VictorJuiz/thesis huggingface dataset:
Electrospun Direct-write Multi-functional Nanofibers

Multi-functional fibers by means of direct-write near-field electrospinning process have been developed for versatile applications on a wide variety of substrates, including flexible ones. Several maskless lithographoy techniques have been established by using the direct-write fibers in dry etching, wet etching and lift-off processes. By selecting the proper functional materials, electrospun direct-write fibers have been demonstrated in prototype working devices, such as large array piezoelectric nanogenerators made of polymeric PVDF (Polyvinylidene fluoride) and direct-write micro heaters made of metallic copper nanoparticles./nIn the first example, continuous yet uniform PVDF fibers have been electrospun on a flexible substrate. A post, electrical poling process has been introduced on electrodes with PDMS (Polydimethylsiloxane) as the filling media to achieve an electrical potential of 2×10^7 V/m. In the prototype device, 500 energy harvesting points formed by 50 pairs of fibers and 10 pairs of comb-shape electrodes have generated about 30nA of electrical current on a flexible substrate under an estimated strain of 0.1%. Both FTIR (Fourier Transform Infrared Spectroscopy) and XRD (X-Ray Diffraction) have been utilized to characterize the electrospun fibers and good beta-phase formation, an essential property for piezoelectricity, has been confirmed./nFor the next example, electrospun direct-write fibers have been employed to show three maskless lithography techniques; lift-off, wet-etching and dry-etching. These include the demonstration of sub-micrometer wide gaps between a thin metallic gold film using the lift-off process; 20um-wide, 20mm-long lineshape micro heaters made of 30nm-thick copper film by a wet-etching process; and a 2um-wide, 10um-long graphene channel FET (Field Effect Transistor) via a dry-etching process. Electrospun PEO (Polyethylene oxide) fibers have been utilized in the aformentioned processes which has shown strong adhesion to the Kapton substrate, robust chemical resistance to wet copper etchant and good resistance to oxygen plasma for the related lift-off, wet etching and dry etching processes, respectively. Experimentally, a fabricated copper micro heater has reached 92°C under an input power of 37mWatt. The graphene-based channel FET on 285nm-thick gate dioxide has 30uA of current under 1V of applied bias voltage while the gate voltage sweep has shown Diract point at +21V./nIn the final demonstration example, electropun direct-write conductive copper wire has been constructed on top of a glass substrate. Copper dinitrate and PVP have been tested as the best polymer mixture for the electrospinning process. A two-step post annealing process has been developed to decompose the polymer and reduce copper oxide to copper for good conductively. The prototype copper wires are 20~100um in length and 500nm in height with an average measrued resistivity of 5.6×10-6Ohm*m from tested 25 samples. As such, electrospun direct-write fibers could find potential applications in various fields, including low-cost electronics.

Advisor: Lin, Liwei
The Role of microRNAs in Olfactory Regeneration

The mammalian main olfactory epithelium is the sensory tissue dedicated to detecting volatile chemical odorants that contribute to our social and natural environment. Natural neuronal turnover throughout adulthood and the ability to regenerate large amounts of damaged tissue are unique properties of the main olfactory epithelium in adult mammals. Independent stem cell populations are activated to give rise to two distinct modes of neurogenesis: transit amplifying globose basal cells maintain homeostatic neuronal turnover while horizontal basal cells enter the cell cycle and regenerate all cell types of the OE upon severe injury. Recent evidence has pointed toward the role of specific miRNAmRNA interactions in the regulation of stem cell self-renewal and differentiation/nThe ability to observe these two modes of adult neurogenesis in vivo,/nhomeostatic maintenance and regeneration after severe injury, makes the main/nolfactory epithelium an excellent model in which to study the molecular regulation/nof stem cells as they enter the cell cycle and differentiate into mature neuronal/nprogeny. However, to fully understand the mechanisms regulating these/nprocesses it is imperative to elucidate both the nature and extent of these/ninteractions at the genome-wide level. Our work in profiling the horizontal basal/ncell transcriptome provides supporting evidence that a large portion of the/ntranscriptome may be regulated by miRNA mediated repression, which acts by/nreinforcing an undifferentiated state. Genetic ablation of miRNA biogenesis/nmachinery shows that miRNA are necessary to repress aberrant cell cycle reentry/nand may promote the expression of the stem cell maintenance gene/nTransforming protein 63./n1

Advisor: Ngai, John
Prescribed Mean Curvature Systems

Let (M,g) be a Riemannian manifold of dimension greater or equal to 3, and let Sigma in M be/nan immersed hypersurface with prescribed mean curvature. I study the geometry of Euler-Lagrange equations in this particular context. This includes a characterization of those prescribed mean curvature systems that are Euler-Lagrange, and I prove that these are locally conformally equivalent to basic systems. Finally, I study Emmy Noether's theorem for first-order conservation laws in the special case of minimal surfaces in Riemannian 3-manifolds. In particular, I am able to identify which conservation laws do arise from symmetries of the system in the sense of Noether and which ones do not.

