Patents by Inventor Denis Zaccarin

Denis Zaccarin 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).

  • Patent number: 9689800
    Abstract: Processes for making high multiplex arrays for use in analyzing discrete reactions at ultra high multiplex with reduced optical noise, and increased system flexibility. The high multiplex arrays 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.
    Type: Grant
    Filed: August 27, 2014
    Date of Patent: June 27, 2017
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Denis Zaccarin, Stephen Turner, Pezhman Monadgemi, Ravi Saxena
  • Patent number: 8993307
    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.
    Type: Grant
    Filed: July 18, 2012
    Date of Patent: March 31, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Denis Zaccarin, Paul Lundquist, Peiqian Zhao, Cheng Frank Zhong, Stephen Turner, Yanqiao Huang, Pezhman Monadgemi, Ravi Saxena, Annette Grot, Aaron Rulison
  • Publication number: 20150053641
    Abstract: Processes for making high multiplex arrays for use in analyzing discrete reactions at ultra high multiplex with reduced optical noise, and increased system flexibility. The high multiplex arrays 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.
    Type: Application
    Filed: August 27, 2014
    Publication date: February 26, 2015
    Inventors: Denis Zaccarin, Stephen Turner, Pezhman Monadgemi, Ravi Saxena
  • Publication number: 20130023039
    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.
    Type: Application
    Filed: July 18, 2012
    Publication date: January 24, 2013
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Denis Zaccarin, Paul Lundquist, Peiqian Zhao, Cheng Frank Zhong, Stephen Turner, Yanqiao Huang, Pezhman Monadgemi, Ravi Saxena, Annette Grot, Aaron Rulison
  • Patent number: 8264687
    Abstract: Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.
    Type: Grant
    Filed: May 6, 2011
    Date of Patent: September 11, 2012
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Paul Lundquist, Denis Zaccarin, Yves Lacroix, Mark Maxham, Mathieu Foquet, Stephen Turner
  • Patent number: 8247216
    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.
    Type: Grant
    Filed: September 25, 2009
    Date of Patent: August 21, 2012
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Denis Zaccarin, Paul Lundquist, Peiqian Zhao, Cheng Frank Zhong, Stephen Turner, Yanqiao Huang, Pezhman Monadgemi, Ravi Saxena, Annette Grot, Aaron Rulison
  • Patent number: 8149399
    Abstract: Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.
    Type: Grant
    Filed: May 9, 2011
    Date of Patent: April 3, 2012
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Paul Lundquist, Denis Zaccarin, Yves Lacroix, Stephen Turner, John Dixon
  • Publication number: 20110291027
    Abstract: Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.
    Type: Application
    Filed: May 6, 2011
    Publication date: December 1, 2011
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Paul Lundquist, Denis Zaccarin, Yves Lacroix, Mark Maxham, Mathieu Foquet, Stephen Turner
  • Publication number: 20110287981
    Abstract: Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.
    Type: Application
    Filed: May 9, 2011
    Publication date: November 24, 2011
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Paul Lundquist, Denis Zaccarin, Yves Lacroix, Stephen Turner, John Dixon
  • Patent number: 7995202
    Abstract: Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.
    Type: Grant
    Filed: February 9, 2007
    Date of Patent: August 9, 2011
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Paul Lundquist, Denis Zaccarin, Yves Lacroix, Mark Maxham, Mathieu Foquet, Stephen Turner
  • Patent number: 7961314
    Abstract: Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.
    Type: Grant
    Filed: October 26, 2007
    Date of Patent: June 14, 2011
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Paul Lundquist, Denis Zaccarin, Yves Lacroix, Stephen Turner, John Dixon
  • Publication number: 20100331212
    Abstract: Methods and systems are described for determining information about template sequences by simultaneously providing excitation over time to a plurality of confined sources on a substrate, each confined source carrying out a template mediated addition of nucleotides with a polymerase enzyme. The nucleotides have different labels, each with a different emission wavelength profile. Optical elements direct optical signals from the different NTPs within each optical confinement to different detector locations. Observing the optical signals over time allows for obtaining sequence information about the template nucleic acids.
    Type: Application
    Filed: September 3, 2010
    Publication date: December 30, 2010
    Applicant: Pacific Bioseciences of California, Inc.
    Inventors: Paul Lundquist, Stephen Turner, Denis Zaccarin
  • Patent number: 7805081
    Abstract: Methods and systems for monitoring a plurality of different optical signals from a single source of such signals, where each such different optical signal is spatially separated from other such signals and directed to different detectors or locations upon a single detector, which direction is generally accomplished through the use of a small number of optical components and/or manipulations.
