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Atomically thin two-dimensional (2D) materials come in all necessary flavors to make semiconductor devices: conductors, semiconductors, and insulators. Graphene, transition metal dichalcogenides (TMDCs), and hexagonal boron nitride (hBN) are the quintessential building blocks. The van der Waals nature of the bonds in 2D films allows the ability to stack materials to achieve novel properties because of their exceptional mechanical, electronic, and optical properties and interactions, which enables various applications of 2D materials in transistors, biosensors, light-emitting devices, and photodetectors. Spectroscopic measurements such as Raman and photoluminescence (PL) reveal a wealth of information since 2D materials are affected by their environment and other local perturbations, e.g., strain and charge doping. My research focused on developing efficient and noninvasive optical methods to evaluate and characterize the properties of 2D materials. In particular, we investigated strain-tunable properties, the effects and signature of charge doping, and the environmental screening properties of graphene and TMDCs. Identifying the charge density and impurities in graphene is vital for graphene-based applications, which require high-quality graphene. I developed an effective optical method to determine the doping level and the local charge density variations in graphene before any fabrication process. This method differentiates charge density variations in graphene via the Raman 2D peak asymmetry that manifests at low charge 1-25 × 1010 cm-2. We explore the effect of charge inhomogeneity, "charge puddles", within the laser spot using simulated Raman 2D spectra, revealing a different signature for large or small charge puddles. Our work provides a simple and noninvasive optical method for estimating the doping level, local charge density variation, and transport properties of graphene, with up to two orders of magnitude higher precision than previously reported optical methods. Strain is another crucial factor that significantly impacts the properties of 2D materials. We studied the charge distribution and radiative efficiency of excitonic complexes in strained monolayer TMDCs, especially WSe2. Straining and electrostatic gating are combined to investigate the dynamics of quasi-particles in WSe2. We found that negative trions accumulate while positive trion emission is near zero, indicating that both conduction and valence bands are bent downwards in the strained area. Finite element analysis of strain distribution and density functional theory calculations of band structures of WSe2 support the experimental results. Hence, localized strain allows locally separating electrons and holes in WSe2 and manipulating light-matter interaction for applications in novel strained-engineered optoelectronics. I applied machine learning and deep learning techniques to improve the efficiency and accuracy of data processing and analysis since traditional methods require domain expertise and have the potential to introduce artifacts. I categorized the wealth of information and data by applying machine learning to spectroscopic information to separate different influences, e.g., strain, charge doping, and dielectric environment. We developed deep learning models to classify graphene Raman spectra according to different charge densities and dielectric environments. To improve the accuracy and generalization of all models, we use data augmentation through additive noise and peak shifting. Using a convolutional neural net (CNN) model, we demonstrated the spectra classification with 99% accuracy. Our approach has the potential for fast and reliable estimation of graphene doping levels and dielectric environments. The proposed model paves the way for achieving efficient analytical tools to evaluate the properties of graphene. / 2022-11-23T00:00:00Z

Femtosecond laser filamentation in gaseous media is a new source of broadband, ultrashort radiation that has the potential for application to many fields of research. In this dissertation filamentation is studied with a view to understanding the underlying physics governing the formation and propagation dynamics of filamentation, as well as to developing a method for vibrational spectroscopy based on the filament-induced impulsive vibrational excitation of molecules in the filamentation region. In pursuit of a better understanding of the underlying physical processes driving filamentation, the development of a new method for characterizing high intensity ultrashort laser pulses is presented, wherein two laser beams generate a transient grating in a noble gas, causing the pulse undergoing filamentation to diffract from the grating. Measuring the spectrum as a function of time delay between the filament and probe beams generates a spectrogram that can be inverted to recover the spectral and temporal phase and amplitude of the filamentary pulse. This technique enables measurement of the filamentary pulse in its native environment, offering a window into the pulse dynamics as a function of propagation distance. The intrinsic pulse shortening observed during filamentation leads to the impulsive excitation of molecular vibrations, which can be used to understand the dynamics of filamentation as well. Combined measurements of the longitudinally-resolved filament Raman spectrum, power spectrum, and fluorescence intensity confirm the propagation dynamics inferred from pulse measurements and show that filamentation provides a viable route to impulsive vibrational spectroscopy at remote distances from the laser source. The technique