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In order to determine the actual threshold level of habitual physical activity necessary to obtain protective effects against degenerative diseases, valid, reliable, nonreactive, and precise instruments are needed. Because regular, low-intensity exercise provides prophylactic effects, the ability to distinguish activity patterns should be a primary consideration when choosing an instrument to assess activity in the field. Although self-report methods in the form of questionnaires are the instruments of choice when large populations are to be assessed, they are somewhat limited in their objectivity. The doubly labeled water (DLW) technique is a highly accurate and objective technique for assessing total daily energy expenditure that should be utilized more as a criterion measure for validating questionnaires that assess energy expenditure. However, the DLW technique remains too costly to be considered practical for large-scale studies. Supplementing questionnaires with a personal interview does elicit more detailed data, but activity monitors provide a more objective measure of activity that can be used as an adjunct to questionnaires. Several models of activity monitors are capable of collecting and storing data for many days, weeks, or even months. More importantly, the internal real-time clocks of these monitors allow the discrimination of activity patterns. Future studies should combine the use of these monitors with a suitable questionnaire.

The influences of deposition rate and alloying with aluminum (0 to 65 at.%) on the structure and optical properties of magnesium films on quartz are examined. Results show that increasing the deposition rate improves the plasmonic figure of merit (FOM) values, and decreases the surface roughness and grain size. Addition of Al to Mg blue shifts the localized surface plasmon (LSP) figure of merit peak position and improves LSP FOM values over portions of the ultraviolet (UV) region. Nanotriangles (NTs) of Mg and Mg-Al on quartz were fabricated using colloidal lithography. Mg-Al NTs show improved LSP resonance (LSPR) response compared to Mg particles due to improved structural integrity.

Early-generation waveguide arrays made of silicon (Si) and fused silica (SiO 2 ) were micromachined for infrared (IR) neural stimulation and optogenetics applications in able to provide comprehensive and selective access to distributed targets. Edge-coupled multimode fibers delivered light through the optrodes. Maximum normalized output power from the tips, with respect to the fiber output, was determined as 0.33 and 0.71 for silicon and glass optrodes, respectively.

Advancements in silicon photonics technology are enabling large scale integration of electro-optical circuits and systems. To fully exploit this potential, automated techniques for design space exploration and physical synthesis for integrated optics must be developed. This paper investigates how conventional VLSI physical design automation techniques can be adapted for integrated optics applications. We present an overall methodology for cell-placement, global routing, and detail routing for physical synthesis of optical circuits. In addition, we highlight optics-specific constraint models, design rules and optimization criteria that will have to be accounted for in physical design automation.

We study the effects of nanotransducer fill fraction on the molecular capture efficiency contribution to overall sensor response. Contrary to expectation, we show that the relative capture efficiency can exceed the fill fraction in the transient regime. However, at thermodynamic equilibrium, the relative efficiency equals the fill fraction in the probe-limited case. When the number of target molecules in solution is the limiting factor in capture, then gains in capture efficiency can be obtained even at thermodynamic equilibrium. The important implication of these results is that significant intrinsic nanotransducer enhancement is necessary in order to provide net gain in sensor response, but that nanotransducer enhancement does not need to exceed the inverse fill fraction. In addition, net gain in overall sensor response is more readily achievable at low target concentrations.

We report on the design, fabrication and optical characterization of a slow light waveguide created using a linear array of coupled resonators in a large cross-section rib waveguide. Structures with as many as 25 high aspect ratio resonators are experimentally investigated. The measured propagation loss, group velocity, and delay-bandwidth product (DBP) are presented. The metric DBP/unit loss is also introduced, with a value 38/dB. Finally we discuss a method for further reducing loss in the slow-light rib waveguide.

