Chemical and Biomolecular Engineering Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/2751
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Item Battery Studies with Particular Reference to Organic Depolarizers(1955) Monson, William L.; Huff, W. J.; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, MD)Since Volta's invention of the first primary cell, using silver and zinc, numerous other cell combinations have been studied, covering a wide variety of anode and cathode materials. The latter have included both inorganic and organic substances capable of electrochemical reduction, although, historically, organic cathode materials have received very much less attention than the inorganic. It was the purpose of this investigation to study the actual behavior of a selected number of quinones as depolarizers in primary cells. Performance of experimental cells was compared with cells of the usual dry cell composition but of the same size and construction as cells of experimental composition. The results show that certain substituted anthraquinones possess good depolarizing ability as measured by discharge voltage and coulombic capacity. Energy output in some cases was higher than that of the manganese dioxide control cells (zinc anodes in all cases) because of higher effective coulombic capacities. A qualitative study of the effect of substituents on the discharge voltages of various quinones showed that cell working voltages were much more sensitive to quinone substitution than were the calculated reversible potentials. Also, in the case of nitro-substituted anthraquinones more coulombic capacity was obtained than could be accounted for by the simple reduction to the corresponding hydroquinone. The possibility of a reduction of the nitro-group of this compound was considered. Substances investigated were benzoquinone, naphthoquinone, anthraquinone, and certain of their derivatives, using various electrolytes. The size of the experimental cells was such that about 0.2 gram of the various depolarizers could be studied conveniently.Item ENGINEERING THE B1 DOMAIN OF STREPTOCOCCAL PROTEIN G: STRUCTURAL INVESTIGATIONS BY MULTlDIMENSIONAL HETERONUCLEAR NMR(2000) Frank, Mary Kirsten; Thirumalai, Devarajan; Institute for Physical Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, MD)The B1 domain of streptococcal protein G provides a well-characterized system for structural investigations of proteins. In this thesis, the urea-unfolded state has been characterized, the tolerance towards hydrophobic substitutions in the core has been surveyed, the hydrogen exchange behavior of the backbone amides has been elucidated, and structural information on a tetrameric mutant of this domain has been gathered. The chemical shifts of the urea-unfolded state were assigned. The secondary chemical shifts, the 3JHNa coupling constants and the short-range NOEs gave no indication of residual structure. Measurement of the backbone 15N relaxation parameters revealed a region of restricted motion in the β3- β4 turn of the native protein. Motion in the rest of the protein was uniform, with the exception of 3-4 residues at either end of the chain. A series of hydrophobic substitutions were made in the hydrophobic core. The resulting mutants were assayed for stability and overall fold . The core of the protein is particularly sensitive to substitutions at position 26. One of the mutants was unable to adopt the GB1 fold and optimized its stability by adopting a homotetrameric form. Hydrogen exchange in the backbone amides was measured at 25 °C. Rates of hydrogen exchange were inversely correlated with burial of the amide nitrogen. The slow-exchanging backbone amides did not correlate with the hydrogen bonds formed early in protein folding. Hydrogen exchange rates from NH to ND and from ND to NH were similar. The ratio between these two rates does not correlate with any obvious physical parameters of the hydrogen bonds. Chemical shifts for the tetrameric mutant (HS#124) were determined using three-dimensional heteronuclear NMR techniques. Measurement of the backbone dynamics revealed a highly flexible region between positions 8 and 22. The secondary structure and β-sheet interactions of this mutant were characterized. The β-sheet interactions were intermolecular and only one of the three β-strand pairings was similar to the β-strand pairings found in wild type GB1 . The novel pairing is between β1 of one monomer and β1 of another monomer and a shift in register is observed for the β3-β4 pairing.Item Interface Broadening and Radiation Enhanced Diffusion During Sputter Depth Profiling(1988) Chambers, George Paul; Rousch, Marvin; Chemical and Nuclear Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)The process of ion bombardment of solids has been investigated using Monte Carlo Computer Code simulation in conjunction with ultra-high vacuum experimental techniques. The computer code EVOLVE has been used to study the shape of the resultant collision cascade as well as the origins of