Browsing by Subject "Nanoscience"
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Item Embargo A Neural Circuit for Gut Microbial Patterns to Regulate Satiety(2024) Liu, Winston WGut microbes and their host need to eat, but microbes rely on their host to control nutrient intake. Thus, microbes might use their metabolites and molecular patterns to influence the appetite of their host, including the quantity and timing of food intake. But the specific receptors, cells, transmitters, and circuits used by the host to sense and respond to the luminal stimuli of microbial patterns in real time remain unknown. In the small intestine, nutrients elicit fast sensory cues from epithelial neuropod cells that guide appetitive choice. Here, we found that in the mouse colon, microbial flagellin activates toll-like receptor 5 (TLR5) expressed on neuropod cells to reduce food intake. Mice lacking TLR5 in neuropod cells become hyperphagic and overweight. The microbial signal does not act directly on a nerve; instead, it triggers the release of peptide YY by epithelial neuropod cells, which acts on the Y2 receptor expressed in vagal nodose neurons innervating the colon. This feeding behavior change is independent of the common innate immune adaptor MyD88 or metabolic inflammation. Our results reveal a novel sensory modality, distinct from inflammatory responses, that enables an animal host to adjust its appetitive behavior by detecting patterns from its resident microbes in the colon.
Item Open Access A Theoretical and Experimental Study of DNA Self-assembly(2012) Chandran, HarishThe control of matter and phenomena at the nanoscale is fast becoming one of the most important challenges of the 21st century with wide-ranging applications from energy and health care to computing and material science. Conventional top-down approaches to nanotechnology, having served us well for long, are reaching their inherent limitations. Meanwhile, bottom-up methods such as self-assembly are emerging as viable alternatives for nanoscale fabrication and manipulation.
A particularly successful bottom up technique is DNA self-assembly where a set of carefully designed DNA strands form a nanoscale object as a consequence of specific, local interactions among the different components, without external direction. The final product of the self-assembly process might be a static nanostructure or a dynamic nanodevice that performs a specific function. Over the past two decades, DNA self-assembly has produced stunning nanoscale objects such as 2D and 3D lattices, polyhedra and addressable arbitrary shaped substrates, and a myriad of nanoscale devices such as molecular tweezers, computational circuits, biosensors and molecular assembly lines. In this dissertation we study multiple problems in the theory, simulations and experiments of DNA self-assembly.
We extend the Turing-universal mathematical framework of self-assembly known as the Tile Assembly Model by incorporating randomization during the assembly process. This allows us to reduce the tile complexity of linear assemblies. We develop multiple techniques to build linear assemblies of expected length N using far fewer tile types than previously possible.
We abstract the fundamental properties of DNA and develop a biochemical system, which we call meta-DNA, based entirely on strands of DNA as the only component molecule. We further develop various enzyme-free protocols to manipulate meta-DNA systems and provide strand level details along with abstract notations for these mechanisms.
We simulate DNA circuits by providing detailed designs for local molecular computations that involve spatially contiguous molecules arranged on addressable substrates via enzyme-free DNA hybridization reaction cascades. We use the Visual DSD simulation software in conjunction with localized reaction rates obtained from biophysical modeling to create chemical reaction networks of localized hybridization circuits that are then model checked using the PRISM model checking software.
We develop a DNA detection system employing the triggered self-assembly of a novel DNA dendritic nanostructure. Detection begins when a specific, single-stranded target DNA strand triggers a hybridization chain reaction between two distinct DNA hairpins. Each hairpin opens and hybridizes up to two copies of the other, and hence each layer of the growing dendritic nanostructure can in principle accommodate an exponentially increasing number of cognate molecules, generating a nanostructure with high molecular weight.
We build linear activatable assemblies employing a novel protection/deprotection strategy to strictly enforce the direction of tiling assembly growth to ensure the robustness of the assembly process. Our system consists of two tiles that can form a linear co-polymer. These tiles, which are initially protected such that they do not react with each other, can be activated to form linear co-polymers via the use of a strand displacing enzyme.
Item Open Access Attentional Biases in Value-Based Decision-Making(2014) San Martin Ulloa, ReneHumans make decisions in highly complex physical, economic and social environments. In order to adaptively choose, the human brain has to learn about- and attend to- sensory cues that provide information about the potential outcome of different courses of action. Here I present three event-related potential (ERP) studies, in which I evaluated the role of the interactions between attention and reward learning in economic decision-making. I focused my analyses on three ERP components (Chap. 1): (1) the N2pc, an early lateralized ERP response reflecting the lateralized focus of visual; (2) the feedback-related negativity (FRN), which reflects the process by which the brain extracts utility from feedback; and (3) the P300 (P3), which reflects the amount of attention devoted to feedback-processing. I found that learned stimulus-reward associations can influence the rapid allocation of attention (N2pc) towards outcome-predicting cues, and that differences in this attention allocation process are associated with individual differences in economic decision performance (Chap. 2). Such individual differences were also linked to differences in neural responses reflecting the amount of attention devoted to processing monetary outcomes (P3) (Chap. 3). Finally, the relative amount of attention devoted to processing rewards for oneself versus others (as reflected by the P3) predicted both charitable giving and self-reported engagement in real-life altruistic behaviors across individuals (Chap. 4). Overall, these findings indicate that attention and reward processing interact and can influence each other in the brain. Moreover, they indicate that individual differences in economic choice behavior are associated both with biases in the manner in which attention is drawn towards sensory cues that inform subsequent choices, and with biases in the way that attention is allocated to learn from the outcomes of recent choices.
Item Open Access Contaminant Interactions and Biological Effects of Single-walled Carbon Nanotubes in a Benthic Estuarine System(2013) Parks, AshleySingle-walled carbon nanotubes (SWNT) are highly ordered filamentous nanocarbon structures. As their commercial and industrial use becomes more widespread, it is anticipated that SWNT will enter the environment through waste streams and product degradation. Because of their highly hydrophobic nature, SWNT aggregate and settle out of aqueous environments, especially in saline environments such as estuaries. Therefore, sediments are a likely environmental sink for SWNT once released. It is important to understand how these materials will impact benthic estuarine systems since they are the probable target area for SWNT exposure in addition to containing many lower trophic level organisms whose survvial and contaminant body burdens can have a large impact on the overall ecosystem. Disruptions in lower trophic level organism survival can have negative consequences for higher trophic levels, impacting the overall health of the ecosystem. It is also important to consider contaminant bioaccumulation, trophic transfer and biomagnification. If SWNT are taken up by benthic invertebrates, there is the possibility for trophic transfer, increasing the exposure of SWNT to higher trophic level organisms that otherwise would not have been exposed. If this type of transfer occurs in environmentally important species, the potential for human exposure may increase. My research aims to determine the magnitude of the toxicity and bioaccumulation of SWNT in benthic estuarine systems, as well as determine how they interact with other contaminants in the environment. This research will contribute to the knowledge base necessary for performing environmental risk assessments by providing information on the effects of SWNT to benthic estuarine systems.
