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Characterizing Membrane Protein-Lipid Interactions by Native Mass Spectrometry
No full textNative mass spectrometry (MS) is a powerful tool for quantitatively characterizing protein complexes and the interactions between protein and ligands due to the capability of preserving non-covalent interactions during measurement. However, preserving non-covalent interactions in native MS studies for membrane protein complexes can be challenging. Higher activation energy is usually needed for desolvation and detergent release, resulting in higher charge states on membrane protein, disrupting the tertiary structure and non-covalent interactions. Therefore, reducing the charges carried on membrane protein is crucial for native MS study. A series of distinct charge-reducing molecules, polyamines, were investigated for their application in reducing charges on membrane protein. The results indicate that polyamines exhibit enhanced charge-reduction potency, presenting innovative strategies to modulate charge states and preserve non-covalent interactions during native MS studies.
In addition to discovering charge-reducing molecules, native MS was applied to characterize bacterial ATP-binding cassette (ABC) transporter MsbA, a crucial player in bacteria lipopolysaccharides (LPS) biogenesis, and its interactions with lipids. This study discovered the binding of copper (II) to MsbA that modulates MsbA-lipid interactions, with atomic structure resolved by X-ray crystallography. In addition, the results of this study revealed the conformation-dependent lipid binding affinities of MsbA by native MS, especially for the LPS precursor, 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). This finding from native MS guided the structural biology study that resolved a 3.6 ��-resolution structure of MsbA in an open, outward-facing conformation, revealing previously undiscovered KDL binding sites that are important for the functions of MsbA.
This study also explored the thermodynamics of the interactions between MsbA and KDL. Despite identifying two distinct LPS binding sites on MsbA, the thermodynamic basis for the interactions of MsbA-KDL remained unclear. Native MS revealed that KDL binding to MsbA is mainly driven by entropy. Basic residues contribute to the binding of KDL through positive coupling entropy, overcoming unfavorable coupling enthalpy. These findings indicated the effect of solvent reorganization, specifically the desolvation of lipid binding sites and the lipid headgroup, in driving KDL binding to MsbA. This study provides new insights into thermodynamic contributions from residues in membrane proteins to lipid binding
Uncertainty-Aware Data-Driven Approaches for Modelling Sparse Agricultural Datasets to Sustain a Society
No full textThe objective of my dissertation is to tackle the issue of sparse datasets in case of agricultural domain to design data-driven approaches that can be used to make Decision Support Systems (DSS) for optimal growth of plants, thereby reducing the cost of labor as well as improving the overall food security and environmental sustainability. In order to achieve this, my research is structured into three primary components. Firstly, it focuses on utilizing Machine Learning (ML) models and data-driven approaches to optimize nutrients in hydroponic and aquaponic environments, enhancing the growth of fish and plants within a unified system using two distinct methodologies. This addresses the inherent sparsity in agricultural datasets. Secondly, the thesis delves into the development of forecasting models for in-season prediction of canopy features in cotton crops. This predictive capability enables timely management decisions to maximize crop yield. The third objective involves the creation of data-driven approaches to model growth stages and nutrient uptake of soybeans cultivated in hydroponic environments, spanning from seeding to maturation
Quantitative Analysis of Strain Response Measured by Low-Frequency Distributed Acoustic Sensing During Hydraulic Fracturing
No full textThis master's thesis investigates the pivotal role of strain measurements in hydraulic fracturing operations, employing Low-Frequency Distributed Acoustic Sensing (LF-DAS) technology to monitor strain changes during treatments. A significant gap in the existing research is addressed by systematically analyzing strain decay beyond the fracture domain corridor. The thesis investigates the impact of parent-well depletion and completion design on hydraulic fracture geometry, employing a decline factor of the strain decay curve as a key analytical tool. This analysis is supported by a geomechanics model, providing a comprehensive understanding of the dataset. Furthermore, the study conducts a comprehensive analysis of Hydraulic Fracture Test Site-2 (HFTS-2), considering the maximum cumulative strain change and decline factor of the strain decay curves. The thesis outlines a well-structured workflow for processing and analyzing LF-DAS cross-well strain data
Accuracy of Three Digital Impression Techniques for Implant-Fixed Complete Dentures
No full textEvidence comparing accuracy of implant-fixed complete denture (IFCD) impression techniques is unclear. The purpose of this in vitro study was to compare the accuracy of three digital impression techniques for IFCD.
