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Title: An individual differences approach to improving low target prevalence visual search performance
Creator: Peltier, Chad
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "Critical real-world visual search tasks such as radiology and baggage screening rely on the detection of rare targets that may only be present on as few as .3% of searches (Gur et al., 2004). When targets are rare, observers search for a shorter amount of time and miss targets more often than when targets are common, a phenomenon known as the low prevalence effect (LPE). Given the real-world importance of the detection of low prevalence targets, researchers have attempted to improve search...
Show more"Critical real-world visual search tasks such as radiology and baggage screening rely on the detection of rare targets that may only be present on as few as .3% of searches (Gur et al., 2004). When targets are rare, observers search for a shorter amount of time and miss targets more often than when targets are common, a phenomenon known as the low prevalence effect (LPE). Given the real-world importance of the detection of low prevalence targets, researchers have attempted to improve search performance. There have been several experimental attempts to reduce the LPE, but none have been wholly successful, as even the best methods have increased hits at the cost of more false alarms. As an alternative to improving visual search performance through experimental manipulations, researchers have recently started using an individual differences approach to predict those who would be best at rare target detection. The individual differences approach has shown that it is possible to predict low prevalence target detection using working memory capacity (WMC) (Peltier & Becker, 2016b; Schwark et al., 2012) and moderate prevalence target detection using a personality assessment (Biggs, Clark, & Mitroff, 2017) and vigilance (Adamo, Cain, & Mitroff, 2016). Experiment 1 expands on the previous research by predicting low prevalence visual search performance using measures of WMC, near transfer high prevalence visual search accuracy, vigilance, attentional control, and introversion. The regression using these predictors accounts for 52% of the variance in accuracy. Experiment 2 addresses practical and theoretical limitations of Experiment 1 by replicating the original finding, including new potential predictors of low prevalence search performance (fluid intelligence, task unrelated thought frequency, and far transfer search accuracy), using more realistic search stimuli to increase external validity, and using eye tracking to investigate how individual differences relate to specific components of performance. The results show that near transfer search, far transfer search, WMC, introversion, and fluid intelligence account for 53% of the variance in accuracy in a more realistic low prevalence search. Using the beta weights from Experiment 1's significant predictors and each observer's score on the corresponding measures in Experiment 2, I find that the old predictors account for 42% of the variance in a novel search task's accuracy. Finally, the eye-tracking results show that we can significantly predict quitting thresholds (the number of items inspected before terminating search), selection error rates (misses caused by never inspecting the target), identification error rates (misses caused by misidentifying an inspected target), item re-inspection rates, target decision times, and distractor decision times. I conclude that the individual differences approach has the potential to be a highly effective tool in selecting those who are most likely to perform at a high level in real-world searches."--Pages ii-iii.
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Title: An investigation of cerebellar morphology in childhood stuttering
Creator: Johnson, Chelsea Anna
Date: 2022
Collection: Electronic Theses & Dissertations
Description: While many studies have connected structural and functional cerebellar differences to developmental stuttering, there are limited studies of cerebellar gray matter morphology in young children who stutter. These examinations include small sample sizes of children and use morphometry methods that might not be best suited for examining the cerebellum (e.g., Chang et al., 2008). This dissertation examines how the structure of specific cerebellar lobules differs in a larger cohort of children who...
Show moreWhile many studies have connected structural and functional cerebellar differences to developmental stuttering, there are limited studies of cerebellar gray matter morphology in young children who stutter. These examinations include small sample sizes of children and use morphometry methods that might not be best suited for examining the cerebellum (e.g., Chang et al., 2008). This dissertation examines how the structure of specific cerebellar lobules differs in a larger cohort of children who stutter and children who do not stutter as well as in persistent and recovered children who stutter. These data will provide evidence to better inform predictions of how the morphology of cerebellar areas are likely involved in aspects of speech motor control in developmental stuttering. In this study, gray matter morphology of the cerebellum was examined in children who do and do not stutter using voxel-based morphometry and a specialized toolbox and atlas for the cerebellum (Diedrichsen, 2006). Here we examined cerebellar gray matter volume (GMV) based on structural MRI data from children who stutter and children who do not stutter, 116 preschool-age children (stuttering N= 57) between the ages of 3-5 years, and a school-age cohort of 72 children (stuttering N=37) six years of age and up. This dissertation is the first study to examine cerebellar GMV in a large group of children who stutter using a specialized toolbox and atlas for the cerebellum. Results from this study showed that there were no overall significant group differences of lobular GMV between the stuttering and non-stuttering groups in any of the groups of children. There were significant age-related associations, however, that differentiated children who do and do not stutter in specific age ranges. In particular, the following cerebellar lobules differed significantly in GMV between children who do and do not stutter with age: 1) cerebellar lobule VII, which may correspond with cerebellar functions that support speech planning, 2) lobule VIII, which has been linked to various functions including corrections during perturbation studies, and 3) lobule IV which has been reported to be involved in feedforward control speech motor control processes. Notably, GMV of cerebellar lobule VI was associated negatively with Stuttering Severity Instrument (SSI) score in preschool-age persistent children who stutter. Associations between SSI score and GMV in cerebellar lobule VI may mean that feedforward control mechanisms are associated with the frequency of stuttering in children who stutter. In summary, significant findings of this investigation indicate that 1) children who do and do not stutter do not show an overall difference in cerebellar GMV, 2) GMV of the cerebellum is associated with SSI score, 3) age-related differences in GMV in the cerebellum differentiate children who do and do not stutter. The results from this study indicate that feedforward control is associated with disfluencies while age-related variations of cerebellar areas that may support both the feedback and feedforward control pathways are connected to aspects of stuttering, such as age.
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Title: Analysis of drinking water quality and sanitation in a peri-urban area of Dar es Salaam, Tanzania
Creator: Ngasala, Tulakemelwa Mhamilawa
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "While the Sustainable Development Goal 6 called for universal access to water and sanitation by 2030, the challenge of achieving this goal seems daunting in the context of the bourgeoning peri- urban communities of the developing world. These areas are often in a regulatory grey area, receiving municipal water on an irregular basis and lacking sanitation and other basic services. And yet, SDG 6 recognizes that improving global health and wellbeing is critically linked to addressing this...