Before investigating the environmental effects of SWNT, it is imperative that a measurement method is established to detect and quantify SWNT once they enter the environment. This research utilized pristine, semiconducting SWNT to develop extraction and measurement methods to detect and quantify these specific materials in environmental media using near infrared fluorescence (NIRF) spectroscopy. Semiconducting SWNT fluoresce in the near infrared (NIR) spectrum when excited with visible&ndashNIR light. This unique optical property can be used to selectively measure SWNT in complex media.
The fate, bioavailability, bioaccumulation and toxicity of SWNT have not been extensively studied to date. Pristine SWNT are highly hydrophobic and have been shown to strongly associate with natural particulate matter in aquatic environments. In light of this, I have focused my research to examine the influence of sediment and food exposure routes on bioavailability, bioaccumulation, and toxicity of structurally diverse SWNT in several ecologically-important marine invertebrate species. No significant mortality was observed in any organism at concentrations up to 1000 mg/kg. Evidence of biouptake after ingestion was observed for pristine semiconducting SWNT using NIRF spectroscopy and for oxidized 14C&ndashSWNT using liquid scintillation counting. After a 24 hour depuration period, the pristine semiconducting SWNT were eliminated from organisms to below the method detection limit (5 &mug/mL), and the 14C&ndashSWNT body burden was decreased by an order of magnitude to a bioaccumulation factor (BAF) of <0.01. Neither pristine SWNT nor oxidized 14C&ndashSWNT caused environmentally relevant toxicity or bioaccumulation in benthic invertebrates. Overall, the SWNT were not bioavailable and appear to associate with the sediment.
In addition to investigating the toxicity and bioaccumulation of SWNT as an independent toxicant, it is important to consider how they will interact with other contaminants in the environment (i.e., increase or decrease toxicity and bioaccumulation of co&ndashcontaminants, alter the environmental transport of co&ndashcontaminants, induce degradation of co&ndashcontaminants, etc.). I wanted to investigate the effects of SWNT on a complex mixture of contaminants already present in a natural system. New Bedford Harbor (NBH) sediment, which is contaminated with polychlorinated biphenyls (PCBs), was amended with pristine SWNT to determine if the presence of SWNT would mitigate the toxicity and bioaccumulation of the PCBs in deposit-feeding invertebrates. A dilution series of the NBH sediment was created using uncontaminated Long Island Sound (LIS) sediment to test 25% NBH sediment, 50% NBH sediment, 75% NBH sediment, and 100% NBH sediment. The results of this work showed increased organism survival and decreased bioaccumulation of PCBs in treatments amended with SWNT, with the greatest reduction observed in the 25% NBH sediment treatment group amended with 10 mg SWNT/g dry sediment. Polyethylene (PE) passive samplers indicated a reduction of interstitial water (ITW) PCB concentration of greater than 90% in the 25% NBH sediment + 10 mg SWNT/g dry sediment amendment. The ITW concentration was reduced because PCBs were not desorbing from the SWNT. Lower bioavailability leads to reduced potential for toxic effects, supporting the observation of increased survival and decreased bioaccumulation. Once in the sediment, not only are SWNT not bioavailable, they act as a highly sorptive phase, such as black carbon (BC), into which hydrophobic organic contaminants (HOCs), such as PCBS and polycyclic aromatic hydrocarbons (PAHs), can partition, thereby reducing the toxicity and bioavailability of co-occurring HOCs.
To more fully understand the impact of SWNT in this environment, their biodegradability also needs to be investigated. Biodegradation of SWNT could lead to release and/or transformation of sorbed HOCs as well as a change in the inherent transport, toxicity, and bioaccumulation of SWNT in the estuarine environment. Because the persistence of SWNT will be a primary determinant of the fate of these materials in the environment, I conducted experiments to determine if the fungus Trametes versicolor, the natural bacterial communities present in NBH sediment, and municipal wastewater treatment plant sludge could degrade or mineralize oxidized 14C&ndashSWNT. Over a six month time period, no significant degradation or mineralization was observed. In all treatments, approximately 99% of the 14C-SWNT remained associated with the solid phase, with only approximately 0.8% of added 14C present as dissolved species and only 0.1% present as 14CO2. These small pools of non-SWNT 14C were likely due to trace impurities, as no differences in production were observed between treatments and abiotic (killed) controls.
Item Open Access Copper-Based Nanowires for Printable Memory and Stretchable Conductors(2018) Catenacci, Matthew JosephIn the field of electronic materials, metal nanowires have been extensively studied for both their syntheses and their properties in electronic composites and devices. This dissertation addresses challenges in the field of electronic materials development with the use of copper nanowires synthesized in gram-scale syntheses, as well as provides analysis of devices and composites that could only be feasibly manufactured thanks to the large-scale syntheses.
In the field of printed electronics, there has been research into the development of fully printed memories. One of the challenges has been developing a memory that has switching characteristics that are on par with existing commercial memories, such as Flash memory. This can be achieved with a composite of Cu-SiO2 nanowires dispersed in ethylcellulose, which acts as a resistive switch when between printed Cu and Au electrodes. A 16-cell crossbar array of these memristors was printed with an aerosol jet. The memristors exhibited moderate operating voltages (~3 V), no degradation over 104 switching cycles, write speeds of 3 µs, and extrapolated retention times of 10 years. The low operating voltage enabled the programming of a fully printed 4-bit memristor array with an Arduino. The excellent performance of these fully printed memristors could help enable the creation of fully printed RFID tags and sensors with integrated data storage. Thanks to the large-scale synthesis of copper nanowires, this can allow for the expanded production of high-quality, fully printed memories.