A polyurethane edentulous mandible with four implant analogs served as the master model. A reference scan was made using a laboratory scanner. Test scans (n=10 per group) were made for the three groups: splinted IOS (Group S), non-splinted IOS (Group NS), and photogrammetry (Group PG). All scans were exported in standard tessellation language (STL) format and superimposed to compare linear, angular, and RMS deviations using a three-dimensional metrology software. Statistical analysis was performed using Kruskal-Wallis test for non-normally distributed data (a = 0.05).
No significant difference in overall accuracy was seen between the three groups. No significant difference in accuracy was seen when splinting ISBs. Significant differences in accuracy were seen within each group depending on position in the arch; higher angular deviation was seen at position RM1 in Group PG and Group S (p<.001).
Digital impressions for IFCD using either IOS or PG yielded similar results. Splinting ISBs did not seem to have a beneficial effect on accuracy. All three methods produced clinically acceptable results
Pair Production in Strong Fields
No full textThe correction to the Coulomb energy due to virtual production of e+e��� pairs, which is on the order of one percent of the Coulomb energy at nuclear scales, is discussed. The effects of including a pair-production term in the semi-empirical mass formula and the correction to the Coulomb barrier for a handful of nuclear collisions using the Bass and Coulomb potentials are studied. With an eye toward future work using Constrained Molecular Dynamics (CoMD) model, we also calculate the correction to the Coulomb energy and force between protons after folding with a Gaussian spatial distribution.
In the collision of two heavy ions the strong repulsion coming from the Coulomb field is enough to produce real e+e��� pair(s) from vacuum fluctuations. The energy is provided by the kinetic energy of the ions and the Coulomb interaction at the production point. If, for instance the electron is located at the center of mass (C.M.) of the two ions moving along the z-axis, and the positron at a distance x from the electron, the ions can be accelerated towards each other since the Coulomb barrier is lowered by the presence of the electron. This screening results in the increase of the kinetic energy of the colliding ions and may result in an increase of the fusion probability of light ions above the adiabatic limit.
Nuclear scattering is not the only situation where real pairs can be produced by this mechanism. In particular, the fields involved in �� decay and nuclear fission are strong enough to produce pairs. The energy of the e+e��� pair is related to the relative distance and velocity of the daughter nuclei. Thus, the energy distribution of the produced pairs can give information about the dynamics of the fission and �� decay processes. A neck model of nuclear fission is used to illustrate how the pairs can be used as a probe of the dynamics.
