Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.

Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.

Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.

Abstract: Apparatus and methods for producing ultrashort optical pulses are described. A high-power, solid-state, passively mode-locked laser can be manufactured in a compact module that can be incorporated into a portable instrument for biological or chemical analyses. The pulsed laser may produce sub-100-ps optical pulses at a repetition rate commensurate with electronic data-acquisition rates. The optical pulses may excite samples in reaction chambers of the instrument, and be used to generate a reference clock for operating signal-acquisition and signal-processing electronics of the instrument.

Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.

Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.

Abstract: Apparatus and methods for producing ultrashort optical pulses are described. A high-power, solid-state, passively mode-locked laser can be manufactured in a compact module that can be incorporated into a portable instrument for biological or chemical analyses. The pulsed laser may produce sub-100-ps optical pulses at a repetition rate commensurate with electronic data-acquisition rates. The optical pulses may excite samples in reaction chambers of the instrument, and be used to generate a reference clock for operating signal-acquisition and signal-processing electronics of the instrument.

Abstract: Compact optical sources and methods for producing short and ultrashort optical pulses are described. A semiconductor laser or LED may be driven with a bipolar waveform to generate optical pulses with FWHM durations as short as approximately 85 ps having suppressed tail emission. The pulsed optical sources may be used for fluorescent lifetime analysis of biological samples and time-of-flight imaging, among other applications.

Abstract: Apparatus and methods for producing ultrashort optical pulses are described. A high-power, solid-state, passively mode-locked laser can be manufactured in a compact module that can be incorporated into a portable instrument for biological or chemical analyses. The pulsed laser may produce sub-100-ps optical pulses at a repetition rate commensurate with electronic data-acquisition rates. The optical pulses may excite samples in reaction chambers of the instrument, and be used to generate a reference clock for operating signal-acquisition and signal-processing electronics of the instrument.

Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.

Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.

Abstract: Techniques and devices for producing short laser pulses based on chirped pulse amplification.

Abstract: Techniques and devices for producing short laser pulses based on chirped pulse amplification.

Abstract: Methods and structures are disclosed demultiplexing optical signals transmitted over an optical fiber into a silicon substrate and to multiple detectors. The silicon substrate has two spaced-apart surfaces and a diffractive element disposed adjacent to one of the surfaces. Each of the optical signals corresponds to one of multiple wavelengths. The optical signals are directed into the silicon substrate along a path through the first surface to be incident on the diffractive element. The path is oriented generally normal with the first surface and/or with the diffractive element, which angularly separates the optical signals such that each of the wavelengths traverses through the substrate in a wavelength dependent direction to the first surface. Each optical signal is steered from the first surface towards the second surface to be incident on different optical elements that direct them generally normal to the first surface to be incident on one of the detectors.

Abstract: An optical assembly is formed with a silicon substrate having a first surface and a second surface confronting the first surface. A reflective coating is formed over the first surface. Multiple diffraction gratings are formed integrally within the second surface of the silicon substrate. An optical absorber is formed over the second surface between the diffraction gratings.

Abstract: A method of fabricating on a substrate an optical detector in an optical waveguide, the method involving: forming at least one layer on a surface of the substrate, said at least one layer comprising SiGe; implanting an impurity into the at least one layer over a first area to form a detector region for the optical detector; etching into the at least one layer in a first region and a second region to form a ridge between the first and second regions, said ridge defining the optical detector and the optical waveguide; filling the first and second regions with a dielectric material having a lower refractive index than SiGe; and after filling the first and second regions with the dielectric material, removing surface material to form a planarized upper surface.

Abstract: Methods are disclosed of fabricating an optical assembly. An active optical element is disposed near or on a first surface of a slab of optical material. A passive optical element is formed on a second surface of the slab, with the second surface being substantially parallel to the first surface. An optical axis of the passive optical element is aligned with an optical path between the passive optical element and an active region of the active optical element using a lithographic alignment process.

Abstract: A method of fabricating a detector that involves: forming a trench in a substrate, the substrate having an upper surface; forming a first doped semiconductor layer on the substrate and in the trench; forming a second semiconductor layer on the first doped semiconductor layer and extending into the trench, the second semiconductor layer having a conductivity that is less than the conductivity of the first doped semiconductor layer; forming a third doped semiconductor layer on the second semiconductor layer and extending into the trench; removing portions of the first, second and third layers that are above a plane defined by the surface of the substrate to produce an upper, substantially planar surface and expose an upper end of the first doped semiconductor layer in the trench; forming a first electrical contact to the first semiconductor doped layer; and forming a second electrical contact to the third semiconductor doped layer.

Abstract: Methods and structures are disclosed demultiplexing optical signals transmitted over an optical fiber into a silicon substrate and to multiple detectors. The silicon substrate has two spaced-apart surfaces and a diffractive element disposed adjacent to one of the surfaces. Each of the optical signals corresponds to one of multiple wavelengths. The optical signals are directed into the silicon substrate along a path through the first surface to be incident on the diffractive element. The path is oriented generally normal with the first surface and/or with the diffractive element, which angularly separates the optical signals such that each of the wavelengths traverses through the substrate in a wavelength dependent direction to the first surface. Each optical signal is steered from the first surface towards the second surface to be incident on different optical elements that direct them generally normal to the first surface to be incident on one of the detectors.

Abstract: A circuit including: an optical detector for detecting an optical pulse and generating therefrom a current pulse on an output; a pulse detector circuit having an input electrically connected to the optical detector and having an output for outputting a detection pulse in response to detecting the current pulse on its input, said pulse detector circuit including: a resettable amplifier including an input for receiving the current pulse from the optical detector, a reset terminal for resetting the amplifier after the amplifier detects the current pulse on its input, and an output for outputting a signal from which the detection pulse is derived; and a reset delay chain feeding back to the reset terminal of the resettable amplifier a feedback signal derived from the output signal of the resettable amplifier.