VictorJuiz/thesis huggingface dataset:
Design and control of soft shape-changing robots
Keywords: Mechanical Engineering.

For robots to be useful in the real world, they must be human-safe, adaptable to different tasks, robust to uncertainty, and untethered from external power. Enabling these capabilities requires the codesign of both the physical robot and its controller. In this talk, I will illustrate this approach through the development of a large-scale, shape-changing, inflated soft robot. First, I will describe the control of robotic trusses, or robots that consist of many linear actuators connected at universal joints to form a shape-changing structure. Using techniques from rigidity theory, I present a kinematic model and control methodology that enables control of arbitrary structures. Then, I will demonstrate these controllers in practice for a new type of inflated truss robot called an "Isoperimetric" Truss Robot, or a truss in which the total edge length is conserved. In this case, the vertices of the truss-structure consist of robotic rollers that pinch inflated fabric tubes that comprise the robot's structure, inducing effective joints. The robot changes its shape by driving the rollers along the tube, lengthening one edge and shortening another by moving the joint. As the overall edge length, and hence inflated volume, remains constant no tether to external air is required. The resultant robot can locomote with a punctuated rolling gait, grasp objects using its inherent compliance, operate safely around humans, and can be manually reconfigured based on its task. Last, I will present a distributed control framework for truss-like robots. In this framework each individual actuator utilizes local computation and communication to determine how to act individually to allow the overall robot to accomplish a task. Together these contributions allow for modular, human-safe robots that are capable of controllably changing their shape
Design and demonstration of on-chip integrated laser-driven particle accelerators
Keywords: Physics.

In this thesis, I present the first demonstration of a waveguide-integrated dielectric laser accelerators (DLA), designed using a photonic inverse design approach. I first review the operation of DLAs and describe how one can formulate a figure-of-merit for the optimization of these structures. I then briefly introduce the inverse design framework that allows for efficient free-form optimization of these structures, enabling search of a design-space that goes far beyond that of the tuning of a few geometric parameters. With an integrated accelerator design obtained, attention is turned to on-chip coupling methods for DLA applications. Here again, the inverse design framework is employed to produce broadband grating couplers. Experimental results of our single-stage on-chip integrated accelerator are shown, from which a maximum energy gain of 0.915 keV over 30 um, corresponding to an acceleration gradient of 30.5 MeV/m is inferred. Lastly, I explore new directions to reach higher on-chip acceleration gradients and larger energy-gain, including utilizing foundry fabrication for multi-stage accelerators
Design and fabrication improvements for the dielectric laser accelerators
Keywords: Electrical Engineering.

Accelerated particle beams have already played and will continue a growing role in the analysis and fabrication of commercially important products, particularly in the development of the next generation of electronics, advanced engineering and smart materials. Without accelerators, major advances in the biosciences of the past 50 years would not have happened, and future developments in accelerator technology will stimulate a better understanding of living processes, leading to new medicines and therapies. However, the size and cost of the conventional radio-frequency (RF) accelerators limit the wide distribution of the accelerator technology. Dielectric laser accelerators (DLAs) aim to shrink down the dimension of the RF accelerators by using near-infrared (NIR) ultrafast femto-second laser to drive dielectric structures as well as provide higher acceleration gradient. The driving wavelength for DLA is 1000X smaller than RF accelerators, which leads to 1000X smaller in accelerator dimension. Additionally, dielectric material, like silicon and silicon dioxide, can survive under one to two orders of magnitude higher energy compared with metal used in RF accelerators. DLA can provide acceleration gradient upwards of 1GV/m, compared to 30-100MV/m for RF accelerators limited by material damage. In this thesis, I will discuss the design and fabrication improvements for DLA in both sub-relativistic and relativistic regime. In the sub-relativistic regime, silicon pillars have been used as accelerators. Hydrogen annealing process can decrease the variation of laser induced damage threshold (LIDT) for silicon pillars, and also makes the damage site positions agree with corresponding field hotspots. A thin film of low-stress nitride coating on silicon pillars can improve LIDT by 27% and acceleration gradient by 11%. In the relativistic regime, eutectic bonding is applied in chip-level fused silica bonding to fabricate accelerators. Single grating /DBR design is proposed and fabricated to provide better symmetric acceleration gradient distribution and remove alignment requirement during bonding process. In order to move towards multi-stage integrated DLA, silicon nitride waveguide-based power delivery DLA is proposed and fabricated. Nitride grating coupler efficiency is measured to be 20.5% and damage at input pulse energy of 15nJ. These results enable the accelerators powered by on-chip couplers and waveguides
Design of a Current Source for Low-Power Electromagnet Excitation in Giant Magnetoresistive-based Biosensors
Keywords:  Department of Electrical Engineering
GMR
PCR
power
point-of-care
biosensor
Thesis

