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- All Subjects: Synthetic Biology
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Description
Polymer and polymer matrix composites (PMCs) materials are being used extensively in different civil and mechanical engineering applications. The behavior of the epoxy resin polymers under different types of loading conditions has to be understood before the mechanical behavior of Polymer Matrix Composites (PMCs) can be accurately predicted. In many structural applications, PMC structures are subjected to large flexural loadings, examples include repair of structures against earthquake and engine fan cases. Therefore it is important to characterize and model the flexural mechanical behavior of epoxy resin materials. In this thesis, a comprehensive research effort was undertaken combining experiments and theoretical modeling to investigate the mechanical behavior of epoxy resins subject to different loading conditions. Epoxy resin E 863 was tested at different strain rates. Samples with dog-bone geometry were used in the tension tests. Small sized cubic, prismatic, and cylindrical samples were used in compression tests. Flexural tests were conducted on samples with different sizes and loading conditions. Strains were measured using the digital image correlation (DIC) technique, extensometers, strain gauges, and actuators. Effects of triaxiality state of stress were studied. Cubic, prismatic, and cylindrical compression samples undergo stress drop at yield, but it was found that only cubic samples experience strain hardening before failure. Characteristic points of tensile and compressive stress strain relation and load deflection curve in flexure were measured and their variations with strain rate studied. Two different stress strain models were used to investigate the effect of out-of-plane loading on the uniaxial stress strain response of the epoxy resin material. The first model is a strain softening with plastic flow for tension and compression. The influence of softening localization on material behavior was investigated using the DIC system. It was found that compression plastic flow has negligible influence on flexural behavior in epoxy resins, which are stronger in pre-peak and post-peak softening in compression than in tension. The second model was a piecewise-linear stress strain curve simplified in the post-peak response. Beams and plates with different boundary conditions were tested and analytically studied. The flexural over-strength factor for epoxy resin polymeric materials were also evaluated.
ContributorsYekani Fard, Masoud (Author) / Chattopadhyay, Aditi (Thesis advisor) / Dai, Lenore (Committee member) / Li, Jian (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Rajadas, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
Plasmon resonance in nanoscale metallic structures has shown its ability to concentrate electromagnetic energy into sub-wavelength volumes. Metal nanostructures exhibit a high extinction coefficient in the visible and near infrared spectrum due to their large absorption and scattering cross sections corresponding to their surface plasmon resonance. Hence, they can serve as an attractive candidate for solar energy conversion. Recent papers have showed that dielectric core/metallic shell nanoparticles yielded a plasmon resonance wavelength tunable from visible to infrared by changing the ratio of core radius to the total radius. Therefore it is interesting to develop a dispersion of core-shell multifunctional nanoparticles capable of dynamically changing their volume ratio and thus their spectral radiative properties. Nanoparticle suspensions (nanofluids) are known to offer a variety of benefits for thermal transport and energy conversion. Nanofluids have been proven to increase the efficiency of the photo-thermal energy conversion process in direct solar absorption collectors (DAC). Combining these two cutting-edge technologies enables the use of core-shell nanoparticles to control the spectral and radiative properties of plasmonic nanofluids in order to efficiently harvest and convert solar energy. Plasmonic nanofluids that have strong energy concentrating capacity and spectral selectivity can be used in many high-temperature energy systems where radiative heat transport is essential. In this thesis，the surface plasmon resonance effect and the wavelength tuning ranges for different metallic shell nanoparticles are investigated, the solar-weighted efficiencies of corresponding core-shell nanoparticle suspensions are explored, and a quantitative study of core-shell nanoparticle suspensions in a DAC system is provided. Using core-shell nanoparticle dispersions, it is possible to create efficient spectral solar absorption fluids and design materials for applications which require variable spectral absorption or scattering.
ContributorsLv, Wei (Author) / Phelan, Patrick E (Thesis advisor) / Dai, Lenore (Committee member) / Prasher, Ravi (Committee member) / Arizona State University (Publisher)
Created2012
Description
Currently in synthetic biology only the Las, Lux, and Rhl quorum sensing pathways have been adapted for broad engineering use. Quorum sensing allows a means of cell to cell communication in which a designated sender cell produces quorum sensing molecules that modify gene expression of a designated receiver cell. While useful, these three quorum sensing pathways exhibit a nontrivial level of crosstalk, hindering robust engineering and leading to unexpected effects in a given design. To address the lack of orthogonality among these three quorum sensing pathways, previous scientists have attempted to perform directed evolution on components of the quorum sensing pathway. While a powerful tool, directed evolution is limited by the subspace that is defined by the protein. For this reason, we take an evolutionary biology approach to identify new orthogonal quorum sensing networks and test these networks for cross-talk with currently-used networks. By charting characteristics of acyl homoserine lactone (AHL) molecules used across quorum sensing pathways in nature, we have identified favorable candidate pathways likely to display orthogonality. These include Aub, Bja, Bra, Cer, Esa, Las, Lux, Rhl, Rpa, and Sin, which we have begun constructing and testing. Our synthetic circuits express GFP in response to a quorum sensing molecule, allowing quantitative measurement of orthogonality between pairs. By determining orthogonal quorum sensing pairs, we hope to identify and adapt novel quorum sensing pathways for robust use in higher-order genetic circuits.