Advisor: Bryant, Robert L
Development of Scaffolds for Light Harvesting and Photocatalysis from the Coat Protein of Tobacco Mosaic Virus

The utility of a previously developed TMV-based light harvesting system has been dramatically expanded through the introduction of reactive handles for the site-specific modification of the interior and exterior surfaces. Further experiments to reengineer the coat protein have produced structures with unique, unexpected, and useful assembly properties that complement the newly available surface modifications. Energy transfer from chromophores in the RNA channel of self-assembled TMV structures to the exterior was made possible by conjugation of acceptor dyes and porphyrins to the N-terminus. By repositioning the N-terminus to the pore through circular permutation, this process was repeated to create structures that mimic the light harvesting 1 complex of photosynthetic bacteria. To study and improve upon natural photosynthesis, closely packed chromophore arrays and gold nanoparticles were tethered to the pore of stabilized TMV disks through introduction of a uniquely reactive lysine. Finally, a dimeric TMV coat protein was produced to control the distribution and arrangement of synthetic groups with synergistic activity.

Advisor: Francis, Matthew B
The Far Reach of Megathrust Earthquakes: Evolution of Stress, Deformation and Seismicity Following the 2004 Sumatra-Andaman Rupture

Starting with the 2004 Mw 9.2 megathrust event, Southeast Asia has been home to an exceptional amount of seismic activity over the past eight years. The series of megathrust earthquakes have been imperfect dominoes, rupturing the northernmost section of the Sunda subduction zone in 2004, then the Nias segment next in line to the south in 2005, followed by the Bengkulu earthquake ∼750 km further south in 2007. The Bengkulu earthquake skipped over the northern Mentawai segment, which has not ruptured in a great event since 1797. However, the subduction zone has not been silent is this section. Analysis of focal mechanisms and geodetic data reveals the reactivation of the Mentawai backthrust system in the overriding plate, and a large, deep earthquake near the city of Padang in 2009 is shown through finite fault inversions and aftershock analysis to have obliquely ruptured the subducting slab. At the same time, the entire region spanning from the Indian Ocean, through the trench and forearc islands, and throughout Thailand has been aseismically deforming in response to the stress changes in the mantle following the megathrust earthquakes. Geodetic observations of postseismic deformation during the first five years following the 2004 earthquake have shown that the far-field regions of Thailand and the Malay Peninsula have moved more postseismically than coseismically, peaking at ∼0.4 m of horizontal displacement in Phuket. In 2012, the stress changes associated with this continued postseismic deformation, along with the initial push from the megathrust earthquakes, appears to have triggered the largest instrumentally recorded strike-slip earthquake. This was a complex earthquake, consisting of four conjugate fault segments, that ruptured the diffuse India-Australia plate boundary zone. Understanding how the faults interact throughout the subduction system, from the incoming plate, to the slab, to the megathrust interface, and overriding plate is an essential part of determining the future seismic hazard for Southeast Asia.

Advisor: Burgmann, Roland
Partnerships for Community Benefit: Exploring Non-Profit Health Systems as Corporate Citizens in the Communities They Serve.

