Split grating coupler with improved beam alignment sensitivity

Abstract

The invention discloses an apparatus and a method for coupling radiation from an incident beam (1-122) into a plurality of waveguides (1-, 2-, 3-212a ... e) by means of a grating coupler (1-, 2-, 3-210). The grating coupler (1-, 2-, 3-210) may have an offset receiving region and a grating portion with an offset periodicity to increase the sensitivity of the grating coupler (1-, 2-, 3-210) to misalignment of the incident beam.

Description

[0001] Related Applications

[0002] This application claims priority under 35 USC §119(e) to U.S. Provisional Application No. 62 / 861,832, filed on June 14, 2019, entitled “SLICEDGRATING COUPLER WITH INCREASED BEAM ALIGNMENT SENSITIVITY,” the entirety of which is incorporated herein by reference. Technical Field

[0003] The present application relates to coupling radiation into a plurality of optical waveguides by means of one or more gratings. Background Art

[0004] In the field of optical instruments and integrated optical devices, optical radiation can be delivered to multiple discrete sites on a chip. For a communication device or an analytical device, the optical radiation can be delivered to multiple waveguides formed on the chip, which can transport the optical radiation to one or more sites on the chip (e.g., for signal processing or for sample detection). One method of delivering radiation to multiple sites is to couple radiation from an incident beam into multiple waveguides using one or more grating couplers. Summary of the invention

[0005] The present invention describes an apparatus and method for coupling optical radiation into one or more waveguides formed on a substrate. In certain embodiments, a grating coupler is patterned to have offset or staggered entrances to two or more waveguides, such that the offset of the entrance provides a signal from the waveguide that eliminates movement of the optical beam on the grating coupler in a direction toward or away from the entrance. In certain embodiments, a grating coupler is patterned to have regions of different grating periodicities adjacent to the entrances to the two or more waveguides, such that the varying periodicity provides a signal from the waveguide that eliminates changes in the angle of incidence of the optical beam on the grating coupler. In other embodiments, the offset and varying pitch of the entrance can be combined in the grating coupler to eliminate both movement of the optical beam on the grating coupler and changes in the angle of incidence. The elimination of beam motion and angle of incidence can improve the sensitivity of the grating coupler to calibration and misalignment of the incident beam.

[0006] Certain embodiments relate to an integrated device comprising: a grating disposed on a substrate and configured to couple radiation incident on the grating into a plurality of optical waveguides disposed on the substrate; a first entrance to a first receiving region of the plurality of optical waveguides; and a second entrance to a second receiving region of the plurality of optical waveguides, wherein the second entrance is offset by a first amount relative to the first entrance in a first direction perpendicular to a line of the grating.

[0007] Certain embodiments relate to a method of coupling radiation into multiple optical waveguides formed on a substrate, the method comprising the following actions: receiving one or more radiation beams on a grating formed on the substrate; coupling radiation from the one or more beams into multiple receiving areas connected to the multiple optical waveguides; monitoring a first amount of radiation received from a first waveguide of the multiple optical waveguides; and determining whether the one or more beams are moving toward or away from an entrance of the first waveguide in a direction perpendicular to a line of the grating based at least in part on the monitored amount of radiation.

[0008] Certain embodiments relate to a method of manufacturing an integrated device. The method may include the following acts: forming a plurality of waveguides on a substrate; forming an entrance grating on the substrate that spans the plurality of waveguides; positioning a first entrance to a first waveguide of the plurality of waveguides along a reference line of the grating; and offsetting a second entrance to a second waveguide of the plurality of waveguides by a first distance from the reference line, wherein the first distance is in a first direction perpendicular to the line of the grating.

[0009] Certain embodiments relate to an integrated device comprising: a grating disposed on a substrate and configured to couple radiation incident on the grating into a plurality of optical waveguides disposed on the substrate; a first inlet to a first waveguide of the plurality of optical waveguides; and a second inlet to a second waveguide of the plurality of optical waveguides, wherein a first portion of the grating positioned adjacent to the first inlet has a different periodicity than a second portion of the grating positioned adjacent to the second inlet.

[0010] Certain embodiments relate to a method of coupling radiation into a plurality of optical waveguides formed on a substrate, the method comprising the following acts: receiving one or more radiation beams on a grating; coupling radiation from the one or more beams into the plurality of optical waveguides; monitoring a signal received from a first waveguide of the plurality of optical waveguides; and determining, based at least in part on the signal monitored from the first waveguide, whether an incident pitch angle of the one or more beams on the grating changes in a direction perpendicular to a line of the grating.

[0011] Certain embodiments are directed to a method of manufacturing an integrated device. The method may include the following acts: forming a plurality of waveguides on a substrate, each waveguide having an entrance adjacent to a grating; and forming a grating on the substrate to span the entrances to the waveguides, wherein a first portion of the grating positioned adjacent to a first entrance to a first waveguide of the plurality of waveguides has a different periodicity than a second portion of the grating positioned adjacent to a second entrance to a second waveguide of the plurality of waveguides.

[0012] The foregoing and other aspects, implementations, acts, functionalities, features and embodiments of the present invention may be more fully understood from the following description in conjunction with the accompanying drawings. BRIEF DESCRIPTION OF THE DRAWINGS

[0013] Those skilled in the art will appreciate that the figures described herein are for illustration purposes only. It should be understood that in some examples, various aspects of the present invention may be shown as enlarged or magnified to facilitate understanding of the present invention. In the accompanying drawings, similar reference characters generally refer to similar features, functionally similar and / or structurally similar elements throughout the various figures. The drawings are not necessarily drawn to scale, but rather, emphasis is placed on illustrating the principles of the present teachings. The drawings are not intended to limit the scope of the present teachings in any way.

[0014] Figure 1-1 is a perspective diagram depicting an optical pulse incident on a grating coupler, according to certain embodiments.

[0015] Figure 1-2 is a plan view depicting an example of a grating coupler configured to couple optical radiation into a plurality of waveguides, according to certain embodiments.

[0016] Figure 1-3 is an elevation view of a grating coupler according to some embodiments.

[0017] Figure 2-1 is a plan view of an example grating coupler with improved sensitivity for beam alignment in accordance with certain embodiments.

[0018] Figure 2-2 is a plan view of an example grating coupler with improved sensitivity for beam alignment in accordance with certain embodiments.

[0019] Figure 2-3 is a plan view of an example grating coupler having improved sensitivity for beam alignment for multiple incident beams in accordance with certain embodiments.

[0020] Figure 2-4 Signal characteristics of a signal received from a receiving region of a grating coupler having improved sensitivity to beam alignment according to certain embodiments are depicted.

[0021] Figure 3-1 is a plan view of an example grating coupler with improved sensitivity for beam alignment in accordance with certain embodiments.

[0022] Figure 3-2 is a plan view of an example grating coupler with improved sensitivity for beam alignment in accordance with certain embodiments.

[0023] Figure 3-3 Signal characteristics of a signal received from a receiving region of a grating coupler having improved sensitivity to beam alignment according to certain embodiments are depicted.

[0024] Figure 3-4Depicted are examples of receiving regions and corresponding grating portions according to certain embodiments.

[0025] Figure 3-5 is a flowchart description of a method for calibrating and maintaining calibration of an incident beam on a grating coupler in accordance with certain embodiments.

[0026] Figure 4 Depicted are cross-sectional perspective views of portions of integrated devices according to certain embodiments.

[0027] Figure 5-1A is a block diagram depiction of an analytical instrument including a compact mode-locked laser module according to certain embodiments.

[0028] Figure 5-1B Depicted is a compact mode-locked laser module incorporated into an analytical instrument in accordance with certain embodiments.

[0029] Figure 5-2 Depicted are optical pulse trains according to certain embodiments.

[0030] Figure 5-3 An example of parallel reaction chambers that can be optically excited by a pulsed laser via one or more waveguides according to certain embodiments is depicted and further shows a corresponding detector for each chamber.

[0031] Figure 5-4 Illustrates optical excitation of a reaction chamber from a waveguide, according to certain embodiments.

[0032] Figure 5-5 Further details of an integrated reaction chamber, optical waveguide, and time-fractionated light detector are depicted according to certain embodiments.

[0033] Figure 5-6 Depicted are examples of biological reactions that may occur within a reaction chamber according to certain embodiments.

[0034] Figure 5-7 The emission probability curves of two different fluorophores with different decay characteristics are depicted.

[0035] Figure 5-8 Depicted is temporally fractionated detection of fluorescence emission according to certain embodiments.

[0036] Figure 5-9 A time-graded light detector is depicted in accordance with certain embodiments.

[0037] Figure 5-10A Depicted are pulsed excitation and time-fractionated detection of fluorescent emission from a reaction chamber, according to certain embodiments.

[0038] Figure 5-10BDepicted are histograms of accumulated fluorescence photon counts in various time bins following repeated pulse excitation of an analyte, according to certain embodiments.

[0039] Figure 5-11A to Figure 5-11D Depicted are different histograms that may correspond to four nucleotides (T, A, C, G) or nucleotide analogs according to certain embodiments.

[0040] Features and advantages of the present invention will become more apparent from the detailed description set forth below in conjunction with the accompanying drawings. When describing embodiments with reference to the accompanying drawings, directional references ("above", "below", "top", "bottom", "left", "right", "horizontal", "vertical", etc.) may be used. Such references are intended only to assist the reader in viewing the drawings in a normal orientation. These directional references are not intended to describe preferred or exclusive orientations of features of the embodied device. Other orientations may be used to embody the device. DETAILED DESCRIPTION

[0041] I. Grating Coupler

[0042] A grating coupler is a useful integrated optical device for coupling optical radiation from an external optical beam into an integrated optical waveguide located on a substrate. For explanation purposes, Figure 1-1 An example of a grating coupler 1-100 integrated on a substrate 1-105 is shown. The grating coupler 1-100 may include an optical grating 1-110 and a receiving region 1-112 of an optical waveguide having an inlet 1-111. In the example shown, the grating 1-110 is positioned adjacent to the inlet 1-111, and the grating coupler 1-100 is configured to redirect and couple incident optical radiation (depicted as a beam of optical pulses 1-122 traveling along an optical axis 1-101 of the beam) via the inlet 1-111 into the receiving region 1-112 of the waveguide. The receiving region 1-112 may be connected to one or more waveguides downstream of the inlet 1-111, such as Figure 1-2 As shown in . Figure 1-1 For directional reference in the illustration of , the coordinate axes are selected so that the x and y directions are parallel to the top surface of the substrate 1-105 on which the grating coupler is formed. However, the present invention is not limited to the illustrated orientation of the Cartesian coordinate reference system. Other reference systems (polar, spherical) and other orientations may be used to describe the present invention.

[0043] When a component is described as being "on" or "over" a substrate or layer, the component may be directly on the substrate or layer, or there may be one or more intervening material layers and / or one or more intervening components between the component and the substrate or layer. The phrase "directly on" is used to indicate that the component is in direct physical contact with the adjacent substrate or layer.

[0044] Figure 1-2 1-105. The grating coupler 1-100 may be connected to and couple radiation into a first waveguide 1-213, which may be connected to two or more waveguides 1-213a, 1-213b. Any of the waveguide segments may be a single transverse mode or multimode waveguide. Any of the waveguide segments may include a waveguide core formed of a first dielectric material having a first refractive index and one or more cladding layers surrounding or partially surrounding the core. The refractive index of the one or more cladding layers may have a value less than the refractive index of the waveguide core.

