Advances in the construction of nanoscale biomedical devices requires
increasingly realistic descriptions of interactions with biomolecules,
and with fluid flow within micro- and nanochannels. We have made
progress in both areas for nanostructures fabricated from amorphous
silica. Silica is a material commonly used to fabricate biomedical
devices, and the interactions of silica with aqueous solutions and
biomolecules are of great importance in many fields. We developed a
tractable model for biomolecules at the water/amorphous silica
interface. This interaction model is based on one previously
developed for the amorphous silica/water interface. Quantum chemical
calculations of a series of probe molecules that mimic the common
functional groups found in biomolecules were performed near a
characteristic silica fragment. Our interaction model was designed to
best reproduce the quantum chemical results. Then we investigated
binding of two tripeptides (lys-trp-lys and glu-trp-glu) at the
amorphous silica/water interface using molecular dynamics simulations.
The preliminary studies reveal the great variety of binding motifs
possible when biomolecules interact with silica, and illustrate how a
peptide with overall negative charge like glu-trp-glu might bind to
silica by hydrophilic/hydrophobic interactions on the highly
inhomogeneous silica surface.
Electroosmotic transport of electrolyte solution in a nozzle geometry
induced by an applied electric field was investigated with atomic
level detail using non-equilibrium molecular dynamics (NEMD)
simulations. Both ends of the nozzle are connected to flat channels
and the walls consist of realistically modeled amorphous silica. The
research is motivated by interesting issues arising from
electrokinetic transport through the micro/nano interface such as ion
concentration polarization and achieving optimum transport of
biomolecules, ions and fluid. We found that the concentration of both
counterions and coions are depleted in the nozzle region and
consequently, a concentration gradient was generated in the direction
of the flow.
In addition, the flow pattern is not uniform along the channel
unlike the uniform pore. The local back flow was observed in flat
channel connected to the nozzle due to the combined effects of induced
adverse pressure and electroosmotic flow.
To understand the underlying mechanism of this
phenomena, we compared the results of non-equilibrium molecular
dynamics simulations to the predictions of continuum hydrodynamics,
using both exact solutions to the Stokes equation and testing the
standard lubrication approximation. In addition, the water
polarization charge that accumulates near a wall which is not parallel
to the external electric field was investigated.