is applied to thermometry in air and in flames, and an analytical expression is derived to describe the short-time dynamics of the rovibrational wave-packet dispersion experienced by diatomic molecules in the wave of the filament. It is found that no energy is initially partitioned into the distribution of rovibrational states during the filamentation process. Filament-assisted impulsive stimulated Raman spectroscopy of more complex systems is also performed, showing that filament-assisted vibrational measurements can be used as an analytical tool for gas phase measurements and has potential for use as a method for standoff detection. Finally, a study of the nonlinear optical mechanisms driving the filamentation process is conducted using spectrally-resolved pump-probe measurements of the transient birefringence of air. Comparison to two proposed theories shows that a newly described effect, ionization grating-induced birefringence, is largely responsible for saturation and sign inversion of the birefringence at 400 nm and 800 nm, while the magnitude of contributions described by a competing theory that relies on negative terms in the power series expansion of the bound electron response remain undetermined. / Chemistry

No / Raman spectra of an extremophile cyanobacterial colony in hydromagnesite from Lake Salda in Turkey have revealed a biogeological modification which is manifest as aragonite in the stratum associated with the colony. The presence of key spectral biomarkers of organic protectant molecules such as (8-carotene and scytonemin indicate that the survival strategy of the cyanobacteria is significantly one of UV-radiation protection. The terrestrial location of this extremophile is worthy of consideration further because of its possible putative link with the White Rock formations in Sabaea Terra and Juventae Chasma on Mars.

This dissertation will have three chapters. In chapter one, a comprehensive review on defects in two dimensional materials will be presented. The aim of this review is to elaborate on different types of defects in two dimensional (2D) materials like graphene and transition metal dichalcogenides (TMDs). First, different types of point and line defects, e.g. vacancies, anti-sites, guest elements, adatoms, vacancy clusters, grain boundaries, and edges, in these materials are categorized in terms of structure. Second, interactions among defects are discussed in terms of their rearrangement for low-energy configurations. Before studying the electronic and magnetic properties of defective 2D materials, some of the structures are considered in order to see how defect structure evolves to a stable defect configuration. Next, the influence of defects on electronic and magnetic properties of 2D materials is discussed. Finally, the dynamic behavior of defects and 2D structures under conditions such as electron beam irradiation, heat treatment, and ambient conditions, is discussed. Later as a case study, defects in a two dimensional transition metal dichalcogenide will be presented. Among two-dimensional (2D) transition metal dichalcogenides (TMDs), platinum diselenide (PtSe2) stands at a unique place in the sense that it undergoes a phase transition from type-II Dirac semimetal to indirect-gap semiconductor as thickness decreases. Defects in 2D TMDs are ubiquitous and play crucial roles in understanding and tuning electronic, optical, and magnetic properties. Here intrinsic point defects in ultrathin 1T-PtSe2 layers grown on mica were investigated through the chemical vapor transport (CVT) method, using scanning tunneling microscopy and spectroscopy (STM/STS) and first-principles calculations. Five types of distinct defects were observed from STM topography images and the local density of states of the defects were obtained. By combining the STM results with first-principles calculations, the types and characteristics of these defects were identified, which are Pt vacancies at the topmost and next monolayers, Se vacancies in the topmost monolayer, and Se antisites at Pt sites within the topmost monolayer. Our study shows that the Se antisite defects are the most abundant with the lowest formation energy in a Se-rich growth condition, in contrast to cases of 2D molybdenum disulfide (MoS2) family. Our findings would provide critical insight into tuning of carrier mobility, charge carrier relaxation, and electron-hole recombination rates by defect engineering or varying growth condition in few-layer 1T-PtSe2 and other related 2D materials. Also, in order to investigate the layer dependency of vibrational and electronic properties of two dimensional materials, 2M-WS2 material was selected. Raman spectroscopy and DFT calculation proved that all Raman active modes have a downshift when material is thinned to few layers (less than 5 layers). It was proven that there is a strong interaction between layers such that by decreasing the number of layers, the downshift in Raman active modes is mostly for the ones which belong to out-of-plane atomic movements and the most downshift is for the Ag2 Raman active mode. Also, I investigated the effect of number of layers on the band structure and electronic properties of this material. As the number of layers decreases, band gap does not change until the materials is thinned down to only a single monolayer. For a single monolayer of 2M-WS2, there is an indirect band gap of 0.05eV; however, with applying in-plane strain to this monolayer, the material takes a metallic behavior as the strain goes beyond ±1%. / Doctor of Philosophy / Graphite (consisting of graphene as building blocks) and TMDS in bulk form are layered and with exfoliation