abstract: The increasing pervasiveness of infections caused by multidrug-resistant bacteria (MDR) is a major global health issue that has been further exacerbated by the dearth of antibiotics developed over the past 40 years. Drug-resistant bacteria have led to significant morbidity and mortality, and ever-increasing antibiotic resistance threatens to reverse many of the medical advances enabled by antibiotics over the last 40 years. The traditional strategy for combating these superbugs involves the development of new antibiotics. Yet, only two new classes of antibiotics have been introduced to the clinic over the past two decades, and both failed to combat broad spectrum gram-negative bacteria. This situation demands alternative strategies to combat drug-resistant superbugs. Herein, these dissertation reports the development of potent antibacterials based on biomolecule-encapsulated two-dimensional inorganic materials, which combat multidrug-resistant bacteria using alternative mechanisms of strong physical interactions with bacterial cell membrane. These systems successfully eliminate all members of the ‘Superbugs’ set of pathogenic bacteria, which are known for developing antibiotic resistance, providing an alternative to the limited ‘one bug-one drug’ approach that is conventionally used. Furthermore, these systems demonstrate a multimodal antibacterial killing mechanism that induces outer membrane destabilization, unregulated ion movement across the membranes, induction of oxidative stress, and finally apoptotic-like cell death. In addition, a peptide-encapsulation of the two-dimensional material successfully eliminated biofilms and persisters at micromolar concentrations. Overall, these novel systems have great potential as next-generation antimicrobial agents for eradication of broad spectrum multidrug-resistant bacteria. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2019

We employ a four-band continuum model to study the transport and confinement in an n-p-n junction in bilayer chiral borophene for both the identical- and oppositechirality configurations. The conditions for transport and confinement are elucidated in terms of the pseudospin. We study the transmission and reflection probabilities, conductances, and bound states. We demonstrate the existence of topological states in a domain wall between domains of opposite-chirality bilayer chiral borophene with reversed layer stacking. We find that changing the interlayer bias modifies the conductance of the identical-chirality configuration but not that of the opposite-chirality configuration, and that it induces a layer localization of the bound and topological states. Our findings suggest paths towards utilization of the layer degree of freedom in bilayer chiral borophene in future electronic devices.

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The major challenge associated with saving energy in the pumping stations of the fluid transportation in the pipeline networks, especially the crude oil transportation for long-distance is drag forces. In other words, this grossly increases the drag form force and friction losses making fluids transport inside pipeline taken a long time to pass, that increases energy consumption and costs. Therefore, the effective solution to overcome these problems is added drag reduction materials (DRMs) with the main fluid using the drag reduction technique (DR). One of the most important drag reduction technique to enhance flow in the pipeline is an active drag reduction using DRMs. Where the DRMs can reduce drag forces in relatively small amounts part per million (ppm), as well as environment friendly. Thereby, the drag reduction enhancement is highly important in terms of fluid transportation in the many industrial applications. An experimental and mathematical study have been performed in the fully development flow to measure fluid characteristics and to evaluate %DR using various DRMs: polymers, surfactants, and nanoparticles in pipeline network. The active drag reduction experiments have been conducted in the rotational disk apparatus (RDA) and in the closed-loop recirculation system (CLRS) using different solutions of DRMs: individual, binary, and triple at different Reynolds numbers (Re) and at different concentrations. The morphological tests have been done employing XDR, TEM and SEM techniques. Mathematical model was presented to validate the experimental results using the statistic softwareV6.2. The results have been displayed with complete explanation, analysis, and conclusions. The results show that the %DR increases with increasing the velocity (Re) and concentration for the most of DRMs solutions. Also, the results confirm that the use of nanoparticle in complex solutions is more effective than using nanoparticle individually within the same work condition. further, the new complex solutions were formed in a manner that can contribute significantly to increase drag reduction performance and enhance shear resistance of the DRMs. Finally, all microscopy techniques confirm the fact that complex solutions were effectively formed and homogenized within the main fluid.

