VictorJuiz/thesis huggingface dataset:
Nanomaterial design via ALD : new methods and applications in catalysis

Producing chemicals and liquid fuels from renewable carbon monoxide and hydrogen (syngas) is a key route towards an environmentally sustainable economy. Alcohols beyond methanol are key targets for fuel and chemical production; however despite almost a century of research, there are no industrially appropriate catalysts for the direct formation of these compounds. New methods are needed to synthesize catalysts for higher alcohol production from syngas. Atomic layer deposition (ALD) is one such synthetic strategy. In this thesis, a new method for ALD nanoparticle synthesis was developed that can be used to prepare catalysts. Using oxygen gas as the co-reactant, area-selective ALD of metal oxides by metalorganic precursors that typically reactive strong oxidants to proceed was achieved selectively on noble metal surfaces by exploiting the catalytic dissociation of oxygen molecules at the metal surface. To explore metal alloy catalysts for syngas conversion, CoZn and PtCo catalysts were synthesized through a combination of traditional wet synthesis and ALD. During synthesis, the number ALD cycles was tuned to optimize catalytic performance with precise control. These catalysts had greatly improved selectivity for the alcohols during syngas conversion. By performing in-situ measurements of CoZn at high pressure, it was discovered that the presence of Zn leads to Co2C formation during catalyst operation. The resulting Co2C was found to be critical in alcohol formation on these catalysts. Beyond CO, CO2 is an emerging feedstock for renewable chemical production. New CoGa catalysts were synthesized for CO2 hydrogenation. The Co:Ga ratio was found to play a critical role in the selectivity, with increasing Co content favoring methane production and increasing Ga content favoring dimethyl ether production.

Keywords: Chemistry.
Advisor: Bent Stacey 
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Kanan Matthew William
Nanophotonics for enhanced solar efficiency, electrostatic screening, and polarization control

Nanophotonics offers a variety of applications including renewable energy, telecommunication and electronics. This thesis explores optical and electrical aspects of nanophotonic devices in three different areas: enhancing the efficiency of solar cells, controlling electrostatic screening using metamaterials, and manipulating polarization with dielectric chiral metamaterials. As the first area, a combined optical and electrical analysis is developed for nanophotonic solar cells. The analysis is applied to two types nanophotonic structures: nanostructured films and nanowires. Such a combined analysis approach is critical for nanophotonic solar cells as they typically have large absorption enhancement but more recombination losses. This combined analysis determines the current and voltage characteristics simultaneously and computes an upper bound on the efficiency while incorporating the fundamental losses due to Auger and surface recombinations. Moreover, an analytical model is introduced, which simplifies the analysis and is used in place of electrical simulations. The second area investigates electrostatic screening in metamaterials. Electrostatic behaviors of metamaterials have not been studied before, and in order to demonstrate different kinds of electrostatic responses, two classes of metamaterials (cubic arrays and wire media) are studied in the electrostatic limit. While cubic arrays are described by a local dielectric function and have a relative permittivity constant like dielectrics do, wire media are described by a nonlocal dielectric function that gives rise to an exponentially decaying electric potential like in bulk metals. The properties of electrostatic screening in both classes of metamaterials are determined by the geometrical parameters of metamaterials, which shows that metamaterials offer geometrical control of electrostatic screening and, therefore, the Coulomb interaction. In the third area, dielectric helices are shown to exhibit strong circular dichroism and to have polarization stop gaps for light propagating perpendicular to helices. Band structures and reflectance spectra are used to illustrate such effects. Perturbation theory is applied to give a quantitative reasoning of how the effects emerge. These effects enable a practical application as a chiral mirror, which completely reflects normally incident light of one circular polarization while preserving the handedness of polarization.

Keywords: Electrical Engineering.
Advisor: Fan Shanhui
Harris J. S. (James Stewart)
Vuckovic Jelena
Nanoscale membrane structure : from lateral organization to proton permeability

