The Electrical Double Layer at the Water-Silica Interface: Structure, Dynamics, Response to External Fields, and Biomolecules Adsorption

Silica is one of the common materials used to fabricate microand nano-scale biomedical devices. The negatively charged silica surface at most pH values leads to an electrical double layer, resulting in electrokinectic phenomena that take place in fluid region. Understanding the interface between water and silica is important for our understanding of fundamental double layer physics, and also aids the design of biomedical devices fabricated from silica or silicon. This dissertation explores the fundamental properties of water and biomolecules, such as DNA and peptides, in the electrical double layer region near the silica-water interface. We investigate the DNA-silica binding mechanism using molecular dynamics simulations. This system is of technological importance, and also of interest to explore how negatively charged DNA can bind to a negatively charged silica surface. We find that the two major binding mechanisms are attractive interactions between DNA phosphate and surface silanol groups, and hydrophobic bonding between DNA base and silica hydrophobic region. Umbrella sampling and the Weighted Histogram Analysis Method are used to calculate the free energy surface for detachment of DNA from a binding configuration to a location far from the silica surface. In experiments, single-stranded DNA (ssDNA) has been observed to bind to silica more strongly than double-stranded DNA (dsDNA). Several factors that emerge from out calculations explain this observation: 1) ssDNA is more flexible and therefore able to maximize the number of binding interactions. 2) ssDNA has free ii unpaired bases to form hydrophobic attachment to silica while dsDNA has to break hydrogen bonds with base partners to get free bases. 3) The linear charge density of dsDNA is twice that of ssDNA. Motivated by recent fluorescence depolarization experiments, we also study binding of the lys-trp-lys and glu-trp-glu tripeptides at the water-silica surface. A wide variety of binding motifs is observed, including both electrostatic and non-electrostatic (hydrophobic) interactions. The long-time limit of the fluorescence anisotropy is calculated. The anisotropy is largest for configurations in which indole fluorophore is directly bound to the surface. To fully understand electrokinetic effects in nano-scale devices, it is important to calculate the internal electric field. Part of that internal field arises from polarization charge. Polarization charge occurs whenever an electric field is applied across an interface and it is assumed infinitely thin in the theory of macroscopic dielectrics and also in most treatments of electrokinetic phenomena in nanoscale structures. In our work, we explore the polarization charge layer in molecular detail. Various formal relations and a linear response theory for the polarization charge are presented. Properties of the polarization charge layer are studied for three aqueous interfaces: air-water, a crystalline silica surface with water, and an amorphous silica surface with water. The polarization charge is calculated from equilibrium simulations via linear response theory, and from non-equilibrium simulations, and the results are within statistical error. The polarization charge is found to be distributed within a region whose width is on the order of a nanometer. We also studied the polarization charge due to ion movement. Poisson-Boltzmann equation is used to describe the system with an electrolyte solution sandwiched by two parallel plates. Molecular simulations are