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Bioinspired Nanostructures for Biomedical Applications
Get PDFNature boasts a myriad examples of coloration achieved purely through the physical interaction of light with nano-scale features also known as biophotonic nanostructures. From reptiles to insects, birds to flora, structural coloration has been achieved through a variety of fascinating nano-architectures that leverage different physics. Beyond structural coloration, these nanostructures are often truly multifunctional. For instance, biophotonic nanostructures can also serve as self-cleaning and bactericidal surfaces, gas and thermal sensors, waveguides and beam splitters. With the growing need for robust and compact biomedical devices, the requirement to embed multiple functionalities towards sensing, monitoring, diagnostics and therapeutics within a diminutive device footprint becomes crucial. In this regard, inspiration from the multifunctionality of biophotonic nanostructures can prove to be greatly beneficial for medical applications. Consequently, this work attempts to showcase various examples of the utilization of nanostructures inspired from biophotonic nanostructures for biomedical applications under various overlapping themes such as ophthalmic sensors, bioinspired optics and plasmonic biosensing.
This thesis is summarized in two parts. The first part (Chapters 2--4) introduces a proof-of-concept optical intraocular pressure (IOP) sensor implant and various challenges faced during its in vivo implementation. In Chapter 3, nanostructures inspired by light-trapping epidermal micro-/nanostructures on flower petals are proposed and embedded onto the sensor platform to improve its in vivo optical signal-to-noise ratio and biocompatibility. Chapter 4 covers nanostructures inspired by biophotonic nanostructures on longtail glasswing butterfly wings that improve the in vivo angle of acceptance and biocompatibility of the sensor.
The second part (Chapters 5 and 6) presents the use of bioinspired nanostructures in plasmonic biosensors. Chapter 5 discusses an on-chip platform consisting of bioinspired plasmonic nanostructures to detect various nucleic acid sequences of relevance in the pathogenesis of HIV-1 via plasmon-enhanced fluorescence. Chapter 6 describes the employment of bioinspired quasi-ordered nanostructuring on flexible substrates for broadband surface-enhanced Raman spectroscopy (SERS). Here, SERS-based biosensing enabled by quasi-ordering is used to detect uric acid -- a biomarker of various pathologies in human tears.</p
Symbiotic Diversity and Mineral-Associated Microbial Ecology in Marine Microbiomes
Get PDFThis thesis investigates ecological interactions in the seafloor between microbial taxa (Chapters 1 and 2) and between these microorganisms and their mineral hosts (Chapters 2 through 4). In seafloor sediments, electron acceptors are often limited, forcing microorganisms inhabiting these sediments to acquire symbiotic partners and/or perform extracellular electron transfer to insoluble electron acceptors. Seafloor methane seeps present an endmember case wherein extremely reducing fluids charged with methane advect through sediment. In these benthic ecosystems, anaerobic methanotrophic archaea (ANME) form symbiotic partnerships with sulfate-reducing bacteria (SRB), but it remained unclear if certain ANME exhibit a preference for certain SRB partners. In Chapter 1, I present results documenting such a pattern of partnership specificity in ANME-SRB consortia. In Chapter 2, I further examine these patterns in rare ANME taxa through development and application of a density-separation protocol refined from published work. This protocol exploits the co-association of microbial taxa on mineral surfaces to aid in the detection of novel symbioses, and further is useful to detect microbial interactions with certain minerals. In Chapter 3, I focus on the interaction between ANME-SRB consortia and authigenic silicates that have been observed on consortium exteriors, finding evidence to support that the precipitation of these silicates is actively mediated by ANME-SRB. In Chapter 4, I perform geochemical modeling benchmarked by synchrotron X-ray analysis to examine the imprint of extracellular electron transport by metal-reducing microorganisms on Precambrian manganese-rich sedimentary rocks
Temporally Changing Roles of Morphogen Dorsal in the Drosophila Early Embryo
