This PDF file contains the front matter associated with SPIE Proceedings Volume 7035, including the Title Page, Copyright information, Table of Contents, and the Conference Committee listing.

The transmission of normally incident light through arrays of subwavelength holes (nanoholes) in gold thin films is enhanced at the wavelengths that satisfy the surface plasmon resonance (SPR) condition. Our group has been active on the implementation of schemes for the application of this phenomenon for chemical sensing. For instance, we have shown that the interaction between adsorbates with nanoholes modified the SP resonance conditions, leading to a shift in the wavelength of maximum transmission. The output sensitivity of this substrate was found to be 400 nm RIU-1 (refractive index units), which is comparable to other grating-based surface plasmon resonance devices. The array of nanoholes was also integrated into a microfluidic system and the characteristics of the solution flow and detection systems were evaluated. In this work, we will concentrate on improving the efficiency of the nanohole arrays for applications in chemical in chemical sensing. Attempts to improve the sensitivity of the device will be discussed. In-hole sensing is suggested as an alternative to decrease the number of probe molecules, and enhance sensitivity. A biaxial sensing scheme will also be introduced. The biaxial scheme allows for polarization-modulation detection that can account for background fluctuations. A flow-through approach should lead to an optimized transport situation of the analytes to the immobilized species at the surface, which should significantly improve the time and sensitivity of the analysis. Finally, we will discuss the implementation of multiplexing detection using these arrays. Multiplexing detection in zero-order transmission is simpler to implement than the common multiplexing imaging from angle-resolved SPR.

Large-scale studies of biomolecular interactions required for proteome-level investigations can benefit from a new class of emerging surface plasmon resonance (SPR) sensors: nanohole arrays and surface plasmon (SP) enhanced optical transmission. In this paper we present a real-time, label-free multiplex SPR imaging sensor in a microarray format. The system presented is built around a low-cost microscope with laser illumination, integrated with microfluidics. The specific binding kinetics of biotin and streptavidin are measured from several sensing elements simultaneously, demonstrating the feasibility of using nanohole arrays as a high-throughput SPR microarray sensor.

Surface Plasmon Resonance imaging (SPRi) is a label-free technique for the quantitation of binding affinities and concentrations for a wide variety of target molecules. Although SPRi is capable of determining binding constants for multiple ligands in parallel, current commercial instruments are limited to a single analyte stream and a limited number of ligand spots. Measurement of target concentration also requires the serial introduction of different target concentrations; such repeated experiments are conducted manually and are therefore time-intensive. Likewise, the equilibrium determination of concentration for known binding affinity requires long times due to diffusion-limited kinetics to a surface-immobilized ligand. We have developed an integrated microfluidic array using soft lithography techniques for SPRi-based detection and determination of binding affinities for DNA aptamers against human alphathrombin. The device consists of 264 element-addressable chambers isolated by microvalves. The resulting 700 pL volumes surrounding each ligand spot promise to decrease measurement time through reaction rate-limited kinetics. The device also contains a dilution network for simultaneous interrogation of up to six different target concentrations, further speeding detection times. Finally, the element-addressable design of the array allows interrogation of multiple ligands against multiple targets.

Phospholipid, which is a building block of biological membranes, plays an important role in compartmentalization of cellular reaction environment and control of the physicochemical conditions inside the reaction environment. Phospholipid bilayer membrane has been proposed as a natural biocompatible platform for attaching biological molecules like proteins for biosensing related application. Due to the enormous potential applications of biomimetic model biomembranes, various techniques for depositions and patterning of these membranes onto solid supports and their possible biotechnological applications have been reported by different groups. In this work, patterning of phospholipid thin-films is accomplished by interferometric lithography as well as using lithographic masks in liquid phase. Surface Enhanced Raman Spectroscopy and Atomic Force microscopy are used to characterize the model phospholipid membrane and the patterning technique. We describe an easy and reproducible technique for direct patterning of azo-dye (NBD)-labeled phospholipid (phosphatidylcholine) in aqueous medium using a low-intensity 488 nm Ar⁺ laser and various kinds of lithographic masks.

