VictorJuiz/thesis huggingface dataset:
Characterization of the 3D nanostructure of Calcium Silicate Hydrates by using Transmission Electron Microscope (TEM)

Calcium silicate hydrate (C-S-H) is the main hydration product of Portland cement that mainly contributes to concrete's physical and mechanical properties. The porosity of C-S-H plays a vital role in the durability-based performance of concrete. Most of the information about the microstructure of C-S-H now is only in 2D due to the complex morphologies of hydration products. This dissertation aims to investigate synthetic C-S-H and C-A-S-H with various Ca/Si ratios and curing temperatures using Transmission Electron Microscope (TEM) tomography. The 3D reconstructions of all samples were done using the simultaneous iterative reconstruction technique (SIRT). The highest beam dose that doesn’t damage the samples for TEM tomography is 5000 e-/(nm2 s) for all samples. The 3D reconstructions and selected ROI analysis confirm that there are only foil-like structures for all C-S-H and C-A-S-H samples. Both CPSD and CMIP reveal that most of the pore sizes of all samples are below 40 nm. However, C-S-H at Ca/Si ratio 1.0 and 1.6 seem to have pore sizes larger than 100 nm. The curing temperature causes a lower porosity in the structure of both C-S-H and C-A-S-H. However, the porosity is not affected by chemical composition. Scanning transmission electron microscopy (STEM) is used to compare the results with TEM. The 3D results of both TEM and STEM tomography show no significant difference. Still, the continuous pore size distribution with CMIP simulations shows a remarkable difference. C-S-H at Ca/Si ratio 1.0 from TEM tomography has 3 dominant pore sizes at 22.2, 28.8 and 37.7 nm, while STEM tomography has only one dominant pore size at 6.0 nm. The pore network’s size of TEM_C-S-H 1.0 is significantly larger but less dense than STEM_C-S-H 1.0. A preliminary study of a fluid flow model has been accomplished. Both porosity and permeability increase with samples higher Ca/Si ratio, and higher equilibrated temperatures. The successful model will enhance the understanding of the relationship of mechanical properties and porosity of cement and concrete. TEM tomography combine with Xlib plugin in ImageJ shows the capability to determine the 3D nanostructure and pore networks of C-S-H and C-A-S-H. To determine the sustainability of cements and concrete, the understanding of the relationship of mechanical properties and porosity is needed. The resulting information of 3D nanostructure and pore analysis provide these critical information for developing a new generation of optimized green cement and concrete.

Advisor: Wenk, Hans-Rudolf
Advancing enabling technology and genome editing in monocot crops for disease resistance and sustainability

It is projected that by the year 2050, global agriculture will need to increase the output of staple crops by 60% to feed the world’s rapidly growing population amidst threats posed by climate change and crop disease. One strategy to meet this challenge is to develop new genetic diversity in the germplasm to generate robust and resilient lines with beneficial traits. Conventional breeding has played an essential and major role in crop trait improvement. However, those methods can be difficult, laborious, and time-consuming. The development of effective technology for precision and time-saving plant breeding is required. A breakthrough tool to this end has been CRISPR-Cas9. Noteworthy for its simple sequence-specific programmability, the gene editing system has unleashed remarkable potential for plant biotechnology and functional genomics. Here, we explore several aspects and parameters to advance Cas9-mediated gene editing technology in the essential monocot food crops: rice and wheat. Early-stage plant gene-editing projects benefit greatly from a rapid transient pipeline using protoplasts to evaluate the efficacy of gene editing reagents. We describe here a novel and sustainable method for protoplast isolation from rice tissue and demonstrate their use in ribonucleoprotein (RNP) based Cas9 gene editing assays. Next, we focus on applications of Cas9 technology in wheat to engineer disease resistance. Wheat is a critical target organism because the complexity of its large allohexaploid genome has rendered genetic manipulation by classic methods extremely difficult. Using DNA plasmids encoding CRISPR-Cas9 gene editing reagents, we optimize conditions and demonstrate that all three homoeologous copies of genes in allohexaploid wheat can be simultaneously edited within a single generation. We recognize, however, that DNA plasmid gene editing approaches have a number of limitations including random integration into the plant genome and unpredictability of expression. To address this, we finally present significant improvements to DNA-free Cas9-RNP based gene editing in wheat. We show that increased temperature treatment greatly enhances Cas9-mediated editing efficiency and regenerate transgene-free edited wheat plants at a high rate. Lastly, we utilize this DNA-free gene editing method to generate de novo partial resistance to the agronomically important pathogen Parastagonospora nodorum.