Methylation of DNA is responsible for gene silencing by establishing heterochromatin structure that represses transcription, and studies have shown that cytosine methylation of CpG islands in promoter regions acts as a precursor to early cancer development. The naturally occurring methyl binding domain (MBD) proteins from mammals are known to bind to the methylated CpG dinucleotide (mCpG), and subsequently recruit other chromatin-modifying proteins to suppress transcription. Conventional methods of detection for methylated DNA involve bisulfite treatment or immunoprecipitation prior to performing an assay. We focus on proof-of-concept studies for a direct microarray-based assay using surface-bound methylated probes. The recombinant protein 1xMBD-GFP recognizes hemi-methylation and symmetric methylation of the CpG sequence of hybridized dsDNA, while displaying greater affinity for the symmetric methylation motif, as evaluated by SPR. From these studies, for symmetric mCpG, the KD for 1xMBD-GFP ranged from 106 nM to 870 nM, depending upon the proximity of the methylation site to the sensor surface. The KD values for non-symmetrical methylation motifs were consistently greater (> 2 µM), but the binding selectivity between symmetric and hemi-methylation motifs ranged from 4 to 30, with reduced selectivity for sites close to the surface or multiple sites in proximity, which we attribute to steric effects. Fitting skew normal probability density functions to our data, we estimate an accuracy of 97.5% for our method in identifying methylated CpG loci, which can be improved through optimization of probe design and surface density.

We have been studying fluorescence enhancement from labeled oligonucleotides immobilized inside metallic nanoapertures. Fluorescence enhancement is a direct result of the localized field intensity enhancement within these nanoapertures from plasmonic excitation. We have also been developing specific surface chemistries for metallic films to localize capture oligos only inside these nanoapertures. Some of our recent results are overviewed.

International audience; Nanoapertures milled in opaque metallic films offer a simple and robust photonic tool to significantly enhance the fluorescence of single molecules. We provide a detailed physical characterization of this phenomenon for apertures milled in gold and aluminum, and discuss its application to biophotonics. For the first time, the most general figures are provided to predict the awaited enhancement factors for almost every kind of fluorescent molecule. This knowledge is essential to discuss the ability to detect low-quantum yield species. We also report the first demonstration of single metal nanoapertures to perform DNA hybridization sensing, and measure similar enhancement factors as for experiments on diffusing molecules.

We experimentally investigate the optical properties of a slow-light waveguide realized on a silicon chip. We measure the group index, bandwidth and propagation loss.

A new low-latency, cascadable optical logic gate with gain, high contrast, and three-terminal input-output isolation is introduced. The interaction between two orthogonally polarized spatial solitons brought into coincidence at the boundary of a saturating nonlinear medium and propagating in different directions results in the phase-insensitive spatial dragging of a strong pump soliton by a weaker signal. As a result, the strong pump is transmitted through an aperture when the weak signal is not present, and it is dragged to the side by more than a beam width and blocked in the presence of the weak signal, thus implementing an inverter with gain. A multi-input, logically complete NOR gate also can be implemented in a cascaded system.

A nanoscale layer of chromium or titanium is commonly used in plasmonic nanoantennas to firmly adhere a gold film to a glass substrate, yet the influence of this layer on the antenna performance is often ignored. As a result, the need for the use of potentially better materials is not widely recognized. Using a single aperture milled in a gold film with 120 nm diameter as a nanobench for these investigations, we present the first experimental report of the strong dependence of the plasmonic enhancement of single-molecule fluorescence on the nature of the adhesion layer. By combining fluorescence correlation spectroscopy and fluorescence lifetime measurements, we show that this structure is very sensitive to the properties of the adhesion layer, and we detail the respective contributions of excitation and emission gains to the observed enhanced fluorescence. Any increase in the absorption losses due to the adhesion layer permittivity or thickness is shown to lower the gains in both excitation and emission, which we relate to a damping of the energy coupling at the nanoaperture. With this nanobench, we demonstrate the largest enhancement factor reported to date (25×) by using a TiO(2) adhesion layer. The experimental data are supported by numerical simulations and argue for a careful consideration of the adhesion layer while designing nanoantennas for high-efficiency single-molecule analysis.