Transmembrane proteins and ion channels are important drug targets and have been explored as single molecule sensors. For these proteins to function normally they must be integrated within lipid bilayers; however, the labor and skill required to create artificial lipid bilayers have the limited the possible applications utilizing these proteins. In order to reduce the complexity and cost of lipid bilayer formation and measurement, we have modified a previously published lipid bilayer formation technique using mechanically contacted monolayers so that the process is automatable, requiring minimal operator input. Measurement electronics are integrated with the fluid handling system, greatly reducing the time and operator feedback characteristically required of traditional bilayer experiments. To demonstrate the biological functionality of the resultant bilayers and the system's capabilities as a membrane platform, the ion channel gramicidin A was incorporated and measured with this system.

We describe the fabrication of sub-100-nanometer-sized channels in a fused silica lab-on-a-chip device and experiments that demonstrate detection of single fluorescently labeled proteins in buffer solution within the device with high signal and low background. The fluorescent biomolecules are transported along the length of the nanochannels by electrophoresis and/or electro-osmosis until they pass into a two-focus laser irradiation zone. Pulse-interleaved excitation and time-resolved single-photon detection with maximum-likelihood analysis enables the location of the biomolecule to be determined. Diffusional transport of the molecules is found to be slowed within the nanochannel, and this facilitates fluidic trapping and/or prolonged measurements on individual biomolecules. Our goal is to actively control the fluidic transport to achieve rapid delivery of each new biomolecule to the sensing zone, following the completion of measurements, or the photobleaching of the prior molecule. We have used computer simulations that include photophysical effects such as triplet crossing and photobleaching of the labels to design control algorithms, which are being implemented in a custom field-programmable-gate-array circuit for the active fluidic control.

Giant magnetoresistive (GMR) biochips using magnetic nanoparticle as labels were developed for molecular diagnosis. The sensor arrays consist of GMR sensing strips of 1.5 μm or 0.75 μm in width. GMR sensors are exquisitely sensitive yet very delicate, requiring ultrathin corrosion-resistive passivation and efficient surface chemistry for oligonucleotide probe immobilization. A mild and stable surface chemistry was first developed that is especially suitable for modifying delicate electronic device surfaces, and a practical application of our GMR biosensors was then demonstrated for detecting four most common human papillomavirus (HPV) subtypes in plasmids. We also showed that the DNA hybridization time could potentially be reduced from overnight to about ten minutes using microfluidics.

Monitoring cancer after the first treatment requires ultra-sensitive personalized biosensors with high specificity. We present here some of the nanoparticle based microfluidic techniques pursued at the Nano Tumor Center towards this goal.

DNA has shown great promise as a template for the controlled localization of various materials and the construction of wires with nanometer-dimension cross sections. We have recently developed a strategy for fabrication of nanocapillaries, using DNA-templated nanowires as a sacrificial material. We first form metal nanowires through the selective electrochemical deposition of nickel atop a surface-aligned DNA molecule. We then deposit a thin layer of silicon dioxide on top of the DNA nanostructures. Next, we photolithographically pattern openings over the ends of the wires and etch through the silicon dioxide layer to expose the metal nanowires. Finally, we etch out the DNA-templated nickel nanowires. This process results in the formation of nanocapillaries having the same dimensions as the originally formed DNA-templated nanowires. We have characterized these DNA-templated nanocapillaries using atomic force microscopy, optical microscopy and scanning electron microscopy. These constructs have potential for application in nanofluidics, power generation, sample preconcentration, and chemical sensing.

Although functional molecular constructs promise a variety of interesting properties in combination with parallel realization and molecular precision, the utilization requires usually integration into the macroscopic world such as electrodes or other technical environments. Dielectrophoresis (DEP) represents an interesting approach to manipulate and control objects at the nanoscale, and especially to position them at controlled locations in microelectrode arrangements. Over the years this technique was established in our group and is now able to arrange either metal nanoparticles and/or DNA into these gaps in a highly reproducible manner. Microscopic tools were optimized in order to be able to follow single particles/molecules during the process. This ability greatly improves the potential, because now the key parameters can be easily tuned during live imaging of the controlled objects and their behavior. It was possible to realize bridges of nanoparticles as well as of a few stretched DNA molecules on gold microelectrode structures at chip surfaces. Moreover, DNA positioned by DEP in electrode gaps was metallized and the resulting metal nanostructure characterized. Work is in process to combine the various units as well as processes in order to access more complex functionalities.

