Bloodborne pathogens are wide spread and can pose risks to health care workers and vulnerable patient populations alike. Conventional diagnostic tests for bloodborne pathogens are costly and time intensive, so fast, affordable, and sensitive diagnostic methods are needed that can be performed under low-resource conditions by untrained personnel. Microfluidic self-digitization technology, developed in the Chiu Laboratory, provides the foundation for such low-cost diagnostics. As undergraduates, we work on the fabrication and optimization of cheap, robust devices used to load samples, as well as dPCR of samples required to detect diseases. As part of a larger research endeavor, we are developing a portable instrument that, in combination with our proprietary microfluidic chip technology, will expand rapid diagnostics to low-resource settings around the world. Expanding diagnostics for bloodborne pathogens will both help prevention as well as monitoring treatment of patients already infected.

Metal catalysts exhibit greater catalytic activity as nanoparticles rather than bulk-like particles. Metal oxide supports can promote the activity and stability of metal catalysts due to the strong metal-support interaction, which can change the electronic properties and structure of metal nanoparticles. Metal-on-oxide-support systems are important for fundamental research and applications in heterogeneous catalysis. Nickel-based catalysts are widely used in industrial purposes such as carbon monoxide oxidation for industrial exhaust cleaning. However, nickel can rapidly deactivate due to solid carbonaceous material (coke) formation and nanoparticle coalescence (sintering) on the surface during a catalytic reaction. Metal oxide supports, such as ceria (CeO₂), improve metal catalytic performance by preventing coke formation and sintering, and in particular, ceria has a high oxygen storage and release capacity during catalytic reactions. Here, the adsorption energies, growth morphology, and charge transfer of adsorbed nickel on stoichiometric ceria (CeO₂(111)) and reduced ceria (CeO_1.8(111)) thin films at 300 K and 100 K are studied using single-crystal adsorption calorimetry (SCAC) in ultra-high vacuum (UHV) and surface sensitive techniques such as low-energy He⁺ ion scattering spectroscopy (LEIS), X-ray photoelectron spectroscopy (XPS), and low energy electron diffraction (LEED). The initial heat of adsorption of nickel atoms on stoichiometric ceria was ~45 kJ/mol greater at 300 K than at 100 K and ~65 kJ/mol greater than reduced ceria at 300 K. The calorimetry results indicate that nickel prefers step edges over terraces and binds stronger to stoichiometric ceria than reduced ceria due to nickel's oxophilicity. LEIS growth mode measurements indicate that nickel grows as 3D nanoparticles. XPS charge transfer experiments show that adsorbed nickel transfers electron charge to ceria below a coverage of 2 monolayers. These results encourage additional study of the adsorption energetics of other group 8 transition metals on ceria supports.

The receptor human protein kinase EphA2 has emerged as a therapeutic drug target for cancer and infectious diseases. However, the dearth of selective EphA2 inhibitors in the field is hampering EphA2-based research and therapies. Our lab recently developed a novel selective small molecule EphA2 inhibitor I268 using medicinal chemistry. Surprisingly, we observed the same inhibitory effects on cell proliferation paradoxically when inhibiting EphA2 with I268 or activating EphA2 with its agonist EphrinA1. We hypothesized that both I268 (inhibitor) and EphrinA1 (agonist) may lead to the same protein-protein interaction network of EphA2 that caused this paradoxical inhibition. We used a chemical proteomic method developed in our lab called “co-clickable precipitation (Co-CP)” to study the interaction network of EphA2 in colon cancer cell line HCT-116. We observed that the onset of inhibitory effect by I268 concurred with the association between EphA2 and a protein interactor called c-RAF, a key player in activating proliferation pathways in cancer cells containing Ras mutations such as HCT-116 cells. We are currently performing confirmatory experiments to characterize whether upon inhibition by I268 or activation by EphrinA1, EphA2 sequesters c-RAF in a form unable to transmit proliferative signals downstream. Our results may demonstrate a possible mechanism for inhibitory effects of EphA2 inhibition on cancer cell growth. These results validated EphA2 as a drug target and may provide novel ways for treating cancer cells by inhibiting cell proliferation pathways indirectly using EphA2 inhibitors.

Synthetic CRISPR–Cas transcription factors enable the construction of complex gene expression programs, and chemically–inducible systems allow for precise, rheostatic-like control over the transcriptional dynamics. We have constructed a bio-orthogonal, chemically–inducible synthetic CRISPR regulatory system to activate and repress gene expression in yeast. By fusing chemically inducible transcriptional regulators to specific RNA binding proteins, we have expanded the tunability of this system of constructs. The RNA binding proteins are fused to half of one chemically-inducible system while the other half is fused to an effector. Upon addition of drug, the two halves come together to form the complete chemically-inducible system and either activate or repress the target gene. We use reporter gene assays to probe the dose-dependence, time-dependence, and reversibility of the systems. The use of multiple, orthogonal chemically-inducible systems and unique guide RNAs allows for more sophisticated, multi-gene programs that still maintain precise control of gene expression dynamics independently at different sites.

New techniques in genome mapping have revealed a high degree of 3D spatial organization in the nucleus. Long-range loops connect enhancers to their gene targets to regulate expression. In order to assess the mechanisms and functions behind 3D spatial organization of the nucleus we need a system that allows us to engineer DNA loops. We use programmable CRISPR-Cas DNA binding domains to target specific sites in the genome. The CRISPR-Cas complex is tethered to a targeting domain (TD) that can dimerize with another TD at a distant DNA locus. To promote interactions between TDs that are bound to DNA, we have designed an allosteric switch that assembles the TD only when the CRISPR-Cas complex has engaged its DNA target. To validate that our switch proteins can act as a DNA sensor we have developed a simple reporter assay; upon successful switch protein activation on DNA a transcription factor is recruited to drive expression of a fluorescent protein. Our results indicate that the protein switches activate when they are recruited to DNA, effectively acting as a sensor for DNA binding. Future steps include optimizing our reporter assay design and modifying the design for DNA looping.

