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Semi-rational evolution of pyruvate carboxylase from Rhizopus oryzae for elevated fumaric acid synthesis in Saccharomyces cerevisiae
No full textBiochemical Engineering Journal, 177, 108238Note : if this item contains full text it may be a preprint, author manuscript, or a Gold OA copy that permits redistribution with a license such as CC BY. The final version is available through the publisher’s platform.Dicarboxylic acids are widely used in food, pharmaceutical, and chemical industries. Pyruvate carboxylase (PYC) plays a pivotal role in the production of dicarboxylic acids in microbial fermentation process. Our previous work showed that heterologous expression of pyruvate carboxylase (RoPYC) from Rhizopus oryzae resulted in an increase in fumaric acid titer to 226.0 ± 2.2 mg/L from 194.0 ± 4.0 mg/L in the S. cerevisiae pdc1adh1fum1 strain. However, PYC still remained the metabolic step limiting the production of target carboxylic acids. In this study, semi-rational evolution of pyruvate carboxylase by site-saturation mutagenesis combined with codon optimization was conducted to further improve fumaric acid synthesis. We demonstrated that each of three mutations (N315F, R485P and N1078F) or codon optimization of RoPYC significantly increased the production of fumaric acid. A maximal titer of 465.5 ± 6.5 mg/L was achieved in flasks by the strain expressing codon-optimized RoPYC mutant (R485P). Enzyme assays of these mutants showed higher PYC activities, while homology modeling indicated that the increased PYC activities could be attributed to the modulation of the allosteric domain and the biotin carboxylation domain. In addition, both calcium ion and carbon dioxide displayed positive effects on the fumaric acid production by this mutant. Overall, the strategy described here demonstrated an effective way for elevating PYC activity and further enhance the synthesis of dicarboxylic acids.National Natural Science Foundation of Chinahttps://login.libproxy.rpi.edu/login?url=https://doi.org/10.1016/j.bej.2021.10823
Modeling viscoelasticity in network materials (stress relaxation analysis)
No full text2021 DecemberSchool of EngineeringDecember 2021School of EngineeringStress relaxation in network materials with permanent crosslinks is due to the transport of fluid within the network (poroelasticity), the viscoelasticity of the matrix and the viscoelasticity of the network. While relaxation associated with the matrix was studied extensively, the contribution of the network remains unexplored. In this work we consider two and three-dimensional stochastic fiber networks with viscoelastic fibers and explore the dependence of stress relaxation on network structure. We observe that relaxation has two regimes – an initial exponential regime, followed by a stretched exponential regime – similar to the situation in other disordered materials. The stretch exponent is a function of density, fiber diameter and the network structure, and has a minimum at the transition between the affine and non-affine regimes of network behavior. The relaxation time constant of the first, exponential regime is similar to the relaxation time constant of individual fibers and is independent of network density and fiber diameter. The relaxation time constant of the second, stretched exponential regime is a weak function of network parameters. The stretched exponential emerges from the heterogeneity of relaxation dynamics on scales comparable with the mesh size, with higher heterogeneity leading to smaller stretch exponents. In composite networks of fibers whose relaxation time constant is selected from a distribution with set mean, the stretch exponent decreases with increasing the coefficient of variation of the fiber time constant distribution. As opposed to thermal glass formers and colloids, in these athermal systems the dynamic heterogeneity is introduced by the network structure and does not evolve during relaxation. While in thermal systems the control parameter is the temperature, in this athermal case the control parameter is a non-dimensional structural parameter which describes the degree of non-affinity of the network.M
Solution-based all inorganic perovskites with enhanced stability and functionality