Gold and silver nanoparticles functionalized with oligonucleotides can be used for the detection of specific sequences of DNA. We show that gold nanoparticles modified with locked nucleic acid (LNA) form stronger duplexes with a single stranded DNA target and offer better discrimination against single base pair mismatches than analogous DNA probes. Our LNA nanoparticle probes have also been used to detect double stranded DNA through triplex formation, whilst still maintaining selectivity for only complementary targets. Nanoparticle conjugates embedded with suitable surface enhanced resonance Raman scattering (SERRS) labels have been synthesized enabling simultaneous detection and identification of multiple DNA targets.

By incorporating DNA as addressable linkers, we can direct and coordinate the simultaneous, parallel self-assembling and binding of multiple different redox proteins to designated nanoelectrodes. As a result, we have formed a nanoelectronic-protein transducer array which is capable of real-time, multiplexed detection of several analytes in parallel. The sequence-specificity of DNA hybridization provides the means of encoding spatial address instruction to the otherwise random self-assembling process and enables the desired programmability, scalability, and renewability. Results of this study, under an AFOSR MURI program, demonstrate the feasibility of a new paradigm of biosensing: detection of not only the presence of target substances but also the real-time activities of multiple biomolecules. In this system, the conjugated biomolecules and nanoelectronic components provide the active monitoring and mediating functions in real time, and can be integrated en masse into large arrays in a silicon-based integrated circuit.

Nucleic acids circulating in body fluids are drawing great attention due to their potential use for disease diagnostics and prognostics. Current detection methods have yet to demonstrate the capability to selectively detect the low abundance nucleic acids. The challenge lies in the separation of circulating DNA from the genomic DNA in normal cells. Here we present an approach employing a nano-structured tip, which directly concentrates nucleic acids to the tip from a sample solution. The high aspect ratio tip is able to collect nucleic acid molecules out of a buffer solution by using dielectrophoretic (DEP) and surface tension force. The DEP force attracts DNA and other biomolecules in the vicinity of a nanotip from the sample solution. Among the attracted molecules, circulating nucleic acids whose dimensions are much smaller than the nanotip diameter are selectively captured to the tip while other bioparticles comparable to or larger than the tip diameter remain in the solution due to surface tension induced force. The concentrated DNA molecules are characterized by SEM, X-ray, and fluorescent microscopy, which demonstrate DNA capturing out of a sample solution having a 1pg/mL DNA concentration. The nanotip-based capturing method will facilitate rapid, but highly sensitive detection of circulating DNA directly from minimally treated- or raw samples.

A 16-channel chip for wireless in vivo recording of chemical and electrical neural activity is described. The 7.83-mm² IC is fabricated using a 0.5-μm CMOS process and incorporates a 71-μW, 3rd-order, reconfigurable, ΔΣ modulator per channel, achieving an input-referred noise of 4.69 μV_rms in 4-kHz BW and 94.1 pA_rms in 5-kHz BW for electrical and fast-scan voltammetric chemical neurosensing, respectively. The chip has been externally interfaced with carbon-fiber microelectrodes implanted acutely in the caudate-putamen of an anesthetized rat, and, for the first time, extracellular levels of dopamine elicited by electrical stimulation of the medial forebrain bundle have been successfully recorded wirelessly across multiple channels using 300-V/s fast-scan cyclic voltammetry.

Information processing and propagation in the central nervous system is mostly electrical in nature. At synapses, electrical signals cause the release of neurotransmitters like dopamine, glutamate etc., that are sensed by post-synaptic neurons resulting in signal propagation or inhibition. It can be very informative to monitor electrical and neurochemical signals simultaneously to understand the mechanisms underlying normal or abnormal brain function. We present an integrated system for the simultaneous wireless acquisition of neurophysiological and neurochemical activity. Applications of the system to neuroscience include monitoring EEG and glutamate in rat somatosensory cortex following global ischemia.