Get PDFMorphogen gradients provide positional cues during development, with cell fate specification proceeding in a morphogen concentration-dependent manner during patterning. However, morphogens also are dynamic as their concentrations change not only in space but also in time, but how these dynamics are translated into cell fate specification over time is not well understood. To provide a better understanding of morphogens’ temporal roles, we studied how Drosophila dorsal-ventral body patterning is controlled by the dynamic morphogen Dorsal (Dl). Dl is present in a nuclear-cytoplasmic gradient along the dorsal-ventral (DV) axis, but Dl levels also continuously increase between and within nuclear cell divisions associated with the early syncytial embryo. To experimentally manipulate Dl levels in time in order to determine whether these dynamics are important, we developed a light-activated degradation system. The blue light inducible degron domain, BLID, was fused to the C-terminus of Dl by genomic editing using CRISPR-Cas9. To assay effects on temporally manipulated Dl levels, we combined this light-inducible degradation system with the MS2-MCP.GFP nascent transcript imaging system, and used to monitor transcription changes in vivo at the snail (sna) locus, a gene requiring high Dl levels. We found that while high Dl levels are required for sna activation at early nuclear cycle 14, late expression can be supported even if Dl levels are extinguished. Twist, an early Dl target gene, is later auto-activating and can support the later sna expression without Dl. Surprisingly, we found that peak levels of Dl, present at late nuclear cycle 14, are required only to fine tune, in particular to decrease, sna levels. This differential action of Dl, first functioning as an activator and next as a damper of expression, is manifest by the coordinate action of two enhancers acting at the sna locus. Here, we highlight how morphogen roles change in time, and suggest that this may be a general characteristic of dynamic morphogens that allows them to control developmental patterning.</p
Exhumed Fluvial Deposits: New Paleohydrological Tools Indicate Long-Duration Fluvial Activity on Early Mars
Get PDFFluvial sinuous ridges are common landforms on Mars that have been used for interpreting the history of ancient martian rivers. They are typically interpreted as eroded casts of an ancient river at a snapshot in time. However, some ridges might instead be channel belts that preserve river history, leading to significant differences in interpretation of paleohydrology, including flow direction, duration, and discharge. In this thesis, I used analog sites on Earth and techniques from fluvial sedimentology and fluvial geomorphology to determine that many ridges are exhumed channel belts, and to create and apply new tools for measuring bankfull discharge and duration of river flow from remote-sensing observations of these sedimentary deposits. I found evidence that rivers on ancient Mars were comparable in size to those on Earth today, and that they flowed for at least millions of years.
I examined sinuous ridges in three terrestrial sites to better understand ridges on Mars: the Cretaceous Cedar Mountain Formation and Jurassic Morrison Formation of Eastern Utah, and the Miocene Caspe Formation of Northeast Spain. Ridges at all sites are capped with sandy units rich with dune and bar strata atop a mudstone pedestal and they cross each other at different stratigraphic levels, observations that together indicate that ridges are channel belts exhumed from floodplain sediments — the most common arrangement of fluvial stratigraphy. By compiling measurements of hundreds of terrestrial channel belts and their associated channels, I found that the best methods to reconstruct paleochannel bankfull geometry from such deposits are to use thickness of channel belts (1-4 times paleochannel depth) or radius of curvature of lateral accretion sets (half the channel width). Ridge width and planview wavelength, common proxies for paleochannel width, are significantly more uncertain due to channel amalgamation and ridge erosion by scarp retreat, which I quantified with geometry and a new erosion model. Intermittency factor converts bankfull discharge to average discharge, enabling measurement of duration of river flow. I calculated the intermittency factor for 206 fluvial deposits and USGS streamgages, and found that it ranges between 0.003-0.7 with a median of 0.10, with values depending on the ratio of catchment-averaged erosion rate to average precipitation but independent of timescale, river size, climate, or grainsize.