Tuberculosis (TB) kills more than one million people annually. Bacteria of the Mycobacterium genus, including M. tuberculosis, build a complex cell wall containing mycolic acids. This cell wall is difficult to penetrate, so specialized antibiotics are needed. Even with newly developed drugs, bacteria adapt quickly and exhibit resistance at an alarmingly rapid pace. One adaptation that allows the community to survive is production of biofilms. Formation of biofilm is one of many quorum sensing behaviors known in pathogenic mycobacteria. This additional layer surrounds a microenvironment where bacteria can thrive with a very low concentration of antibiotic. Thus, one alternative method to treat TB is to control biofilm formation. In this research, a set of marine bacterial strains, including several bacteria that exhibited swarming behaviors and several from the same environmental samples that did not, were cultured, extracted, and analyzed by 1H NMR and LC-MS as well as in newly-developed biofilm and growth inhibition assays. Initial results showed one group of bacteria produced an organic compound that induced biofilm production in mycobacteria. This was an unexpected result. One representative strain producing a strong biofilm inducer was grown on large scale (10L) then extracted using progressively less polar eluents on a reversed-phase SPE column. The biofilm-inducing fraction was then separated using flask column chromatography. One major component was analyzed spectroscopically using 1D and 2D NMR techniques along with Mass Spectrometry. This compound could result in a strategy to interfere with biofilm formation in mycobacteria, thus making antibiotics more effective.

Modern cells discriminate among the amino acids chosen to be included in protein synthesis: some, like leucine, serine, glycine, and alanine appear in most proteins across most cells, whereas other amino acids, like (g)-aminobutyric acid and aminoisobutyric acid do not appear. This raises the question of how selectivity among amino acids arose – does the selectivity rely on modern protein machinery or could it have arisen in the first protocells of the Early Earth? For example, could certain amino acids have, by some mechanism, associated more strongly with protocell membranes, increasing their chances of being integrated into the first peptide chains? To test this hypothesis, our group assembles rudimentary protocells from molecules that would have been present on the early-Earth: decanoic acid (a fatty acid), sodium mono-phosphate, salt, and water. Vesicles of the decanoic acid spontaneously form. We then add different amino acids to the solutions and measure their turbidity to determine whether each amino acid causes the number of lamellae in the vesicles to increase or decrease. Increased lamellarity correlates with a sturdier vesicle. If certain amino acids increase lamellarity of protocells, that could serve as a method of selection for certain amino acids rather than others. Our results are that particular amino acids (most notably serine, glycine, and alanine) do in fact increase the lamellarity of fatty acid vesicles significantly, whereas other, less common, amino acids do not. We are currently exploring the plausibility of a mechanism for this occurrence involving ease of rotation around the alpha carbon of the amino acids, and we are investigating other ways in which interactions between amino acids and fatty acid membranes might be manifested, for example by a shift in the solution’s critical vesicle concentration. Our results will fit into the overarching goal of understanding peptide formation and protocell stability in order to gain insight into the origins of life on Earth.

Long non-coding (lnc)RNAs have multiple biological functions, including recruitment of kinases to regulate signaling pathways involved in tumorigenesis and other human diseases. Of particular interest is the proposed interaction between Long Intergenic Noncoding RNA for Kinase Activation (LINK-A) and the membrane component phosphatidylinositol-3,4,5-triphosphate (PIP₃). The proposed interaction between PIP₃-LINK-A would be the first example of a direct interaction between a non-coding RNA and phospholipid. I investigated the proposed interaction between LINK-A and PIP₃ using Nuclear Magnetic Resonance (NMR) spectroscopy. Multiple NMR-based experiments were performed to assess the degree of binding on the basis of line-width broadening of NMR spectra. Wild-type and mutated RNA constructs were titrated into a 100 uM solution of PIP₃, but the NMR data showed no evidence of line-width broadening, indicating that no direct interaction occurs between wild-type or mutated RNA constructs. Presumably, the reported cellular interaction is not direct and might require an additional mediating factor. I determined the 3D structure of the LINK-A RNA hairpin, required to recruit PIP₃, using biophysical molecular modeling and NMR data. My results provide a biophysical foundation to elucidate the functional role of LINK-A in PIP₃ recruitment and kinase activation.

Electronic movement can be modeled using the Schrodinger equation. For many-electron systems, however, these equations are not algebraically solvable, which is why this research uses direct numerical integration of Schrodinger’s equation to model time dependent electronic characteristics of molecules. The choice of numerical integration scheme can drastically change the outcomes of the simulation – even causing qualitative changes in molecular behavior. First, an advanced numerical integration technique (4th order Magnus propagator) has been implemented in the ChronusQuantum software package. Next, the effects on molecular behavior of choosing this integration scheme over preexisting schemes are evaluated. The implemented integration algorithms can be used to model the elementary steps of chemical reactions, as well as analyzing the effects of light on electron movement. The research provides meaningful information about the impacts of different implementations of algorithms along with analyzing the simulated behavior of electrons.

A protein's function is dependent on its structure, which is made up of amino acids. Proline, (an amino acid) is known to cause the kinks and turns in protein structures. However, little is known about the influence of pH on the isomeric preference of proline-attached dipeptides. For this experiment, the isomeric preference of methionine-proline was measured in 10% solutions for pH levels of 7 and 11, the pH of the human body falls between the range of 6 and 9. At pH 11, NMR-90 spectra showed that the cis- isometric form was preferred at a rate of 14% more than the trans- isometric form, measured by the alpha hydrogen. At neutral pH of 7 trans- isomers are preferred 36% more than the cis- form measured by the alpha hydrogen and 73% more measured by the delta hydrogen. In conclusion, this experiment supports the hypothesis that proline-attached dipeptides’ isomerization is pH dependent and is more likely to be in cis- form when in high pH in comparison to a neutral pH. The purpose of this experiment is to determine if pH levels can change the structure of a protien, with further research exploring if the change of structure changes the function. This is important to determine if medications containing amino acids can have an optimal or range of pH.

The environment in which a molecule resides can drastically affect both its reactivity and its spectroscopic properties. These effects can be clearly seen in phenomena such as solvochromism or increased reactivity in a protein active site. The most accurate models that can capture these effects are purely quantum mechanical, but they also have a steep computational scaling cost that prohibits their use on large molecular systems. In order to circumvent this, less expensive models, such as molecular mechanics, can be used for the environment while maintaining the accurate model for the system of interest. In recent years, development of polarizable molecular mechanics has enhanced the accuracy of this technique for time-independent systems, but a gap still exists for time-dependent systems. In particular, the frequency dependence of polarizability has yet to be addressed. This research uses frequency dependent polarizabilities to parameterize a novel molecular mechanics scheme. Specifically, a machine learning model is trained to predict the best locations to place isotropic polarizabilities in order to recover the molecular, frequency-dependent polarizability.