No full textDecember 2020School of EngineeringHalide perovskite materials have attracted considerable attentions owing to their high light absorption coefficient, long carrier diffusion length, remarkable optoelectronic properties and high efficiency in solar cells. However, due to the inevitable moisture instability for organic-inorganic hybrid perovskites, all inorganic perovskites with inherent stability have become research hotspots as promising candidates for commercial perovskite solar cells and advanced optoelectronics. In this thesis, all inorganic lead-free perovskites (Cs2SnIxCl6-x) have been synthesized by a solution-based method and the mechanisms governing their stability and degradation behavior are investigated. We were able to tune the optical properties and stability of the Cs2SnIxCl6-x all inorganic perovskites through controlling the incorporation ratios of iodide and chloride. The optical absorption can be systematically tuned into a wide range from UV to infrared. Meanwhile, the mixed halide perovskite with low chloride contents can significantly enhance the optical property with much higher PL intensity. The synthesized all inorganic mixed halide perovskites show greatly improved environmental stability without degradation in ambient conditions. The incorporation of Cl further enhances the phase stability of the binary system Cs2SnIxCl6-x with increased phase decomposition temperature. However, these materials can still decompose upon exposure to high humidity or aqueous condition and show different degradation behaviors as controlled by different compositions of the hybrid all inorganic perovskites (Cs2SnIxCl6-x). Several in-situ techniques have been adopted to monitor the interaction between perovskites (Cs2SnIxCl6-x) and water molecules to understand the mechanisms governing the environmental stability. The dissolution-precipitation processes of Cs2SnX6 perovskites (Cs2SnI6, Cs2SnCl6, and Cs2SnI0.9Cl5.1) have been investigated by direct exposure to water via in-situ measurements. The isostructural Cs2SnI6 and Cs2SnCl6 display different dissolution behaviors. Cs2SnI6 experiences direct dissolution. Through the application of in-situ synchrotron XRD and Raman spectroscopy, we determine Cs2SnI6 decomposes into CsI and SnI4 in water and a hydrolysis product Sn(OH)4 can be identified in the solution. A partially reversible reaction also occur with the formation of Cs2SnI6 with the dehydration process Cs2SnCl6 displays an enhanced stability and its crystallinity can be well maintained in water when exposure at the same condition as Cs2SnI6, except partial hydrolysis leading to amorphous precipitation during the dehydration process. As to the mixed halide lead free perovskite (Cs2SnI0.9Cl5.1), it shows two different dissolution stages while exposure to water. The iodide in the crystal structure dissolves fast with water addition and transforms to a more chloride-rich phase. The new phase displays a slower iodide dissolution rate and remains crystalline in water similar to Cs2SnCl6. Therefore, these results can help elucidate the fundamental decomposition pathways in Cs2SnIxCl6-x perovskite and understand their mechanisms of the dissolution-precipitation process, which is expected to in turn lead to new material preparation strategies and device optimization methods.
To further improve the quality of the all-inorganic perovskite and enhance their functionality for optoelectronic applications, we develop a new method to synthesize single crystalline mm-sized Cs2SnI6 perovskite at a liquid-liquid interface. By controlling solvent conditions and Cs2SnI6 supersaturation at the liquid-liquid interface, Cs2SnI6 crystals can be obtained from three-dimensional (3D) to two-dimensional growth (2D) with controlled geometries such as octahedron, pyramid, hexagon and triangular nanosheets. The formation mechanisms and kinetics of complex shapes/geometries of high quality Cs2SnI6 crystals were investigated. Free-standing single crystalline 2D nanosheets can be fabricated as thin as 25 nm, and the lateral size can be controlled up to sub-mm-regime. Electronic property of the high quality Cs2SnI6 2D-nanosheets was also characterized, featuring a n-type conduction with a high carrier mobility of 35 cm2V-1s-1.
Currently, the performance of Sn4+ based perovskite optoelectronics is still low. The lower performance can be attributed to nonoptimized device architecture and film preparation methods to obtain high quality crystals with reduced defect density (e.g. Sn vacancy defects) within the structure. A solution-based metal ion doping strategy is developed to incorporate Nd3+ into Cs2SnCl6 perovskite. By inducing a sub-band absorption, the Nd3+-doped Cs2SnCl6 perovskite exhibits strong photoluminescence intensity. By fabricating UV photodetectors with a design of interfacial charge-controlled hole-injection structure, high performance UV photodetectors could be achieved with a maximum detectivity of 6.3×1015 jones at 372 nm, fast photo-response speed with rise time and fall time on the order of milliseconds, and a large linear dynamic range of 118 dB.
