Liquid core waveguide for full imaging of electrophoretic separations

We employed a liquid core waveguide to image both DNA electrophoresis separations and isoelectric focusing of proteins. The utility of the system is demonstrated for DNA fragment sizing and protein separations. The system utilizes the liquid-core waveguide as an efficient window for both the excitation of separated samples and the collection of light through total internal reflectance, with an ability to detect target molecules in the zeptomolar range. Scanning the excitation laser along the length of the electrophoresis capillary excites individually separated analyte bands, while the fluorescence is collected end-on by an optical fiber coupled to a photomultiplier, thus, creating an image of the separation along the length of the capillary.     

Analysis of an optically controlled photonic switch

The principle that the coupling of light between two fiber waveguides can be controlled by the resonant interference of a third waveguide has been developed [Attard, Appl. Opt. 37, 2296-2302 (1998)]. Here significant details concerning the operation of a photonic switch are obtained, and a more complete analysis is presented. Multiple-resonant conditions are identified for slab and fiber control waveguides at large indices of refraction. Thus a selection of materials with an appropriate refractive index and a Kerr coefficient is rendered more easily. Furthermore it is shown that the light used to control the index of refraction in the control waveguide does not enter the output of the photonic switch but remains confined to the control waveguide, for either a slab or a multimode fiber control waveguide. Spatial fluctuations of the control light beam in the control waveguide do not affect the operation of the photonic switch. Tolerances have been determined for the spacing between the control waveguide and the photonic coupler and also for the index of refraction of the control waveguide.     

Efficiency of integrated waveguide probes for the detection of light backscattered from weakly scattering media

A semianalytical model for light collection by integrated waveguide probes is developed by extending previous models used to describe fiber probes. The efficiency of waveguide probes is compared to that of different types of fiber probes for different thicknesses of a weakly scattering sample. The simulation results show that integrated probes have a collection efficiency that is higher than that of small-core fiber probes, and, in the particular case of thin samples, also exceeds the collection efficiency of large-core highly multimode fiber probes. An integrated waveguide probe with one excitation and eight collector waveguides is fabricated and applied to excite and collect luminescence from a ruby rod. The experimental results are in good agreement with the simulation and validate the semianalytical model.     

Modal analysis and device considerations of thin high index dielectric overlay slab waveguides

The effect of adding a thin high index dielectric overlay layer onto a 3-layer slab waveguide demonstrates several interesting features that can be exploited in integrated optical device configurations. A simple modal analysis is employed to examine the behavior of guided light launched from a 3-layer waveguide structure then coupled and propagated in the 4-layer overlay region. Modal properties typically overlooked in conventional slab waveguides are made use of in the design and theoretical analysis of an MMI device and optical index of refraction sensor. The optical structure presented here can form the backdrop waveguide design for more complex and active devices.     

Metal nanoparticle plasmon-enhanced light-harvesting in a photosystem I thin film

Silver metal nanoparticle (NP) enhanced fluorescence is investigated in thin films of cyanobacterial Photosystem I trimer complexes (PSI) by correlating confocal laser scanning microscopy, dark-field imaging, and fluorescence lifetime measurements. PSI represents an interesting light-harvesting complex with a 20 nm diameter that is not uniformly contained within the surface-localized plasmon field of the NPs. With weak far-field illumination, 5- to 20-fold fluorescence enhancement is observed for PSI complexes adjacent to NPs, arising from efficient nanoparticle light collection and subsequent localized, surface plasmon excitation of PSI. Enhanced PSI fluorescence is detected most prominently near "rafts" of aggregated NPs that more completely fill the confocal field of view. These results demonstrate opportunities to probe energy transfer within photosynthetic complexes using plasmonic excitation and to design nanostructures for optimizing artificial light-harvesting systems.     

Fabrication and analysis of a low-loss in-fiber active polymer waveguide

We present a method for fabricating an in-fiber electro-optic polymer waveguide within a D-shaped optical fiber. A combined process of selective chemical etching and spin coating creates a 2-cm in-fiber poly(methyl methacrylate)-DR1 dye polymer waveguide section with an overall insertion loss of micro 1.6 dB at 1550 nm. Numerical simulations show that, for in-fiber polymer waveguides to have low loss, the polymer layer's thickness must be kept below a certain value so that it will not support slab waveguide modes. Long transition regions between the unetched fiber and the polymer waveguide section also reduce loss. We analyze the efficiency of an in-fiber polymer waveguide by simulating its theoretical performance as an electro-optic modulator.     

Modulation of coupling in a photonic switch by resonant interference

A novel photonic switch structure is described in which the coupling of light between two fiber waveguides is controlled by the resonant interference of a third waveguide. The switching action is controlled by a small variation of the index of refraction of the control waveguide by the application of either photo-optical (Kerr) techniques or electro-optical (Pockels) techniques. The control waveguide can be either a fiber waveguide or a slab waveguide. The equations for the waveguide coupling were obtained by analytical approximations from coupled-mode theory. A beam-propagation simulation was also used. The results of the two models were compared. Multiple resonant interferences were observed in the case of a slab waveguide.     

