Spectroscopic Tagging Lucas A. Lane,† Ximei Qian,† and Shuming Nie*,†,‡ †Departments of Biomedical Engineering and Chemistry, Emory University and Georgia Institute of Technology, Health Sciences Research Building, Room E116, 1760 Haygood Drive, Atlanta, Georgia 30322, United States ‡College of Engineering and Applied Sciences, Nanjing University, 22 Hankou Road, Nanjing, Jiangsu Province 210093, China

SERS Nanoparticles in Medicine: From Label-Free Detection to Spectroscopic Tagging.

Metallic nanostructures now play an important role in many applications. In particular, for the emerging fields of plasmonics and nanophotonics, the ability to engineer metals on nanometric scales allows the development of new devices and the study of exciting physics. This review focuses on top-down nanofabrication techniques for engineering metallic nanostructures, along with computational and experimental characterization techniques. A variety of current and emerging applications are also covered.

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Engineering metallic nanostructures for plasmonics and nanophotonics

A topical review of numerical and experimental studies of supercontinuum generation in photonic crystal fiber is presented over the full range of experimentally reported parameters, from the femtosecond to the continuous-wave regime. Results from numerical simulations are used to discuss the temporal and spectral characteristics of the supercontinuum, and to interpret the physics of the underlying spectral broadening processes. Particular attention is given to the case of supercontinuum generation seeded by femtosecond pulses in the anomalous group velocity dispersion regime of photonic crystal fiber, where the processes of soliton fission, stimulated Raman scattering, and dispersive wave generation are reviewed in detail. The corresponding intensity and phase stability properties of the supercontinuum spectra generated under different conditions are also discussed.

Supercontinuum generation, photonic crystal fiber

Resonant waveguide gratings (RWGs), also known as guided mode resonant (GMR) gratings or waveguide-mode resonant gratings, are dielectric structures where these resonant diffractive elements benefit from lateral leaky guided modes from UV to microwave frequencies in many different configurations. A broad range of optical effects are obtained using RWGs such as waveguide coupling, filtering, focusing, field enhancement and nonlinear effects, magneto-optical Kerr effect, or electromagnetically induced transparency. Thanks to their high degree of optical tunability (wavelength, phase, polarization, intensity) and the variety of fabrication processes and materials available, RWGs have been implemented in a broad scope of applications in research and industry: refractive index and fluorescence biosensors, solar cells and photodetectors, signal processing, polarizers and wave plates, spectrometers, active tunable filters, mirrors for lasers and optical security features. The aim of this review is to discuss the latest developments in the field including numerical modeling, manufacturing, the physics, and applications of RWGs. Scientists and engineers interested in using RWGs for their application will also find links to the standard tools and references in modeling and fabrication according to their needs.

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Recent Advances in Resonant Waveguide Gratings

The integration of microfluidics and photonic biosensors has allowed achievement of several laboratory functions in a single chip, leading to the development of photonic lab-on-a-chip technology. Although a lot of progress has been made to implement such sensors in small and easy-to-use systems, many applications such as point-of-care diagnostics and in vivo biosensing still require a sensor probe able to perform measurements at precise locations that are often hard to reach. The intrinsic property of optical fibers to conduct light to a remote location makes them an ideal platform to meet this demand. The motivation to combine the good performance of photonic biosensors on chips with the unique advantages of optical fibers has thus led to the development of the so-called lab-on-fiber technology. This emerging technology envisages the integration of functionalized materials on micro- and nano-scales (i.e. the labs) with optical fibers to realize miniaturized and advanced all-in-fiber probes, especially useful for (but not limited to) label-free chemical and biological applications. This review presents a broad overview of lab-on-fiber biosensors, with particular reference to lab-on-tip platforms, where the labs are integrated on the optical fiber facet. Light-matter interaction on the fiber tip is achieved through the integration of thin layers of nanoparticles or nanostructures supporting resonant modes, both plasmonic and photonic, highly sensitive to local modifications of the surrounding environment. According to the physical principle that is exploited, different configurations - such as localized plasmon resonance probes, surface enhanced Raman scattering probes and photonic probes - are classified, while various applications are presented in context throughout. For each device, the surface chemistry and the related functionalization protocols are reviewed. Moreover, the implementation strategies and fabrication processes, either based on bottom-up or top-down approaches, are discussed. In conclusion we highlight some of the further development opportunities, including lab-in-a-needle technology, which could have a direct and disruptive impact in localized cancer treatment applications.

Lab-on-fiber technology: a new vision for chemical and biological sensing

Direct and quantitative detection of unlabeled glycerophosphoinositol (GroPIns), an abundant cytosolic phosphoinositide derivative, would allow rapid evaluation of several malignant cell transformations. Here we report label-free analysis of GroPIns via surface-enhanced Raman spectroscopy (SERS) with a sensitivity of 200 nM, well below its apparent concentration in cells. Crucially, our SERS substrates, based on lithographically defined gold nanofeatures, can be used to predict accurately the GroPIns concentration even in multicomponent mixtures, avoiding the preliminary separation of individual compounds. Our results represent a critical step toward the creation of SERS-based biosensor for rapid, label-free, and reproducible detection of specific molecules, overcoming limits of current experimental methods.

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Reproducible surface-enhanced Raman quantification of biomarkers in multicomponent mixtures.