New investigations are carried out on the optical spectral response of grating based nanophotonic structures and their sensitivity to refractive index variations of a liquid like analyte embedded within and on top of nanometer-sized grating structure. The phenomena examined are guided wave resonances in dielectric grating/waveguide structures, respectively, and scatterometric effects in non-resonant structures. Both resonant and non-resonant configurations are shown to allow refractive index detection limit on the level of 10^-6 - 10^-5. The spectroscopic scatterometry approach offers also specificity in particular when the analyzed materials are dispersive and absorptive. The planarity and operation at normal incidence as well as possibility of fabrication using silicon technologies are advantages for these structures that permit building arrays of sensors for biochip applications.

A novel short wave infrared single photon detector was conceived for wavelengths beyond 1 μm. The detector, called the nano-injection photon detector, is conceptually designed with biological inspirations taken from the eye. Based on a detection process similar to the human visual system, the detector couples a nano-scale sensory region with a large absorption volume to provide a low-noise internal amplification mechanism, high signal-to-noise ratio and quantum efficiency. Tens of thousands of devices were fabricated in different configurations with conventional processing methods in more than 20 iterations. For low speed imaging applications, the detectors have shown gain values reaching 10,000 with bias voltages around 1 V. Ultra-low noise levels were measured at gain values exceeding 4,000 at room temperature: Fano factors as low as 0.55 has been achieved, which indicated a statistically stable amplification mechanism and resulting sub-Poissionian shot noise. An alternate version of the detector, which is specialized towards high-speed applications, has also been developed with slight changes in processing steps. The fast detectors with bandwidth beyond 3 Ghz were demonstrated which provide gain values around 20. The measured risetime was less than 200 ps. Femtosecond pulsed illumination measurements exhibited ultra-low jitter around 15 ps. Transient delay experiments revealed that the measured jitter is due to the transit time in the large absorption region. Hence the amplification process has insignificant time-uncertainty in addition to low amplitude-variance (noise), which is consistent with statistically stable nature of amplification.

Fluorescence has important applications in chemical and biological sensing and analysis due to the large selection of fluorescent markers and their specificity in staining. In order to achieve high sensitivity, the strength and the collection efficiency for the fluorescence signal is a critical issue that needs to be addressed. In this paper, we study the use of one dimensional photonic band gap (1D PBG) structures to enhance the florescence excitation and collection. The 1D PBG structure is designed to create an enhanced evanescent field for the excitation wavelength at the interface of last layer of the PBG and the sample. Meanwhile, the 1D PBG also serves as an omnidirectional reflector for the florescence signal, leading to higher collection efficiency. The combination of both effects provides a significant enhancement of florescence signal. In order to verify the feasibility, GaP/SiO₂ multilayer thin film stack is designed and fabricated. High quality GaP/SiO₂ multilayer thin film stack is fabricated using sputtering technique. The sputtered GaP thin film is characterized using ellipsometer. GaP thin film with very high refractive index (n=3.45 at 633 nm) was obtained. The performance of the multilayer stack as omnidirectional reflector is also reported.

The integration of optical components on microfluidic devices is needed for downscaling analytical processes to portable, integrated and low-cost lab-on-a-chip systems for point-of-care applications. We have developed a micro-optical detection unit for both laser induced fluorescence and absorbance analysis in fused silica capillaries for microfluidic chromatographic applications. We present the use of non-sequential ray tracing simulations to design the system and to perform a tolerance analysis to define theoretically for each parameter in the system the acceptable fabrication and alignment errors. The system is prototyped using Deep Proton Writing and characterized by means of an optical non-contact profiler, in order to check for every parameter if the realized alignment and fabrication errors do not exceed the theoretically acceptable tolerance ranges. These measurements show that Deep Proton Writing is appropriate for the fabrication of the designed micro-optical detection system. In addition the tolerance study shows for which parameters the alignment is most critical. Finally we demonstrate by means of optical simulations that the same micro-optical design can be applied in different materials (index of refraction between 1.3 and 1.5) and used for sensing fluorescence of a variety of molecules in a wide spectral window (from 400nm up to 1550nm).