Show more"While the Sustainable Development Goal 6 called for universal access to water and sanitation by 2030, the challenge of achieving this goal seems daunting in the context of the bourgeoning peri- urban communities of the developing world. These areas are often in a regulatory grey area, receiving municipal water on an irregular basis and lacking sanitation and other basic services. And yet, SDG 6 recognizes that improving global health and wellbeing is critically linked to addressing this problem. A multi-method study of the peri-urban area of Dar es Salaam was conducted to determine the extent of the problem and to make recommendations for system-wide approaches to alleviate the risk of waterborne disease. Existing water sources in the area were identified. Water collection and storage practices were assessed at the household level to determine how water from relatively clean sources becomes contaminated. Escherichia coli (E. coli), nitrate, and total dissolved solid (TDS) were analyzed as indicators for the sewage contamination. Bivariate correlation and univariate regression analyses were used to identify the sources of contamination. The assessment focused on the relationship and association of water contamination with site-specific variables. The variable that had the highest negative impact to the water source was analyzed by using a groundwater flow and contaminant transport model as a tool to make recommendations for proper site-specific sanitation practices. Of the three water sources identified (city water, vendors, and domestic wells), water quality analysis showed that city water at the point of collection (POC) was deemed excellent, whereas it diminished at the point of use (POU) for all three water sources. Reasons for change in water quality at POU and POC were due to mixing of water from different water sources at homes during storage. Using a multinomial regression model, the main reason for mixing water was determined to be the dilution of the salty taste of well water (p < 0.05) and insufficient storage containers (p < 0.05). Of the three water sources identified, domestic wells were found to be the most contaminated. Further analysis on the domestic wells showed a significant contamination, where 80% of wells tested contained E. coli. Also, 58% and 81% of wells tested had concentrations of nitrate and TDS, respectively, that exceeded the WHO guidelines. Univariate regression analysis confirmed the association of contaminants with distance of a well from a sanitation system and well depth (p < 0.05). Groundwater transport modeling showed a strong correlation between the tracer and contaminants and the tracer and distance and helped identify the safe well setback distance that is specific to site conditions, soil type, and aquifer properties. Groundwater modeling was shown to be a good assessment tool for contamination within an aquifer system in urban overpopulated areas of developing countries. Our findings also indicate that the risk of exposure to waterborne disease comes from a combination of factors that involve multiple actors, from improved awareness and sanitation practices to improved regulatory oversight, supply practices, and sanitation technologies."--Pages ii-iii.
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Title: Analysis of wind turbine blade vibration and drivetrain loads
Creator: Ramakrishnan, Venkatanarayanan
Date: 2017
Collection: Electronic Theses & Dissertations
Description: The reliability of wind turbines is a major issue for the industry. Drivetrain and blade failures are common, costly and not fully understood. Designers must thus examine and understand the key parameters that influence reliability. As wind turbines increase in size, the blades are designed to be more lightweight and flexible, increasing the potential for large-displacement oscillations during operation. This necessitates the incorporation of nonlinearity in the formulation of the blade model...
Show moreThe reliability of wind turbines is a major issue for the industry. Drivetrain and blade failures are common, costly and not fully understood. Designers must thus examine and understand the key parameters that influence reliability. As wind turbines increase in size, the blades are designed to be more lightweight and flexible, increasing the potential for large-displacement oscillations during operation. This necessitates the incorporation of nonlinearity in the formulation of the blade model to better understand the dynamics and stability characteristics. Also, oscillations in the blade impart dynamic loading onto the gearbox. Understanding these dynamic loads is essential for the design of reliable gears and bearings, and hence economically viable wind turbines. Traditional studies of wind turbines have focused on the aerodynamic performance of the blades, the reliability of gearbox and its components, grid connectivity and improvements in power distribution. The aspect of blade vibration from a dynamics point of view has garnered interest but not been fully developed and understood. In this work, the partial and ordinary differential equations that govern the in-plane and out-of-plane motion of a wind turbine blade subject to gravitational and aerodynamic loading are developed using Hamilton's principle and Lagrange formulations respectively. These differential equations include nonlinear terms due to nonlinear curvature and nonlinear foreshortening, as well as parametric and direct excitation at the frequency of rotation. The equations are reduced using an assumed uniform cantilevered beam mode to produce single second-order ordinary differential equations (ODE) to approximate the blade model for the case of constant rotation rate. Embedded in the ODE's are terms of a forced Mathieu equation with cubic nonlinearity. Different variations of the forced Mathieu equation are analyzed for resonances by using the method of multiple scales. The forced Mathieu equation has instabilities and resonances at multiple superharmonic and subharmonic frequencies. Second-order expansions are used to unfold the expressions that govern the amplitude of response at these critical resonances. The equations of motion (EOM's) also have regions of instability and we employ perturbation analysis to identify the stability transition curves of the system. These calculations compare well with numerical simulations for simple systems under study. The formulation is then extended to wind turbine blades. The effect of various parameters on the amount of blade oscillation is demonstrated using the amplitude-frequency curve. Aerodynamic forces on the wind turbine blades are calculated using the Blade Element Momentum (BEM) theory and its extensions. Commercial software, such as FAST, have also been used to simulate responses for specific blades to understand influence of various blade parameters. For current production wind turbine blades, the parameters are such that the superharmonic resonances are not excited significantly. From parametric studies of the blade EOM we can understand the parameter values at which these resonances become dominant. It is shown that as wind turbine blades become larger they are prone to superharmonic resonances, whose existence may not be within the scope of current design strategies. The amplitude of response at all resonances tend to become amplified for much larger blades. Both in-plane and out-of-plane responses will increase the loading at the rotor hub and consequently, increase the loads and moments on the wind turbine drivetrain. To capture the effect of increased loading on the wind turbine drivetrain, we follow two approaches. First, using RomaxWind, we model the 750 kW gearbox used as a part of the Gearbox Reliability Collaborative (GRC) headed by National Renewable Energy Labs (NREL). For this, we partnered with Romax Technology Ltd. to analyze the sensitivities of the load on the elements of the gearbox to variations in the input loads. Using the Romax gearbox model, we suggest methods to optimize the gear geometry to improve reliability of the drivetrain by minimizing influence of manufacturing and assembly tolerances and misalignments. We also designed novel approaches to predict gearbox vibration using the models and suggested changes that are required to improve the overall design of the gearbox (these have been implemented while manufacturing newer generations of the NREL GRC gearbox). Second, for the case of in-plane blade vibration, we use a simple torsional model of the wind turbine gearbox to study the influence of a time varying load on the torsional response of the drivetrain. The effect of increased loading on larger wind turbine systems is shown by scaling values of blade and gearbox properties. The fundamental work formulated in this thesis can be extended to more complex models to understand other system level dynamics of interest (multi-mode interaction, multi-blade resonance, etc.). More detailed formulation of aerodynamic loads (for example by using ONERA semi-empirical approach) would also improve model fidelity for predicting the influence of aerodynamic loads on blade vibration.
