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BACKGROUND:Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse environments. This quality makes them an attractive bacterial target for research in bioremediation and microbial fuel cell applications. Constraint-based modeling is a useful tool for helping researchers gain insights into the metabolic capabilities of these bacteria. However, Shewanella oneidensis MR-1 is the only strain with a genome-scale metabolic model constructed out of 21 sequenced Shewanella strains.RESULTS:In this work, we updated the model for Shewanella oneidensis MR-1 and constructed metabolic models for three other strains, namely Shewanella sp. MR-4, Shewanella sp. W3-18-1, and Shewanella denitrificans OS217 which span the genus based on the number of genes lost in comparison to MR-1. We also constructed a Shewanella core model that contains the genes shared by all 21 sequenced strains and a few non-conserved genes associated with essential reactions. Model comparisons between the five constructed models were done at two levels - for wildtype strains under different growth conditions and for knockout mutants under the same growth condition. In the first level, growth/no-growth phenotypes were predicted by the models on various carbon sources and electron acceptors. Cluster analysis of these results revealed that the MR-1 model is most similar to the W3-18-1 model, followed by the MR-4 and OS217 models when considering predicted growth phenotypes. However, a cluster analysis done based on metabolic gene content revealed that the MR-4 and W3-18-1 models are the most similar, with the MR-1 and OS217 models being more distinct from these latter two strains. As a second level of comparison, we identified differences in reaction and gene content which give rise to different functional predictions of single and double gene knockout mutants using Comparison of Networks by Gene Alignment (CONGA). Here, we showed how CONGA can be used to find biomass, metabolic, and genetic differences between models.CONCLUSIONS:We developed four strain-specific models and a general core model that can be used to do various in silico studies of Shewanella metabolism. The developed models provide a platform for a systematic investigation of Shewanella metabolism to aid researchers using Shewanella in various biotechnology applications.

Our ability to understand and predict the fate and transport of contaminants in natural systems is vital if we are to be successful in protecting our water resources. One important aspect of understanding chemical fate and transport in natural systems is identifying key kinetic controls on important redox reactions such as sulfate reduction. Anaerobic microbial activities like sulfate reduction are of particular interest because of the important role they play in the degradation of contaminants in the subsurface. However, current rate estimates for sulfate reduction have a wide range in the literature making it difficult to determine representative rates for a given system. These differences in rate data may be explained by varying kinetic controls on reactions. Push-pull tests were used to evaluate sulfate reduction rates at the wetland-aquifer interface. Anaerobic aquifer water containing abundant sulfate was injected into sulfate-depleted wetland porewater. The injected water was subsequently withdrawn and analyzed for geochemical indicators of sulfate reduction. Complexities in rate data, such as presence of a lag phase, changing rate order and spatial variability, were observed and are hypothesized to be linked to activities of the native microbial population. Subsequent experiments explored the response of native microorganisms to geochemical perturbations using a novel approach to measure directly the effects of a geochemical perturbation on an in situ microbial population and measure rates of resulting reactions. In situ experiments involved colonization of a substrate by microorganisms native to the wetland sediments followed by introductions of native water amended with sulfate and tracer. Experimental results showed that higher sulfate concentrations and warmer seasonal temperatures result in faster sulfate reduction rates and corresponding increases in sulfate reducing bacteria. Findings from this research provide quantitative evidence of how geochemical and microbiological processes are linked in a system not at equilibrium.

