Patents by Inventor Aaron Rulison

Aaron Rulison has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20210311254
    Abstract: 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.
    Type: Application
    Filed: March 15, 2021
    Publication date: October 7, 2021
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Alexey KURITSYN, Mark MCDONALD, Aaron RULISON, Russell BERMAN
  • Publication number: 20210285881
    Abstract: Provided herein are highly multiplexed optical analytical systems for improved nucleic acid sequencing. The systems include a plurality of highly multiplexed optical chips, at least one optical source, and a plurality of optical delivery devices for illuminating an array of nanoscale rection regions on each of the optical chips. In use, the reaction regions contain fluorescent nucleic acid sequencing reagents and are arranged to report nucleic acid sequence information to optical detectors associated with the multiplexed optical chips in real time. The systems enable a massive increase in the scale of nucleic acid sequencing reactions capable of being performed within a single instrument without a corresponding increase in size, complexity, or cost of the instrument.
    Type: Application
    Filed: February 18, 2021
    Publication date: September 16, 2021
    Inventors: Alexey KURITSYN, Mark MCDONALD, Aaron RULISON, Annette GROT
  • Publication number: 20210215607
    Abstract: Provided herein are cartridges, packaged devices, and systems for improved nucleic acid sequencing. The cartridges, devices, and systems include a highly multiplexed optical chip comprising a plurality of nanoscale reaction regions that is configured to perform and report nucleic acid sequencing reactions. The chips are, in some embodiments, packaged for use in analytical nucleic acid sequencing reactions. The chips may be attached to a printed circuit board, may be surrounded by a protective enclosure, may include a flow cell, and may include optical features to minimize or block photobleaching of the sequencing reagents and background fluorescent signals. Also provided are analytical systems for nucleic acid sequencing that comprise the disclosed cartridges and packaged devices.
    Type: Application
    Filed: January 14, 2021
    Publication date: July 15, 2021
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Russell BERMAN, Jaime Juan BENITEZ-MARZAN, Natasha POPOVICH, Aaron RULISON, Ravi SAXENA
  • Patent number: 11054576
    Abstract: 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.
    Type: Grant
    Filed: July 18, 2019
    Date of Patent: July 6, 2021
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Shang Wang, Mathieu Foquet, Paul Lundquist, Aaron Rulison, Mark McDonald, Ariel Herrmann
  • Patent number: 10948652
    Abstract: 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.
    Type: Grant
    Filed: November 3, 2018
    Date of Patent: March 16, 2021
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Alexey Kuritsyn, Mark McDonald, Aaron Rulison, Russell Berman
  • Publication number: 20210033788
    Abstract: 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.
    Type: Application
    Filed: July 10, 2020
    Publication date: February 4, 2021
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Shang WANG, Mathieu FOQUET, Paul LUNDQUIST, Aaron RULISON, Mark MCDONALD, Ariel HERRMANN
  • Patent number: 10871460
    Abstract: The present invention provides novel methods and devices that employ microfluidic technology to generate molecular melt curves. In particular, the devices and methods in accordance with the invention are useful in providing for the analysis of PCR amplification products.
    Type: Grant
    Filed: May 25, 2018
    Date of Patent: December 22, 2020
    Assignee: Canon U.S.A., Inc.
    Inventors: Ivor T. Knight, Deborah John Boles, Aaron Rulison, Wesley B. Dong, Andrew Fabans, Allen Boronkay, Edward Donlon, Robert Moti, Michael Slater, Steven A. Sundberg, Michael R. Knapp
  • Publication number: 20200049882
    Abstract: 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.
    Type: Application
    Filed: July 18, 2019
    Publication date: February 13, 2020
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Shang WANG, Mathieu FOQUET, Paul LUNDQUIST, Aaron RULISON, Mark MCDONALD, Ariel HERRMANN
  • Patent number: 10487356
    Abstract: 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.
    Type: Grant
    Filed: March 16, 2016
    Date of Patent: November 26, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Paul Lundquist, Mark McDonald, Aaron Rulison
  • Publication number: 20190317340
    Abstract: 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.