Long non-coding RNAs (ncRNAs) play a significant role in transcriptional regulation; therefore, mutations in their sequences can lead to human disease. An example is provided by the promoter associated non-coding RNA (paRNA) that, when bound with Argonaut 1 (Ago1) and a miRNA, plays a key role in coordinating gene silencing of the tumor suppressor CDH1 in epithelial cells. The paRNA expression can be implicated with cancer. This is due to a single nucleotide polymorphism (SNP) at positions -160(C/A) relative to the CDH1 promoter. The -160(A) isoform favors a unique secondary structure of the paRNA, distinct from more common -160(C), which favors over-suppression of CDH1 and leads to increased cancer risk. To better understand how the -160(A) isoform mechanistically drives increased suppression of CDH1, our lab is applying NMR-based methods to determine the 3D structure of the paRNA. However, the T7 RNA polymerase used to synthesize RNA is prone to producing heterogeneous products in longer RNAs such as this one. Having exact lengths of the transcript is important for improving signal-to-noise and peak sharpness in NMR spectra, which is critical for 3D structure determination. To overcome this problem, I designed a pUC19 plasmid containing the paRNA -160(A) sequence with a downstream self-cleaving hepatitis delta virus (HDV) ribozyme. Following transcription, the HDV ribozyme undergoes self-cleavage, producing homogenous ends at the 3’ end of the paRNA. My results show that HDV incorporation produces a single species of RNA with no 3’ overhang and improves NMR spectra quality. This cloning tool is easily adaptable to other large RNAs, facilitating data collection for other large RNAs used in our lab. Ultimately, our ability to predict the 3D structure of this paRNA could someday lead to its use as a potential drug target.

Tin-doped indium oxide (ITO) is a n-type semiconducting material that have been widely used in solar cells, smart windows, and transistors. This material conducts electricity due to excess free charge carriers which charge-compensate the tin dopants. We are working to develop new chemical treatment methods to build optoelectronic devices from ITO nanocrystals. Colloidal nanocrystals are well-suited for solution-processing and low-temperature deposition techniques. These routes can be ideal for fabrication of thin-film electronics, especially on flexible substrates; however, increasing electronic communication between nanocrystals require post-deposition treatments. Few low-temperature methods to create conductive films from oxide nanocrystals have yet been reported. We seek to increase the conductivity of ITO nanocrystal films with ligand-exchange procedures to decrease the distance between each nanocrystal, then chemically crosslinking them. We synthesized ITO nanocrystals, then resuspended in solvents at high concentrations for film deposition. We first modify the surface of our nanocrystals by replacing the native long nonpolar ligands with short polar ligands. The modified crystals were deposited by spin-coating onto glass substrates and a variety of solvents/conditions were tested to optimize uniformity and thickness. Four-point probe measurements resulted in sheet resistance (R_s) ranging from 1 MΩ/square (ligand exchanged nanocrystals) to 2 TΩ/square (untreated nanocrystals). Profilometer measurements probed film thickness that can be used to calculate our films' bulk resistivity. Next, we used zinc and aluminum compounds as chemical solders to build bridges between nanocrystals to increase the material’s conductivity. R_s drops to ~0.15 MΩ/square with aluminum bridges and ~0.10 MΩ/square with zinc bridges. We plan on using other undoped metal oxides with this same scheme and apply them to thin-film field effect transistors (FET) to investigate how these treatments improve FET performance. We are also working on using similar techniques with SnO₂ nanocrystal films for application as electron-transport layers in perovskite solar cells.

Fossil Fuels are associated with contemporary energy crises and climate change. The combustion of fossil fuels is leading to increased greenhouse gas emissions, which in turn have increased the overall earth’s temperatures and is predicted to grow at an alarming rate. Fuel cells are alternative, sustainable sources of energy that uses hydrogen (or hydrogen-rich fuel) and oxygen to generate electricity through electrochemical processes. I conducted a survey, focused on Bellevue College’s (BC) Chemistry Department, that indicated broad support for a simple hydrogen proton exchange membrane (PEM) fuel cell lab to be incorporated into the introductory chemistry curriculum. I will design a lab that will spark student interest in sustainability and expose students to real-world electrochemistry applications while addressing electrochemical, thermodynamic, transport phenomena, and clean energy concepts. The educational goals of this lab are to promote a deeper conceptual understanding of electrochemistry, to improve quantitative reasoning, and to improve explanations of observed scientific phenomena. I collaborated with BC’s Chemistry Department to determine learning outcomes and a systematic process to quantifiably assess fuel cell labs from other institutions. This information was used to design an effective lab and lesson plan surrounding fuel cells. Four fuel cell labs were evaluated: (1) A pre-constructed Hydrogen PEM Fuel Cell from Horizon Fuel Cell Technologies (2) A microbial fuel cell, (3) A fuel cell using platinum electrodes that is bathed in an acid solution (4) A fuel cell using graphite electrodes that is immersed in an acid solution. This research produced an economical and introspective laboratory experience that utilized basic laboratory equipment and materials. The results were presented in an engineering framework that details how aspects of the lab promote critical thinking and engagement, addresses learning objectives, and was cost-effective.

In recent years, researchers have dedicated much effort to overcoming the ~250 nm spatial resolution limit of light in order to reveal biological details that have been obscured by diffraction. A new form of super-resolution microscopy called expansion microscopy (ExM) relies on physically expanding a fixed specimen in a swellable hydrogel polymer and offers a simple, inexpensive approach to achieving ~70 nm resolution with conventional confocal microscopy. A critical and understudied step in this process is the homogenization of the embedded sample by proteolytic enzymes, enabling artifact-free expansion. However, in large and complex samples like Drosophila, enzymatic digestion is time-consuming and sensitive to experimental parameters such as fixation, hydrogel composition, and tissue type. To overcome the limitations of enzymatic digestion, I have explored parameter space for rapid peptide cleavage using air-tight stainless-steel vessels to achieve high temperatures and pressures not typically accessible in the lab. Additionally, a small-molecule digestion agent, dimethoxyiodobenzene, was tested in order to provide site-specific peptide cleavage and enhance tissue homogenization. The modified digestion process was first validated using standard immunofluorescent microtubules in cell culture. Next, Drosophila tissue was treated using thermal digestion to confirm the applicability of this technique in robust, difficult-to-expand tissues. This improved ExM protocol holds the potential to increase sample throughput, reduce expansion-related sample distortions, and extend ExM to be applicable to a wide range of previously incompatible tissues types, enabling pathologists to better analyze and assess diseases in human tissues.

