Herein we demonstrate a novel electroless etching synthesis of monolithic, single-crystalline, mesoporous silicon nanowire arrays with a high surface area and luminescent properties consistent with conventional porous silicon materials. The photoluminescence of these nanowires suggest they are composed of crystalline silicon with small enough dimensions such that these arrays may be useful as photocatalytic substrates or active components of nanoscale optoelectronic devices. A better understanding of this electroless route to mesoporous silicon could lead to facile and general syntheses of different narrow bandgap semiconductor nanostructures for various applications.

The everlasting battles between humans and bacteria entered a new stage with the discovery of antibiotics that saved millions of lives in the 20th century. However, the rise of antibiotic-resistant strains, often resistant to multiple classes of antibiotics, poses a renewed threat to human health. Compared to the quick and swift evolution of the resistant phenotypes, the development of new antibiotics has stagnated for decades, exacerbated by a limited understanding of the evolutionary mechanisms driving antibiotic resistance.

Bacteria, thriving in diverse and harsh environments, have evolved myriad strategies to survive various stresses, including starvation, osmotic stress, heavy metals, antimicrobial agents, and so on. Understanding bacterial responses to these stresses is critical for delaying the emergence of antibiotic resistance mutations, reducing pathogenic bacterial tolerance to adverse environments, and optimizing industrial production processes.

In this work, different tools were deployed to detect, visualize, quantify, and eventually predict bacterial behavior under different stresses. A widely used molecule resazurin was found to be an ideal candidate for a novel accurate, cheap, and highly effective bioassay that could monitor intracellular NADH level and bacterial stress response in real time. An algorithm depicting bacterial metabolite profile was developed to detect minor heavy metal contamination in the drinking water, harnessing bacteria as powerful indicators to pollution. Lastly, we adapted a novel model to study the persistent bacterial community known as biofilms. Biofilm attaches to biotic or abiotic surfaces, is resistant to adverse conditions, and causes great pain to our patients. We simulated the osmotic pressure perturbation in vivo to explain the mechanisms of cross-protection between different stresses and found inspiration to postulate new strategies to eliminate stubborn bacterial communities.

Thermoelectric power generation could be crucial in a sustainable energy future through waste heat energy recycling. Typical nanoengineering of thermoelectric materials requires energy intensive and expensive methods of device fabrication. We employ a facile solution processed device fabrication method that can easily be scaled up for manufacturing while maintaining its cost effectiveness. In this work, we establish and qualify a thermopower measurement system for thin film and bulk devices. To qualify the measurement system, we show that trends in the signs and magnitudes of the Seebeck coefficients of known silicon standards are correct. We also show that PbSe nanocrystal thin film devices exhibit a large Seebeck coefficient (~1500-2000 μV/K) prior to alumina infilling and a reduced Seebeck coefficient (~800-1200 μV/K) post alumina infilling. With this measurement tool, we are able to view differences in thermopower before and after atomic layer deposition treatment within an oxygen-free atmosphere.

Bacterial biofilms cause persistent and deadly infections in medical settings, which are resistant to conventional antibiotic doses. Medical biofilms are often multi-species communities of bacteria which are maintained through chemical signaling and metabolite exchange. An improved understanding of the interactions between bacteria governing community behavior will facilitate the discovery of drug targets for biofilm prevention and eradication. In this thesis, I describe coculture interactions between different species of bacteria and a method to track metabolic states of bacteria in different environments.

One example of such coculture interactions is illustrated in the competition for iron in an in vitro infection model. Salmonellaenterica serovar Typhimurium (STm) causes acute infections in the gut, but STm infections are abolished in coculture with a probiotic bacterium, Escherichia coli Nissle (EcN). EcN outcompetes STm in the gut via a class of bactericidal compounds, called microcins, which are conjugated to iron scavenging siderophore molecules. In vitro biofilm models show that STm uses EcN siderophores to acquire iron, and that siderophore conjugation is an anti-cheating strategy employed by EcN to outcompete STm for nutrients.

In another example of novel coculture interactions, E. coli and Pseudomonas aeruginosa have competitive interactions governing biofilm establishment and dispersal. The E. coli biofilm dispersal is triggered by P. aeruginosa quorum sensing (QS) compounds. However, E. coli biofilms grown on periodic microcturctures, resembling the stomach micro-villi, are shown to modulate this pathway by metabolite accumulation in engineered microenvironments. Substrate structures induce changes in E. coli biofilm morphology, which in turn increase the concentration of indole, a constitutively produced metabolite within the biofilm. Moreover, the monoculture biofilms grown on microstructured substrates are significantly more susceptible to antibiotics than monocultures on flat substrates. FLIM is a label free, non-invasive technique and has immense potential for use as a means to probe interactions in microbial communities. Fluorescence lifetime imaging microscopy (FLIM), demonstrates that this increased antibiotic susceptibility is due to changes in cellular metabolism induced by an altered microenvironment. The research in this thesis demonstrates more long term and permanent strategies for biofilm infections and will provide guidelines and inspiration for improved diagnostics, and treatments for biofilm infections.

The increasing demand for fossil fuels and the need to reduce greenhouse gases require clean energy sources and more efficient utilization of energy. Thermoelectric materials provide a means toward achieving these goals since they convert heat, including waste heat, directly into an electric potential difference. Metal-semiconductor heterostructures can work as Schottky barriers in thermoelectric materials to increase thermoelectric efficiency.