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Title: Analysis techniques and diagnostics of non-relativistic hadron beams
Creator: Richard, Christopher
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Beam diagnostics are essential to the operation of hadron particle accelerators. They are used to tune the accelerator, verify beamline modes, ensure minimal beam losses, and characterize and monitor the beam quality. By adding and improving the measurements of the beam properties, the operation of the accelerator can be better informed and improved. Addition and improved measurements of the beam properties can be realized by developing new analysis techniques for the existing diagnostic...
Show moreBeam diagnostics are essential to the operation of hadron particle accelerators. They are used to tune the accelerator, verify beamline modes, ensure minimal beam losses, and characterize and monitor the beam quality. By adding and improving the measurements of the beam properties, the operation of the accelerator can be better informed and improved. Addition and improved measurements of the beam properties can be realized by developing new analysis techniques for the existing diagnostic devices.This dissertation presents further analysis of measurements from two devices. Firstly, it discusses converting phase space measurements taken with an Allison scanner from position-angle coordinates to action-phase coordinates. In this coordinate system, the distribution is stable under changes to linear optics. This allows for direct comparison of phase space measurements taken at different locations or with different transverse focusing. In addition, this stability can make it easier to visualize and quantify the beam tails.Secondly, beam profile measurements taken with Beam Position Monitors (BPMs) by measuring multiple harmonics are presented. The measurements are primarily focused on non-relativistic beams where the transverse and longitudinal profiles can be fit to the BPM signals. While these measurements were unsuccessful, it understood why they failed and how to avoid the same issues for future measurements.Lastly, the design of a test stand to calibrate BPMs for non-relativistic effects is presented. The test stand relies on a helical transmission line can can propagate signals with phase velocity of 0.03c. It is shown, with the appropriate geometry, that the phase velocity, pulse propagation, and field profiles from the helical transmission line can match the those of a non-relativistic bunch.
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Title: Analytical and computational study of electron bunch dynamics
Creator: Xiang, Xukun
Date: 2020
Collection: Electronic Theses & Dissertations
Description: This dissertation is centered on the analytical and numerical study of ellipsoidal electron bunch dynamics. We are particularly interested in the focusing process of the probing electron bunches in the ultrafast electron diffraction/microscopy system, so that we can improve the temporal and spectral resolution of the ultrafast experiments. More specifically, to understand the collective space charge effects throughout the bunch evolution, we employed several analytic models to describe the...
Show moreThis dissertation is centered on the analytical and numerical study of ellipsoidal electron bunch dynamics. We are particularly interested in the focusing process of the probing electron bunches in the ultrafast electron diffraction/microscopy system, so that we can improve the temporal and spectral resolution of the ultrafast experiments. More specifically, to understand the collective space charge effects throughout the bunch evolution, we employed several analytic models to describe the bunch dynamics. We start with an extension of the mean-field model using ordinary differential equations. Analysis of this mean-field model leads to the identification of a longitudinal critical chirp, which separates two regimes for particle trajectories for the longitudinal focusing of the bunches: (1) bounce-back, where the particles reverse their direction at the waist of the focusing process, and (2) cross-over, where the bunch experiences a singularity where the bunch width reduces to zero. We show that time can be scaled by the initial plasma frequency, and that the critical chirp becoming dimensionless and depends solely on the initial bunch aspect ratio. In order to study the emittance effect on the bunch dynamics, we introduce the self-similar analytical (SSA) model, a statistical method describing the second order moments dynamics to model the evolution of an ellipsoidal electron bunch. We also discussed its linear chirp assumption, explaining how it is the key assumption that leads to the emittance conservation according to the SSA model. We discuss the statistical nature of bunch emittance noting that the space charge effect of the uniform density profile and of the Gaussian profile are close to each other in the SSA model. The impact from a changing emittance is captured by an additional term in the modified SSA model, which is then equivalent to the Kapchinsky-Vladimirsky (K-V) envelope equation in accelerator physics. We point out that the application of the statistical methods can extend beyond the uniform ellipsoidal bunch, while the accuracy of the SSA prediction is mainly related to the discrepancy between the actual density profile and the uniform density profile.We present the Molecular Dynamics (MD) simulation results for the longitudinal focusing process of uniform spheroidal electron bunches. The comparison of the longitudinal width evolution between the MD simulations and the SSA predictions shows the impact of a varying emittance on bunch evolution. We propose two competing mechanisms for the change of emittance throughout the compression process. The disorder-induced heating (DIH) increases the emittance in both degrees of freedom while the difference in the SSA temperature generates emittance transfer between degrees of freedom. In addition, the non-uniform density profile at the focal point introduces significant emittance growth in both the longitudinal and transverse directions.
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Title: Anarchist Mathematics Education : Ethic, Motivation, and Praxis
Creator: Bowers, David
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Anarchists and (mathematics) education researchers generally share convergent interests regarding social (in)equality—that is to say, both groups share a concern over noticing inequality and making efforts to pursue social justice. In this dissertation, I employ three tenets of anarchism (cooperation; mutual aid; freedom from unjustified, coercive hierarchy) to formulate and live out the beginnings of a mathematics education research approach rooted anarchism, in pursuit of the larger goal of...
Show moreAnarchists and (mathematics) education researchers generally share convergent interests regarding social (in)equality—that is to say, both groups share a concern over noticing inequality and making efforts to pursue social justice. In this dissertation, I employ three tenets of anarchism (cooperation; mutual aid; freedom from unjustified, coercive hierarchy) to formulate and live out the beginnings of a mathematics education research approach rooted anarchism, in pursuit of the larger goal of developing cohesion between my anarchist worldview and the possible/probable products of a career in research. In so doing, I aim to simultaneously: (1) Respond productively to critiques of mathematics education as atheoretical, (2) articulate one possible cohesion between anarchist worldview and research methods, (3) unsettle some of the taken-for-granted assumptions of the mathematics education research community, and (4) invite others into more radical forms of anti-oppressive research and praxis.
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Title: Application of earth observation and related technology in agro-hydrological modeling
Creator: Herman, Matthew Ryan
Date: 2018
Collection: Electronic Theses & Dissertations
Description: Freshwater is vital for life on Earth, and as the human population continues to grow so does the demand for this limited resource. However, anthropogenic activities and climate change will continue to alter freshwater systems. Therefore, there is a need to understand how the hydrological cycle is changing across the landscape. Traditionally, this has been done by single point monitoring stations; however, these stations do not have the spatial variability to capture different aspects of the...