ContributorsMuller, Ryan (Author) / Haynes, Karmella (Thesis director) / Wang, Xiao (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
One of the primary bottlenecks to chemical production in biological organisms is the toxicity of the chemical. Overexpression of efflux pumps has been shown to increase tolerance to aromatic compounds such as styrene and styrene oxide. Tight control of pump expression is necessary to maximize titers and prevent excessive strain on the cells. This study aimed to identify aromatic-sensitive native promoters and heterologous biosensors for construction of closed-loop control of efflux pump expression in E. coli. Using a promoter library constructed by Zaslaver et al., activation was measured through GFP output. Promoters were evaluated for their sensitivity to the addition of one of four aromatic compounds, their "leaking" of signal, and their induction threshold. Out of 43 targeted promoters, 4 promoters (cmr, mdtG, yahN, yajR) for styrene oxide, 2 promoters (mdtG, yahN) for styrene, 0 promoters for 2-phenylethanol, and 1 promoter for phenol (pheP) were identified as ideal control elements in aromatic bioproduction. In addition, a series of three biosensors (NahR, XylS, DmpR) known to be inducible by other aromatics were screened against styrene oxide, 2-phenylethanol, and phenol. The targeted application of these biosensors is aromatic-induced activation of linked efflux pumps. All three biosensors responded strongly in the presence of styrene oxide and 2-phenylethanol, with minor activation in the presence of phenol. Bioproduction of aromatics continues to gain traction in the biotechnology industry, and the continued discovery of aromatic-inducible elements will be essential to effective pathway control.
ContributorsXu, Jimmy (Author) / Nielsen, David (Thesis director) / Wang, Xuan (Committee member) / School of Life Sciences (Contributor) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
This dissertation focuses on the biosynthetic production of aromatic fine chemicals in engineered Escherichia coli from renewable resources. The discussed metabolic pathways take advantage of key metabolites in the shikimic acid pathway, which is responsible for the production of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. For the first time, the renewable production of benzaldehyde and benzyl alcohol has been achieved in recombinant E. coli with a maximum titer of 114 mg/L of benzyl alcohol. Further strain development to knockout endogenous alcohol dehydrogenase has reduced the in vivo degradation of benzaldehyde by 9-fold, representing an improved host for the future production of benzaldehyde as a sole product. In addition, a novel alternative pathway for the production of protocatechuate (PCA) and catechol from the endogenous metabolite chorismate is demonstrated. Titers for PCA and catechol were achieved at 454 mg/L and 630 mg/L, respectively. To explore potential routes for improved aromatic product yields, an in silico model using elementary mode analysis was developed. From the model, stoichiometric optimums maximizing both product-to-substrate and biomass-to-substrate yields were discovered in a co-fed model using glycerol and D-xylose as the carbon substrates for the biosynthetic production of catechol. Overall, the work presented in this dissertation highlights contributions to the field of metabolic engineering through novel pathway design for the biosynthesis of industrially relevant aromatic fine chemicals and the use of in silico modelling to identify novel approaches to increasing aromatic product yields.
ContributorsPugh, Shawn (Author) / Nielsen, David (Thesis advisor) / Dai, Lenore (Committee member) / Torres, Cesar (Committee member) / Lind, Mary Laura (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2016
Description
A hybrid molecular dynamics (MD) simulation framework is developed to emulate mechanochemical reaction of mechanophores in epoxy-based nanocomposites. Two different force fields, a classical force field and a bond order based force field are hybridized to mimic the experimental processes from specimen preparation to mechanical loading test. Ultra-violet photodimerization for mechanophore synthesis and epoxy curing for thermoset polymer generation are successfully simulated by developing a numerical covalent bond generation method using the classical force field within the framework. Mechanical loading tests to activate mechanophores are also virtually conducted by deforming the volume of a simulation unit cell. The unit cell deformation leads to covalent bond elongation and subsequent bond breakage, which is captured using the bond order based force field. The outcome of the virtual loading test is used for local work analysis, which enables a quantitative study of mechanophore activation. Through the local work analysis, the onset and evolution of mechanophore activation indicating damage initiation and propagation are estimated; ultimately, the mechanophore sensitivity to external stress is evaluated. The virtual loading tests also provide accurate estimations of mechanical properties such as elastic, shear, bulk modulus, yield strain/strength, and Poisson’s ratio of the system. Experimental studies are performed in conjunction with the simulation work to validate the hybrid MD simulation framework. Less than 2% error in estimations of glass transition temperature (Tg) is observed with experimentally measured Tgs by use of differential scanning calorimetry. Virtual loading tests successfully reproduce the stress-strain curve capturing the effect of mechanophore inclusion on mechanical properties of epoxy polymer; comparable changes in Young’s modulus and yield strength are observed in experiments and simulations. Early damage signal detection, which is identified in experiments by observing increased intensity before the yield strain, is captured in simulations by showing that the critical strain representing the onset of the mechanophore activation occurs before the estimated yield strain. It is anticipated that the experimentally validated hybrid MD framework presented in this dissertation will provide a low-cost alternative to additional experiments that are required for optimizing material design parameters to improve damage sensing capability and mechanical properties.