sputtered particles while experimental studies of interface regions have been performed to elucidate the physical processes occurring during sputtering. The EVOLVE code models the target as an amorphous multicomponent semi-infinite solid. The target composition during ion bombardment is simulated. The study concludes that recoil activity grows in size and tends to move away from the target surface with increasing time. It is further concluded that the majority of sputtered atoms originate from early generations and are produced from sites near the entry point of the bombarding ion. Low energy noble gas ion bombardment of thin-film Cr/Ni multilayered structures has been performed in conjunction with Auger electron spectroscopy under UHV conditions. An accurate, reliable, and systematic parameterization of the interface region between metallic layers is presented. It is concluded from this study that the extent of the distortion of the interface region due to ion induced broadening is dependent not only on the material system used but on the experimental conditions employed as well. Lastly, radiation enhanced diffusion (RED) has been studied using Ag/Ni thin-film multilayered structures. A physical mathematical model of the radiation broadened Ag layer, capable of successfully deconvoluting the contributions to interface broadening due to RED from those due to cascade mixing and microstructure development, is presented and shown to be an accurate characterization of the interface region. It is concluded from the application of this model that RED can contribute substantially to interface broadening in multicomponent systems with low activation energies of diffusion. It is further concluded from this study that elevated temperatures, sustained during the depth profiling process, can cause the effects of RED to subside dramatically. This phenomenon is most probably due to the dispersion of complex defects responsible for the RED process.Item Dynamics of Elastic Capsules in Cross-Junction and T-Junction Microfluidic Channels(2017) Mputu udipabu, Pompon; Dimitrakopoulos, Panagiotis; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In this dissertation, we investigate via numerical computations the dynamicsof elastic capsules (made from a thin strain-hardening elastic membrane) in two microfluidic channels of cross-junction and T-junction geometries. For the cross-junction microfluidic channel, we consider an initially spherical capsule with a size smaller than the cross-section of the square channels comprising the cross-junction, and investigate the effects of the capsule size, flow rate, and lateral flow rates on the transient dynamics and deformation of low-viscosity and equiviscous capsules. In addition, we also study the effects of viscosity ratio on the transient capsule dynamics and deformation. Our investigation shows that the intersecting lateral flows at the cross-junction act like a constriction. Larger capsules, higher flow rates and higher intersecting lateral flows result in stronger hydrodynamic forces that cause a significant capsule deformation, i.e., the capsule’s length increases while its height decreases significantly. The capsule obtains different dynamic shape transitions due to the asymmetric shape of the cross-junction. Larger capsules take more time to pass through the cross-junction owning to the higher flow blocking. As the viscosity ratio decreases, the capsule’s transient deformation increases and tail formation develops transiently, especially for low-viscosity capsules owing to the normal-stress effects of the surrounding fluid on the capsule’s interface. However, the viscosity ratio does not affect much the capsule velocity due to a weak inner circulation. Our findings suggest that the tail formation of low-viscosity capsule may promote membrane breaking and thus drug release of pharmaceutical capsules in the microcirculation. Furthermore, we investigate via numerical computations the motion of an elastic capsule (made from an elastic membrane obeying the strain-hardening Skalak law) flowing inside a microfluidic T-junction device. In particular, we consider the effects of the capsule size, flow rate, lateral flow rate, and fluid viscosity ratio on the motion of the capsule in the T-junction micro-channel. As the capsule’s initial lateral position increases, the capsule moves faster and reaches different final lateral positions. As the capsule size increases, the gap between the capsule’s surface and the channel wall decreases. This results in the development of stronger hydrodynamic forces and a decrease in the capsule velocity due to flow blocking. As the capsule size increases, there is a small lateral migration towards the micro-channel centerline, which is the low-shear region of the T-junction micro-channel. This migration is in agreement with experimental and numerical studies on non-inertial lateral migration of vesicles in bounded Poiseuille flow by Coupier et al. [13] who showed that the combined effects of the walls and of