Membranes composed of lipids and proteins are universal features of living organisms. These layers that are only a few nanometers thick differentiate between life and death for cells. Despite the importance of biological membranes in compartmentalizing cellular space and separating the cell from its surroundings, many aspects of membrane structure and functional organization remain a mystery. The plasma membrane of mammalian cells contains thousands of different membrane proteins and thousands of different lipid species, and the absolute and relative amounts of these components are tightly regulated. Given this dizzying molecular complexity, how these molecules are functionally organized to optimize biochemical processes that occur at the membrane remains poorly understood. In addition to this complexity, non-mammalian cells contain structurally exotic lipids, whose physical properties and functions in their membranes remain unexplored. This thesis describes my work on elucidating the structure and biophysics of lipid membranes and the functional consequences of membrane structure. I have applied biophysical characterization techniques, imaging mass spectrometry, and chemical synthesis to address these questions. I take a reductionist approach and utilize model membranes and single cell analysis to unravel the complexities of biological systems. I will first describe the development of new methods for using nanoscale secondary ion mass spectrometry (NanoSIMS) to measure the distance between isotopically labeled molecules in lipid bilayers. I take advantage of a process called atomic recombination, in which atoms in sample from different molecules rearrange to form secondary ions when bombarded by a high energy ion beam. This process depends on the distance between the molecules and can therefore be used to measure the distance between the molecules. After benchmarking this new method, I use it to show that there are nanoscale lipid clusters in bilayers that had previously been observed indirectly or not at all. I then describe recent results from the structurally unique ladderane lipids, which are exclusively found in bacteria that perform anaerobic ammonium oxidation (anammox). The biological role of these lipids and biophysics of membranes containing them are unknown due to a lack of pure lipids. We approach this problem by synthesizing the natural lipids and unnatural analogs and performing structure-function studies. These experiments reveal an anomalously low proton permeability for ladderane bilayers, suggesting a role for ladderane lipids in preventing the breakdown of transmembrane proton gradients. We further explore the structure-function relationships between lipid molecular structure and resulting lipid bilayer structure.

Keywords: Chemistry.
Advisor: Boxer Steven G. (Steven George)
Burns Noah
Cegelski Lynette
Narratives of detachment and literary transculturation : Catalan exiles in Mexico

In 1939, due to Franco's victory in the Spanish Civil War and the fall of the Second Spanish Republic, hundreds of thousands of citizens had to emigrate from the country and find refuge in different parts of the world. Among them, a group of writers went into exile in Mexico, after being incarcereted in inhumane concentration camps in France. This dissertation is a study of narrative works written by Agustí Bartra (1908-1982), Viçens Riera Llorca (1903-1991), Avel·lí Artís-Gener (Tísner) (1912-2000), Pere Calders (1912-1994), and Lluís Ferran de Pol (1911-1995), inspired by their decades-long Mexican exile. In my analysis, I demonstrate that just as the authors crossed the national border, the literature they wrote in exile crosses multiple boundaries, including those of language, identity, and literary traditions. Through their writings, the Catalan authors did the opposite of what the Franco regime sought to do with them: instead of persecuting and annihilating difference, they embraced it and let it live.

Keywords: Iberian and Latin American Cultures.
Advisor: Resina Joan Ramon 
Hoyos Ayala Héctor 
Ruffinelli Jorge
Nartshell: A Time Travel Journey for Creativity in Art

Creative skills and creative confidence in problem-solving efforts are demanded in all fields, from art, literature to STEM fields. Research shows that art education is strongly connected with creative skills and creative confidence development, but oftentimes students have limited access to creative art resources and personal attention in art curriculum at school (Davies, 2000; White, 2018). Learning opportunities outside of classrooms like drawing apps claim to foster creativity in children. However, most of these apps only focus on teaching artistic techniques, rather than utilizing learning mechanics to reinforce the creative aspect of art. Without quality learning experiences in or outside of school, students in underserved communities are left behind in developing their creativity and confidence.
Nartshell is a browser-based digital game that offers students a safe space to take creative challenges with adaptive difficulty and personalized feedback. Nartshell is a virtual world where students can travel around to learn from game characters that are based on famous artists (e.g., Andy Warhol). Students explore art challenges in order to unlock art tools and cities on the virtual map. They can use the art tools later to create their own paintings. Preliminary tests indicated that learners performed more creatively in art challenges when receiving art-tool rewards, and felt more positive about their accomplishments when receiving constructive feedback. The game can be accessed by any student for free on a website. In future, the game will be introduced to students by collaborating with schools, daycare centers, afterschool programs and local public libraries in underserved communities.

