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Three-Dimensional Quantitative Visualization for Mechanics of Discontinuous Materials
Get PDFThe complexity and multiscale nature of material microstructures introduces significant intricacies to many mechanics problems for which we do not have a full theoretical understanding. Under loading, these microstructures can introduce significant nonlinearities that cannot be described sufficiently by current theories and models. This leads us to consider experiments we could perform to improve our understanding of such effects. This thesis describes the design of experiments exploring two aspects of material microstructure effects: (i) crack propagation and renucleation in soft brittle polymers and (ii) interparticle forces in granular materials.
First, experimental and analysis methods are developed to study fracture mechanics in soft brittle polymers with the goal of developing a more detailed understanding of the effects of microstructural heterogeneities on crack propagation and renucleation in three-dimensions. To better understand these processes, experiments on crack propagation in thin soft polymers using confocal microscopy images are conducted. Traditional metrics associated with crack propagation including stress intensity factor (SIF, K) and energy release rate (ERR, G) are calculated by direct measurement of the crack tip opening displacement (CTOD, δt) on the sub-millimeter scale. Errors in these calculations are comparable to those reported in the literature for more traditional fracture experiment geometries. Fluorescent speckle images are captured using confocal microscopy imaging, a fast and low cost 3D optical imaging technique, to study crack geometry during propagation. Images of renucleation events are also captured allowing investigation of factors contributing to slow crack roughening observed by earlier researchers. The goal of this study is to provide an experimental method to enhance understanding of crack interactions with microstructural heterogeneities and of renucleation events, which can significantly improve our ability to design material toughness.
To begin to understand the effects of engineered microstructural heterogeneities such as inclusions in materials, we must be able to produce such engineered systems and understand the interparticle interactions. To this end, a method to manufacture volumetrically speckled spheres in-house with controlled diameters was developed. Additionally, an experimental method combining confocal microscopy with digital volume correlation (DVC) was also used to study interparticle force transmission in 3D. Analysis of an in-plane 2D projection of volumetric surface data shows that three-dimensional effects play a significant role in the deformation of granular assemblies. Study of a single grain in 3D demonstrates progress in experimental capabilities and highlights the need for more studies to validate existing numerical models and theories for granular matter. Analysis of particle scale deformations and strains with the Granular Element Method (GEM) allows us to determine interparticle forces and understand the development and evolution of force chains in a granular assembly under a wide variety of loading conditions. These experiments can also lead to development of new understanding of the effects of inclusions on material properties, processes, and damage evolution.</p
Formal Design and Analysis for DNA Implementations of Chemical Reaction Networks
Get PDFIn molecular programming, the Chemical Reaction Network model is often used to describe systems of interacting molecules. This model can describe either real systems, allowing us to analyze and determine their computational function; or describe hypothetical systems, with known computational function but perhaps no known physical example. One significant breakthrough in the field is that any Chemical Reaction Network can be approximated by a system using DNA Strand Displacement mechanisms. This allows the Chemical Reaction Network model to be treated like a programming language, where programs can be written in the abstract and then compiled into physical molecules. Given a programming language and a proof-of-concept compiler, one would want to take the compiler from the proof-of-concept stage into a more reliable, more systematic, and better understood process. This thesis is made up of my contributions to that effort.
First, given a programming language and a compiler, it would be useful to formally verify that the compiler is correct. My collaborators, Qing Dong and Erik Winfree, and I defined a Chemical Reaction Network-specific form of bisimulation equivalence, which can compare two such networks and verify that one is (or is not) a correct implementation of the other. For example, the compiler-produced DNA circuit can be verified as an implementation of its abstract program, although this is not the only possible use. After defining this concept of equivalence, we show that it can be checked by algorithm; although various parts of the problem are NP-complete or PSPACE-complete, we give algorithms that meet these lower bounds. We also prove a number of interesting properties of Chemical Reaction Network bisimulation equivalence, including transitivity and modularity properties which are particularly useful for stepwise checking of large systems. We further extend this bisimulation method to linear Polymer Reaction Networks, a strictly more powerful abstraction which has been occasionally used in molecular programming. Again we prove complexity hardness results, which in this case are as expected uncomputable in the general case; however, many practical systems can still be verified, and we give one such example. Finally, we use bisimulation to identify a class of single-locus networks that are practical to implement. Thus we show a method of verification which can simplify use of the above-mentioned compiler by proving general statements of correctness about its results.