In addition to the study of mechanochemical reaction analysis, an atomistic model of interphase in carbon fiber reinforced composites is developed. Physical entanglement between semi-crystalline carbon fiber surface and polymer matrix is captured by introducing voids in multiple graphene layers, which allow polymer matrix to intertwine with graphene layers. The hybrid MD framework is used with some modifications to estimate interphase properties that include the effect of the physical entanglement. The results are compared with existing carbon fiber surface models that assume that carbon fiber has a crystalline structure and hence are unable to capture the physical entanglement. Results indicate that the current model shows larger stress gradients across the material interphase. These large stress gradients increase the viscoplasticity and damage effects at the interphase. The results are important for improved prediction of the nonlinear response and damage evolution in composite materials.
In addition to the study of mechanochemical reaction analysis, an atomistic model of interphase in carbon fiber reinforced composites is developed. Physical entanglement between semi-crystalline carbon fiber surface and polymer matrix is captured by introducing voids in multiple graphene layers, which allow polymer matrix to intertwine with graphene layers. The hybrid MD framework is used with some modifications to estimate interphase properties that include the effect of the physical entanglement. The results are compared with existing carbon fiber surface models that assume that carbon fiber has a crystalline structure and hence are unable to capture the physical entanglement. Results indicate that the current model shows larger stress gradients across the material interphase. These large stress gradients increase the viscoplasticity and damage effects at the interphase. The results are important for improved prediction of the nonlinear response and damage evolution in composite materials.
ContributorsKoo, Bonsung (Author) / Chattopadhyay, Aditi (Thesis advisor) / Dai, Lenore (Committee member) / Jiang, Hanqing (Committee member) / Jiao, Yang (Committee member) / Rajadas, John (Committee member) / Arizona State University (Publisher)
Created2017
Description
The engineering of microbial cell factories capable of synthesizing industrially relevant chemical building blocks is an attractive alternative to conventional petrochemical-based production methods. This work focuses on the novel and enhanced biosynthesis of phenol, catechol, and muconic acid (MA). Although the complete biosynthesis from glucose has been previously demonstrated for all three compounds, established production routes suffer from notable inherent limitations. Here, multiple pathways to the same three products were engineered, each incorporating unique enzyme chemistries and/or stemming from different endogenous precursors. In the case of phenol, two novel pathways were constructed and comparatively evaluated, with titers reaching as high as 377 ± 14 mg/L at a glucose yield of 35.7 ± 0.8 mg/g. In the case of catechol, three novel pathways were engineered with titers reaching 100 ± 2 mg/L. Finally, in the case of MA, four novel pathways were engineered with maximal titers reaching 819 ± 44 mg/L at a glucose yield of 40.9 ± 2.2 mg/g. Furthermore, the unique flexibility with respect to engineering multiple pathways to the same product arises in part because these compounds are common intermediates in aromatic degradation pathways. Expanding on the novel pathway engineering efforts, a synthetic ‘metabolic funnel’ was subsequently constructed for phenol and MA, wherein multiple pathways were expressed in parallel to maximize carbon flux toward the final product. Using this novel ‘funneling’ strategy, maximal phenol and MA titers exceeding 0.5 and 3 g/L, respectively, were achieved, representing the highest achievable production metrics products reported to date.