We demonstrate the operation of a flexible optical filter based on guided mode resonances that operates in the visible regime. The filter is fabricated on a free standing polymeric membrane of 1.3 μm thickness and we show how the geometrical design parameters of the filter determine its optical properties, and how various types of filter can be made with this scheme. To highlight the versatility and robustness of the approach, we mount a filter onto a collimated fibre output and demonstrate successful wavelength filtering.

Optical guided mode resonance filter on a flexible substrate

We demonstrate a method to add photonic functionalities to the tip of hollow photonic crystal fibers, for ultracompact and integrated lab-on-fiber applications. Specifically we present an angularly robust passband filter that is directly applied to the facet of a fiber, without adhesive or etching. The filter exploits the engineered plasmonic response of metallic features realized on a polymeric membrane and works over a range of 10 degrees, with a passband of 50 nm, centered at a wavelength of 800 nm. This result extends the available functionalities offered by the lab-on-fiber methodology to photonic crystal fibers, as well as providing a reversible method of functionalizing any type of fiber.

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Nanoplasmonic Filters for Hollow Core Photonic Crystal Fibers

In this chapter we discuss a versatile method to functionalize the tip of optical fibers for lab-on-fiber applications. At variance with traditional direct writing methods, the photonic functionality is implemented on a flexible, ultrathin support hosting metallic nano-features that is applied on the tip of a fiber. Here we present and discuss several fabrication strategies that combine different substrates with alternative approaches to realize the metallic photonic layer. As a specific application example we focus on a method to filter spectrally the broadband light transmitted through a standard multimode fiber. The filter consists of a metallic nanowire grating on a polymeric substrate, which acts as a guided mode resonance filter with an additional Fano resonance. The advantages and limitations of the presented technique are discussed as well.

Functional Metamaterials for Lab-on-Fiber

Nanoplasmonics has provided a way to control light with extremely high precision, into nanoscale volumes. In many circumstances, the nanoplasmonic devices which can be realised are fabricated using processing techniques which rely on planar technologies. This thesis provides a general method to make nanoplasmonic devices on a flexible membrane structure, which can be free standing, extremely thin (less than the wavelength of visible light), but retains the ability to be manipulated without loss of optical function. These devices are very pliant and conformable. Flexibility allows the integration of nanoplasmonic devices into many new applications where curved surfaces or the ability to conform to another object is required, as well as providing a route for post-fabrication tunability. Two specific applications are considered: lab-on-fibre technology and surface enhanced Raman spectroscopy. Lab-on-fibre technologies have been advancing the ability to miniaturise experiments which would normally require a whole laboratory. Fabricating a membrane and then later applying it to the fibre decouples the choice of fibre from the design of the device. Surface enhanced Raman spectroscopy is a powerful diagnostic tool which can uniquely identify an optical fingerprint of different molecules. The technique has been held back from widespread clinical adoption because of the difficulty of reproducibility of the substrates used. A repeatable and reliable rigid substrate is demonstrated, which can identify the concentration of a three component mixture of physiologically relevant biomolecules. This same design is then shown in a flexible form factor, which is applied to a non-planar landscape where it can identify the locations where a molecule of interest has been deposited. This thesis details the development of the fabrication protocol, the construction of experimental apparatus for characterisation, and the use of numerical modelling to advance the flexible nanoplasmonic membrane platform. Candidate’s declarations: I, Peter Reader-Harris, hereby certify that this thesis, which is approximately 40,000 words in length, has been written by me, and that it is the record of work carried out by me, or principally by myself in collaboration with others as acknowledged, and that it has not been submitted in any previous application for a higher degree. I was admitted as a research student in September 2011 and as a candidate for the degree of Doctor of Philosophy in September 2011; the higher study for which this is a record was carried out in the University of St Andrews between 2011 and 2015. Date Signature of candidate Supervisor’s declaration: I hereby certify that the candidate has fulfilled the conditions of the Resolution and Regulations appropriate for the degree of Doctor of Philosophy in the University of St Andrews and that the candidate is qualified to submit this thesis in application for that degree. Date Signature of supervisor Permission for publication: In submitting this thesis to the University of St Andrews I understand that I am giving permission for it to be made available for use in accordance with the regulations of the University Library for the time being in force, subject to any copyright vested in the work not being affected thereby. I also understand that the title and the abstract will be published, and that a copy of the work may be made and supplied to any bona fide library or research worker, that my thesis will be electronically accessible for personal or research use unless exempt by award of an embargo as requested below, and that the library has the right to migrate my thesis into new electronic forms as required to ensure continued access to the thesis. I have obtained any third-party copyright permissions that may be required in order to allow such access and migration, or have requested the appropriate embargo below. The following is an agreed request by candidate and supervisor regarding the publication of this thesis: PRINTED COPY No embargo on print copy ELECTRONIC COPY No embargo on electronic copy Date Signature of candidate Signature of supervisor

Peter Reader-Harris

Papers

Reproducible surface-enhanced Raman quantification of biomarkers in multicomponent mixtures.

Optical guided mode resonance filter on a flexible substrate

Nanoplasmonic Filters for Hollow Core Photonic Crystal Fibers

Functional Metamaterials for Lab-on-Fiber

Flexible membranes for nanoplasmonic applications