Second, given a programming language and a concept of compiling it, it would be useful to optimize the result of the compilation. One particular area of optimization is the number of DNA strands per prepared complex; some experiments suggest that systems with no more than 2 strands per complex are more robust. Lulu Qian and I developed some proposed DNA Strand Displacement schemes for general Chemical Reaction Network implementations with no more than 2 strands per complex, and a number of other desirable properties. Meanwhile, having been shown to be useful for many reasons, the mechanisms of DNA Strand Displacement have recently been formalized, abstracted, and analyzed. I show that this formalization, combined with the bisimulation methods above, can prove various statements about the limits of DNA Strand Displacement systems. For example, a set of desirable conditions including the 2-strand limit cannot be achieved by any general Chemical Reaction Network implementation scheme. I also observe that two of the new schemes we discovered, each meeting all but one condition of the impossible set, were found in the process of coming up with this proof. I thus argue that through formalization of DNA Strand Displacement we can have a more systematic method of finding and designing molecular programs, and of knowing when the programs we want do not exist.</p
Neurons that Control Social States in Drosophila melanogaster
Get PDFAnimal behaviors are influences not only by the immediate stimuli they are receiving but also by internal states. Internal states such as fear, hunger, and arousal can change subjective "feeling", and result in complex behavioral outcome even if animals receive the same stimuli. In most cases, these state-dependent behavioral changes persist long after the sensory input that caused internal state change is removed, and affect future behavior, reflexing previous experience. This feature of state-control allows animals to adapt their behavior to be more suitable for their internal demands.
The influence of the internal state on animal behavior has been emphasized for decades. There are multiple studies and attempts to identify persistent neuronal mechanisms which are the important feature of the internal state. However, how persistency makes the behavioral state interact with behavioral process to induce input/output relationship has been largely unknown. In addition, it is not clear what the behavioral functions of the persistence are, and what the circuit implementation of persistent activity is. Are there neurons that are persistently activated by external stimulus? Here we approached these questions by investigating social state of fruit flies, Drosophila melanogaster.
Fruit flies exhibit complex social behaviors that are appropriate for given social cues. For example, male flies show courtship behavior toward female flies, and show aggressive behavior such as wing threat and fighting when they encounter opponent male files. Previous studies have been focused on what sensory cues induce these behaviors: detection of female specific pheromones, 7,11-HD, causes male files to court, and male specific pheromone, cVA, induces inter-male aggression. In this study, we have focused more on how these cues might affect internal state changes rather than immediate behavioral response.
Studying persistent social state change has been challenging due to the difficulty of precise, time-resolved presentation of the social cues. For instance, courtship behaviors require constant presence of female object toward which male flies show oriented behavior. The male-male aggressive behaviors such as lunging and tussling require constant interaction between two animals, and removal of opponent male fly is technically impossible. Therefore, we first developed an optogenetic tool in fly systems to study persistent feature of the social state change to mimic transient presentation of the social cue. In Chapter II, we describe an optogenetic tool that allows the manipulation of neural activity in a freely moving fly. We used Red activatable Channelrhodopsin (ReachR), which enabled us to manipulate activation of neurons in freely behaving adult flies in millisecond precision without interfering normal visual function. Using such an activation tool, we show that activation of female sensing neurons, P1 neurons, induces persistent courtship behaviors in male flies that last several minutes after the stimulation of P1 neurons.
Although we show that persistent internal state change can be induced by transient stimulation of the sensory cues in Chapter II, the circuit implementation of such a persistency is not clear. In Chapter III, we show that activation of P1 neurons triggers persistent activity in its downstream neurons, pCd neurons, that is necessary for the persistent social behavior induced by transient social behaviors. Interestingly, manipulation of the pCd neurons do not affect immediate behavioral response that are shown during the presentation of social cues (P1 stimulation), implying that there are parallel and dissociable pathways for the immediate response and enduring response derived from persistent internal state change, although these responses are caused by common cue. Although the neural mechanism to encode persistent activity is still unclear, this finding shows how internal state and command pathway interact with each other to affect behavioral outcome.
Altogether, these findings described in this dissertation offer new insights for future researchers to understand behavioral state control.</p
Additive Manufacturing of 3D Nano-Architected Metals and Ceramics
Get PDFAdditive manufacturing (AM) represents a set of manufacturing processes that create complex 3D parts out of polymers, metals, and ceramics. AM of metals and ceramics is widely used to produce parts for aerospace, automotive, and medical applications. At the micro- and nano-scales, AM is poised to become the enabling technology for efficient 3D microelectromechanical systems (MEMS), 3D micro-battery electrodes, 3D electrically small antennae, micro-optical components, and photonics. Today, the minimum feature size for most commercially available metal and ceramic AM is limited to ~20-50 μm. Currently, no established processes can reliably produce complex 3D metal and ceramic parts with sub-micron features.
