Intel Corporation

Siros Technologies, Inc.

Pacific Biosciences of California, Inc.

Emcore Corporation

Solfocus, Inc.

Other

Foveon, Inc.

Optiteck, Inc.

Mark E McDonald

Andrew J Daiber

Aaron J Rulison

Paul M Lundquist

Shang Wang

Robert R McLeod

William B Chapman

Sergei L Sochava

Mathieu Foquet

Marc A Finot

Ariel Herrmann

Lambertus Hesselink

William J Kozlovsky

Alexey Kuritsyn

Mark Rice

Russell Berman

Michael V Morelli

Brad Vaughn Johnson

Hua Li

Alexander V Tuganov

Paul Chi-Hwa Lin

Deborah Pao-Tung Kwo

Sanjoy Ghose

Shunichi Nishimura

Tsuei-Lian Wang

Stephen Wilson Turner

Wei W Wang

Richard Francis Lyon

Jiro Yoshinari

Hideki Hirata

John F Heanue

Nadim I Maluf

Takuya Tsukagoshi

Naoki Hayashida

Marc Epitaux

Peter E Kirkpatrick

Stephen John Horne

Richard Becker

Herman Ferrier

George W Hopkins, Ii

John E Sell

Tokuyuki Honda

Matthew Lipson

Ingolf Sander

Thomas Kridl

Nathan Shou

David Ross Pace

LeRoy A Volz

Timothy M Slagle

Dana Rose

James R Amble

John Steffen Jensen

Jan Peeters Weem

Balaki Venkateshwaran

Timothy F Slagle

Andy Daiber

Tokyuki Honda

Lambrerrtus Hesselink

Yu Chuan Lee

Integrated target waveguide devices and optical analytical systems comprising such devices are provided. The target devices include an optical coupler that is optically coupled to an integrated waveguide and that is configured to receive optical input from an optical source through free space, particularly through a low numerical aperture interface. The devices and systems 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 provide for the efficient and reliable coupling of optical excitation energy from an optical source to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination. The devices and systems are well suited for miniaturization and high throughput.

Integrated target waveguide devices and systems for optical coupling

Provided herein are systems, devices, and methods for improved optical waveguide transmission and alignment in an analytical system. Waveguides in optical analytical systems can exhibit variable and increasing back reflection of single-wavelength illumination over time, thus limiting their effectiveness and reliability. The systems are also subject to optical interference under conditions that have been used to overcome the back reflection. Novel systems and approaches using broadband illumination light with multiple longitudinal modes have been developed to improve optical transmission and analysis in these systems. Novel systems and approaches for the alignment of a target waveguide device and an optical source are also disclosed.

Systems, devices, and methods for improved optical waveguide transmission and alignment

We describe methods of producing gratings such as Bragg gratings with optical waveguides. Described are the writing and erasing of gratings within SiON waveguides by forming standing waves. Methods, systems, instruments, and devices are described that provide improved transmission of light through such waveguides.

Producing bragg gratings in optical waveguides

Optical delivery devices and integrated analytical systems comprising the optical delivery devices are provided. The optical delivery devices include optical inputs, optical outputs, and integrated optical waveguides that are configured for coupling of optical energy to a target waveguide device through free space. The integrated analytical systems include the optical delivery devices in combination with the target waveguide device. The devices and systems 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 provide for the efficient coupling of optical excitation energy from an optical source to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination. The devices and systems are well suited for miniaturization and high throughput.

Integrated devices and systems for free-space optical coupling

We have seen that some waveguides exhibit variable and increasing back reflection of single wavelength illumination over time, limiting their effectiveness and reliability. We have developed approaches to improve the transmission of these waveguides. We have found that by modulating the illumination wavelength over a small wavelength range we can reduce or eliminate this back reflection from the waveguide. In addition, we describe the writing and erasing of gratings within SiON waveguides by forming standing waves. Methods, systems, instruments, and devices are described that provide improved transmission of light through such waveguides.

Waveguide transmission

Apparatus, systems and methods for use in analyzing discrete reactions are provided. The analytical devices of the invention use an array of nanoscale regions (a chip) that has discrete patches, for example, patches of nanoscale regions. In some embodiments an analytical system is provided that has an analysis chip with an array of patches, each of the patches comprising nanoscale regions that emit fluorescent light when illuminated. The system has a two-dimensional (x, y) array of dichroic prisms, each prism comprising a dichroic element that diverts illumination light up in the z dimension of the array to a patch on the analysis chip above it. Each dichroic element transmits fluorescent light emitted by the patch that it illuminates, whereby the emitted light from each patch passes down through each dichroic prism. The analytical system also has a detector below the array of dichroic prisms that detects the transmitted fluorescent light. Such systems are useful for monitoring many analytical reactions at one time including single molecule sequencing reactions.

Analytical devices having dichroic prism arrays

Apparatus, systems and methods for use in analyzing discrete reactions are provided. The analytical devices of the invention use an array of nanoscale regions (a chip) that has discrete patches of nanoscale regions. The chip mates with a collection device comprising an array of compact lens trains (CLTs) where each of the CLTs corresponds to a single patch of nanoscale regions. Each CLT collects the emitted light from a patch on the chip, collimates the light, performs color separation on the collimated emitted light, and focuses the separated light onto a portion of pixels on the detector below the CLT. Such systems are useful for monitoring many analytical reactions at one time including single molecule sequencing reactions.

Analytical devices having compact lens train arrays

An approach to the design of the set of filters which allows for the collection of a larger portion of the optical signal while still distinguishing the presence of the various fluorophores is described. In some embodiments, the filter sets of the invention each block a smaller portion of the spectrum, allowing for a larger portion of the emitted light to be detected. The combined information from the light passing through two or more of the filters is then used to determine the presence of a given fluorophore. The filter sets of the invention can be particularly useful in integrated devices in which the light from a single molecule reaction in a small reaction region is directed to a detector or to a specific portion of a detector.

Filter architecture for analytical devices

A method comprising forming two or more frames from a first wafer, forming two or more etalons from a second wafer, disposing a resistive thermal device on each of the two or more frames, dicing the first wafer and the second wafer, and bonding each of the frames to a corresponding one of the etalons to form optical subassemblies of optical filters.

Thermal control of optical filter with local silicon frame

A method comprising generating an optical beam with a laser, filtering the optical beam to select a desired wavelength with an etalon positioned in a path of the optical beam, heating the etalon to an operational temperature using a heater, monitoring the operational temperature of the etalon with a resistive thermal device disposed in or on a thermally conductive frame bonded to the etalon, and applying feedback control of the heater based on the monitoring to select the desired wavelength.

Growing community of inventors

Mill Valley, CA, United States of America

Mark E McDonald