the curvature of the velocity profile induce a lateral migration toward the centerline of the channel. As the capillary number Ca increases, the stronger hydrodynamic forces cause the capsule to extend along the flow direction (i.e., the capsule’s length Lx increases as the capsule enters the T-junctions and decreases as the capsule exits the T-junction). There is a small lateral migration away from the micro-channel centerline as the flow rate Ca increases. The capsule lateral position zc, main-flow velocity Ux and migration velocity Uz are practically not affected by the fluids viscosity ratio λ. As the channel’s lateral flow rate increases, the capsule migrates downwards towards the bottom of the device. Our findings on the lateral migration in the T-junction micro-channel suggest that there is a great potential for designing a T-junction microfluidic device that can be used to manipulate artificial and biological capsules.Item Local Atomic Arrangments and Solution Strengthening of Ta-Mo and Ta-Nb Alloys(1975) Predmore, Roamer Edward; Arsenault, Richard J.; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)Ta-Nb alloys are shown to form random solid solutions by x-ray diffuse scattering measurements. These alloys have equal size atoms in their pure state with lattice parameters that are invariant in composition, obey Vegard's law, and exhibit an absence of solid solution hardening and an absence of fracture embrittlement at high solute concentrations. Ta-Mo atoms of about 5% difference in atomic size form short range ordered solid solutions with large atomic displacement effects. The Ta-Mo, and Ta-W, Nb-Mo and Nb-W alloys have in common a lattice parameter that varies in composition with a negative deviation from Vegard's Law. There is also a negative heat of mixing which is well correlated with short range order. In addition, all these alloys show linear solid solution hardening to high solute concentrations at room temperature and fracture embrittlement at high solute concentrations. Diffuse ex-ray scattering measurements on Ta-Mo alloys give the short range order parameters and atomic size displacements. The hardening is attributed to a combination of size effect induced substitutional solid solution hardening and short range order induced hardening.Item Self-Assembly in Polar Organic Solvents(2019) Agrawal, Niti; Raghavan, Srinivasa R; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Self-assembly of amphiphilic molecules occurs extensively in water, and can result in a variety of large, nanoscale aggregates, including long cylindrical chains called wormlike micelles (WLMs), as well as nanoscale containers called vesicles. However, in organic solvents of polarity lower than water, such as formamide, glycerol, and ethylene glycol, self-assembly has been demonstrated only to a limited extent. While there are reports of small micelles in these solvents, there are no reports of large structures such as WLMs and vesicles (with at least one length scale > 100 nm). In this dissertation, we show that both WLMs and vesicles can be formed in these solvents, and thereby our work expands the possibilities for self-assembly to new systems. Applications for the fluids developed here could arise in cosmetics, pharmaceutics, antifreeze agents, and lubricants. In the first part of this study, we demonstrate the formation of WLMs in polar solvents like glycerol and formamide. WLMs in water are induced by combining a cationic surfactant and a salt, but the combinations that work for water mostly do not work in polar solvents. The combination that does work in the latter involves a cationic surfactant with a very long (erucyl, C22) tail and an aromatic salt such as sodium salicylate. These WLMs display viscoelastic and shear-thinning rheology, as expected. By using a low-freezing mixture of glycerol and ethylene glycol, we are able to devise formulations in which WLMs remain intact down to sub-zero temperatures (–20°C). Thereby, we have been able to extend the range for WLM existence to much lower temperatures than in previous studies. Next, in the second part, we focus on the dynamic rheology of WLMs in glycerol, which is shown to be very different from that of WLMs in water. Specifically, WLMs in glycerol exhibit a double-crossover of their elastic (G′) and viscous (G″) moduli within the range of frequencies accessible by a rheometer. We believe that the high viscosity of glycerol influences the rheology at high frequencies. We also hypothesize that the WLMs in glycerol are shorter and weakly entangled compared to WLMs in water. Moreover, in terms of their dynamics, we suggest that WLMs in glycerol are similar to polymers – i.e., the chains will remain intact and not break and re-form frequently. In the last study, we demonstrate the formation of vesicles in polar solvents (glycerol, formamide and ethylene glycol) using the simple phospholipid, lecithin. Lecithin dissolves readily in polar solvents and gives rise to viscous fluids at low concentrations (~ 2 to 4%). At