Proteins are essential to life, but many structural methods fail to capture the dynamic nature of proteins. This means researchers are left with an incomplete view of how protein function and structure relate. The Stoll lab uses electron paramagnetic resonance (EPR) to study the dynamic structure of proteins. The project I am working on is investigating the way in which the measurement conditions in EPR affect the determined protein structure. We use maltose binding protein (MBP) as a model system, since its structure has been previously well-characterized. My primary role has been to create new mutants for site-directed spin labeling, in which a radical spin label is attached to the protein. This radical is measured by placing the sample in a magnetic field and results in a probability distribution of distances. Common spin labels used in EPR, however, have many rotatable bonds, andd can cause uncertainty in the extracted distance distribution. Our project is investigating the contribution of spin labels to the EPR experiment. I use polymerase chain reaction to create new mutants of MBP by swapping a native residue with a cysteine residue in the mutants. Each mutant has one or two amino acids replaced with a cysteine. After mutating the DNA, I then transform the mutant DNA into wild type cells to grow the mutant protein and purify the protein. The spin label forms a disulfide bond with the cysteine residue in the mutant, providing an unpaired electron for measurement. By using various commonly used spin labels on many different site pairs in MBP, we hope to develop a model in which the contribution of spin labels to the probability distribution of distances is accounted for. This will ensure more accurate results in determining protein structure and will aid in structural characterization of many proteins.

The objective of this study is to evaluate vaping products that contain vitaminB12 (cyanocobalamin). Breathable vitamin supplements claim to be moreeffective than oral and injectable methods. Vitamin B12 is known to bechemically unstable when exposed to certain variables such as heat, light,oxygen, etc. in biochemistry related studies. The recent popularity of usingvaping devices as delivery methods for flavorings and other substances(including vitamins) prompts the need to study the chemical composition ofe-juices after vaping conditions to evaluate their safety.

Reactions of titanium oxide and silicon dioxide are of importance in materials used in high temperature environments. There are questions concerning the reaction of titanium dioxide (rutile) with silica. Both are important as potential materials or reaction products in thermal barrier coatings or environmental barrier coatings in combustion environments, as for example in gas turbine technologies. The extent of reaction and temperature range are important questions to answer for this chemical system. Experimental evidence would suggest that a third cation is necessary to have compound formation. Presently we are exploring the reaction of titanium dioxide with silicon dioxide with small amounts of yttrium oxide being added. Mixtures of the three oxides are being subjected to heatings at various temperatures from ca. 1200-1500°C. Samples are characterized before and after heating by means of X-ray diffraction and diffuse reflectance infrared spectroscopy, transmission infrared spectroscopy, and/or diffuse reflectance UV/Vis spectroscopy as appropriate. There hasn’t been any evidence of reactions between titanium dioxide (rutile) and silica. The sample will be continued to be heated at longer times and higher temperatures, and results in experiments to date at1300 °C will be presented.

Ion Mobility-Mass Spectrometry (IM-MS) is an analytical technique that is useful for analyzing large biomolecules with minimal disruption to their natural structure. One of the most common methods of introducing proteins to the gas phase in IM-MS is electrospray ionization (ESI), whereby a large voltage applied to a sample induces a spray of droplets that quickly evaporate and leave the desired analyte as a gas-phase ion. It is established that the high voltages of this process lead to a buildup of charge via electrochemistry in the sample solution, which may cause changes to the pH of the solution. However, this phenomenon has primarily been characterized in systems with continuously replenishing samples that form a steady state between excess charge formation and incoming sample flow. This work establishes a method to identify these changes in small, non-replenishing systems, which have not yet been characterized and are the standard practice for IM-MS analysis of proteins. Using SNARF-4F, a pH-sensitive fluorescent dye; a series of filters and a camera; and Python scripts for image processing; the rates and spatial position of pH changes under non-equilibrium conditions were determined with high accuracy. Additionally, several methods of preventing or slowing pH changes are examined. These include the use of buffers such as ammonium dihydrogen phosphate and ammonium bicarbonate, or periodic cycling between positive and negative electrospray. Preliminary findings indicate that these buffers can affect pH change, but at high enough concentrations, may also reduce the quality of mass spectra.

Black phosphorus, an allotrope of phosphorus with a unique layered structure, can be exfoliated to form a few layer variant called phosphorene.  Phosphorene has recently emerged in the field of 2D materials as a promising candidate for use in novel electronic and optical devices.  Phosphorene's Achilles' heel, however, is its air-sensitivity.  When exposed to air, phosphorene is rapidly oxidized, losing its valuable optoelectronic properties.  Herein, we propose Lewis acids such as GaCl3, AlCl3, and AlBr3 as effective reagents for protecting phosphorene.  This Lewis acid-based strategy has advantages over previous methods because it is reversible and leaves phosphorene optically and electronically accessible.  A Lewis acid can act as an electron acceptor for the lone electons pairs on the surface of black phosphorus.  By sterically blocking oxygen's access to these lone pairs, ambient degradation in phosphorene is drastically slowed.

Crucial processes in clean energy research, such as the splitting of water into H₂ and O₂ and the reduction of CO₂, require multi-electron redox events throughout a catalytic cycle. Noble metals such as iridium and platinum prefer such events, while more abundant and consequently cheaper base metals prefer single-electron events. Redox-active ligands offer the potential of enabling noble metal behavior in base metals by combining a single-electron transformation at both the metal and the ligand to create an overall two-electron process. While redox non-innocent ligands are typically comprised of organic components, cobalt selenide clusters offer an attractive alternative given their wide variety of accessible oxidation states. Here, I present the synthesis of heteroleptic cobalt selenide clusters [cis-Co₆Se₈(PEt₃)₄(RNHP(C₆H₅)₂)₂ Et = ethyl, R = alkyl, aryl] containing ditopic aminophosphine ligands. The cluster was then metallated using copper(II) triflate and the product was fully characterized by multi-nuclear nuclear magnetic resonance, ultraviolet-visible, and infrared spectroscopies. Further analysis was performed using cyclic voltammetry and the solid-state structure has been solved via single-crystal X-ray crystallography. Upon spectroscopic analysis, it appears that copper(II) is reduced to copper(I) by the cluster. This result is encouraging, as using clusters as redox-active ligands would require facile electron transfer between the metal atom and the cluster core.

