Chemical & Biomolecular Engineering

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Formerly known as the Department of Chemical Engineering.

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End date: 2019Subject: search.filters.subject.Chemical engineering

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    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.
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    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 investigated
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    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.
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    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.
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    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.
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    A HIGH ENERGY AND POWER DUAL-ION BATTERY
    (2019) Wang, Boyu; Wang, Chunsheng; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    As the alternative of Lithium-ion Batteries, Dual-Ion Batteries (DIBs), utilizing the intercalation mechanisms of anions into graphite cathode and cations into anode materials, have been proposed as a novel energy storage system for the long cycle life, low cost and environmental impact. However, due to the high potential of anions intercalation into graphite, electrolytes with high oxidizing stability are required. Herein, all-fluorinated electrolyte (1 M LiPF6 in fluoroethylene carbonate (FEC)/ bis(2,2,2-trifluoroethyl) carbonate (FDEC)/ hydrofluoroether (HFE) 2:6:2 by volume) enables the DIB to be operated within a wide voltage window with excellent cycling stability. Moreover, Li2TiSiO5 anode material with high reversibility and proper working potential (0.28 V vs. Li+/Li), which supports high-rate operation due to free of lithium dendrite compared with graphitic anode, is applied here. This dual ion cell (graphite // Li2TiSiO5) exhibits high cycling stability with 71% capacity retention after 500 cycles and excellent rate performance (15 C).
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    MOLECULAR SIMULATION OF ANTIMICROBIAL PEPTIDE WLBU2-MOD BINDING WITH GRAM-NEGATIVE INNER MEMBRANE MIMIC
    (2019) Cline, Tyler Newman; Klauda, Jeffery; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Since the discovery of Penicillin in 1928 by Sir Alexander Fleming, antibiotics have been one of the most important technologies in modern medicine. Due to the lack of novel innovative methods and the gross abuse of antibiotics both in human use and agriculture, we currently face an antibiotic resistance crisis. In the last fifty years only a handful of new class of antibiotics that target gram-positive bacteria have been introduced and, in that time, no new class of antibiotics that target gram-negative bacteria have been introduced. This thesis focuses on the molecular dynamic simulations involving the cationic α-helical antibacterial peptide, WLBU2-mod (RRWVRRVRRVWRRVVRVVRRWVRR), binding with a gram-negative bacterial inner membrane (IM) mimic composed of palmitoyloleoyl PE (POPE), palmitoyloleoyl PG (POPG), and 1,1’,2,2’-tetraoctadecenoyl CL (TOCL2) in a 7:2:1 ratio respectively. The structure of WLBU2-mod was predicted using Robetta to be either a single extended α-helical structure or a bent α-helical structure. Replica exchange with solute tempering with an improved Hamiltonian acceptance protocol (REST2) was performed on WLBU2-mod to relax the peptide to an unstructured conformation in an ii explicit aqueous solution. WLBU2-mod relaxed with REST2 consists of mainly random coil and β-sheet secondary structure which matches experimental circular dichroism (CD) results collected by Aria Salyapongse and Dr. Tristram-Nagle. Experimental CD results with the IM predicted the peptide to be structured with majority α-helical secondary structure, contrary to the unstructured results of the peptide in water. Both structured and unstructured WLBU2-mod were placed in parallel 10 Å above the IM mimic and molecular dynamics (MD) was performed to observe the binding mechanism. Simulations failed to see significant bilayer thinning or penetration into the hydrophobic core but there is strong indication that our simulations represent in intermediate state toward the final binding mechanism. In order to observe more substantial binding to the IM, future projects should consider increasing the length of the simulations and flipping the orientation of the peptide to have the hydrophobic components face inward toward the bilayer. Future projects in combination with the groundwork laid out here will hopefully provide insight into how antibacterial peptides can become the answer to the resistance crisis we face today.
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    Protein Engineering Approaches to Improve the Therapeutic Potential of Histatin-5 for Candida albicans Infections