Throughout the work, I applied the methods to sinuous ridges on Mars to demonstrate their applicability. I found that many ridges are likely channel belts, and that the ancient rivers they represent are likely smaller but longer than previously studies have indicated. Altogether, this contribution enables new quantitative analyses of ancient rivers on Earth and Mars, and provides evidence that ancient Martian climate was capable of supporting liquid water at many locations across the surface for at least millions of years.</p
Spectroscopy and Kinetics of Atmospheric and Astrochemical Reactions
Get PDFThe reactions between reactive radicals and other neutral compounds have long been known to be important in atmospheric chemistry and astrochemistry. This work uses pulsed-laser photolysis cavity ringdown spectroscopy and laser-induced fluorescence to measure the rate constants and branching ratios of chemical reactions over a wide range of temperatures and pressures relevant to both polluted atmospheres, and the interstellar medium. This includes studying the OH + NO₂ reaction in the 253 – 333 K range, the reaction of CN with benzene (C₆H₆) and toluene (C₇H₈) down to 16 K, and the OH + CO reaction down to 30 K.</p
The Whisper and the Bang: Cosmic Fireworks in the Lives of Compact Binaries
Get PDFCompact binaries, comprising of a white dwarf, neutron star or black hole in a tight orbit around another star are produced from binary evolution through a complex range of astrophysical processes -- ranging from eruptive mass loss episodes ('the whisper') to spectacular explosions ('the bang') that have shaped the universe as we see it today. In pursuit of a complete road-map of the explosive lives of high mass and low mass stars in compact binaries, I undertook two major experiments.
In the first two parts of this thesis, I describe the largest volume-limited supernova classification experiment undertaken till date, using the Zwicky Transient Facility optical time domain survey. I present the identification of a new class of 'ultra-stripped' supernovae that form neutron stars in compact binary systems, that are likely direct progenitors of merging neutron stars detectable in LIGO/Virgo. Using the systematic sample of supernovae, I identify a class of helium shell explosions on low mass white dwarfs that likely represent the final fates of helium accreting white dwarfs. In the third part of this thesis, I present the development of Palomar Gattini-IR (PGIR), the first wide-field infrared survey capable of studying the dynamic infrared sky from timescales of seconds to years. I present a systematic search for nova eruptions in the Milky Way using PGIR, and show that optical surveys have systematically missed a large fraction of dust obscured novae to derive the first quantitative estimate of the Galactic nova rate. I present the first infrared constraints on the second-timescale emission from a Galactic Fast Radio Burst identified with a dust obscured Galactic magnetar.
This thesis helps set the stage for a systematic exploration of the local stellar graveyard using i) the Vera Rubin Observatory to probe the lowest luminosity stellar deaths in the local universe and ii) the upcoming assemblage of infrared surveys to study variability in Galactic compact objects in conjunction with the rich landscape of X-ray and radio sky surveys. By mapping out the demographics of explosive phenomena, it helps us interpret the astrophysical populations detectable with current and future gravitational wave observatories.</p
Multi-Functional Metamaterials
Get PDFOptimally designing interdependent mechanical properties in a structure allows for it to be used in application where an arbitrary combination of properties is desired. Architected materials have proven to be an effective way of attaining mechanical behaviors that are unattainable using their constituent materials alone, such as unusual static mechanical properties, unusual wave propagation behavior, and shape morphing. The advent of 3-D printing has allowed for fabricating metamaterials with complex topologies that display engineered mechanics. However, much of the current efforts have focused on optimally designing simple mechanical behaviors such as designing for stiffness and weight, particular frequency bandgaps, or bi-stability. In this work, we study two metamaterial systems where we control and optimize a wide set of static and dynamic properties, and one complex multi-stable structure.
Most studies on the optimal design of static properties have focused on engineering stiffness and weight, and much remains unknown about ways to decouple the critical load to failure from stiffness and weight. This is the focus of the first part of our work. We show that the addition of local internal pre-stress in selected regions of architected materials enables the design of materials where the critical load to failure can be optimized independently from the density and/or quasistatic stiffness. We propose a method to optimize the specific load to failure and specific stiffness using sensitivity analysis, and derive the maximum bounds on the attainable properties. We demonstrate the method in a 2-D triangular lattice and a 3-D octahedral truss, showing excellent agreement between experimental and theoretical results. The method can be used to design materials with predetermined fracture load, failure location and fracture paths.