With existing numerical models for fluid particle systems in CHEM, the acoustic-particle interactions associated with two-phase dilute dispersed flow can be captured and the particle model can be validated using experimental and analytical data and verified using numerical techniques. The experimental and analytical data come from Zink and Delsasso and provides data for particles of diameters 5 to 15 microns for frequencies between 500Hz to 13600Hz. In the particle number density measurements by Zink and Delsasso there was a 10% estimated error range. Using the fourth order skew symmetric flux in CHEM and the built in Eulerian and Lagrangian particle models, the sound wave dissipation was captured and found to be within the margin of error. Two additional tests were conducted to measure the effect of nonlinear acoustics and increased bulk density on the dissipation. Nonlinear effects showed no significant effect and the linear increase in bulk density showed a linear increase in dissipation.

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Proteins are of primary importance to the structure and function of all living cells. Study of proteins relies on the ability to separate a complex mixture so that individual proteins can be more easily processed by other techniques. Since protein samples often exist at low concentration in a small volume, the trend in chemical analysis is toward micro total analysis systems (µTAS) or lab-on-a-chip devices. Among µTAS separation methods, the relatively new electric field gradient focusing (EFGF) technique has shown potential. It focuses and separates analytes based on their electrophoretic migration in an opposing hydrodynamic flow. The detection principles that are compatible with µTAS separation may not always scale down. This thesis represents the development of laser-induced two-photon fluorescence detection on a microchip separation device. This detection is based on excitation of native fluorescence of aromatic amino acids by simultaneous absorption of two photons. First, a compact two-photon prototype detector was investigated. Its sensitivity was improved after discovery of the source of the background and subsequent reduction of background levels. Simple CE separation on a square capillary was coupled to this detector to demonstrate its ability for micro-scale detection. However, this detector did not provide a way to view the location illuminated by a laser and was difficult to use for on-microchip detection. A two-photon microscope was constructed on the frame of a commercial Olympus microscope to solve this problem. The eyepiece of this microscope enabled viewing of the detection volume, and the removal of a glass compensator from the trinocular head allowed for UV detection. This detection system was carefully aligned and optimized before coupling to microchip CE. Two microchip substrates including poly (methyl methacrylate) (PMMA) and glass, and two chip layouts were explored for their compatibilities with the microscope detector. It was found that the PMMA chip with conventional chip layout was not suitable for two-photon detection; therefore, a novel chip layout on PMMA was designed. Through testing the new design, it was concluded that precise focusing of the laser was essential to successful detection on microchips. Although the precise focusing of the laser inside microchip channels was not achieved completely in the limited research period, it is believed that this new design should be an appropriate solution to coupling PMMA chips with the two-photon microscope. Finally, glass chips were employed to successfully demonstrate the detection of amino acids.

Over the past several decades the phenomenon of luminescence (divided into fluorescence and phosphorescence) has received great attention in the field of biological science. This quest has motivated scientists for a variety of applications, including fluorescence imaging. Fluorescence microscopy techniques that provide unique advantages, such as high spatial resolution and superior sensitivity, have been regarded as attractive tools in biophotonics. With the progress of ultrafast laser sources, two-photon absorption (2PA), in which a molecule absorbs two photons simultaneously, has opened possibilities of using it for various applications. Two-photon fluorescence microscopy (2PFM), which affords deeper tissue penetration and excellent three-dimensional (3D) images, is now being widely employed for bioimaging. This dissertation focuses on the design, synthesis, and photophysical characterization of new fluorophores, as well as desirable applications. Chapter 1 gives an account of a brief introduction of luminescence and 2PA, as well as their utilities in biological applications. In chapter 2, a series of new BODIPY derivatives are presented along with their comprehensive linear and nonlinear characteristics. They exhibited excellent photophysical properties including large extinction coefficients, high fluorescence quantum yields, good photostability, and reasonable two-photon absorption cross sections. Two promising compounds were further evaluated as NIR fluorescent probes in one-photon and two-photon fluorescence imaging. Chapter 3 provides the design, synthesis, and photophysical characterization of two BODIPY dyes. In order to assess the potential of using the dye as a fluorescent probe, Lysotracker Red, a commercial lysosomal marker, was investigated for comparison purposes. The results indicate that figure of merit of both compounds were three orders of magnitude higher than that of Lysotracker Red. With an eye towards applications, one of the compounds was encapsulated in silica-based nanoparticles for in vitro and ex vivo one-photon and two-photon fluorescence imaging, in which the surface of the nanoparticle was modified with RGD peptides for specific targeting. The nanoprobe exhibited good biocompatibility and highly selective RGD-mediated uptake in ?V?3 integrin-overexpressing cancers, while maintaining efficient fluorescence quantum yield and high photostability. In chapter 4, the synthesis and photophysical properties of a novel photosensitizer with heavy atoms (halogen) were presented. The dye exhibited low fluorescence quantum yield, resulting in high singlet oxygen generation quantum yield. In vitro photodynamic studies demonstrated that photosensitization of the agent can induce cellular damage, subsequently leading to cell death by a necrotic cell death mechanism, supporting the therapeutic potential of using the agent for photodynamic therapy.