Rapid biomarker identification and detection at low concentrations in biological fluids opens the door to early-detection and treatment of not only chronic diseases that develop over many years, but also acute infectious diseases where rapid diagnosis is often a necessity. To enable rapid-testing, high sensitivity biosensors have to be moved to the point-of-care (POC). One of the most sensitive biosensors cited in literature are giant-magneto-resistive spin-valve (GMR-SV) biosensors. Proof-of-concept point-of-care GMR platforms have been developed but suffer from high power consumption and low in-field life-time. To transfer this GMR biosensor into a point-of-care setting for DNA detection it must be readily integrated with a method of DNA amplification, such as polymerase-chain reaction (PCR). PCR is also a very power-intensive process needed for sample preparation for sensing and analysis, further constraining the power budget of the GMR system and increasing the sizes, voltages, currents, and converter sizes for a deployable POC device. This honors thesis aims to significantly decrease the power consumption needed for the PCR-GMR POC platform by (1) decreasing the power budget needed for GMR-biosensor readout, (2) improving efficiency of on-board voltage conversion and regulation, and (3) exploring the feasibility and opportunity in integrating PCR and GMR into a single die using multi-physics simulations.
Design principles of green fluorescent proteins - Why are they green and fluorescent?
Keywords: Chemistry.

Since its discovery in jellyfish around the early 1960s, green fluorescent protein (GFP) and its derivatives have become the most widely used in vivo imaging tools for biological studies. Mutants of GFPs have been engineered to exhibit a palette of colors, wide range of fluorescence quantum yields (FQYs), and photoswitching characteristics, enabling advanced applications such as optogenetics and super-resolution microscopy. However, tailoring GFPs for specific purposes heavily relies on extensive screening and/or directed evolution as it is unclear how the protein environment modulates the photophysics of the chromophore in quantitative terms. Thanks to the semisynthetic split GFP method and the recently popularized technique for incorporating noncanonical amino acids (i.e., amber suppression), we created conventionally inaccessible GFP mutants with systematically altered electrostatic properties and/or steric bulk of the chromophore and the surrounding protein environment. Correlations between various photophysical properties of these mutants led to transparent models describing how the protein-chromophore interactions affect the chromophore's color and FQY. The models provide quantitative predictions for designing GFPs with desired phenotypes and infer physically imposed limitations. In addition, our finding of how electrostatics biases photoisomerization pathways in GFPs could shed light on the general phenomenon of bond-specific photoisomerization, a defining characteristic of the retinal chromophore within rhodopsins central to vision and important to the field of photoactive molecular devices
Designing bioinks for 3D bioprinting in gel-based support baths
Keywords: Materials Science and Engineering.

3D bioprinting has emerged as a powerful tool to pattern extracellular matrix (ECM) and living cells to produce biological structures that mimic native tissues and organs ex vivo. Bioinks, the cell- and ECM-laden mixtures used during bioprinting, have primarily been composed of biopolymers appropriated from traditional 3D tissue engineering to form hydrogels following printing. These materials are not particularly well suited to meet the challenges introduced through bioprinting, namely, cell sedimentation, mechanical damage while printing, printing in gel-based support baths, and tunability of the mechanics and bioactivity of the biopolymer hydrogels. New bioink materials can be produced through intentional design of the crosslinking scheme of the hydrogel network before and after bioprinting into a gel-based support bath. The work presented in this thesis explores the benefits of designing new bioink materials for 3D bioprinting that move beyond the simplest crosslinking strategies used in traditional tissue engineering materials. Specifically, bioinks that employ two different stages of crosslinking, a first-stage crosslinking before the material is printed and a second stage following printing in a bath, prove to be effective for 3D bioprinting. One example of the increased versatility of bioinks from a dual-crosslinking approach is a bioprinted stem cell expansion lattice for stem cell manufacturing made using a traditional bioink material, sodium alginate. The second half of this thesis introduces two new crosslinking schemes that are made possible only by bioprinting into a gel-based support bath. Both bioorthogonal and hydrazone dynamic covalent chemistries are explored for producing new bioinks. The work put forward in this thesis is a step toward designing new bioinks for 3D bioprinting. An array of crosslinking schemes for bioinks are presented alongside creative uses of existing biopolymers to produce more adaptable bioinks
Designing Embodied Dialogue Systems: A Way of Thinking about Character Conversation in Video Games
Keywords:  Symbolic Systems Program
RPG
Game Design
Sonification
Embodied Dialogue
Dialogue System
Symbolic Systems Program
School of Humanities and Sciences
Symbolic Systems
SYMSYS
Thesis

