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Plasmonics and Electron Optics in Graphene
Get PDFThe field of plasmonics has been attracting wide interest because it has provided routes to guide and localize light at nanoscales by utilizing metals as its major building block. Meanwhile, graphene, a two-dimensional lattice of carbon atoms, has been regarded as an ideal material for electronic applications owing to its remarkably high carrier mobility and superior thermal properties. Both research fields have been growing rapidly, but quite independently. However, a closer look reveals that there are actually numerous similarities between them, and it is possible to extract useful applications from these analogies. Even more interestingly, these research fields are recently overlapping to create a new field of research, namely graphene plasmonics.
In this thesis, we present a few examples of these intertwined topics. First, we investigate "rainbow trapping" structures, broadband plasmonic slow light systems composed of single or double negative materials. We clarify the mode-conversion mechanism and the light-trapping performance by analyzing the dispersion relation. We then show that electrons in graphene exhibit photonlike dynamics including Goos-Hanchen effect and the rainbow trapping effect, but quantitatively differently. To study the dynamics of graphene electrons numerically, we develop a finite-difference time domain simulator. We also present a way to enhance electron backscattering in graphene by engineering the dispersion of electron eigenmodes in a Kronig-Penney potential. Finally, we discuss physics of graphene plasmon cavities. We report the resonant mid-infrared transmission across a plasmonic waveguide gap that is governed by the Fano interference between transmission through plasmon modes in graphene and nonresonant background transmission. An ultracompact graphene plasmon cavity, which resonates at near-infrared telecommunication frequencies, is also proposed.</p
Selective Functionalization of the Protein N-Terminus with N-Myristoyl Transferase in Bacteria
Get PDFProteins are involved in myriad processes in all organisms. They provide structural support in the membrane and scaffolding of each cell; they aid in the transmission of biochemical signals within and between cells; and they play central roles in combating various disease states. The development of techniques enabling selective and site-specific functionalization of proteins is an active area of investigation, as such modifications are critical to many studies and uses of proteins. For instance, with the addition of a unique reactive handle, a protein may be conjugated to a polymer for the production of protein-based therapeutics exhibiting improved bioavailability. Alternatively, proteins may be attached to slides to prepare diagnostic microarrays, reacted with hydrogels to create functional biomaterials, or decorated with fluorophores for in vivo imaging. Site-specific protein tagging techniques have already contributed greatly to biomedical research and will continue to advance the state of the field.
The focus of my thesis research has been the development of a novel site-specific protein labeling method centered on the eukaryotic enzyme N-myristoyl transferase (NMT). In a process called myristoylation, NMT appends a fatty acid to the N-terminus of numerous substrate proteins. Previous work demonstrated that NMT tolerates a wide range of chemically functionalized analogs of its natural fatty acid substrate. Here, we describe efforts that exploit various features of NMT: its ability to bind and utilize reactive fatty acid analogs, its exquisite selectivity toward its protein substrates, and its orthogonality toward those proteins naturally present in bacteria.
First, in Chapter II, we discuss the development of a model system for NMT-mediated protein labeling in the bacterium Escherichia coli. We synthesized an azide fatty acid analog that can participate in bioorthogonal chemistries, and we prepared two GFP-based substrate proteins, each displaying a recognition sequence derived from a known substrate of NMT. Our experiments indicate that labeling by NMT is site-specific, quantitative, and highly selective for each engineered substrate within the bacterial milieu.
As summarized in Chapter III, the model system was extended to the N-terminal labeling of two neuronal proteins, calcineurin (CaN) and calmodulin (CaM). While CaN is naturally myristoylated, CaM was engineered to achieve labeling by NMT. Experiments with CaN and CaM confirmed that our NMT-based system is quantitative and selective in its labeling of both natural and engineered substrate proteins. Extensive characterization of each protein allowed us to identify constructs that retain wild-type levels of activity even after labeling with the azide fatty acid.
Three of the protein constructs reported in Chapters II and III were utilized for microarray studies, as described in Chapter IV. We achieved rapid surface immobilization of each azide-labeled protein directly from lysate, a significant advantage when considering the time and resources normally required to purify proteins for downstream applications. The experiments and methods summarized in this chapter will be adapted for high-throughput biochemical research with protein microarrays.
