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The water-amorphous silica interface: electrokinetic phenomena in a complex geometry, and treatment of interactions with biomolecules

Shin, Yun Kyung

Abstract Details

2011, Doctor of Philosophy, Ohio State University, Chemistry.

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.

Sherwin J. Singer, PhD (Advisor)
A. T. Conlisk, PhD (Committee Member)
James V. Coe, PhD (Committee Member)
286 p.

Recommended Citations

Citations

  • Shin, Y. K. (2011). The water-amorphous silica interface: electrokinetic phenomena in a complex geometry, and treatment of interactions with biomolecules [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1299587783

    APA Style (7th edition)

  • Shin, Yun Kyung. The water-amorphous silica interface: electrokinetic phenomena in a complex geometry, and treatment of interactions with biomolecules. 2011. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1299587783.

    MLA Style (8th edition)

  • Shin, Yun Kyung. "The water-amorphous silica interface: electrokinetic phenomena in a complex geometry, and treatment of interactions with biomolecules." Doctoral dissertation, Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1299587783

    Chicago Manual of Style (17th edition)