In summary, based on a systematic study of the Cs2SnI6- Cs2SnCl6 binary system, new synthesis sciences have been achieved with the controlled chemical compositions and tunable bandgaps and optoelectronic properties. High quality and large-sized single crystal perovskites are demonstrated and the kinetics of crystal growth are investigated. The degradation mechanisms of the all-organic perovskites exposed to high moisture and aqueous environments are elucidated by various in-situ and ex-situ materials characterization, and their environmental stability is correlated with chemical compositions and key structure characteristics. To further improve their properties and functionalities, a new doping strategy is demonstrated to effectively increase the photoluminescence and device performance used as an UV-detector. The fundamental understanding of growth kinetics and degradation mechanisms and the combination of the new synthesis science will open up opportunities to design new types of perovskite materials with enhanced environmental stability, dimensionality and film quality, enabling their applications with improved functionalities and device performance.Ph
Fault tolerant control of multirotor vehicles
No full textDecember 2021School of EngineeringThe future of vertical takeoff and landing (VTOL) vehicles involves many exciting and novel configurations, among which are electric multirotor vehicles and high-speed coaxial helicopters. These concepts move away from the conventional ``pod and boom" single main rotor helicopters, instead utilizing multiple rotors to generate the forces and moments required to control the vehicle. In the case of electric multirotor vehicles, the anticipated use cases involve human transport (``air taxis"), package delivery, and surveillance (among others), while the high speed coaxial helicopter is being developed to serve military missions, including aerial scout missions (assault and reconnaissance) and troop transport. The missions are markedly different, but both require safe operation, even when faults occur, to be deployed in the future of VTOL aircraft.
In the electric multirotor field, aircraft range in size from small package delivery drones to large manned air taxis. Research on these platforms consider the entire range of scale, considering things like control design using simplified physics models that ignore much of the physics of the problem. Additional work applies high-fidelity computational fluid dynamics analyses that consider the entire complexity of the physics, but at the cost of high computational time. The present work applies a developed medium-fidelity analysis tool to analyze a small (2 kg) hexacopter trim and performance with single rotor failure. The application of medium-fidelity tools allows for more confidence in the predicted results relative to low-fidelity models, at a significantly lower cost than high-fidelity analyses.
For coaxial helicopters, limited publication is available in the open literature due to ongoing development of the aircraft at present. Established comprehensive codes have been utilized to conduct studies on these platforms, but limited flight test data is available to validate predictions against. For analysis in the present body of work, the RPI Coaxial Helicopter Analysis and Dynamics (CHAD) code is developed and validated against available rotor test stand measurement, aircraft steady trim performance and control setting data, and identified flight test dynamic characteristics. This code is developed using a coupled finite state dynamic wake model to predict aerodynamic interference between rotors, as well as a coupled fuselage and elastic flap-lag blade dynamic model to account for coupled blade and rigid body motion as the vehicle operates.
Safety in the operation of coaxial helicopters, as in any air vehicle, is imperative to the successful deployment of the platform. One of the interesting features of this configurations relative to conventional single main rotor aircraft is control redundancy, which (like the aforementioned electric multirotor vehicles) can allow for control reconfiguration and tolerance to control failure during operation. CHAD is utilized to analyze coaxial helicopter fault tolerance in two ways: steady trimmed flight and dynamic simulation.