In this project, nickel silicide phases were introduced into silicon nanowires (SiNWs) to build up the Schottky barrier. SiNW arrays were fabricated using a metal-assisted chemical process, creating SiNWs about 200 nm in diameter and 30ìm in length. Different methods were adopted for nickel deposition: electroless nickel deposition, electro nickel deposition, E-beam deposition, and thermal evaporation. The samples were examined by X-ray diffraction (XRD) and scanning electron microscopy (SEM). The results show that depositing nickel on SiNWs in an aqueous solution without electricity is a simple way to deposit nickel particles, and the morphology of nickel particles depends on the concentration of the deposition bath. However, an aqueous solution will cause oxidation of the SiNWs and hinder the formation of nickel silicide. To solve this problem, depositing nickel on SiNWs in organic solutions inside an oxygen-free glove box is a way to prevent oxidation, and nickel can diffuse into silicon substrates easily via annealing when there no oxidation layer on the surface of SiNWs. The dominant phase formed in these samples is NiSi2 after being annealed at 650°C for one hour in a tube furnace.

Antibiotic resistant pathogens cause more than 2.8 million infections and 35000 deaths in the United States each year. We need unique and effective therapies that will eradicate bacterial colonization, reduce patient suffering, and improve our ability to deliver necessary medications with reduced complications. Unfortunately, making new classes of antibiotics will not solve the antibiotic resistant problem.Bacteria face different stressful conditions which have an adverse effect on the physiological welfare of bacterial cells. Stress response mechanisms protect cells against stress and make them tolerant to antibiotics. As a result, tolerant cells might be a source of resistance. Targeting the stress response mechanisms can be a good tool to prevent tolerance. Throughout this research, different analytical and characterization methods were used to investigate different stress responses from pathogens in different environmental conditions. Additionally, the effects of stress response mechanisms on making cells tolerant to antibiotics was studied. Consequently, this approach was used to develop some strategies for preventing infection. For example, a small molecule was found to be effective against bacterial survival in some stressful environments, and one type of probiotic strain was used to interact with pathogens and prevent the growth by using its stress response mechanism. Using this knowledge, we can find the ways tolerance arises to target mechanisms of tolerance to combat antibiotic resistance as a more time saving strategy.

At present, very little is known about the development of tolerance in response to osmotic stress. Although cells undergo similar adaptations to both antibiotic and osmotic stress, there exists a need to elucidate the relationship, observed through growth rate patterns, metabolic perturbations, and membrane alterations, in response to simultaneous exposure to both stresses. A better understanding of these interactions will produce new strategies for treating persistent and recalcitrant bacterial infections. We show here that osmotic stress cross-protects E. coli to bactericidal antibiotics, conferring tolerance to antibiotics.

The colloidal synthesis and surface modification of germanium and germanium-based nanomaterials is a developing area of research with potential applications in a variety of fields. Colloidal germanium nanocrystal syntheses have improved significantly in recent years, but there has been little exploration into the synthesis of Ge-based nanomaterials, especially metal-germanium nanocrystals. A solution-phase synthesis of nickel germanide nanocrystals was developed to produce colloidal particles possessing an unexpected Ni¬19Ge12 crystal phase. The mechanism of this synthesis was explored to show that the Ni19Ge12 phase formed over a wide range of experimental conditions, but the use of a trioctylphosphine cosolvent allowed formation of a Ni1Ge1 phase that was not thermally stable. Many proposed applications of colloidal Ge nanocrystals require thorough particle surface modification. To this end, surface ligand exchange of Ge nanocrystals was examined and improved through the development of a high-temperature sulfur treatment. Finally, Ge nanocrystal films were cast from solution and their electrical conductivity was characterized.

Nanomaterials derived from silicon and germanium have demonstrated several desirable properties for a variety of materials applications, such as optoelectronics, spintronics, catalysis, and thermoelectrics. Currently, the synthetic library for the production of technologically relevant Group IV nanomaterials comprised of silicon–germanium alloys, metal-silicides, and metal germanides are extremely limited, particularly with regard to solution-phase approaches. The work presented in this dissertation demonstrates the expansion of existing protocols to produce a variety of new Group IV-based nanomaterials using solution-phase syntheses. For the first time, silicon–germanium alloy nanocrystals are produced from a solution-phase approach. In addition, a new, generalizable scheme for the production of a variety of metal germanide nanocrystals is demonstrated through the use of metal(0) precursors. This methodology is then adapted to existing electroless etching methodologies used to produce silicon nanowire arrays, leading to the production of heterostructured silicon/metal silicide nanowires.

Proteins and peptides may be a promising route to develop conductive materials capable of interfacing biological components with electronics for bioelectronic applications. Amino acid sequences can drive the self-assembly of supramolecular nanostructures, whose high surfaces area, soft material surfaces may be suitable for interfacing with biology. These sequences can be coupled with conjugated small molecules or metals to drive the aqueous self-assembly of water soluble, electronically-conductive nanomaterials, or these sequences, by themselves, can form electronically-conductive supramolecular structures. In this work, we demonstrate long-range, non-redox, and non-thermally activated electron transport in biological protein nanofibers purified from Geobacter sulfurreducens, and we replicate these unique conduction properties in non--stacked, self-assembled nanofibers constructed from a de novo peptide sequence. We demonstrate that natural amino acids can be used to form supramolecular nanofibers with high conductivities, comparable to conjugated materials, in the absence of delocalization. This micrometer-scale transport does not fit within the framework of long-range conduction mechanisms in organic materials, and thus suggests a rethinking of current electron transport models. We also characterize electronic and electrostatic properties in two other amino acid based supramolecular systems, demonstrating how amino acids can be used to tune the self- assembly and electronic properties of conductive materials. These findings suggest that amino acid based materials may be a viable platform for designing functional bioelectronic materials.