[0045] According to certain embodiments, a power divider 1-225 may divide the power received from the first waveguide 1-213 into the two waveguides 1-213a, 1-213b shown. In certain embodiments, the power from the first waveguide 1-213 may be divided into more than two waveguides. In certain cases, a power divider may not be used and only a single waveguide 1-213 may extend from the grating coupler 1-100. In certain cases, the waveguides 1-213a, 1-213b may be connected to additional power dividers so that the optical power in the waveguides may be further distributed into a plurality of waveguides.

[0046] Some examples of power divider 1-225 include waveguide couplers or waveguide splitters, in which a propagation mode in a first waveguide is transiently coupled to one or more propagation modes in one or more adjacent waveguides. Other examples of power divider 1-225 include interference splitters, such as Mach-Rend interferometers and multimode interference couplers. Regardless of the type of power divider 1-225 and the number of downstream waveguides, the power from the first waveguide 1-213 can be equally or unequally distributed among the downstream waveguides by selecting a suitable design and splitting ratio of the power divider 1-225.

[0047] Figure 1-3 Depicted is a schematic diagram roughly corresponding to Figure 1-1 . An elevation view of the structure shown in . The optical grating 1-110 may be patterned as lines 1-116 in a first material having a higher (or in some cases lower) refractive index than an adjacent material 1-310 adjacent to the grating lines. Figure 1-1 ) In some embodiments, the optical grating 1-110 is embedded in one or more surrounding materials. For example, instead of a single adjacent material 1-310 surrounding the grating 1-110, the grating may be formed between two or more different material layers. The lines (or teeth) 1-116 of the grating 1-110 may be formed from a single material layer (e.g., Figure 1-1), or may include two or more material layers (such as Figure 1-3 ). For example, the second material 1-312 can be placed above the first material 1-311 and patterned when forming the lines 1-116. The addition of one or more layers of the second material can improve the diffraction efficiency of the grating 1-110. When two or more layers are used, the materials that can be used to form the grating lines 1-116 include, but are not limited to, dielectrics (oxides, nitrides), semiconductors, metals, and combinations of these materials. These example materials include silicon oxide, tantalum oxide, aluminum oxide, silicon nitride, nitrogen-rich silicon nitride (e.g., a nitride with more than the stoichiometric ratio of Si3N4), silicon, silicon-germanium, germanium, aluminum, tungsten, and polymer materials. In an example embodiment, the grating 1-110 can be primarily formed of nitrogen-rich silicon nitride and the adjacent material 1-310 surrounding the grating can include silicon oxide.

[0048] The one or more adjacent materials 1-310 surrounding the optical grating 1-110 may be optically transparent to optical radiation to be coupled into the receiving region 1-112 through the optical grating 1-110. Preferably, the one or more adjacent materials 1-310 exhibit low optical losses to the optical radiation to be coupled into the waveguide. Materials that may be used for the one or more adjacent materials 1-310 include, but are not limited to, oxides, nitrides, and polymers as described above.

[0049] According to some embodiments, the optical grating 1-110 may have a periodicity P between 200 nm and 800 nm. In other embodiments, the grating 1-110 may have a periodicity P less than 200 nm or greater than 800 nm. The duty cycle of the grating (the ratio of the width of the grating line 1-116 in the x-direction to the periodicity P) may be between 20% and 80%. According to some embodiments, the thickness t of the grating line 1-116 may be between 20% and 80%. g The width w of the grating teeth 1-116 associated with coupling into a single inlet 1-111 may be between 20 nm and 500 nm. g According to some embodiments, the last line 1-116 of the grating 1-110 adjacent to the entrance 1-111 may be spaced from the entrance 1-111 by a distance equivalent to the spacing between the grating lines 1-116 (eg, Figure 1-1 ). In some cases, the last line 1-116 of the grating 1-110 may be spaced from the entrance 1-111 by a distance that is an integer number of spacings between grating lines 1-116 or a non-integer number of spacings between grating lines 1-116.

[0050] The receiving region 1-112 and the optical waveguide 1-213 may be patterned in a first material having a higher refractive index than an adjacent material 1-310 of the receiving region 1-112 and / or waveguide 1-213. In certain embodiments, the receiving region 1-112 and the optical waveguide 1-213 may be embedded in one or more surrounding materials. The receiving region, the waveguide, and the one or more surrounding materials may be optically transparent to radiation conveyed by the waveguide. Preferably, the receiving region 1-112, the waveguide 1-213, and the one or more adjacent materials 1-310 exhibit low optical loss (e.g., less than 1 dB / cm) to the optical radiation conveyed by the waveguide. Materials that may be used for the receiving region 1-112, the waveguide 1-213, the downstream waveguides 1-213a, 1-213b, and the one or more second materials 1-310 include, but are not limited to, oxides and nitrides as described above. As an example, the waveguide 1-213, the receiving region 1-112, and the downstream waveguides 1-213a, 1-213b may be formed of silicon nitride (or nitrogen-rich silicon nitride) and one or more adjacent materials 1-310 may be formed of silicon oxide.

[0051] According to some embodiments, the receiving area 1-112 may be tapered, such as Figure 1-1 Along the tapered region, the width w of the waveguide core in the receiving region t may decrease in size in the x-direction, moving away from the inlet 1-111, until it matches the width w of the core in the uniform portion of the waveguide 1-213 at a downstream location, as shown Figure 1-2 In other embodiments, the width w of the waveguide core in the tapered region 1-112 is t may increase in size in the x-direction, moving away from the entrance 1-111, until it matches the width w of the uniform portion of the core of the waveguide 1-213. Additionally or alternatively, the thickness t of the core in the receiving region 1-112 may be w The core of the receiving region 1-112 may be tapered so as to change in size until it matches the thickness of the core of the connected waveguide 1-213. For example, when the lateral size (mode profile) of the incident beam is significantly different from the size of the optical mode (e.g., fundamental mode size) supported by the waveguide 1-213, tapering the width and / or thickness of the core in the receiving region 1-112 may improve the coupling efficiency of the optical radiation into the receiving region and downstream waveguide.

[0052] According to some embodiments, the width w of the core in the uniform portion of the waveguide 1-213 may be between 200 nm and 800 nm. The thickness t of the core in the uniform portion of the waveguide 1-213 may be between 200 nm and 800 nm. wThe width w of the core in the tapered receiving region 1-112 may be between 20 nm and 500 nm. In some embodiments, the width and thickness of the waveguide core are selected so that the waveguide 1-213 supports only a single transverse optical mode (the fundamental optical mode) within the waveguide. In some cases, the waveguide 1-113 may support more than one transverse optical mode. t In some cases, the core at the inlet 1-111 may be less than 200 nm, or in other cases, it may be greater than 800 nm at the inlet. In some embodiments, the receiving region may not be tapered. The thickness t of the core at the inlet of the receiving region 1-112 w It can be between 20nm and 500nm.

[0053] The grating 1-110, receiving region 1-112, and waveguide 1-213 may be fabricated using planarized microfabrication techniques, such as those described in U.S. Patent Application No. 15 / 844,403, filed on December 15, 2017, and entitled “Optical Coupler and Waveguide System,” which is incorporated herein by reference in its entirety. Such microfabrication techniques may include the steps of patterning the grating and waveguide in a resist using a mask and photolithography techniques; and etching the pattern of the grating and waveguide in an oxide and / or nitride layer using an etching procedure such as anisotropic reactive ion etching. Such microfabrication techniques may also include the steps of depositing resist and layers for forming a grating coupler; and removing portions of the residual resist and layers.

[0054] In operation, the grating coupler 1-100 can diffract incident optical radiation into one or more different directions away from the path of the incident beam (which travels along the optical axis 1-101). By carefully designing the grating coupler (e.g., selecting an appropriate pitch P of the grating 1-110 for the operating characteristic wavelength) and properly orienting the incident beam, a majority of the incident optical radiation can be diffracted from the grating 1-100 toward the entrance 1-111 and substantially coaxial with the receiving region 1-112. Thus, a majority of the incident radiation can be coupled into the receiving region 1-112 and the downstream waveguide 1-213. The incident beam can be described by the position of the beam and the angle of incidence (in Figure 1-1 1-122). For example, in some cases, the position of the beam on the grating 1-110 can be described as the position of the center of the beam (e.g., the optical axis 1-101) relative to the center of the grating 1-110 or the center of the entrance 1-111 (in the x and y directions). The angle of incidence of the beam can be represented by a first angle of incidence or a pitch angle θ i (e.g., measured from the z-axis toward the x-direction, rotated about the y-axis) and a second angle of incidence or tilt angle φ i(e.g., measured from the z-axis toward the y-direction, rotating around the x-axis) describes the position of the beam on the grating 1-110, the pitch angle θ i and the tilt angle φ i Changes in can change the coupling efficiency of the incident beam into the receiving region 1-112 and the downstream waveguide 1-213.

[0055] The above article targets Figure 1-1 , Figure 1-2 and Figure 1-3 The features, materials, and dimensions described in the embodiments of the grating coupler may be implemented in the grating coupler described in the following embodiments in which coupling is directly from the grating 1-110 to one or more receiving regions.

[0056] The inventors have recognized and appreciated that once an incident beam of optical pulses 1-122 (or a continuous wave incident beam) is calibrated to the grating coupler 1-100 for maximum coupling efficiency, when a reduction in power coupled into the receiving region 1-112 or in a downstream waveguide is detected, there can be ambiguity or uncertainty in knowing how the orientation of the beam has changed. For example, when oriented for maximum coupling efficiency with respect to the position of the incident beam on the grating 1-110, movement of the beam toward or away from the entrance 1-111 produces very similar characteristic reductions in coupling efficiency. Therefore, by detecting a reduction in power in the downstream waveguide, it cannot be easily determined whether the incident beam has moved toward or away from the entrance 1-111. Therefore, automatic correction of the beam position to maintain high coupling efficiency is complicated by the ambiguity in the movement in the x-direction of the beam.

[0057] Similar results are obtained at pitch angle θ i For example, after the highest coupling efficiency with respect to the pitch angle is obtained, an increase or decrease in the pitch angle produces substantially the same decrease in coupling efficiency. i The ambiguity of directional motion further complicates automatic correction of the beam position to maintain high coupling efficiency.

[0058] Figure 2-1An embodiment of a grating coupler 2-100 with improved beam calibration sensitivity is depicted, in which the direction of movement of the incident beam 2-102 in the x-direction (resulting in reduced coupling efficiency) can be eliminated. The diagram shows a plan view of the grating coupler. In the illustrated embodiment, the grating coupler 2-100 includes five receiving areas 2-112a to 2-112e having five entrances 2-111a to 2-111e, some of which are offset relative to other entrances in the x-direction or in a direction perpendicular or substantially perpendicular to the line 2-116 of the grating. In some embodiments, there may be fewer than or more than five receiving areas. For some applications, there may be dozens or more than one hundred receiving areas and entrances in the grating coupler 2-100. To simplify the illustration, only the receiving areas of the grating lines and waveguides are shown. The receiving areas 2-112a to 2-112e of the grating lines 2-116 and the waveguides can be formed on the substrate 1-105 together with the surrounding material, as described above in conjunction with Figure 1-1 to Figure 1-3 As described.