Advisor: Cate, Jamie H.D.
Staskawicz, Brian J.
Safe and Efficient Human-Robot Collaboration

As the emphasis on manufacturing is shifting from mass production to mass customization, the demands for flexible automation keep increasing. Human-robot collaboration (HRC), as an effective and efficient way to enhance flexibility, has attracted lots of attention both in industry and academia in the past decade. These robots are called co-robots. The fundamental research question is how to ensure that co-robots operate efficiently and safely with human partners./nTo achieve that, two problems should be addressed: 1) co-robots should know the human's future trajectory and avoid potential collisions to guarantee safety, and 2) co-robots should know the human's intentions and take corresponding actions to ensure task efficiency. Therefore, a robotic system is adopted, which reasons about human behavior and makes human-aware planning using the reasoning information. For reasoning about human behavior, a hierarchical probabilistic modeling method and two online adaptation algorithms are proposed for human plan recognition and human trajectory prediction. The hierarchical probabilistic modeling method explicitly utilizes the hierarchical behavior of the human and uses a pipeline to identify human intention through the trajectory, the trajectory type, the action, and finally the plan, which is explainable and data-efficient.Two online adaptation algorithms, the adaptable neural network and the adaptable lognormal method, are proposed for short-term and long-term trajectory prediction. These two adaptation algorithms enable the prediction models to online accommodate different human behaviors and to deal with the lack of human data. For short-term prediction, the adaptable neural network utilizes the recursive least square-parameter adaptation algorithm to online adapt the last layer of a neural network model, the prediction of which is employed to the real-time collision avoidance. For long-term prediction, the adaptable lognormal method uses an objective-based adaptation algorithm to online adapt the sigma-lognormal model, from which the duration of the whole trajectory is estimated and later will be used in the task planner that optimizes the task completion time. For making human-aware planning, a separation task planner is proposed, which uses the knowledge of human intention and makes the robot execute actions that are parallel to the human actions, while minimizing the task completion time. Different from those methods that only consider time efficiency, this separation task planner additionally improves human satisfaction and avoids potential conflicts, which can be shown in the experiment results.

Advisor: Tomizuka, Masayoshi
Geochronologic Constraints on Earth Surface Processes and Their Response to Climate Change

Earth’s topography is constantly evolving in response to surface processes that are modulated by changes in climate, tectonics, and sea level. Geochronology can used to identify the timing and rates of past Earth surface change and thereby advance our understanding of how these changes relate to different Earth processes that interplay over different geologic timescales. In this thesis, I contribute new geochronologic constraints on the extent to which Earth surface processes varied in the past and how that variation relates to past climate change. Chapter 1 describes the fundamentals of geochronology and provides an overview of the specific techniques used in this thesis. In Chapter 2, I present a quantitative framework for determining the timing and patterns of km-scale topographic change at the high-latitude Antarctic Peninsula using detrital apatite (U-Th)/He thermochronometry and 3D thermo-kinematic numerical modeling. While Plio-Pleistocene cooling accelerated glacial erosion rates at many mid-latitude glacial landscapes, my results reveal that Plio-Pleistocene cooling suppressed glacial erosion at the Antarctic Peninsula. These results highlight that landscapes at different latitudes had different responses to global cooling. In Chapter 3, I apply the approach developed in Chapter 2 to seven additional fjords along a latitudinal transect at the Antarctic Peninsula to investigate how the timing of km-scale topographic change relates to changes in climate and tectonics. At this site, the onset of km-scale topographic change occurs more than 15 million years after the initiation of glaciation and generally covaries with the arrival time of spreading ridge. These are among the first empirical results to show that a tectonic history, and its control on the regional topography of a landscape, has influenced glacial erosion rates over geologic timescales. In Chapter 4, I use the uranium-series comminution age technique to constrain sediment transport times to the Bengal Fan over the last 200 thousand years. I find pronounced variability in transport time that appears to be modulated by the climate and hydrological changes associated with the Late Pleistocene climate cycles. Because sediment transport times are more than 100 times smaller than the age of the Bengal Fan, Himalayan sediment transport keeps pace with erosion on million-year timescales. Each chapter demonstrates that the response of Earth surface processes to climate change depends on the geologic history of landscape. Thus, the past not only informs on the extent to which climate change can perturb Earth surface processes; the past influences how Earth surface processes will respond to future climate change.