Keywords: Creativity
creative confidence
art education
Thesis
Nearly-Kähler 6-manifolds of cohomogeneity two : local theory

We study nearly-Kahler 6-manifolds equipped with a cohomogeneity-two Lie group action for which each principal orbit is coisotropic. If the metric is complete, this last condition is automatically satisfied. We will show that the acting Lie group must be 4-dimensional and non-abelian. We partition the class of such nearly-Kahler structures into three types (called I, II, III) and prove a local existence and generality result for each type. Metrics of Types I and II are shown to be incomplete. We also derive a quasilinear elliptic PDE system on a Riemann surface that nearly-Kahler structures of Type I must satisfy. Finally, we remark on a relatively simple one-parameter family of Type III structures that turn out to be incomplete metrics cohomogeneity-one under the action of a larger group.

Keywords: Mathematics.
Advisor: Mazzeo Rafe 
Schoen Richard (Richard M.) 
Bryant Robert L.
The needfinding machine

This thesis develops and evaluates a method for allowing designers to perform needfinding by remotely interacting with users in real-time through computer-enabled interactive devices. While interactive systems present new opportunities for creating intelligent products that adapt to their users, these devices may also help designers understand people's needs by providing a view into users' everyday experiences. This thesis asks: how can designers use interactive devices to connect with users to receive information and feedback about their in-context experiences with interactive products? To answer this question, I develop the Needfinding Machine. Using the Needfinding Machine method, a designer in-the-loop observes the user, asks questions through an interactive machine, and remotely performs the machine's behaviors in real-time as a way to conduct problem-space exploration in-context. This thesis has four major components. Part one gives an overview of the Needfinding Machine and situates the method among other design methods for understanding people and their needs. Part two presents a lab-based study exploring how we can use machines that speak to elicit meaningful information from people. I then move out of the lab and evaluate how practicing designers can use a needfinding machine to understand their users. Part three develops a needfinding machine for use in automobiles called WoZ Way. I then discuss a case study with designers from Renault using WoZ Way to understand driver experience with currently available advanced driving assistance features. Finally, part four presents a case study with an interaction research team from Spotify using a needfinding machine I developed, called DJ Bot, to explore people's experience with music in two contexts, the car and the home. These projects present a proof-of-concept for using interactive devices for real-time remote needfinding and describe how designers can engage with the Needfinding Machine method.

Keywords: Mechanical Engineering.
Advisor: Ju Wendy
Leifer Larry J. 
Hinds Pamela 
Landay James A.
The neural basis of tactile attention

Spatial tactile attention is the ability to improve the processing of tactile stimuli at particular, attended, parts of our body. In order to investigate the neural and behavioral characteristics of spatial tactile attention, we combined measurements of tactile sensory regions using functional magnetic resonance imaging, with a novel tactile behavioral paradigm that included an attentional manipulation. We find an improvement in amplitude discrimination performance when a cue directs attention to a particular hand, and a corresponding increment in neural activity in the primary and secondary somatosensory cortices contralateral to the attended hand. Taking inspiration from the literature on visual attention, we consider whether the observed behavioral and cortical changes are more likely to be caused by a change in processes to do with the selection of stimuli (operationalized as an offset in neural activity), or if they are instead the outcome of a change in sensitivity to stimuli (operationalized as a change in the gain of the stimulus drive). We find that both behavioral and neural data are most consistent with the selection (neural offset) hypothesis. This is consistent with findings with functional imaging in the visual attention literature, suggesting that mechanisms for allocating spatial attention in sensory regions of cortex might be similar across sensory modalities. The implications of these results are considered in light of previously documented inconsistencies between functional imaging and electrophysiological measurements in the visual attention literature.

Keywords: Psychology.
Advisor: Gardner Justin
Norcia Anthony Matthew
Wagner Anthony David
Neural dynamics of motor preparation and tools for large scale neuroscience

A central goal of systems neuroscience is to relate an organism's neural activity to behavior. Current state of the art experimental methods are limited both in the capability of recording from large populations of neurons simultaneously, as well as in the complexity of the behaviors studied. In this work, I describe the development of new tools and methods for recording from large populations of neurons in rhesus macaque nonhuman primates (NHP). In addition, I describe the development of a haptic robotic interface to implement more complex motor tasks. I use this apparatus to study how short timescale adaptation to dynamic loads alters neural preparatory activity in premotor and primary motor cortices prior to movements. Chapter 1 provides an introduction and in-depth overview of the work covered in the remaining four chapters of this dissertation. Chapter 2 describes efforts to estimate neural population dynamics using multiunit threshold crossings in place of well isolated single units, which potentially eliminates a time consuming, difficult, and inexact portion of data analysis that serves as bottleneck for discovery. In Chapter 3, I describe the development of two-photon calcium imaging for rhesus macaque monkeys performing motor behaviors and the implementation of an optical brain machine interface (oBMI). In Chapter 4, I describe the development of techniques for using high-density silicon electrodes, such as the Neuropixels probe, in NHP. Lastly, in Chapter 5, I describe the development of a haptic experiment in which we introduce a simulated drag force and investigate the impact of short timescale adaptation to these dynamic loads on motor preparation.