Quantum confined nanomaterials have become an important field of study with many applications from color displays to low-energy alternative lighting sources. Discovered in the early 1980s, these semiconducting nanocrystals continue to draw attention; their unique properties differ from their bulk counterpart’s due to a quantum confinement effect rising from their small nanometer-scale size. Indium phosphide (InP), a group III-V semiconductor, is a promising nontoxic, environmentally innocuous material. The morphology of the synthesized InP nanocrystal is commonly a quantum dot quantum-confined in all three dimensions. However, the utility of the dot in biological imaging and display applications is hindered due to reabsorption resulting from overlap in its absorption and emission properties. This dims the light of an indicator and limits efficiency in catalysis. The subject of this investigation—InP quantum rods— offers a solution to this problem, as it is quantum confined in two dimensions and exhibits bulk semiconductor characteristics in the third, separating the absorptive and emissive features and improving the photoluminescent quantum yield. My procedure involves a hot-injection method. Currently, a magic sized cluster hot-injection synthesis in N-methyl pyrrolidone at 150 °C is known to afford InP rods (Dr. Friedfeld, UW Cossairt lab). I explore multiple experiment sets that manipulate the reaction length and temperature of the synthesis, cluster identity and concentration, and the identity of the aprotic polar solvent in which the reaction takes place. I characterize all material via UV-vis spectroscopy and imaged on a transmission electron microscope. The aim of the investigation is to learn why these rods form and what reaction conditions favor their formation. In understanding how to efficiently control the distribution of InP rods v. dots using chemical tools, the usefulness of nanocrystals in nanobiotechnology and clean energy science can be improved.

Increasing energy demand coupled with over-reliance on fossil fuels and other non-renewable energy sources has created a need for alternative renewable energy sources. The sun is one of the most promising sources and photovoltaic cells are one way to capture solar energy. Halide perovskite thin-films have recently emerged as ideal materials for solar cells due to low fabrication costs, bandgap tunability, high extinction coefficients, and high carrier mobility. Moreover, they have demonstrated rapid gains in power conversion efficiencies from 3.8% to 23.7% in nine years. Halide perovskites have the molecular formula ABX3, where A and B are cations while X is a halide. Past research has shown that methylammonium(MA) lead triiodide, a commonly used perovskite, can be changed into formamidinium(FA) lead triiodide by exchanging the A-site cation in a formamidinium iodide solution. This highlights high ion mobility and interchangeability in perovskites. However, in perovskites with mixed-ion composition, high ion diffusion adversely affects the device performance due to ion segregation, but little is known about inter-diffusion of different ions in perovskites. Here, we investigate the inter-diffusion of A-site and X-site ions in halide perovskite films by creating a lateral heterojunction of the ions. We confirm the creation of the gradient using UV-Vis and steady-state photoluminescence (PL) measurements. We further confirm that there is no change in the film morphology and crystallinity as evidenced by SEM and XRD, respectively. With PL line scans across the lateral gradient, we image the inter-diffusion of the ions as a function of position and time. Using Fick’s Diffusion equations to fit the PL line scans, we determine the ion inter-diffusion coefficient and extract the activation energy using temperature dependent measurements. This study demonstrates a facile quantitative method of probing the ion inter-diffusion in halide perovskites and furthers understanding of mixed-ion perovskite compositions.

Space travel and exploration provides a new perspective of the universe and our place within it. Private companies are taking the leading role in driving the aerospace industry. Many of these companies are looking for new technologies that will lower the cost of spacecraft production and operation. This goal could be achieved through the development of a multi-use modular launch vehicle. This project created a scaled modular rocket utilizing an adjustable ring fin design. The adjustable ring fin allows the user to easily and quickly change the aerodynamics of the rocket to compensate for a variety of payloads. Four test models were created using Callisto rocketry kits. Three of the Callistos were modified with a variety of ring fin diameters, and one was kept as an unmodified control. The live test parameters were based on rail velocity, visual stability, and altitude. After the baseline performance of each ring fin was established, the lengths of the rockets were adjusted to simulate different payloads. This work demonstrates that adjusting the ring fin allows the same base rocket to fly a variety of payloads without needing to construct a new rocket. Successful flights of the test vehicles, with improved performance based on our alterations, provide a new avenue of research into incorporating small modifications to garner a wide array of uses without extensive and costly modification. Further research will involve scaling up to rockets with motors with an impulse up to 10,000 newton seconds, as well as testing other innovative concepts related to modularity and revisions to the ring fin design. The ultimate goal is the design of a single rocket with a changeable ring fin that can be used in a wide variety of applications, saving money on research and development of new launch systems.

Mercury (Hg) is widely known to be a neurotoxin. Mercury in our environment is found in many different forms, and the key difference between them is evident in the way they are absorbed by organisms. Hydrophobic methylmercury (Me-Hg) readily bioaccumulates in the tissues of all organisms, leading to Hg exposures involving higher doses. Recent research shows that sulfate-reducing bacteria (SRBs) play a role in methylating mercury only when they possess the hgcAB gene cluster. Gaining a more comprehensive understanding of the aqueous conditions required for SRBs to thrive and consequently methylate inorganic mercury is essential for addressing the ongoing problems associated with Hg toxicity. In the initial phase of this study, ion chromatography was used to quantify sulfate (SO42-) concentrations along an urban river in an industrial region of Seattle (the Duwamish/Green River Watershed). The measurements revealed that SO42- concentrations as high as 5300 ppm were present at several sites along the lower portion of the Duwamish River. A number of previous studies also showed significant amounts of mercury in this region’s sediments and fish tissues. The secondary phase of this study involved an investigation determining whether the measured high sulfate concentrations were related to the production of Me-Hg and additionally examined if SRBs likewise played a role. River sediment was analyzed for the presence of the hgcAB gene cluster. Ongoing studies are focused on quantifying Me-Hg at sites where SRBs were found and on the identification of key indicators for mercury methylation conditions along a watershed. This study provides further insight into the relationship between mercury, sulfates, and SRBs when found in combination in an aqueous environment.