Materials that retain a high conductivity under strain are essential for wearable electronics. I describe a new conductive, stretchable composite consisting of a Cu-Ag core-shell nanowire felt infiltrated with a silicone elastomer. This composite exhibits a retention of conductivity under strain that is superior to any composite with a conductivity greater than 1000 S cm-1. This work also shows how the mechanical properties, conductivity, and deformation mechanisms of the composite changes as a function of the stiffness of the silicone matrix. The retention of conductivity under strain was found to decrease as the Young’s modulus of the matrix increased. This was attributed to void formation as a result of debonding between the nanowire felt and the elastomer. The nanowire composite was also patterned to create serpentine circuits with a stretchability of 300%. Composites of this scale and density could only be feasibly manufactured thanks to large-scale syntheses of copper nanowires and the silver coating of copper nanowires. With the advances made in the quality of stretchable conductive composites, alternate methods were employed as to manufacture new composites and structures, such as the cofiltration of nanowires and waterborne rubber to accelerate production, or the manufacturing of Cu-Ag nanowire aerogels with density tunable via the aspect ratio of the nanowires.
Item Open Access Design Optimization of Encapsulating 3D DNA Nanostructures with Curvature and Multi-layers(2022) Fu, DanielDNA origami has been a paradigm-shifting technique for synthesizing and manipulating matter with nanoscale precision. The simple design principle of using numerous short (<100 nts) oligonucleotides to "fold" a long (>1000 nts) DNA strand achieved both simplicity in design and greatly increased yields in comparison to previous motifs for DNA nanostructure design. Various approaches have been explored that have resulted in DNA nanostructures rapidly growing in mass and complexity while also becoming more accessible for a wide scientific community, such as developing computer-aided design graphical user interfaces, establishing design principles for classes of structures with algorithmic regularity, and refining synthesis strategies and the respective design criteria to exploit them.
These directions are all fundamentally a straight extension of the DNA origami technique and pursuits towards large, functional DNA origami have been amply rewarded. Yet due to the nature of how a primary driving factor of scaling designs upwards has been the exploitation of repeatable motifs, several assumptions underlie conventional strategies for the DNA origami design of complex shapes. This thesis formally classifies a geometry of curved DNA origami nanostructures and discusses how such structures do not align with existing assumptions for DNA nanostructure design. While it is class of structures that has high biotechnological relevance, the tedium of design challenges arising from this departure have limited accessibility and enthusiasm for utilizing them. To achieve greater functional relevance, DNA origami must undoubtedly retread on the establishment of strategies for scaling up mass and shape complexity in DNA nanostructures; this time beyond regular, repeating subunits, and towards supramolecular assemblies with distinct, bespoke geometric features. As such, this thesis entreats an approach towards formalizing local and global properties in DNA origami design that can be quantified and characterized for their effects on DNA nanostructure yield and stability. Thus, a generalized strategy for DNA origami design can be born.
This thesis first consolidates and proposes a hierarchy of properties active in DNA origami design. It then suggests and evaluates two heuristic optimization algorithms to attempt a multi-variable optimization of those properties to achieve rapid generation of oligonucleotide sequences to generate desired DNA origami shapes. This thesis then discusses the existing challenges and potential applications of curved DNA origami nanostructures. Lastly, the application of the aforementioned optimization algorithms are applied to generate examples in this class of nanostructures, and the results are hither reported and discussed.
Item Open Access Development of Methods for Biomedical Diagnostics and Therapy using Plasmonic Nanoplatforms(2023) Odion, Ren ArriolaPlasmonic nanoplatforms have fundamentally changed the landscape of biomedical sciences, particularly in the fields of early disease detection and treatment. Metallic nanoparticles with unique geometries and compositions such as gold nanostars (GNS) and nanorattles (NR) have allowed for the development of highly sensitive and effective platforms for detecting early disease biomarkers such as RNA without the need for laboratory-based sample amplification tools such as polymerase chain reaction (PCR). Furthermore, these plasmonics-active particles have also enabled novel optical methods for deep tissue tumor detection without the associated energy concerns and technical complexity of traditional imaging methods such as X-Ray computed tomography (CT) or magnetic resonance imaging (MRI). Finally, these particles can also be used for their effective photon to heat conversion capabilities for highly specific treatment of cancer tissue. The body of work described here is a culmination of several applications of plasmonic nanoparticles ranging from biomarker disease detection to deep tumor localization and photothermal treatment.
Recent advances in the of plasmonic nanoplatforms utilizing gold nanoparticles have resulted in many applications for point-of-care (POC) diagnostics. Upon laser excitation, the surface plasmons on the gold nanoparticles strongly oscillate, generating a strong electromagnetic field (EF) in the vicinity of the nanoparticle surface. This EF field enhancement, often referred to as the plasmonic effect, can be utilized to greatly increase the Raman scattering signal of molecules near the particle’s surface. This phenomenon called Surface-Enhanced Raman Scattering (SERS) can then be utilized for highly specific diagnostic and therapeutic applications. Our group has developed numerous biosensors that take advantage of this unique plasmonic property for use in non-invasive and non-amplifying biomarker detection. Due to its strong SERS signal, the ultrabright SERS nanorattles were developed as a unique sandwich hybridization biosensor for nucleic acid detection. We have demonstrated their successful use in detecting unamplified RNA genetic biomarkers of squamous cell carcinoma (SCC) for Head and Neck Cancers (HNCs) in a joint project with our clinical collaborator, Dr. Walter Lee, MD.
Nanoparticle platforms have also allowed for the development of novel optical and spectroscopic detection of deeply seated tumors. The unique spectroscopic fingerprint of SERS spectra on Raman-labelled GNS can be paired with optical techniques that separate the excitation laser source from the detector, which allows for deep tissue interrogation. approach This Surface-Enhanced Spatially Offset Raman Spectroscopy (SESORS) modality has allowed for the detection of GNS in tissue model systems such as through the centimeter-thick bone of a monkey skull. This spatial offset detection mechanism was further developed into a more general system known as Optical Recognition of Constructs using Hyperspectral Imaging and Detection (ORCHID). This system takes advantage of the two-dimensional charge-coupled detection (CCD) system itself as a means of physical separation between the source and detector, and by binning pixels of specific radial distances, a novel and digital-based spatial offset system can be utilized for probing deep tissue layers.
Finally, nanoparticles are utilized for the improved and highly targeted treatment of cancer tissue by taking advantage of the enhanced permeation and retention (EPR) effect in tumors. The photothermal heat treatment with GNS allows for highly specific targeted treatment of tumor, thereby minimizing off-target healthy tissue heating. We have demonstrated this in a brain tumor in a mouse model in a collaborative project with our clinical collaborator Dr. Peter Fecci, MD. We have also developed several simulation models utilizing Monte Carlo Photon propagation as well as analytical thermal diffusion models to demonstrate this effect in tissue containing GNS accumulated in a tumor volume. These simulations were then complemented with experimental studies showing the extent of heat using MRI heat imaging and direct contact thermocouples.