    Type: Grant
    Filed: August 11, 2005
    Date of Patent: September 28, 2010
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Paul Lundquist, Stephen Turner, Denis Zaccarin
  • Patent number: 7791792
    Abstract: An apparatus for suppressing optical power transients includes a variable optical attenuator receiving an input optical signal and outputting an output optical signal; an optical power sensing element coupled to the input optical signal and sensing a portion of the input optical signal; and a feedforward loop controller coupled to the variable optical attenuator and to the optical power sensing element; the feedforward control loop providing feedforward control of the variable optical attenuator to reduce optical power transients of the input optical signal and maintain a substantially constant output power based on the input optical power and a reference value; the variable optical attenuator having a default opaque state in which the input optical signal is substantially attenuated when power is not being supplied to said variable optical attenuator. Variations include feedback loop controllers and a combination feedback and feedforward loop controllers.
    Type: Grant
    Filed: July 16, 2008
    Date of Patent: September 7, 2010
    Assignee: Ciena Corporation
    Inventors: Paul Lundquist, Marc Levesque, Denis Zaccarin
  • Publication number: 20100167413
    Abstract: Mitigative and remedial approaches to reduction of autofluorescence background noise are applied in analytical systems that rely upon sensitive measurement of fluorescent signals from arrays of fluorescent signal sources. Such systems are for particular use in fluorescence based sequencing by incorporation systems that rely upon small numbers or individual fluorescent molecules in detecting incorporation of nucleotides in primer extension reactions. Systems and methods for analyzing highly multiplexed sample arrays using highly multiplexed, high-density optical systems to illuminate high-density sample arrays and/or provide detection and preferably confocal detection off signals emanating from such high-density arrays. Systems and methods are applied in a variety of different analytical operations, including analysis of biological and biochemical reactions, including nucleic acid synthesis and derivation of sequence information from such synthesis.
    Type: Application
    Filed: May 9, 2008
    Publication date: July 1, 2010
    Inventors: Paul Lundquist, Cheng Frank Zhong, Denis Zaccarin, Pegian Zhao, Stephen Turner
  • Patent number: 7715001
    Abstract: Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.
    Type: Grant
    Filed: February 9, 2007
    Date of Patent: May 11, 2010
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Paul Lundquist, Denis Zaccarin, Yves Lacroix, Stephen Turner, John Dixon
  • Patent number: 7714303
    Abstract: Mitigative and remedial approaches to reduction of autofluorescence background noise are applied in analytical systems that rely upon sensitive measurement of fluorescent signals from arrays of fluorescent signal sources. Such systems are for particular use in fluorescence based sequencing by incorporation systems that rely upon small numbers or individual fluorescent molecules in detecting incorporation of nucleotides in primer extension reactions.
    Type: Grant
    Filed: May 9, 2008
    Date of Patent: May 11, 2010
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Paul Lundquist, Cheng Frank Zhong, Denis Zaccarin, Stephen Turner
  • Publication number: 20100099100
    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.
    Type: Application
    Filed: September 25, 2009
    Publication date: April 22, 2010
    Applicant: Pacific Biosciences of California, Inc.
    Inventors: Denis Zaccarin, Paul Lundquist, Peiqian Zhao, Cheng Frank Zhong, Stephen Turner, Yanqiao Huang, Pezhman Monadgemi, Ravi Saxena, Annette Grot, Aaron Rulison
  • Patent number: 7692783
    Abstract: Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.
    Type: Grant
    Filed: July 7, 2006
    Date of Patent: April 6, 2010
    Assignee: Pacific Biosciences of California
    Inventors: Paul Lundquist, Denis Zaccarin, Yves Lacroix, Stephen Turner, John Dixon
  • Publication number: 20090303576
    Abstract: An apparatus for suppressing optical power transients includes a variable optical attenuator receiving an input optical signal and outputting an output optical signal; an optical power sensing element coupled to the input optical signal and sensing a portion of the input optical signal; and a feedforward loop controller coupled to the variable optical attenuator and to the optical power sensing element; the feedforward control loop providing feedforward control of the variable optical attenuator to reduce optical power transients of the input optical signal and maintain a substantially constant output power based on the input optical power and a reference value; the variable optical attenuator having a default opaque state in which the input optical signal is substantially attenuated when power is not being supplied to said variable optical attenuator. Variations include feedback loop controllers and a combination feedback and feedforward loop controllers.
    Type: Application
    Filed: July 16, 2008
    Publication date: December 10, 2009
    Inventors: Paul Lundquist, Marc Levesque, Denis Zaccarin