one can reach to few layers which is called two-dimension. Two dimensional materials like graphene have been used in researches vastly due to their unique properties, e.g. high carrier mobility, and tunable electronic properties. Transition metal dichalcogenides (TMDs) with a general formula of MX2, where M represents transition metal elements (groups 4-10) and X represents chalcogen elements (S, Se or Te), are another family of two-dimensional materials which have been extensively studied in the past few years. Besides exfoliation, there are also synthesis methods to produce two dimensional materials, e.g. chemical vapor deposition and chemical vapor transport. Normally, after synthesizing these materials, researchers investigate structure and electronic properties of these materials. There might be some atoms which no longer exist in the structure; hence, those are replaced by either vacancies or other elements which all of them are called defects. In chapter 1, defects in graphene and transition metal dichacolgenides were investigated, carefully. Later, dynamic behavior of defects in these materials were investigated and finally, the effect of defects on the electronic properties of the two dimensional materials were investigated. Chapter two talks about a case study which is two dimensional 1T-PtSe2. In this chapter, 5 different kinds of defects were studied using scanning tunneling microscopy and spectroscopy investigations and density functional theory was used to prove our assumptions of the origin of defects. Also, another thing which is investigated by researcher is that how atoms in two dimensional materials vibrate and how the number of layers in the two dimensional material influences vibrations of atoms. Other than this, electronic properties of these materials is dependent upon the number of layers. When these materials are synthesized, there is a stress applied to the material due the mismatch between the material and its substrate, so it is worth investigating the effect of stress (strain) on the structure, and electronic properties of the material of interest. For this purpose, 2M-WS2 was exfoliated on Si/SiO2 substrate and the layer dependency of its vibrational modes was investigated using Raman spectroscopy and density functional theory calculation. Also, in order to investigate the influence of stress (strain) on the electronic properties of two dimensional 2M-WS2, a single monolayer of this materials underwent a series of strains in density functional theory calculations and the effect of strain on the electronic properties of this material was investigated.

Adherent microbial communities, known as biofilms, are a major contributing factor in the incidence of healthcare-associated infections (HCAIs). HCAIs are responsible for annually causing 100,000 deaths and medical expenses estimated to be $35-45 billion. Physical and chemical surface modification techniques are thought to be critical in the fight against biofilm formation within medical settings. Nanoscale structural features have been found to have significant effects on bacterial adhesion and biofilm formation, but their effects on fungal pathogens are less explored. This thesis systematically explores the effect of surface topography in the form of nano and microscale polymeric fibers (~0.4-1.2 µm in diameter) on biofilm formation and virulence of a common HCAI-causing fungal pathogen, Candida albicans. We show that both C. albicans attachment density and differentiation to its virulent phenotype significantly vary with fiber diameter and spacing on polymeric fiber-coated surfaces. We further show that high throughput and high content techniques, such as Raman spectroscopy, can be used to track environmental and physical effects on the organism's resulting morphology and associated virulence. Findings from this thesis will inform the design of antifouling surfaces including implantable medical devices. In a prototypical example, we demonstrate the use of fiber coating to modulate C. albicans attachment on polyurethane, silicone, and latex catheters. / Master of Science / Microbial communities that adhere to surfaces, known as biofilms, are largely associated with incidence of healthcare-associated infections (HCAIs). HCAIs are responsible for annually causing 100,000 deaths and medical expenses estimated to be $35-45 billion. Modification of surfaces using physical and chemical techniques is believed to be critical in the fight against biofilm formation on surfaces within medical settings. Nanoscale structural features have been found to have significant effects on bacterial adhesion and biofilm formation, but their effects on fungal pathogens have not been extensively studied. This thesis focuses on the effect of surface topography, or textures, in the form of nano and microscale polymeric fibers (~0.4-1.2 µm in diameter) on biofilm formation and disease-causing ability, or virulence, of a common HCAI-causing fungal pathogen, Candida albicans. We show that both C. albicans attachment density and differentiation to its virulent form significantly vary with fiber diameter and spacing on polymeric fiber-coated surfaces. We also show that high throughput and detailed imaging techniques, such as Raman spectroscopy, can be used to track environmental and physical effects on the organism's resulting morphology and associated virulence. Findings from this thesis can be used to aid in the design of surfaces that discourage biofilm formation, including implantable medical devices. We demonstrate the use of fiber coating to vary C. albicans attachment on polyurethane, silicone, and latex catheters in one of our studies.

