Chemistry & Biochemistry Theses and Dissertations

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DIRECTED AND ELLIPTIC FLOW MEASUREMENTS: A COMPARISON BETWEEN THE PARTICIPANT AND SPECTATOR PLANES IN Pb+Pb COLLISIONS AT √sNN = 5.02 TeV WITH CMS AT THE LHC
(2024) Lascio, Samuel Andrew; Mignerey, Alice C.; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Directed and elliptic flow of unidentified charged hadrons at mid-rapidity are measured as a function of transverse momentum (pT) and pseudorapidity (η) in ultra-relativistic PbPb collisions at √sNN = 5.02 TeV with the Large Hadron Collider (LHC) at CERN. The reaction plane (RP) angle is approximated using participants and spectator neutrons measured with the Compact Muon Solenoid (CMS) detector and the newly installed Spectator Reaction Plane Detector (SRPD), respectively. The SRPD is the latest addition to the existing Zero Degree Calorimeter (ZDC) designed to measure spectator neutrons +/- 140 m from the interaction point at CMS. The Event Plane (EP) Method is used to calculate the v1odd, v1even, and v2 harmonic flow parameters as functions of η and pT. The directed flow measurements using participants and spectators with CMS are compared and contrasted. Overall results are in good agreement between participants and spectators, however v1even(pT) measurements using spectators begin to show the opposite trend to those using participants at pT > 2 GeV/c. Results are compared to those obtained by A Large Ion Collider Experiment (ALICE), which is another experiment at the CERN LHC. Directed flow results do not agree with those obtained by ALICE. Additionally, the first elliptic flow measurements using the EP Method and mixed harmonics with the SRPD are reported. A slight asymmetry in v2(η) is observed using spectators. The elliptic flow results do agree with ALICE. Tracking efficiency as determined by the CMS collaboration is applied to the data and potential corruption as a result is discussed. Results strongly support continued use of the SRPD as a spectator neutron detector for reaction plane determination within the CMS ZDC.
USING VIBRATIONAL SUM-FREQUENCY-GENERATION SPECTROSCOPY TO EXPLORE THE ROLE OF SOLVENT ORGANIZATION IN DETERMINING ION LOCATIONS NEAR SILICA SURFACES
(2024) Singh, Siddharth; Fourkas, John; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Chemical processes occurring at liquid–solid interfaces are fundamental to applications in fields such as energy storage and nanofluidic transport. In this thesis I establish that the general framework used to describe and understand these systems, the electrical double-layer model, is insufficient in describing interfacial electrolyte solutions in polar, aprotic organic solvents. Using vibrational sum-frequency-generation (VSFG) spectroscopy, a nonlinear optical technique that is indispensable for exploring interfacial organization and dynamics, I study different polar aprotic solvents at silica interfaces. These studies highlight the importance of the organization of such solvents in dictating the interfacial distribution of ions. In the first part of this dissertation, I compare electrolyte experiments in acetonitrile (MeCN) and propionitrile (EtCN) to determine how an increase in alkyl chain length can influence solvent organization at a liquid–solid (LS) interface, and thereby influence the interactions of ions with the interface. In the second part of the dissertation, I focus on a solvent mixture of EtCN and deuterated MeCN at a silica interface. VSFG data for solutions with different molar ratios of the two solvents indicate that there is preferential partitioning of each liquid at this surface. In the third part of this dissertation, I examine the effects of solvent chirality on the organizational behavior at an LS interface, and consequently on the effects of this organization on ion partitioning. The key result of my research is that a polar, aprotic, organic solvent’s structure, chirality, and mixing with other solvents, can drive the partitioning of ions in interfacial electrolyte systems, in contradiction to the predictions of the EDL.
