Abstract: Optical analytical devices and their methods of use are provided. The devices are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices include optical waveguides for illumination of the optical reactions. The devices further provide for the efficient coupling of optical excitation energy from the waveguides to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices of the invention are well suited for miniaturization and high throughput.

Abstract: The application relates to methods of manufacture of improved optical containment structures. The invention relates to arrays of zero-mode waveguide structures comprising nanoscale apertures having non-reflective coatings on their walls. The methods provide for selectively coating the walls of the zero mode waveguides, allowing for selective functionalization of the bases.

Abstract: The application relates to methods for producing islands of functionality within nanoscale apertures. Islands of functionality can be produced by growing an aperture constriction layer from the walls, functionalizing the exposed base of the aperture, then removing the aperture constriction layer. The aperture constriction layer can be produced, for example, by anodically growing an oxide layer onto a cladding through which the aperture extends. The islands of functionality can be used to bind a single molecule of interest, such as an enzyme within the nanoscale aperture.

Abstract: Apparatus, systems and methods for use in analyzing discrete reactions at ultra high multiplex with reduced optical noise, and increased system flexibility. Apparatus include substrates having integrated optical components that increase multiplex capability by one or more of increasing density of reaction regions, improving transmission of light to or collection of light from discrete reactions regions. Integrated optical components include reflective optical elements which re-direct illumination light and light emitted from the discrete regions to more efficiently collect emitted light. Particularly preferred applications include single molecule reaction analysis, such as polymerase mediated template dependent nucleic acid synthesis and sequence determination.

Abstract: An optical navigation device with a phase grating for beam steering. The optical navigation device includes a light source, and image sensor, and a beam steering element. The light source directs a light beam toward a navigation surface. The image sensor receives light along an imaging path and generates a navigation image of the navigation surface from the light received along the imaging path. The beam steering element is disposed between the navigation surface and the image sensor. The beam steering element receives reflected light from the navigation surface along a specular reflection path. The beam steering element directs a first portion of the reflected light along the imaging path toward the image sensor. The beam steering element directs a second portion of the reflected light along a beam steering path away from the imaging path.

Abstract: Apparatus, systems and methods for use in analyzing discrete reactions at ultra high multiplex with reduced optical noise, and increased system flexibility. Apparatus include substrates having integrated optical components that increase multiplex capability by one or more of increasing density of reaction regions, improving transmission of light to or collection of light from discrete reactions regions. Integrated optical components include reflective optical elements which re-direct illumination light and light emitted from the discrete regions to more efficiently collect emitted light. Particularly preferred applications include single molecule reaction analysis, such as polymerase mediated template dependent nucleic acid synthesis and sequence determination.

Abstract: The application relates to methods for producing islands of functionality within nanoscale apertures. Islands of functionality can be produced by growing an aperture constriction layer from the walls, functionalizing the exposed base of the aperture, then removing the aperture constriction layer. The aperture constriction layer can be produced, for example, by anodically growing an oxide layer onto a cladding through which the aperture extends. The islands of functionality can be used to bind a single molecule of interest, such as an enzyme within the nanoscale aperture.

Abstract: The application relates to improved optical containment structures, methods of manufacture and use, and systems for employing same. The optical containment structures generally comprise zero-mode waveguide structures having non-reflective walls. The non-reflective walls allow the preparation of optical containment regions in which the optical containment dimensions can be decoupled from the solution containment dimensions. The application also relates to methods for producing islands of functionality within nanoscale apertures.

Abstract: Each opto-mechanical pointing device includes a housing having a base that two or more rollers extend beyond to make contact with a surface. An optical module that includes a light source and a detector track the motion of the opto-mechanical pointing device directly or indirectly. Light reflecting off markings positioned opposite of each detector is used to determine the speed and distance traveled by an opto-electrical pointing device. Alternatively, the speed and distance traveled by an opto-electrical pointing device is determined by monitoring the tilt or rotation of the opto-mechanical pointing device with respect to the surface beneath the pointing device.

Abstract: An optical navigation device with a phase grating for beam steering. The optical navigation device includes a light source, and image sensor, and a beam steering element. The light source directs a light beam toward a navigation surface. The image sensor receives light along an imaging path and generates a navigation image of the navigation surface from the light received along the imaging path. The beam steering element is disposed between the navigation surface and the image sensor. The beam steering element receives reflected light from the navigation surface along a specular reflection path. The beam steering element directs a first portion of the reflected light along the imaging path toward the image sensor. The beam steering element directs a second portion of the reflected light along a beam steering path away from the imaging path.

