Abstract: Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. These have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy of polynucleotide sequencing applications.

Abstract: Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. These may have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy of polynucleotide sequencing applications.

Abstract: Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. These have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy of polynucleotide sequencing applications.

Abstract: Disclosed herein is a high throughput optical scanning device and methods of use. The optical scanning device and methods of use provided herein can allow high throughput scanning of a continuously moving object with a high resolution despite fluctuations in stage velocity. This can aid in high throughput scanning of a substrate, such as a biological chip comprising fluorophores. Also provided herein are improved optical relay systems and scanning optics.

Abstract: Disclosed herein is a high throughput optical scanning device and methods of use. The optical scanning device and methods of use provided herein can allow high throughput scanning of a continuously moving object with a high resolution despite fluctuations in stage velocity. This can aid in high throughput scanning of a substrate, such as a biological chip comprising fluorophores. Also provided herein are improved optical relay systems and scanning optics.

Abstract: Methods are provided for carrying out DNA sequencing on a device having upper and lower conductive layers separated by an insulative layer. Holes in the upper conductive layer create discrete attachment sites for DNA fragments. Voltage is applied to the surface to control affinity between the attachment sites and the DNA fragments, and to compact the DNA fragments for discrete optical detection.

Abstract: Electrical detection methods are used to identify and further characterize single-molecule target analytes such as proteins and nucleic acids. A composition including a probe region and a tail region is contacted with a target analyte. The probe region specifically binds to the target analyte. The tail region is coupled to the probe region, and includes a nucleic acid template for polynucleotide synthesis. When conditions are such that polynucleotide synthesis occurs along the tail region, one hydrogen ion is released for every nucleotide that is incorporated into the tail region. A transistor such as an ISFET detects and measures changes in ion concentration, and these measurements can be used to identify the tail region and thus characterize the corresponding target analyte.

Abstract: Methods are provided for carrying out nucleic acid analysis, including sequence identification, employing voltage and/or controlled electric charge to enhance operation. A device comprises substrates for nucleic acid analysis, a first electrically conductive layer, a first electrically insulative layer of dielectric material on the first conductive layer, a second electrically conductive layer disposed upon the first insulative layer in a pattern to define discrete attachment sites for macromolecules on the first insulative layer, the second conductive layer provided with means for resisting affinity for the macromolecules to impede their attachment to sites on the second conductive layer, and terminals for the first and second conductive layers for applying a voltage pattern between the first and the second conductive layers to control affinity between the macromolecules and the discrete attachment sites.

Abstract: A grating light valve has with a plurality of spaced reflective ribbons are spatially arranged over a substrate with reflective surfaces. The grating light valve is configured to optimized the conditions for constructive and destructive interference with an incident light source having a wavelength ?. The grating light valve preferably has a set of movable active ribbons alternating between the set of stationary bias ribbons. The active ribbons and the bias ribbons are spatially separated over the substrate surface such that reflective regions of the substrate surface correspond to the spaces between the ribbons. The ribbons and reflective regions of the substrate optically and geometrically optimized for to generate the conditions for constrictive and destructive interference with the incident light source.

Abstract: One embodiment disclosed relates to a method for calibrating an array of light-modulating elements. The method includes illuminating the array of elements, modulating an intensity of light diffracted by the elements over a modulation range, and measuring the modulated light intensity from each element of the array using a linear detector. Other embodiments disclosed relate to an apparatus and system for calibrating an array of light-modulating elements. The apparatus includes a light source for illuminating the array of elements and a linear detector for measuring light intensities at points along a line segment. The apparatus is configured so that modulated light from each of the elements impinges upon a different point of the line segment. The system includes means for modulating an intensity of light diffracted by the elements over a modulation range and a detector for measuring the modulated light intensity from each element of the array.

Abstract: A device comprising movable micro-structures configured to contact a substrate is disclosed. The substrate has a metal-insulator-metal construction with an upper metal layer and an insulator being patterned to provide substrate contact regions to a lower metal layer. The micro-structures have metal under layers for providing ribbon contact regions and non-contact regions. In use, a bias voltage is applied across the micro-structures and the top metal layer of the substrate causing the micro-structures and the substrate to contact through the contact regions. During contact, the contact regions are maintained at a potential that is substantially less than the applied bias voltage, thereby reducing the formation of asperities and/or sticking between contacting parts. The micro-structures are preferably ribbon structures in an optical MEM device configured to modulate light.

Abstract: One embodiment disclosed comprises a method for bipolar operation of a light-modulating array. The method includes driving light-modulating elements of the array in a first polarity, switching polarities from the first polarity to a second polarity, driving the light-modulating elements of the array in a second polarity, switching polarities from the second polarity to the first polarity, and repeating the steps. Another embodiment disclosed comprises an apparatus utilizing a light-modulating array. The apparatus includes a first look-up table storing data for operating elements the light-modulating array in a first polarity mode, and a second look-up table storing data for operating the elements of the light-modulating array in a second polarity mode. The apparatus also includes a drive system for driving the elements of the light-modulating array. The drive system is coupled to both the first and second look-up tables.

Abstract: A device comprising movable micro-structures configured to contact a substrate is disclosed. The substrate has a metal-insulator-metal construction with an upper metal layer and an insulator being patterned to provide substrate contact regions to a lower metal layer. The micro-structures have metal under layers for providing ribbon contact regions and non-contact regions. In use, a bias voltage is applied across the micro-structures and the top metal layer of the substrate causing the micro-structures and the substrate to contact through the contact regions. During contact, the contact regions are maintained at a potential that is substantially less than the applied bias voltage, thereby reducing the formation of asperities and/or sticking between contacting parts. The micro-structures are preferably ribbon structures in an optical MEM device configured to modulate light.

Abstract: A grating light valve has with a plurality of spaced reflective ribbons are spatially arranged over a substrate with reflective surfaces. The grating light valve is configured to optimized the conditions for constructive and destructive interference with an incident light source having a wavelength &lgr;. The grating light valve preferably has a set of movable active ribbons alternating between the set of stationary bias ribbons. The active ribbons and the bias ribbons are spatially separated over the substrate surface such that reflective regions of the substrate surface correspond to the spaces between the ribbons. The ribbons and reflective regions of the substrate optically and geometrically optimized for to generate the conditions for constrictive and destructive interference with the incident light source.