Finally, the orthogonality of NMT toward bacterial systems was probed further for the purpose of selective labeling of individual bacterial proteins for live-cell imaging. In addition to identifying an azide fatty acid suitable for such studies, we also selected two bacterial proteins that exhibit interesting functions and localization patterns, and we developed corresponding protein constructs for NMT-mediated labeling. Progress toward the use of NMT for in vivo imaging applications in bacteria is described in Chapter V.
Ultimately, our objective throughout the design and execution of these projects was to create and validate a new technique to achieve site-specific protein labeling. The particular advantages of NMT include its tolerance of reactive fatty acid analogs and engineered substrate proteins, and its lack of interaction with proteins present in the widely used E. coli expression host. We believe that the ideas and results presented in this thesis establish NMT-mediated protein labeling as a valuable tool for addition to the existing set of site-specific protein labeling methods. Development of such methods represents an important and exciting area within the field of modern chemical biology.</p
I: Solid Materials for Low Temperature Thermochemical Water Splitting. II: Structure-Property Relationships on the Zeolite Catalyzed Conversion of Methanol to Light Olefins
Get PDFThis thesis describes two separate projects. The first part of the thesis involves the synthesis of materials for enabling thermochemical water splitting at temperatures below 1000ºC, while the second part focuses on the structure-property relationships for the catalytic conversion of methanol-to-olefins.
In the first project, metal oxide clusters are impregnated in a silica support and tested as catalysts for the thermochemical splitting of water at temperatures below 1000ºC. These supported catalysts are able to do either the oxidation or reduction half cycle, but not both. Thermodynamic analyses reveal that for most common metal / metal oxide pairs, a thermochemical water splitting cycle can not occur in two steps below 1000ºC. Thus, a multi-step thermochemical cycle is developed using Mn3O4 and Na2CO3. This new cycle can be closed at temperatures that do not exceed 850ºC. Additionally, three metal spinels (Mn, Fe and Co based) are investigated with three alkali metal carbonates (Li, Na and K) for both thermochemical water splitting and thermochemical CO2 reduction. The manganese, sodium system is found to be the optimal combination for water splitting.
The second project explores the effects that zeolite structure has on the product selectivity in the methanol-to-olefins (MTO) reaction. After first ensuring that literature results on the more common MTO catalysts could be reproduced, the effects of several zeolite structure features on product selectivity are elucidated. Structural features such as channel width and channel eccentricity, cage size (tested on the LEV, CHA and AFX frameworks) and framework composition (tested on the LEV, AEI, CHA and AFX frameworks) are explored. It is found that the product selectivity does not have a strong correlation with channel width and eccentricity. Ethylene selectivity did increase with a reduction in cage size, while propylene selectivity is a maximum with the CHA cage. The most consistent theme noted is that between the aluminosilicates (zeolites) and the silicoaluminophosphates (SAPOs), the effect of temperature on the C3=/C2= is the same (if the aluminosilicate shows an increase in C3=/C2= with an increase in temperature, so does the silicoaluminophosphate, etc.).</p
Tissue Engineering Active Biological Machines: Bio-Inspired Design, Directed Self-Assembly, and Characterization of Muscular Pumps Simulating the Embryonic Heart
Get PDFBiological machines are active devices that are comprised of cells and other biological components. These functional devices are best suited for physiological environments that support cellular function and survival. Biological machines have the potential to revolutionize the engineering of biomedical devices intended for implantation, where the human body can provide the required physiological environment. For engineering such cell-based machines, bio-inspired design can serve as a guiding platform as it provides functionally proven designs that are attainable by living cells. In the present work, a systematic approach was used to tissue engineer one such machine by exclusively using biological building blocks and by employing a bio-inspired design. Valveless impedance pumps were constructed based on the working principles of the embryonic vertebrate heart and by using cells and tissue derived from rats. The function of these tissue-engineered muscular pumps was characterized by exploring their spatiotemporal and flow behavior in order to better understand the capabilities and limitations of cells when used as the engines of biological machines
Coupled Plasmonic Systems and Devices: Applications in Visible Metamaterials, Nanophotonic Circuits, and CMOS Imaging
Get PDFWith the size of transistors approaching the sub-nanometer scale and Si-based photonics pinned at the micrometer scale due to the diffraction limit of light, we are unable to easily integrate the high transfer speeds of this comparably bulky technology with the increasingly smaller architecture of state-of-the-art processors. However, we find that we can bridge the gap between these two technologies by directly coupling electrons to photons through the use of dispersive metals in optics. Doing so allows us to access the surface electromagnetic wave excitations that arise at a metal/dielectric interface, a feature which both confines and enhances light in subwavelength dimensions - two promising characteristics for the development of integrated chip technology. This platform is known as plasmonics, and it allows us to design a broad range of complex metal/dielectric systems, all having different nanophotonic responses, but all originating from our ability to engineer the system surface plasmon resonances and interactions. In this thesis, we demonstrate how plasmonics can be used to develop coupled metal-dielectric systems to function as tunable plasmonic hole array color filters for CMOS image sensing, visible metamaterials composed of coupled negative-index plasmonic coaxial waveguides, and programmable plasmonic waveguide network systems to serve as color routers and logic devices at telecommunication wavelengths