INVESTIGATION OF AMBIENT METHANE CONCENTRATION, SOURCES, AND TRENDS IN THE BALTIMORE-WASHINGTON REGION
(2024) Sahu, Sayantan; Dickerson, Russell Professor; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Methane, an important and not yet fully understood greenhouse gas, has a global warming potential 25 times that of carbon dioxide over 100 years, although with an atmospheric lifetime much shorter than carbon dioxide. Controlling methane emissions is a useful way to avoid some of the adverse effects of climate change at least on short time scales. Natural sources include wetlands, ruminants, and wildfires, while anthropogenic sources include the production, transmission, distribution, and use of natural gas, livestock, and landfills. In the US, natural gas and petroleum systems, anthropogenic sources, are the second-largest source of methane emissions. Urban areas are a significant source of anthropogenic methane emissions, primarily fugitive emissions from natural gas distribution and usage.We studied methane observations from five towers in the Baltimore-Washington (BWR) region – two urban towers ARL (Arlington, VA), NEB (Northeast Baltimore, MD), and one rural tower, BUC (Bucktown, MD). Methane measurements from these three towers displayed distinct seasonal and diurnal cycles with maxima at night and in the early morning, which indicated significant local emissions. We concluded from our analysis that anthropogenic methane emissions dominate at the urban sites whereas wetland emissions dominate at the rural site. We compared observed enhancements (mole fractions above the 5th percentile) to simulated methane enhancements using the WRF-STILT model driven by two EDGAR inventories – EDGAR 4.2 and EDGAR 5.0. We did a similar comparison between model and observations with vertical gradients. We concluded that both versions of EDGAR underestimated the regional anthropogenic emissions of methane, but version 5.0 had a more accurate spatial representation. We ran the model with WETCHARTs to account for wetland emissions which significantly reduced the bias between model and observations especially in summer at the rural site. We investigated winter methane observations from three towers in the BWR including a ten-year record, 2013-2022, from BUC, located ~100 km southeast of these urban areas. We combined the observations with a HYSPLIT clustering analysis for all years to determine the major synoptic patterns influencing methane mixing ratios at BUC. For methane concentrations above global background, the cluster analysis revealed four characteristic pathways of transport into BUC – from the west (W), southwest (SW), northwest (NW), and east (E) and these showed significant differences in methane mixing ratios. We corroborated our conclusions from BUC using 2018-2022 data from towers in Stafford, Virginia (SFD), and Thurmont, Maryland (TMD); results confirmed the influence of synoptic pattern, typically associated with frontal passage, on methane. No significant temporal trend over the global background was detected overall or within any cluster. For BUC, low concentrations were observed for air off the North Atlantic Ocean (E cluster) and flowing rapidly behind cold fronts (NW cluster). High methane mixing ratios were observed, as expected, in the W cluster due to the proximity of the BWR and oil and gas operations in the Marcellus. Less expected were high mixing ratios for the SW cluster – we attribute these to agricultural sources in North Carolina. Swine production, ~500 km to the SW, impacts methane in eastern Maryland as much or more than local urban emissions plus oil and gas operations 100–300 km to the west; this supports the high end of emission estimates for animal husbandry and suggests strategies for future research and mitigation.
NONEQUILIBRIUM STATISTICAL PHYSICS OF FEEDBACK-CONTROLLED AND AUTONOMOUS INFORMATION-THERMODYNAMIC SYSTEMS
(2024) Bhattacharyya, Debankur; Jarzynski, Christopher; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
This thesis investigates the nonequilibrium dynamics of a variety of systems evolving under control protocols. A control protocol can involve feedback based on measurements performed by an external agent, or it can be a predefined protocol that does not rely on explicit measurements of the system’s state. In the context of information thermodynamics, the former setup belongs to the paradigm of non-autonomous or feedback-controlled Maxwell's demons, and the latter to the paradigm of autonomous demons. The thesis begins with a framework for analyzing non-autonomous feedback control, when the control protocol is applied by an agent making continuous measurements on the system. A multiple-timescales perturbation theory, applicable when there exists an appropriate separation of timescales, is developed. This framework is applied to a classical two-state toy model of an information engine – a device that uses feedback control of thermal fluctuations to convert heat into work. Additionally, quantum trajectory simulations are used to study a feedback-controlled model of Maxwell's demon in a double quantum dot system. Next, a modeling scheme for converting feedback-controlled Maxwell's demons to autonomous (non-feedback) systems is developed. This scheme explicitly accounts for the thermodynamic costs of information processing, by incorporating an information reservoir, modeled as a sequence of bits. This modeling scheme is then applied for converting the classical analogue of the non-autonomous double quantum dot Maxwell's demon, discussed previously, to an autonomous model. Using analytical, semi-analytical and stochastic simulation-based approaches, it is shown that the obtained model can act either as an information engine, or as a “Landauer eraser”, and then the phase diagrams that identify these regimes of behavior are constructed. Finally, fast-forward shortcuts to adiabaticity for classical Floquet-Hamiltonian systems is developed, and applied to a periodically driven asymmetric double well (without feedback control). Tools from dynamical systems theory are then used to characterize the system’s angle-variable dynamics.
USING DNA LOOPING PROTEINS TO ENHANCE HOMOLOGY DIRECTED REPAIR IN VIVO FOLLOWING A CAS9 INDUCED DOUBLE STRAND BREAK
(2024) Ferencz, Ian Theodore; Kahn, Jason D; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Genome engineering methods that start with a CRISPR/Cas9 targeted genomic DNA double strand break proceed through cellular DNA repair mechanisms after the induction of the break. Imprecise nonhomologous end-joining (NHEJ) is useful for knockouts, but precise homology-directed repair (HDR) is necessary for gain of function changes. NHEJ tends to be more efficient, so directing the cell to knock in a precise sequence via HDR is an active area of research. The system we have designed uses a bivalent protein to recruit HDR donor DNA to the site of a specific DNA double strand break induced by a Cas9/sgRNA nuclease. Previously described leucine zipper dual-binding (LZD) proteins areused because they are small and stable. The system was designed to reduce the effort needed for screening, shorten the time required for the repair process, and/or decrease the amount of donor DNA needed, reducing potential off-target effects. We developed a model system in Saccharomyces cerevisiae to measure gene disruption and HDR frequencies in yeast that contain combinations of non-replicating donor DNA plasmid or linear DNA, expression plasmids of four LZD variants, and a plasmid expressing Cas9 and an sgRNA targeting either the AGC1 or ADE2 genes. The donor DNA includes a gene coding for G418 resistance in yeast. It also includes an INV-2 site recognized by the C-terminal DNA binding domain of LZDs adjacent to suboptimal regions of homology to the target gene. The N-terminal DNA binding domain of the LZDs recognizes an endogenous CREB site near the target gene. The desired recombinants are scored by their inability to grow on acetate as a sole carbon source (for AGC1) or their red color (ADE2), accompanied by resistance to G418. We believe that LZD enhancement can become a simple and valuable adjunct to any other method of improving the efficiency of HDR, in any system. We were able to show that the inclusion of LZD73 in recombination experiments increased the number of colonies presenting with the desired phenotype and genotype nearly eight-fold in the absence of a designed DNA break. We also provide evidence suggesting that the presence of LZD73 has a slight positive effect on the efficiency of Cas9 targeting. Desired recombinants were recovered after Cas9/sgRNA cleavage in an experiment where there was no apparent recombination in the absence of LZD73. Future work on this project includes optimization of the homologous sequences to improve background recombination so a more quantitative measure of the improvement observed in the presence of LZD proteins. This work can be transferred laterally to enhance other recombination-based methods in other organisms: the LZD proteins could be analogous to an adjuvant that increases overall efficiency.
