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In this dissertation, we present work on the first-principles informed phenomenological modeling of the optical properties of materials. We use density functional theory and time-dependent density functional theory calculations to inform parameterized models of the response to light in materials. We include the effect of ultrafast nonequilibrium effects, as well as the importance of quantum mechanical lattice vibrations. Using these models, we validate the approaches, and predict the effect of both ultrafast phenomena as well as quantum mechanical vibrations on the optical properties of bulk and 2D materials. Such modeling opens up avenues for efficient phenomenological approaches to describing optical phenomena in materials while keeping the accuracy of first-principles simulations.

In this dissertation, I present methods to improve the sensitivity and specificity of Silicon nanowires field-effect transistors (SiNWs FETs)-based biosensors. Our detection mechanism is based on ion-sensitive field-effect transistors (ISFET) and biosensor field-effect transistors (bioFET), allowing chemical ion and protein biomarker concentrations to be monitored in physiologically relevant solutions, such as 1x PBS buffer solutions. Our results have important implications and applications in fundamental sciences, environmental monitoring, disease diagnosis, drug discovery, pharmacology, and medicine. SiNWs FETs aroused great attention in the past few years due to their unique characteristics, such as high surface-to-volume ratio, sensitivity, mechanical strength, and stability in solutions. However, their major limitation is to detect the biomarkers in the high-salt buffer environments, such as 1x PBS, human serum, or whole blood. The sensing scheme is that the binding of charged entities such as protein or DNA biomolecules onto the nanowire surface (applying a top gate voltage) will induce a field-effect, therefore a change in the conductance of the semiconducting SiNWs underneath in which SiNWs act as the conductance channel between the source and drain of FET device. The difference in conductance provides valuable information on the selective binding of the biological target analyte species to their covalently linked counterparts on the nanowire surface. The experimental part of this dissertation presents the experimental details, a newly designed top-down wafer fabrication process with scalable manufacturing enabled, the optimized parameters for sequential processes were chosen to produce a complete silicon nanowire (down to 50 nm wire width) measurement circuit on silicon on insulator (SOI) wafers. I also refined the surface functionalization chemistry recipes for improved performance. The results show that after surface functionalization including salination, SiNWs FETs biosensors can be used as efficient and sensitive pH sensors. After the application of an external electric field on the side-gate field pads, there is a growing dipolar separation due to the increasing DC electric field which causes a better signal-to-noise ratio and higher conductance. A new biomarker sensing technique using RF electric field has been developed for the detection of protein biomarkers in the frequency domain. The RF signals have a clear biomarker concentration dependence and RF signals from the biomarkers are easily distinguishable from the control groups. Lastly, the results after the application of DC superimposed AC electric field show a slight shift in the concentration sensitive region and DC offset enhances the signals in the concentration range of interest. Our results provide further insights into overcoming the Debye length limitations of SiNWs FETs biosensors, bringing the real-time, label-free, high-selectivity, and high-specificity silicon nanowire-based biosensor platforms one step closer to being realized for Point-of-Care (POC) medical healthcare applications. / 2029-05-31T00:00:00Z

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Advances in functional coatings and methods to deposit them are critical in enhancing the functionality and performance of 3D micro-architected devices in applications encompassing energy storage, electronics, as well as selective and high-capacity molecular adsorption. Electrodeposition as a non-line-of-sight fabrication method for thin films is readily adapted to modify micro 3D substrates with functional coatings. However, most polymer electrodeposition so far has been achieved by electrochemically initiated chain-growth polymerization which causes uncontrolled polymer formation when applied on 3D micro-architected substrate. Here, this project developed the electrodeposition of polymer thin films utilizing electrocoupling reaction between bromoisobutyrate (bib) and acrylate functionalities to form a step-growth polymer network. The influence of molecular concentration, solvents, and end-group ratio are investigated on planar gold electrodes, enabling tailorable control over the film thickness, molecular permeability, and chemical composition. The optimized method is applied to coat a layer with solid polymer electrolyte on a low-tortuosity 3D Carbon electrode with high aspect ratio pores of micron-scale diameters. As a result, the entire pore surface of the 3D carbon electrode is effectively enveloped by a sub-micron polymer film. The deposited polymer film exhibits high electronic resistance and can serve as a solid polymer electrolyte. This approach decouples the polymer functionality from its electrodeposition chemistry while preventing uncontrolled polymer formation away from the surface and can therefore be a universal method to coat various conductive micro-architected 3D substrates with tailorable functional polymers. / 2025-08-29T00:00:00Z