A procedure for fabricating nanopatterned surfaces at the sub-500 nm scale comprising a hexagonal close packed array of bioadhesive gold nanoareas in a protein resistant matrix (PEO-like polymer), has been optimized. The surfaces were characterized by AFM analysis and their interaction with amino functionalised gold nanoparticles as models were investigated. The AFM images show the crystalline arrangement of nanopattern array and the localized adsorption of the H2N-Au nanoparticles in the bioadhesive nanoareas. A Surface Plasmon Resonance imaging (SPRi) system was used to assess the detection performances of these surfaces when employed as a transduction platform for studying biomolecule interactions. The investigated surfaces showed an enhancement of the affinity reaction efficiency with respect to the non structured surfaces. The obtained preliminary results show that nanostructuring the surfaces improve the binding site accessibility of the immobilized biological probes without significantly modifying the native biomolecule conformation.

We have developed a numerical model of Small Target Motion Detector neurons, bio-inspired from electrophysiological experiments in the fly brain. These neurons respond selectively to small moving features within complex moving surrounds. Interestingly, these cells still respond robustly when the targets are embedded in the background, without relative motion cues. This model contains representations of neural elements along a proposed pathway to the target-detecting neuron and the resultant processing enhances target discrimination in moving scenes. The model encodes high dynamic range luminance values from natural images (via adaptive photoreceptor encoding) and then shapes the transient signals required for target discrimination (via adaptive spatiotemporal high-pass filtering). Following this, a model for Rectifying Transient Cells implements a nonlinear facilitation between rapidly adapting, and independent polarity contrast channels (an 'on' and an 'off' pathway) each with center-surround antagonism. The recombination of the channels results in increased discrimination of small targets, of approximately the size of a single pixel, without the need for relative motion cues. This method of feature discrimination contrasts with traditional target and background motion-field computations. We improve the target-detecting output with inhibition from correlation-type motion detectors, using a form of antagonism between our feature correlator and the more typical motion correlator. We also observe that a changing optimal threshold is highly correlated to the value of observer ego-motion. We present an elaborated target detection model that allows for implementation of a static optimal threshold, by scaling the target discrimination mechanism with a model-derived velocity estimation of ego-motion.

We present a synchronous time-based dual-threshold imager that experimentally achieves 95.5 dB dynamic range, while consuming 1.79 nJ/pixel/frame, making it one of the most wide-dynamic-range energy-efficient imagers reported. The imager has 150×256 pixels, with a pixel pitch of 12.5μm × 12.5μm and a fill factor of 42.7%. The imager is intended for use in a brain-machine visual prosthesis for the blind where energy efficiency and power are of paramount importance. Such prostheses will also need to convey visual information to patients with relatively few electrodes and in a manner that minimizes electrode interactions, just as cochlear implants have accomplished for deaf subjects. To achieve these goals, we present a strategy that compresses visual information into the basis coefficients of a few image kernels that encode enough information to provide reasonably good image reconstruction with 60 electrodes. The strategy also uses time-multiplexed stimulation of electrodes to minimize channel interactions like the continuous interleaved sampling (CIS) strategy used in cochlear implants. Some of the image kernels that we employ are similar to the receptive fields observed in biology and may thus be natural to learn, just as cochlear-implant subjects have learned to reconstruct sound from a few filter basis coefficients.

Advances in micro-nano-biosensor fabrication are enabling technology that can integrate a large number of biological recognition elements within a single package. As a result, hundreds to millions of tests can be performed simultaneously and can facilitate rapid detection of multiple pathogens in a given sample. However, it is an open question as to how to exploit the high-dimensional nature of the multi-pathogen testing for improving the detection reliability a typical biosensor system. In this paper, we discuss two complementary high-dimensional encoding/decoding methods for improving the reliability of multi-pathogen detection. The first method uses a support vector machine (SVM) to learn the non-linear detection boundaries in the high-dimensional measurement space. The second method uses a forward error correcting (FEC) technique to synthetically introduce redundant patterns on the biosensor which can then be efficiently decoded. In this paper, experimental and simulation studies are based on a model conductimetric lateral flow immunoassay that uses antigen-antibody interaction in conjunction with a polyaniline transducer to detect presence or absence of pathogen in a given sample. Our results show that both SVM and FEC techniques can improve the detection performance by exploiting cross-reaction amongst multiple recognition sites on the biosensor. This is contrary to many existing methods used in pathogen detection technology where the main emphasis has been reducing the effects of cross-reaction and coupling instead of exploiting them as side information.