Item Open Access Electron Transport through Carbon Nanotube Quantum Dots in A Dissipative Environment(2012) Mebrahtu, Henok TesfamariamThe role of the surroundings, or environment , is essential in understanding funda- mental quantum-mechanical concepts, such as quantum measurement and quantum entanglement. It is thought that a dissipative environment may be responsible for certain types of quantum (i.e. zero-temperature) phase transitions. We observe such a quantum phase transition in a very basic system: a resonant level coupled to a dissipative environment. Specifically, the resonant level is formed by a quantized state in a carbon nanotube, and the dissipative environment is realized in resistive leads; and we study the shape of the resonant peak by measuring the nanotube electronic conductance.
In sequential tunneling regime, we find the height of the single-electron conductance peaks increases as the temperature is lowered, although it scales more weakly than the conventional T-1. Moreover, the observed scaling signals a close connec- tion between fluctuations that influence tunneling phenomenon and macroscopic models of the electromagnetic environment.
In the resonant tunneling regime (temperature smaller than the intrinsic level width), we characterize the resonant conductance peak, with the expectation that the width and height of the resonant peak, both dependent on the tunneling rate, will be suppressed. The observed behavior crucially depends on the ratio of the coupling between the resonant level and the two contacts. In asymmetric barriers the peak width approaches saturation, while the peak height starts to decrease.
Overall, the peak height shows a non-monotonic temperature dependence. In sym- metric barriers case, the peak width shrinks and we find a regime where the unitary conductance limit is reached in the incoherent resonant tunneling. We interpret this behavior as a manifestation of a quantum phase transition.
Finally, our setup emulates tunneling in a Luttinger liquid (LL), an interacting one-dimensional electron system, that is distinct from the conventional Fermi liquids formed by electrons in two and three dimensions. Some of the most spectacular properties of LL are revealed in the process of electron tunneling: as a function of the applied bias or temperature the tunneling current demonstrates a non-trivial power-law suppression. Our setup allows us to address many prediction of resonant tunneling in a LL, which have not been experimentally tested yet.
Item Open Access Engineering Exquisite Nanoscale Behavior with DNA(2012) Gopalkrishnan, NikhilSelf-assembly is a pervasive natural phenomenon that gives rise to complex structures and functions. It describes processes in which a disordered system of components form organized structures as a consequence of specific, local interactions among the components themselves, without any external direction. Biological self-assembled systems, evolved over billions of years, are more intricate, more energy efficient and more functional than anything researchers have currently achieved at the nanoscale. A challenge for human designed physical self-assembled systems is to catch up with mother nature. I argue through examples that DNA is an apt material to meet this challenge. This work presents:
1. 3D self-assembled DNA nanostructures.
2. Illustrations of the simplicity and power of toehold-mediated strand displacement interactions.
3. Algorithmic constructs in the tile assembly model.
Item Open Access Foundational Studies of the Deposition of Metal-Halide Perovskite Thin Films by Resonant Infrared, Matrix-Assisted Pulsed Laser Evaporation(2020) Barraza, Enrique TomasMetal-halide perovskites (MHP) comprise a diverse family of crystalline materials whose optoelectronic properties have gathered significant interest recently. Their use in transistors, solar cells, light emitting diodes, and many other applications with significant real-world impacts has been enabled by synthesis techniques that can deposit high quality MHP thin films. The simple yet powerful chemistry involved in solution-processing techniques has allowed for MHP thin films to be deposited in a variety of different ways like spin-coating, inkjet printing, and doctor blading. However, solvent in these techniques can preclude the creation of advanced MHP structures like graded composition films or all-MHP heterojunctions. Additionally, the poor solubility of complex organic moieties in the polar solvents used in solution-processing of MHP materials could prevent the creation of MHP materials with unique photophysical properties. The development of vapor-processing techniques which circumvent the use of solvent to vaporize MHP precursors and deposit thin films has shown promise in addressing these concerns with solution-processing. However, the use of highly energetic precursor vaporization mechanisms has itself raised worries about its broad applicability.
In this dissertation, the deposition of MHP thin films using Resonant Infrared, Matrix-Assisted Pulsed Laser Evaporation (RIR-MAPLE) is developed as an alternative to current MHP thin film deposition techniques. The ‘dry’ deposition of materials under dynamic vacuum and the use of a low energy infrared laser directly address shortcomings of solution- and vapor-processing techniques, respectively. Using the understanding of RIR-MAPLE developed by previous studies, a double solvent approach was first developed to solubilize and deposit MHP precursors in a manner which maintained the integrity of the resulting films. The viability of this baseline approach was confirmed through the creation of MHP solar cells with competitive performance and thin films of MHP materials with complex organic moieties that demonstrate unique photophysical properties. Subsequent studies of nuanced aspects in RIR-MAPLE deposition of MHP thin films helped develop an understanding of the process-structure-property relationships in play during RIR-MAPLE deposition and in post-processing of the resulting MHP thin films.
Following these baseline studies, unique precursor delivery schemes were developed to demonstrate the versatility of RIR-MAPLE. These schemes were shown to reliably deposit continuous films of MHP materials despite differences in the state of precursors during deposition and crystallization. Finally, a comprehensive study of MHP film formation mechanisms during RIR-MAPLE deposition was undertaken. These experiments categorically described the wetting, nucleation, diffusion, and accumulation essential to MHP film development during RIR-MAPLE deposition. Overall, this work demonstrates some of the most promising aspects of the RIR-MAPLE deposition technique and develops the candidacy of RIR-MAPLE as an MHP thin film technique uniquely positioned to address the shortcomings of other currently established methods.
Item Unknown Functionalization of DNA Nanostructures for Cell Signaling Applications(2014) Pedersen, RonnieTransforming growth factor beta (TGF-beta) is an important cytokine responsible for a wide range of different cellular functions including extracellular matrix formation, angiogenesis and epithelial-mesenchymal transition. We have sought to use self-assembling DNA nanostructures to influence TGF-beta signaling.
