Hydrodynamic Radius Fluctuations in Model DNA-Grafted Nanoparticles

We utilize molecular dynamics simulations (MD) and the path-integration program ZENO to quantify hydrodynamic radius (R-h) fluctuations of spherical symmetric gold nanoparticles (NPs) decorated with single-stranded DNA chains (ssDNA). These results are relevant to understanding fluctuation-induced interactions among these NPs and macromolecules such as proteins. In particular, we explore the effect of varying the ssDNA-grafted NPs structural parameters, such as the chain length (L), chain persistence length (l(p)), NP core size (R), and the number of chains (N) attached to the nanoparticle core. We determine R-h fluctuations by calculating its standard deviation (sigma R-h) of an ensemble of ssDNA-grafted NPs configurations generated by MD. For the parameter space explored in this manuscript, sigma R-h shows a peak value as a function of N, the amplitude of which depends on L, l(p) and R, while the broadness depends on R.