The introduction of the IRS Form 990 Schedule H and the 2010 Patient Protection and Affordable and Care Act (ACA) has challenged not-for-profit (NFP) health systems and hospitals to reassess the charitable practices that afford them tax-exemption. Many NFP health systems have been prompted to reexamine their roles, contributions, and impact in the communities they serve. These organizations have begun to explore alternative means to plan and strategically provide community benefit. As the regulatory landscape changes, the decision-making of leadership around community engagement may call for more transparent community engagement and efficient strategies that target specified needs. This will ultimately affect the goals and types of partnerships that are formed with various community stakeholders./nThis research examines how large not-for-profit health care delivery systems establish partnerships aimed to improve community health. It is an exploratory project that examines the types of partnerships that these organizations engage in at system and hospital levels to affect the social and environmental conditions of their communities. Case studies were built around three different types of partnerships implemented by NFP health systems and hospitals through their projects and programs with community stakeholders. Each case study analyzed what took place before and while NFP health providers implemented partnerships directed toward community health. Through cross-case analysis, the degree to which principles of community-based public health and corporate social responsibility factor into the form, structure, and purposes of those partnerships were assessed./nBased on qualitative and quantitative data, four key characteristics were found to be consistent across the three partnership strategies examined. The findings emphasize the importance of purposeful strategic planning that is aligned with an organization's mission and responsive to its market environments. They also highlight the value of stakeholder engagement that is flexible, empowered, and sustained. I explore the implications of these findings in the context of the evolving policy and market landscapes shaped by new requirements of the IRS and the Affordable Care Act.

Advisor: Shortell, Stephen M.
Microengineered Platforms For Assessing Cell-Cell Communication And Single-Cell Influences On Adult Neural Stem Cell Fate

The signaling environment experienced by a single cell is highly dependent on its interactions with its neighbors, which may secrete locally acting factors or act via membrane bound receptor-ligand systems. Stem cells are particularly sensitive to these signals, which act in concert to regulate self-renewal and discrete transitions into distinct fates. In the case of the adult neural stem cell, decades of in vivo and in vitro work have illustrated specific roles for different types of niche cells and some of the molecular mediators of their instructive roles. However, these studies have not investigated the strengths of these fate-inducing or fate-repressing cues as presented by single neighboring cells at endogenous expression levels. In this work, we have developed and applied microengineered tools to examine the transmission of signals between small populations of cells and to assess their impact on neural stem cell fate./nFirst, we measured gap junction coupling between cells by using microfluidic flow focusing of calcein/AM dye and timelapse imaging to measure the dynamics of dye transfer through gap-junction coupled glioma cells. Secondly, we developed single-cell micropatterning methods to investigate the potential for single neural progenitor cells to influence their neighbor's fate. Size-matched circular and hourglass shaped polystyrene microwells achieved up to 80% efficiency in capturing single and paired neural progenitor cells, a large improvement over Poisson-distributed random seeding. In conjunction, we also developed a method to fabricate and align PDMS meshes to corral patterned cells into non-connected arenas so that single cells and cell pairs can be grown in isolation for six days before immunostaining for fate markers. Lastly, we applied a simplified micropatterning technique in conjunction with automated high-throughput imaging to enforce persistent interactions between initially patterned cells. We discovered that single neural progenitor cells can significantly bias their neighbor's fate in mixed differentiation medium. Although the initial number of cells on a pattern did not affect the overall distribution of different fates, we saw reduced fate asymmetry on patterns with initially paired cells, indicating that single cells may be inducing a similar fate in their neighbors, or repressing differentiation. By tracking cell populations on micropatterns on every day of the experiment via brightfield imaging, we also ascertained that the initial patterning state was maintained for approximately two days, suggesting that fate specification or repression occurred early in the process. Our discovery that a single as-yet undifferentiated neural stem cell can significantly bias its neighbor's fate paves the road for future work in elucidating how conflicting signals from various types of niche cells are arbitrated in a single recipient stem cell.

Advisor: Maharbiz, Michel M
An Optimized Video-on-Demand System: Theory, Design and Implementation

Internet on-demand video traffic has seen explosive growth in recent years. This brings a number of challenges in deploying video-on-demand services at large scale. The first challenge has to do with the enormity of the video catalog size. Traditionally, content providers replicate the entire video library in different locations, but this is wasteful and non-scalable as the video catalog size expands. The second challenge comes with the increase in video quality, which calls for efficient utilization of the scarce network bandwidth resources that continue to be economically expensive to expand. The emergence of different device modalities, including smart-phones, high-definition and 3D TV, tablets and etc poses another challenge in designing efficient systems and algorithms that cater to all device characteristics and user needs./nIn this dissertation, we aim to present a general approach to designing, optimizing and architecting a video-on-demand system. Our approach considers the practical constraints of disk space, network link bandwidth, and node connection degree bound. In general, the joint optimization problem is combinatorially difficult. To tackle this, we first design a simple fractional storage architecture, which uses a class of regeneration codes that fluidifies the content, thereby enabling a distributed content placement and link rate allocation algorithm. We show that by storing only a fractional of the entire catalog everywhere, the system is able to fully support user demand at large scale. Second, we develop a Markov approximation technique to solve the problem of topology selection under node degree bound using a simple distributed algorithm. We prove that our algorithm achieves close-to-optimal solution, which we verify using extensive realworld trace simulations./nOn the system side, we show extensive results to test the algorithm's scalability and robustness to changes in user dynamics and demand patterns. We show that our solution achieves high utilization of cache nodes storage and bandwidth resources, and automatically learns and caches the video according to the demand patterns. We observe that there exists a complex interplay between disk space, network bandwidth and node degree bound. We also present guidelines to important practical design choices including caching update intervals, demand prediction and provisioning. We also demonstrate the feasibility and efficiency of our design choice by building and experimenting a prototype system at Berkeley.

