Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the…
Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement.…
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We…
Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices.
The culture of the 1970s in the United States of America was progressive and revolutionary. Due to various events that were unfavorable to the public, U.S. citizens began to lose trust in their government. Signs of the public's revolt and dissention began to show in laws and propositions voters passed.…
The culture of the 1970s in the United States of America was progressive and revolutionary. Due to various events that were unfavorable to the public, U.S. citizens began to lose trust in their government. Signs of the public's revolt and dissention began to show in laws and propositions voters passed. In California, Proposition 13 was one of many anti-tax laws taxpayers voted for to cut back the control of the government. As a result, revenues for public services and improvements decreased and maintenance allocations for infrastructure systems were considerably reduced. Fast-forwarding to today, infrastructure systems in the U.S. are reaching their retirement period and are requiring extreme maintenance and attention. Los Angeles has been experiencing severe water main breaks in its water distribution system for several years now, but the city is lacking funds to replace the aging pipes. The lack of funds paired with aging infrastructure indicates there is a flaw in the forecasting analysis techniques used today to project infrastructure costs. Therefore, an alternative discounting function to the exponential is proposed: the hyperbolic discounting function. A comparative analysis was performed using a hyperbolic and an exponential discounting function. The two functions were calibrated over the course of 50 years and the parameters r and a were determined. Then the discounts were applied to a 50-year expenditure projection for pipe replacements of a water distribution system. The present value was computed with each discount function and results were obtained. By year 50, the hyperbolic function yielded a higher present value of $25.06 million and the exponential function yielded a present value of $14 million. These results lead to the conclusion that the hyperbolic discounting function is the preferred methodology when calculating long-term expenditures, especially those dependent on tax revenue.
As inhabitants of a desert, a sustainable water source has always been and will continue to be a crucial component in developing the cities Arizonans call home. Phoenix and the surrounding municipalities make up a large metropolitan area that continues to grow in spatial size and population. However, as climate…
As inhabitants of a desert, a sustainable water source has always been and will continue to be a crucial component in developing the cities Arizonans call home. Phoenix and the surrounding municipalities make up a large metropolitan area that continues to grow in spatial size and population. However, as climate change becomes more of an evident challenge, Arizona is forced to plan and make decisions regarding its ability to safely and efficiently maintain its livelihood and/or growth. With the effects of climate change in mind, Arizona will need to continue to innovatively and proactively address issues of water management and the effects of urban heat island (UHI). The objective of this thesis was to study the socioeconomic impacts of four extreme scenarios of the future Phoenix metropolitan area. Each of the scenarios showcased a different hypothetical extreme and uniquely impacted factors related to water management and UHI. The four scenarios were a green city, desert city, expanded city into desert land, and expanded city into agricultural land. These four scenarios were designed to emphasize different aspects of the urban water-energy-population nexus, as the future of the Phoenix metropolitan area is dynamic. Primarily, the Green City and Desert City served as contrasting viewpoints on UHI and water sustainability. The Expanded Cities showed the influence of population growth and land use on water sustainability. The socioeconomic impacts of the four scenarios were then analyzed. The quantitative data of the report was completed using the online user interface of WaterSim 5.0 (a program created by the Decision Center for a Desert City (DCDC) at Arizona State University). The different scenarios were modeled in the program by adjusting various demand and supply oriented factors. The qualitative portion as well as additional quantitative data was acquired through an extensive literature review. It was found that changing land use has direct water use implications; agricultural land overtaken for municipal uses can sustain a population for longer. Though, removing agricultural lands has both social and economic implications, and can actually cause the elimination of an emergency source. Moreover, it was found that outdoor water use and reclaimed wastewater can impact water sustainability. Practices that decrease outdoor water use and increase wastewater reclamation are currently occurring; however, these practices could be augmented. Both practices require changes in the publics' opinions on water use, nevertheless, the technology and policy exists and can be intensified to become more water sustainable. While the scenarios studied were hypothetical cases of the future of the Phoenix metropolitan area, they identified important circumscribing measures and practices that influence the Valley's water resources.
The current EPA regulation for total chromium in drinking water is the MCL standard of 0.1 milligrams per liter or 100 parts per billion (ppb) to avoid dermatological effects. With a toxicology study released in 2008 by the Department of Health and Human Services noting that hexavalent chromium is carcinogenic,…
The current EPA regulation for total chromium in drinking water is the MCL standard of 0.1 milligrams per liter or 100 parts per billion (ppb) to avoid dermatological effects. With a toxicology study released in 2008 by the Department of Health and Human Services noting that hexavalent chromium is carcinogenic, the EPA is currently reviewing this MCL standard. During this review, the EPA provides monitoring guidance that requires quarterly sampling of surface water for hexavalent chromium. However, these samples monitor the instant in time that they were taken, and do not account for varying concentrations that are time-dependent. This research seeks to develop a method for monitoring hexavalent chromium in water. Using ion exchange technology, passive samplers were developed and installed at the Chandler Water Treatment Plant for a week-long monitoring event. Results show that passive samplers using ion exchange technology provide an accurate assessment of the average concentration of total chromium within the water treatment plant's effluent with 90.3% recovery of Cr(VI) in SIR-100 resin and 62.6% recovery in SIR-700.