Show moreFreshwater is vital for life on Earth, and as the human population continues to grow so does the demand for this limited resource. However, anthropogenic activities and climate change will continue to alter freshwater systems. Therefore, there is a need to understand how the hydrological cycle is changing across the landscape. Traditionally, this has been done by single point monitoring stations; however, these stations do not have the spatial variability to capture different aspects of the hydrologic cycle required for detailed analysis. Therefore, hydrological models are traditionally calibrated and validated against a single or a few monitoring stations. One solution to this issue is the incorporation of remote sensing data. However, the proper use of these products has not been well documented in hydrological models. Furthermore, with a wide variety of different remote sensing datasets, it is challenging to know which datasets/products should be used when.To address these knowledge gaps, three studies were conducted. The first study was performed to examine whether the incorporation of remotely sensed and spatially distributed datasets can improve the overall model performance. In this study, the applicability of two remote sensing actual evapotranspiration (ETa) products (the Simplified Surface Energy Balance (SSEBop) and the Atmosphere-Land Exchange Inverse (ALEXI)) were examined to improve the performance of a hydrologic model using two different calibration techniques (genetic algorithm and multi-variable). Results from this study showed that the inclusion of ETa remote sensing data along with the multi-variable calibration technique could improve the overall performance of a hydrological model.The second study evaluated the spatial and temporal performance of eight ETa remote sensing products in a region that lacks observed data. The remotely sensed datasets were further compared with ETa results from a physically-based hydrologic model to examine the differences and describe discrepancy among them. All of these datasets were compared through the use of the Generalized Least-Square estimation with Autoregressive models that compared the ETa datasets on temporal (i.e., monthly and seasonal basis) and spatial (i.e., landuse) scales at both watershed and subbasin levels. Results showed a lack of patterns among the datasets when evaluating the monthly ETa variations; however, the seasonal aggregated data presented a better pattern and fewer variances, and statistical difference at the 0.05 level during spring and summer compared to fall and winter months. Meanwhile, spatial analysis of the datasets showed that the MOD16A2 500 m ETa product was the most versatile of the tested datasets, being able to differentiate between landuses during all seasons. Finally, the ETa output of the model was found to be similar to several of the ETa products (MOD16A2 1 km, NLDAS-2: Noah, and NLDAS-2: VIC).The third study built upon the first study by expanding the use of remotely sensed ETa products from two to eight while examining a new calibration technique, which was the many-objective optimization. The results of this analysis show that the multi-objective calibration still resulted in better performing models compared to the many-objective calibration. Furthermore, the ensemble of all of the ETa products produced the best performing model considering both streamflow and evapotranspiration.
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Title: Application of free energy methods to drug discovery
Creator: Song, Lin, 1992-
Date: 2020
Collection: Electronic Theses & Dissertations
Description: With the increasing power of computers, computational studies have become more and more significant in drug discovery. High binding free energy is one of the major requirements for an effective drug molecule, hence much effort has been spent to develop fast and accurate computational free energy methods. In this thesis, different free energy methods, i.e. umbrella sampling, thermodynamic integration, and double decoupling method, are applied to different systems related to drug discovery. For...
Show moreWith the increasing power of computers, computational studies have become more and more significant in drug discovery. High binding free energy is one of the major requirements for an effective drug molecule, hence much effort has been spent to develop fast and accurate computational free energy methods. In this thesis, different free energy methods, i.e. umbrella sampling, thermodynamic integration, and double decoupling method, are applied to different systems related to drug discovery. For the first study, umbrella sampling studies are performed to calculate the absolute binding free energies of host-guest systems which serve as great model systems to assess free energy methods due to the small size of the systems, etc. We find that benchmarking our method with known systems can significantly improve the results for the unknown systems: the overall RMSE of the binding free energy versus experiment is reduced from 5.59 kcal/mol to 2.36 kcal/mol. The source of error could be from the un-optimized force constants used in umbrella sampling (hence possibly poor window overlaps), as well as force field, sampling issues, etc. Our results ranked 4th best in the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL6) blind challenge. For the second study, GPU accelerated thermodynamic integration (GPU-TI) is used to compute the relative binding free energies of a protein-ligand dataset originally assembled by Schrodinger, Inc. The calculations of relative binding free energies between different ligands are the typical process in the lead optimization of computer-aided drug discovery. In our study using GPU-TI from AMBER 18 with the AMBER14SB/GAFF1.8 force field, we obtained an overall MUE of 1.17 kcal/mol and an overall RMSE of 1.50 kcal/mol for the 330 perturbations contained in this data set. They are comparable to the overall MUE of 0.9 kcal/mol and RMSE of 1.14 kcal/mol using their GPU free energy code (FEP+) and the OPLS2.1 force field combined with the REST2 enhanced sampling by Schrodinger, Inc. Notably, after we published our work, several other research groups reported their benchmarking results on the other free energy software using the same dataset.The third study of this thesis focuses on modeling the thermodynamics of transition metal (TM) ions binding to a protein. TM ions are very common in biology and are important in drug discovery as well, because many TM ions are in the active site of the protein where the inhibitors bind, for example, the histone deacetylase. While the structural details of TMs bound to metalloproteins are generally well understood via experimental and computational means; studies accurately describing the thermodynamics of TM ion binding are less common. Herein, we demonstrate that we can obtain accurate structural and absolute binding free energies of Co2+ and Ni2+ to the enzyme glyoxalase I (GlxI) using an optimized 12-6-4 (m12-6-4) potential. Optimizing the 12-6-4 potential to accurately model the interactions between the TMs and the binding site residues, as well as protonation state changes associated with TMs (un)binding, are found to be crucial. Given the success of this study, we are now in a position to explore more complicated processes associated with TM-based drug discovery.
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Title: Application of nuclear Density Functional Theory to exotic nuclei
Creator: Chen, Mengzhi
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Nuclear density functional theory (DFT) is the method of choice to study the nuclear properties of medium-mass and heavy nuclei.This dissertation employs the Skryme Hartree-Fock-Bogoliubov (HFB) approach to study nuclear reflection-asymmetric deformations and collective rotation.Nuclear ground states with stable reflection-asymmetric shapes, predicted by theory, have been confirmed experimentally.To explore the microscopic origin of reflection-asymmetric nuclear shapes, we applied the density...