As one of the most promising solar cell technologies, organic solar cells have unique superiorities distinct from inorganic counterparts, such as semitransparency, flexibility and solution-processability, as well as tunable photophysical properties, which originate from the structural verstailities of organic semiconductors. A major breakthrough in OSCs was the exploration of novel non-fullerene electron acceptor (NFAs): In comparison with traditional fullerene derivative acceptors, NFA possesses several advantages, such as low synthesis cost, tunable absorption range and adjustable energetic level, which effectively provides a wide light-harvesting window with low energetic loss. In recent decades, fused-ring electron acceptors (FREAs) have obtained an irreplaceable status in the development of OSCs. However, there are still initial drawbacks to FREA-based devices including: 1: the degree of molecular packing and the corresponding impact on device performance, which has not been studied in depth; 2: the feasibility of approaches for controlling the bulk heterojunction morphology of the film, which also has not been systemic researched; 3: the presence of bulk (geminate and non-geminate) and surface recombination which significantly affects the efficiency and stability of working devices. In this thesis, I took the above three issues as my main doctoral research subjects. In the first part of the thesis, I shine light onto the strength of π-conjugated backbones in FREA molecular structures, which strongly affect the intramolecular interaction. Herein, two FREA with different conjugated framework (IDT core vs IDTT core) are synthesized and employed as electron acceptors in OSCs. A significantly enhanced power conversion efficiency of 11.2% is obtained from IDTTIC-based devices in comparison with that of IDTIC-based devices (5.6%). After considering the electron-donating part in FREA molecules, I also study the effect of the terminal unit, which has a strong relationship with the intramolecular charge transfer effect and intermolecular interactions. Solvent additives are another powerful strategy to further improve the photovoltaic efficiency. 1-chloronaphthalene (CN) was found to be useful in the PTB7-Th:IEICO-4F system, which show a PCE improvement from 9.5% to 12.8%. Furthermore, by utilizing a small molecule donor, BIT-4F-T, as a third component, an optimum PCE of 14.0% is achieved in the devices based on PTB7-Th:IEICO-4F.

Abstract: Even though improvements in the efficiency of organic solar cells encouraged the commercialization of this technology in the past two decades, the stability of organic solar cells is still an active area of research. The effect of photo-oxidative degradation on the performance of organic solar cell devices is significant. One way to lower the rate of photooxidation degradation is by preventing oxygen molecules from reaching the active layer of organic solar cells. This could be achieved by fabricating the devices in an inert environment in the absence of oxygen. Once the devices are fabricated, they would be encapsulated in a transparent material.1, 2 Even though this is a viable solution, there are two main issues. First, it was shown that oxygen molecules could diffuse through the encapsulating material and degrade the devices.3 Second, implementing this solution would increase the fabrication cost of these devices, which would make this solution commercially unfeasible compared to other solar cell technologies.3 Speller and his colleges reported a possible mechanism of the photo-oxidative degradation and showed a relationship between the rate of degradation and LUMO energy levels of electron acceptor molecule4. In this thesis, we report the photo-oxidative degradation rate of O-IDTBR and O-IDTBR-(C3N2)2. The later electron acceptor is analogous to O-IDTBR with deeper LUMO by 0.1 eV. After four hours of constant irradiation from a 1-sun intensity xenon solar simulator, the maximum UV-Vis absorbance of O-IDTBR is reduced by 12% relative to O-IDTBR-(C3N2)2. Lower absolute degradation rates were observed when 1-sun LED solar simulator was used compare to xenon solar simulator.