One of the salient challenges of sustainability is the Tragedy of the Commons, where individuals acting independently and rationally deplete a common resource despite their understanding that it is not in the group's long term best interest to do so. Hardin presents this dilemma as nearly intractable and solvable only…
One of the salient challenges of sustainability is the Tragedy of the Commons, where individuals acting independently and rationally deplete a common resource despite their understanding that it is not in the group's long term best interest to do so. Hardin presents this dilemma as nearly intractable and solvable only by drastic, government-mandated social reforms, while Ostrom's empirical work demonstrates that community-scale collaboration can circumvent tragedy without any elaborate outside intervention. Though more optimistic, Ostrom's work provides scant insight into larger-scale dilemmas such as climate change. Consequently, it remains unclear if the sustainable management of global resources is possible without significant government mediation. To investigate, we conducted two game theoretic experiments that challenged students in different countries to collaborate digitally and manage a hypothetical common resource. One experiment involved students attending Arizona State University and the Rochester Institute of Technology in the US and Mountains of the Moon University in Uganda, while the other included students at Arizona State and the Management Development Institute in India. In both experiments, students were randomly assigned to one of three production roles: Luxury, Intermediate, and Subsistence. Students then made individual decisions about how many units of goods they wished to produce up to a set maximum per production class. Luxury players gain the most profit (i.e. grade points) per unit produced, but they also emit the most externalities, or social costs, which directly subtract from the profit of everybody else in the game; Intermediate players produce a medium amount of profit and externalities per unit, and Subsistence players produce a low amount of profit and externalities per unit. Variables influencing and/or inhibiting collaboration were studied using pre- and post-game surveys. This research sought to answer three questions: 1) Are international groups capable of self-organizing in a way that promotes sustainable resource management?, 2) What are the key factors that inhibit or foster collective action among international groups?, and 3) How well do Hardin's theories and Ostrom's empirical models predict the observed behavior of students in the game? The results of gameplay suggest that international cooperation is possible, though likely sub-optimal. Statistical analysis of survey data revealed that heterogeneity and levels of trust significantly influenced game behavior. Specific traits of heterogeneity among students found to be significant were income, education, assigned production role, number of people in one's household, college class, college major, and military service. Additionally, it was found that Ostrom's collective action framework was a better predictor of game outcome than Hardin's theories. Overall, this research lends credence to the plausibility of international cooperation in tragedy of the commons scenarios such as climate change, though much work remains to be done.
The rising need for water reuse in the Southwest United States has increased awareness of the quality of wastewater. This need is caused by an increased population having basic water needs; inefficient water use, such as overwatering lawns and leaking pipes; and recent drought conditions all over the southwestern US.…
The rising need for water reuse in the Southwest United States has increased awareness of the quality of wastewater. This need is caused by an increased population having basic water needs; inefficient water use, such as overwatering lawns and leaking pipes; and recent drought conditions all over the southwestern US. Reclaimed water is a possible solution. It's used for a variety of non-potable, or non-drinkable, reasons. These uses include: cooling power plants, concrete mixing, artificial lakes, and irrigation for public parks and golf courts. Cooling power plants utilizes roughly 41% of the total water consumed by the United States, which makes it the highest user of water in the US. The attention is turned to optimizing mechanical processes and reducing the amount of water consumed. Wet-recirculating systems reuse cooling water in a second cycle rather than discharging it immediately. Cooling towers are commonly used to expose water to ambient air. As the water evaporates, more water is withdrawn while the rest continues to circulate. These systems have much lower water withdrawals than once-through systems, but have higher water consumption. The cooling towers in wet-recirculating plants and other warm machinery have two major limitations: evaporation of pumped water and scale formation in the components. Cooling towers circulate water, and only draw as it evaporates, which conserves water. The scale formation in the components is due to the hardness of the water. Scale occurs when hard water evaporates and forms solid calcium carbonate. This formation can lead to reduced flow or even clogging in pipes, fouling of components or pipes, and reduced cooling efficiency. Another concern from the public over the use of reclaimed water is the possibility of there being fecal contamination. This fear stems from the stigma associated with drinking water that essentially came from the toilet. An emerging technology, in order to address these three issues, is the use of an electromagnetic device. The wires have a current flowing through which induces a magnetic field perpendicular to the direction of the flow, while the electrical field is proportional to the flow velocity. In other words, the magnetic and electrical fields will create an effect that will concentrate cations at the center of the pipe and anions at the wall of the pipe or the other way depending on the direction of the flow. Reversing the field will then cause the cations and anions to move toward one another and increase the collision frequency and energy. The purpose of these experiments is to test the effects of the electromagnetic device on the aforementioned topics. There are three tests that were performed, a surface tension test, a hardness test, and a microbial test. The surface tension test focused on the angle of a water droplet until it burst. The angle would theoretically decrease as the bond between water molecules increased due to the device. The results of this test shows a lower angle for the treated water but a higher angle for the untreated one. This means the device had an effect on the surface tension of the water. Hard water is caused by calcium and magnesium ions in the water. These ions are dissolved in the water as it travels past soil and rocks. The purpose of this test is to measure the free calcium ion amount in the water. If the free calcium number lowers, then it can be assumed it collided with the carbonate and formed calcium carbonate. This calcium carbonate causes a reduction in hardness in the water. The result of the test showed no correlation between ion concentrations in the treated/untreated system. The e. coli test focused on testing the effects of an electromagnetic device on inhibiting fecal contamination in water/wastewater at a treatment facility. In order to detect fecal contamination, we test for bacteria known as fecal coliforms, more specifically e. coli. The test involved spiking the system with bacteria and testing its concentrations after time had passed.The e. coli results showed no trend in the inactivation of the bacteria. In conclusion, the device had varying results, but multiple steps can be taken in the future in order to continue research.