We measure second-harmonic generation from arrays of sub-wavelength apertures in transmission using fundamental input at 800 nm. Lattice arrangements include disordered, Penrose (quasi-periodic or aperiodic), and square (periodic). Strong angular dependence of SHG is observed, with maxima located at angular positions that roughly correspond to incidence angles of extraordinary optical transmission (EOT) for the fundamental. In addition, even at incidence normal to the sample, strong secondary maxima are observed at off-normal scattering angles for the arrangements with higher degree of order. Breaking the inversion symmetry of the aperture allows second harmonic peaks at normal incidence and detection. These measurements help to resolve the role that symmetry plays in second-harmonic generation from arrays of apertures.

We propose a new method for molecular detection that retains the sensitivity of fluorescence, but without requiring fluorescence labeling of the sample. The method works by spiking the sample solution with one or more labeled molecular species of known concentration. With proper choice of these “competitor” species, their binding kinetics can be used to quantitatively determine the concentration of unlabeled target species. This method can be applied to any fluorescence transduction mechanism that allows real-time signal acquisition, and represents an advance in mitigating certain sample processing steps. We demonstrate the method for the detection of a DNA sequence containing a single-nucleotide polymorphism (SNP).

The selective adsorption of reagents is often essential for bioarray and lab-on-a-chip type devices. As the starting point for a bioarray, alkyl monolayer terminated silicon shards were photopatterned in a few nanoseconds with thousands of wells (spots) using an optical element, a microlens array. Polyallylamine (PAAm), a primary amine containing polymer, adsorbed with little selectivity to the spots, i.e., silicon oxide, over the hydrophobic background. However, at appropriate concentrations, addition of a cationic surfactant to the PAAm deposition solution, cetyltrimethylammonium chloride, prevented the nonspecific adsorption of PAAm onto the hydrophobic monolayer, while directing it effectively to the active spots on the device. A nonionic surfactant was less effective in preventing the nonspecific adsorption of PAAm onto the hydrophobic monolayer. The localized reactions/interactions of adsorbed PAAm with four species that are useful for bioconjugate chemistry: glutaric anhydride, phenylenediisothiocyanate, biotin NHS ester, and an oligonucleotide (DNA) were shown in the spots of an array. The reactivity of PAAm was further demonstrated with an isocyanate. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) played an important role in confirming selective surface reactivity and adsorption. X-ray photoelectron spectroscopy (XPS), spectroscopic ellipsometry, and wetting confirmed PAAm reactivity on planar substrates.

In any microarray hybridization experiment, there are contributions at each probe spot due to the match and numerous mismatch target species (i.e., cross-hybridizations). One goal of temperature optimization is to minimize the contribution of mismatch species; however, achieving this goal may come at the expense of obtaining equilibrium reaction conditions. We employ two-component thermodynamic and kinetic models to study the trade-offs involved in temperature optimization. These models show that the maximum selectivity is achieved at equilibrium, but that the mismatch species controls the time to equilibrium via the competitive displacement mechanism. Also, selectivity is improved at lower temperatures. However, the time to equilibrium is also extended, so that greater selectivity cannot be achieved in practice. We also employ a two-color real-time microarray reader to experimentally demonstrate these effects by independently monitoring the match and mismatch species during multiplex hybridization. The only universal criterion that can be employed is to optimize temperature based upon attaining equilibrium reaction conditions. This temperature varies from one probe to another, but can be determined empirically using standard microarray experimentation methods.

The fluorescence enhancement found in gold nanoapertures is demonstrated to increase the signal-to-noise ratio (SNR) in fluorescence correlation spectroscopy (FCS). Starting from a general discussion on noise in FCS experiments, we show that fluorescence enhancement leads to a dramatic increase in the SNR. This prediction is confirmed by experiments where we report an experimental gain in SNR of about 1 order of magnitude, corresponding to a 100-fold reduction of the experiment duration. This technique is then applied to monitor the kinetics of a fast enzymatic cleavage reaction. This set of experiments evidence the feasibility of FCS analysis with fast integration times of about 1 s, opening the way to the monitoring of a variety of biochemical reactions at reduced time scales.

