Simulating DNA Confined in Slit-like Geometry Using Stochastic Rotation Dynamics
Date Issued
2012
Date
2012
Author(s)
Chang, En-Cheng
Abstract
We simulate the behavior of DNA in slit-like confinement using stochastic rotation dynamics(SRD) and molecular dynamics hybrid method. We examine the static and dynamic properties of DNA at equilibrium, and make comparison with the recent experimental observation.
SRD is a particle-based mesoscale simulation method which coarse-grains small fluid molecules to large fluid parcels, but it still can simulate the large length scale and long-time scale behavior of pure solvents precisely. The behavior of DNA is simulated using bead-spring model with molecular dynamics. The complex fluid system consists of simple fluid and DNA is then described by the SRD-MD hybrid method.
We first verify the ability of SRD to simulate the behavior of simple fluids. The results of SRD for unsteady Poiseuille flow and Couette flow agree perfectly with the theoretical prediction given by the exact solution of the Navier-Stokes equation. Next, we simulate the relaxation and diffusion of single DNA molecule at equilibrium. The scaling between radius of gyration, relaxation time and diffusivity versus DNA length is also in agreement with the theoretical prediction and experimental data.
One important feature of SRD is that it can easily “turn” on or off the hydrodynamic interaction between DNA molecules. Using this feature, we discover that the hydrodynamic interaction has significant effects on DNA dynamics, even when DNA is highly confined. This is different from the common anticipation based on polymer physics.
Finally, we simulate the behavior of DNA confined in slit-like geometry. The scaling of static and dynamic properties with DNA length and slit height agrees with recently experiment results. We compare the results with blob theory and confirm the blobs in confinement are partial draining, not nondraining.
Subjects
stochastic rotation dynamics
SRD-MD hybrid method
mesoscale
blob theory
DNA
slit-like confinement
hydrodynamic interaction
Type
thesis
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