Arrays of integrated analytical devices and their methods for production are provided. The arrays 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 integrated devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The arrays and methods of the invention make use of silicon chip fabrication and manufacturing techniques developed for the electronics industry and highly suited for miniaturization and high throughput.

Arrays of integrated analytical devices and their methods for production are provided. The arrays 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 integrated devices allow the highly sensitive discrimination of optical signals using features such as spectra, amplitude, and time resolution, or combinations thereof. The arrays and methods of the invention make use of silicon chip fabrication and manufacturing techniques developed for the electronics industry and highly suited for miniaturization and high throughput.

An optical waveguide comprises at least two TIR surface and contains a grating. Input TIR light with a first angular range along a first propagation direction undergoes at least two diffractions at the grating. Each diffraction directs light into a unique TIR angular range along a second propagation direction.

An optical waveguide comprises at least two TIR surface and contains a grating. Input TIR light with a first angular range along a first propagation direction undergoes at least two diffractions at the grating. Each diffraction directs light into a unique TIR angular range along a second propagation direction.

An apparatus with a grating structure and a method for forming the same are disclosed. The grating structure includes forming a wedge-shaped structure in a grating layer using a grayscale resist and photo lithography. A plurality of channels is formed in the grating layer to define slanted grating structures therein. The wedge-shaped structure and the slanted grating structures are formed using a selective etch process.

A free space coupling system comprising a waveguide horizontally positioned on an integrated circuit, and a silicon housing coupled to the waveguide, wherein the silicon housing comprises a reflective surface, a first port, wherein the first port is configured to receive light from an optic source positioned substantially parallel to the waveguide at a coupling point, and a second port, wherein the second port is oriented at about ninety degrees with respect to the first port, and wherein the second port is aligned with a grating port on the waveguide.

A free space coupling system comprising a waveguide horizontally positioned on an integrated circuit, and a silicon housing coupled to the waveguide, wherein the silicon housing comprises a reflective surface, a first port, wherein the first port is configured to receive light from an optic source positioned substantially parallel to the waveguide at a coupling point, and a second port, wherein the second port is oriented at about ninety degrees with respect to the first port, and wherein the second port is aligned with a grating port on the waveguide.

A semiconductor device includes a substrate, a trench in the substrate, the trench having an inclined sidewall, a reflective layer over the inclined sidewall, a grating structure over the substrate, and a waveguide in the trench. The waveguide is configured to guide optical signals between the grating structure and the reflective layer.

A semiconductor device includes a substrate, a trench in the substrate, the trench having an inclined sidewall, a reflective layer over the inclined sidewall, a grating structure over the substrate, and a waveguide in the trench. The waveguide is configured to guide optical signals between the grating structure and the reflective layer.

An optical phased array includes, in part, a multitude of optical signal emitters and a multitude of optical signal phase/delay elements each associated with and disposed between a different pair of the optical signal emitters. Each optical signal phase/delay element is adapted to cause a phase/delay shift between the optical signals emitted from its associated pair of optical signal emitters. Each optical signal phase/delay element is optically a ring resonator that includes a p-i-n junction. By varying the bias applied to the p-i-n junction, the phase/delay generated by the ring resonator is varied. Furthermore, each optical signal emitter is optionally an optical grating having a multitude of grooves. The groove lengths of the optical gratings are optionally selected so as to increase along the direction of travel of the input optical signal through the optical phase array.