This model of pair production is also applied to situations with strong fields involving lasers. In particular, lasers can fully ionize clusters of atoms, which then expand in a ���Coulomb explosion," and when a laser irradiates the surface of a metal, a shower of protons is ejected in a phenomenon known as Target Normal Sheath Acceleration (TNSA). The fields involved in these cases were found to be too weak to produce pairs with this mechanism. Likewise, no pairs are produced by the gravitational field at the event horizon of a black hole, indicating that this mechanism is different from Hawking radiation
Characteristics of Atomic Mirrors in Waveguide QED
No full textThis thesis presents a detailed study of photon-atom interactions in one-dimensional waveguide systems, exploring the dynamics of photon decay in atomic cavities and the emission characteristics of single photons from two-level emitters. The study focuses on the decay dynamics of single-photon pulses in cavities formed by atomic mirrors coupled to waveguides and reveals strategies to increase photon storage times by optimizing system parameters such as coupling strength, cavity length, and atomic separation. In addition, the emission of single photons from two-level emitters in atomic cavities is investigated, demonstrating the potential for frequency combing and spectral narrowing through appropriate control of atomic separations. The results of this work contribute to the understanding of light-matter interactions in waveguide quantum electrodynamics and provide insight into the design of novel photonic devices for quantum information processing and communication
Testing the Benefits of Using Silicon Photomultipliers on Organic Scintillator Portal Monitors
No full textRapid and accurate detection of radiation at checkpoints is of vital importance to national security. One proposed method for improving radiation detection capabilities is using Silicon Photomultipliers (SiPMs) on the organic scintillation panels used at checkpoints to detect radiation. Research on SiPMs has been relegated to small detectors with volumes in the cubic millimeter range, but large portal monitors are often used at ports of entry and traffic control points to monitor radiation. This research examined the efficacy of SiPMs placed on larger plastic scintillators with volumes orders of magnitude larger than previous tests have analyzed. For this research two arrays of SiPMs were determined to be the most advantageous due to superior intrinsic efficiency and were tested on plastic scintillators using three different gamma emitting isotopes. Experiments testing a single SiPM to a PMT when placed in geometrically similar configurations gave an average SiPM to PMT total count ratio of 0.0963 �� 0.0006 for the highest-energy gammas, which was within 5% of the expected value based on the ratio of the active areas of the single SiPM and PMT. However, when two arrays of SiPMs were selected based on numerical simulations and tested, the best ratio of SiPM to PMT total count ratio for a single array observing a source was 0.394 �� 0.001, which was within 5% of the active area ratio. SiPM arrays and PMTs were also compared by the ratio of source counts to background counts observed for each isotope, with the best SiPM array observing a ratio of 1.391 �� 0.003 while the PMT���s ratio was 1.584 �� 0.003 for the same isotope. Ultimately, the results of the study do not suggest that SiPMs are an optimal substitute for PMTs on large-volume plastic scintillators, but this result is not concluded decisively by the experiment���s results
Framework for Interactive, Individualized Feedback Design to Improve Thinking Skills in Construction Education
No full textOrganizational improvement relies heavily on having a competent workforce. To facilitate continuous improvement in the construction industry, this study examined the weaknesses in problem-solving skills among today's students (the future workforce). Based on these findings, a new educational approach was proposed, taking today���s student characteristics such as Acquired Attention Deficit Disorder (AADD) into consideration. This proposed educational approach was proved to have immediate and lasting effects beyond class periods on students��� learning through improved thinking skill exercises.
Initial investigations focused on identifying weaknesses in exercising adequate thinking skills in problem-solving and determining the cause beyond the weaknesses. Weaknesses were identified when faced with information processing, locating inputs from multiple sources, repeating the same cognitive processes over extended periods, unfamiliar calculation direction, and ignoring industry common sense due to a calculation-oriented mindset. The lack of fundamentals was identified as the primary cause of the weakness.
To resolve the weaknesses by addressing the cause behind the weaknesses, a new educational approach was proposed and validated through a mixed method. First, a feedback framework was designed which functions for knowledge delivery. Feedback was designed to deliver highly relevant knowledge to the problem at hand and to be presented in a size to allow easy information consumption in real-time considering the target students��� characteristics and learning preferences, Generation Z.
Feedback, a knowledge delivery tool, had immediate effects on exercising thinking skills in problem-solving on a sample of 13 graduate-level students in the Department of Construction Science at Texas A&M University who volunteered for the experiment and the following interview. Especially, two factors of feedback were counted as the key to improving thinking skills, and they are the feedback that was given immediately in real-time when it was in need (when in need) and the feedback that matched the target knowledge in question (what is needed).