Show moreNuclear density functional theory (DFT) is the method of choice to study the nuclear properties of medium-mass and heavy nuclei.This dissertation employs the Skryme Hartree-Fock-Bogoliubov (HFB) approach to study nuclear reflection-asymmetric deformations and collective rotation.Nuclear ground states with stable reflection-asymmetric shapes, predicted by theory, have been confirmed experimentally.To explore the microscopic origin of reflection-asymmetric nuclear shapes, we applied the density expansion method to decompose the total HFB energy into different multipolarities. We demonstrated that the reflection-asymmetric deformation is driven by the isoscalar part of the interaction energy. We also confirmed the importance of high-multipolarity fields for stabilizing reflection-asymmetric deformations.The nucleon localization function (NLF) has been successfully applied to characterize nuclear shell structure and collective motion.In our work, we extended the application of NLF to study the nuclear response to fast rotation. By solving the cranked harmonic-oscillator and comparing it with cranked Hartree-Fock results, we defined the simplified localization measure and demonstrated its usefulness as an indicator of nuclear rotation. The above nuclear DFT calculations were performed using existing HFB solvers.However, the current HFB solvers are deficient in the study of exotic nuclei whose properties are strongly affected by the quasiparticle continuum space. For this purpose, we developed a three-dimensional Skyrme-HFB solver HFBFFT in the coordinate-space representation using the canonical basis approach. We implemented the soft energy cutoff and pairing annealing to solve the problem of pairing collapse; a sub-iteration method to improve the convergence, and an algorithm to restore the Hermiticity of differential operators brought by Fourier-transform-based differentiation. The accuracy and performance of HFBFFT were tested by benchmarking it against other HFB codes, both spherical and deformed, for a set of well-bound and weakly-bound nuclei.
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Title: Application of topological data analysis and machine learning for mutation induced protein property change prediction
Creator: Wang, Menglun
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Mutagenesis is a process by which the genetic information of an organism is changed, resulting in a mutation. A lot of diseases are caused by mutation of protein, including Cystic fibrosis, Alzheimer's Disease and most of cancer. To get a better understanding of mutation induced protein properties change, accurate and efficient computational models are urgently needed. For protein-protein binding affinity changes upon mutation ($\Delta\Delta G$), we built a prediction model called TopNetTree....
Show moreMutagenesis is a process by which the genetic information of an organism is changed, resulting in a mutation. A lot of diseases are caused by mutation of protein, including Cystic fibrosis, Alzheimer's Disease and most of cancer. To get a better understanding of mutation induced protein properties change, accurate and efficient computational models are urgently needed. For protein-protein binding affinity changes upon mutation ($\Delta\Delta G$), we built a prediction model called TopNetTree. Algebraic topology, a champion in recent worldwide competitions for protein-ligand binding affinity predictions, is a promising approach for simplifying the complexity of biological structures. Here, we introduce element-specific and site-specific persistent homology, a new branch of algebraic topology, to simplify the structural complexity of protein-protein complexes and embed crucial biological information into topological invariants. Additionally, we propose a new deep learning algorithm called NetTree, to take advantage of convolutional neural networks and gradient boosting trees. A topology-based network tree (TopNetTree) is constructed by integrating the topological representation and NetTree for predicting PPI $\Delta\Delta G$. Tests on major benchmark datasets indicate that the proposed TopNetTree significantly improves the current state-of-art in $\Delta\Delta G$ prediction.For mutation induced protein folding energy change, we proposed a local topological predictor (LTP) based machine learning model. To characterize molecular structure, Hessian matrix of local surface is generated from Exponential and Lorentz density kernel. Eigenvalues of Hessian matrix are calculated as local topological predictor, which are then fed into gradient boost machine learning model as features. Our LTP model obtained state-of-art results for various benchmark data sets of mutation induced protein folding energy change
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Title: Approaching exact quantum chemistry by stochastic wave function sampling and deterministic coupled-cluster computations
Creator: Deustua Stahr, Jorge Emiliano
Date: 2020
Collection: Electronic Theses & Dissertations
Description: One of the main goals of quantum chemistry is the accurate description of ground- and excited-state energetics of increasingly complex polyatomic systems, especially when non-equilibrium structures and systems with stronger electron correlations are examined. Size extensive methods based on coupled-cluster (CC) theory and their extensions to excited electronic states via the equation-of-motion (EOM) framework have become the de facto standards for addressing this goal. In the vast majority of...
Show moreOne of the main goals of quantum chemistry is the accurate description of ground- and excited-state energetics of increasingly complex polyatomic systems, especially when non-equilibrium structures and systems with stronger electron correlations are examined. Size extensive methods based on coupled-cluster (CC) theory and their extensions to excited electronic states via the equation-of-motion (EOM) framework have become the de facto standards for addressing this goal. In the vast majority of chemistry problems, the traditional single-reference CC hierarchy, including CCSD, CCSDT, CCSDTQ, etc., and its EOM counterpart provide the fastest convergence toward the exact, full configuration interaction (FCI), limit, allowing one to capture the leading many-electron correlation effects, in a systematic manner, by employing particle-hole excitations from a single reference determinant. Unfortunately, computational costs associated with the incorporation of higher-than-two-body components of the cluster and excitation operators of CC and EOMCC, which are required to achieve a fully quantitative description of molecular systems, are usually prohibitive. This has exacerbated the need for new ideas in quantum chemistry leading to computationally affordable methodologies that do not suffer from failures of lower-order, less expensive approximations. In this dissertation, I propose two novel and computationally cost-effective strategies for acquiring accurate electronic energetics, equivalent to those obtained with high-level CC/EOMCC methods, such as CCSDT, EOMCCSDT, and CCSDTQ, and the exact, FCI, theory, even when wave function quasi-degeneracies and other higher-order correlation effects become significant.The first strategy consists in merging the deterministic CC framework, abbreviated as, CC(P;Q), with the stochastic CI Quantum Monte Carlo (QMC) approaches, such as CISDT-MC, CISDTQ-MC, FCIQMC, and their CCSDT-MC counterpart with the intention of using wave functions resulting from QMC propagations to identify the leading higher-than-doubly excited components entering deterministic CC and EOMCC calculations.The second proposed methodology provides a direct way of recovering FCI energetics following the ideas of the externally corrected CC theories. In the resulting approach, that we denominate CAD-FCIQMC, we utilize the cluster analysis of FCIQMC wave functions to obtain the connected three- and four-body cluster components, which are the only clusters that directly couple to the one- and two-body components of the cluster operator. In general, the externally corrected CC methods are guaranteed to attain the exact, FCI, ground-state energy, if the triply and quadruply excited cluster components extracted from a non-CC source entering the suitably corrected CCSD-like equations approach their exact values. Since the long-time FCIQMC propagations converge the exact FCI wave functions, our new CAD-FCIQMC method is assured to produce numerically exact energies.All of the above approaches, including the semi-stochastic CC(P;Q) and CAD-FCIQMC methodologies, are discussed in this dissertation. This includes their mathematical foundations, computer implementation, and numerical tests using bond breaking in the F2, H2O, and CH+ molecules and the automerization of cyclobutadiene.