Organic photovoltaics has emerged as a promising technology for electricity generation. The essential component in an organic solar cell is the bulk heterojunction absorber layer, typically a blend of an electron donor and an electron acceptor. Efforts have been made to design new materials such as donor polymers and novel acceptors to improve the power conversion efficiencies. New fullerene free acceptors providing low cost synthesis routes and tenability of their optoelectronic and electrochemical properties have been designed. Despite the efforts, still not much is known about the photopysical processes in these blends that limit the performance. In this respect, time-resolved spectroscopy such as transient absorption and time-resolved photoluminescence, can provide in-depth insight into the various (photo) physical processes in bulk heterojunction solar cell. In this thesis, PCE10 was used as donor and paired with different non fullerene acceptors. In the first part of this thesis the impact of the core structure (cyclopenta-[2, 1-b:3, 4-b’]dithiophene (CDT) versus indacenodithiophene (IDTT)) of malononitrile (BM)-terminated acceptors, abbreviated as CDTBM and IDTTBM, on the photophysical characteristics of BHJ solar cells is reported. The IDTT-based acceptor achieves power conversion efficiencies of 8.4%, higher than the CDT-based acceptor (5.6%), due to concurrent increase in short-circuit current and open-circuit voltage. Using (ultra)fast transient spectroscopy we demonstrate that reduced geminate recombination in PCE10: IDTTBM blends is the reason for the difference in short-circuit currents. External quantum efficiency measurements indicate that the higher energy of interfacial charge-transfer states observed for the IDTT-based acceptor blends is the origin of the higher open-circuit voltage. In the second part of this thesis, I report the impact of acceptor side chains on the photo-physical processes of BHJ solar cells using three different IDT-based acceptors, namely O-IDTBR, EH-IDTBR and O-IDTBCN blended with PCE10. Power conversion efficiencies as high as 10 % were achieved. The transient absorption spectroscopy experiments provide insight into sub-picosecond exciton dissociation and charge generation which is followed by nanosecond triplet state formation in PCE10:O-DTBR and PCE10:EH-IDTBR blends, while in O-IDTBCN triplets are not observed. Time delayed collection field experiments (TDCF) were performed to address the charge carrier generation and examine its dependence on the electric field.

The state-of-the-art organic solar cells (OSC) use bulk heterojunction (BHJ) blend architecture in the photo-active layer. The BHJ is formed by finely mixing polymer donor and small molecule acceptor, which was predominantly fullerene derivatives until the last five years. However, the emergence of non-fullerene acceptor (NFA) materials has been the viable alternative to overcome high synthetic costs, limited optical absorption, and poor bandgap tunability of fullerene-based acceptors. These unique properties of NFA has resulted in a rapid improvement of OSC efficiency and opened doors for wide variety of applications including building integrated photovoltaics, green houses and agrivoltaics. Despite these advantages, the shorter device lifetime under light and heat is a major concern for their commercialization. This dissertation is focused on improving poor photo- and thermal stability of high efficiency OSC based on the widely used NFA, ITIC and Y-series derivatives. The light-induced changes in the acceptor molecular structure and the active layer nanostructure results in the photo-induced traps in photo-aged devices. The selective addition of third component to the active layer impedes the changes in the active layer nanostructure and suppress trap formation. Under constant thermal stress, the growth of acceptor crystals results increases the trap-assisted recombination in thermally aged devices. Similar to photo-stability the selective addition of third or more component/s arrests the crystal growth by minimizing the Gibbs free energy. The results suggest that the fabricated hexanary and ternary OSC display a superior thermal stability than the respective binary devices. In addition, the hexanary devices displayed thickness independent thermal stability, which is essential for the active layer thermal stability printed via high throughput techniques.

A numerical model for subsurface solute transport is developed and applied to a contaminated field site. The model is capable of depicting multiple species transport in a three-dimensional, anisotropic, heterogeneous domain as influenced by advection, dispersion, adsorption, and biodegradation. Various hydrocarbon contaminants are simulated as electron donors for microbial growth, with electron acceptors utilized in the following sequence: oxygen, nitrate, Mn(IV), Fe(III), sulfate, and CO₂. In addition, the model accounts for products of biodegradation such as Mn (II), Fe(II), H₂S, and CH₄. Biodegradation of each hydrocarbon substrate follows Monod kinetics, modified to include the effects of electron acceptor and nutrient availability. Inhibition functions permit any electron acceptor to inhibit utilization of all other electron acceptors that provide less Gibbs free energy to the microbes. The model assumes that Fe(III) and Mn(IV) occur as solid phase ions, while the other electron acceptors are dissolved in the aqueous phase. Microbial biomass is simulated as independent groups of heterotrophic bacteria that exist as scattered microcolonies attached to the porous medium. Diffusional limitations to microbial growth are assumed to be negligible. In order to verify the accuracy of the computer code, the model was applied to simple, hypothetical test cases, and the results were compared to analytical solutions. In addition, a sensitivity analysis showed that variations in model inputs caused logical changes in output. Finally, the capabilities of the model were tested by comparing model output to observed concentrations of hydrocarbons, electron acceptors, and endproducts at a leaking UST site. The model was calibrated using historical site data, and predictive capabilities of the model were tested against subsequent sets of field data. The model was used to examine the effect of porous media heterogeneities on contaminant transport and biodegradation. The turning bands method was used to produce hypothetical, yet realistic heterogeneous fields describing hydraulic conductivity, initial biomass concentration, and the maximum rate of substrate utilization. When the available electron acceptor concentrations were small compared to the hydrocarbon concentration, the overall rate of hydrocarbon mass loss increased with time, even as hydrocarbon concentrations decreased. This trend is the opposite of what would be predicted by a first order decay model. / Ph. D.