[0059] By using multiple inlets 2-111a through 2-111e, the grating coupler 2-100 can couple radiation from the high power beam 2-102 directly into multiple waveguides. 2 An example lateral beam profile of width is indicated as a dashed ellipse. ) Direct coupling into multiple waveguides can be advantageous to avoid damaging the optical waveguides and to avoid undesirable nonlinear optical behavior that can occur at higher powers. In addition, the lateral width w of the inlets 2-111a to 2-111e in the y direction is t The dimensions may be determined to obtain a desired power ratio among the receiving regions 2-112a to 2-112e. For example, the outer entrances 2-111a, 2-111e may be wider than the central entrance 2-111c so that each receiving region 2-112a, 2-112c, and 2-112e couples approximately the same amount of optical power from the incident beam. In some embodiments, all receiving regions may couple approximately the same amount of optical power from the incident beam so that each waveguide downstream of the receiving regions carries approximately the same amount of optical power. In other embodiments, other power coupling ratios may be implemented by selecting appropriate widths of the entrances 2-111a to 2-111e and the receiving regions 2-112a to 2-112e.

[0060] According to some embodiments, one or more of the inlets 2-111a to 2-111e may be positioned substantially along the same reference line 2-115 (which may be straight or curved). Figure 2-1 As depicted in the example shown, most of the inlets 2-111a, 2-111c, 2-111e are along the same reference line 2-115 (at x=X i102 is depicted as a dotted line). Although the reference line is shown as straight in the illustration, in some embodiments, the reference line 2-115 may be curved (e.g., to adjust the curvature of the shape of the incident beam 2-102). The reference line 2-115 may correspond to the following position: when the incident beam is positioned on the grating to achieve the highest coupling efficiency into one of the two or more receiving regions, two or more entrances of the receiving region will be positioned to provide the highest coupling efficiency to the two or more receiving regions. For the grating coupler 2-100 with improved x-direction sensitivity, at least one entrance is positioned away from the reference line 2-115 in the x-direction by an amount |Δx|. In some embodiments, two or more entrances are positioned away from the reference line 2-115 in the x-direction by an amount |Δx| or two different amounts. In some cases, it is possible to position most of the entrances away from the reference line 2-115 in the x-direction by an amount |Δx| or multiple different amounts. In such cases, the reference line 2-115 may be calibrated with as few as one inlet (eg, an inlet positioned at the average x-position among all the inlets).

[0061] The amount by which one or more portals 2-111b, 2-111d may be offset from the reference line 2-115 may be between 0.5 microns and 10 microns, or may be approximately these values ​​according to certain embodiments, and for the wavelength of the incident beam, may be between 400 nm and 800 nm, or may be approximately these values. The offset portals 2-111b, 2-111d and receiving regions 2-112b, 2-112d may couple less power than if they were located on the reference line 2-115. In certain embodiments, the widths of the offset portals and receiving regions may be sized to couple a desired power ratio among all portals and receiving regions (e.g., the same amount of power into each portal and receiving region).

[0062] The cancellation of beam motion can be sensed by monitoring the power in the waveguide connected to the offset inlet (e.g., inlet 2-112d). Figure 2-1, the initial beam calibration can optimize the power coupled into one or more inlets and receiving regions (e.g., inlet 2-111c and receiving region 2-112c) placed along the reference line 2-115. For optimization of coupling efficiency, the power or intensity can be monitored from the waveguide connected to the one or more inlets and receiving regions placed along the reference line 2-115. In some cases, the monitoring can be performed at one or more sites on the chip to which the waveguide delivers power. For example, the site on the chip can include a photodetector that can sense the amount of radiation intensity in the waveguide. After optimization of the coupling efficiency, the power or intensity monitored in one or more offset inlets and receiving regions can indicate in which direction (in x) the incident beam has moved. For example, if the power is monitored in the waveguide connected to the receiving region 2-112d, an increase in power will indicate that the incident beam 2-102 has moved in the -x (upstream) direction. A decrease in power will indicate that the incident beam 2-102 has moved in the +x (downstream) direction. Alternatively or additionally, although the examples described herein refer to the power of the incident beam, the intensity may be monitored.

[0063] For the same grating coupler 2-100, the power monitored in the waveguide connected to the receive region 2-112b will show opposite behavior to the power monitored in the waveguide connected to the receive region 2-112d. Movement of the incident beam 2-102 in the -x direction will result in a decrease in the power coupled into the receive region 2-112b. Movement of the incident beam 2-102 in the +x direction will result in an increase in the power coupled into the receive region 2-112b. Differentiating the power signals from the two waveguides connected to the two receive regions 2-112b, 2-112d can increase the sensitivity of detecting movement of the input beam 2-102.

[0064] Figure 2-2 Another embodiment of a grating coupler 2-200 with improved beam alignment sensitivity is depicted. The grating coupler 2-200 can be nearly identical to Figure 2-1 The grating coupler 2-100 is the same as the grating coupler 2-100, except that the entrance and receiving regions 2-112a to 2-112e are spatially separated in the y direction rather than being adjacent and touching at their edges. The grating 2-210 may include separated portions 2-210a to 2-210e, such as Figure 2-2 As shown in , or can be formed as a continuous line 2-116, such as Figure 2-1. Separating the entrances 2-111a to 2-111e and the receiving regions 2-112a to 2-112e in the y direction may result in reduced coupling efficiency, but may improve the optical mode profile in the receiving region by reducing the effect of discontinuities directly adjacent to the entrance facets. The grating 2-210 and the receiving regions 2-112a to 2-112e may be formed on the substrate 1-105 together with the surrounding material, as described above in conjunction with Figure 1-1 to Figure 1-3 As described.

[0065] In certain applications, it may be desirable to couple multiple incident beams 2-330 into multiple integrated waveguides. Figure 2-3 Another embodiment of a grating coupler 2-300 with improved beam alignment sensitivity for such applications is shown. The grating coupler 2-300 may include a grating 2-310 and a plurality of receiving regions 2-312a to 2-312d adjacent to the grating 2-310. The grating may include separate portions 2-310a to 2-310d, as shown, or may be formed as Figure 2-1 1-14. The receiving regions 2-312a to 2-312d may be separated in the y-direction, as shown, or may be directly adjacent to each other. At least one of the receiving regions and the portals may be offset in the x-direction from the reference line 2-115. According to certain embodiments, the widths of the receiving regions and portals may be approximately the same. In certain embodiments, the widths of the receiving regions and portals of the offset grating may be greater than the widths of the receiving regions and portals of the portals placed on the reference line 2-115 (e.g., so as to obtain the same amount of power in each receiving region).

[0066] If the multiple incident beams 2-330 are moved together as a unit rather than independently, the movement of the multiple incident beams 2-330 in the x-direction will produce the same power change coupled into the offset receiving area, as described above in conjunction with Figure 2-1 As described. For example, movement of the incident beam 2-330 in the +x direction can be detected as an increase in power of the waveguide connected to the receiving region 2-312b and a decrease in power of the waveguide connected to the receiving region 2-312c. Also, movement of the incident beam 2-330 in the -x direction can be detected as a decrease in power of the waveguide connected to the receiving region 2-312b and an increase in power of the waveguide connected to the receiving region 2-312c. The grating 2-310 and the receiving regions 2-312 to 2-312e can be formed on the substrate 1-105 together with the surrounding material, as described above in conjunction with Figure 1-1 to Figure 1-3 described.

[0067] Figure 2-4 A grating coupler with improved sensitivity to changes in the x-position of the incident beam (e.g. Figure 2-1The first curve 2-402 shows the signal S received from the receiving area 2-112c having an inlet placed on the reference line 2-115. c For an incident beam positioned at a reference x-position (arbitrarily set to 0 microns), the highest coupling efficiency into the receiving region 2-112c is obtained. As can be seen from the first curve 2-402, the signal level changes similarly for increases or decreases in the beam position along the x-direction. Although there is an asymmetry in the curves, the differences may be small and difficult or impossible to reliably discern in an implemented automated system. For example, every signal value between -20 microns and 20 microns does not uniquely identify the beam position. The second curve 2-404 shows the difference signal S received from two receiving regions (which are offset from the reference line 2-115). d -S b changes, such as Figure 2-1 . The difference signal shows a continuous increase in the change of the beam position from x≈-7 microns to x≈+7, and the motion of the beam in the -x direction can be clearly distinguished from the motion of the beam in the +x direction. The nonlinearity in the curve can be corrected and compensated electronically. For this simulation, the two receiving areas were offset by +5 microns and -5 microns, but the invention is not limited to only these offset values. In some embodiments, smaller or larger offsets can be used.

[0068] Figure 3-1 Another embodiment of a grating coupler 3-100 with improved beam alignment sensitivity is depicted in FIG. The example shown can eliminate the pitch angle θ of the incident beam 2-102. i ( Figure 1-1 ). For such an embodiment, the grating coupler 3-100 may include a grating 3-110 having a plurality of portions 3-110a to 3-110e, at least two of the plurality of portions having different or offset grating periodicities (e.g., P1, P2). In certain embodiments, the entrances to the receiving regions 3-112a to 3-112e may be placed along a common reference line 2-115, which may be straight or curved, as described above. The grating portions 3-110a to 3-110e and the receiving regions 3-112a to 3-112e may be directly adjacent to each other in the y direction, as shown, or may be separated from each other (e.g., Figure 2-2 In some embodiments, the grating portions 3-110a to 3-110e and the receiving regions 3-112a to 3-112e may be separated and sized so as to be as described above. Figure 2-3 Multiple incident beams are coupled into multiple waveguides as depicted in FIG.

[0069] One or more of the grating portions 3-110a, 3-110c, 3-110e may have the same grating periodicity P1, which may be a reference periodicity. In some cases, most of the grating portions 3-110a, 3-110c, 3-110e may have the same reference grating periodicity P1. The reference periodicity may be a reference periodicity that provides the highest coupling efficiency to each of the corresponding receiving regions (e.g., receiving regions 3-112a, 3-112c, 3-112e) when the incident beam 2-102 is directed for the highest coupling efficiency to each of the corresponding receiving regions. At least one of the grating portions 3-110b may have an offset periodicity P2 that is different from the reference periodicity P1. The offset periodicity may result in a reduced coupling efficiency to the corresponding receiving region 3-112b. In some cases, there may be one or more additional grating portions 3-110d having one or more additional offset periodicities P3. The grating 3-110 and receiving regions 3-112a to 3-112e may be formed on the substrate 1-105 together with the surrounding material, as described above in conjunction with Figure 1-1 to Figure 1-3 described.

[0070] For a grating portion 3-110a having a reference periodicity P1, diffraction of a portion of the incident beam may be substantially in the y-direction (e.g., directly into a corresponding entrance) and substantially coaxial with the core of the receiving region. i The change in spacing in the –θ direction will produce the same i The spacing changes in the direction have essentially the same power reduction behavior (again refer to Figure 1-1 ). For a grating portion 3-110b having a period P2 less than P1, diffraction of a portion of the incident beam may be primarily in the y direction but may also be partially in the -z direction (not in the paper). This may result in reduced coupling efficiency into the receiving region 3-112b. However, the incident beam at +θ i The change in spacing in the direction will reduce the power coupled into the receiving region 3-112b, while the incident beam is at –θ i A change in spacing in the direction of θ will increase the power coupled into the receiving region 3-112b. Monitoring the power or intensity from the waveguide coupled into the receiving region 3-112b can then eliminate the incident beam 2-102 in the ±θ i The spacing in the direction changes.