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Title: Artful teaching and learning abroad : an arts-based education abroad research (ABEAR) study
Creator: Creps, Karenanna Boyle
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Over the last three decades, there has been a surge in short-term, faculty-directed education abroad programs sponsored by U.S.-based postsecondary institutions. Surprisingly, there is little research that examines the pedagogies faculty program directors enact on these programs, which can leave them with few resources to support their work with students abroad beyond their own on-campus teaching experience. This arts-based education abroad research (ABEAR) project is designed to provide an...
Show moreOver the last three decades, there has been a surge in short-term, faculty-directed education abroad programs sponsored by U.S.-based postsecondary institutions. Surprisingly, there is little research that examines the pedagogies faculty program directors enact on these programs, which can leave them with few resources to support their work with students abroad beyond their own on-campus teaching experience. This arts-based education abroad research (ABEAR) project is designed to provide an opportunity for discourse and reflection on the multiple pedagogies I enacted as a faculty program director by asking: how do I, as a faculty program director, perceive student learning from arts-oriented, experiential, and place-based pedagogies on two education abroad programs designed to introduce rising freshmen to undergraduate education? I will respond to this research question through an examination of the program pedagogies I created and enacted on two such programs, contextualized within Elliot Eisner's curriculum theory (2002) and John Dewey's experiential learning theory (1938, 2005), as well as within the education abroad research literature. Through the methodological frameworks of performative autoethnography and a/r/tography, I examine my design and enactment of arts-oriented, experiential, intercultural education abroad pedagogy on two Michigan State University (MSU) First-Year Seminar Abroad (FSA) programs. MSU offers these programs to rising freshmen as an introduction to life in a university community. My "findings" chapter is offered as both a dramatic and performance text (a performance of the dramatic text for a live audience), both of which extend the examination of a/r/tifacts, the evidence of pedagogy I collected for this study, to a larger conversation about the pedagogical possibilities of education abroad programming. I approach this dissertation project as an a/r/tographer, which is to say that my combined identities of artist, researcher, and teacher inform and resonate throughout the project. This dissertation makes two important contributions to the education abroad research community: first, it is designed to inspire dialogue about the pedagogical possibilities of arts-oriented intercultural education abroad; and second, this study introduces a new methodological term, Arts-Based Education Abroad Research (ABEAR), to signal the application of Arts-Based Education Research (ABER) methodologies to the unique learning context of education abroad.
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Title: Asserting sovereignty through strategic accommodation : the Rukai people and collaborative conservation in Pingtung, Taiwan
Creator: Lin, Ying-Jen
Date: 2020
Collection: Electronic Theses & Dissertations
Description: This dissertation examines how the Rukai, an Indigenous people of Taiwan, have engaged in community-based ecotourism and the state's conservation projects in order to assert Indigenous sovereignty over traditional territories. This study focuses on the Adiri and the Labuwan communities, which are communities of the Rukai people living in the Wutai Township in Pingtung, Taiwan. The two Rukai communities have actively collaborated with the government on various conservation projects although...
Show moreThis dissertation examines how the Rukai, an Indigenous people of Taiwan, have engaged in community-based ecotourism and the state's conservation projects in order to assert Indigenous sovereignty over traditional territories. This study focuses on the Adiri and the Labuwan communities, which are communities of the Rukai people living in the Wutai Township in Pingtung, Taiwan. The two Rukai communities have actively collaborated with the government on various conservation projects although the relationship between Indigenous peoples of Taiwan and the settler state's forest governance system has been riddled with conflicts. Existing research has portrayed collaborative environmental governance either as an instrument for co-optation of Indigenous interests or as a catalyst for a more equitable relationship between the state and Indigenous peoples. This dissertation builds on and extends this body of work by examining how the Rukai people have continued to assert sovereignty in the community-based ecotourism and collaborative conservation projects. Using a combination of ethnographic observations, interviews, and archival research, this dissertation explores how the Rukai community members have positioned themselves vis-a-vis the government and non-Indigenous society and how the Rukai people have articulated their relationship to ancestral lands in ecotourism and conservation projects.My findings suggest that the Rukai people have used ecotourism and collaborative conservation projects as a strategic platform to ensure their needs and goals for land-based self-determination are met and to assert sovereignty over ancestral lands, while remaining wary and critical of the colonial dimensions and constraints of the state's laws and policies. I argue that the positions and actions taken by the Rukai people were the "third space of sovereignty" (Bruyneel 2007; Diver 2016) that is neither outright resistance nor full compliance with the settler state's political and cultural systems. My analyses indicate that the Rukai people's engagement with the state's conservation projects was not simply a form of co-optation into the dominant discourses and practices; instead, it was one of the strategies employed by the Rukai people to seek their broader goals of Indigenous sovereignty and self-determination given the political and economic realities and available options.
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Title: Assessing species distributions and the effects of habitat fragmentation : the case of the giant panda
Creator: Connor, Thomas
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "Environmental degradation has become a ubiquitous feature in the modern world. This degradation is resulting in widespread loss and fragmentation of wildlife habitat, leading to increased extinction risks and population declines. In order to stem these threats, it is imperative to accurately predict species' habitats, how to optimize the restoration and protection of these habitats, and better understand how their ecology interacts with habitat requirements. I used both simulated and...