Controlled Nucleation and Growth of Carbon Nanotubes
(2024) Alibrahim, Ayman; Wang, YuHuang; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Single-walled carbon nanotubes (SWCNTs) exhibit exceptional electrical, mechanical, and optical properties, making them potential game changers for diverse applications. However, the synthesis of SWCNTs faces significant challenges, including low yield, inadequate control over catalyst particle size, and prevalent impurities. This dissertation focuses on elucidating SWCNTs' nucleation and growth mechanisms to address these challenging issues. First, I applied in-situ absorption spectroscopy to monitor the SWCNT production by chemical vapor deposition. Second, I investigated the factors affecting metal catalyst nucleation and introduced a confinement strategy that enabled a record-breaking growth rate of 4500 meters per hour for SWCNTs. Furthermore, I developed a novel “seed doping” technique to control the nucleation of metal catalysts, significantly reducing catalyst particle size and producing purer, smaller-diameter SWCNTs continuously. Finally, I explored the role of ethanol in enabling the controlled growth of double-walled carbon nanotubes by building on SWCNTs as templates.
TOWARDS FULLY AUTOMATED ENHANCED SAMPLING OF NUCLEATION WITH MACHINE-LEARNING METHODS
(2024) Zou, Ziyue; Tiwary, Pratyush; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Molecular dynamics (MD) simulation has become a powerful tool to model complex molecular dynamics in physics, materials science, biology, and many other fields of study as it is advantageous in providing temporal and spatial resolutions. However, phenomena of common research interest are often considered rare events, such as nucleation, protein conformational changes, and ligand binding, which occur on timescales far beyond what brute-force all-atom MD simulations can achieve within practical computer time. This makes MD simulation difficult for studying the thermodynamics and kinetics of rare events. Therefore, it is a common practice to employ enhanced sampling techniques to accelerate the sampling of rare events. Many of these methods require performing dimensionality reduction from atomic coordinates to a low-dimensional representation that captures the key information needed to describe such transitions. To better understand the current challenges in studying crystal nucleation with computer simulations, the goal is to first apply developed dimensionality reduction methods to such systems. Here, I will present two studies on applying different machine learning (ML) methods to the study of crystal nucleation under different conditions, i.e., in vacuum and in solution. I investigated how such meaningful low-dimensional representations, termed reaction coordinates (RCs), were constructed as linear or non-linear combinations of features. Using these representations along with enhanced sampling methods, I achieved robust state-to-state back-and-forth transitions. In particular, I focused on the case of urea molecules, a small molecule composed of 8 atoms, which can be easily sampled and is commonly used in daily practice as fertilizer in agriculture and as a nitrogen source in organic synthesis. I then analyzed my samples and benchmarked them against other experimental and computational studies. Given the challenges in studying crystal nucleation using molecular dynamics simulations, I aim to introduce new methods to facilitate research in this field. In the second half of the dissertation, I focused on presenting novel methods to learn low-dimensional representations directly from atomic coordinates without the aid of a priori known features, utilizing advanced machine learning techniques. To test my methods, I applied them to several representative model systems, including Lennard Jones 7 clusters, alanine dipeptide, and alanine tetrapeptide. The first system is known for its well-documented dynamics in colloidal rearrangements relevant to materials science studies, while the latter two systems represent problems related to conformational changes in biophysical studies. Beyond model systems, I also applied my methods to more complex physical systems in the field of materials science, specifically iron atoms and glycine molecules. Notably, the enhanced sampling method integrated with my approaches successfully sampled robust state-to-state transitions between allotropes of iron and polymorphs of glycine.