Molecules that are non-superimposable on their mirror image are named chiral or optically active compound. Over the years, molecular chirality has played an essential role in the understanding of fundamental aspects associated the origin of life, drug and food technologies and, asymmetric catalysis, among others. Moreover, most of the groundbreaking discoveries and advances made in this field have happened due to the development of spectroscopic techniques based on the natural asymmetry of the enantiomers and their ability to preferentially absorb right or left polarized light. For instance, circular dichroism (CD), which measures the difference in absorption between these two states of polarized light, has emerged as one of the most useful spectroscopic methods to identify and characterize chiral compounds. Unfortunately, CD is based on linear absorption which, in most common organic molecules, takes place in the UV region of the spectrum where the majority of organic solvents absorb as well. This certainly imposes limitations in the indiscriminated applicability of this technique to the study of chiral chromophores of biological interest in non-aqueous solutions. Consequently, a systematic and comprehensive characterization of the electronic and optical properties of such molecular entities still remains a major issue to be addressed. On this regard, nonlinear optics offers new alternatives to overcome some of the shortcomings of the standard linear CD-based spectroscopy. In order to surmount the existent limitations in this field and deepen in the fundamental understanding of chiral systems, we have mainly directed the attention of our research to the experimental and theoretical study of the polarization dependent two-photon absorption (2PA) of several chiral azo-compounds and binaphthol derivatives in solution. The first part of this dissertation (Chapters I-IV) covers a full characterization of the linear and nonlinear optical properties of a series of non-chiral and chiral azo derivatives. The combination of experimental techniques such as absorption, fluorescence, excitation anisotropy, circular dichroism, two-photon absorption and two-photon absorption circular-linear dichroism in combination with density functional theory calculations allowed us to unambiguously distinguish and assign the spectral position of the main electronic transitions (n-[pi]* and [pi]-[pi]*) in azobenzene derivatives. Our results represent a major contribution to the understanding of the electronic structure of these organic chromophores which have been reported of potential interest in the design of optoelectronic devices. Then, Chapter V describes the development of a novel experimental technique called the synchronized double L-scan for the study of polarization dependent multiphoton absorption in chiral samples. The high sensitivity of this technique resides in the use of "twin" pulses to account for energy and mode fluctuations of the excitation pulse when determining absorption nonlinearities as a function of the light polarization. The robustness of this method was validated by measuring the first ever reported two-photon absorption circular dichroism (2PA-CD) spectrum on a chiral binaphthol derivative in solution. Finally, Chapters VI and VII compile an ample experimental and theoretical investigation of the chirality-dependent 2PA of axial enantiomers in solution. We combined the use of the synchronized double L-scan technique with state-of-the-art density functional theory calculations to provide a precise and reliable description of the contribution of the different electronic excited states to the 2PA-CD and 2PA-CLD spectra. Our findings are foreseen to have a tremendous impact in the comprehension of some of the most fundamental aspects of chiral phenomena.