Virtual reality augmentation of therapy has advanced a long way since its beginnings. Virtual reality technologies have been found effective for treatment of post-traumatic stress disorder and phobias as well as a potential aid as an in-treatment distraction for burn patients undergoing dressing changes. The advent of increasingly advanced displays, tracking, and comfort have transformed virtual reality from a novelty into a highly beneficial clinical device. The increasing presence of virtual reality devices in clinical settings necessitates additional investigation into sterilization techniques. The diversity of materials in the devices makes a single method of sterilization difficult. The device’s vulnerable surfaces can be separated into categories: lenses, casing, straps, and facial interface. The delicate electronics preclude the use of autoclave sterilization and the porous nature of the straps and cushioning preclude the use of surface wipes. Finally, the delicate lenses need special care to facilitate cleaning while retaining structure. In the present study UV, steam autoclave, and water-based benzalkonium chloride antibacterial foam were compared to standard procedures by Oculus, one of the leading commercial manufacturers of virtual reality devices. Oculus Go virtual reality headsets were disassembled for testing. After determining baseline presence of environmental bacteria, Staphylococcus Aureus was applied to the tested surfaces. The previously mentioned methods were applied to the newly contaminated surfaces and the surfaces were swabbed and cultured. Effectiveness of sterilization was determined through numerical analysis of colony forming units. While Oculus' standard procedures have adequately disinfected some of the diverse materials tested here, more rigorous methods are needed for complete sterilization. A hospital setting may benefit from a multifaceted and specialized approach that addresses the needs of different materials to prevent increases in resistant strains. Proper sterilization procedures for this rising technology will allow for safe widespread implementation as a medical device.

Lecture demonstrations have a long history of use in science learning spaces. While extant research in STEM education show that demonstrations can be used to rouse student interest, some studies suggest that demonstrations have little to no effect on improving students’ understanding of the concepts taught in class. In chemistry, demonstrations are commonly used in lectures with the belief that student understanding of chemical concepts improves from observations of chemical phenomena. The purpose of this mixed methods study was to investigate students’ perceptions of lecture demonstrations and their usefulness in preparing for exams. To measure students’ perception of lecture demonstrations, a survey was administered to first year students (n <1500) in nine introductory chemistry classes over two quarters. Initial findings reveal that while students do in fact remember and enjoy lecture demonstrations, they found it difficult to apply demonstration concepts to problems on exams. Results also suggest a strong link between student engagement and exam performance. Overall this study highlights the importance of soliciting student feedback for improving and designing course materials and tools. Various strategies and implications for practice are also addressed.

A study conducted by Dunning and Kruger suggested that people with high skills usually under evaluate their performance, whereas relatively lower skilled individuals tend to over evaluate the performance due to a limited amount of knowledge. This research aims to model the relationship between students’ self-assessed and actual performance on exams in general chemistry courses at the University of Washington. Using a two-stage least squares regression analysis, we examined student’s’ estimation of their test performance following course examinations and their actual performance. The results indicated the magnitude of overestimation was on average greater for students receiving lower exam scores, while high performers tended to under evaluate their performance, consistent with the so-called Dunning-Kruger effect. In addition, the degree of overfidence was more pronounced for men with lower performance; however, higher scoring women tended to underestimate their performance relative to men with equivalent scores. The immense number of external factors that contribute to students’ exam performance threatens the validity of estimates of the Dunning-Kruger effect. Therefore, this research also examined the role of measurement bias in estimating the relationship between students’ self-assessment and actual exam performance.

Antibiotics are an environmental contaminant increasingly found in aquatic ecosystems, adversely affecting wildlife and contributing to antibiotic drug resistance. Sources include untreated agricultural runoff entering rivers and estuaries, outdated or leaking septic systems in rural areas, and large urban populations excreting unmetabolized medications into sewage systems. Current wastewater treatment methods are unable to effectively mitigate the release of these environmental toxins, thus new approaches are needed. White-rot fungi produce lignin-modifying enzymes which can degrade persistent organic pollutants, including antibiotics. Previous studies have demonstrated that the mycelia of turkey tail (Trametes versicolor) and shiitake (Lentinula edodes) mushrooms can reduce concentrations of the common antibiotics erythromycin and cefuroxime, respectively. In this study, three species of fungus (turkey tail, shiitake, and oyster mushrooms/Pleurotus ostreatus) were combined to create a more dynamic and effective approach to removing antibiotics from wastewater, using commonly available equipment and low-maintenance growth conditions. The fungi were cultivated at room temperature in modular bins, connected in series with removable tubing. The mycelia of the fungi were exposed to antibiotic solutions (erythromycin and cefuroxime dissolved in water) and tested for rates of removal in two phases. The first phase established a baseline rate of removal for each single fungus/antibiotic pair; the second phase optimized the sequence of fungus species and method of exposure (continuous flow vs. batch mode) to improve filtration of a synthetic wastewater solution containing both antibiotics. Results suggest that combining fungal species may be a more efficient method of filtration compared to methods using a single species. This is a promising step towards advancing the practical technologies available for complex wastewater treatment in various settings.

 In vivo animal models are an advanced tool for testing complex biological phenomena and functions in humans, yet are difficult to adapt due to high cost, biological and anatomical differences, and ethical concerns. As an alternative to in vivo models, in vitro organotypic models have been created that can accurately and efficiently reproduce biological processes, allowing researchers to probe specific factors without the difficulties associated with in vivo models. We present further development of a novel microfluidic platform, called Stacks, which uses open and suspended microfluidic principles to enable spatial and temporal manipulation of 3D cultures in suspended collagen plugs. We are developing the Stacks platform to accurately reflect morphology exhibited in the air-liquid interface (ALI) of the epithelial layer of the lung and allow analysis of lung pathophysiology, cell signaling, and immune responses of the lung in both monoculture and coculture. Furthermore, using the flat faces of the device that allow for stacking, we have connected a layer of human lung endothelial cells, representing a model vascular system, with a second layer of immune cells and mycobacterium, representing a model infection system, to study soluble factor signaling in granulomatous infections. Through the modification of the Stacks device, we can achieve granuloma formation and utilize soluble factor analyses (e.g., immunoassay) to observe and characterize infection-dependent changes in vasculature resulting from the exchange of chemical signals generated by the infection model. Future development of the platform will build on these newly developed lung models to combine them for studies involving signaling and disease mechanisms between the lung ALI and the underlying tissue layers.