    Type: Application
    Filed: April 11, 2019
    Publication date: October 17, 2019
    Inventors: Mark McDonald, Aaron Rulison, Paul Lundquist, Tsuei-Lian Wang, Deborah Pao-Tung Kwo, Shang Wang
  • Patent number: 10365434
    Abstract: 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.
    Type: Grant
    Filed: June 11, 2016
    Date of Patent: July 30, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Shang Wang, Mathieu Foquet, Paul Lundquist, Aaron Rulison, Mark McDonald, Ariel Herrmann
  • Publication number: 20190179078
    Abstract: 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.
    Type: Application
    Filed: November 3, 2018
    Publication date: June 13, 2019
    Inventors: Alexey KURITSYN, Mark MCDONALD, Aaron RULISON, Russell BERMAN
  • Patent number: 10302972
    Abstract: 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.
    Type: Grant
    Filed: January 21, 2016
    Date of Patent: May 28, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Mark McDonald, Aaron Rulison, Paul Lundquist, Tsuei-Lian Wang, Deborah Pao-Tung Kwo, Shang Wang
  • Publication number: 20180321170
    Abstract: The present invention provides novel methods and devices that employ microfluidic technology to generate molecular melt curves. In particular, the devices and methods in accordance with the invention are useful in providing for the analysis of PCR amplification products.
    Type: Application
    Filed: May 25, 2018
    Publication date: November 8, 2018
    Applicants: Canon U.S. Life Sciences, Inc., CALIPER LIFE SCIENCES, INC.
    Inventors: Ivor T. Knight, Deborah John Boles, Aaron Rulison, Wesley B. Dong, Andrew Fabans, Allen Boronkay, Edward Donlon, Robert Moti, Michael Slater, Steven A. Sundberg, Michael R. Knapp
  • Patent number: 9983155
    Abstract: The present invention provides novel methods and devices that employ microfluidic technology to generate molecular melt curves. In particular, the devices and methods in accordance with the invention are useful in providing for the analysis of PCR amplification products.
    Type: Grant
    Filed: March 15, 2013
    Date of Patent: May 29, 2018
    Assignees: Canon U.S. Life Sciences, Inc., CALIPER LIFE SCIENCES, INC.
    Inventors: Ivor T. Knight, Deborah John Boles, Aaron Rulison, Wesley B. Dong, Andrew Fabans, Allen Boronkay, Edward Donlon, Robert Moti, Michael Slater, Steven A. Sundberg, Michael R. Knapp
  • Patent number: 9945781
    Abstract: 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.
    Type: Grant
    Filed: January 17, 2017
    Date of Patent: April 17, 2018
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Aaron Rulison, Mark McDonald, Paul Lundquist
  • Publication number: 20170167979
    Abstract: 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.
    Type: Application
    Filed: January 17, 2017
    Publication date: June 15, 2017
    Inventors: Aaron Rulison, Mark McDonald, Paul Lundquist
  • Patent number: 9581550
    Abstract: 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.
    Type: Grant
    Filed: May 29, 2014
    Date of Patent: February 28, 2017
    Assignee: Pacific Biosciences of California
    Inventors: Aaron Rulison, Mark McDonald, Paul Lundquist
  • Publication number: 20160377562
    Abstract: The present invention provides novel methods and devices that employ microfluidic technology to generate molecular melt curves. In particular, the devices and methods in accordance with the invention are useful in providing for the analysis of PCR amplification products.
    Type: Application
    Filed: June 27, 2016
    Publication date: December 29, 2016
    Applicants: CALIPER LIFE SCIENCES, INC., CANON U.S. LIFE SCIENCES, INC.
    Inventors: Steven A. Sundberg, Michael R. Knapp, Ivor T. Knight, Deborah J. Boles, Aaron Rulison, Wesley B. Dong, Andrew Fabans, Allen Boronkay, Edwawrd Donlon, Robert Moti, Michael Slater
  • Publication number: 20160363728
    Abstract: 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.
    Type: Application
    Filed: June 11, 2016
    Publication date: December 15, 2016
    Inventors: Shang WANG, Mathieu FOQUET, Paul LUNDQUIST, Aaron RULISON, Mark MCDONALD, Ariel HERRMANN