The former approach considers the allowable variation in control settings in low, moderate, and high speed flight, identifying potential ranges of flight control settings where the aircraft could retain trim even when a locked-in-place fault has occurred, considering assumed geometric limits on controls and observed tip clearance limits between the coaxial counter-rotating rotors. The latter examination explores control reallocation for a locked-in-place flight control fault during dynamic simulation. To this end, an explicit model following closed loop flight control system is designed, and a pseudoinverse control allocation is implemented to distribute control effort among the available effectors. Various control faults are considered in low and high speed flight, the pseudoinverse allocation is recalculated based on the available effectors, and the vehicle behavior post-failure is examined and compared across different fault cases.Ph
Building integrated agriculture simulation (BIA-sim) development of a simulation based software for the implementation of building integrated agriculture in urban contexts
No full textAugust 2022School of ArchitectureSince the world's population is growing at an alarming rate, scientists and researchers are trying to find ways to increase both the quality and quantity of food available. However, the current methods used in the agriculture industry lead to the wastage of fresh water, the generation of waste, environmental degradation, and excessive energy use. Agriculture is responsible for about 30% of the world's yearly consumption of fossil fuels (FAO, 2015) and for the consumption of over 70% of the world's freshwater resources (AQUASTAT, n.d.). Aiming to reduce food and water waste, pollution, and energy needs, researchers are exploring the viability of bringing agriculture into urban areas and even buildings. On the other hand, cities are also known to be sinks for natural resources, intensively using fresh water and energy and creating waste. Buildings account for around one-third of global CO2 emissions (IEA, 2015) and account for almost 20% of total energy (EIA, 2019).While scholars are currently approaching these issues independently, I believe that by bringing these two fields together we may be able to uncover some of the answers that have been hiding within them. There is potential for agriculture and buildings to share waste products in a mutually beneficial way. It is vital that we develop a kind of software that can not only suggest design guidelines for integrating agriculture into a building, but also provide visual and quantifiable results of the benefits of Building Integrated Agriculture early in the designing stages. This will persuade people to adopt these new kinds of buildings. Efforts towards a sustainable lifestyle are expected to play a more prominent role in people's daily lives in the future. This type of software will assist users in determining which resource – food, water, air, or energy – is most critical to them according to their location/climatic conditions on the globe. It will introduce a whole new range of factors in terms of thinking of design other than the social, economic and cultural factors.
The motivation for this research came from the works of several researchers who have shown great potential for improving the energy efficiency of agricultural production facilities that lies in the use of Building Performance Simulation (BPS) tools. A recent example is an initiative by MIT to develop a plugin for Rhinoceros 3D called HARVEST. This plugin can calculate the quantity of crops produced in Controlled Environment Agriculture farms.
By using the HARVEST plugin as a base of study, the goal of this project is to provide the basic framework for a Building Integrated Agriculture Simulation Tool. This tool can visualize and quantify the mutually beneficial interactions between buildings and agriculture other than just crop produce including:
a. Greywater generation and reuse between the building and farm
b. CO2 exchange between the occupants of the building and the plants in the agricultural farms.
c. Reduction in the Building operation energy due to the farm.
A framework was created to establish the software's workflow. To demonstrate several use scenarios a site in New Delhi, India was chosen for an urban agriculture-integrated residential building. India is a developing country facing issues like population expansion, fast urbanization, food insecurity, and climate change. The country is no stranger to news of floods, droughts, and heat waves terrifying the nation. Additionally, Delhi, India's capital, struggles with a significant level of pollution. The tomato plant was chosen as the example for all a calculation.
The software’s user input includes location, 3D site model, site and building details, number of occupants, farm type and crops. Greywater, CO2 from occupants and building energy usage are calculated. Outputs demonstrate how a software framework informed by an extensive database of plants, their properties and their farming requirements can be utilized to identify, design and exploit feedback loops between building and urban agriculture waste products.