In any microarray hybridization experiment, there are contributions at each probe spot due to the match and numerous mismatch target species (i.e., cross-hybridizations). One goal of temperature optimization is to minimize the contribution of mismatch species; however, achieving this goal may come at the expense of obtaining equilibrium reaction conditions. We employ two-component thermodynamic and kinetic models to study the trade-offs involved in temperature optimization. These models show that the maximum selectivity is achieved at equilibrium, but that the mismatch species controls the time to equilibrium via the competitive displacement mechanism. Also, selectivity is improved at lower temperatures. However, the time to equilibrium is also extended, so that greater selectivity cannot be achieved in practice. We also employ a two-color real-time microarray reader to experimentally demonstrate these effects by independently monitoring the match and mismatch species during multiplex hybridization. The only universal criterion that can be employed is to optimize temperature based upon attaining equilibrium reaction conditions. This temperature varies from one probe to another, but can be determined empirically using standard microarray experimentation methods.

Third-harmonic generation from arrays of sub-wavelength apertures is measured. Strong angular dependence of THG is observed, which roughly corresponds to that of fundamental transmission. Influence of hole size and adhesion layers is also experimental studied.

We study the effects of pulse distortion on four-wave mixing (FWM) for different slow-light architectures. REMZI has the highest FWM conversion. Distortion constraint limits the FWM conversion in CROW with higher number of stages.

The three-terminal spatial-soliton angular-deflection geometry provides the characteristics of an inverting logic gate with gain, and phase-insensitive implementations can be realized by a number of specific nonlinear interactions between orthogonally polarized waves. In particular, numerical simulations of spatial-soliton dragging and collision are used to calculate the transfer functions of inverter and multiple configurations of two-input nor gates and to address their cascadability. These transfer functions converge in cascaded operation and suggest that fan-out greater than 2 with a large noise margin is attainable in a system with standardized signal levels. These results are obtained with the material properties of fused silica and are representative of low-loss Kerr media.

Quantitative analysis of DNA microarray data is complicated by uncertainties inherent to the experimental setup. Using computer simulations and real-time experimental results, we have previously demonstrated effects of multiplex reactions on a single sensing zone of an array, which may be a leading factor in erroneous interpretation of experimental data. We suggest here that a simplified three-component kinetic model may present a sufficient approximation to describe the general case of DNA sensing in a complex sample milieu. We show that, by analyzing the real-time hybridization kinetics of a nontarget species, we can perform quantitative analysis of unlabeled targets of interest within a broad dynamic range of concentrations.

A bare nanometric aperture milled in a metallic film forms a simple nanophotonic device that can strongly enhance the optical properties of nearby emitters such as fluorescent molecules. In this paper, we experimentally and numerically compare the properties of circular apertures milled in gold and aluminum, and discuss the influence of a noble metal holding plasmonic resonances in the visible range such as gold. We report that nanometric apertures milled in gold exhibit significantly higher fluorescence enhancement factors than apertures in aluminum. We relate this effect to a larger enhancement of the excitation intensity and radiative rate for an aperture milled in gold. A spectrally resolved analysis of the fluorescence emission from apertures is also presented. Comparison with numerical simulations shows that the enhancement factor is maximum when the photonic density of modes is maximum. Altogether, these results provide crucial knowledge for the design of nanoapertures towards high-efficiency single-molecule analysis.

Influence of adhesion layers on gold bowtie antennae are numerical considered, which depends on refractive-index and absorption of adhesion material and whether it is continuous or etched. A simple near-field optimization method is also demonstrated.

Under the constraint of fixed pulse distortion, REMZI architecture has the highest bandwidth-delay product compared to SCISSOR and CROW. Nonlinear response of CROW fails to improve with increasing number of resonators, but inter-pulse interaction decreases.

We show that the nonlinear phase shift produced by a ring resonator constructed from a given nonlinear optical material can be greater than the phase shift produced by a single pass through an infinite length of the same material when linear and nonlinear absorption are taken into consideration. The figure of merit (defined by the phase shift times the throughput) also improves for the ring resonator over that of the native nonlinear absorbing material. We finally show that these benefits of using the ring resonator as a nonlinear phase-shifting element can enhance the switching characteristics of a Mach-Zehnder interferometer.