Advisor: Shuster, David L
DePaolo, Donald J
Instrumentation for Radio Interferometers with Antennas on a Regular Grid

In the past two decades, a rebirth of interest in low-frequency radio astronomy, for 21\,cm tomography of the Epoch of Reionization, has given rise to a new class of radio interferometers with $N \gg 100$ antennas. The availability of low-noise receivers that do not require cryogenic cooling has driven down the cost of antennas, making it affordable to build sensitivity with numerous small antennas rather than traditional large dish structures. However, the computational- and storage-costs of such radio arrays, determined by the $\mathcal{O}(N^2)$ scaling of visibility products that need to be computed for calibration and imaging, become proportional to the cost of the array itself and drive up the overall cost of the radio telescope./nWhen antennas in the array are built on a regular grid, direct-imaging methods based on spatial Fourier transforms of the array can be exploited to avoid computing the intermediate visibility matrices that drive the unfavorable scaling. However, such methods rely on the availability of calibrated antenna voltages which are themselves difficult to obtain without using visibility matrices. In this thesis, I explore two real-time calibration strategies that can operate on subsets of visibility matrices, which can be computed without compromising on the $\mathcal{O}(N\log{N})$ scaling of direct-imaging systems./nFor more general radio interferometer layouts, baseline-dependent averaging with fringe stopping can be used to decrease the data rate of visibility products. While the computational cost is nearly unchanged, this technique can decrease the data volume of cross-correlation products, making it more tenable to store, process, and calibrate the output of the correlator. In this thesis, I describe the entire signal processing pipeline built for the Hydrogen Epoch of Reionization Array (HERA), which is currently being commissioned for detecting and characterizing the power spectrum of neutral hydrogen in the redshift range $5 < z < 28$. The HERA correlator implements both fringe stopping and baseline dependent averaging to bring down the data rate from nearly 1 Tbps to 15 Gbps.

Advisor: Parsons, Aaron R
Disrupting Environments: Boarding School Domesticity and the Making of Catholic Colombians and Socialist Cubans in Twentieth-Century Latin America

"Disrupting Environments" explores how boarding school domesticity was a central tool to instill Catholic and Socialist values in two twenty-century Latin American nations. In Colombia, an elementary boarding school for indigenous children that operated between 1913 and 1958 in La Guajira region was the most influential component of a project of Christianization and “Colombianization” of the Wayúu indigenous group. Founded by the Catholic Capuchin order with funding from the Colombian government, the boarding school was set to be the center of a new town meant to facilitate missionaries’ control of the indigenous territory. In Cuba, a program of rural boarding schools for middle-school students that operated between 1971 and the early 1990s was intended to shape the "hombre nuevo" (new man) for the emerging Socialist society. Hundreds of these boarding schools were built in rural areas across Cuba as part of the government’s push to upgrade the countryside’s physical conditions. This dissertation shows how the social transformation campaigns in both Colombia and Cuba relied heavily on the built environment and used boarding schools as their catalyst elements. I contend that the Capuchin order and the Cuban government used their power to produce physical interventions while simultaneously spreading narratives prescribing how to interpret these interventions. Such narratives shaped the boarding schools’ domesticities, situating them as part of larger coherent landscapes (physical and rhetorical), making it difficult for students to contest the values they were set to learn. The two ideologies promoted in both campaigns, Catholicism and Socialism, were carefully spatialized and domesticated to change children’s lives through quotidian activities. "Disrupting Environments," therefore, understands boarding schools as domestic spaces. It claims that the academic activities performed in these institutions are secondary to their domestic use. It also shows that readings of domesticity require the analysis of the narratives that shape it, which circulate beyond the traditionally understood boundaries of domestic space.