ContributorsThompson, Brian (Author) / Nielsen, David R (Thesis advisor) / Nannenga, Brent (Committee member) / Green, Matthew (Committee member) / Wang, Xuan (Committee member) / Moon, Tae Seok (Committee member) / Arizona State University (Publisher)
Created2017
Description
Metabolic engineering of bacteria has become a viable technique as a sustainable and efficient method for the production of biochemicals. Two main goals were explored: investigating styrene tolerance genes in E. coli and engineering cyanobacteria for the high yield production of L-serine. In the first study, genes that were shown to be highly differentially expressed in E. coli upon styrene exposure were further investigated by testing the effects of their deletion and overexpression on styrene tolerance and growth. It was found that plsX, a gene responsible for the phospholipid formation in membranes, had the most promising results when overexpressed at 10 µM IPTG, with a relative OD600 of 706 ± 117% at 175 mg/L styrene when compared to the control plasmid at the same concentration. This gene is likely to be effective target when engineering styrene- and other aromatic-producing strains, increasing titers by reducing their cytotoxicity.In the second study, the goal is to engineer the cyanobacterium Synechococcus sp. PCC 7002 for the overproduction of L-serine. As a robust, photosynthetic bacteria, it has potential for being used in such-rich states to capture CO2 and produce industrially relevant products. In order to increase L-serine titers, a key degradation gene, ilvA, must be removed. While ilvA is responsible for degrading L-serine into pyruvate, it is also responsible for initiating the only known pathway for the production of isoleucine. Herein, we constructed a plasmid containing the native A0730 gene in order to investigate its potential to restore isoleucine production. If functional, a Synechococcus sp. PCC 7002 ΔilvA strain can then be engineered with minimal effects on growth and an expected increase in L-serine accumulation.
ContributorsAbed, Omar (Author) / Nielsen, David R (Thesis advisor) / Varman, Arul M (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2021
Description
Functional materials can be characterized as materials that have tunable properties and are attractive solutions to the improvement and optimization of processes that require specific physiochemical characteristics. Through tailoring and altering these materials, their characteristics can be fine-tuned for specific applications. Computational modeling proves to be a crucial methodology in the design and optimization of such materials. This dissertation encompasses the utilization of molecular dynamics simulations and quantum calculations in two fields of functional materials: electrolytes and semiconductors. Molecular dynamics (MD) simulations were performed on ionic liquid-based electrolyte systems to identify molecular interactions, structural changes, and transport properties that are often reflected in experimental results. The simulations aid in the development process of the electrolyte systems in terms of concentrations of the constituents and can be invoked as a complementary or predictive tool to laboratory experiments. The theme of this study stretches further to include computational studies of the reactivity of atomic layer deposition (ALD) precursors. Selected aminosilane-based precursors were chosen to undergo density functional theory (DFT) calculations to determine surface reactivity and viability in an industrial setting. The calculations were expanded to include the testing of a semi-empirical tight binding program to predict growth per cycle and precursor reactivity with a high surface coverage model. Overall, the implementation of computational methodologies and techniques within these applications improves materials design and process efficiency while streamlining the development of new functional materials.
ContributorsGliege, Marisa Elise (Author) / Dai, Lenore (Thesis advisor) / Derecskei-Kovacs, Agnes (Thesis advisor) / Muhich, Christopher (Committee member) / Emady, Heather (Committee member) / Zhuang, Houlong (Committee member) / Arizona State University (Publisher)
Created2021
Description
The purpose behind this research was to identify unknown transport proteins involved in lactate export. Lactate bioproduction is an environmentally beneficial alternative to petroleum-based plastic production as it produces less toxic waste byproduct and can rely on microbial degradation of otherwise wasted biomass. Coupled with appropriate product refinement, industrial microbial producers can be genetically engineered to generate quantities of bioplastic approaching 400 million metric tons each year. However, this process is not entirely suitable for large investment, as the fermentative bottlenecks, including product export and homeostasis control, limit production metrics. Previous studies have based their efforts on enhancing cellular machinery, but there remain uncharacterized membrane proteins involved in product export yet to be determined. It has been seen that deletion of known lactate transporters in Escherichia coli resulted in a decrease in lactate production, unlike the expected inhibition of export. This indicates that there exist membrane proteins with the ability to export lactate which may have another similar substrate it primarily transports.To identify these proteins, I constructed a genomic library of all genes in an engineered lactate producing E. coli strain, with known transporter genes deleted, and systematically screened for potential lactate transporter proteins. Plasmids and their isolated proteins were compared utilizing anaerobic plating to identify genes through sanger sequencing. With this method, I identified two proteins, yiaN and ybhL-ybhM, which did not show any significant improvement in lactate production when tested. Attempts were made to improve library diversity, resulting in isopropyl-β-D-1-thiogalactopyranoside induction as a likely factor for increased expression of potential fermentation-associated proteins. A genomic library from Lactobacillus plantarum was constructed and screened for transport proteins which could improve lactate production. Results showed that isolated plasmids contained no notable inserts, indicating that the initial transformation limited diversity. Lastly, I compared the results from genomic screening with overexpression of target transporter genes by computational substrate similarity search. Induced expression of ttdT, citT and dcuA together significantly increased lactate export and thus production metrics as well as cell growth. These positive results indicate an effective means of determining substrate promiscuity in membrane proteins with similar organic acid transport capacity.
ContributorsLee-Kin, Jared (Author) / Wang, Xuan (Thesis advisor) / Nielsen, David (Committee member) / Varman, Arul (Committee member) / Arizona State University (Publisher)
Created2022