In this thesis, we first demonstrate a nanoscale metal AM process that can produce ~300 nm features out of nanocrystalline, nanoporous nickel using synthesized hybrid organic-inorganic materials, two-photon lithography, and pyrolysis. We study microstructure and mechanical properties of as-fabricated nickel architectures and compare their structural strength to established AM processes. We then show how this process can be extended to other metals and metalloids, including Mg, Ge, Si, and Ti.
This study extends further into nanoscale AM of transparent, high refractive index materials for micro-optics and photonic crystals. We develop an AM process to 3D print fully dense nanocrystalline rutile titanium dioxide (TiO₂) with feature dimensions down to ~120 nm. We carefully study and model the relationship between feature dimensions and process parameters to achieve a <2% variation in critical dimensions. We then use this understanding of the process to fabricate and study 3D dielectric photonic crystals with a full photonic bandgap in the infrared.
Finally, a microscale AM process of titanium dioxide is demonstrated for photocatalytic water treatment. We show how synthesized hybrid organic-inorganic materials can be applied for stereolithography to print TiO₂ architectures with 100 μm features. We use the developed 3D printing process to investigate the effect of 3D architecture on the efficiency of photocatalytic water treatment.
This work establishes a versatile and efficient pathway to create three-dimensional nano-architected metals and ceramics and to investigate their properties for applications in 3D MEMS, micro-optics, photonics, and photocatalysis.</p
Quantum Storage of Light Using Nanophotonic Resonators Coupled to Erbium Ion Ensembles
Get PDFThis thesis presents on-chip quantum storage of telecommunication wavelength light using nanophotonic resonators coupled to erbium ions. Storage of light in an optical quantum memory has applications in quantum information and quantum communication. For example, long distance quantum communication using quantum repeater protocols is enabled by quantum memories. Efficient and broadband quantum memories can be made from resonators coupled to ensembles of atoms. Like other rare earth ions, erbium is appealing for quantum applications due to its long optical and hyperfine coherence times in the solid state at low temperatures. However, erbium is unique among rare earth ions in having an optical transition in the telecommunication C band (1540 nm), making it particularly appealing for quantum communication applications. In this work, we use nano-scale resonators coupled to erbium-167 ions in yttrium orthosilicate crystals (167Er 3+:Y2SiO5).
We demonstrate quantum storage in two types of resonators. In a nanobeam photonic crystal resonator milled directly in 167Er 3+:Y2SiO5, we show storage of weak coherent states using the atomic frequency comb protocol. The storage fidelity for single photon states is estimated to be at least 93.7% ± 2.4% using decoy state analysis, Storage of up to 10 μs and multimode storage are demonstrated. Using a hybrid amorphous silicon 167Er 3+:Y2SiO5 resonator and on-chip electrodes, we demonstrate a multifunctional memory using the atomic frequency comb protocol with DC Stark shift control. In addition dynamic control of memory time, Stark shift control allows modifications to the frequency and bandwidth of stored light. We show tuning of the output pulse by ± 20 MHz relative to the input pulse, and broadening of the pulse bandwidth by more than a factor of three. The storage efficiency in both devices was limited to < 1%.
On the way to these results, we describe 167Er 3+:Y2SiO5 spectroscopy measurements including optical coherence times and hyperfine lifetimes below 1 K, and we estimate the linear DC stark shift along two crystal directions. The design and fabrication of the on-chip resonators is presented. We discuss the limitations to storage time and efficiency, including superhyperfine coupling and resonator parameters, and we outline a path forward for improving the storage efficiency in these types of devices.</p
Functional Acrylate Resins for Shape Memory Polymer Microarchitectures
Get PDFShape memory polymers (SMPs) are materials that can undergo programmable shape change in response to a specific stimulus. The ability to undergo this reliable, three-dimensional shape change makes SMPs promising smart materials for applications like biomedical stents and sutures. However, to access areas like blood vessels in the eye, these materials must be fabricated with micron or submicron resolution. In this work, benzyl methacrylate-based, heat-responsive SMP microstructures were fabricated using two-photon lithography in a variety of three-dimensional designs. The effects of different fabrication conditions on the structures were studied, and Raman spectroscopy was used to probe network properties, including degree of polymerization.