Developing Peptide Based Capture Agents for Diagnostics and Therapeutics
Get PDFIterative in situ click chemistry (IISCC) is a robust general technology for development of high throughput, inexpensive protein detection agents. In IISCC, the target protein acts as a template and catalyst, and assembles its own ligand from modular blocks of peptides. This process of ligand discovery is iterated to add peptide arms to develop a multivalent ligand with increased affinity and selectivity. The peptide based protein capture agents (PCC) should ideally have the same degree of selectivity and specificity as a monoclonal antibody, along with improved chemical stability. We had previously reported developing a PCC agent against bovine carbonic anhydrase II (bCAII) that could replace a polyclonal antibody. To further enhance the affinity or specificity of the PCC agent, I explore branching the peptide arms to develop branched PCC agents against bCAII. The developed branched capture agents have two to three fold higher affinities for the target protein. In the second part of my thesis, I describe the epitope targeting strategy, a strategy for directing the development of a peptide ligand against specific region or fragment of the protein. The strategy is successfully demonstrated by developing PCC agents with low nanomolar binding affinities that target the C-terminal hydrophobic motif of Akt2 kinase. One of the developed triligands inhibits the kinase activity of Akt. This suggests that, if targeted against the right epitope, the PCC agents can also influence the functional properties of the protein. The exquisite control of the epitope targeting strategy is further demonstrated by developing a cyclic ligand against Akt2. The cyclic ligand acts as an inhibitor by itself, without any iteration of the ligand discovery process. The epitope targeting strategy is a cornerstone of the IISCC technology and opens up new opportunities, leading to the development of protein detection agents and of modulators of protein functions
Investigation of Hypervelocity Impact Phenomena Using Real-time Concurrent Diagnostics
Get PDFHypervelocity impact of meteoroids and orbital debris poses a serious and growing threat to spacecraft. To study hypervelocity impact phenomena, a comprehensive ensemble of real-time concurrently operated diagnostics has been developed and implemented in the Small Particle Hypervelocity Impact Range (SPHIR) facility. This suite of simultaneously operated instrumentation provides multiple complementary measurements that facilitate the characterization of many impact phenomena in a single experiment. The investigation of hypervelocity impact phenomena described in this work focuses on normal impacts of 1.8 mm nylon 6/6 cylinder projectiles and variable thickness aluminum targets. The SPHIR facility two-stage light-gas gun is capable of routinely launching 5.5 mg nylon impactors to speeds of 5 to 7 km/s. Refinement of legacy SPHIR operation procedures and the investigation of first-stage pressure have improved the velocity performance of the facility, resulting in an increase in average impact velocity of at least 0.57 km/s. Results for the perforation area indicate the considered range of target thicknesses represent multiple regimes describing the non-monotonic scaling of target perforation with decreasing target thickness. The laser side-lighting (LSL) system has been developed to provide ultra-high-speed shadowgraph images of the impact event. This novel optical technique is demonstrated to characterize the propagation velocity and two-dimensional optical density of impact-generated debris clouds. Additionally, a debris capture system is located behind the target during every experiment to provide complementary information regarding the trajectory distribution and penetration depth of individual debris particles. The utilization of a coherent, collimated illumination source in the LSL system facilitates the simultaneous measurement of impact phenomena with near-IR and UV-vis spectrograph systems. Comparison of LSL images to concurrent IR results indicates two distinctly different phenomena. A high-speed, pressure-dependent IR-emitting cloud is observed in experiments to expand at velocities much higher than the debris and ejecta phenomena observed using the LSL system. In double-plate target configurations, this phenomena is observed to interact with the rear-wall several micro-seconds before the subsequent arrival of the debris cloud. Additionally, dimensional analysis presented by Whitham for blast waves is shown to describe the pressure-dependent radial expansion of the observed IR-emitting phenomena. Although this work focuses on a single hypervelocity impact configuration, the diagnostic capabilities and techniques described can be used with a wide variety of impactors, materials, and geometries to investigate any number of engineering and scientific problems
Discovery of New Roles for Chondroitin Sulfate in Neurotrophin Signaling and Retinotopic Development
Get PDFChondroitin sulfate (CS), a member of the glycosaminoglycan family of linear polysaccharides, is involved in the formation and maintenance of neuronal networks. CS has dual roles in regulating neuronal morphology: promoting or inhibiting neuronal outgrowth, depending on the context. A single sulfated epitope, CS-E, is capable of inducing both types of activity.