Advisor: Ramchandran, Kannan
Parekh, Abhay
Photonic Design: From Fundamental Solar Cell Physics to Computational Inverse Design

Photonic innovation is becoming ever more important in the modern world. Optical systems are dominating shorter and shorter communications distances, LED's are rapidly emerging for a variety of applications, and solar cells show potential to be a mainstream technology in the energy space. The need for novel, energy-efficient photonic and optoelectronic devices will only increase. This work unites fundamental physics and a novel computational inverse design approach towards such innovation./nThe first half of the dissertation is devoted to the physics of high-efficiency solar cells. As solar cells approach fundamental efficiency limits, their internal physics transforms. Photonic considerations, instead of electronic ones, are the key to reaching the highest voltages and efficiencies. Proper photon management led to Alta Device's recent dramatic increase of the solar cell efficiency record to 28.3%. Moreover, approaching the Shockley-Queisser limit for any solar cell technology will require light extraction to become a part of all future designs./nThe second half of the dissertation introduces inverse design as a new computational paradigm in photonics. An assortment of techniques (FDTD, FEM, etc.) have enabled quick and accurate simulation of the "forward problem" of finding fields for a given geometry. However, scientists and engineers are typically more interested in the inverse problem: for a desired functionality, what geometry is needed? Answering this question breaks from the emphasis on the forward problem and forges a new path in computational photonics. The framework of shape calculus enables one to quickly find superior, non-intuitive designs. Novel designs for optical cloaking and sub-wavelength solar cell applications are presented.

Advisor: Yablonovitch, Eli
Watering the Desert: Environment, Irrigation, and Society in the Premodern Fayyum, Egypt

Through a study of its natural environment and irrigation system, this dissertation investigates the evolution of the landscape of Egypt's Fayyum depression across sixteen centuries, from the third century BCE to the thirteenth century CE. From the evidence of Greek papyri, Arabic fiscal documentation, early modern travel literature, archaeology, and contemporary scientific work, I chart the changes in human relationships with earth and water over time, changes which constantly altered the inhabited and cultivated regions of the Fayyum. My main argument throughout is that it was local agency and not state governments that continuously remade the landscape./nThe history of the Fayyum after the fourth century CE has long been viewed by ancient historians as one of decline from its ancient heights due to the failure of the late Roman and Muslim successor states to properly manage its irrigation system. I locate the genesis of this narrative within nineteenth century perceptions of the docility of nature and the belief that ancient governments had achieved centralized control over the Nile and the Egyptian environment. This anachronistic retrojection of the characteristics of the modern irrigation system has had a considerable afterlife in historical scholarship on Egyptian irrigation./nEschewing a narrow focus on the state, this dissertation argues that that nature is a potent agent in its own right. Ancient farmers could not control nature so they adapted to it, creating four distinct irrigated sub-regions in the Graeco-Roman Fayyum, each tailored to the particulars of the local environment. Our papyri stem from only one of these sub-regions, the water-scarce margins, which lay at the tail end of the irrigation system. Here, inadequate irrigation and fertilization progressively led to soil salinization and degradation, which helped to spur the eventual abandonment of these areas. By the medieval period, only the central floodplain remained inhabited. Only here was sustainable agriculture under the regime of premodern technology possible./nAlthough the Roman state coordinated local labor on the canals, nothing could bind Fayyum villagers to the degrading margins in perpetuity. Fourth century papyri hint that some cultivators had moved to other nomes and were prospering. Still later documents of the sixth to eighth centuries CE reveal greatly increased settlement density in the central Fayyum. Thus, it was local cultivators who made and remade the landscape of the Fayyum over the centuries according to their own needs. Government could both guide and benefit from this local labor but it could never fully control it.

Advisor: Hickey, Todd M.