DECIPHERING THE MOLECULAR MECHANISM BEHIND THE SARS-COV-2 FUSION DOMAIN
(2024) Birtles, Daniel; Lee, Jinwoo; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
SARS-CoV-2 is an extremely infectious virus, yet despite a plethora of research the viral lifecycle is still not well understood, particularly the process of membrane fusion. The traditional means by which viral glycoproteins facilitate fusion is that of the six-helix bundle, within which a short, conserved sequence known as the fusion domain (FD) initiates the process as it embeds within and perturbs the target cell membrane, in turn lowering the energetic barrier necessary to coalesce two opposing membranes. Furthermore, the highly conserved coronavirus FD is found to be available on the SARS-CoV-2 spike protein surface, which along with its integral role within the viral lifecycle makes it an ideal therapeutic target. However, limited knowledge of the exact molecular mechanism by which the SARS-COV-2 FD conducts its role within the fusion process has prevented the production of antiviral treatments. Here we describe the elucidation of key molecular details regarding how the SARS-CoV-2 FD initiates the process of membrane fusion. Firstly, the FD was found to contain a unique assembly of fusogenic regions, known as a fusion peptide (FP) and fusion loop (FL), which operate in synergy to elicit efficient fusion. This was followed by the discovery of a preference for the FD to fuse within conditions akin to the late endosomal membrane, with both pH and lipid composition significantly impacting fusion. It was found that the endosomal resident anionic lipid BMP imparts a negative impact on lipid packing within the membrane, which positively correlates with fusion. The unique mechanism by which the coronavirus FD initiates fusion was cemented when we uncovered the importance of several positively charged residues towards the FDs function. This also led to unearthing a mutant of the FD (K825A), which if found to have naturally occurred within the full spike protein, has the potential to produce a more virulent strain of SARS-CoV-2.
SCALING NANOFABRICATION: CARBON NANOTUBE-BASED SMART MATERIALS AND DEVICES
(2024) Lin, Qinglin; Wang, YuHuang Y.H.W; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
This dissertation introduces groundbreaking approaches to scaling up the nanofabrication of carbon nanotube (CNT)-based materials and devices, with diverse applications ranging from biosensors to smart textiles. The research begins in Chapter 2 with developing a CNT hydrogel that enables the direct alignment of CNTs across a trench. This approach paves the way for a new sensor design that detects SARS-CoV2 RNA with high sensitivity. In Chapter 3, I optimized this hydrogel system and applied it to effectively align CNTs simply by spin-coating. The alignment is comprehensively characterized by multiple methods, and I further demonstrated that this method could be applied to aligning other 1D nanostructures for innovative semiconductor device design. In Chapter 4, I further applied the CNT hydrogel to achieve an ultrafast assembly of CNTs on polymer fibers, with production rates reaching 100 meters per second. This rapid assembly process facilitates the development of cutting-edge FET-on-a-fiber devices, crucial for advanced biosensing of neurotransmitters. Finally, Chapter 5 explores the design of a humidity-responsive fiber for personal thermal regulation. This composite fiber, driven by torsional actuation, features dynamic inter-fiber distance control, making the material suitable for next-generation smart textiles.
Matrix Isolation and Gas-Phase Kinetics of Astrochemically Relevant Species
(2024) Hockey, Emily K.; Dodson, Leah G.; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Following the first detection of an interstellar molecule in 1937, there have been over 300 detected chemical species as of the writing of this dissertation. Interstellar molecules typically exist in a range of conditions including very low-temperature environments, making their existence unexpected and their chemistry exotic. The formation and evolution of such molecules can be strikingly different than here on Earth. This dissertation work reproduced the reaction conditions of astrophysical environments for laboratory experiments. Two classes of chemicals were studied to gain a more complete understanding of the potential energy surfaces of astrophysically relevant molecules. First, the formation of transient species was studied using a custom-built matrix-isolation spectrometer (detailed in Chapter 2). Second, the destruction of astrochemically relevant molecules via ultraviolet (UV) radiation was studied using multiplexed photoionization mass spectrometry. In the first portion of this dissertation, spanning Chapters 3−5, we study (a) the noncovalent interactions that lead to the formation of weakly bound complexes, (b) the structure of transient intermediates, and (c) fundamental effects of different matrix environments. In Chapter 3, we demonstrate the utility of this instrument by isolating and characterizing the weakly bound complexes between hydrogen cyanide (HCN) and methyl chloride (CH3Cl) using FTIR spectroscopy and quantum chemistry calculations. The study ultimately led to a hypothesis that the formation of weakly bound complexes with CH3Cl could catalyze formation of the isomers of prebiotic molecules. Isomerism became the focus of subsequent studies using this instrumentation, as an emphasis was placed on the importance of considering how host/guest interactions may perturb gas-phase isomer ratios during matrix deposition. Chapter 4 demonstrates the change in conformer abundance of methyl nitrite (CH3ONO) in relation to the gas-phase ratio as a result of depositing with different low-temperature matrices, an important finding in the continued development of matrix-isolation techniques. Chapter 5 continues this investigation, expanding to investigate how different matrices influence the photodynamics of CH3ONO upon UV irradiation. These chapters reiterate the need for a deeper understanding of not only the chemical systems, but the methods used to study them as well. The second portion—Chapters 6 and 7—investigates the fate of a molecule important both on Earth and in space: methanol (CH3OH). The products formed upon UV excitation of CH3OH have not been well-constrained previously. In a collaborative project with Sandia National Laboratories (SNL) and Lawrence Berkeley National Laboratory (LBNL), we carried out UV photodissociation studies on CH3OH at the Advanced Light Source (ALS) synchrotron, identifying and quantifying the photodissociation products via Multiplexed Photoionization Mass Spectrometry. Chapter 6 provides direct observation of the formation mechanism and subsequent reactivity under gas-phase reaction conditions of hydroxymethylene (HCOH)—an elusive singlet carbene—which was previously unattainable due to the transient nature of the molecule. Additionally, the results in Chapter 7 inform scientists of the destruction processes possible for this important astrochemical in regions of space with high ultraviolet radiation fields, as well as quantitatively assign branching ratios for all of the major photodissociation channels of CH3OH for the first time. Finally, Chapter 8 details future work that will utilize both instruments to completely characterize the potential energy surface of possible formation routes to polycyclic aromatic hydrocarbon and other unique transient species.