higher concentrations (> 10 wt%), lecithin forms clear gels that are strongly birefringent at rest. Dynamic rheology of the latter reveals an elastic, gel-like response. Images from cryo-scanning electron microscopy (cryo-SEM) indicate that the concentrated samples are ‘vesicle gels’, where multilamellar vesicles (MLVs, also called onions), with sizes between 50 to 600 nm, are close-packed across the sample volume. This structure explains both the rheology and the birefringence.Item EFFECT OF LIPID-PROTEIN INTERACTIONS ON THE CONDUCTANCE OF THE TRANSMEMBRANE PROTEIN ALPHA HEMOLYSIN USING MOLECULAR DYNAMICS SIMULATIONS(2019) Tammareddy, Tejaswi; Klauda, Jeffery; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Alpha-hemolysin (aHL) is a transmembrane ion-conducting channel which finds application in single molecule sensing using nanopore technology. Biomolecules are allowed to pass through the pore of the protein and, as a result, there is a change in the ion current, which is monitored to quantify single-molecule sensing. However, it has been established that the change in current is also affected by the lipid membrane in which the protein is present. It is also known that cholesterol has a concentration-dependent reduction in the current through the pore, experimentally. The understanding of current reduction at a single-molecule level and theoretical models replicating these conditions are lacking. In the current thesis, molecular dynamics simulations are performed on aHL inserted into a 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline (POPC) lipid bilayer with varying concentrations of cholesterol to investigate the effect on ionic current. Effect of lipid interactions, especially of cholesterol, on the protein structure and hence functioning of the ion channel is investigatedItem Ultra-Small Metal Nanoparticles: Aerosol- and Laser-Assisted Nanomanufacturing, Characterization, and Applications(2019) Yang, Yong; Zachariah, Michael R.; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Ultrasmall metal nanoparticles (1-10 nm) are certain to be the building blocks of the next generation of electronic, catalytic, and energy storage devices. Despite their importance, synthesizing these extremely small nanoparticles, at least in sufficient quantities to enable their industrial utility however, is challenging due to their low stability and tendency to agglomerate. Numerous techniques developed thus far typically generate metal nanoparticles in small quantities with a main difficulty in industrial scale-up being poor thermal control. This shortcoming often leads to wide size distributions, inhomogeneous dispersion, and aggregation. Thus, there is a pressing need for developing new strategies for scalable manufacturing of ultrasmall metal nanoparticles towards industrial applications. This dissertation identifies two techniques for scalable manufacturing of ultrasmall metal nanoparticles with tunable size, constituency, microstructure, and other properties: an aerosol droplet mediated approach and an ultrafast laser shock approach. The aerosol droplet mediated approach employs the fast heating and quenching nature of aerosol droplet nanoreactors containing precursor species to produce ultrasmall metal nanoparticles uniformly dispersed in polymer or graphene matrices. The fast heating and quenching nature intrinsic to the aerosol droplets is also employed to fabricate a new type of engineering material, notably high entropy alloy nanoparticles, defined as five or more well-mixed metal elements in near equimolar ratios. As an example of application, I further employ the aerosol droplets to create antimony nanoparticles incorporated carbon nanosphere network and the resulting architecture offered one of the best potassium ion battery anode performances in terms of both capacity and cycling stability. This dissertation also introduces an ultrafast laser shock technique to decorate metal nanoparticles onto carbon nanofibers (CNFs) in-situ with kinetically tunable size and surface density. A shorter laser shock enables the formation of metal nanoclusters with higher number densities and smaller sizes while longer laser shock leads to the further growth of metal nanoclusters and the achievement of their equilibrium shape. The catalytic performance towards electrocatalytic hydrogen evolution was greatly enhanced for CNF supported metal nanoclusters with a smaller size and higher number density.Item Advancements in Label-free Biosensing Using Field-Effect Transistors and Aided by Molecular Dynamics Simulations(2019) Guros, Nicholas; Klauda, Jeffery B; Balijepalli, Arvind; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Biosensors are used to characterize or measure concentrations of physiologically or pathologically significant biomarkers that indicate the health status of a patient, for example, a biomarker associated with a specific disease or cancer. Presently, there is a need to improve the capabilities of biosensors, which includes their rate of