The predictable Watson Crick base pairing allows for designing selfassembling nanoscale structures using oligonucleotides. We have used the method of DNA origami to assemble structures functionalized with multiple peptides that bind TGF-beta receptors outside the ligand binding domain. This allows the nanostructures to cluster TGF-beta receptors and lower the energy barrier of ligand binding thus sensitizing the cells to TGF-beta stimulation. To prove efficacy of our nanostructures we have utilized immunofluorescent staining of Smad2/4 in order to monitor TGF-beta mediated translocation of Smad2/4 to the cell nucleus. We have also utilized Smad2/4 responsive luminescence constructs that allows us to quantify TGF-beta stimulation with and without nanostructures.
To functionalize our nanostructures we relied on biotin-streptavidin linkages. This introduces a multivalency that is not necessarily desirable in all designs. Therefore we have investigated alternative means of functionalization.
The first approach is based on targeting DNA nanostructure by using zinc finger binding proteins. Efficacy of zinc finger binding proteins was assayed by the use of enzyme-linked immunosorbent (ELISA) assay and atomic force microscopy (AFM). While ELISA indicated a relative specificity of zinc finger proteins for target DNA sequences AFM showed a high degree of non-specific binding and insufficient affinity.
The second approach is based on using peptide nucleic acid (PNA) incorporated in the nanostructure through base pairing. PNA is a synthetic DNA analog consisting of a backbone of repeating N-(2-aminoethyl)-glycine units to which purine and pyrimidine bases are linked by amide bonds. The solid phase synthesis of PNA allows for convenient extension of the backbone into a peptide segment enabling peptide functionalization of DNA nanostructures. We have investigated how the neutral character of PNA alters the incorporation in DNA based nanostructures compared to a DNA control using biotinylation and AFM.
Results indicate that PNA can successfully be used as a way of functionalizing DNA nanostructures. Additionally we have shown that functionalized nanostructures are capable of sensitizing cells to TGF-beta stimulation.
Item Unknown Gallium-based Ultraviolet Nanoplasmonics(2013) Yang, YangNanometer-scale metallic structures have been widely and intensively studied over the last decade because of their remarkable plasmonic properties that can enhance local electromagnetic (EM) fields. However, most plasmonic applications are restricted to the visible and near infrared photon energies due to the limitations of the surface plasmon resonance energies of the most commonly used plasmonic metals: Au and Ag. Plasmonic applications in ultraviolet (UV) are of great interest because Raman scattering sections are larger and do not overlap fluorescence spectra. UV plasmonics also benefit from high spatial resolution and low penetration depth. However, an appropriate UV plasmonic material must be identified.
We proposed and demonstrated that gallium is a highly-promising and compelling material for UV nanoplasmonics through synthesis of size-controlled nanoparticle arrays, EM modeling of local field enhancement, ellipsometric and spatial characterization of the arrays, and analytical measurement of UV- enhanced Raman and fluorescence spectra. Self-assembled arrays of hemispherical gallium nanoparticles deposited by molecular beam epitaxy on a sapphire support are characterized with spatial and ellipsometric measurements. Spin-casting a thin film of crystal violet upon these nanoparticles permitted the demonstration of surface-enhanced Raman spectra, fluorescence, and molecular photodegradation following excitation by a HeCd laser operating at 325 nm (UV). Measured local Raman enhancement factors exceeding 107 demonstrated the potential of gallium nanoparticle arrays for plasmonically-enhanced ultraviolet detection and remediation.
Item Unknown Growth, Characterization, and Properties of Hybrid Graphene-Carbon Nanotube Films and Related Carbon Nanostructures(2016) Ubnoske, Stephen M.Graphene, first isolated in 2004 and the subject of the 2010 Nobel Prize in physics, has generated a tremendous amount of research interest in recent years due to its incredible mechanical and electrical properties. However, difficulties in large-scale production and low as-prepared surface area have hindered commercial applications. In this dissertation, a new material is described incorporating the superior electrical properties of graphene edge planes into the high surface area framework of carbon nanotube forests using a scalable and reproducible technology.
The objectives of this research were to investigate the growth parameters and mechanisms of a graphene-carbon nanotube hybrid nanomaterial termed “graphenated carbon nanotubes” (g-CNTs), examine the applicability of g-CNT materials for applications in electrochemical capacitors (supercapacitors) and cold-cathode field emission sources, and determine materials characteristics responsible for the superior performance of g-CNTs in these applications. The growth kinetics of multi-walled carbon nanotubes (MWNTs), grown by plasma-enhanced chemical vapor deposition (PECVD), was studied in order to understand the fundamental mechanisms governing the PECVD reaction process. Activation energies and diffusivities were determined for key reaction steps and a growth model was developed in response to these findings. Differences in the reaction kinetics between CNTs grown on single-crystal silicon and polysilicon were studied to aid in the incorporation of CNTs into microelectromechanical systems (MEMS) devices. To understand processing-property relationships for g-CNT materials, a Design of Experiments (DOE) analysis was performed for the purpose of determining the importance of various input parameters on the growth of g-CNTs, finding that varying temperature alone allows the resultant material to transition from CNTs to g-CNTs and finally carbon nanosheets (CNSs): vertically oriented sheets of few-layered graphene. In addition, a phenomenological model was developed for g-CNTs. By studying variations of graphene-CNT hybrid nanomaterials by Raman spectroscopy, a linear trend was discovered between their mean crystallite size and electrochemical capacitance. Finally, a new method for the calculation of nanomaterial surface area, more accurate than the standard BET technique, was created based on atomic layer deposition (ALD) of titanium oxide (TiO2).
Item Unknown Impact of Particle Aggregation on Nanoparticle Reactivity(2011) Jassby, DavidThe prevalence of nanoparticles in the environment is expected to grow in the coming years due to their increasing pervasiveness in consumer and industrial applications. Once released into the environment, nanoparticles encounter conditions of pH, salinity, UV light, and other solution conditions that may alter their surface characteristics and lead to aggregation. The unique properties that make nanoparticles desirable are a direct consequence of their size and increased surface area. Therefore, it is critical to recognize how aggregation alters the reactive properties of nanomaterials, if we wish to understand how these properties are going to behave once released into the environment. The size and structure of nanoparticle aggregates depend on surrounding conditions, including hydrodynamic ones. Depending on these conditions, aggregates can be large or small, tightly packed or loosely bound. Characterizing and measuring these changes to aggregate morphology is important to understanding the impact of aggregation on nanoparticle reactive properties. Examples of decreased reactivity due to aggregation include the case where tightly packed aggregates have fewer available surface sites compared to loosely packed ones; also, photocatalytic particles embedded in the center of large aggregates will experience less light when compared to particles embedded in small aggregates. However, aggregation also results in an increase in solid-solid interfaces between nanoparticles. This can result in increased energy transfer between neighboring particles, surface passivation, and altered surface tension. These phenomena can lead to an increase in reactivity. The goal of this thesis is to examine the impacts of aggregation on the reactivity of a select group of nanomaterials. Additionally, we examined how aggregation impacts the removal efficiency of fullerene nanoparticles using membrane filtration.