Two-dimensional model for three-dimensional index-guided multimode plasmonic waveguides and the design of ultrasmall multimode interference splitters

We demonstrate that a three-dimensional (3D) index-guided multimode plasmonic waveguide can be approximated to a two-dimensional (2D) lossy slab waveguide by using an effective-index method. It is found that this 2D approximation is more accurate when the width of the multimode waveguide increases. Such a 2D approximation can be used for a quicker and more efficient design of complicated multimode plasmonic devices. 1 x N ultrasmall multimode interference splitters based on multimode surface plasmon waveguides are designed by using this 2D model and the designs are validated with a 3D finite-difference time-domain method.     

A slab optical waveguide with negative effective thickness

Two new asymmetric slab optical waveguides with a left-handed media (LHM) cover or substrate are studied. The effective thickness is derived by using normalized waveguide parameters. An analytical method is then proposed to calculate the universal effective thickness. We show that negative effective thickness exists in the waveguide with a LHM substrate, unlike in conventional waveguide or other LHM waveguides studied previously. However, for the waveguide with a LHM substrate, the shape of high-order mode behaves like that of a traditional slab waveguide, and neither the fundamental mode nor the other higher order modes have the novel phenomena of negative effective thickness. Both TE and TM modes are discussed.     

Resonant scattering and mode coupling in two-dimensional textured planar waveguides

A heuristic formalism is developed for efficiently determining the specular reflectivity spectrum of two-dimensionally textured planar waveguides. The formalism is based on a Green's function approach wherein the electric fields are assumed to vary little over the thickness of the textured part of the waveguide. Its accuracy, when the thickness of the textured region is much smaller than the wavelength of relevant radiation, is verified by comparison with a much less efficient, exact finite difference solution of Maxwell's equations. In addition to its numerical efficiency, the formalism provides an intuitive explanation of Fano-like features evident in the specular reflectivity spectrum when the incident radiation is phase matched to excite leaky electromagnetic modes attached to the waveguide. By associating various Fourier components of the scattered field with bare slab modes, the dispersion, unique polarization properties, and lifetimes of these Fano-like features are explained in terms of photonic eigenmodes that reveal the renormalization of the slab modes due to interaction with the two-dimensional grating. An application of the formalism, in the analysis of polarization-insensitive notch filters, is also discussed.     

Narrow-band Resonant Grating Waveguide Filters Constructed with Azobenzene Polymers.

Resonant grating waveguide structures were used to fabricate narrow-bandwidth optical filters. Azopolymer films were deposited on top of slab waveguides, and surface relief gratings were optically inscribed on them to be used as couplers. This technique is a simple one-step process and produces efficient gratings with high accuracy. Sharp resonant peaks are observed in the transmission and the reflection spectra of these structures. The thickness and the index of refraction of the waveguide can be accurately determined from these resonances by use of modal theory. These parameters are then used in the design of an optical filter. Bandwidths of less than 1 nm and a decrease in transmitted signal of 60% are reported. Measurement of these values was limited by the divergence of the probe beam.     

Long-range surface plasmon polariton mode cutoff and radiation in slab waveguides

The normal-mode-analysis method is used to model the radiative spreading of long-range surface plasmon polariton modes injected into regions where the bound surface mode is cutoff or radiative. Mode cutoff is induced by an asymmetry between the index of refraction of the top cladding layer and that of the bottom. The analysis was performed at lambda(0)=1.55 microm for infinite-width (slab) metal waveguides where the metal was Au and the bounding dielectrics were SiO(2). Results show that a change in insertion loss of > 20 dB is possible for an appropriate waveguide geometry and dielectric asymmetry.     

Microfabrication and characterization of liquid core waveguide glass channels coated with Teflon AF

We report on the microfabrication and testing of liquid core waveguides (LCW) using Teflon AF for integration in microfabricated microanalysis systems. Teflon AF has an index of refraction less than that of water allowing it to function as a waveguide when used as a cladding layer surrounding an aqueous core. Straight microchannels (400-/spl mu/m width, 60-/spl mu/m depth) etched into Pyrex and soda-lime glass wafers were coated with Teflon AF and sealed with a Teflon AF coated capping wafer. Aqueous fluorescein solutions with varying concentrations were injected into the channels and were illuminated transversely using an ultraviolet light emitting diode. For studying the waveguide attenuation performance, light was focused to a point on the channel. Fluorescence generated in the channel was used to quantify the light collection and waveguide characteristics. The Teflon coating produces a significant enhancement in the amount of light collected in the channel, allowing light to be collected from the 16-mm length tested. This is compared to a control microchannel in glass (no coating), for which the fluorescence drops to the background level in an illumination-detection separation of <4 mm. For sensitivity performance, the entire channel was illuminated. The lower detection limit for spectroscopically resolved fluorescence was /spl sim/10 nMolar.     