This thesis argues for a new way of thinking about designing engaging dialogue systems for video games. The proposed approach – called designing “embodied dialogue” systems – stands in contrast to and goes beyond designing traditional “descriptive” dialogue systems to create an intrinsically engaging moment-to-moment dialogue experience. On this basis, this work proposes three design principles for creating embodied dialogue systems, namely, such systems should be (1) expressive, (2) autonomy-inspiring, and (3) true to the underlying game genre. These principles are put into motion in a proof of concept game prototype called Embodied Dialogue; the ways in which the design approach shaped the game design are discussed in detail. This tangible instantiation of the proposed approach was qualitatively evaluated by play-testers as a way of assessing its initial effectiveness. Furthermore, the game itself serves as a critical exploration of embodied dialogue elements including strongly-timed audiovisual sonification of dialogue, audiovisual inner speech, and an expressive personality system. Overall, this thesis argues that designing embodied dialogue systems (and the various game elements that can be derived from using this approach) is a compelling way of thinking for creating more engaging video game dialogue systems.
Designing in situ interaction with ubiquitous robots
Keywords: Mechanical Engineering.

We are nearing an era of ubiquitous robots. They will be in our home doing our dishes and laundry, in our workplace helping us carry heavy loads and performing repetitive tasks, and on the road driving us to our destinations and delivering packages. Due to this wide variety of potential tasks, robots will take different forms, sizes, and numbers resulting in a diverse set of robots ranging from a humanoid robot, specifically designed for interacting with humans, to a swarm of small mobile robots, used to collectively gather information in a large unstructured environment. Of these, particularly important are swarms of centimeter-scale non-anthropomorphic robots. Their appearance and size enable seamless transition between blending into the environment, becoming "invisible" to the users, and doing everyday tasks such as object manipulation through collective means and interaction with users through their motion and touch. While roboticists have made great strides in enabling swarms to move objects and control formation, the topic of in situ human-multirobot interaction is crucial and timely, given the rise in interaction with a group of robots in our daily environment. My thesis centers on ubiquitous human-centered robotics that facilitate in situ interactions with people. I introduce the concept of Ubiquitous Robotic Interfaces (URIs), multi-robot systems that are capable of mobility, manipulation, sensing, display, and interaction both with the user and the environment. In order to better understand interaction with this new class of robots, specifically on how to enable robots to effectively interact and communicate with people, I develop new tabletop swarm robot platforms, design multimodal multi-robot interaction, and evaluate them through a set of human subject experiments. As non-humanoid robots lack anthropomorphic features that have been heavily relied upon for human interaction, I leverage a feature common across most, if not all, types of robots: mobility. Specifically, I study how to visually display information like expresssivenss and intent to users through multi-robot motion, and how to convey information through touch from the robots. Closing the loop, I also investigate how people naturally communicate with a swarm of robots. In summary, this thesis provides a deeper understanding of interactive ubiquitous robots as well as generating a rich set of guidelines to increase effective human-multirobot interaction
Determining the bacterial response to environmental stresses
Keywords: Microbiology and Immunology.

Bacteria are highly resilient to environmental insults due to their sophisticated abilities to adapt to diverse stressors. As a primary level of response, they carefully regulate thousands of genes in response to changes in their surroundings. Moreover, evolution can provide genetic enhancements to stress adaptation. Perhaps less appreciated are physiological adaptations, often occurring on short time scales that improve growth and survival in dynamic environments. Most experimental studies of bacteria are carried out in near ideal conditions for growth, which are ultimately poor replicas of the harsher natural environments in which cells typically exist. Expanding our knowledge of how bacteria function in inhospitable and dynamic environments is crucial to understanding and capitalizing on bacterial physiology. In this thesis, I provide multiple novel perspectives on physiological adaptation to stress in bacteria. Chapter 1 provides an introduction to the ways bacteria can adapt to environmental conditions and methods for measuring adaptation. In chapter 2, I investigate how starvation introduces heterogeneity in a populations of cells, in which different subpopulations exhibit vastly different potentials for growth. In chapter 3, I explore the genetic mechanisms by which bacteria adapt to a variety high osmolarity conditions in a long-term laboratory evolution experiment. Chapter 4 concludes with a summary of my work and a discussion of future directions with broad impacts for the microbiology field
Determining the Role of the Nlgn3 Mutation R451C on Myelin-forming Cell Dynamics in Autism Spectrum Disorders
Keywords:  Department of Biology
oligodendrocyte
myelination
neuroligin-3
Autism Spectrum Disorders
myelin plasticity
Thesis