Metal-organic frameworks (MOFs) represent an important new class of adsorbent materials, catalysts, and catalytic supports. As such, it is important to fundamentally understand its adsorption capacity and selectivity of simple gases. NU-1000 is a prototypic zirconium-based MOF which has shown to be thermally stable up to 250 C and has a number of interesting catalytic and adsorbent properties. It is composed of zirconium oxide nodes connected by pyrene linkers with COO- end groups. We determined the isosteric heats of adsorption (Qst) versus coverage of four gases (N2, CO, Ar, and CH4) on NU-1000 by measuring volume-pressure equilibrium isotherms at very low coverages (under 0.1 monolayer) and above 90K. We then compared our experimental measurements to density functional theory (DFT) calculations of adsorption enthalpies at 77 K for the zero-coverage adsorption of the same gases at seven different types of sites of the MOF lattice. These comparisons showed remarkable agreement between the measured and theoretical isosteric heats in trend as well as reasonable agreement in magnitude, indicating that the sites predicted by DFT calculations are populated sequentially in order of decreasing absolute enthalpyt. This study further increased our understanding of adsorption on this prototype MOF at very low coverages and reaffirmed the accuracy of theoretical calculations.

To keep peace with increasing world energy demands, scientific research has shifted to devising sustainable energy alternatives. Unlike widely used fossil fuels, solar energy is carbon-free and globally abundant, and therefore a promising energy supplement to aid global efforts in reducing anthropogenic carbon footprint. My project sought to employ light-harvesting colloidal semiconductor nanoparticles, namely quantum dots (QDs), to drive the energy-intensive depolymerization of lignocellulosic biomass and to store solar energy in chemical bonds. Accounting for 40% of biomass’ energy content, lignin is one of few naturally existing polymers composed of valuable functionalized aromatic species and is the target substrate for the decomposition reaction. Recently, iridium-based catalysts have been used to cleave β-O-4 linkages (predominant C-O lignin linkers), however, iridium’s high cost and poor long-term stability hinder its utility in extensive production and application. In contrast, prior work from my research team has demonstrated that QD photocatalysts boast lower synthetic costs, higher turnover frequencies (up to 15x faster), lower catalyst loading (333x less catalyst), and various traits desirable for industrial reproduction over iridium. Beyond QDs, my studies also looked at the synthesis of anisotropic nanoparticle photocatalysts such as nanorods and nanotetrapods. QDs are quantum confined, meaning photoexcited, oppositely-charged electrons and holes (electrons’ counter charges) recombine quickly in all dimensions, which endows them with size-tunable semiconductor functionalities. Nanorods and tetrapods are quantum confined in the width but not along the length dimension, which delays the recombination of paired electrons and holes (excitons). This elongated exciton lifetime allows more time for substrates to interact with our nanomaterials which facilitates photocatalysis. As pioneers in studying photoredox-active nanomaterials, we were motivated to decipher how nanomaterial design dictates photocatalytic performance, which not only furthers the search for most efficient photocatalysts but advances contemporary research on effectively using solar energy to derive solutions to presently-unfeasible, energy-demanding reactions.

Cysteine is an infrequently occurring but important amino acid critical to tertiary and quaternary structure. While peptide chains typically undergo post-translational modifications, cysteine is susceptible to further modification due to its reactive thiol group. The effects of these modifications are unclear, as they could either represent normal cell-cell communication or potentially harmful by-products. Common agents that affect the thiol group of cysteine are by-products from other biological processes, for example metabolic processes (which creates H₂O₂), natural toxicant defense (p450 or glutathione), and inflammation (HOCl). This experiment sought to discern the products that form when cysteine is exposed to biologically relevant concentrations of these oxidants. Liquid chromatography-mass spectrometry (LC-MS) was used to perform the analysis of the oxidation products. Cysteine was mixed with 5 mM bleach in vitro and pH buffered and the resulting solution was analyzed. Methods were developed by optimizing instrumental conditions—including molarity of solutions, voltage spray and flow rate, and acidity of the samples—in order to use LC-MS. Pending results will allow for the identification and quantity of the cysteine oxidation products.

Omega-3 fatty acids provide numerous health related benefits, and are commercially available in the form of supplements. However, these fatty acids have the tendency to oxidize over time and can have potentially harmful effects on the human body. Additionally, neutrophil oxidation of fatty acids in vitro has been shown to be a marker for oxidative stress. Oils oxidized with a biologically relevant concentration of sodium hypochlorite were used to simulate the behavior of neutrophils in the human body and these results were analyzed and compared to control samples. In order to characterize the oxidation byproducts of common fatty acids, the oxidation products and control samples were treated with acidified methanol in toluene to perform a fatty acid methyl esterification (FAMEs). This facilitated the analysis by gas chromatography and mass spectrometry (GC-MS) and provided proof-of-concept for the fatty acid analysis method. This methodology was applied to 0.29 mmols of each sample of oil oxidized with .05 mMols of sodium hypochlorite to evaluate the products of this reaction to simulate the behavior of neutrophils in the human body. GC-MS data for the composition of the FAMEs and oxidation derivatives detected will be presented as well as their relative amounts.

Harmful radiation, such as UV photons from the sun, can damage DNA in a manner that results in cation-radical formation which leads to nucleobase loss and strand breakage. In the Frantisek Tureček research group, DNA cation-radicals were generated in the gas phase, isolated and subjected to incremental wavelengths between 210-700 nm with intent to observe their absorption action spectra that can be used to assign structures and intrinsic properties. The difficulty with these experiments is the ability to effectively communicate the experimental set-up of mass spectrometers, tunable lasers, and various other pieces of equipment in a supporting manner that delivers concise information to be understood regardless of prior knowledge in this specific field. I had the unique opportunity to take two-dimensional, over-simplified schematics and transform them into three-dimensional, professional and photorealistic images of our experimental arrangements using Siemens NX CAD modeling software.