Application of microarrays for single nucleotide polymorphims (SNPs) has a limited appeal currently due to low reliability of experimental results. Theoretical and experimental studies of surface hybridization of heterozygous samples allow us to identify two factors of observed instabilities. First, reactions may not reach thermodynamic equilibrium in the course of the experiment and second, competitive displacement of low affinity species by high affinity species is the mechanism defining specificity of molecular recognition. Here we describe a real time optical detection arrangement that facilitated the detection of competitive displacement between a wild-type target and a SNP target. Results show that even when the SNP is an order of magnitude lower in concentration (100 pM) then the wild-type target, the kinetics of the SNP hybridization affects hybridization of the wild-type target. Additionally, results show that observed binding kinetics can be altered by adjusting the concentration of the SNP without changing the concentration of the wild-type target. These results have significance when considering what needs to be accounted for when analyzing real time hybridization data.

We measure second-harmonic generation from arrays of sub-wavelength metallic apertures in transmission using square, triangular, Penrose, and disordered lattice arrangements.

We introduced a new type of 1-D PC rib waveguide (PCRW). Simulations of the structure showed an extremely wide photonic band gap. Furthermore, the loss can be controlled by increasing the waveguide height.

Under the constraint of fixed pulse distortion, the nonlinear response of coupled-resonator slow light waveguides fails to improve with increasing number of resonators, even though improvement in bandwith-delay product is obtained.

Aluminum and magnesium have a strong plasmonic response in the ultraviolet part of the spectrum. Due to the differences in their dielectric responses, however, there are qualitative differences in the fluorescence enhancement factors for Al and Mg nanoapertures. In order to make our results applicable to experimental studies, we further investigate fluorescence enhancement in these nanoapertures using UV emitters that excite near 270 nm and emit near 340 nm with both high and low quantum yields (QY). Our results suggest that Al nanoapertures may perform better for molecules with low QY, while Mg may perform better for molecules with high QY. We further consider the effects of bulk and surface oxidation of the two metals. In order to improve fluorescence enhancement, avoiding bulk oxidation during film deposition is important, although bulk oxidation could be used as an optimization parameter for some enhancement mechanisms.

We demonstrate that the inclusion of aluminum (Al) seed layers allows for the growth of finer grain, smoother magnesium (Mg) films, allowing for improved plasmonic response in the UV spectral range. We deposit Al seed layers and Mg films using DC/RF magnetron sputtering. For Al seed layer thicknesses of 2, 5, 10 and 15 nm, we measure the corresponding optical constants over the wavelength range of 250 to 600 nm using a variable angle spectroscopic ellipsometer and compare the results to a reference 100 nm thick Mg film deposited without a seed layer. The optical constants of Mg depend on the seed layer thicknesses and the surface morphology of Mg films. The surface morphology of the Mg films are characterized using scanning electron microscopy, atomic force microscopy and x-ray diffraction and the surface oxide layer on Mg is examined using x-ray photoelectron spectroscopy. We observe that the presence of the seed layer improves the LSP figure of merit in the UV spectral range of 250–400 nm. From the perspective of plasmonics applications, we find that the best localized surface plasmon resonance (LSP) figures of merit are observed for the 10 nm thick Al seed layer. In fact, the LSP figure of merit of the 100 nm Mg film with and without the Al seed layer is found to be greater than Al films in the spectral range of 250–400 nm, confirming earlier findings with thicker Mg films.

We explore theoretic limits of convective flux effects, as a function of species concentrations and sample volume, in biosensing systems containing target species with differing affinities. A finite element method is used to simulate mass transport of DNA through a microfluidic chamber to the sensing surface where hybridization of DNA is modeled using the corresponding kinetic equations. Our results show enhancements due to convection are controlled by the concentration and sample volume of the lower affinity species, while the upper-limit of the enhancements are determined by the concentration and sample volume of the higher affinity species. Additionally, enhancements are controlled by the degree of competition between the two species, which is related to the total fraction of binding sites used.

