Paper Citing NAMD - Abstract
Lee, One-Sun; Schatz, George C.
Molecular Dynamics Simulation of DNA-Functionalized Gold Nanoparticles
JOURNAL OF PHYSICAL CHEMISTRY C, 113:2316-2321, FEB 12 2009
Molecular dynamics methods have been used to study a 2 nm gold nanoparticle that is functionalized with four single stranded DNAs at the atomistic level. The DNA strands, which are attached to the [111] faces of a 201 atom truncated octahedral gold particle with a -S(CH(2))(6)- linker, are found to be perpendicular to the surface of the particle, with the alkane chain lying on the surface. There are no significant hydrogen bonding interactions between the adsorbed ss-DNAs during the simulation. Even though the expected radius would be 49 angstrom (3.4 angstrom per base) for a Watson-Crick DNA structure, the simulation with 0.5 M salt shows a radius of about 29 angstrom (2.2 angstrom per base), which is a result that is consistent with recent experimental reports. It is also found that the sodium concentration within 30 angstrom of the gold particle is about 20% higher than the bulk concentration. This is consistent with an observed increase in the melting temperature of DNA when many functionalized gold particles are hybridized together.