Structural Investigation into RioK1 for Cancer Therapeutics
(2024) Hunter, Daniel Arthur; Weber, David; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Cancer was the second leading cause of death in the United States in 2020.1 Cancer shares many similarities with healthy cells, making it a difficult therapeutic target.2 Current developments of cancer therapeutics are governed by targeting key proteins responsible for distinct features in each type of cancer phenotype. (e.g. decreased apoptosis, metastasis, immortalization, etc.). However, finding a rational therapeutic target, engineering a lead compound, and lead compound optimization is time-consuming and expensive. With the use of high-throughput screens and structure-based drug design it is possible to design lead compounds in a more efficient manner. Techniques such as x-ray crystallography and cryo-electron microscopy are used to observe how compounds interact with the target protein at atomic resolution, which helps facilitate optimization.2-4 Kinases in particular, have benefitted greatly from these techniques.5 Kinases play key roles in signal transduction and its regulation in many cellular pathways. The catalytic active site is highly conserved among many kinase families, so designing drugs targeting a single enzyme’s catalytic site could have potential off target effects as many kinases could be inhibited. Strategies to target kinases therefore use distinct features of each kinase that take both conserved and nonconserved residues into consideration as well as for active and inactive forms of the kinase being targeted, so tailormade therapeutic solutions are derived, as with the case of reading open frame kinase 1 (RioK1).2, 4, 5 RioK1 was identified as a key enzyme in both lung and colorectal cancer, cancer subtypes with some of the most severe prognoses.6 In a study done by Kiburu et al., toyocamycin was demonstrated to bind tightly to RioK1 from archaeoglobus fulgidus (afRioK1), thereby discovering the first scaffold for RioK1.7 Toyocamycin is an adenosine analog, commonly used as inhibitor, and thus making this drug scaffold non-specific with off-target effects other than for RioK1.8-12 To address this issue, computer aided drug design was used to find toyocamycin-like compounds that have improved selectivity for afRioK1 inhibition. A series of these compounds were identified via screening approaches and then co-crystallized with afRioK1 with the goal of elucidating useful structure-activity relationship data for next stage drug-design. Furthermore, one of the most newly studied interactions of RioK1 is with protein arginine methyltransferase type 5 (PRMT5), so understanding the details of this interaction provides yet another means to develop afRioK1 inhibition strategies as part of an approach to block cancer progression.
BLANKET AND PATTERNED REPROGRAMMING OF AZOPOLYMER NANORIDGES AND APPLICATIONS TO CELLULAR BIOPHYSICS
(2024) Abostate, Mona Hamdy Abdelrahman; Fourkas, John J; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
The objective of this project is to tailor nanotopographies previously fabricated on large areas through photomodification. The original master patterns consist of nanoridges created using conventional lithography. Using an azopolymer as a photoresponsive material, replicas of the original master were prepared using soft lithography. The entire surface of the azopolymer nanoridges underwent photomodification using a 532 nm laser with varying polarizations and durations, in a process referred to as blanket reprogramming. This process resulted in controllable widening, buckling, or removal of the nanoridges due to photoisomerization and subsequent mass migration of the azopolymer. To replicate the reprogrammed surfaces, a molding procedure was employed using an acrylatic resin. The blanket reprogramming process was monitored in situ during exposure through diffraction of another reading laser beam. Cellular behaviors can be modulated in various biological contexts through interactions with their surroundings. The relationship between nanotopography and cell behavior is crucial, and has a wide range of biological consequences and medical applications. For example, nanotopography is employed to design antibacterial surfaces, preventing the adhesion of bacteria and biofilm formation, thereby reducing the risk of infections associated with medical devices. Nanostructured surfaces can inhibit the migration of cancer cells, offering insights into potential therapeutic strategies. Nanotopography is also used in nerve-regeneration scaffolds to guide neurite outgrowth, aiding in the repair of damaged neural tissue. We investigated the response of MCF10A breast epithelial cells to buckled acrylic nanoridges replicated from a master of azopolymer ridges photomodified by laser. The nanoridges became buckled after exposure to 532 nm light polarized parallel to the ridges. The impact of buckling on the dynamics and location of actin polymerization was investigated, as well as the distribution of lengths of contiguous polymerized regions. Azopolymers, known for their biocompatibility, have been employed by various research groups to create nanotopographies on which cells are plated and imaged. We conducted experiments using a spinning-disk confocal fluorescence microscope, testing exposure wavelengths ranging from 405 nm to 640 nm. Our objective was to assess the feasibility of live-cell imaging on azopolymer nanotopographies without inducing surface alterations. Our findings revealed the capability of live-cell imaging at high frame rates across a wide range of wavelengths. This result stands in contrast to prior studies, in which the selection of fluorescent dyes compatible with these materials was limited to those excited in the red spectrum and emitting in the near-infrared. I demonstrate that different patterns can be created through patterned reprogramming of the azopolymer nanoridges. A periodic arrangement of light strips was projected perpendicular to the ridges, thereby projecting an amplitude grating onto the azopolymer nanoridges. The spacing of this pattern can be adjusted by altering the mask or adjusting the magnification of the optical system. Furthermore, varying the direction of light polarization expands the potential for creating a wider variety of designs. Different types of reprogramming motifs can be implemented by projecting patterns at angles that are not perpendicular to the substrate, by tilting the incoming laser beam away from the horizontal. Various intriguing patterns, such as repeating curves, were observed, dependent on both the angle of the incident light and the direction of light polarization relative to the direction of the ridges.