[0071] For a grating portion 3-110d having a periodicity P3 greater than P1, the opposite behavior to that of the grating portion 3-110b may be obtained. In the case where the periodicity P3 is greater than the reference periodicity P1, the diffraction of part of the incident beam may be mainly in the y direction but also partially in the +z direction (in the plane of the figure). The incident beam at +θ iThe change in spacing in the direction will increase the power coupled into the receiving region 3-112d, while the incident beam is at –θ i The change in spacing in the direction will reduce the power coupled into the receiving area 3-112d. Differentiating the signals received from the receiving areas 3-112b and 3-112d can increase the incident beam direction within ±θ i The sensitivity of detecting changes in direction.

[0072] According to some embodiments, the offset of the grating periodicity from the reference periodicity P1 may be between 0.1% and 1% of the reference periodicity P1. For some visible optical configurations, the periodicity change of the offset grating may be between 0.5nm and 4nm, or between about 0.5nm and about 4nm.

[0073] Figure 3-2 An example of a grating coupler 3-200 combining an offset receiving region 3-212b, 3-212d with an offset grating periodicity P2, P3 is depicted. The grating coupler 3-200 may include a grating 3-210 comprising a grating portion 3-210b having a reference periodicity P1 and one or more additional portions 3-210a, 3-210c having one or more offset periodicities P2, P3. The grating coupler 3-200 may further include: one or more receiving regions 3-212a, 3-212c, 3-212e having an entrance positioned along a reference line 2-115 and one or more receiving regions 3-212b, 3-212d having an entrance offset from the reference line 2-115 in the x-direction. For the example shown, a power change detected from a waveguide connected to receiving regions 3-212b and / or 3-212d may unambiguously indicate movement of the incident beam position on the grating 3-210 in the +x or -x direction. A power change detected from a waveguide connected to receiving regions 3-212a, 3-212e may unambiguously indicate movement of the incident beam position on the grating 3-210 in the +θ direction. i or –θ i Movement in direction.

[0074] Figure 3-3 The elevation angle θ of the incident beam is plotted i The change of the grating coupler with improved sensitivity (e.g. Figure 3-1 The first curve 3-302 shows the signal S received from the receiving area 3-112c adjacent to the grating with the reference periodicity P1. cFor the selected grating design and characteristic wavelength, the highest coupling efficiency into the receiving region adjacent to the grating portion having the reference periodicity is obtained for an incident pitch angle of -4.0 degrees. It can be seen from the first curve 3-302 that the signal level changes substantially equally for an increase or decrease in the incident pitch angle of the beam from the calibration position of -4.0 degrees. Each signal level does not uniquely identify the incident angle of the beam. The second curve 3-304 shows the difference in the signal level from adjacent to the grating portion having the offset periodicity (P2<P1,P3> The difference signal S received by the two receiving areas of the two grating parts of P1) d -S b The difference signal is essentially linear over the range of incident angles and clearly indicates the direction of the change in pitch angle. For this simulation, the difference between the offset grating periodicity and the periodicity P1 of the reference grating was +1 nm and -1 nm, although the offset of the grating periodicity is not limited to these values. Smaller or larger offsets of the grating periodicity can be used.

[0075] Despite Figure 2-1 to Figure 3-2 In the embodiments shown in , the grating lines and the entrance to the receiving region are depicted as straight, but in certain embodiments, the grating lines and the entrance may be curved in any of the embodiments. Figure 3-4 An example is shown in which a grating 3-410 adjacent to a receiving region 3-412 has a curved line 3-416. Additionally, an entrance 3-411 to the receiving region 3-412 may have a curved surface. The curved grating lines 3-416 and / or the curved entrance 3-411 may improve the coupling efficiency into the receiving region 3-412. In some cases, additionally or alternatively, the curved grating lines 3-416 and / or the curved entrance 3-411 may improve the optical mode profile in the receiving region 3-412.

[0076] Figure 3-5 is a flow chart illustrating an example method 3-500 for calibrating or maintaining calibration of an incident beam on a grating coupler of an embodiment of the present invention. Some or all of the acts of the method may be automatic (e.g., by using an automatic beam steering and positioning instrument). The method 3-500 may include an act of first calibrating the incident beam 2-102 on the grating 2-110 of the grating coupler 2-100 (act 3-510). The calibrated position may be an orientation that provides the highest or approximately the highest coupling efficiency into a reference receiving area (e.g., a receiving area having an inlet 2-111 placed on a reference line 2-115 and / or a receiving area having an inlet for a corresponding reference grating periodicity P1). After obtaining the calibrated orientation, the incident beam 2-102 may be calibrated at x and / or θ. iThe beam orientation is scanned in a direction to calibrate (action 3-520) the sensor and signal levels within a set of uncalibrated orientations. For each independent degree of freedom, the calibration signal level can be monitored (action 3-530). The calibration signal level can be monitored by one or more sensors integrated on a substrate on which the waveguide and grating coupler are formed. In certain embodiments, the sensor can be located in a pixel of the analytical instrument, which will be described in further detail below. The automatic system can test for an increase (action 3-540) or decrease (action 3-550) in the signal level. If an increase in the signal level is detected (for example, caused by beam movement in the +x direction), the automatic system can move the beam in the -x direction (action 3-545) until the signal level is restored to the originally calibrated signal level and the monitoring signal (action 3-530) is restored. The calibrated signal level can be a voltage level V determined during calibration (action 3-520) of the automatic calibration system. a , and the system can be configured to accept the V a A value range within a few percent of θ as an indication of calibration. If a decrease in the signal level is detected (e.g., caused by beam motion in the -x direction), the automated system may move the beam in the +x direction (act 3-555) until the signal level returns to the calibrated level and resumes monitoring the signal (act 3-530). According to some embodiments, movement of the beam may be implemented using a galvanometer or stepper motor to move the optical assembly in the path of the incident beam and thereby move or change the pitch angle of the incident beam. Similar actions may be performed for detecting the beam pitch angle θ i changes and restore the beam to the calibrated orientation.

[0077] The grating coupler described in the foregoing embodiments can be used in various optical applications mentioned above. One area in which such a grating coupler can be used is with respect to analyzing one or more samples on a chip (e.g., a chip lab application). Instruments for analyzing samples continue to improve and can incorporate microfabricated components (e.g., electronic chips, microfluidic chips), which can help reduce the overall size of the instrument. Samples to be analyzed may include air (e.g., sensing hazardous gas leaks, combustion byproducts, or toxic chemical components), water or other ingestible liquids, food samples, and biological samples extracted from subjects (blood, urine, etc.). In some cases, it may be desirable to have a portable, handheld instrument for analyzing samples so that technicians or medical personnel can easily carry the instrument to the site where services can be performed and samples need to be analyzed quickly and accurately. In a clinical setting, a desktop-sized instrument may be expected to be used for more complex sample analysis, such as sequencing human genes or proteins or performing a complete blood cell count analysis.

[0078] In advanced analytical instruments (such as those described in U.S. Patent Application No. 2015 / 0141267 and U.S. Patent No. 9,617,594, both of which are incorporated herein by reference), disposable integrated devices (which may be referred to as "wafers" and "disposable chips" for the purpose of brevity) can be used to perform large-scale parallel sample analysis. The disposable integrated device may include a packaged biophotoelectric chip on which there may be a large number of pixels having reaction chambers for parallel analysis of one sample or different samples. For example, the number of pixels having reaction chambers on the biophotoelectric chip may be between about 10,000 and about 10,000,000 in some cases and between 100,000 and about 100,000,000 in some cases. The grating couplers and waveguides described above may deliver optical radiation to each of the pixels on the biophotoelectric chip. In some embodiments, the disposable chip may be mounted in a receptacle of an advanced analytical instrument and connected to optical and electronic components in the instrument. The disposable chip can be easily replaced by the user for each new sample analysis.

[0079] Figure 4 An example structure 4-100 of a disposable chip according to certain embodiments is shown in FIG. The disposable chip structure 4-100 may include a biophotovoltaic chip 4-110 having a semiconductor substrate 4-105 and including a plurality of pixels 4-140 formed on the substrate. In an embodiment, there may be columns or rows of waveguides 4-115 that provide excitation radiation to columns or rows of pixels 4-140. The excitation radiation may be coupled into the waveguide using a grating coupler of the embodiments described above. For example, a grating coupler may be formed on a surface of the biophotovoltaic chip 4-110 to couple excitation radiation from a focused laser beam into one or more receiving waveguides connected to the plurality of waveguides 4-115.

[0080] The disposable chip structure 4-100 may further include a wall 4-120 formed around the pixel area of ​​the biophotovoltaic chip 4-110. The wall 4-120 may be part of a plastic or ceramic housing that supports the biophotovoltaic chip 4-110. The wall 4-120 may form at least one reservoir 4-130 in which at least one sample may be placed and in direct contact with a reaction chamber 1-130 on the surface of the biophotovoltaic chip 4-110. For example, the wall 4-120 may prevent the sample in the reservoir 4-130 from flowing into an area containing an optical port 4-150 and a grating coupler. In certain embodiments, the disposable chip structure 4-100 may further include electrical contacts on the external surface of the disposable chip and interconnects within the package so that electrical connections can be made between circuits on the biophotovoltaic chip 4-110 and circuits in an instrument into which the disposable chip is mounted.

[0081] II. Example Bioanalytical Applications

[0082] Example bioanalysis applications are described where integrated grating couplers can be used in advanced analytical instrumentation. For example, grating couplers of embodiments of the present invention can be used to improve the ability to automatically maintain alignment of an incident beam with the grating coupler and maintain a constant power level in a downstream waveguide over a period of time.

[0083] When installed in the receptacle of the instrument, the disposable chip 4-100 (like Figure 4 The chip (like the one shown in ) can communicate optically and electronically with optical and electronic devices within advanced analytical instruments. The instrument may include hardware for an external interface so that data from the chip can be transferred to an external network. In an embodiment, the term "optical" may refer to ultraviolet, visible, near infrared, and short-wave infrared spectral bands. Although various types of analysis can be performed on various samples, the following explanation describes gene sequencing and is at least partially applicable to protein sequencing. However, the present invention is not limited to instruments configured for gene or protein sequencing.

[0084] In the overview and reference Figure 5-1AThe portable advanced analytical instrument 5-100 may include one or more pulsed light sources 5-108 that are installed in the instrument 5-100 as replaceable modules or otherwise coupled to the instrument 5-100. The portable analytical instrument 5-100 may include an optical coupling system 5-115 and an analytical system 5-160. The optical coupling system 5-115 may include a combination of optical components (e.g., it may not include or include one or more components from the following components: lenses, mirrors, optical filters, attenuators, beam steering components, beam shaping components) and is configured to operate on the analytical system 5-160 and / or couple the output optical pulses 5-122 from the pulsed light source 5-108 to the analytical system 5-160. The analytical system 5-160 may include a plurality of components that are arranged to direct optical pulses to at least one reaction chamber for sample analysis, receive one or more optical signals (e.g., fluorescence, backscattered radiation) from at least one reaction chamber, and generate one or more electrical signals representing the received optical signals. In some embodiments, the analysis system 5-160 may include one or more photodetectors and may also include signal processing electronics (e.g., one or more microcontrollers, one or more field programmable gate arrays, one or more microprocessors, one or more digital signal processors, logic gates, etc.) configured to process electrical signals from the photodetectors. The analysis system 5-160 may also include data transmission hardware configured to transmit data to an external device (e.g., the instrument 5-100 may be connected to one or more external devices on its network via one or more data communication links) and receive data from the external device. In some embodiments, the analysis system 5-160 may be configured to receive a biophotoelectric chip 5-140 that holds one or more samples to be analyzed.