The materials we selected to study include ZnS - a metal chalcogenide nanoparticle that photoluminesces after exposure to UV; TiO2 and ZnO nanoparticles - photocatalytic nanoparticles that generate reactive oxygen species upon UV irradition; and, fullerene nanoparticles used in the filtration experiments, selected for their potential use, small size, and surface chemistry. Our primary methods used to characterize particle and aggregate characteristics include dynamic light scattering used to describe particle size, static light scattering used to characterize aggregate structure (fractal dimension), transmission electron microscopy used to verify primary particle sizes, and electrophoretic mobility measurements to evaluate suspension stability. The reactive property of ZnS that was measured as a function of aggregation was photoluminescence, which was measured using a spectrofluorometer. The reactive property of TiO2 and ZnO that was studied was their ability to generate hydroxyl radicals; these were measured by employing a fluorescent probe that becomes luminescent upon interaction with the hydroxyl radical. To detect the presence of fullerene nanoparticles and calculate removal efficiencies, we used total organic carbon measurements. Additionally, we used UV-vis spectroscopy to approximate the impact of particle shadowing in TiO2 and ZnO aggregates, and Fourier transformed infrared spectroscopy to determine how different electrolytes interact with fullerene surface groups.
Our findings indicate that the impact of aggregation on nanoparticle reactivity is material specific. ZnS nanoparticles exhibit a 2-fold increase in band-edge photoluminescence alongside a significant decrease in defect-site photoluminescence. This is attributed to aggregate size-dependent surface tension. Additionally, we used photoluminescence measurements to develop a new method for calculating the critical coagulation concentration of a nanoparticle suspension.
The ability of both TiO2 and ZnO to generate hydroxyl radicals was significantly hampered by aggregation. The decline in hydroxyl radical generation could be attributed to two key parameters. First, increased aggregate size was associated with increased particle shadowing, as determined from the observed decrease in the rate of optically induced transitions. Secondly, aggregate structure was associated both with increased shadowing (denser aggregates exhibited more shadowing than similarly sized loose aggregates), and with an increase in radical quenching on neighboring particle surfaces in an aggregate.
Aggregation had a positive impact on hydroxylated fullerene membrane separation, increasing removal efficiency to around 80%, regardless of transmembrane pressure. However, the type of electrolyte used determined whether aggregation was successful at increasing removal. Divalent ions, capable of forming strong covalent bonds with surface oxygen groups, increased removal efficiency and made it pressure insensitive. In contrast, monovalent ions increased removal efficiency slightly, but maintained the pressure dependence of the removal efficiency. Evidence is presented to support the hypothesis that divalently aggregated hydroxylated fullerenes deform under increased pressure and partially penetrate the membrane.
Finally, nanoparticle reactive properties depend on the primary particle aggregation state. Both size and structure are key factors when evaluating nanomaterial reactivity under aggregation-inducing conditions. However, the impact of aggregation is not easily predicted. Some materials exhibit a decreased reactivity while others experience an increase. Therefore, the impact of aggregation on nanoparticle reactive properties must be evaluated on a material-by-material basis, while considering all of the particle and aggregate characteristics as well as environmental ones.
Item Unknown Lasing From Single Film-Coupled Nanoparticles(2022) Deputy, XanderPlasmonic nanostructures and metamaterials have found many applications as small-scale sources of controllable emission. Of particular interest is utilizing these types of structures as potential coherent radiation sources. Plasmonic Film-coupled Nanoparticles(FCNP), or nanopatch antennas, are good candidates for low-threshold, room-temperature nanolasing that can be predicted analytically. In this dissertation, I present results from multiphysical numerical models used to validate the predictions of a recent analytical theory, using optical pump intensity, population inversion, and pump photon count as metrics of lasing threshold. I show that a single cylindrical nanopatch antenna made of silver with an embedded fluorescent dye is capable of lasing at a threshold on the order of $10^4$ W/cm$^2$. I go beyond the hypotheses of the theoretical model by investigating the impact of spectrally non-separated absorption and emission transitions through the influence of lasing signal/absorption line and pump/emission line interactions. Furthermore, I tighten the model constraints and analytical predictions to facilitate experimental verification and ultimately demonstrate predicted lasing behavior. Thresholds on the order of $10^5$ W/m$^2$ are verified from fabricated experimental samples through spectral and coherence measurements of emission as a function of incident optical pump intensity from single film-coupled nanocubes with a variety of embedded dyes corresponding favorable geometric and material parameters. Agreement between analytically predicted thresholds and experimentally measured thresholds validates the previously developed theory and demonstrates the utility of the single film-coupled nanoparticle platform for lasing.
Item Unknown Lights, Camera, Reaction! The Influence of Interfacial Chemistry on Nanoparticle Photoreactivity(2016) Farner Budarz, Jeffrey MichaelThe ability of photocatalytic nanoparticles (NPs) to produce reactive oxygen species (ROS) has inspired research into several new applications and technologies, including water purification, contaminant remediation, and self-cleaning surface coatings. As a result, NPs continue to be incorporated into a wide variety of increasingly complex products. With the increased use of NPs and nano-enabled products and their subsequent disposal, NPs will make their way into the environment. Currently, many unanswered questions remain concerning how changes to the NP surface chemistry that occur in natural waters will impact reactivity. This work seeks to investigate potential influences on photoreactivity – specifically the impact of functionalization, the influence of anions, and interactions with biological objects - so that ROS generation in natural aquatic environments may be better understood.
To this aim, titanium dioxide nanoparticles (TiO2) and fullerene nanoparticles (FNPs) were studied in terms of their reactive endpoints: ROS generation measured through the use of fluorescent or spectroscopic probe compounds, virus and bacterial inactivation, and contaminant degradation. Physical characterization of NPs included light scattering, electron microscopy and electrophoretic mobility. These systematic investigations into the effect of functionalization, sorption, and aggregation on NP aggregate structure, size, and reactivity improve our understanding of trends that impact nanoparticle reactivity.