Show more"Environmental degradation has become a ubiquitous feature in the modern world. This degradation is resulting in widespread loss and fragmentation of wildlife habitat, leading to increased extinction risks and population declines. In order to stem these threats, it is imperative to accurately predict species' habitats, how to optimize the restoration and protection of these habitats, and better understand how their ecology interacts with habitat requirements. I used both simulated and empirical study systems to investigate these topics and focused heavily on giant panda (Ailuropoda melanoleuca) populations across Wolong Nature Reserve and Southwest China.Given the uncertainty and debate surrounding the relative effects of habitat amount and habitat fragmentation on ecological responses (Chapter 1), I set out to accurately define habitat before further investigating these effects. I found that the grain size of environmental predictor variables had important effects on modeling the distributions of virtual species simulated on real landscapes, and that modeling with grain sizes farther away from the "true" grain size used to simulate the species resulted in lower predictive accuracy and incorrect ecological inferences about the importance of environmental variables to habitat (Chapter 2). I then went a step further and investigated interactive spatial scale effects on species distribution modeling by varying the total extent of the study areas and grain size of the environmental variables used to predict panda habitat and distributions across Southwest China (Chapter 3). I found that increasing total extent offset the negative effects of increasing grain size on model accuracy and that total extent can be optimized as both larger (at smaller spatial scales) and smaller (at the geographic range scale) than the study area of interest. I then further improved the accuracy of our species habitat and distribution modeling by leveraging empirical movement distributions derived from GPS-collar data to transform the environmental predictor variables, and used the resulting habitat map to investigate the effects of habitat amount and fragmentation on functional connectivity in the panda population in Wolong (Chapter 4). I found that the standard deviation of the core area index, a measure of habitat configuration, was the best predictor of functional connectivity. Habitat amount was the second-best predictor and we found that in our study system it could optimized to cover about 80% of a local landscape to maximize functional connectivity. Habitat fragmentation also showed a nonlinear and threshold-dependent relationship with functional connectivity-important findings to consider in the spatial planning of protected areas. Finally, I used the noninvasive genetics data to "capture" and "recapture" unique individuals across a core habitat area in Wolong and conduct the first social network analysis of pandas (Chapter 5). I found strong evidence of two to three social clusters in the population, defined as groups of pandas that associated with each other at a significantly higher rate than individuals outside the cluster. These clusters may represent cryptic family structuring, as genetic relatedness was a significant positive predictor of associations between individuals. My detailed approaches to investigating the habitat and ecology of giant pandas used throughout this manuscript resulted in unique insights into this threatened habitat specialist species, and we recommend they be applied widely to other species. Optimizing the way in which we predict and conserve habitat in each landscape and system, as opposed to relying on expert opinion or competing theories, will be increasingly important as environmental degradation continues in the Anthropocene."--Pages ii-iii.
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Title: Assessment as growth : teaching the working alliance through systematic evaluation of professional dispositions in counselor education
Creator: Levine, Allison
Date: 2018
Collection: Electronic Theses & Dissertations
Description: "The 2016 CACREP Standards call for the formal assessment of student professional dispositions throughout a counselor education program. This is a complex and often unwelcome task for faculty given the subjective nature of assessing non-academic competencies. Furthermore, considering the ethical and legal implications of this task, an empirically-based instrument would benefit faculty in counselor education programs in a variety of ways including ensuring due process during evaluations. Using...
Show more"The 2016 CACREP Standards call for the formal assessment of student professional dispositions throughout a counselor education program. This is a complex and often unwelcome task for faculty given the subjective nature of assessing non-academic competencies. Furthermore, considering the ethical and legal implications of this task, an empirically-based instrument would benefit faculty in counselor education programs in a variety of ways including ensuring due process during evaluations. Using a two-phase methodology, the current study began with a Delphi panel to establish items to be included in an instrument. The second phase involved validation of the instrument items using a survey distributed to Certified Rehabilitation Counselors (n = 148). Instrument items were rated on Relevance and Utility to assess their appropriateness for being included in the instrument. The Assessment as Growth Inventory (AGI), was developed, being framed using the working alliance in order to encourage the development of student professional dispositions in line with this evidence-based practice. AGI comprises four sections, with 48 items (Professional Dispositions - 13, Tasks - 10, Goals - 8, and Bonds - 17). Implications for research, counselor education, and clinical practice are discussed at length."--Page ii.
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Title: Assessment of equation-of-motion coupled-cluster methods with approximate treatments of higher-order excitations and development of novel schemes for accurate calculations of diradical electronic spectra and bond breaking
Creator: Ajala, Adeayo Olayinka
Date: 2017
Collection: Electronic Theses & Dissertations
Description: The development and implementation of electronic structure methods based on the exponential wave function ansatz of the single-reference coupled-cluster (CC) theory and its extensions to excited states exploiting the equation-of-motion (EOM) and linear responseframeworks have witnessed great success in a wide range of applications, but there are areas of chemistry, especially studies of chemical reaction pathways and photochemistry, where further improvements in the existing CC and EOMCC...
Show moreThe development and implementation of electronic structure methods based on the exponential wave function ansatz of the single-reference coupled-cluster (CC) theory and its extensions to excited states exploiting the equation-of-motion (EOM) and linear responseframeworks have witnessed great success in a wide range of applications, but there are areas of chemistry, especially studies of chemical reaction pathways and photochemistry, where further improvements in the existing CC and EOMCC methodologies are needed. In order to make progress in this area, it is important to evaluate the quality of the results that the existing CC/EOMCC methods provide, particularly in applications involving the interpretation and prediction of photochemical phenomena and electronic excitations spectra involving closed- and open-shell molecules. Thus, in the rst part of this PhD project we use a database set of 28 organic molecules ranging from linear polyenes, unsaturated cyclic hydrocarbons, aromatic hydrocarbons, and heterocycles to aldehydes, ketones, amides, and nucleobases to examine the performance of the completely renormalized (CR) EOMCC approaches forexcited electronic states, in which the relatively inexpensive non-iterative corrections due to triple excitations are added to the energies obtained with the standard EOMCC approach with singles and doubles, abbreviated as EOMCCSD. We focus on two variants of the approximately size-intensive CR-EOMCC methodology with singles, doubles, and noniterative triples, abbreviated as delta-CR-EOMCCSD(T), and the analogous two variants of the newer, rigorously size-intensive, left-eigenstate delta-CR-EOMCC(2,3) approach based on the biorthogonal formulation of the method of moments of CC equations.In the second part of this dissertation, we focus on the development of new EOMCC methods that are particularly well-suited for accurate calculations of diradical electronic spectra and single bond breaking. They are the cost-effective variants of the doubly electron-attached (DEA) EOMCC methodologies with up to 3-particle---hole (3p-1h) or 4-particle--2-hole (4p-2h) excitations, abbreviated as DEA-EOMCC(3p-1h)fNug and DEA-EOMCC(3p-1h,4p-2h){Nu}, respectively, which utilize the idea of applying a linear electron-attaching operator to the correlated CC ground state of an (N -2)-electron closed-shell reference system in order to generate the ground and excited states of the N-electron open-shell species of interest, while using Nu active unoccupied orbitals to select the dominant 3p-1h and 4p-2h terms. We demonstrate that the relatively inexpensive DEA-EOMCC(3p-1h,4p-2h){Nu} method signicantly reduces the computational costs of the parent active-space DEA-EOMCC(4p-2h){Nu} and full DEA-EOMCC(4p-2h) approaches, which are needed to obtain highly accurate results for open-shell systems having two electrons outside the closed-shell cores, such as diradicals, with virtually no loss in accuracy of the resulting excitation and dissociation energies. We also show that the active-space DEA-EOMCC(3p-1h){Nu} method accurately reproduces the results of the parent DEA-EOMCC(3p-1h) calculations at the small fraction of the cost. In addition to a series of benchmark examples that illustrate the performance of the DEA-EOMCC(3p-1h){Nu}, DEA-EOMCC(3p-1h,4p-2h){Nu}, and other DEA-EOMCC approaches with 3p-1h and 4p-2h excitations, including singlet{triplet gaps in methylene, trimethylenemethane, and several antiaromatic diradicals and bond breaking in the fluorine molecule, we provide the most essential details of DEA-EOMCC equations with an active-space treatment of 3p-1h and 4p-2h terms, as implemented in the compactcodes developed in this work and interfaced with the GAMESS package.