[0085] Figure 5-1BAnother detailed example of a portable analytical instrument 5-100 including a compact pulsed light source 5-108 is depicted. In this example, the pulsed light source 5-108 includes a compact passive mode-locked laser module 5-110. The passive mode-locked laser can generate optical pulses autonomously without applying an external pulse signal. In some embodiments, the module can be mounted to an instrument rack or frame 5-102 and can be located inside the outer housing of the instrument. According to some embodiments, the pulsed light source 5-108 may include additional components that can be used to operate the light source and operate the output beam from the light source 5-108. The mode-locked laser 5-110 may include an element (e.g., a saturated absorber, an acousto-optic modulator, a Kerr lens) in or coupled to the laser cavity, which induces phase locking of the longitudinal frequency mode of the laser. The laser cavity may be partially defined by cavity end mirrors 5-111, 5-119. This locking of the frequency mode results in pulsed operation of the laser (eg, intracavity pulses 5-120 bounce back and forth between the cavity end mirrors) and produces a stream of output optical pulses 5-122 from one end mirror 5-111 that is partially transmitting.

[0086] In some cases, the analytical instrument 5-100 is configured to receive a removable packaged biophotovoltaic or optoelectronic chip 5-140 (also referred to as a "disposable chip"). The disposable chip may include a biophotovoltaic chip 4-110, such as Figure 4 As shown in , the biophotoelectric chip includes: a plurality of reaction chambers; an integrated optical component arranged to deliver optical excitation energy to the reaction chambers; and an integrated light detector arranged to detect fluorescence emission from the reaction chambers. In some embodiments, the chip 5-140 can be discarded after a single use, while in other embodiments, the chip 5-140 can be reused two or more times. When the chip 5-140 is received by the instrument 5-100, it can communicate electrically or optically with the pulsed light source 5-108 and the equipment in the analysis system 5-160. For example, electrical communication can be performed through electrical contacts on the chip's package.

[0087] In certain embodiments and with reference to Figure 5-1B, the disposable chip 5-140 may be mounted (e.g., via a socket connection) on an electronic circuit board 5-130, such as a printed circuit board (PCB), which may include additional instrument electronics. For example, the PCB 5-130 may include circuitry configured to provide electrical power, one or more clock signals, and control signals to the chip 5-140, and signal processing circuitry configured to receive signals representative of fluorescent emissions detected from the reaction chamber. Data returned from the chip 5-140 may be processed in part or in whole by electronics on the instrument 5-100, although in some embodiments, the data may be transmitted to one or more remote data processors via a network connection. The PCB 5-130 may also include circuitry configured to receive feedback signals from the chip regarding the optical coupling and power level of the optical pulses 5-122 in the waveguide coupled to the chip 5-140. The feedback signals may be provided to one or both of the pulsed light source 5-108 and the optical system 5-115 to control one or more parameters of the output beam of the optical pulses 5-122. In some cases, the PCB 5-130 may provide or route power to the pulsed light source 5-108 in order to operate the light source and associated circuitry in the light source 5-108.

[0088] According to some embodiments, the pulsed light source 5-108 includes a compact mode-locked laser module 5-110. The mode-locked laser may include a gain medium 5-105 (which may be a solid state material in some embodiments), an output coupler 5-111, and a laser cavity end mirror 5-119. The optical cavity of the mode-locked laser may be defined by the output coupler 5-111 and the end mirror 5-119. The optical axis 5-125 of the laser cavity may have one or more folds (turns) to increase the length of the laser cavity and provide a desired pulse repetition rate. The pulse repetition rate is determined by the length of the laser cavity (e.g., the time it takes for an optical pulse to make a round trip within the laser cavity).

[0089] In some embodiments, there may be additional optical elements in the laser cavity ( Figure 5-1B The end mirror 5-119 may include a saturated absorber mirror (SAM) that induces passive mode locking of the longitudinal cavity mode and results in pulsed operation of the mode-locked laser. The mode-locked laser module 5-110 may further include a pump source (e.g., a laser diode, Figure 5-1B (not shown) for exciting the gain medium 5-105. Further details of the mode-locked laser module 5-110 can be found in U.S. Patent Application No. 15 / 844,469, entitled “Compact Mode-Locked Laser Module,” filed on December 15, 2017, which is incorporated herein by reference.

[0090] When the laser 5-110 is mode locked, the intracavity pulse 5-120 may circulate between the end mirror 5-119 and the output coupler 5-111, and a portion of the intracavity pulse may be transmitted as an output pulse 5-122 via the output coupler 5-111. Figure 5-2 As shown in the graph of , as the intracavity pulses 5-120 bounce back and forth between the output coupler 5-111 and the end mirror 5-119 in the laser cavity, a train of output pulses 5-122 can be detected at the output coupler.

[0091] Figure 5-2 The temporal intensity profile of the output pulses 5-122 is depicted, although the illustration is not drawn to scale. In some embodiments, the peak intensity values ​​of the transmitted pulses may be approximately equal, and the profile may have a Gaussian temporal profile, although the peak intensity values ​​of the transmitted pulses may be approximately equal ... and the profile may have a Gaussian temporal profile, although the peak intensity values ​​of the transmitted pulses may be approximately equal, such as the sech 2 Other profiles of the profile are also possible. In some cases, the pulses may not have a symmetrical temporal profile, but may have other temporal shapes. The duration of each pulse may be characterized by a full width at half maximum (FWHM) value, such as Figure 5-2 According to some embodiments of the mode-locked laser, the ultrashort optical pulses may have a FWHM value of less than 100 picoseconds (ps). In some cases, the FWHM value may be between about 5 ps and about 30 ps.

[0092] The output pulses 5-122 may be separated by a regular interval T. For example, T may be determined by the round trip travel time between the output coupler 5-111 and the cavity end mirror 5-119. According to certain embodiments, the pulse separation interval T may be between about 1 ns and about 30 ns. In some cases, the pulse separation interval T may be between about 5 ns and about 20 ns, corresponding to a laser cavity length (approximate length of the optical axis 5-125 within the laser cavity) between about 0.7 meters and about 3 meters. In an embodiment, the pulse separation interval corresponds to the round trip travel time in the laser cavity, such that a cavity length of 3 meters (round trip distance of 6 meters) provides a pulse separation interval T of approximately 20 ns.

[0093] According to certain embodiments, the desired pulse separation interval T and laser cavity length can be determined by a combination of the number of reaction chambers on the chip 5-140, the fluorescence emission characteristics, and the speed of the data handling circuit used to read data from the chip 5-140. In an embodiment, different fluorophores can be distinguished by their different fluorescence decay rates and characteristic lifespans. Therefore, there needs to be sufficient pulse separation intervals T to collect sufficient statistical data for the selected fluorophores to distinguish their different decay rates. In addition, if the pulse separation interval T is too short, the data handling circuit cannot keep up with the large amount of data collected by a large number of reaction chambers. A pulse separation interval T between about 5ns and about 20ns is suitable for fluorophores with decay rates up to about 2ns and is suitable for handling data from between about 60,000 and 10,000,000 reaction chambers.

[0094] According to certain embodiments, the beam steering module 5-150 can receive output pulses from the pulsed light source 5-108 and is configured to at least adjust the position and angle of incidence of the optical pulses to the optical coupler (e.g., grating coupler) of the chip 5-140. In some cases, the output pulses 5-122 from the pulsed light source 5-108 can be operated by the beam steering module 5-150 to (additionally or alternatively) change the beam shape and / or beam rotation at the optical coupler on the chip 5-140. In certain embodiments, the beam steering module 5-150 can further provide focusing and / or polarization adjustment of the beam of the output pulse to the optical coupler. An example of a beam steering module is described in U.S. patent application No. 15 / 161,088, entitled "Pulsed Laser and Bioanalytic System," filed on May 20, 2016, which is incorporated herein by reference. Another example of a beam steering module is described in separate U.S. patent application Ser. No. 62 / 435,679, filed Dec. 16, 2016, and entitled “Compact Beam Shaping and Steering Assembly,” which is incorporated herein by reference.

[0095] refer to Figure 5-3For example, output pulses 5-122 from a pulsed light source may be coupled into one or more optical waveguides 5-312 on a disposable bio-photovoltaic chip 5-140. In some embodiments, the optical pulses may be coupled to the one or more waveguides via one or more grating couplers 5-310, although in some embodiments one end of one or more optical waveguides coupled to the chip 5-140 may be used. A simplified example of a grating coupler is shown in the diagram. According to some embodiments, a four-quadrant detector 5-320 may be located on a semiconductor substrate 5-305 (e.g., a silicon substrate) to assist in the alignment of the beam of the optical pulses 5-122 with the grating coupler 5-310. One or more waveguides 5-312 and a reaction chamber or reaction chambers 5-330 may be integrated on the same semiconductor substrate with an intervening dielectric layer (e.g., a silicon dioxide layer) between the substrate, waveguides, reaction chambers, and the optical detector 5-322.

[0096] Each waveguide 5-312 may include a tapered portion 5-315 below the reaction chamber 5-330 to equalize the optical power coupled to the reaction chamber along the waveguide. The reduced taper may force more optical energy outside the core of the waveguide, thereby increasing coupling to the reaction chamber and compensating for optical losses along the waveguide, including losses of radiation coupled into the reaction chamber. A second grating coupler 5-317 may be located at one end of each waveguide to direct the optical energy to an integrated photodiode 5-324. For example, the integrated photodiode may detect the amount of power coupled along the waveguide and provide a detected signal to a feedback circuit that controls the beam steering module 5-150.

[0097] The reaction chamber 5-330 or reaction chambers 5-330 may be aligned with the tapered portion 5-315 of the waveguide and recessed in the well seat 5-340. For each reaction chamber 5-330, there may be a photodetector 5-322 located on the semiconductor substrate 5-305. In certain embodiments, the semiconductor absorber ( Figure 5-5 A plurality of optical filters 5-530 (shown as optical filters 5-530 in FIG. 5 ) may be positioned between the waveguide and the photodetector 5-322 at each pixel. A metal coating and / or multi-layer coating 5-350 may be formed around the reaction chamber and over the waveguide to prevent optical excitation of fluorophores that are not in the reaction chamber (e.g., dispersed in solution over the reaction chamber). The metal coating and / or multi-layer coating 5-350 may be raised beyond the edge of the well seat 5-340 to reduce absorption losses of optical energy in the waveguide 5-312 at the input and output ends of each waveguide.

[0098] There may be multiple columns of waveguides, reaction chambers, and time-graded photodetectors on the chip 5-140. For example, in some embodiments, there may be 128 columns, each with 512 reaction chambers, for a total of 65,536 reaction chambers. Other embodiments may include fewer or more reaction chambers, and may include other layout configurations. The optical power from the pulsed light source 5-108 may be distributed to the multiple waveguides via one or more star couplers or multimode interference couplers or by any other component located between the optical coupler 5-310 to the chip 5-140 and the multiple waveguides 5-312.