Abstract: Apparatus, systems and methods for use in analyzing discrete reactions at ultra high multiplex with reduced optical noise, and increased system flexibility. Apparatus include substrates having integrated optical components that increase multiplex capability by one or more of increasing density of reaction regions, improving transmission of light to or collection of light from discrete reactions regions. Integrated optical components include reflective optical elements which re-direct illumination light and light emitted from the discrete regions to more efficiently collect emitted light. Particularly preferred applications include single molecule reaction analysis, such as polymerase mediated template dependent nucleic acid synthesis and sequence determination.

Abstract: Photonic crystal sensors may be created from two and three dimensional photonic crystals by introducing defects. The localization of the optical field in the defect region affords the ability to sense small volumes of analyte.

Abstract: An apparatus and method for measuring a target environmental variable (TEV) that employs a film-bulk acoustic resonator with motion plate. The film-bulk acoustic resonator (FBAR) includes an acoustic reflector formed in an FBAR wafer and a surface. A first electrode is formed on the surface of the acoustic reflector and has a surface. A piezoelectric layer is formed on the surface of the first electrode and has a surface. A second electrode is formed on the surface of the piezoelectric layer. A motion plate is suspended in space at a predetermined distance relative to the surface of the second electrode and is capacitively coupled to the FBAR.

Abstract: Each opto-mechanical pointing device includes a housing having a base that two or more rollers extend beyond to make contact with a surface. An optical module that includes a light source and a detector track the motion of the opto-mechanical pointing device directly or indirectly. Light reflecting off markings positioned opposite of each detector is used to determine the speed and distance traveled by an opto-electrical pointing device. Alternatively, the speed and distance traveled by an opto-electrical pointing device is determined by monitoring the tilt or rotation of the opto-mechanical pointing device with respect to the surface beneath the pointing device.

Abstract: An optical navigation system includes an illumination system, an image sensor, and a processing system. The illumination system directs a beam of output light toward an object so that a first portion of the output light beam reflects off the object front surface to form a first reflected light beam and a second portion of the output light beam reflects off the object back surface to form a second reflected light beam, where the first and second reflected light beams overlap in a region of space to produce an interference pattern. The image sensor captures images of the interference pattern. The processing system produces motion signals indicative of movement of the image sensor in relation to the object from comparisons of ones of the images captured by the image sensor.

Abstract: A diagnostic system in accordance with the invention is housed in a hand-held personal communications device (PCD). The diagnostic system includes a data capture system that is used to capture diagnostic data. The diagnostic system also includes a data storage system and a processing system. The data storage system stores reference diagnostic data that is used by the processing system in conjunction with the captured diagnostic data to obtain a diagnostic result.

Abstract: A wafer-level device fabrication process forms standing structures around emitting areas of multiple VCSELs. The standing structures can be shaped to hold ball lenses or other optical elements for respective VCSELs or can include platforms on which optical elements are formed. Ball lenses that are attached to the standing structures either during chip-level or wafer-level processes fit into the standing structures and are automatically aligned. Wafer level fabrication of optical elements can align the optical elements with accuracies associated with photolithographic processes. The optical elements can be formed using a molding or replication process, a printing method, or surface tension during a reflow of lithographically formed regions.

Abstract: A humidity sensor that includes a resonant structure and a structure for altering a resonant frequency of the resonant structure in response to a change in humidity. The structures of a humidity sensor according to the present teachings may be formed in relatively small form factors and are well suited to remote applications and providing mechanisms for compensating for temperature drift.

Abstract: A surface sensing system including at least two sensors located on the end of the same optical fiber. The sensors are configured such that they exhibit resonant frequencies or Q-factors that are distinguishable from each other, where the Q-factor is defined as the resonant frequency divided by the resonance spectrum at full-width half maximum (FWHM). Because the sensors have distinguishable resonant frequencies or Q-factors and are located on the end of the same optical fiber, they can be monitored in parallel with little or no optical interference.

Abstract: An apparatus for analyzing a lateral flow test strip having a plurality of types of markers for binding to analytes corresponding, respectively, to the types of markers. The apparatus includes a plurality of emitters corresponding, respectively, to the plurality types of markers on the lateral flow test strip. Each emitter emits light in a predetermined range near an optimum absorption wavelength for the corresponding type of marker to excite the marker.