Chemical & Biomolecular Engineering
Permanent URI for this communityhttp://hdl.handle.net/1903/2219
Formerly known as the Department of Chemical Engineering.
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Item Dynamic Modeling for the Design and Cyclic Operation of an Atomic Layer Deposition (ALD) Reactor(MDPI, 2013-08-19) Travis, Curtisha D.; Adomaitis, Raymond A.A laboratory-scale atomic layer deposition (ALD) reactor system model is derived for alumina deposition using trimethylaluminum and water as precursors. Model components describing the precursor thermophysical properties, reactor-scale gas-phase dynamics and surface reaction kinetics derived from absolute reaction rate theory are integrated to simulate the complete reactor system. Limit-cycle solutions defining continuous cyclic ALD reactor operation are computed with a fixed point algorithm based on collocation discretization in time, resulting in an unambiguous definition of film growth-per-cycle (𝑔𝑝𝑐). A key finding of this study is that unintended chemical vapor deposition conditions can mask regions of operation that would otherwise correspond to ideal saturating ALD operation. The use of the simulator for assisting in process design decisions is presented.Item Shape-Changing Tubular Hydrogels(MDPI, 2018-02-22) Raghavan, Srinivasa R.; Fernandes, Neville J.; Cipriano, Bani H.We describe the creation of hollow tubular hydrogels in which different zones along the length of the tube are composed of different gels. Our method to create these gels is adapted from a technique developed previously in our lab for creating solid hybrid hydrogels. The zones of our tubular gel are covalently bonded at the interfaces; as a result, these interfaces are highly robust. Consequently, the tube can be picked up, manipulated and stretched without suffering any damage. The hollow nature of these gels allows them to respond 2–30-fold faster to external stimuli compared to a solid gel of identical composition. We study the case where one zone of the hybrid tube is responsive to pH (due to the incorporation of an ionic monomer) while the other zones are not. Initially, the entire tube has the same diameter, but when pH is changed, the diameter of the pH-responsive zone alone increases (i.e., this zone bulges outward) while the other zones maintain their original diameter. The net result is a drastic change in the shape of the gel, and this can be reversed by reverting the pH to its original value. Similar localized changes in gel shape are shown for two other stimuli: temperature and solvent composition. Our study points the way for researchers to design three-dimensional soft objects that can reversibly change their shape in response to stimuli.Item Effect of a Cationic Surfactant on Microemulsion Globules and Drug Release from Hydrogel Contact Lenses(MDPI, 2019-06-06) Torres-Luna, Cesar; Hu, Naiping; Koolivand, Abdollah; Fan, Xin; Zhu, Yuli; Domszy, Roman; Yang, Jeff; Yang, Arthur; Wang, Nam SunThe present study evaluates the in vitro release of diclofenac sodium (DFNa) from contact lenses based on poly-2-hydroxyethyl methacrylate (pHEMA) hydrogels containing an embedded microemulsion to extend release duration. The oil (ethyl butyrate)-in-water microemulsion systems are prepared with two non-ionic surfactants, Brij 97 or Tween 80, together with a long-alkyl chain cationic surfactant, cetalkonium chloride (CKC). Without CKC, Brij 97 or Tween 80-based microemulsions showed average droplet sizes of 12 nm and 18 nm, respectively. The addition of CKC decreased the average droplet sizes to 2–5 nm for both non-ionic surfactants. Such significant reduction in the average droplet size corresponds to an increase in the DFNa release duration as revealed by the in vitro experiments. Contact lens characterization showed that important properties such as optical transparency and water content of Brij 97-based contact lenses with cationic microemulsions was excellent. However, the optical transparency of the corresponding Tween 80 based contact lenses was unsatisfactory. The results indicate that cationic microemulsion-laden contact lenses can benefit from combinatory effects of microemulsions and cationic surfactant at low CKC weight percentage, e.g., with the release of 70% of the drug in 45, 10, and 7 h for B97-CKC-0.45%, CKC-0.45%, and control lenses, respectively. However, the microemulsion effect on extending DFNa release became negligible at the highest CKC weight percentage (1.8%).Item Formation of Drug-Participating Catanionic Aggregates for