Paper Citing NAMD - Abstract
Ngo, Van A.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya
Supercrystals of DNA-Functionalized Gold Nanoparticles: A Million-Atom Molecular Dynamics Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 116:19579-19585, SEP 13 2012
We use million-atom molecular dynamics simulations to study body-centered cubic (BCCS) and face-centered cubic (FCCS) supercrystals of DNA-functionalized gold nanopartides, which are solvated with water and neutralized with sodium ions. The two supercrystals contain 2.77 and 5.05 million atoms. Having large numbers of DNAs and hexanethiols attached to 3 nm diameter gold nanoparticles, we observe smooth changes of the averaged DNA structures over the simulation time. We find that, after 10 ns, the DNA structures are different from the canonical B-DNA structures in terms of root-mean-square deviations, base-base stacking structures, and hydrogen bonds. We also examine ion distributions around DNAs and estimate the melting temperature increases for the supercrystals from the ion distributions, which are Delta T-BCCS = 12.9 K and Delta T-FCCS = 8.0 K The radial distribution functions for the correlation between ions and DNA show that ions bind stronger in BCCS than FCCS. This correlation explains the higher melting temperature increase in BCCS and supports that there are more entropic effects in FCCS than in BCCS. We also report the Young's and bulk moduli of the supercrystals, which resemble those of water. The Possion ratios for both supercrystals (similar to 0.39) are close to the ideal value (=1/3).