Advisor: Shenoy Krishna V. (Krishna Vaughn) 
Clandinin Thomas R. (Thomas Robert)
Ganguli Surya
Newsome William T.
Neural ensemble dynamics in behaving animals : computational approaches and applications in amygdala and striatum

The brain must integrate many sensory signals and decide appropriate actions to take given prior knowledge and the current state of the world. Many fundamental questions remain about how exactly neural circuits perform these critical functions. A confluence of novel technologies is allowing neuroscientists to address these old biological questions and ask new ones, but has also led to new challenges in handling and analyzing large-scale neural datasets. In this dissertation, I conducted a series of studies that give novel insights into the neural coding of pain, rewarded actions, and locomotion along with new and improved computational methods for analyzing large-scale calcium imaging datasets. First, I studied how the rodent amygdala codes for pain, demonstrating that a specific neural ensemble codes for noxious stimuli and that a subset of this ensemble is stable across days to weeks. I then show that heightened behavioral responses after nerve injury parallel alterations in the neural pain code and we find that this neural ensemble is necessary to produce certain pain behaviors. Next, I demonstrate enhanced analysis and development of methods for calcium imaging cell extraction and automated cell classification. Finally, in a pair of studies, we apply large-scale calcium imaging techniques in two genetically defined neuronal populations in the mammalian striatum to detail the ensemble neural codes used for action initiation in a learning paradigm and locomotion during spontaneous behavior. Taken together, this dissertation provides new insights into pain and action selection along with powerful examples of how large-scale optical and computational methods can broaden our understanding of neural circuits.

Keywords: Biology.
Advisor: Schnitzer Mark Jacob
Chen Xiaoke
Malenka Robert C.
Scherrer Gregory 
Yamins Daniel
Neural mechanisms underlying spatial navigation and memory

An animal's survival depends intimately on its ability to navigate the environment. While the neural processes underlying spatial navigation have long intrigued scientists, only recently have we begun to understand how external sensory inputs are integrated into a mental representation of space. In the first of three sections in this thesis, I introduce two of the main classes of cells fundamental to generating this internal map: 'place cells' in the hippocampus and 'grid cells' in the medial entorhinal cortex. The discoveries of each cell type brought about experimental and computational efforts to uncover the mechanisms underlying their precise spatial coding. In the first section of Chapter 1, I review recent discoveries into the mechanisms governing the formation of place cells, while focusing in particular on the role of input from grid cells to provide background for my main experimental project, detailed in Chapter 2. Additionally, I hope to bring a new perspective into discussions of place cell formation by highlighting how newly discovered heterogeneity in the genetic profiles, biophysical properties and connectivity of hippocampal pyramidal neurons supports place cells' diverse functional coding properties. I then describe the prevailing model of grid cell formation and recent experimental manipulations probing the role of grid cells in behavior to provide context for the insights into these topics uncovered by my own experimental findings. Chapter 2 contains the primary research project that I conducted during my Doctoral training. This work involves several components, each of which make new contributions to the topics outlined above. First, using a combination of electrophysiological recordings and a viral-mediated knockout strategy, I determined that the scale of grid cell representations is modulated by HCN1 channels in the entorhinal cortex. This discovery has key implications for models of grid cell formation. Moreover, it afforded me the unique opportunity to investigate the roles of grid scale in downstream hippocampal place coding and spatial memory. I found that specifically increasing grid scale leads to parallel increase in the scale of place cell representations. While prominent models of place cell formation had long predicted this result, demonstrating it conclusively was only made possible by the discovery of a means to alter grid scale without impacting other types of spatially modulated cells. Surprisingly, increasing grid scale also reduced the long-term stability of place maps. In this chapter I describe the results from a computational model that we developed to help explain mechanistically how grid scale may play this unexpected role. I also describe the impact of increasing grid and place representations on a behavioral task requiring the formation of new place memories across days. Lastly, in a final section (Chapter 3), I discuss insights gained from my experimental findings and future directions that arise from the work presented in this dissertation.

Advisor: Giocomo Lisa
Hestrin Shaul
Huguenard John 
Raymond Jennifer L.