Epifluorescence collection in two-photon microscopy

We present a simple model to describe epifluorescence collection in two-photon microscopy when one images in a turbid slab with an objective. Bulk and surface scattering determine the spatial and angular distributions of the outgoing fluorescence photons at the slab surface, and geometrical optics determines how efficiently the photons are collected. The collection optics are parameterized by the objective's numerical aperture and working distance and by an effective collection field of view. We identify the roles of each of these parameters and provide simple rules of thumb for the optimization of the epifluorescence collection efficiency. Analytical results are corroborated by Monte Carlo simulation.     

Analysis of optical fibers by the effective-index method

The effective-index method for determining waveguide dispersion is derived from the scalar wave equation and applied to optical fibers of arbitrary cross-sectional shapes. In the simplest use of the method, the optical fiber is replaced by an equivalent slab waveguide with an index profile derived from the geometrical shape of the fiber. Results from analyzing circular, elliptical, and cusp-shaped fibers are used to illustrate the general features of the method. A procedure is also given for improving the accuracy of the method applied to a class of single-mode fiber.     

Laser-induced fluorescence detection by liquid core waveguiding applied to DNA sequencing by capillary electrophoresis

A new laser-induced fluorescence detector for capillary electrophoresis (CE) is described. The detector is based on transverse illumination and collection of the emitted fluorescent light via total internal reflection along the separation capillary. The capillary is coated with a low refractive index fluoropolymer and serves as a liquid core waveguide (LCW). The emitted light is detected end-on with a CCD camera at the capillary exit. The observed detection limit for fluorescein is 2.7 pM (550 ymol) in the continuous-flow mode and 62 fM in the CE mode. The detector is applied to DNA sequencing. One-color G sequencing is performed with single-base resolution and signal-to-noise ratio approximately 250 for peaks around 500 bases. The signal-to-noise ratio is approximately 50 for peaks around 950 bases. Full four-color DNA sequencing is also demonstrated. The high sensitivity of the detector is suggested to partly be due to the efficient rejection of scattered laser light in the LCW. The concept should be highly suitable for capillary array detection.     

Single-scattering theory of light diffraction by a circular subwavelength aperture in a finitely conducting screen

A perturbation theory based on a single-scattering approximation is developed from the rigorous differential theory of diffraction in cylindrical coordinates. It results in analytical formulas in the inverse space for the field amplitudes providing results that are in quantitative agreement with the results of the rigorous method, in both the near- and far-field regions, when a proper correction to the incident field inside the aperture is made by using the renormalized Born approximation. When working in reflection by a screen having permittivity high in modulus, the method proposes an equivalence with the simple model consisting of the emission by a single magnetic dipole excited inside the pierced layer, emission that is then transferred back into the cladding following the Fresnel's coefficients of transmission from the layer into the cladding. The theory predicts a directivity of the radiation pattern that increases for smaller values of modulus of permittivity, both for dielectrics and metals, thus independently of the possibility of plasmon surface wave excitation along the interface. The theory can take into account such surface wave resonances, as well as the waveguide supported by a dielectric slab, but cannot implicitly recognize the modes carried out by the cylindrical waveguide corresponding to the aperture. This fact limits its domain of validity when used in transmission, although the far- and near-field maps can be reconstructed sufficiently well within a multiplicative factor corresponding to the enhanced transmission due to the excitation of these modes.     

Slab waveguide with conducting interfaces as an efficient optical sensor: TE case

In this paper, three-layer slab waveguide structure is treated for optical sensing applications. Four waveguide configurations including different guiding films and analytes are assumed. A conducting two-dimensional free charge layers with a surface conductivity is assumed to exist at the substrate/film and film/cladding interfaces. The sensing sensitivity of the proposed structure to any changes in an analyte refractive index uniformly distributed in the cladding layer is investigated. Positive as well as negative surface conductivities are considered. It is found that utilizing positive surface conductivity can enhance the sensitivity, whereas using negative values of the surface conductivity reduces the sensitivity.     

Transmission and radiation in a slab waveguide coupled to a whispering-gallery resonator: volume-integral-equation analysis

The excitation of a whispering gallery resonator by a surface wave guided in a dielectric slab is analyzed with a rigorous volume-integral-equation approach. The analysis is based on the Green's function concept and the application of the entire-domain Galerkin technique through expansion of the electric field in the resonator in terms of cylindrical wave functions. The algorithm developed yields highly accurate results for the transmission and reflection coefficients in the waveguide. The radiated far field is computed, and the effect of the excitation of a whispering gallery mode on the radiation pattern is studied.     

Axial resolution limit of a fiber-optic fluorescence probe

We examine the limit of spatial resolution achievable when a sine optical fiber is used for excitation and collection of fluorescence from a bulk specimen. We calculate the probability of detecting a fluorescent particle as a function of its position relative to the fiber face, using excitation wavelength lambda, radius a, numerical aperture N.A., and the particle's fluorescence and absorbance spectra. Treating Rhodamine B as a model fluorescent analyte and using appropriate fiber parameters, we show that the maximum axial resolution (defined as the axial distance in a homogenous solution within which 50% of the detected signal originates) achievable is approximately 10 microm. We experimentally measured the axial resolution for a 500-microM aqueous solution of Rhodamine B with lambda = 543 nm, a = 1.31 microm, and a N.A. of 0.16 and found good qualitative agreement with the calculation.