Engineered functionalization of FNPs was shown to impact NP aggregation, ROS generation, and viral affinity. Fullerene cage derivatization can lead to a greater affinity for the aqueous phase, smaller mean aggregate size, and a more open aggregate structure, favoring greater rates of ROS production. At the same time however, fullerene derivatization also decreases the 1O2 quantum yield and may either increase or decrease the affinity for a biological surface. These results suggest that the biological impact of fullerenes will be influenced by changes in the type of surface functionalization and extent of cage derivatization, potentially increasing the ROS generation rate and facilitating closer association with biological targets.
Investigations into anion sorption onto the surface of TiO2 indicate that reactivity will be strongly influenced by the waters they are introduced into. The type and concentration of anion impacted both aggregate state and reactivity to varying degrees. Specific interactions due to inner sphere ligand exchange with phosphate and carbonate have been shown to stabilize NPs. As a result, waters containing chloride or nitrate may have little impact on inherent reactivity but will reduce NP transport via aggregation, while waters containing even low levels of phosphate and carbonate may decrease “acute” reactivity but stabilize NPs such that their lifetime in the water column is increased.
Finally, ROS delivery in a multicomponent system was studied under the paradigm of pesticide degradation. The presence of bacteria or chlorpyrifos in solution significantly decreased bulk ROS measurements, with almost no OH detected when both were present. However, the presence of bacteria had no observable impact on the rate of chlorpyrifos degradation, nor chlorpyrifos on bacterial inactivation. These results imply that investigating reactivity in simplified systems may significantly over or underestimate photocatalytic efficiency in realistic environments, depending on the surface affinity of a given target.
This dissertation demonstrates that the reactivity of a system is largely determined by NP surface chemistry. Altering the NP surface, either intentionally or incidentally, produces significant changes in reactivity and aggregate characteristics. Additionally, the photocatalytic impact of the ROS generated by a NP depends on the characteristics of potential targets as well as on the characteristics of the NP itself. These are complicating factors, and the myriad potential exposure conditions, endpoints, and environmental systems to be considered for even a single NP highlight the need for functional assays that employ environmentally relevant conditions if risk assessments for engineered NPs are to be made in a timely fashion so as not to be outpaced by, or impede, technological advances.
Item Open Access Localized DNA Computation(2017) Bui, Hieu TrungRecently, solution-based systems for DNA computation have demonstrated the enormous potential of DNA nanosystems to do computation at the molecular-scale. These use DNA strands to encode values and use DNA hybridization reactions to perform computations. But most of these prior DNA computation systems relied on the diffusion of DNA strands to transport values during computations. During diffusion, DNA molecules randomly collide and interact in a three-dimensional fluidic space. At low concentrations and temperatures, diffusion can be quite slow and could impede the kinetics of these systems whereas at higher concentrations and temperature, unintended spurious interactions during diffusion can hinder the computations. Hence, increasing the concentration of DNA strands to speed up DNA hybridization reactions has the unfortunate side effect of increasing leaks, which are undesired hybridization reactions in the absence of input strands. Also, diffusion-based systems possess global states encoded via concentration of various species and hence exhibit only limited parallel ability.
To address these challenges, this dissertation describes a novel design for DNA computation called a localized hybridization network, where diffusion of DNA strands does not occur. Instead all of the DNA strands are localized by attaching them to an addressable substrate such as DNA nanotrack and DNA origami. This localization increases the relative concentration of the reacting DNA strands thereby speeding up the kinetics. This dissertation demonstrated a localized hybridization network that executed a chain reaction of five DNA hybridizations which executes faster than non-localized DNA reactions.
Another advantage of this approach is that each copy of the localized hybridization network operates independently of each other, allowing for a high level of parallelism. Localized hybridization networks also allow one to reuse the same DNA sequence to perform different actions at distinct location on the addressable substrate, increasing the scalability of such systems by exploiting the limited sequence space. An advantage of localized hybridization computational circuit is sharper switching behavior as information is encoded over the state of a single molecule. This also eliminates the need for thresholding as computation is performed locally eliminating the need for a global consensus.
There are many applications for localized hybridization networks. These include counting the number of disease marker molecules in a patient, detecting various cancer DNA sequences, and detecting and distinguishing bacteria by their distinguishing DNA. The results from localized DNA hybridization reactions may also be of practical use in performing surface computation on cellular membranes for disease detection and prevention.
Item Open Access Manipulation of Nonlinear Optical Processes in Plasmonic Nanogap Cavities(2020) Shen, QixinNonlinear generation of optical fields has enabled many exciting breakthroughs in light science such as nonlinear imaging, all-optical switching and supercontinuum generation. The intrinsic nonlinear response from bulk materials is extremely weak and phase matching conditions need to be satisfied for efficient generation. Plasmonic structures have proven to be a promising platform to investigate nonlinear optics due to the capability to enhance and localize electromagnetic fields within subwavelength volumes beyond the diffraction limit. However, the origin of the large nonlinear response observed in the plasmonic structures is not fully understood and the investigations of nonlinear processes involving multiple excitation wavelengths are limited. Furthermore, simultaneous enhancement and precise manipulation of multiple nonlinear optical processes have not been experimentally demonstrated.
In this dissertation, I describe a specific film-coupled plasmonic nanogap cavity structure consisting of arrays of nanoparticles separated from a metallic ground plane by an ultrathin dielectric layer. Polarization-dependent, dual-band and spatially-overlapped resonances are obtained with arrays of rectangle nanoparticles where the two resonances can be tuned independently. Highly efficient third harmonic generation (THG) is achieved by integrating dielectric materials in plasmonic nanogap cavities, resulting in more than six orders of magnitude enhancement in the THG response compared with a bare gold film. Utilizing comprehensive spectral analysis and finite-element simulation, it is concluded that the main contributing nonlinear source is dielectric material in the gap. Furthermore, I demonstrate simultaneous enhancement of three nonlinear responses from THG, sum frequency generation (SFG) and four wave mixing (FWM) by integrating 1-7 nm Al2O3 layer in the nanocavities formed by a gold ground plane and silver nanorectangles. Enhancement up to 106-fold for both THG and FWM and 104-fold for SFG is achieved when the excitation wavelengths overlap with the resonance wavelengths from transverse and longitudinal modes of the nanorectangles. Precise control of the relative strength of these nonlinear responses is demonstrated either actively by varying the ratio between excitation powers or passively by changing the Al2O3 gap thickness. Moreover, a metasurface-based efficient frequency mixer is realized utilizing diamond and a novel polymer transfer process is employed for creating nanoparticle arrays. This new insight into the nonlinear response in ultrathin gaps between metals is expected to be promising for both the fundamental understanding of nonlinear optics at the deep nanoscale and efficient on-chip nonlinear devices such as ultrafast optical switching and entangled photon sources. The capability to precisely manipulate nonlinear optical processes at the nanoscale could find important applications for nonlinear imaging and quantum communication.