The resin was also chemically functionalized prior to polymerization with BOC-protected amine groups via the thiol-Michael addition reaction, which allows for attachment of other useful functional groups to the surface of the structures. This chemistry was utilized for attachment of a dye as well as gold nanoparticles. When exposed to laser light, these nanoparticles can undergo localized surface plasmon resonance and serve as heat generators. The theoretical feasibility of using this heating technique to induce shape change in SMP microstructures is examined in this work.</p
First-Principles Calculations of Electron-Defect Interactions and Defect-Limited Charge Transport
Get PDFCrystallographic defects and impurities govern charge transport at low temperature, where the electron-defect (e-d) interactions limit the carrier mobility and manifest themselves in a wide range of phenomena of broad relevance in condensed matter physics. Theoretical treatments of e-d interactions have so far relied on heuristic approaches and analytic models. However, the band structure, electronic wave functions, and defect perturbation potential are far more complex in real materials than in these simplified models. First-principles calculations can provide atomistic details of the atomic and electronic structures of the material and make accurate predictions of their properties. Yet, ab initio calculations of e-d interactions are still in their infancy, mainly because they require large simulation cells and computationally expensive workflows. This thesis aims to overcome the open challenge of computing the e-d interactions and the associated e-d matrix elements, e-d relaxation times, and defect-limited mobility using first-principles methods. We develop an efficient first-principles method to compute the e-d matrix elements and apply it to neutral vacancy and interstitial defects in silicon. Using the new approach, we demonstrate systematic convergence of the e-d relaxation times with respect to supercell size, defect position, and Brillouin zone sampling. To speed up the e-d calculations, we formulate and implement an interpolation scheme to compute the e-d matrix elements using maximally-localized Wannier functions. We show for the first time fully ab initio calculations of the temperature dependent defect-limited carrier mobility and investigate its numerical convergence. To treat charged defects, we develop a different interpolation method and apply it to a charged point defect in silicon. We use this approach together with importance sampling integration to effectively compute the e-d relaxation times for charged defects. Finally, we provide technical details of the e-d routines and discuss their integration in the open source code PERTURBO developed in the Bernardi group. In summary, the methods developed in this thesis have laid a solid foundation for future ab initio e-d interaction calculations, which can be applied broadly to address materials design challenges in electronics, energy, and quantum technologies.</p
Insights Into Stellar Explosions From Infrared Light
Get PDFMassive stars are the workhorse of the Universe. While accounting for a minute fraction of baryonic mass, their influence on the cosmos is profound. Their lives and deaths lead to nucleosynthesis of all elements heavier than helium, including those essential to life. They produce some of the most energetic eruptions and explosions, core-collapse (CC) supernovae (SNe) at the end of their life. These explosions are common, about once per century per galaxy, and are one of the primary drivers of the gas dynamics of their host galaxies. Despite their importance, many facets of the massive stars' evolution and their eventual death in CCSNe are still uncertain. In this thesis, I use a variety of observations in the infrared (IR) part of the electromagnetic spectrum to probe aspects of these stellar explosions elusive to visible light.
IR observations of SNe remain sparse compared to the optical, even for the most nearby events. I present the first systematic study of CCSNe light curves from the Spitzer Space Telescope showing trends in IR properties of CCSNe and identifying outliers that exhibit signs of interactions between the SN shock and the circumstellar medium (CSM) ejected from the star. I also present in-depth explorations of nearby SN 2017eaw, a typical and common hydrogen-rich explosion; and SN 2014C, a hydrogen-poor explosion whose shock wave crashes into the CSM containing material lost from the star. IR observations provide insights into the chemical evolution and circumstellar environment in these SNe.
In the second part of this thesis, I present the development and commissioning of a near-IR spectropolarimeter WIRC+Pol at Palomar Observatory. WIRC+Pol utilizes a novel, highly efficient polarization grating as its polarimetric beam splitter and spectral disperser. The resulting high sensitivity allows WIRC+Pol to observe sources as faint as J = 14.5 to 0.1% polarimetric accuracy in 2 hours. I also present the first scientific results from the instrument: the spectropolarimetric measurements of four nearby SNe, which are the first such observations in the IR. We detected polarization from SN 2018hna, which allowed us to constrain that its explosion geometry looks similar to the very well-studied SN 1987A observed from a different angle, suggesting the same underlying geometry.</p
Borel Matchings and Analogs of Hall's Theorem
Get PDFIn classical graph theory, Hall’s theorem gives a necessary and sufficient condition for a bipartite graph to have a perfect matching. The analogous statement for Borel perfect matchings is false. If we instead consider Borel perfect matchings almost everywhere or Borel perfect matchings generically, results similar to Hall’s theorem hold. We present Marks’ proof that König’s theorem, a special case of Hall’s theorem, fails in the context of Borel perfect matchings. We then discuss positive results about the existence of Borel matchings that are close to perfect in the measure theory and Baire category settings
Exogenesis
No full text[Introduction] The trip into the city takes longer than anticipated. By the time Amelia’s maglev car drops her off in front of the hotel, classical music and bright lights are already spilling out of the windows and the open lobby doors