Members of the neurotrophin (NT) family of growth factors are required for CS- E-induced neurite outgrowth in hippocampal neurons. Here, we demonstrate that CS is capable of forming ternary complexes with NTs and their receptors. These complexes were discovered using a novel, carbohydrate microarray-based approach that allows for the rapid screening of such interactions. To support these findings, we computationally determined the CS-E-binding site of the complexes, suggesting a structural basis for the interaction. In addition, we showed that CS-E is capable of attenuating NT signaling in cells, consistent with our computational and microarray data. This is the first demonstration that CS-E is involved in NT signaling and that CS is capable of supporting multimeric signaling complexes.
In addition to stimulating growth factor signaling, CS has been known to repulsively guide retinal ganglion cell (RGC) axons for over twenty years. However, its function in vivo is unknown. RGCs are the only neuron type that transmits visual information to the brain, and their guidance, which maps a topographic projection of the retina to the superior colliculus (SC), is tightly regulated. Here, we show that CS-E is required for the proper formation of this topographic order. CS-E, but not the other major sulfation patterns, is a repellent guidance cue for RGC axons, with a graded activity profile from low to high along the dorsal-ventral axis of the retina, congruent with EphB3 expression. EphB3 binds specifically to CS-E with physiologically relevant affinity, and is required for CS-E-mediated guidance. CS-E-null mice have defects in topographic mapping in which ventral axons form ectopic termina- tions medial to their correct location in the SC. These results indicate that CS is a repulsive guidance cue required to map the dorsal-ventral axis of the retina along the lateral-medial axis of the SC. This is the first report of a non-protein topographical
guidance cue.</p
Experimental Analysis of Dynamic Interactions between Micrometer-Scale Stainless Steel Spheres
No full textThe quasi-static interactions between macroscopic, spherical particles are well described by the Hertzian
contact law. However, little is known about the interaction law at the micrometer scale, where the
effects of electrostatic and hydrodynamic forces at the contact are no longer negligible. Contact
dynamics at the micrometer scale have been relatively unexplored due to experimental challenges, since
the particles are too small in size to be excited by actuators but too massive to be manipulated by
electromagnetic fields. In this work, we experimentally study the dynamic interactions between two
micrometer-scale spheres colliding in a v-shaped groove. From our experiments we determine physical
parameters of interest that inform us about the force laws that apply before, during and after the
collision. These parameters include the coefficient of air resistance, the coefficient of friction between
the spheres and the groove, the coefficient of friction between two spheres in contact, and the
coefficient of restitution
Blood Cell Count On-a-Chip
Get PDFWhite blood cell (WBC) count is one of the most frequently ordered clinical tests in hospitals. There are five types of WBCs in the circulating blood, including lymphocyte, monocyte, neutrophil, eosinophil and basophil. The WBC count test enumerates not only the total number of WBCs in per volume blood, but also the percentage of each WBC type. A portable instrument for the WBC count test is currently in demand by the NASA human spaceflight, and also by the on-earth telemedicine application. However, the commercially available tests do not meet the requirement of the portable applications, because of their large instrument size and the large reagent volume consumed per test.
This study describes the development of a WBC count technology optimized for portable applications. First, a sheathless microfluidic cytometer is developed for WBC count. This technology consumes only a small amount of blood (5 microlitre) and a minimal volume of reagents (50 microlitre). Second, fluorescent dye assays are developed for the WBC differential count by measuring fluorescent emissions on the microfluidic cytometer. Based on this technology, a portable instrument is built with high test accuracy (maximum error less than 10%).
Furthermore, this study explores two key components for future integrating this technology into a self-contained chip. First, a microvalve actuated by thermal blood clogging is developed. This valve has a simple structure suitable for on-chip integration. Second, a micromixer is used to demonstrate the staining of blood with dye assays, and the following fluorescent detection of WBCs on the cytometer.</p