It is the intent of this research to determine the feasibility of utilizing industrial byproducts in cementitious systems in lieu of Portland Cement to reduce global CO2 emissions. Class C and Class F Fly Ash (CFA and FFA, respectively) derived from industrial coal combustion were selected as the replacement materials…
It is the intent of this research to determine the feasibility of utilizing industrial byproducts in cementitious systems in lieu of Portland Cement to reduce global CO2 emissions. Class C and Class F Fly Ash (CFA and FFA, respectively) derived from industrial coal combustion were selected as the replacement materials for this study. Sodium sulfate and calcium oxide were used as activators. In Part 1 of this study, focus was placed on high volume replacement of OPC using sodium sulfate as the activator. Despite improvements in heat generation for both CFA and FFA systems in the presence of sulfate, sodium sulfate was found to have adverse effects on the compressive strength of CFA mortars. In the CFA mixes, strength improved significantly with sulfate addition, but began to decrease in strength around 14 days due to expansive ettringite formation. Conversely, the addition of sulfate led to improved strength for FFA mixes such that the 28 day strength was comparable to that of the CFA mixes with no observable strength loss. Maximum compressive strengths achieved for the high volume replacement mixes was around 40 MPa, which is considerably lower than the baseline OPC mix used for comparison. In Part 2 of the study, temperature dependency and calcium oxide addition were studied for sodium sulfate activated systems composed of 100% Class F fly ash. In the presence of sulfate, added calcium increased reactivity and compressive strength at early ages, particularly at elevated temperatures. It is believed that sulfate and calcium react with alumina from fly ash to form ettringite, while heat overcomes the activation energy barrier of fly ash. The greatest strengths were obtained for mixes containing the maximum allowed quantity of calcium oxide (5%) and sodium sulfate (3%), and were around 12 MPa. This is a very low compressive strength relative to OPC and would therefore be an inadequate substitute for OPC needs.
The civil engineering curriculum includes the engineering fields of environmental, geotechnical, hydrology, structural, and transportation. A particular focus on the structural engineering curriculum outline involves courses in mathematics, engineering mechanics, structural analysis, and structural design. The core structural analysis and design course at Arizona State University (CEE 321) is a…
The civil engineering curriculum includes the engineering fields of environmental, geotechnical, hydrology, structural, and transportation. A particular focus on the structural engineering curriculum outline involves courses in mathematics, engineering mechanics, structural analysis, and structural design. The core structural analysis and design course at Arizona State University (CEE 321) is a transition course to connect realistic structural design and analysis concepts to an engineering foundation created by the first and second year mathematics and mechanics courses. CEE 321 is styled after a flipped classroom model and students are assessed through quizzes, midterms, design projects, and a final exam. Student performance was evaluated for the Spring 2013 and Fall 2013 semesters through an error analysis technique designed to categorize student mistakes based on type of error and related topic. This analysis revealed that student's basic engineering mechanics skills improved throughout the course as well as identified the areas that students struggle in. The slope-deflection and direct stiffness methods of analysis and calculating cross-sectional properties are the primary areas of concern. Using appropriate technology in the engineering classroom has the potential to enhance the learning environment and address the areas of inadequacy identified by the performance analysis. A survey of CEE 321 students demonstrated that technology is a highly integrated and useful portion of student's lives. Therefore, the engineering classroom should reflect this. Through the use of analysis and design software, students are able to begin to develop design intuition and understanding while completing realistic engineering projects in their third year of undergraduate studies. Additionally, incorporating internet resources into and outside of the classroom allows students to be connected to course content from any web-enabled device of their choice. Lecture videos posted online covering the course content were requested by many CEE 321 students and are an emerging resource that supplements the flipped classroom model. The availability of such a tool allows students to revisit concepts that they do not understand or pause, rewind, and replay the lectures when necessary. An expansion of the structural analysis and design online lecture videos for CEE 321 are expected to address and improve the areas that students struggle in as identified by the error analysis.