Understanding and establishing reaction mechanisms is an important area in heterogeneous catalysis. This dissertation describes the use of in situ laser Raman spectroscopy combined with kinetic measurements and dynamic experiments to determine the mechanism of catalytic reactions. Two cases involving ozone reactions on manganese oxide catalysts were treated. Manganese oxide was chosen because it is the most active of the transition metal oxides for ozone decomposition and because it is a well-known catalyst for complete oxidation reactions. The first case studied was that of the ozone decomposition reaction on a supported manganese oxide catalyst. An adsorbed species with a Raman signal at 884 cm-1 was observed and assigned to a peroxide species based on results of in situ Raman spectroscopy, 18O isotopic substitution measurements, and ab initio MO calculations. The reaction pathway of ozone decomposition was elucidated with carefully designed isotopic experiments. The reaction sequence was found to involve two irreversible, kinetically significant steps: 1) dissociative adsorption of ozone to form a peroxide species and an atomic oxygen species, and 2) desorption of the peroxide intermediate. The kinetic behavior of the peroxide species and the overall decomposition reaction were investigated to test the validity of the proposed sequence. The transient kinetics were found to be consistent with the steady state kinetics, and both were well represented by the two-step sequence, indicating that the proposed reaction sequence accurately described the mechanism of decomposition. The surface was found to be non-uniform, with activation energies that varied linearly with coverage. At zero surface coverage the activation energy for ozone adsorption was found to be 6.2 kJ mol-1, while that for desorption of the peroxide species was found to be 69.0 kJ mol-1. The second case investigated was that of ethanol oxidation using ozone on alumina and silica supported manganese oxide catalysts. Ethanol was found to react with ozone at lower temperatures than with oxygen, and also with a lower activation energy. The reaction kinetics was found to be well described by a power law equation with the reaction orders on ozone and ethanol being 0.89 and 0.81 respectively. The oxidation reactivity was found to be closely related to that of ozone decomposition, suggesting an important role of ozone decomposition in the reaction mechanism. In situ laser Raman spectroscopic studies showed the existence of adsorbed ethoxide species on the catalyst surface under reaction conditions, however, at a much lower concentration than when oxygen alone was used as the oxidant. Transient experiments provided direct evidence that surface peroxide (an adsorbed species due to ozone) and surface ethoxide (an adsorbed species due to ethanol) reacted with each other on the catalyst surface. / Ph. D.