Microarray analysis has become increasingly complex due to the growing size of arrays. In this work we explore the effects of diffusion and convective fluxes on the time of hybridization and sensing specificity in a single component system. A .nite element software is used to simulate the diffusion of DNA through a microfluidic chamber to the sensing surface where hybridization of DNA is modeled using the corresponding kinetic equation. The differences between diffusion controlled and convection controlled mass transport are investigated as a function of concentration and hybridization time. Hybridization enhancement produced by microfluidics versus stationary diffusion is introduced as a useful metrics for quantitation of mass transport effects.

We study enhancement of fluorescence of molecular species bound within metallic nanocavities. An electromangetic model of dipole radiation within a nanocavity shows an increase in radiative output consistent with experimental yield estimates and also verifies the strong fluorescence isolation from species lying outside the nanocavity.

We propose and demonstrate the application of concepts from digital filter design in order to optimize artificial optical resonant structures to produce a nearly ideal nonlinear phase shift response. Multistage autoregressive moving average (ARMA) optical filters (ring-resonator-based Mach–Zehnder interferometer lattices) are designed and studied. The filter group delay is used as a measure instead of finesse or quality factor to study the nonlinear sensitivity for multiple resonances. The nonlinearity of a four-stage ARMA filter is 17 times higher than that of the intrinsic material of the same group delay. We demonstrate that the nonlinear sensitivity can be increased within constant bandwidth by allocating more in-band phase or by using higher-order filter structures and that the nonlinear sensitivity enhancement improves with increasing group delay. We also investigate methods to precompensate the nonlinear response to reduce the occurrence of optical bistabilities. The effect of optical loss, including linear absorption and two-photon absorption, is discussed in postanalysis. In addition, we discuss how the improvement in nonlinear response scales with respect to various filter parameters.

In this paper, we study the linear and nonlinear responses of 1-D photonic bandgap (PBG) structures. We show that, the nonlinear interaction can be greatly enhanced by the use of Kerr defect modes in a 1D dielectric photonic crystal structure, such as low-intensity bistability and multistability, and by optimizing the design of the layer sequence. 1-D PBG structure can also be promising candidate as low-intensity nonlinear phase shifter. Nonlinear z-scan measurements of a 3-cavity thin-film PBG sample show that the nonlinearity is enhanced over the native material by a factor over 30, while maintaining a bandwidth greater than 1T Hz, which is great for all-optical switching.

Research world-wide on biosensing techniques is motivated by numerous applications in clinical diagnostics, genetic screenings, proteomics, and single-molecule detection, for example. However, the important problem of detecting in parallel a large number of molecular species from very small samples remains an elusive goal. This work represents a step in that direction through the development of a biosensor platform in which enhanced fluorescence transduction occurs through the optical excitation of molecules located within metallic nanocavities. This study also demonstrates that the phenomenon of enhanced transmission can be used as a technique for molecular transduction in optical biosensor applications with the important benefits of an apparent increase in fluorescence yield and isolation from fluorescence produced by unbound species. Finally, we demonstrate that real-time biosensing can be performed by monitoring the fluorescence signal produced due to the hybridization between probe oligonucleotide's immobilized within the nanocavities and complementary target oligonucleotides in solution introduced through a microfluidic channel.

We demonstrate the generation of second-harmonic radiation in transmission through periodic and disordered arrays of sub-wavelength metallic apertures. For circular apertures in a square lattice, the second-harmonic signal peaks at incidence angles corresponding to enhanced transmission of the fundamental beam of 800~nm wavelength except at small incidence angles where the local symmetry minimizes the effective second-order nonlinear susceptibility of the apertures. Even though the linear transmission of the fundamental beam can be more than five times greater through the periodic array as compared to a disordered array, the strength of the second harmonic from the disordered array is greater at large incidence angles. By breaking the local symmetry through the use of apertures of non-centrosymmetric shape, the second-harmonic output occurs at fundamental transmission resonances at small incidence angles.