[0099] Figure 5-4 Optical energy coupled from an optical pulse 5-122 within a tapered portion 5-315 of a waveguide to a reaction chamber 5-330 is shown. The figure is generated based on an electromagnetic field simulation of a light wave that accounts for the waveguide dimensions, the reaction chamber dimensions, the optical properties of different materials, and the distance of the tapered portion 5-315 of the waveguide from the reaction chamber 5-330. For example, the waveguide may be formed of silicon nitride in a surrounding medium 5-410 of silicon dioxide. The waveguide, surrounding medium, and reaction chamber may be formed by the microfabrication procedures described in U.S. Application No. 14 / 821,688, filed on August 7, 2015, and entitled "Integrated Device for Probing, Detecting and Analyzing Molecules." According to certain embodiments, the evanescent optical field 5-420 couples the optical energy transported by the waveguide to the reaction chamber 5-330.

[0100] Figure 5-5 A non-limiting example of a biological reaction occurring in a reaction chamber 5-330 is depicted in FIG. This example depicts the sequential incorporation of nucleotides or nucleotide analogs into a growing strand complementary to a target nucleic acid. Sequential incorporation can occur in the reaction chamber 5-330 and can be detected by an advanced analytical instrument to sequence DNA. The reaction chamber can have a depth between about 150 nm and about 250 nm and a diameter between about 80 nm and about 160 nm. A metallization layer 5-540 (e.g., metallization for an electrical reference potential) can be patterned above the photodetector 5-322 to provide an aperture or iris that blocks stray radiation from adjacent reaction chambers and other unwanted radiation sources. According to certain embodiments, a polymerase 5-520 can be located within the reaction chamber 5-330 (e.g., attached to a substrate of the chamber). The polymerase can grab a target nucleic acid 5-510 (e.g., a portion of a nucleic acid derived from DNA) and sequence the growing strands of complementary nucleic acids to produce growing strands of DNA 5-512. Nucleotides or nucleotide analogs labeled with different fluorophores can be dispersed in the above solution and in the reaction chamber.

[0101] When the labeled nucleotide or nucleotide analog 5-610 is incorporated into the growing strand of complementary nucleic acid, e.g. Figure 5-6 As shown in , one or more attached fluorophores 5-630 can be repeatedly excited by optical energy pulses coupled from the waveguide 5-315 into the reaction chamber 5-330. In certain embodiments, one or more fluorophores 5-630 can be attached to one or more nucleotides or nucleotide analogs 5-610 by means of any suitable connector 5-620. The incorporation event can last for a time period of up to about 100ms. During this time, for example, a pulse of fluorescence emission caused by the excitation of the fluorophore by the pulse from the mode-locked laser can be detected by means of a time-graded light detector 5-322. In certain embodiments, one or more additional integrated electronic devices 5-323 can be present at each pixel for signal processing (e.g., amplification, readout, routing, signal preprocessing, etc.). According to certain embodiments, each pixel may include at least one optical filter 5-530 (e.g., a semiconductor absorber) that passes the fluorescence emission and reduces the transmission of radiation from the excitation pulse. Certain embodiments may not use an optical filter 5-530. By attaching fluorophores with different emission properties (e.g., fluorescence decay rate, intensity, fluorescence wavelength) to different nucleotides (A, C, G, T), the different emission properties are detected and distinguished while the strands of DNA 5-512 are incorporated with nucleic acid and enable the determination of the genetic sequence of the growing strands of DNA.

[0102] According to certain embodiments, an advanced analytical instrument 5-100 configured to analyze a sample based on fluorescence emission characteristics can detect differences in fluorescence lifetime and / or intensity between different fluorescent molecules and / or differences in lifetime and / or intensity between the same fluorescent molecule in different environments. As an explanation, Figure 5-7 Two different fluorescence emission probability curves (A and B) are plotted, which may represent, for example, fluorescence emission from two different fluorescent molecules. Referring to curve A (dashed line), the probability p of fluorescence emission from the first molecule after excitation by a short or ultrashort optical pulse is A (t) can decay with time, as shown in the figure. In some cases, the decrease in the probability of photon emission with time can be described by an exponential decay function Indicates that P Ao is the initial emission probability, and τ1 is a time parameter associated with the first fluorescent molecule, characterizing the emission decay probability. τ1 may be referred to as the "fluorescence lifetime," "emission lifetime," or "lifetime" of the first fluorescent molecule. In some cases, the value of τ1 may be altered by the local environment of the fluorescent molecule. Other fluorescent molecules may have emission characteristics different from those shown in curve A. For example, another fluorescent molecule may have a decay profile different from a single exponential decay, and its lifetime may be characterized by a half-life value or some other metric.

[0103] The second fluorescent molecule may have an exponential decay profile p B (t), but with measurably different lifetimes τ2, e.g. Figure 5-7 In the example shown, the lifetime of the second fluorescent molecule of curve B is shorter than that of curve A, and after exciting the second molecule, the probability of emission p B (t) is higher than curve A. In certain embodiments, different fluorescent molecules can have lifetime or half-life values ​​ranging from about 0.1 ns to about 20 ns.

[0104] The difference of fluorescence emission lifetime can be used to distinguish the presence or absence of different fluorescent molecules and / or to distinguish between different environments or conditions experienced by fluorescent molecules. In some cases, distinguishing fluorescent molecules based on lifetime (for example, rather than emission wavelength) can simplify the state of analytical instrument 5-100. As an example, when distinguishing fluorescent molecules based on lifetime, wavelength distinguishing optical devices (such as wavelength filters, dedicated detectors for each wavelength, dedicated pulsed light sources at different wavelengths and / or diffraction optical devices) can be reduced or eliminated in number. In some cases, a single pulsed light source operating at a single characteristic wavelength can be used to excite different fluorescent molecules, which are emitted within the same wavelength range of the spectrum but have measurable different lifetimes. Using a single pulsed light source instead of multiple sources operating at different wavelengths to excite and distinguish the analysis system of different fluorescent molecules emitted at the same wavelength region can reduce the complexity of operation and maintenance, making it more compact and can be manufactured at a lower cost.

[0105] Although an analysis system based on fluorescence lifetime analysis may have certain benefits, the amount of information obtained by the analysis system and / or the detection accuracy may be increased by allowing additional detection techniques. For example, certain analysis systems 5-160 may additionally be configured to discern one or more properties of a sample based on fluorescence wavelength and / or fluorescence intensity.

[0106] Reference again Figure 5-7 According to some embodiments, different fluorescence lifetimes can be distinguished with the aid of a photodetector that is configured to time bin the fluorescence emission events after excitation of the fluorescent molecule. The time binning can occur during a single charge accumulation cycle of the photodetector. A charge accumulation cycle is the interval between read events during which photogenerated carriers accumulate in the binning grid of the time binning photodetector. The concept of determining fluorescence lifetimes by time binning of emission events is discussed in detail in the literature. Figure 5-8 The time t just before t1 e At the same time, short or ultrashort optical pulses are used to excite the same type (e.g., corresponding to Figure 5-7For a macromolecular ensemble, the emission intensity may have a temporal profile similar to that of curve B, such as Figure 5-8 as shown in .

[0107] However, for a single molecule or a small number of molecules, for this example, according to Figure 5-7 The emission of fluorescent photons occurs according to the statistics of curve B in FIG. The time-graded light detector 5-322 can accumulate carriers generated from emission events into a discrete time-graded grid. Figure 5-8 Three bins are indicated in FIG, although fewer bins or more bins may be used in embodiments. e The grading grid is resolved in time. For example, the first grading grid may accumulate vectors generated during the interval between time t1 and t2, which is the vector generated during the interval between time t1 and t2. e The second classification grid can accumulate carriers generated during the interval between time t2 and t3, and the third classification grid can accumulate carriers generated during the interval between time t3 and t4. When summing up a large number of emission events, the accumulated carriers in the time classification grid can be approximated Figure 5-8 The decay intensity curve shown in , and the graded signals can be used to distinguish different fluorescent molecules or different environments where fluorescent molecules are located.

[0108] Examples of temporal binning photodetectors 5-322 are described in the following applications: U.S. Patent Application No. 14 / 821,656, filed on August 7, 2015, entitled “Integrated Device for Temporal Binning of Received Photons” and U.S. Patent Application No. 15 / 852,571, filed on December 22, 2017, entitled “Integrated Photodetector with Direct Binning Pixel”, both of which are incorporated herein by reference in their entirety. For purposes of explanation, Figure 5-9A non-limiting embodiment of a time-graded photodetector is depicted in . A single time-graded photodetector 5-322 may include a photon absorption / carrier generation region 5-902, a carrier discharge channel 5-906, and a plurality of carrier storage gratings 5-908a, 5-908b, all of which are formed on a semiconductor substrate. A carrier transport channel 5-907 may be connected between the photon absorption / carrier generation region 5-902 and the carrier storage gratings 5-908a, 5-908b. In the example shown, two carrier storage gratings are shown, but there may be more or fewer carrier storage gratings. There may be a readout channel 5-910 connected to the carrier storage gratings. The photon absorption / carrier generation region 5-902, the carrier discharge channel 5-906, the carrier storage gratings 5-908a, 5-908b, and the readout channel 5-910 may be formed by locally doping the semiconductor and / or forming adjacent insulating regions to provide photoelectric detection capabilities, confinement, and transport of carriers. The time-graded photodetector 5-322 may also include a plurality of electrodes 5-920, 5-921, 5-922, 5-923, 5-924 formed on a substrate and configured to generate an electric field in the device to transport carriers through the device.

[0109] In operation, a portion of an excitation pulse 5-122 from a pulsed light source 5-108 (e.g., a mode-locked laser) is delivered to a reaction chamber 5-330 via a time-graded light detector 5-322. Initially, some of the excitation radiation photons 5-901 may arrive at the photon absorption / carrier generation region 5-902 and generate carriers (shown as light shaded circles). There may also be some fluorescence emission photons 5-903 that arrive with the excitation radiation photons 5-901 and generate corresponding carriers (shown as dark shaded circles). Initially, the number of carriers generated by the excitation radiation may be excessively large compared to the number of carriers generated by the fluorescence emission. For example, in the time interval |t e The initial carriers generated during -t1| may be rejected by gating them into the carrier discharge channel 5-906 having the first electrode 5-920.

[0110] At a later time, most of the fluorescent emission photons 5-903 arrive at the photon absorption / carrier generation region 5-902 and generate carriers (represented as dark shaded circles) that provide a useful and detectable signal representative of the fluorescent emission from the reaction chamber 5-330. According to certain detection methods, the second electrode 5-921 and the third electrode 5-923 may be gated at a later time to direct the carriers generated at a later time (e.g., during a second time interval |t1-t2|) to the first carrier storage grading grid 5-908a. Subsequently, the fourth electrode 5-922 and the fifth electrode 5-924 may be gated at a later time (e.g., during a third time interval |t2-t3|) to direct the carriers to the second carrier storage grading grid 5-908b. After an excitation pulse of a large number of excitation pulses, charge accumulation may continue in this manner to accumulate a considerable number of carriers and signal levels in each carrier storage grading grid 5-908a, 5-908b. At a later time, the signal may be read out from the grading grid. In some embodiments, the time interval corresponding to each storage bin is on a sub-nanosecond time scale, although in some embodiments (eg, in embodiments where fluorophores have longer decay times) longer time scales may be used.

[0111] During a single charge accumulation cycle of the time-graded photodetector 5-322, the process of generating and time-grading carriers after an excitation time (e.g., an excitation pulse from a pulsed light source) can occur once after a single excitation pulse or be repeated multiple times after multiple excitation pulses. After charge accumulation is complete, the carriers can be read out from the storage grading grid via the readout channel 5-910. For example, an appropriate biasing sequence can be applied to the electrodes 5-923, 5-924 and at least the electrode 5-940 to remove the carriers from the storage grading grid 5-908a, 5-908b. The charge accumulation and readout process can occur in massively parallel operations on the chip 5-140, resulting in a frame of data.