Pentaerythritol tetranitrate (PETN), a nitrate ester, is widely used as a powerful explosive and is classified as a munitions constituent of great concern by DoD in U.S.A. It is an environmental concern and poses a threat to ecosystem and human health. Our objective was to examine potential remediation strategies for both PETN-contaminated water and soil. Flow-through iron columns were used to determine the potential for using granular iron to degrade PETN in aqueous phase. PETN transformation in both a 100% iron column and a 30% iron and 70% silica sand column followed pseudo-first-order kinetics, with average half-lives of 0.26 and 1.58 minutes, respectively. Based on the identified intermediates and products, the reaction pathway was proposed to be a sequential denitration process, in which PETN was stepwisely reduced to pentaerythritol with the formation of pentaerythritol trinitrate (PETriN) and pentaerythritol dinitrate (PEDN). Although pentaerythrito mononitrate was not detected, an approximately 100% nitrogen mass recovery indicated that all nitro groups were removed from PETN. Nitrite was released in each denitration step and subsequently reduced to NH4+ by iron. Nitrate was not detected during the experiment, suggesting that hydrolysis was not involved in PETN degradation. Furthermore, batch experiments showed that PETN dissolution was likely a rate-limiting factor for PETN degradation, especially in the case with high amount of iron. Using 50% methanol as a representative co-solvent, PETN solubility was greatly enhanced and thus the removal efficiency was improved. The results demonstrate the use of granular iron to remediate PETN-contaminated water. The biodegradability of aqueous PETN was examined with a mixed microbial culture from a site contaminated with PETN. The mixed culture was enriched and selected using a mineral medium containing acetate and yeast extract as carbon and nutrient sources in the presence of nitrate or sulfate. The final enrichment cultures were used as inocula for studying PETN biodegradation under nitrate-reducing and sulfate-reducing conditions. In addition, PETN degradation was tested using the original microbial culture under the mixed electron acceptor conditions of nitrate and sulfate. The results showed that under all conditions tested, PETN was sequentially reduced, apparently following the same pathway as the abiotic reduction by granular iron. Pentaerythritol mononitrate, a suspected intermediate in the abiotic degradation by iron, was identified in this experiment. The presence of nitrate seemed not to affect the kinetics of PETN degradation, with both PETN and nitrate degrading simultaneously. However, the rate of nitrate reduction was much faster than PETN degradation. With respect to sulfate, its presence did not have an adverse effect on PETN degradation, indicated by the very similar degradation rates of PETN in the presence and absence of sulfate. Under all conditions, PETN appeared to act as a terminal electron acceptor for energy generation during biodegradation. A utilization sequence by bacteria in the order of nitrate, PETN, PETriN, PEDN and sulfate was clearly observed. The study in this phase demonstrated that under anaerobic conditions, with carbon sources provided, PETN can be effectively biodegraded by indigenous bacteria in contaminated soil, most likely by denitrifying bacteria. Based on the successful demonstration of abiotic and biotic degradation of PETN in the aqueous phase, both methods were further tested for remediating PETN-contaminated soil in both laboratory and pilot scale. In the laboratory, a systematic soil microcosm experiment was conducted using soil from a contaminated site and additions of either granular iron or organic materials, with deoxygenated Millipore water. Because of the high concentration in the contaminated soil, solid-phase of PETN was initially present in the microcosms. Two types of DARAMEND products, D6390Fe20 (containing 20% iron + 80% botanical materials) and ADM-298500 (100% botanical materials), were used as sources of carbon and other nutrients. During the 84-day incubation period, more than 98% was removed in all DARAMEND treatments, following pseudo-first-order kinetics with half-lives ranging between 8 and 18 days. The results clearly demonstrated that PETN can be effectively degraded under anaerobic conditions with the addition of carbon and possibly