For the second part of our work, we focus on designing acoustically transparent structures, by engineering the acoustic impedance -- a combination of wave speed and density, to match that of the surroundings. Owing to the strong correlation between acoustic wave speed and static stiffness, it is challenging to design acoustically transparent materials in a fluid, while maintaining their high structural rigidity. We provide a sensitivity analysis to optimize these properties with respect to design parameters of the structure, that include localized masses at specific positions. We demonstrate the method on five different periodic, three dimensional lattices, to calculate bounds on the longitudinal wave speed as a function of their density and stiffness. We then perform experiments on 3-D printed structures, to validate our numerical simulations. Further, using the sensitivity analysis together with a data-driven approach, we design and demonstrate a mode demultiplexer, that is capable of splitting arbitrarily mixed modes. The tools developed in this work allow for designing structures in a plethora of applications, including ultrasound imaging, wave filtering, and waveguiding.
Finally, most multi-stable structures are limited by bi-stability either at the macroscopic or the unit cell level owing to the difficulty in engineering a highly non-linear energy landscape using just elements that display convex energy landscapes. We demonstrate a method to design arbitrarily complex multi-stable shape morphing structures, by introducing rigid kinematic constraints together with disengaging energy storing elements. We present the idea on a kagome lattice configuration, producing a quadri-stable unit cell and complex stable topologies with larger tessellations, validated by demonstrations on 3-D printed structures. Most designs that use passive actuation address one-way shape morphing along the direction of least resistance. We demonstrate reversible, thermally actuated shape morphing between stable open and closed topologies using shape memory springs. The designs can be extended to non-planar structures and fabricated at vastly different length scales.</p
Focused Laser Differential Interferometry
Get PDFThe focused laser differential interferometer (FLDI) is a non-imaging optical diagnostic that is sensitive to density disturbances. A distinguishing feature is reduced sensitivity away from the focal plane of its beams. The spatial resolution is sub-mm, and the temporal resolution is restricted only by photodetector bandwidth, typically >10 MHz. These traits make FLDI particularly suited to measurements in hypervelocity ground-testing facilities, where the low densities, short time-scales, and harsh environments preclude the use of intrusive diagnostics. Line of sight integration issues associated with other optical techniques are therefore minimized, a distinct advantage for measurements in impulse facilities, where the core flow of interest is often surrounded by highly-turbulent shear layers.
The systematic design principles for single and double FLDI systems are discussed, based on ray transfer matrix analysis combined with Gaussian optics. A detailed guide is presented for the practicalities of aligning, calibrating, and operating an FLDI.
A modular numerical implementation of Schmidt and Shepherd's FLDI ray-tracing model is developed, capable of accepting arbitrary flow-fields defined via analytical expressions, simulation coupling, or experimental datasets. This numerical implementation is used to perform the first comprehensive experimental validation of the model, using known static and dynamic phase objects. Quantitatively-accurate predictions of the response of real FLDI systems are obtained. Importantly, the spatial sensitivity of the instrument is found to be dependent on disturbance wavelength, with scaling matching that predicted analytically from the model. Propagating shock waves are used as another highly-dynamic test phase object, and it is shown that FLDI maintains its theoretical performance at sub-μs time-scales.
The validated ray-tracing model is used to develop analytical expressions for the response of FLDI to propagating plane waves, extending on the results of Schmidt and Shepherd, and Settles and Fulghum. For the first time, the inverse problem is solved for this class of flow-field, allowing the density fluctuation spectrum to be recovered quantitatively from FLDI phase shift data. This approach is validated using synthetic flow-fields with the numerical ray-tracing scheme, and is also compared with the approximate approach introduced by Parziale et al.
