining. Finally, we investigated the role of hydrodynamic interaction(HI) to DNA behavior by directly “turn” it on and off, and concluded that HI is important even when the dimension of the confinement is much smaller than the size of DNA.