Raman spectroscopy and its counterpart surface-enhanced Raman scattering (SERS) have proven to be effective methods for detecting miniscule changes in the phenotypes of E. coli and other single-celled organisms to aid in the detection of new strains for industrial use and discovery of new antibiotics. The purpose of this study is to develop a method to quickly and accurately detect contaminants in water samples through phenotype changes in E. coli measured through SERS. Contaminated Luria-Bertani (LB) media was inoculated with LB with an OD600 of 1, grown for two hours, and then dried on a flat piece of aluminum foil. These samples were then Raman scanned and processed to determine contaminant-induced changes to the phenotypes of the E. coli. Three types of tests were run to show the effectiveness of this method: single-component, multicomponent, and impure water sources. In single-component tests, it was found that differences due to NaCl contamination could be detected to 5.0E-9 weight percent (wt %), ethanol (EtOH) to 5.0E-7 volumetric percent (% v/v), citric acid (CA) to 2.8E-4 wt %, acetic acid (AA) to 2.6E-4 wt %, kanamycin to 2.5E-11 wt %, ampicillin to 2.5E-10 wt %, CoCl2 to trace amounts, and silver nanoparticles (AgNP) to 5.2E-7 wt %. Many of these are below the detection limits of analytical instrumentation, but their effects on E. coli phenotypes were detectable by Raman spectroscopy. Multicomponent tests showed that in a mixture, the most toxic or most concentrated contaminants have the most effect on cell phenotype. However, it was shown that similar concentrations of similar contaminants may be difficult to discern with current methods. This behavior was also seen in the impure water samples, showing that tap water behaves the closest to a DI control, followed by running water, and finally stagnant bodies. This new method of monitoring E. coli phenotypes with Raman spectroscopy as a biosensor shows promise for the fast, portable, and accurate determination of environmental contaminants with a broad-spectrum and very low detection limits. / Master of Science / Recently, Raman spectroscopy and an enhanced version called surface-enhanced Raman scattering (SERS) have shown promise in showing the effects of a cell’s environment on how it expresses genes and what chemical compounds it produces to survive. It does this through reading the chemical signature it gives off due to these changes, and these readings have been used for showing the effects of antibiotics, finding varieties that are resistant to toxic byproducts of their activities, and as biosensors. The study outlined in this thesis aims to develop a test utilizing SERS to see the reactions of a non-pathogenic strain of E. coli to contaminants in their media and determine their identity. This test was run for three types of contaminated samples: one contaminant, three contaminants, and tests using impure water from a sink tap, a pond, and a stream. For the single contaminants, eight types were tested; NaCl, ethanol, citric acid, acetic acid (AA), kanamycin, ampicillin, CoCl2, and silver nanoparticles. Detection limits for all contaminants were found, with the lowest detectable concentrations all falling below or matching detection limits of common methods. The lowest detectable concentrations came from kanamycin and CoCl2, at 2.5E-11 weight percent and in amounts which are considered beneficial to the environment, respectively. The three-contaminant test shows that it is possible to pinpoint which contaminants are having the highest effect, though if contaminants are similar in nature and in similar concentrations, it may be difficult to pinpoint which is causing the effect. In the final test, similarity of water sources to pure water were found, with tap water being closest, followed by stream water and the most different being pond water. It was also found that pond water and stream water were closest in behavior, showing the power of this method in differentiating sources from each other.

Cyanobacterial blooms are of great concern to the drinking water treatment industry due to their capacity to produce microcystins and other cyanotoxins that are deadly to humans, livestock, pets, and aquatic life at low doses. Unfortunately, the strategies currently employed for cyanotoxin detection involve laborious analyses requiring significant expertise or bioassay kits that are subject to numerous false positives and negatives. These methods are incapable of providing rapid, inexpensive, and robust information to differentiate between the >80 cyanotoxin variants potentially present in an aqueous sample. The use of Raman spectroscopy for identification and quantification of the ubiquitous cyanotoxin microcystin-LR (MC-LR) was examined. Raman spectra readily reflect minute changes in molecular structure, spectra can be collected through water or glass, portable Raman spectrometers are increasingly available, and through surface enhanced Raman spectroscopy (SERS) it is possible to achieve femto or picomolar detection limits for a variety of target species. Drop coating deposition Raman (DCDR) was successfully implemented for quantitation of 2-100 ng of MC-LR deposited in 2 ?L of aqueous sample, even without the use of a specifically designed DCDR substrate or Raman signal enhancements. Reproducible MC-LR Raman spectra were observed for both fresh and aged DCDR samples, and the MC-LR Raman spectrum remained identifiable through a matrix of >80% DOM by mass. DCDR methods show tremendous potential for the rapid, simple, and economical detection of cyanotoxins in environmental matricies at environmentally relevant concentrations. / Master of Science

No / The dissociation constant is one of the most important characteristics of a pharmaceutical chemical moiety which has to be estimated with accuracy. The development of in-situ speciation methods in solutions with parallel measurements using Raman spectroscopy (molecular) and pH (macroscopic) for the identification, characterization, and quantitative determination of citric acid species in aqueous solution by numerical data treatment using a multiwavelength curve fitting program over a range of pH values is described. As a result, the first, second and third stepwise dissociation constants of citric acid have been evaluated as 3.02±0.06, 4.78±0.06 and 6.02±0.04, respectively. From these data over the pH range 2.38-6.16 an excellent agreement with literature values was achieved.