FLDI is used to make freestream density fluctuation measurements on two facilities: a conventional blowdown tunnel, and an expansion tube. On the conventional tunnel, a comparison is made between pitot-probe and FLDI measurements after converting both to freestream pressure fluctuation spectra. A modification of Stainback and Wagner's theory, incorporating recent numerical results from Chaudhry et al., is used to interpret the pitot data, while the new inversion algorithm is applied to the FLDI data. Close agreement is found between the two sets of spectra, showing that accurate quantitative data can be obtained with FLDI, and used to extend spectra beyond the pitot bandwidth.
On the expansion tube, the theory of Paull and Stalker for freestream noise originating in the driver gas is investigated. Their proposed relationship between freestream density fluctuations and the primary interface sound speed ratio is not observed. Spectral banding is also absent, however this is expected due to the relatively low secondary expansion strengths. The envelope of accessible conditions is somewhat restricted due to the low mean freestream densities that lead to signal-to-noise issues.
Significant performance improvements can still be made to FLDI, in terms of its noise and bandwidth limitations, and to the spatial localization of its sensitive region; suggestions are given for possible approaches. With the ray-tracing model now validated, it can be used to optimize FLDI, or even to suggest derivative instruments based on similar principles.</p
Quantum Information at High and Low Energies
Get PDFIn this thesis, we take a look at how quantum information theory can be used to study physical systems at both high and low energies.
In the first part of this thesis, we examine the structure of the low-energy subspaces of quantum many-body systems. We show that the existence of error-correcting properties in low-energy subspaces is a generic feature of quantum systems. Using the formalism of matrix product states, we construct explicit quantum error-detecting codes formed from the momentum eigenstates of a quantum many-body system.
We also examine how topological order can persist past the ground state space into the low-energy subspace of excited states by studying the No Low-Energy Trivial States (NLTS) conjecture. We prove a version of the NLTS conjecture under the assumption of symmetry protection. Moreover, we show that our symmetric NLTS result has implications for the performance of quantum variational optimization algorithms by using it to prove a bound on the Quantum Approximate Optimization Algorithm (QAOA).
In the second part of this thesis, we examine problems related to bulk reconstruction in holography and the black hole firewall paradox. Using the formalism of the tensor Radon transform, we devise and implement a numerical algorithm for reconstructing (perturbatively in AdS₃/CFT₂) the bulk metric tensor from a given boundary entropy profile.
We finally examine the black hole firewall problem from the perspective of quantum error-correction and quantum computational complexity. We argue that the state of the Hawking radiation has the special property of being computationally pseudorandom, meaning that it cannot be distinguished from the maximally mixed state by any efficient quantum computation. We show that this implies that each black hole has a natural structure as a quantum error-correcting code.</p
Biomolecular Tools for Noninvasive Imaging and Manipulation of Engineered Cells
Get PDFToday’s most advanced tools for imaging and controlling cellular function are based on fluorescent or light-controlled proteins, which have limited utility in large organisms or engineered living materials due to the scattering of photons. Deeply penetrant forms of energy such as magnetic fields and sound waves, while routinely used to monitor and treat diseases on the tissue and organism level, do not process the equivalent set of biomolecular tools for interfacing with biology on the molecular and cellular level. Emerging technologies discussed in this thesis aim to bridge this gap by harnessing biomolecules that have the appropriate physical properties to interact with sound waves or magnetic fields in such a way that enables the visualization and control of specific cells (Chapter 1). We describe two additions to the expanding toolkit for noninvasive imaging and control. In the first case, we show that gas vesicles, a class of hollow protein nanostructures naturally found in aquatic single-cell organisms, can be used as acoustic actuators to enable the control of cellular forces, movement, and patterning using ultrasound (Chapter 2). In the second case, we show that aquaporins, a class of membrane water channels, can be used to alter cellular permeability and serve as genetic reporters for magnetic resonance imaging (Chapter 3). These tools provide critical capabilities for interfacing with cellular function noninvasively and could open the door to applications in various research, biomedical, and industrial settings