Extended Delivery of Non-Steroidal Anti-Inflammatory Drugs from Contact Lenses(MDPI, 2019-10-10) Torres-Luna, Cesar; Koolivand, Abdollah; Fan, Xin; Agrawal, Niti R.; Hu, Naiping; Zhu, Yuli; Domszy, Roman; Briber, Robert M.; Wang, Nam Sun; Yang, ArthurThis paper focuses on extending drug release duration from contact lenses by incorporating catanionic aggregates. The aggregates consist of a long-chain cationic surfactant, i.e., cetalkonium chloride (CKC), and an oppositely charged anti-inflammatory amphiphilic drug. We studied three non-steroidal anti-inflammatory (NSAID) drugs with different octanol–water partition coefficients; diclofenac sodium (DFNa), flurbiprofen sodium (FBNa), and naproxen sodium (NPNa). Confirmation of catanionic aggregate formation in solution was determined by steady and dynamic shear rheology measurements. We observed the increased viscosity, shear thinning, and viscoelastic behavior characteristic of wormlike micelles; the rheological data are reasonably well described using a Maxwellian fluid model with a single relaxation time. In vitro release experiments demonstrated that the extension in the drug release time is dependent on the ability of a drug to form viscoelastic catanionic aggregates. Such aggregates retard the diffusive transport of drug molecules from the contact lenses. Our study revealed that the release kinetics depends on the CKC concentration and the alkyl chain length of the cationic surfactant. We demonstrated that more hydrophobic drugs such as diclofenac sodium show a more extended release than less hydrophobic drugs such as naproxen sodium.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 A core microbiome associated with the peritoneal tumors of pseudomyxoma peritonei(Springer Nature, 2013-07-12) Gilbreath, Jeremy J; Semino-Mora, Cristina; Friedline, Christopher J; Liu, Hui; Bodi, Kip L; McAvoy, Thomas J; Francis, Jennifer; Nieroda, Carol; Sardi, Armando; Dubois, Andre; Lazinski, David W; Camilli, Andrew; Testerman, Traci L; Merrell, D ScottPseudomyxoma peritonei (PMP) is a malignancy characterized by dissemination of mucus-secreting cells throughout the peritoneum. This disease is associated with significant morbidity and mortality and despite effective treatment options for early-stage disease, patients with PMP often relapse. Thus, there is a need for additional treatment options to reduce relapse rate and increase long-term survival. A previous study identified the presence of both typed and non-culturable bacteria associated with PMP tissue and determined that increased bacterial density was associated with more severe disease. These findings highlighted the possible role for bacteria in PMP disease. To more clearly define the bacterial communities associated with PMP disease, we employed a sequenced-based analysis to profile the bacterial populations found in PMP tumor and mucin tissue in 11 patients. Sequencing data were confirmed by in situ hybridization at multiple taxonomic depths and by culturing. A pilot clinical study was initiated to determine whether the addition of antibiotic therapy affected PMP patient outcome. We determined that the types of bacteria present are highly conserved in all PMP patients; the dominant phyla are the Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. A core set of taxon-specific sequences were found in all 11 patients; many of these sequences were classified into taxonomic groups that also contain known human pathogens. In situ hybridization directly confirmed the presence of bacteria in PMP at multiple taxonomic depths and supported our sequence-based analysis. Furthermore, culturing of PMP tissue samples allowed us to isolate 11 different bacterial strains from eight independent patients, and in vitro analysis of subset of these isolates suggests that at least some of these strains may interact with the PMP-associated mucin MUC2. Finally, we provide evidence suggesting that targeting these bacteria with antibiotic treatment may increase the survival of PMP patients. Using 16S amplicon-based sequencing, direct in situ hybridization analysis and culturing methods, we have identified numerous bacterial taxa that are consistently present in all PMP patients tested. Combined with data from a pilot clinical study, these data support the hypothesis that adding antimicrobials to the standard PMP treatment could improve PMP patient survival.Item Experimental evidence and isotopomer analysis of mixotrophic glucose metabolism in the marine diatom Phaeodactylum tricornutum(Springer Nature, 