Characterization of a novel Escherichia coli exopolysaccharide and its biosynthesis by NfrB
(2024) Fernando, Sashika Hansini Lakmali; Poulin, Myles B; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Biofilms are made from an association of bacterial cells and extracellular products dominated by a plethora of exopolysaccharides. Accumulating evidence have demonstrated that the bacterial second messenger cyclic-di-guanosine monophosphate (c-di-GMP) promotes the synthesis of these exopolysaccharides through direct allosteric activation of glycosyltransferase enzymes. The Escherichia coli inner membrane protein NfrB, which together with the outer membrane protein NfrA acts as a receptor system for phage N4, contains a N-terminal glycosyltransferase domain and C-terminal c-di-GMP binding domain. Recent research revealed that NfrB is a novel, c-di- GMP controlled glycosyltransferase that is proposed to synthesize a N-acetylmannosamine containing polysaccharide product, though the exact structure and function of this remains unknown. Nfr polysaccharide production impedes bacterial motility, which suggests a possible role of the Nfr proteins in bacterial biofilm formation. Here, we carry out in-vivo synthesis of novelNfr polysaccharide followed by its structural characterization. Preliminary data from MALDI- TOF mass spectrometry and Solid State 13C NMR spectroscopy indicated that the Nfr polysaccharide is mainly a homo polymer of poly-?-(1®4)-N-acetylmannosamine, bound to an aglycone. In addition, we report efforts to develop of a Nfr polysaccharide binding and detection tool, through the mutation of YbcH, a putative Nfr polysaccharide hydrolase enzyme. These studies advance the understanding of Nfr polysaccharide biosynthesis and could offer potential new targets for the development of antibiofilm and antibacterial therapies.
ESOTAXIS: IDENTIFYING THE FACTORS THAT INFLUENCE NANOTOPOGRAPHIC GUIDANCE OF THE DYNAMICS AND ORGANIZATION OF THE ACTIN CYTOSKELETON AND OTHER MOLECULES INVOLVED IN DIRECTED CELL MIGRATION
(2024) Hourwitz, Matt; Fourkas, John T.; Losert, Wolfgang; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Directed migration is a crucial capability of cells in developmental and immunological processes. Defects in cell migration can lead to negative health outcomes. Cell motion depends on the organization and dynamics of internal components, especially the actin cytoskeleton, and the extracellular environment. Microscale and nanoscale topographical cues, with at least one dimension that is much smaller than most cells, can bias cell motion over long distances, due to the guidance of the organization and dynamics of the cytoskeleton and other molecules and assemblies within the cell. In this work, I describe a technique to reproduce patterned nanotopographic substrates for use in the study of esotaxis, the guided organization and dynamics of the actin cytoskeleton and other cellular components in response to nanotopographic cues. The guidance of actin drives directed cell motion along a pattern with dimensions much smaller than the cell. The dimensions of the nanotopography determine the extent to which cellular components are guided. Differences in the physical properties of the plasma membrane and the actin cytoskeleton among cell lines will influence the extent of guidance by nanotopography. Asymmetric patterns can accentuate the distinctions in esotactic responses among cell lines and drive contact guidance in different directions. The cytoskeletal response to nanotopography is a local phenomenon. A cell in contact with multiple nanotopographic cues simultaneously will show distinct organization of actin in the different regions of the cell. The importance of local actin dynamics requires an analysis method, optical flow, that can identify and track the distinct cytoskeletal motions in different parts of the cell. The formation of adhesions attached to the extracellular matrix is a characteristic of the migratory behavior of many types of cells and these adhesions are credited with allowing the cell to sense and interact with the underlying substrate. Actin can sense nanotopographic cues without the widespread availability of adhesive ligands. Although adhesion to the substrate strongly increases the extent of cell spreading and migration on nanoridges, epithelial cells can align with and migrate along nanotopography even with a dearth of adhesive cues. Therefore, actin is a supreme sensor of nanotopography that can drive directed cell migration.