nutrients. As in the aqueous tests, the sequence of microbial utilization was nitrate followed by PETN and sulfate. In contrast to the tests with aqueous PETN, iron was not effective in removing PETN in the contaminated soil, due to iron passiviation caused by the presence of high levels of nitrate in the soil. In addition, a slight enhancement was observed in a combined system of iron and biodegradation over biodegradation only. However, the extent of enhancement is not believed to be significant relative to the extra cost for iron addition. A pilot scale test was conducted at a PETN-contaminated site at Louviers, CO, a waste pond which had received waste water from PETN manufacture for over 20 years. The test involved 10 treatments, one control without amendment, one amended with iron (10%), eight with different types and amounts of organic carbon (1%, 2% and 4% of D6390Fe20; 2% and 4% of ADM-298500 and 1%, 2% and 4% of brewers grain). Each treatment was performed in a plastic tub (45 cm wide × 90 cm long × 25 cm deep), containing approximately 18 cm thick layer of soil and 6-8 cm of standing water. Over 74 days, very little consistent reduction of PETN was found in the iron treatment, which was also due to iron passivation in the presence of nitrate in the soil. In contrast, significant removal of PETN (11,200 to 33,400 mg/kg) was observed in the treatments amended with organic materials, and the extent of removal increased with increasing amounts of organic materials. The pilot test was consistent with the results of the laboratory experiments for iron and biodegradation with carbon addition. For biological treatment, the stoichiometric estimation suggests that the complete remediation in many of the treatments will be ultimately limited by carbon sources. Results of this study showed the great potentials of using granular iron to degrade PETN in solution and using indigenous bacteria present in contaminated soils to biodegrade PETN in both the solution and soil phase. Both iron and biodegradation with carbon addition represent viable approaches for remediation of PETN-contaminated water and soil, though iron may not be appropriate in the presence of high concentration of nitrate.

Pentaerythritol tetranitrate (PETN), a nitrate ester, is widely used as a powerful explosive and is classified as a munitions constituent of great concern by DoD in U.S.A. It is an environmental concern and poses a threat to ecosystem and human health. Our objective was to examine potential remediation strategies for both PETN-contaminated water and soil. Flow-through iron columns were used to determine the potential for using granular iron to degrade PETN in aqueous phase. PETN transformation in both a 100% iron column and a 30% iron and 70% silica sand column followed pseudo-first-order kinetics, with average half-lives of 0.26 and 1.58 minutes, respectively. Based on the identified intermediates and products, the reaction pathway was proposed to be a sequential denitration process, in which PETN was stepwisely reduced to pentaerythritol with the formation of pentaerythritol trinitrate (PETriN) and pentaerythritol dinitrate (PEDN). Although pentaerythrito mononitrate was not detected, an approximately 100% nitrogen mass recovery indicated that all nitro groups were removed from PETN. Nitrite was released in each denitration step and subsequently reduced to NH4+ by iron. Nitrate was not detected during the experiment, suggesting that hydrolysis was not involved in PETN degradation. Furthermore, batch experiments showed that PETN dissolution was likely a rate-limiting factor for PETN degradation, especially in the case with high amount of iron. Using 50% methanol as a representative co-solvent, PETN solubility was greatly enhanced and thus the removal efficiency was improved. The results demonstrate the use of granular iron to remediate PETN-contaminated water. The biodegradability of aqueous PETN was examined with a mixed microbial culture from a site contaminated with PETN. The mixed culture was enriched and selected using a mineral medium containing acetate and yeast extract as carbon and nutrient sources in the presence of nitrate or sulfate. The final enrichment cultures were used as inocula for studying PETN biodegradation under nitrate-reducing and sulfate-reducing conditions. In addition, PETN degradation was tested using the original microbial culture under the mixed electron