Advisor: Castillo, Greg
Generative Models as a Robust Alternative for Image Classification: Progress and Challenge

The tremendous success of neural networks is clouded by the existence of adversarial examples: maliciously engineered inputs can cause neural networks to perform abnormally, causing security and trustworthiness concerns. This thesis will present some progress on an alternative approach for robustly classifying images. Generative classifiers use generative models for image classification, showing better robustness than discriminative classifiers. However, generative classifiers face some unique challenges when images are complex. This thesis will present an analysis of these challenges and remedies./nGenerative classifiers suffer from out-of-domain reconstructions: overpowered generators can generate images out of the training distribution. This thesis demonstrates a method to address out-of-domain reconstructions in generative classifiers. Combined with other extensions, our method has successfully extended generative classifiers from robustly recognizing simple digits to classifying structured colored images. Besides, this thesis conducts a systematic analysis of out-of-domain reconstructions on CIFAR10 and ImageNet and presents a method to address this problem on these realistic images./nAnother challenge of generative classifiers is measuring image similarity. This thesis will demonstrate that similarity measurements are critical for complex images such as CIFAR10 and ImageNet. It also presents a metric that has significantly improved generative classifiers on complex images./nThe challenges of generative classifiers come from modeling image distributions. Discriminative models do not have such challenges because they model label distribution instead of image distribution. Therefore, the last part of this thesis is dedicated to a method that connects the two worlds. With the help of randomized smoothing, the new generative method leverages discriminative models and model image distribution under noises. Experiments showed that such a method improves the robustness of unprotected models, suggesting a promising direction for connecting the world of generative models and discriminative models.

Advisor: Wagner, David
Structure and Ion Transport in Hybrid Organic-Inorganic Copolymer Electrolytes

Block copolymers mixed with lithium salts are promising electrolyte materials for next- generation lithium batteries. One block can aid in the transport of ions, while the other block can provide improved mechanical strength to counteract lithium dendritic growth, a common failure mechanism of lithium metal batteries. Block copolymers often exhibit microphase separation of the two blocks due to thermodynamic repulsions between the two unlike chemical moieties. Understanding the correlations between structure, salt concentration, mechanical strength, and ion transport is important for improving the performance of polymer electrolytes. Significant work in characterization of structure and ion transport has been performed in all- organic diblock copolymers mixed with lithium salts, namely, polystyrene-block-poly(ethylene oxide) (PS-b-PEO; SEO) and lithium bis(trifluoromethanesulfonyl) imide (LiTFSI). However, there is an emerging interest in replacing the mechanically rigid block with an inorganic material, such as polyhedral oligomeric silsesquioxane (POSS). POSS represents a silica caged structure with molecular weight close to 1 kg mol-1 and molecular size of 1 nm.In this dissertation, mixtures of poly(ethylene oxide)-block- acryloisobutyl polyhedral oligomeric silsesquioxane (PEO-POSS) and acryloisobutyl polyhedral oligomeric silsesquioxane)-block- poly(ethylene oxide)-block- acryloisobutyl polyhedral oligomeric silsesquioxane (POSS-PEO-POSS) with LiTFSI are studied. PEO provides good ion solvation and transport, while POSS increases the modulus. PEO-POSS/LiTFSI and POSS-PEO- POSS/LiTFSI microphase separate into distinct morphologies which are a strong function of volume fraction, chain length, salt concentration, and temperature that differ from the phase behavior of SEO/LiTFSI. We study the relationships between the morphology, salt concentration, shear moduli, crystallinity of the POSS block, and ion-transport using small/wide angle X-ray scattering, electron microscopy, ac impedance spectroscopy, chronoampotherapy and rheology. Experiments show that PEO-POSS/LiTFSI and POSS- PEO-POSS/LiTFSI tends to segregate more strongly with increasing temperature, opposite of SEO/LiTFSI. The morphology is strongly dependent upon the crystallization of the POSS block. Block structure and morphology both, in turn, effect the electrochemical properties and the limiting current density.