Optimized simulations of fermionic systems on a quantum computer
(2024) Wang, Qingfeng; Monroe, Christopher; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Quantum computing holds promise for simulating microscopic phenomena, offering profound implications across disciplines such as chemistry, condensed matter physics, and high-energy physics, particularly in the accurate simulation of fermions. However, practical implementation requires the optimization of quantum programs to mitigate quantum noise and decoherence effects. Given the constraints of near-term quantum computers, the Variational Quantum Eigensolver (VQE) emerges as a key approach for estimating molecular ground state energies, crucial for determining chemical properties. This work aims to present advancements in optimizing VQE simulations to minimize quantum computational resources. Specifically, this work explores various optimization strategies, including the utilization of second-order perturbation correction to recover additional energy beyond VQE estimates and select critical ansatz terms. Additionally, circuit optimization techniques are investigated, focusing on achieving shorter equivalent ansatz circuits, particularly for physically-inspired VQE ansatz, through methods such as generalized fermion-to-qubit transformations and Pauli string orderings. Furthermore, this work demonstrates the advantage of a better initial state on a trapped-ion quantum computer.
Using Electric Fields to Modulate Polymeric Materials: Electro-adhesion, Electro-gelation and Electro-carving
(2023) XU, WENHAO; Raghavan, Srinivasa R.; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
This dissertation concerns the effects of electric fields on aqueous polyelectrolytes (solutions and gels), including those of polysaccharides and proteins. Electrical effects on such polymeric systems have not been studied in detail thus far. In this work, we apply electric fields as stimuli to trigger responses in these materials. We have discovered three novel responses: electro-adhesion of a gel to a solid electrode; electro-gelation of a polymer solution, which allows gels to be made in 3D, and localized electro-disruption of gels, which allows gels to be carved or sculpted. In our first study, we show that it is possible to adhere a soft ionic conductor (like a polymeric hydrogel) to a hard, electronically conductive electrode using a low DC voltage without any adhesive. When 5 to 10 V DC is applied between a pair of electrodes (e.g., graphite, copper, etc.) spanning a cylindrical hydrogel (e.g., acrylamide, gelatin, etc.), in 3 to 15 min, the gel strongly adheres to either or both electrodes. The ultimate adhesion strength can exceed 150 kPa and is only limited by the strength of the soft material. This hard-soft electro-adhesion applies to not only lab-synthesized hydrogels but also animal or plant tissues, such as beef, pork, apples, bananas, etc. We show that this adhesion results from electrochemical reactions that form chemical bonds between the polymers in the gel backbone and the electrode surface. Hard-soft electro-adhesion can be used to assemble hybrid materials with hard and soft compartments, which could be useful in robotics, energy storage, underwater adhesion etc. Next, we demonstrate how an electric field can be used to gel a polymer solution with spatial control  thereby, we can ‘print’ gels in 3D. When a solution of alginate (an anionic biopolymer) is subjected to a DC electric field (~ 10 V) using a platinum (Pt) needle as the anode, a gel is formed right around the anode within seconds. By using a mobile anode, gel “voxels” can be formed sequentially and these merge into 3D structures. Similar electro-gelation can also be done with the cationic biopolymer chitosan, but at the cathode instead of the anode. The mechanism for gelation with both alginate and chitosan involves the polymer chains losing their charge next to the electrode. A loss of charge leads to insolubility, and insoluble domains act as crosslinks and connect the chains into networks. We have built a prototype for a 3D-printer that can translate a 3D design into a robust biopolymer gel formed by electro-gelation. Lastly, we show that an electric field applied by an electrode can be used like a knife to carve or sculpt hydrogels into 3D shapes. When we apply a DC electric field across certain gels, the gel shrinks near the anode, while water is expelled out of the gel near the cathode. Ultimately the gel shrinks by more than 50% of its original size. Such shrinkage is observed with a range of anionic gels, including both physical gels of biopolymers like agar and alginate as well as covalent gels such as sodium acrylate. If the ionic strength of the gel is high, the shrinkage does not occur. The origin of this effect lies in a combination of electroosmosis as well as pH changes near the electrodes. Finally, we show that with a focused electric field, the shrinkage can be limited to a specific location in a gel, thereby allowing us to electro-carve gels in 3D.
Spatiotemporal proteomic approaches for investigating patterning during embryonic development
(2024) Pade, Leena Rajendra; Nemes, Peter; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Characterization of molecular events as embryonic cells give rise to tissues and organs raises a potential to better understand normal development and design remedies for diseases. In this work, I integrated bioanalytical chemistry with neurodevelopmental biology to uncover mechanisms underlying tissue induction in a developing embryo. Specifically, I developed ultrasensitive proteomic approaches to study the remodeling of the proteome as embryonic cells differentiate in space and time to induce tissue formation. This dissertation discusses the design and development of proteomic strategies to deepen proteomic coverage from limited embryonic tissues. A novel sample preparation workflow and detection strategy was developed to address the challenge of interference from abundant proteins such as yolk in Xenopus tissues which in turn boosts the sensitivity of detecting low abundant proteins from complex limited amounts of tissues. The refined analytical workflow was implemented to study the development of critical signaling centers and stem cell populations and the tissues they induce to form in developing embryos.