detection, limit of detection, and usability. With respect to usability, it is advantageous to develop biosensors that can detect a biomarker that is not labeled, such as with a conventional fluorescent, magnetic, or radioactive label, prior to characterization or measurement by that biosensor. Such biosensors are known as label-free biosensors and are the primary focus of this work. Biosensors are principally evaluated by two standards: their sensitivity to detect a target biomarker at physiologically relevant concentrations and their specificity to detect only the target biomarker in the presence of other molecules. The elements of biosensing critical to improving these two standards are: biorecognition of the biomarker, immobilization of the biorecognition element on the biosensor, and transduction of biomarker biorecognition to a measurable signal. Towards the improvement of sensitivity, electrostatically sensitive field-effect transistors (FET) were fabricated in a dual-gate configuration to enable label-free biosensing measurements with both high sensitivity and signal-to-noise ratio (SNR). This high performance, quantified with several metrics, was principally achieved by performing a novel annealing process that improved the quality of the FET’s semiconducting channel. These FETs were gated with either a conventional oxide or an ionic liquid, the latter of which yielded quantum capacitance-limited devices. Both were used to measure the activity of the enzyme cyclin-dependent kinase 5 (Cdk5) indirectly through pH change, where the ionic-liquid gated FETs measured pH changes at a sensitivity of approximately 75 times higher than the conventional sensitivity limit for pH measurements. Lastly, these FETs were also used to detect the presence of the protein streptavidin through immobilization of a streptavidin-binding biomolecule, biotin, to the FET sensing surface. To study the biomolecular factors that govern the specificity of biomarker biorecognition in label-free biosensing, molecular dynamics (MD) simulations were performed on several proteins. MD simulations were first performed on the serotonin receptor and ion channel, 5-HT3A. These simulations, which were performed for an order of magnitude longer than any previous study, demonstrate the dynamic nature of serotonin (5-HT) binding with 5-HT3A. These simulations also demonstrate the importance of using complex lipid membranes to immobilize 5-HT3A for biosensing applications to adequately replicate native protein function. The importance of lipid composition was further demonstrated using MD simulations of the ion channel alpha-hemolysin (αHL). The results of these simulations clearly demonstrate the lipid-protein structure-function relationship that regulates the ionic current though a lipid membrane-spanning ion channel. Finally, to demonstrate the impact of MD simulations to inform the design of FET biosensing, a strategy to use FETs to measure the ultra-low ionic currents through the ion channel 5-HT3A is outlined. This strategy leverages critical elements of 5-HT biorecognition and ion channel immobilization extracted from MD simulations for the design of the proposed FET sensing surface interface.Item Nature of Mesoscopic Aggregates in Solutions of Lysozyme(2018) NIKFARJAM, SHAKIBA; Woehl, Taylor J; Anisimov, Mikhail; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)An anomalous class of mesoscopic aggregates have previously been observed in solutions of lysozyme. These aggregates are thought to play an important role in nucleation of protein crystals and ordered protein aggregates, like amyloid fibers. Mesoscopic aggregates are currently thought to be in thermodynamic equilibrium with the protein solution, where transient oligomers of partially unfolded lysozyme monomers are thought to be the formation source of these aggregates. However, there is little experimental evidence to back up this proposed formation mechanism and thermodynamic behavior. Specifically, the effects of temperature on these aggregates and their thermodynamic reversibility have not been systematically tested. In this thesis, we investigate the equilibrium nature and the formation source of mesoscopic aggregates in solutions of model protein, lysozyme. We tested the effects of temperature on aggregate size and concentration and the aggregate reversibility after removal by systematic filtration. We used light and x-ray scattering and chromatography to experimentally characterize the aggregates during this study. Our findings indicate that mesoscopic aggregates are minimally sensitive to temperature changes and do not reform after removal by filtration. Together, these results indicate that mesoscopic aggregates are not in thermodynamic equilibrium with protein monomers or oligomers in solution. Overall, our experimental results contrast the current accepted formation mechanism of these mesoscopic aggregates and suggest they instead form due to contaminants present in solution or a sub-population of partially unfolded proteins.