In one example, using 60% of building grey water for irrigation of tomato, we found 47% of the maximum buildable surface area would be needed for tomato production. More than 100% of the CO2 emitted by building occupants could be absorbed, and the plants' thermal mass could save 50% of cooling energy using farm layouts that, in turn, enhanced food output based on solar exposure. Several other scenarios were seen that demonstrated the broader benefits urban agriculture can have for the built environment beyond food production.M
Origin of region II slow crack growth of glasses : internal friction of crack tip
No full textAugust 2022School of EngineeringThe slow crack growth behavior was observed for oxide glasses under stress in the presence of water vapor. In general, the slow crack growth is divided into three regions: region I, region II and region III slow crack growth. With decreasing applied stress intensity, the slow crack growth transitions from region III to region II and finally to region I. In slow crack growth region II, the crack growth rate is nearly independent of the applied stress intensity, while in region I or region III, the logarithmic crack growth rate linearly depends on the applied stress intensity. The traditional explanation for the region II slow crack growth is the limited rate of the transport of water vapor molecules towards the crack tip. Based on the transport limited theory, the region II slow crack growth rate was predicted to be nearly temperature independent. However, the region II slow crack growth was found to increase with temperature for some glasses under a constant water vapor pressure. It is known that water diffuses into glass during the slow crack growth and that water in glass produces a large internal friction. In this thesis, the region II slow crack growth of oxide glasses is attributed to the transition between region I, where there is a lower relaxed modulus near crack tip, and region III, where the crack tip has a higher unrelaxed modulus. The proposed mechanism is supported by the observation that there is a residual stress pattern near crack tip after region I slow crack growth while no residual pattern is observed near crack tip after region III slow crack growth. The residual stress pattern exhibits a match, ignoring the magnitude variation, to the theoretical stress field near the crack tip predicted by the linear elastic fracture mechanics model for both soda-lime silicate glass and sodium trisilicate glass. Furthermore, the residual stress pattern is found to exhibit a time-dependent behavior: as the time increases, the residual stress pattern decays. The decay process can be modeled using empirical equation: stretched exponential decay function. The time dependent behavior indicates that oxide glasses exhibit the viscoelastic behavior even at room temperature. Due to water diffusion into glass, internal friction plays a role and reduces the strength. These observations support the proposed model of region II slow crack growth.Ph
Loaded Language and Conspiracy Theorizing
No full textLoaded language is an umbrella term for words, phrases, and overall rhetorical strategies that have strong emotional implications and intent to sway others. Belief in conspiracy theories is tied to a range of strong emotions (van Prooijen and Douglas, 2018). Accordingly, language with strong emotional and persuasive content may be expressed by people experiencing the strong emotions associated with conspiracy theorizing. In this research, we examine multiple types of loaded language in two online parenting forums: one historically against vaccination, and another historically accepting of vaccination. It is well-established that conspiracy theories are the most influential contributor to anti-vaccination views (Hornsey et al., 2018) and anti-vaccination beliefs are strongly correlated with belief in unrelated conspiracy theories (Goldberg & Richey, 2020). Results indicate that users of an anti-vaccination forum use a greater frequency of loaded language to express themselves than users of a vaccination-neutral forum
Characterization of evaporation kinetics and wettability using a quartz crystal microbalance
No full textMay 2022School of EngineeringEvaporation of water is ubiquitous, found in a multitude of natural processes and industrial applications. While scientific studies of water evaporation have been performed for over a century, there exists continued interest in determining the fundamental transport phenomena at the liquid-vapor interface. Improved understanding of the rate-limiting transport mechanisms at the liquid-vapor interface would allow designing more efficient thermal systems for electronics cooling, energy storage, and other critical applications. However, the phenomena occurring in the interfacial region are extremely challenging to probe experimentally, often occurring across only a few nanometers to micrometers. High precision sensing techniques are needed to elucidate transport phenomena at the liquid-vapor interface.This thesis develops a megahertz frequency piezoelectric sensing technique using a quartz crystal microbalance (QCM) to quantify evaporation rates with high precision. It identifies the difference in QCM’s frequency response to changes in the droplet contact area and contact angle using a multiphysics computational model validated using experimental measurements. The QCM contact area sensing technique is then combined with side-view contact angle measurement to study sessile droplet evaporation under different conditions. This hybrid QCM-imaging technique provides a higher precision than imaging alone and is used to determine the evaporation rate of water droplets in a dry nitrogen flow at different temperatures.
With the QCM-imaging measurement technique, this thesis studies a series of nominally pure water droplets in a nitrogen cross-flow. The experimental observations are combined with a multiscale computational model to investigate the mass accommodation at the liquid-vapor interface. The computational model combines the macroscopic flow field with the kinetic theory of gasses near the interface to determine the mass accommodation coefficient (AC) during the evaporation process. Further, the QCM determines the amount of non-volatile impurities in the nominally pure water droplets, indicating how challenging it can be to obtain impurity-free water and keep it clean. This research obtains an AC close to 0.001 across multiple droplets in the dry nitrogen (diffusively-limited) environment. This model can provide predictive capabilities for evaporation in non-condensable gas streams. This thesis also extends the model to analyze water droplets with non-volatile impurities. Specifically, the evaporation of aqueous potassium chloride droplets into nitrogen flow was analyzed over a wide range of molality (10-5 – 1 mol/kg). Under these conditions, the accommodation is relatively stable around 0.001. This result indicates that potassium chloride does not strongly influence the accommodation during evaporation.