How Non-Hermitian Superfluids are Special? Theory and Experiments
(2024) Tao, Junheng; Spielman, Ian Bairstow; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Ultracold atoms emerge as a promising advanced platform for researching the principles of quantum mechanics. Its development of scientific understanding and technology enriches the toolbox for quantum simulations and quantum computations. In this dissertation work, we describe the methods we applied to build our new high-resolution 87Rb Bose-Einstein condensate (BEC) machine integrated with versatile quantum control and measurement tools. Then we describe the applications of these tools to the research of novel superfluidity and non-Hermitian physics. Superfluids and normal fluids were often studied in the context of Landau’s two-fluid model, where the normal fluid stemmed from thermally excited atoms in a superfluid background. But can there be normal fluids in the ground state of a pure BEC, at near zero temperature? Our work addressed the understanding of this scenario, and then measured the anisotropic superfluid density in a density-modulated BEC, where the result matched the prediction of the Leggett formula proposed for supersolids. We further considered and measured this BEC in rotation and found a non-classical moment of inertia that sometimes turns negative. We distinguished the roles of superfluid and normal fluid flows, and linked some features to the dipolar and spin-orbit coupled supersolids. As a second direction, we describe our capability to create non-Hermiticity with Raman lasers, digital-micromirror device (DMD), and microwave, and present our work in engineering the real space non-Hermitian skin effect with a spin-orbit coupled BEC. By use of a spin-dependent dissipative channel, we realized an imaginary gauge potential which led to nonreciprocal transport in the flat box trap. We studied the system dynamics by quenching the dissipation, and further prepared stationary edge states. We link our discoveries to a non-Hermitian topological class characterized by a quantized winding number. Finally, we discuss the exciting promises of using these tools to study many-body physics open quantum systems.
Magnetic and Toroidal Symmetry of Lithium Transition Metal Orthophosphates
(2024) Gnewuch, Stephanie Kardia; Rodriguez, Efrain; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
LiCoPO4 is the foremost candidate material for a novel type of ferroic ordering calledferrotoroidicity. In this work, the synthesis of polycrystalline sample of LiCoPO4 is discussed, along with the structural analog LiMnPO4. Their magnetic susceptibility and magnetic structure were determined and analyzed and found to be consistent with previous reports on single crystal materials. This work also provides a thorough introduction to ferrotoroidicity, a history of its theoretical development, and a summary of the most studied candidate materials. The work then presents a detailed methodology for determining the toroidal structure which would result for the magnetic structure in candidate ferrotoroidal materials. The model provides a method for determining how many toroidal moments would be present, where they would be located within the unit cell, and along which crystallographic direction they would be oriented. Detailed examples for determining the magnetic structure are provided for LiCoPO4 and analogous structures with the olivine structure type, as well as several structures with the pyroxene structure type. The results demonstrate a method for understanding ferrotoroidal arrangements, anti-ferrotoroidal arrangements and non-toroidal structures.
UNRAVELING THE ROLE OF LASSA VIRUS TRANSMEMBRANE DOMAIN IN VIRAL FUSION MECHANISM
(2024) Keating, Patrick Marcellus; Lee, Jinwoo; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
Lassa virus (LASV) is the most prevalent member of the arenavirus family and the causative agent of Lassa fever, a viral hemorrhagic fever. Although there are annual outbreaks in West Africa and recently isolated cases worldwide, no current therapeutics or vaccines pose LASV as a significant global public health threat. One of the key steps in LASV infection is the delivery of its genetic material by fusing its viral membrane with the host cell membrane. This process is facilitated by significant conformational changes within glycoprotein 2 (GP2), yielding distinct prefusion and postfusion structural states. However, structural information is missing to understand the changes that occur in the transmembrane domain (TM) during the fusion process. Investigating how the TM participates in membrane fusion will provide new insights into the LASV fusion mechanism and uncover a new therapeutic target sight to combat the dangerous infection. Here, we describe our protocols for expressing and purifying the isolated TM and our GP2 constructs which we use to probe the relationship between the structure of the TM and its influence on the function of GP2.We express TM as a fusion protein with a Hisx9 tag and a TrpLE tag using E. coli bacterial cells. We purify the TM using Nickel affinity chromatography and enzymatic cleavage to remove the tags. Since the TM is prone to aggregation, we must use a strong denaturant, trichloroacetic acid (TCA), to remove the TM from the resin. The isolated TM is then buffer exchanged to a detergent solution for structural studies. Using circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy, our structural studies revealed a pH-dependent structural change resulting in an N-terminal extension of the alpha helix in the postfusion state. To test the importance of this structural change, we used the GP2 construct to perform a modified lipid mixing fusion assay. Our results from the fusion assay and a combined mutational study revealed that this structural change is important for the fusion efficiency of GP2. Loss of this extension resulted in lower fusion activity. To further understand these structural changes and to probe the TM’s environmental interactions, we turned to fluorine NMR. This method gives us a unique and highly sensitive probe to monitor changes in the structure and membrane environment. We describe our incorporation protocol of fluorine into the TM and our method for incorporating the TM into a lipid bilayer system. We describe preliminary results showing sensitive changes in the structure of the TM and the implications this method has to enhance our understanding of the LASV membrane fusion mechanism.

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