[0112] Despite the combination Figure 5-9The described examples include multiple charge storage grading grids 5-908a, 5-908b, but in some cases, a single charge storage grading grid may be used instead. For example, only grading grid 1 may be present in the time-grading photodetector 5-322. In this case, a single storage grading grid 5-908a may be operated in a variable time-gated manner to view different time intervals after different excitation events. For example, after a pulse in a first sequence of excitation pulses, an electrode for the storage grading grid 5-908a may be gated to collect carriers generated at a first time interval (e.g., during a second time interval |t1-t2|), and the accumulated signal may be read out after a first predetermined number of pulses. After a pulse in a sequence of subsequent excitation pulses in the same reaction chamber, the same electrode of the storage grading grid 5-908a may be gated to collect carriers generated during different gaps (e.g., during a third time interval |t2-t3|), and the accumulated signal may be read out after a second predetermined number of pulses. If desired, carriers may be collected in a similar manner during later time intervals. In this way, a single carrier storage grid can be used to generate signal levels corresponding to fluorescent emission during different time periods after the arrival of an excitation pulse at a reaction chamber.

[0113] For example, regardless of how charge accumulation occurs at different time intervals after excitation, the read signal can provide a binned histogram that characterizes the decay of the fluorescence emission. Figure 5-10A and Figure 5-10B , for which two charge storage bins are used to acquire fluorescence emission from a reaction chamber. The bins of the histogram may indicate the number of photons detected during each time interval following excitation of the fluorophore in the reaction chamber 5-330. In some embodiments, the signal for the bins will accumulate after a large number of excitation pulses, such as Figure 5-10A The excitation pulse can occur at time t e1 ,t e2 ,t e3 ,…,t eN, which are separated by the pulse interval time T. In some cases, for a single event observed in the reaction chamber (e.g., a single nucleotide incorporation event in DNA analysis), there may be between 105 and 107 excitation pulses 5-122 (or portions thereof) applied to the reaction chamber during the signal accumulation in the electronic storage grid. In some embodiments, one grid (grid 0) can be configured to detect the amplitude of the excitation energy delivered with each optical pulse and can be used as a reference signal (e.g., to normalize the data). In other cases, the excitation pulse amplitude can be stable, can be determined once or more during signal acquisition, and is not determined after each excitation pulse, so that there is no grid 0 signal acquisition after each excitation pulse. In this case, the carrier generated by the excitation pulse can be combined as described above. Figure 5-9 As described, the photons are rejected and dumped from the photon absorption / carrier generation region 5-902.

[0114] In certain embodiments, only a single photon may be emitted from a fluorophore following an excitation event, such as Figure 5-10A At time t e1 After the first excitation event at f1 The emitted photons at can occur within a first time interval (e.g., between times t1 and t2) such that the resulting electron signal accumulates in the first electron storage lattice (contributing to lattice 1). e2 In the subsequent excitation event, time t f2 The emitted photons at can occur within a second time interval (e.g., between times t2 and t3) such that the resulting electronic signal contributes to the classification grid 2. e3 In the next excitation event at time t f3 , thereby occurring within a first time interval.

[0115] In some embodiments, there may be no emitted and / or detected fluorescent photons following each excitation pulse received at the reaction chamber 5-330. In some cases, there may be as few as one fluorescent photon detected in the reaction chamber for every 10,000 excitation pulses delivered to the reaction chamber. One advantage of implementing the mode-locked laser 5-110 as a pulsed excitation source 5-108 is that the mode-locked laser can produce short optical pulses with high intensity and fast off times at a high pulse repetition rate (e.g., between 50 MHz and 250 MHz). With such a high pulse repetition rate, the number of excitation pulses within a 10 millisecond charge accumulation gap can be 50,000 to 250,000, allowing for accumulation of a detectable signal.

[0116] After a large number of excitation events and carrier accumulation, the carrier storage bins of the time-fractionated photodetector 5-322 can be read out to provide a multi-valued signal (e.g., a histogram of two or more values, an N-dimensional vector, etc.) for the reaction chamber. The signal value of each bin can depend on the decay rate of the fluorophore. For example and again referring to Figure 5-8 , a fluorophore with decay curve B will have a higher signal rate in fractional grid 1 to fractional grid 2 than a fluorophore with decay curve A. The values ​​from the fractional grids can be analyzed and compared to the calibration values ​​and / or to each other to determine the presence of a particular fluorophore. For sequencing applications, for example, identifying a fluorophore can determine a nucleotide or nucleotide analog that will be incorporated into a growing strand of DNA. For other applications, identifying a fluorophore can determine the identity of a molecule of interest or a specimen that can be attached to or labeled with a fluorophore.

[0117] To further assist in understanding the signal analysis, the accumulated multi-level bin values ​​can be plotted as a histogram, such as Figure 5-10B , or can be recorded as a vector or position in N-dimensional space. A calibration run can be performed separately to obtain calibration values ​​(e.g., calibration histograms) for multi-valued signals (e.g., calibration histograms) of four different fluorophores attached to four nucleotides or nucleotide analogs. As an example, a calibration histogram can be visualized as Figure 5-11A (fluorescent label associated with T nucleotide), Figure 5-11B (fluorescent label associated with A nucleotide), Figure 5-11C (fluorescent label associated with C nucleotide) and Figure 5-11D (fluorescent label associated with G nucleotide). The measured multi-value signal (corresponding to Figure 5-10B Comparison of the histogram of the nucleotide signal to the proofreading multivalued signal can determine the identity of the nucleotide or nucleotide analog to be incorporated into the growing strand of DNA "T" ( Figure 5-11A ).

[0118] Additionally or alternatively, in some embodiments, fluorescence intensity can be used to distinguish between different fluorophores. For example, even though certain fluorophore decay rates may be similar, the fluorophores may emit at significantly different intensities or have significant differences in their excitation probabilities (e.g., at least about 35% difference). By referencing the binned signals (bin 5 to 3) to the measured excitation energy and / or other acquired signals, it is possible to distinguish different fluorophores based on intensity levels.

[0119] In certain embodiments, different numbers of fluorophores of the same type can be attached to different nucleotides or nucleotide analogs, so that nucleotides can be identified based on fluorophore intensity. For example, two fluorophores can be attached to a first nucleotide (e.g., "C") or nucleotide analog and four or more fluorophores can be attached to a second nucleotide (e.g., "T") or nucleotide analog. Due to the different numbers of fluorophores, there can be different excitation and fluorophore emission probabilities associated with different nucleotides. For example, there can be more emission events for "T" nucleotides or nucleotide analogs during the signal accumulation gap, so that the apparent intensity of the graded grid is significantly higher than that of "C" nucleotides or nucleotide analogs.

[0120] Differentiating nucleotides or any other biological or chemical sample based on fluorophore decay rate and / or fluorophore intensity enables simplification of the optical excitation and detection systems in the analytical instrument 5-100. For example, optical excitation can be performed with a single wavelength source (e.g., a source that produces one characteristic wavelength rather than multiple sources or a source that operates at multiple different characteristic wavelengths). In addition, wavelength differentiation optics and filters may not be required in the detection system to differentiate between fluorophores of different wavelengths. Moreover, a single light detector can be used for each reaction chamber to detect emissions from different fluorophores.

[0121] The phrase "characteristic wavelength" or "wavelength" is used to refer to the central or dominant wavelength within a finite bandwidth of radiation (e.g., the central or peak wavelength within a 20 nm bandwidth output by a pulsed light source). In some cases, "characteristic wavelength" or "wavelength" may be used to refer to the peak wavelength within the total bandwidth of radiation output by a source.

[0122] Fluorophores with emission wavelengths in the range between about 560nm and about 900nm can provide sufficient amounts of fluorescence to be detected by time-fractionated photodetectors (which can be made on silicon wafers using CMOS programs). These fluorophores can be connected to biomolecules of interest, such as nucleotides or nucleotide analogs for gene sequencing applications. Fluorescence emission in this wavelength range can be detected with a high responsiveness to fluorescence at longer wavelengths in silicon-based photodetectors. In addition, fluorophores and associated linkers in this wavelength range may not interfere with the incorporation of nucleotides or nucleotide analogs into the growing strands of DNA. In certain embodiments, fluorophores with emission wavelengths in the range between about 560nm and about 660nm can be optically excited by means of a single wavelength source. An example fluorophore in this range is Alexa Fluor 647 available from Thermo Fisher Scientific Inc. in Waltham, Massachusetts. Excitation energy at shorter wavelengths (e.g., between about 500nm and about 650nm) can be used to excite fluorophores emitting at wavelengths between about 560nm and about 900nm. In certain embodiments, a time-graded photodetector can efficiently detect longer wavelength emissions from a reaction chamber, for example, by incorporating other materials such as Ge into the active region of the photodetector.

[0123] IV. Conclusion

[0124] Thus, having described several aspects of several embodiments of the system architecture for the advanced analysis system 5-100, it should be understood that various changes, modifications and improvements will readily occur to those skilled in the art. Such changes, modifications and improvements are intended to be part of the present invention and are intended to be within the spirit and scope of the present invention. Although the present teachings have been described in conjunction with various embodiments and examples, it is not intended that the present teachings be limited to these embodiments or examples. On the contrary, the present teachings encompass various alternatives, modifications and equivalent forms, as will be appreciated by those skilled in the art.

[0125] Although various inventive embodiments have been described and illustrated, it will be easy for those skilled in the art to imagine various other methods and / or structures for performing the functions and / or obtaining one or more of the described results and / or advantages, and each of the individual changes and / or modifications is considered to be within the scope of the described inventive embodiments. More generally, it will be easy for those skilled in the art to understand that all the parameters, dimensions, materials, and configurations described are intended to be examples, and the actual parameters, dimensions, materials, and / or configurations will depend on one or more specific applications using the inventive teachings. Those skilled in the art will recognize or be able to determine many equivalents of the described specific inventive embodiments using only routine experiments. Therefore, it should be understood that the aforementioned embodiments are presented only by way of example and within the scope of the attached claims and their equivalents, the inventive embodiments may be practiced differently from the specific descriptions and claims. The inventive embodiments of the present invention are for each individual feature, system, system upgrade, and / or method described. In addition, if such features, systems, system upgrades, and / or methods do not contradict each other, any combination of two or more such features, systems, and / or methods is included in the inventive scope of the present invention.

[0126] Furthermore, although certain advantages of the present invention may be indicated, it should be understood that not every embodiment of the present invention will include every described advantage. Certain embodiments may not implement any of the features described as advantageous. Therefore, the foregoing description and accompanying drawings are by way of example only.

[0127] The full text of all documents and similar materials cited in this application (including but not limited to patents, patent applications, articles, books, papers and web pages) are expressly incorporated by reference regardless of the format of these documents and similar materials. If one or more of the incorporated documents and similar materials are different from or inconsistent with this application, including but not limited to defined terms, term usage, described technology, etc., this application shall prevail.

[0128] The section headings used are for organizational purposes only and are not to be construed as limiting the subject matter described in any way.

[0129] Furthermore, the described techniques may be embodied as a method, of which at least one example has been provided. The actions performed as part of the method may be ordered in any suitable manner. Thus, embodiments may be constructed in which the actions are performed in an order different from that illustrated, which may include performing certain actions simultaneously, even though shown as sequential actions in an illustrative embodiment.