2013-11-14) Zheng, Yuting; Quinn, Andrew H; Sriram, GaneshHeterotrophic fermentation using simple sugars such as glucose is an established and cost-effective method for synthesizing bioproducts from bacteria, yeast and algae. Organisms incapable of metabolizing glucose have limited applications as cell factories, often despite many other advantageous characteristics. Therefore, there is a clear need to investigate glucose metabolism in potential cell factories. One such organism, with a unique metabolic network and a propensity to synthesize highly reduced compounds as a large fraction of its biomass, is the marine diatom Phaeodactylum tricornutum (Pt). Although Pt has been engineered to metabolize glucose, conflicting lines of evidence leave it unresolved whether Pt can natively consume glucose. Isotope labeling experiments in which Pt was mixotrophically grown under light on 100% U-13C glucose and naturally abundant (~99% 12C) dissolved inorganic carbon resulted in proteinogenic amino acids with an average 13C-enrichment of 88%, thus providing convincing evidence of glucose uptake and metabolism. The dissolved inorganic carbon was largely incorporated through anaplerotic rather than photosynthetic fixation. Furthermore, an isotope labeling experiment utilizing 1-13C glucose and subsequent metabolic pathway analysis indicated that (i) the alternative Entner-Doudoroff and Phosphoketolase glycolytic pathways are active during glucose metabolism, and (ii) during mixotrophic growth, serine and glycine are largely synthesized from glyoxylate through photorespiratory reactions rather than from 3-phosphoglycerate. We validated the latter result for mixotrophic growth on glycerol by performing a 2-13C glycerol isotope labeling experiment. Additionally, gene expression assays showed that known, native glucose transporters in Pt are largely insensitive to glucose or light, whereas the gene encoding cytosolic fructose bisphosphate aldolase 3, an important glycolytic enzyme, is overexpressed in light but insensitive to glucose. We have shown that Pt can use glucose as a primary carbon source when grown in light, but cannot use glucose to sustain growth in the dark. We further analyzed the metabolic mechanisms underlying the mixotrophic metabolism of glucose and found isotopic evidence for unusual pathways active in Pt. These insights expand the envelope of Pt cultivation methods using organic substrates. We anticipate that they will guide further engineering of Pt towards sustainable production of fuels, pharmaceuticals, and platform chemicals.Item Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network(Springer Nature, 2013-11-14) Misra, Ashish; Sriram, GaneshGene regulatory networks (GRNs) are models of molecule-gene interactions instrumental in the coordination of gene expression. Transcription factor (TF)-GRNs are an important subset of GRNs that characterize gene expression as the effect of TFs acting on their target genes. Although such networks can qualitatively summarize TF-gene interactions, it is highly desirable to quantitatively determine the strengths of the interactions in a TF-GRN as well as the magnitudes of TF activities. To our knowledge, such analysis is rare in plant biology. A computational methodology developed for this purpose is network component analysis (NCA), which has been used for studying large-scale microbial TF-GRNs to obtain nontrivial, mechanistic insights. In this work, we employed NCA to quantitatively analyze a plant TF-GRN important in floral development using available regulatory information from AGRIS, by processing previously reported gene expression data from four shoot apical meristem cell types. The NCA model satisfactorily accounted for gene expression measurements in a TF-GRN of seven TFs (LFY, AG, SEPALLATA3 [SEP3], AP2, AGL15, HY5 and AP3/PI) and 55 genes. NCA found strong interactions between certain TF-gene pairs including LFY → MYB17, AG → CRC, AP2 → RD20, AGL15 → RAV2 and HY5 → HLH1, and the direction of the interaction (activation or repression) for some AGL15 targets for which this information was not previously available. The activity trends of four TFs - LFY, AG, HY5 and AP3/PI as deduced by NCA correlated well with the changes in expression levels of the genes encoding these TFs across all four cell types; such a correlation was not observed for SEP3, AP2 and AGL15. For the first time, we have reported the use of NCA to quantitatively analyze a plant TF-GRN important in floral development for obtaining nontrivial information about connectivity