Item Open Access Mapping Sensitivity of Nanomaterial Field-Effect Transistors(2020) Noyce, Steven GaryAs society becomes increasingly data-driven, the appetite of individuals, corporations, and algorithms for data sources swells, strengthening the demand for sensors. Chemical sensors are of particular interest as they provide highly human-relevant information, such as DNA sequences, cancer biomarker concentrations, blood glucose levels, antibody detection, and viral testing, to name a few. Among the most promising transduction elements for chemical sensors are nanomaterial field-effect transistors (FETs). The nanoscale size of these devices allows them to operate using very small sample sizes (an extremely small volume of patient blood, for instance), be strongly influenced by low concentrations of the target chemical, and be produced at low-cost, potentially using the same methods developed for consumer electronics (which have achieved a cost of less than 0.000001 cents per device). Nanomaterial FET-based chemical sensors also have the advantage of directly transducing a chemical presence or change to an electrical output signal. This avoids components such as lasers, optics, fluorophores, and more, that are frequently used as a part of the transduction chain in other types of chemical sensors, adding size, complexity, and cost. Much work has focused on demonstrating one-off nanomaterial FET-based sensors, but less work has been done to determine the underlying mechanisms that lead to sensitivity by mapping sensitivity against other variables in experimental devices. With challenges of consistency and reproducible operation stifling progress in this field, there is a significant need to improve understanding of nanomaterial-based FET sensitivity and operation mechanisms.
The work contained in this dissertation maps the sensitivity of nanomaterial FETs across a range of parameters, including space, time, device operating point, and analyte charge. This mapping is performed in an effort to yield insight into the underlying mechanisms that govern the sensitivity of these devices to nearby charges. In order to both draw comparisons between different device types and to make the results of this work broadly applicable to the field as a whole, four types of devices were studied that span a broad range of characteristics. The device types spanned from channels of one-dimensional nanotubes to three-dimensional nanostructures, and from partially printed fabrication to cleanroom-based nanofabrication. Specifically, the devices explored herein are carbon nanotube (CNT) FETs, molybdenum disulfide (MoS2) FETs, silicon nanowire FETs, and carbon nanotube thin-film transistors (CNT-TFTs). Fabrication processes were developed to build devices of each of these types that are capable of undergoing long-term electronic testing with reliable contact strategies. Passivation schemes were also developed for each device type to enable testing in solution and formation of solution-based sensors so that results could be extended to the case of biosensors. An automated experimentation platform was developed to enable tight synchronization between characterization instruments so that each variable impacting device sensitivity could be controlled and measured in tandem, in some cases for months on end.
Many of the obtained results showed similar trends in sensitivity between device types, while some findings were unique to a given channel material. All tested devices showed stability after a period of drain current settling caused by the occupation equilibration of charge trap states – an effect that was found to severely reduce sensitivity and dynamic range. For CNTs specifically, two new decay modes were discovered (intermediate between device stability and breakdown) along with respective onset voltages that can be used to avoid them. For CNT-TFTs, it was found that the relationship between signal-to-noise ratio (SNR) and device operating point remained consistent between ambient air and solution environments, indicating that this relationship is governed primarily by properties of the device. A simple chemical sensor made from the same devices showed a clear peak in the SNR near the device threshold voltage – a result that became increasingly meaningful when combined with similar observations in other device types obtained via separate experimental methods.
For both silicon nanowire and MoS2 FETs, sensitivity was mapped in space with sub-nanometer precise control over analyte position. Both device types manifested distinct sensitivity hotspots spread across the geometry of the channel. These hotspots were found to be stable in time, but their prominence depended heavily on the device operating point. When SNR was mapped across a range of operating points for these devices, a clear peak was discovered, with the hotspot intensity culminating at the peak. Ideal operating points were identified to be near the threshold voltage for both device types, with findings (and a developed numerical model) in MoS2 indicating that the operating point where SNR is maximized may depend upon the extent of the channel that is influenced by the analyte. Observations from multiple devices and approaches revealed that SNR peaks below the point of maximal transconductance, offering increased resolution to a matter that has previously been of some debate in the literature. In MoS2 FETs, a significant asymmetry was discovered in the response of devices to analytes of opposing polarity, with analytes that modulate devices toward their off-state eliciting a much larger response (and, correspondingly, SNR). This asymmetry was confirmed by a numerical model that suggested it to be a general result applicable to all FET-based charge detection sensors, leading to the recommendation that sensor designers select FETs that will be turned off by the target analyte.
Each finding contributed by this dissertation provides insight into future sensor designs and increases clarity of the underlying mechanisms leading to sensitivity in nanomaterial FET-based sensors. The discovery of decay modes, hotspots, ideal operating points, asymmetries, and other trends comprise substantial scientific advancements and propel the field closer to the goal of providing ubiquitous access to critical information, diagnoses, and measurements that promptly and correctly inform decisions.
Item Open Access Metamaterials Analysis, Modeling, and Design in the Point Dipole Approximation(2017) Bowen, PatrickThis dissertation is focused on applying the discrete dipole approximation to modeling metamaterial structures and devices. In particular, it is focused on modeling the linear and nonlinear behavior of one particular kind of metasurface, called a film-coupled metasurface. Film-coupled metasurfaces are periodic structures of metamaterial elements where the elements are placed a deeply subwavelength distance away from a metal film. The optical nanopatch antenna is an example of a particularly interesting film-coupled metasurface, and it is explored in depth in this dissertation. Starting with fundamental coupled mode theory approaches, fully predictive, analytic formula are developed that solve for the polarizabilities of the elements, which in turn are used to compute the reflective properties of the metasurface, including the effects of spatial dispersion using the language of effective medium theory. The theory is able to explain Wood's anomalies of the structure from an effective medium standpoint, again using purely analytic results that show excellent agreement with experiments and full-wave simulations. fThe linear optical theory is extended in later chapters to applications in nonlinear optics including bistability and lasing in four-level systems. The final chapter is devoted to solving for surface modes of the structure with complex eigenfrequencies, which may be useful in future work for explaining recent experiments that show lasing in modes that are spatially coherent across the surface.
Modeling other metamaterial devices using the discrete dipole approximation, including radio frequency metamaterial antennas, is discussed in the appendices.