There has been growing concern regarding rising carbon dioxide concentration in the atmosphere because CO₂ traps excessive heat and warms the planet through the greenhouse effect. One strategy to mitigate this problem is through the capture and conversion of CO₂ via hydrogenation to fuels and chemical feedstocks that are currently produced from fossil fuels. Given the complexity of these multi-electron, multi-proton transformations and the multitude of products that can result, catalysts are required to lower the energy barrier and direct the selectivity of CO₂ conversion reactions. One catalyst currently under development is a Ru(II) bis-(protic N-heterocyclic carbene) phosphine catalyst, which incorporates protic N-H wingtips adjacent to the metal center. The N-H wingtips are an interesting feature due to their ability to activate CO₂ through metal-ligand cooperation, their accessibility as a proton source near a metal active center, and the likelihood that they aid in splitting H₂ between the metal center and the nitrogen. Preliminary results have shown moderate turnover numbers (TONs) for both formate (130) and methanol (7), the latter of which is a rare transformation in a single catalyst system. In order to improve catalytic TONs and understand the role of protic N-H wingtips, a library of catalysts with varying ancillary ligands, including 2,2’-bipyridine, 4,4’-dimethoxy-2,2’-bipyridine (electron donating), 4,4’-dibromo-2,2’-bipyridine (electron withdrawing), and 1,2 bis(diphenylphosphino)ethane (sterics), is synthesized and screened under high pressure and temperature conditions using THF solvent and varying additives (e.g. Li₃PO, K₃PO₄, KPF₆) and additive concentration. It is expected that the ancillary ligands, bound trans to the bis-carbenes, will influence the proton donor ability of the N-H wingtips and catalytic turnover.

Probiotic bacteria grow on the intestinal lining and are essential for optimal digestive health. Understanding the optimal growth conditions for these probiotics is particularly important, since healthy probiotic populations in the gut have been shown to positively impact health in a number of ways. In order to determine the effect of pH and nutrient availability, the following methods were performed; first, probiotic growth was achieved by inoculating Sigma-Aldrich (MRS) and Luria-Bertani media (LBm) at different pH’s ranging from 2 to 7.5. For both MRS and LBm, live cultures of probiotics have been proven to grow successfully in both media while incubated at 37 degrees Celsius at the pH of +/- 6.2. The Bradford protein assay was used to determine protein concentration in samples of both media, and the tryptic digestion of the bacterial cultures were analyzed by liquid chromatography mass spectrometer. These findings will be reported, highlighting important differences in the proteomic data sets in relation to different environmental variables.

Microbial communities are essential to numerous biological systems from aquatic and land ecosystems to the human gut. Our understanding of interactions among bacterial strains can help us understand how these communities form and function. Such interactions may depend on the species themselves but can also be sensitive to the abiotic environment. Harsh environments, where mortality is increased, can reverse the outcome of a competition between species. Simple models predict that increasing mortality favors faster growers, and past experiments repeatedly confirmed this prediction. In these pairwise competition experiments, slow growers excluded fast growers in low-mortality environments, but increasing mortality caused fast growers to dominate. A necessary condition for observing the reversal is that slow growers are good competitors in low-mortality, high-density environments. While this tradeoff between growth rate and competitive ability was common in well-characterized lab strains of bacteria, it was unclear if it might exist elsewhere. In this project, we tested for the existence of a growth/competition tradeoff in a natural community of bacteria collected from MIT’s Killian Court. Contrary to past results and some evidence from the literature, we found a weak positive correlation between competitive ability and growth rate, which does not support the idea of a tradeoff.

Plastics are a ubiquitous part of modern life, without them many issues in the food, medical, and textile industries would be near insurmountable. However, our failure to consider life cycles of materials containing plastics have led to a global environmental threat. As polymers break down through degradation, they can create microplastics (MP’s) or fibers that can escape into the environment. Microplastics are generally less than 5mm. Recent studies have indicated that endangering levels of MP’s have been found in the oceans. Little to no research has been conducted on the quantity of MP’s found in freshwater bodies and land far from the influence of the ocean. Little is known about the amount of MP’s released during a clothing dryer cycle. To address sources of MP’s created from a clothing dryer, samples of lint were collected beneath the dryer vent exits. Aggregate characterization of the samples were performed using attenuated total reflectance infrared (ATR-IR) which allowed samples to be evaluated based on a measured wavelength of a reflected beam of light. Samples collected were representative of MP’s that would shed from textiles during a drying cycle and be distributed into the air. To effectively characterize and count MP’s in solution a fluorescent dye (Nile Red) was used to stain the samples before imaging with a Fluorescent Microscope. Most dryers have a mesh screen to catch lint which has been useful, but it doesn’t capture all the microfibers during a drying cycle. Still, hundreds if not thousands of microfibers evade the lint filter and are likely being released from the vent. The potential consequences of not regulating the release of MP’s correlate with the growth of the textile industries. An important first step to this problem involves similar research to better understand the origin and release of MP’s into the environment.

 A method of negative-pulse partial modulation for comprehensive two-dimensional gas chromatography (GC×GC) using a pulse flow is studied. The capability of a pulse flow valve modulator has been shown to enhance many aspects of GC performance such as chemical selectivity and reduced analysis time, allowing complex GC×GC analysis in a shorter time scale. In our study, we explored a particular configuration of a pulse flow valve that periodically (specified by modulation period, P_M) disrupts the carrier gas flow to achieve partial modulation. This disruption of flow creates a "plug" of higher concentration on top of the primary GC signal, which is further separated in a secondary column. The size of the plug determined by pulse width, P_W, has a direct relationship to chemical selectivity and sensitivity. For our experiment, we determined the ideal P_W to be around 8 ms. Therefore, a 20-component mixture was evaluated using P_W of 8 ms and P_M of 100 ms, producing an average peak width, ²W_b, of 12 ms and approximated ideal peak capacity, ²n_c, of 8 on the second dimension. All 20 compounds were separated in a 12 second separation window. This powerful partial modulation method was achieved by the unique concept of the flow disruption with short modulation period, demonstrating high peak capacity and improved selectivity between compounds and chemical sensitivity. Due to the significant increase in GC performance, this form of partial modulation using a pulse flow valve allows efficient and faster GC×GC analysis that can be implemented in a variety of GC×GC applications.