strengths between TFs and their target genes as well as TF activity. However, since NCA relies on documented connectivity information about the underlying TF-GRN, it is currently limited in its application to larger plant networks because of the lack of documented connectivities. In the future, the identification of interactions between plant TFs and their target genes on a genome scale would allow the use of NCA to provide quantitative regulatory information about plant TF-GRNs, leading to improved insights on cellular regulatory programs.Item Microvessel rupture induced by high-intensity therapeutic ultrasound—a study of parameter sensitivity in a simple in vivo model(Springer Nature, 2017-03-02) Kim, Yeonho; Nabili, Marjan; Acharya, Priyanka; Lopez, Asis; Myers, Matthew R.Safety analyses of transcranial therapeutic ultrasound procedures require knowledge of the dependence of the rupture probability and rupture time upon sonication parameters. As previous vessel-rupture studies have concentrated on a specific set of exposure conditions, there is a need for more comprehensive parametric studies. Probability of rupture and rupture times were measured by exposing the large blood vessel of a live earthworm to high-intensity focused ultrasound pulse trains of various characteristics. Pressures generated by the ultrasound transducers were estimated through numerical solutions to the KZK (Khokhlov-Zabolotskaya-Kuznetsov) equation. Three ultrasound frequencies (1.1, 2.5, and 3.3 MHz) were considered, as were three pulse repetition frequencies (1, 3, and 10 Hz), and two duty factors (0.0001, 0.001). The pressures produced ranged from 4 to 18 MPa. Exposures of up to 10 min in duration were employed. Trials were repeated an average of 11 times. No trends as a function of pulse repetition rate were identifiable, for either probability of rupture or rupture time. Rupture time was found to be a strong function of duty factor at the lower pressures; at 1.1 MHz the rupture time was an order of magnitude lower for the 0.001 duty factor than the 0.0001. At moderate pressures, the difference between the duty factors was less, and there was essentially no difference between duty factors at the highest pressure. Probability of rupture was not found to be a strong function of duty factor. Rupture thresholds were about 4 MPa for the 1.1 MHz frequency, 7 MPa at 3.3 MHz, and 11 MPa for the 2.5 MHz, though the pressure value at 2.5 MHz frequency will likely be reduced when steep-angle corrections are accounted for in the KZK model used to estimate pressures. Mechanical index provided a better collapse of the data (less separation of the curves pertaining to the different frequencies) than peak negative pressure, for both probability of rupture and rupture time. The results provide a database with which investigations in more complex animal models can be compared, potentially establishing trends by which bioeffects in human vessels can be estimated.Item Fluorinated solid electrolyte interphase enables highly reversible solid-state Li metal battery(AAAS, 2018-12-21) Fan, Xiulin; Ji, Xiao; Han, Fudong; Yue, Jie; Chen, Ji; Chen, Long; Deng, Tao; Jiang, Jianjun; Wang, ChunshengSolid-state electrolytes (SSEs) are receiving great interest because their high mechanical strength and transference number could potentially suppress Li dendrites and their high electrochemical stability allows the use of high-voltage cathodes, which enhances the energy density and safety of batteries. However, the much lower critical current density and easier Li dendrite propagation in SSEs than in nonaqueous liquid electrolytes hindered their possible applications. Herein, we successfully suppressed Li dendrite growth in SSEs by in situ forming an LiF-rich solid electrolyte interphase (SEI) between the SSEs and the Li metal. The LiF-rich SEI successfully suppresses the penetration of Li dendrites into SSEs, while the low electronic conductivity and the intrinsic electrochemical stability of LiF block side reactions between the SSEs and Li. The LiF-rich SEI enhances the room temperature critical current density of Li3PS4 to a record-high value of >2 mA cm−2. Moreover, the Li plating/stripping Coulombic efficiency was escalated from 88% of pristine Li3PS4 to more than 98% for LiF-coated Li3PS4. In situ formation of electronic insulating LiF-rich SEI provides an effective way to prevent Li dendrites in the SSEs, constituting a substantial leap toward the practical applications of next-generation high-energy solid-state Li metal batteries.