Advisor: Balsara, Nitash P
Minor, Andrew M
Grieving Labor: Maternal Bereavement, Race, and Gender

Although national crime rates have declined in recent years, African American and Latinx mothers still experience the homicide of a child twice as often as White mothers. Unlike much of the scholarship that describes grief as a universal experience, my work shows how economic, racial, and gender inequities compound and complicate bereavement for historically minoritized groups. My dissertation draws on data collected between 2012 and 2018 in Oakland and Salinas, California and Chicago, Illinois. During this time, I partnered with several community organizations advocating for families impacted by violence. I organically grew closer to four mothers who had lost children to homicide and who became the key participants in my study: Anjanette Albert, Demitra Barnes, Debbie Aguilar, and Princess Beverly Williams. This small sample size of Black and Latina mothers allowed me to observe variation in mothers’ bereavement processes closely. In four case studies, we see how surviving mothers endure at least two forms of symbolic violence. Firstly, they are burdened with sanitizing their children’s public representations, which appear as one-dimensional or criminal or both. Secondly, maternal grief is commodified by members of the media, the not-for-profit industrial complex, and political apparatus for personal and professional gain. Materially, these participants’ labor is exploited, and the stress they experience because of being overworked and underpaid exacerbates the negative symptoms of their already-complex trauma. Mutual aid, nurturance culture, and grief therapy provide frameworks with which to envision new ways of responding to racialized and gendered violence. As the experiences of all the mothers in this study illustrate, it is only by being nurtured and cared for by others that we move through grief.

Advisor: Rodriguez, Juana Maria
Part I. A Concise Total Synthesis of Garsubellin A Part II. Synthetic Studies towards Acutumine Alkaloids

In this two-part dissertation, several different strategies are developed to attempt concise synthesis of complex natural products. In the first part, a concise total synthesis of garsubellin A, is reported. Starting from commercially available 2-methyl cyclopentenone, this synthesis of garsubellin A was enabled by a series of powerful C-C bond forming reactions, including a tandem oxy-Cope/methylation reaction, a diketene annulation, a ring expansion reaction and a novel regioselective prenyl coupling reaction. Meanwhile, a novel palladium catalyzed Wacker-type oxidation was developed to construct the characteristic tetrahydrofuran ring of garsubellin A. As we hoped this synthetic strategy could serve as a modular synthetic solution of diverse PPAP meroterpenes, an enhanced substrate scope of the diketene reaction was reported./nIn the second part of this dissertation, our synthetic studies of acutumine is described. In this chapter, a background introduction is first given, including the isolation and structure determination of acutumine alkaloids, biosynthetic studies, bioactivates of acutumine family, and the prior synthetic studies of (–)-acutumine. Meanwhile, several different strategies for achieving a concise total synthesis of (–)-acutumine were developed and discussed in this dissertation. A novel [3+2] cyclization protocol was developed, which, in three steps, converts commercially available starting materials to a [3.3.0] aza-bicyclic intermediate. From this advanced bicyclic intermediate, a series of efforts to transfer this advanced bicyclic intermediate to (–)-acutumine was explored and reported.

Advisor: Maimone, Thomas J.