acceptor conditions of nitrate and sulfate. The results showed that under all conditions tested, PETN was sequentially reduced, apparently following the same pathway as the abiotic reduction by granular iron. Pentaerythritol mononitrate, a suspected intermediate in the abiotic degradation by iron, was identified in this experiment. The presence of nitrate seemed not to affect the kinetics of PETN degradation, with both PETN and nitrate degrading simultaneously. However, the rate of nitrate reduction was much faster than PETN degradation. With respect to sulfate, its presence did not have an adverse effect on PETN degradation, indicated by the very similar degradation rates of PETN in the presence and absence of sulfate. Under all conditions, PETN appeared to act as a terminal electron acceptor for energy generation during biodegradation. A utilization sequence by bacteria in the order of nitrate, PETN, PETriN, PEDN and sulfate was clearly observed. The study in this phase demonstrated that under anaerobic conditions, with carbon sources provided, PETN can be effectively biodegraded by indigenous bacteria in contaminated soil, most likely by denitrifying bacteria. Based on the successful demonstration of abiotic and biotic degradation of PETN in the aqueous phase, both methods were further tested for remediating PETN-contaminated soil in both laboratory and pilot scale. In the laboratory, a systematic soil microcosm experiment was conducted using soil from a contaminated site and additions of either granular iron or organic materials, with deoxygenated Millipore water. Because of the high concentration in the contaminated soil, solid-phase of PETN was initially present in the microcosms. Two types of DARAMEND products, D6390Fe20 (containing 20% iron + 80% botanical materials) and ADM-298500 (100% botanical materials), were used as sources of carbon and other nutrients. During the 84-day incubation period, more than 98% was removed in all DARAMEND treatments, following pseudo-first-order kinetics with half-lives ranging between 8 and 18 days. The results clearly demonstrated that PETN can be effectively degraded under anaerobic conditions with the addition of carbon and possibly nutrients. As in the aqueous tests, the sequence of microbial utilization was nitrate followed by PETN and sulfate. In contrast to the tests with aqueous PETN, iron was not effective in removing PETN in the contaminated soil, due to iron passiviation caused by the presence of high levels of nitrate in the soil. In addition, a slight enhancement was observed in a combined system of iron and biodegradation over biodegradation only. However, the extent of enhancement is not believed to be significant relative to the extra cost for iron addition. A pilot scale test was conducted at a PETN-contaminated site at Louviers, CO, a waste pond which had received waste water from PETN manufacture for over 20 years. The test involved 10 treatments, one control without amendment, one amended with iron (10%), eight with different types and amounts of organic carbon (1%, 2% and 4% of D6390Fe20; 2% and 4% of ADM-298500 and 1%, 2% and 4% of brewers grain). Each treatment was performed in a plastic tub (45 cm wide × 90 cm long × 25 cm deep), containing approximately 18 cm thick layer of soil and 6-8 cm of standing water. Over 74 days, very little consistent reduction of PETN was found in the iron treatment, which was also due to iron passivation in the presence of nitrate in the soil. In contrast, significant removal of PETN (11,200 to 33,400 mg/kg) was observed in the treatments amended with organic materials, and the extent of removal increased with increasing amounts of organic materials. The pilot test was consistent with the results of the laboratory experiments for iron and biodegradation with carbon addition. For biological treatment, the stoichiometric estimation suggests that the complete remediation in many of the treatments will be ultimately limited by carbon sources. Results of this study showed the great potentials of using granular iron to degrade PETN in solution and using indigenous bacteria present in contaminated soils to biodegrade PETN in both the solution and soil phase. Both iron and biodegradation with carbon addition represent viable approaches for remediation of PETN-contaminated water and soil, though iron may not be appropriate in the presence of high concentration of nitrate.