The design feedback also had a lasting impact on exercising adequate thinking skills, by which improved academic achievement was demonstrated in a sample of 24 students enrolled in a construction estimating course for undergraduate students at Western Kentucky University. The result of the paired t-test evidenced the effectiveness of feedback on knowledge retention and academic achievement. Additionally, 71% of 24 study participants responded to the self-confidence survey, and the positive self-confidence in exercising thinking skills in each category in Bloom���s Taxonomy also denoted the efficacy of knowledge feeding in feedback.
This study theoretically expanded types of feedback by adding knowledge delivery to the existing feedback types. With this addition, feedback now functions not only giving confirmation or correction for the performance, but it also functions as a vehicle for knowledge delivery. Pragmatically, this study proposed a novel educational approach which aligns with today���s students��� learning preferences and weaknesses
System-Level Rotordynamic Analysis of Centrifugal Compressors Using Computational Fluid Dynamics (CFD), Design and Optimization of Novel Swirl Brakes
No full textThe accurate characterization of compressor rotordynamic coefficients during the design phase reduces the risk of subsynchronous vibration (SSV) problems occurring in the field. Although rotordynamists extensively investigate discrete compressor components (such as seals and front shrouds) to tackle instability issues, integrated or system-level analysis of compressor rotordynamics is very scarce. In reality, the impeller, eye labyrinth seal, and the front shroud heavily influence one another; and the collective dynamic behavior of the system differs from the sum of the dynamic behavior of isolated components. Furthermore, American Petroleum Institute (API) level II vibration stability analysis requires inclusion of all possible destabilizing forces including those that stem from seals and the front shroud cavity.
A CFD-based approach is taken to evaluate the dynamic behavior of the system as a whole. The geometry and operating conditions in this work are based on a recently published experimental study on centrifugal compressor. The commercial CFD code CFX 19.0 is used to resolve Reynolds Averaged Navier-Stokes (RANS) equations to quantify the eye labyrinth seal and front cavity stiffness, damping, and added mass. The entire compressor stage is modeled to uncover the coupled behavior of the components and assess the stability of the whole system instead of just discrete components. In the current work, three CFD approaches, namely quasi-steady, transient static eccentricity, and transient mesh deformation techniques are studied and benchmarked against analytical and experimental results from the literature. Having established the efficacy of the proposed approach, 4 types of swirl brakes are proposed and analyzed for stability. The novel swirl brakes create negative swirls at the brake cavities and stabilize both the front shroud and the eye-labyrinth seal simultaneously. The designed swirl brakes are further investigated to identify contribution of each geometric feature of the brakes to the rotordynamic stability of the whole system/stage. The geometric parameters chosen for the parametric study are the height of the slot cavity, the number of slots, the length of slots, the slot angle and the direction of slot curvature
Accelerating Finite Element Analysis Using a Multi-Fidelity Computational Scheme for Nuclear Applications
No full textNext-generation microreactors are currently being designed to be operated terrestrial and ex-traterrestrial for remote surface power production. These systems will provide an alternative source of carbon-free energy that is versatile and can be utilized for various applications. This recent de-sire to design and build next-generation nuclear systems requires high-fidelity analysis to ensure the proposed design can operate safely and as intended. Traditionally, this can be achieved by obtaining a combination of experimental and numerical results, however it has become difficult and expensive to perform integral experiments. Therefore, high-fidelity numerical results have become heavily relied upon to provide the required analysis, specifically finite-element based codes. This reliance on numerical codes has presented its own set of issues as it can take millions of CPU hours to gather the required results for a given design. Therefore, a novel computational scheme is pro-posed to accelerate transient finite element analysis of these next-generation nuclear systems. A discrepancy function between a low and high-fidelity model is approximated and used to actively correct the low-fidelity solution. By exploiting the computational cheap low-fidelity solution and a few snapshots in time of the high-fidelity solution, an approximated discrepancy function can be found to correct the low-fidelity model. This approach aims to produce a solution that is close to the full-order high-fidelity model while requiring a smaller computational cost. The idea was decided to be implemented to work alongside the Abaqus finite element software, and utilized to model a series of transient events for two conceptual reactor designs