Autism Spectrum Disorders (ASDs) are a broad spectrum of neurodevelopmental conditions with high prevalence but no effective therapy. Recently, mutations in the synaptic protein neuroligin-3 (Nlgn3) have been associated with ASDs, resulting in disrupted neuronal connectivity and altered neural circuit function. Although decreased white matter especially in the corpus callosum (CC) has been observed in patients with autism, the effect of autism-related mutations such as Nlgn3R451C on myelination by myelin-forming glial cells called oligodendrocytes has never been studied. Previous work has shown that this mutation leads to decreased Nlgn3 protein levels by 90% at the synapse, suggesting that it may disturb synapse formation between neurons and oligodendrocyte precursor cells (OPCs). In this work, we aim to determine how Nlgn3R451C alters myelination and OPC dynamics and to establish whether this mutation affects the adaptive proliferative response of OPCs to neuronal activity. Using immunostaining and fluorescence confocal microscopy in a conditional knock-in endogenous mouse model, this study reveals that Nlgn3R451C does not alter CC white matter volume. Furthermore, Nlgn3R451C is found to decrease the number of OPCs in white matter CC, but not in gray matter cortex, suggesting particular vulnerability for white matter OPCs. The OPC response to optogenetically increased neuronal activity shows unaltered proliferation despite potential disruption in neuron-to-OPC synapses in Nlgn3R451C. This study sheds light on the link between autism and myelin dynamics and establishes Nlgn3R451C-related myelin impairments that contribute to autism pathology.
Developing computational and experimental tools to understand chromatin dynamics and regulation
Keywords: Bioengineering.

The human genome is condensed yet accessible, allowing cells to execute complex logic needed for cellular programs. The dynamic physical organization of the genome is connected to its instantaneous transcriptional profile. Current sequencing technologies can only recover a static and highly-averaged picture of these dynamic processes. Identification of dynamic signatures from chromatin motion requires an imaging and analysis platform for simultaneous tracking of genes and their transcriptional state in live cells. Advances in microscopy have provided a great opportunity to obtain such information. Unfortunately, segmenting overlapping nuclei is still a major challenge for single cell microscopic measurement. We first reported a deep-learning based model 'Nuclear Segmentation Tool' (NuSeT) that accurately segments multiple types of nuclei from imaging data. Using a hybrid architecture that consists of U-Net and Region Proposal Networks (RPN), followed by watershed processing, NuSeT has achieved superior performance in delineating nuclear boundaries in images of varying complexities. NuSeT further improves nuclear detection and reduces false positives by employing foreground normalization and additional training on synthetic images containing non-cellular artifacts. NuSeT also addresses common bottlenecks in nuclear segmentation such as limited training samples, variability in nuclear signal and shapes, and sample preparation artifacts. NuSeT consistently fares better in generating accurate segmentation masks and assigning boundaries for touching nuclei compared with other state-of-the-art segmentation models. Next, we developed an imaging platform for simultaneous real-time visualization of locus dynamics and transcriptional output. Using a CRISPR/Cas9 based gene knock-in strategy, we have introduced MS2 hairpin cassettes into native genes of interest, which can reveal their transcriptional states. To track these loci for extended periods of time at high spatiotemporal resolution, we have generated optical tag ArrayG/N fusions of the nuclease deactivated Cas9 (dCas9) and a polycistronic cassette of repeating tRNA-sgRNA delivered by lentivirus. This platform enables sustainable tracking of non-repetitive genomic loci. We have further modified ArrayG/N tags to recruit chromatin effectors at selected genomic sites that makes this experimental platform particularly well suited for dynamic monitoring of epigenetic manipulations on selected genes. Using this platform, we have measured dynamic signatures of chromatin accessibility. We have also shown that the motion of gene loci are further constrained when they are transcriptionally active. These image analysis and cellular engineering tools can be used to answer other outstanding questions about the chromatin and gene regulation dynamics
Developing functionalized virus like particles for circulating tumor cell detection and enumeration
Keywords: Chemical Engineering.

Circulating Tumor Cells (CTCs) are released from a primary tumor and circulate in the vasculature to form seeds for metastatic colonization at distant locations. There is strong evidence for their use as prognosis markers to indicate the extent of disease progression in cancer patients. For example, the accurate enumeration of CTCs could provide a minimally invasive method to frequently monitor how the cancer responds to therapeutic interventions. Currently there is only one FDA approved CTC assay, CellSearch, but its clinical acceptance has been limited. We seek to develop a point-of-care assay that would detect CTCs based on tumor specific markers. As a model system, we are targeting prostate specific membrane antigen (PSMA), a glycoprotein that is overexpressed on a majority of metastatic prostate cancer cells. The Swartz Lab has developed virus-like particles (VLPs) derived from the Hepatitis B core protein. The VLPs have been stabilized by an engineered disulfide network and display a non-natural amino acid for precise surface augmentation. Using this VLP as a scaffold, nanoparticles (NP) have been developed that can specifically target prostate cancer cells. These NPs are surface functionalized by: a) scFv antibody fragments derived from the PSMA targeting J591 antibody and b) the Gaussia princeps luciferase to provide a luminescent signal. We present work showing feasibility for a point-of-care, highly parallel CTC assay based on these highly engineered VLPs. This technology can facilitate frequent monitoring of cancer patients to ensure that the best possible interventions are employed