The QCM is also employed to study nanoscale phenomena, including electrochemical fabrication of nanomaterials and evaporation of liquids confined in nanopores. A two-step anodization approach is used to obtain an ordered array of cylindrical alumina nanopores. The creation of these nanopores is monitored during the fabrication process using the QCM to obtain and control the pore geometry. Our analysis indicates that a mass resolution of approximately 20 ng/s can be achieved using the QCM to elucidate the nanoscale phenomenon. Finally, the evaporation of water into pure vapor confined in single-ended nanopores is studied. A one-dimensional theoretical model based on the kinetic theory of gasses is developed that links the far-field temperature and pressure to the QCM measurement of mass flux from the nanopores to determine evaporation kinetics and mass accommodation at the liquid-vapor interface. This modeling approach allowed investigation of the meniscus shape and the tensile pressure in the condensed phase. It was found that confinement in the pore produces high tensile pressure when the liquid meniscus recedes far into the pores, strongly affecting the mass accommodation at the liquid-vapor interface.Ph
Automated grading for advanced topics courses
No full textAugust 2021School of ScienceAs Computer Science course enrollments have increased over recent years, instructors have turned to automated grading systems to help relieve the burden of processing student assignments. However, the available autograding solutions have generally lacked support for traditionally difficult-to-grade advanced topics courses. In this thesis, I explore the "autogradeability" of the assignments presented in advanced topics computer science courses. I assert that automated grading systems can both support such courses and can be designed such that they are easy to use for instructors and of great educational value to students. I introduce a set of six performance axes through which the viability of an autograding system can be assessed: Repeatability, Scalability, Security, Extensibility, Instructor Ease of Use, and Educational Value. I lay out an extensibility-based design philosophy, which promotes system modularity for the simpler integration of features to support new courses, and I champion the inclusion of features which increase educational value to students within an autograding system. I detail the conception, design, implementation, and success of automated grading subsystems to process networked assignments and interactive computer graphics assignments, as well as the advancements in automated grading infrastructure necessary to achieve this success. Finally, I look to assignments which cannot be automatically processed, and turn to peer grading as a method of alleviating instructor burden while providing a valuable learning experience to the student. To that end, I propose a novel algorithm for peer review matching. This algorithm uses stratified sampling informed by a student's likelihood to produce feedback of high quality to increase the probability that a peer assessee will receive actionable, educationally valuable feedback.Ph
Semantically enabled medical image understanding
No full textAugust 2022School of ScienceMedical imaging examination is the most common form of routine medical analysis, which involves several stages of reasoning and careful analysis to reach a final decision by the radiologist. Most deep learning frameworks utilize only the imaging data in its entirety to reach a clinical decision, ignoring important patient information that might be vital for the diagnosis. This includes symptoms, age, and patient history information. Furthermore, Most deep learning systems ignore domain based information and commonsense reasoning when they make their prediction. In this work, we designed and implemented an AI system that can use both the anatomical information and patient history information while making decisions. In particular, we focused on using semantic web technologies, ontologies and knowledge graphs, to bridge the gap in existing deep learning systems. We developed a deep learning system that can detect chest x-ray pathologies within the correct anatomical location. We developed a Medical Imaging and Diagnostic Ontology, MIDO,to provide a standardized format for modelling medical imaging tasks, including disease classification and disease localization. We then generated knowledge graphs from the chest x-ray images using the ontology for modelling the entities are relationships. Furthermore, we demonstrated the possibility of semantic reasoning to enhance transparency, trust, interpretability and explainability of the deep learning system through the application of the knowledge graph to increase the physician's trust in the individual patient's deep learning prediction by determining the likelihood of the system being correct, enriching the knowledge graph with additional domain based knowledge and reasoning causal relationships between different diseases. Not only that, but we conducted an in-depth evaluation of the various parts of our workflow and compared them to existing state-of-the art whenever possible.Ph