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Title: Assuming Ambiguity
Creator: Conklin, Rebecca C.
Date: 2022
Collection: Electronic Theses & Dissertations
Description: This dissertation considers ambiguity throughout the history of Rhetoric and Composition, a discipline generally concerned with clarity, concision, and correctness as key attributes of “good” writing. In the first part of this dissertation, I draw from the theoretical contributions made by Simone de Beauvoir in The Ethics of Ambiguity (1947) and show how the central tensions she wrestled with in that text mirror the tensions experienced at the dawn of this discipline, tensions that have (re...
Show moreThis dissertation considers ambiguity throughout the history of Rhetoric and Composition, a discipline generally concerned with clarity, concision, and correctness as key attributes of “good” writing. In the first part of this dissertation, I draw from the theoretical contributions made by Simone de Beauvoir in The Ethics of Ambiguity (1947) and show how the central tensions she wrestled with in that text mirror the tensions experienced at the dawn of this discipline, tensions that have (re)emerged throughout subsequent decades. I trace the disciplinary conversations in the decades following World War II, as Rhetoric and Composition sought to define itself and its space in increasingly neoliberal, corporate college and university structures. Summarizing field conversations around the problems of relevance, content/standards, teachers and students, and assessment, I show how the gap between disciplinary knowledge/best practices bumps up against the demands of a profit-driven university. This project offers another way of thinking and doing through a praxis of ambiguity, explored and articulated through five guiding verbs: imagine, emerge, expand, intuit, and situate. Through these guiding verbs, I explore how these verbs and the scholarship that supports them may offer ways to intentionally disrupt the presence of white supremacy culture in teaching, research, and administration in the discipline by making visible the characteristics of this culture and sketching the outlines of an interventional framework based on a praxis of ambiguity, offering avenues for future research.
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Title: At the intersection of multiple identities : an examination of the meaning making and leadership experiences of black women community college administrators
Creator: Gaither, Chastity D.
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Although the volume of literature on Black women in higher education is constantly growing, the experiences of Black women community college administrators have not been well documented in research literature. Using qualitative inquiry, this study examined and documented the leadership and meaning making experiences among 12 Black women who serve as community college administrators. The study was presented through a Black Feminist Thought lens that underscored the intersection of multiple...
Show moreAlthough the volume of literature on Black women in higher education is constantly growing, the experiences of Black women community college administrators have not been well documented in research literature. Using qualitative inquiry, this study examined and documented the leadership and meaning making experiences among 12 Black women who serve as community college administrators. The study was presented through a Black Feminist Thought lens that underscored the intersection of multiple marginalized identities in relation to perspectives on leadership and meaning making.
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Title: Atomic simulation on chemical-mechanical coupled deformations in complex nano structures
Creator: Liu, Jialin (Graduate of Michigan State University)
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "Nano-structured materials often exhibit very different mechanical properties comparing with their bulk counterpart and are more sensitive and active to chemical interactions with the environments due to the large surface-to-volume ratio. In this thesis, predictive modeling techniques including density functional theory (DFT) and reactive molecular dynamics method (MD) are designed and applied to understand the deformation mechanisms of complex nano-structured material and describe chemical...
Show more"Nano-structured materials often exhibit very different mechanical properties comparing with their bulk counterpart and are more sensitive and active to chemical interactions with the environments due to the large surface-to-volume ratio. In this thesis, predictive modeling techniques including density functional theory (DFT) and reactive molecular dynamics method (MD) are designed and applied to understand the deformation mechanisms of complex nano-structured material and describe chemical-mechanical coupled interactions. Three technologically important materials are investigated, to understanding the high strain rate toughening mechanism in nacre, predicting the formation and fracture of aluminum oxide bifilms in aluminum castings, and revealing the lithium growth morphology as a function of oxygen partial pressure. For nacre, its hierarchical structure and toughening mechanisms have inspired many materials developments. Recently, a new toughening mechanism, deformation twins was observed in nacre after dynamic loading (103 s--1). The deformation twinning tendency and the competition between fracture and deformation twinning were revealed by DFT calculations. We discovered that the ratio of the unstable and the stable stacking fault energy in aragonite is hitherto the highest in a broad range of metallic and oxide materials and the bonding nature for this high ratio is explained. Both aluminum and lithium have high oxygen affinity. Their interaction with the oxygen environment affects the mechanical properties and vice versa. During casting of aluminum, it has long been proposed that the entrapped alumina "bifilms" are detrimental to the fatigue properties of the cast product. However, its properties have never been measured due to experimental limitations. Therefore, a ReaxFF based MD protocol was designed to simulate aging, folding, and fracture of oxide bifilms. The predicted fracture energy, fracture location, and differences between old and young oxides are explained a series of experimental observations. To illustrate the Li-growth mechanism in a solid-state-battery testing platform, we modeled the morphology of Li nano-structure growth in oxygen environment via ReaxFF-based MD. The simulation revealed that the competition of the Li growth rate and oxidation rate leads to the sphere-nanowire-sphere morphology transition with increasing oxygen partial pressure. Understanding the impact of chemical reaction on Li dendrite growth mechanisms and morphology evolution provided insights on the formation of the solid electrolyte interface (SEI) layer in a Li-ion battery. Finally, a shortcoming of the current charge transfer scheme (qEq) used in the ReaxFF MD simulation is discussed. It is demonstrated that qEq method will lead to overductile ionic materials in the MD simulation. A new Force field method and new parameters are proposed to mitigate this problem."--Pages ii-iii.
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