In this paper, we propose and demonstrate the application of concepts from digital filter design to optimize artificial optical resonant structures to produce a nearly ideal nonlinear phase shift response. Multi-stage autoregressive moving average (ARMA) optical filters (ring resonator based Mach-Zehnder interferometer lattices) are designed and studied. The filter group delay is used as an alternate measure instead of finesse or quality factor to study the nonlinear sensitivity for multiple resonances. The nonlinearity of a 4-stage ARMA filter is 17 times higher than that of the intrinsic material. We demonstrate that the nonlinear sensitivity can be increased within the same bandwidth by allocating more in-band phase or using higher-order filter structures and that the nonlinear enhancement improves with increasing group delay. We also investigate some possible ways to pre-compensate the nonlinear response to reduce the occurrence of optical bistabilities. The impact of optical loss, including linear absorption and two-photon absorption, and fabrication tolerance are discussed in post-analysis.

Research world-wide on biosensing techniques is motivated by numerous applications in clinical diagnostics, genetic screenings, proteomics, and single-molecule detection, for example. However, the important problem of detecting in parallel a large number of molecular species from very small samples remains an elusive goal. This work represents a step in that direction through the development of a biosensor platform in which enhanced fluorescence transduction occurs through the optical excitation of molecules located within metallic nanocavities. This study also demonstrates that the phenomenon of enhanced transmission can be used as a technique for molecular transduction in optical biosensor applications with the important benefits of an apparent increase in fluorescence yield and isolation from fluorescence produced by unbound species. Finally, we demonstrate that real-time biosensing can be performed by monitoring the fluorescence signal produced due to the hybridization between probe oligonucleotide's immobilized within the nanocavities and complementary target oligonucleotides in solution introduced through a microfluidic channel.

This paper presents a case-study of some University/Government/Industry interactions at the University of Utah that build research and academic programs and create opportunities for economic growth in the areas of micro and nano science and engineering.

We present experimental results confirming that both periodic and randomly placed metallic nanoapertures can be used to enhance the output of a fluorescing molecular monolayer. The metallic nanoapertures were fabricated by e-beam lithography using both positive and negative e-beam resists. Measurements show that the peak fluorescence from the periodic apertures occurs under the conditions of the maximum transmission of excitation light through the structures. There is also an enhancement of fluorescence from randomly placed apertures even though there is no enhancement of the transmission light, which is caused by the incident light evanescently coupling directly through the apertures.

Two major activities of this grant were to develop a generalized approach to the enhancement of nonlinear optical effects based upon slow-light propagation in artificial resonators and the study of nonlinear self-focusing in periodic arrays of photonic microcavities, thereby providing a mechanism for the formation of very narrow (i.e. wavelength scale) spatial solitons at very low powers.

We treat the nonlinear phase shift response in the weak perturbation limit as a linear digital filter that can be synthesized into the values of its poles and zeros and mapped onto an optical architecture. This procedure results in a significant enhancement in the nonlinear sensitivity with a response that is robust to frequency changes within the filter passband. A precompensation technique can be used to reduce distortions under strongly driven nonlinear operation to achieve a larger phase shift. We also show that nonlinear sensitivity improves with increasing filter group delay and can be increased within constant linear bandwidth by use of higher-order filters.

Summary from only given. Periodic arrays of photonic microcavities can facilitate significant enhancements of the nonlinear sensitivity over bulk materials. These enhancement occur for very short lengths. Preliminary experimental results are encouraging.

An evanescent field waveguide DNA biosensor coupled with a microfluidic sample delivery system is the platform for our studies. By employing microfluidics our aim is to reduce sample size and scale to large arrays, thereby increasing the efficiency of the sensor. We are studying the hybridization rate in small sensing zones under flow conditions, with a capture oligonucleotide immobilized on the surface of the waveguide. We are also investigating what effect passive mixing structures placed in the sensing zone have on the hybridization kinetics of the system.