    (2019) Leissa, Jesse Alton; Karlsson, Amy J; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The salivary peptide histatin 5 has been studied as a novel therapeutic to address rising drug resistance and limited therapeutics for treating infections caused by the fungal pathogen Candida albicans. While histatin 5 possesses antifungal activity, degradation from secreted aspartic proteases produced by C. albicans hinders its potential. To develop a strategy that will identify variants of histatin 5 with improved proteolytic stability, the peptide was integrated into a yeast surface display system, and the proteolytic degradation conditions were optimized to improve the resolution between proteolytically stable (K11RK17R) and proteolytically susceptible (K13L) variants. Additionally, histatin 5 and K11RK17R were embedded in polyelectrolyte multilayer films (PEMs) to investigate their ability to prevent biofilm formation on surfaces. Significant biofilm formation was prevented at high concentrations of K11RK17R, while histatin 5 encouraged biofilm formation. My results support the therapeutic potential of histatin 5 and will enable the design of improved peptide-based therapeutic approaches.
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    ISOTOPE-ASSISTED METABOLIC FLUX ANALYSIS IN THE INVESTIGATION OF PROSTATE CANCER
    (2019) Graham, Trevor; Sriram, Ganesh; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Understanding cancer metabolism is critical to developing treatment strategies which selectively target malignant cells. Toward this objective, we apply isotope-assisted metabolic flux analysis to the investigation of prostate cancer, which kills over 28,000 men every year in the United States alone. We performed metabolic flux analysis (MFA) on immortal prostate cancer cell lines to determine the relative activity of metabolic pathways that constitute central carbon metabolism. We identified multiple deviations of the malignant phenotype from that of benign cells. We found that all cell lines exhibited a preference for the pentose phosphate pathway over glycolysis for glucose catabolism, with an average flux partition of 53% ± 25% in favor of the pentose phosphate pathway. We also identified a drop in TCA cycle flux from 33.5 ± 10.5 for LNCaP to 19.7 ± 7.8 for CSS90 cells, possibly indicating a preference for glutaminolysis and lipogenesis to fuel rapid proliferation.
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    An experimental and graph theoretic study of atomic layer deposition processes for spacecraft applications
    (2019) Salami, Hossein; Adomaitis, Raymond A; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Accurate understanding of the atomic layer deposition (ALD) process kinetics is necessary for developing new ALD chemistries to produce novel nanomaterials, and also optimization of typical ALD processes used in industrial applications. Proposing a potential reaction sequence alongside with accurate kinetic data is among the very first steps in studying the ALD process kinetics and forms the backbone of further engineering analysis. A valid and proper ALD reaction net work (RN) must be able to reflect the self-limiting and cycle to cycle reproducibility behavior experimentally observed for practical ALD processes. Otherwise, the mathematical model built based on it fails to precisely capture and reproduce ALD behavior no matter how accurate the available kinetic data are. In this work, a RN analysis method based on species-reaction graphs and the principles of convex analysis is developed to study the mathematical structure and dynamical behavior of thin-film deposition RN models. The key factor in ALD RN analysis is the presence of consistent surface-originated invariant states for each ALD half-cycle. Therefore, the primary focus of the proposed approach is on identifying and formulating physically-relevant RN invariant states, and to study the chemical significance of these conserved modes for ALD reaction mechanisms. The proposed method provides a well-defined framework, applicable to all ALD systems, to examine the above criteria of a proper ALD RN without requiring any information on the reaction rates. This method fills a gap in the procedure of ALD process modeling before the time-consuming step of calculating individual reaction rates which is usually done through ALD experiments in reactors equipped with in-situ measurement instruments or computationally expensive computational chemistry-based calculations such as density functional theory. The presented approach is also extended to study the variant states of a RN. The generalized method provides information on different variant states dynamically depending on each individual reaction in the network which facilitates the study and ultimately the formulation of different reaction rates in the system. In the second part of this dissertation, an experimental study of ALD of indium oxide and indium tin oxide films using the trimethylindium, tetrakis (dimethylamino) tin(IV), and ozone precursor system is conducted to first, investigate the potential application of this ALD process for producing high-quality transparent conducting layers; and second, to understand the relationship between the thickness of the deposited films and their electrical and optical properties. The optimized recipe was then used to process commercial Z93 heat radiator pigments used in manufacturing spacecraft thermal radiator panels to enhance their electrical conductivity to avoid the differential charging that may occur due to the interaction with charged particles in Van Allen radiation belts. To this aim a specialized ALD reactor was designed and constructed capable of processing standard flat substrates as well as coating micron-sized particles. The results confirm that the proposed process can be used to coat the heat radiator pigment particles and that the indium oxide film can nucleate and grow on their surface. This provides an example from a variety of potential space-related applications that can benefit from the ALD process.