[0130] As defined and used, all definitions should be understood to control over dictionary definitions, definitions in documents incorporated by reference, and / or ordinary meanings of the defined terms.

[0131] Numerical values ​​and ranges can be described in this specification and claims as approximate or exact values ​​or ranges. For example, in some cases, the terms "about", "approximately" and "substantially" can be used to refer to a value. Such reference is intended to cover the reference value and the positive and negative reasonable changes of the value. For example, the phrase "between about 10 and about 20" is intended to mean "between exactly 10 and exactly 20" in some embodiments, and "between 10 ± δ1 and 20 ± δ2" in some embodiments. The variation δ1 and δ2 of the value can be less than 5% of the value in some embodiments, less than 10% of the value in some embodiments, and less than 20% of the value in some embodiments. In embodiments where a large range of values ​​is given (e.g., a range comprising two or more orders of magnitude), the variation δ1 and δ2 of the value can be as high as 50%. For example, if the operable range extends from 2 to 200, "about 80" can cover values ​​between 40 and 120, and the range can be as large as 1 and 300. When an exact value is desired, the term "just" is used, for example, "between exactly 2 and exactly 200".

[0132] The term "adjacent" may refer to two elements that are arranged in close proximity to each other (e.g., within a distance that is less than about one-fifth of the lateral or vertical dimension of the larger of the two elements). In some cases, there may be intervening structures or layers between adjacent elements. In some cases, adjacent elements may be in close proximity to each other without intervening structures or elements.

[0133] Unless explicitly indicated to the contrary, the indefinite articles "a" and "an" used in the specification and in the claims should be understood to mean "at least one."

[0134] As used in the specification and in the claims, the phrase "and / or" should be understood to mean "either or both" of the elements so combined, i.e., elements that exist in combination in some cases and in separation in other cases. Multiple elements listed with "and / or" should be considered to be in the same manner, i.e., "one or more" of the elements so combined. Other elements may be present, whether related or unrelated to those elements specifically identified, in addition to the elements specifically identified by the "and / or" clause. Thus, as a non-limiting example, when used in conjunction with open language such as "comprising", references to "A and / or B" may refer to only A (optionally including elements other than B) in one embodiment; to only B (optionally including elements other than A) in another embodiment; to both A and B (optionally including other elements) in yet another embodiment; and so on.

[0135] As used in the specification and in the claims, "or" should be understood to have the same meaning as "and / or" defined above. For example, when separating items in a list, "or" or "and / or" should be interpreted as inclusive, i.e., including at least one of several elements or lists of elements, but also including more than one, and optionally, additional unlisted items. Only the term is clearly indicated as the opposite, such as when used in the claims, "only one of them" or "exactly one of them" or "consisting of..." will refer to including exactly one element in several elements or lists of elements. In general, the term "or" as used should only be interpreted as indicating exclusive alternatives (i.e., "one or the other, but not two") before exclusive terms, such as "either", "one of them", "only one of them" or "exactly one of them". When used in the claims, "essentially consisting of..." should have its general meaning as used in the field of patent law.

[0136] As used in the specification and in the claims, the phrase "at least one" referring to a list of one or more elements should be understood to mean at least one element selected from any one or more elements in the list of elements, but does not necessarily include at least one of each element specifically listed in the list of elements, and does not exclude any combination of elements in the list of elements. This definition also allows for the optional presence of elements other than the elements specifically identified in the list of elements to which the phrase "at least one" refers, whether related or unrelated to those specifically identified elements. Thus, as a non-limiting example, in one embodiment, "at least one of A and B" (or equivalently, "at least one of A or B", or equivalently, "at least one of A and / or B") may refer to at least one (optionally including more than one) A, without B (and optionally including elements other than B); in another embodiment, to at least one (optionally including more than one) B, without A (and optionally including elements other than A); in yet another embodiment, to at least one (optionally including more than one) A and at least one (optionally including more than one) B (and optionally including other elements); and so on.

[0137] In the claims and in the description above, all transitional phrases (e.g., "comprising," "including," "carrying," "having," "containing," "involving," "maintaining," "consisting of," etc.) should be understood as open-ended, i.e., meaning including but not limited to. Only the transitional phrases "consisting of" and "consisting essentially of" should be closed or semi-closed transitional phrases, respectively.

[0138] The claims should not be interpreted as limited to the described order or elements unless described to that effect. It should be understood that one of ordinary skill in the art may make various changes in form and details without departing from the spirit and scope of the appended claims. All embodiments within the spirit and scope of the appended claims and their equivalents are claimed.

Claims

1. An integrated device comprising: a grating disposed on a substrate and arranged to couple radiation incident on the grating into a plurality of optical waveguides disposed on the substrate; a first access to a first receiving region of the plurality of optical waveguides; a second entrance to a second receiving region of the plurality of optical waveguides, wherein the second entrance is offset from the first entrance by a first amount in a first direction perpendicular to the lines of the grating; and A third entrance to a third receiving region of the plurality of optical waveguides, wherein the third entrance is offset from the first entrance by a second amount in a second direction perpendicular to the lines of the grating, the second direction being opposite to the first direction.

2. The integrated device according to claim 1, wherein: A first portion of the grating positioned adjacent to the first entrance has a first periodicity that is different from a second periodicity of a second portion of the grating positioned adjacent to a fourth entrance to a fourth receiving region of the plurality of optical waveguides.

3. The integrated device according to any one of claims 1 to 2, further comprising: a first optical sensor arranged to receive radiation coupled into the first waveguide; as well as A second optical sensor is arranged to receive radiation coupled into the second waveguide.

4. The integrated device according to claim 1, wherein: The first inlet is at a first position angle to the first receiving area, and the second inlet is at a second position angle to the second receiving area.

5. The integrated device according to claim 1, wherein: The first inlet has a different width than the second inlet.

6. The integrated device according to claim 1, wherein: The first amount of the offset is any value between 1 micron and 20 microns.

7. The integrated device according to claim 1, wherein: The grating includes a plurality of separated grating portions.

8. The integrated device according to claim 1, wherein: The lines of the grating include a first dielectric material embedded in a second dielectric material, the second dielectric material having a lower refractive index than the first dielectric material.

9. The integrated device according to claim 1, wherein: The lines of the grating comprise metal.

10. The integrated device according to claim 9, wherein: The first dielectric material is the same material and layer used to form the plurality of optical waveguides.

11. The integrated device according to claim 1, wherein: Each waveguide of the plurality of optical waveguides includes a first dielectric material embedded within a second dielectric material, the second dielectric material having a lower refractive index than the first dielectric material.

12. The integrated device according to claim 11, wherein: The first dielectric material is silicon nitride.

13. The integrated device according to claim 1, wherein: The second receiving area has a tapered width.

14. The integrated device according to claim 13, wherein: The width of the first inlet is different from the width of the second inlet.

15. The integrated device of claim 1, further comprising a plurality of pixels formed on the substrate, each comprising a reaction chamber and an optical sensor, wherein At least one waveguide is configured to provide excitation radiation to the plurality of reaction chambers.

16. The integrated device according to claim 15, wherein: Each reaction chamber is configured to receive a sample for gene sequencing, protein sequencing, or another biological analysis.

17. A method of coupling radiation into a plurality of optical waveguides formed on a substrate, the method comprising: receiving one or more radiation beams at a grating formed on the substrate; coupling the radiation from the one or more beams into a plurality of receiving regions connected to the plurality of optical waveguides; monitoring an amount of a first radiation received from a first waveguide of the plurality of optical waveguides; determining, based at least in part on the monitored amount of radiation, whether the one or more beams are moving in a direction perpendicular to the lines of the grating toward or away from an entrance of the first waveguide; and monitoring an amount of a second radiation received from a second waveguide of the plurality of optical waveguides; Obtaining a difference between the first radiation amount and the second radiation amount received by the first waveguide and the second waveguide; If the difference increases, determining that the motion of the one or more beams is in a first direction perpendicular to the line of the grating; as well as If the difference decreases, it is determined that the movement of the one or more beams is in a second direction opposite to the first direction.

18. The method according to claim 17, further comprising: performing an initial calibration of the one or more beams on the grating by maximizing an amount of radiation coupled into a third waveguide of the plurality of waveguides; moving the beam across the grating in the first and second directions perpendicular to the lines of the grating; as well as A reference value of the difference between the first and second amounts of radiation received from the first and second waveguides is recorded as a function of the position of the beam in the direction perpendicular to the lines of the grating.

19. The method according to claim 18, wherein: The inlet is positioned at an angle to the third waveguide that is different from another angle of position of another inlet to another waveguide.

20. The method according to claim 17, wherein: The monitoring includes detecting the first radiation amount and the second radiation amount by means of a sensor integrated on the substrate.

21. The method according to claim 20, further comprising: Signals from the sensor are averaged over a plurality of data frames, wherein the sensor is located in a plurality of pixels formed on the substrate and the data frames include outputs from the sensor.

22. The method according to claim 17, wherein: The coupling includes coupling a same amount of the radiation within 25% into two or more of the plurality of waveguides.

23. The method according to claim 22, wherein: Two or more of the plurality of waveguides each have an entrance and a tapered receiving region adjacent to the entrance, and wherein a first width of a first tapered receiving region at an entrance to a first of the two or more waveguides is different from a second width of a second tapered receiving region at an entrance to a second of the two or more waveguides.

24. The method of claim 17, further comprising delivering radiation from one or more of the plurality of optical waveguides to a plurality of reaction chambers formed on the substrate.

25. The method of claim 24, further comprising the step of performing gene sequencing or protein sequencing or another biological analysis at two or more of the reaction chambers.

26. The method of claim 17, further comprising delivering radiation from one or more of the plurality of optical waveguides to a plurality of sensors formed on the substrate.

27. The method of claim 17, further comprising outputting at least one signal from a sensor integrated on the substrate in response to determining that the one or more beams have moved toward or away from the entrances of the first waveguide and the second waveguide to cause automatic recalibration of the one or more beams on the grating.

28. A method of manufacturing an integrated device, comprising: forming a plurality of waveguides on a substrate; forming a grating on the substrate spanning entrances to the plurality of waveguides; a first inlet positioned along a reference line of the grating to a first waveguide of the plurality of waveguides; offsetting a second entrance to a second waveguide of the plurality of waveguides from the reference line by a first distance, wherein the first distance is in a first direction perpendicular to the line of the grating; and The inlet and the waveguide form a position angle which is different from another position angle between another inlet and another waveguide.

29. The method according to claim 28, wherein: The first distance is a value between 0.1 micrometers and 20 micrometers.

30. The method of claim 28, further comprising: forming a first tapered receiving region adjacent to the first inlet of the first waveguide of the plurality of waveguides; as well as A second tapered receiving region is formed adjacent to the second inlet of the second waveguide of the plurality of waveguides.

31. The method of claim 28, further comprising forming a first portion of the grating positioned adjacent to the first inlet to have a different periodicity than a second portion of the grating positioned adjacent to a third inlet to a third waveguide of the plurality of waveguides.

32. The method of claim 28, further comprising forming the grating at least in part from the same material and in the same layer used to form the plurality of waveguides.

33. An integrated device comprising: a grating disposed on a substrate and arranged to couple radiation incident on the grating into a plurality of optical waveguides disposed on the substrate; a first access to a first receiving region of the plurality of optical waveguides; a second entrance to a second receiving region of the plurality of optical waveguides, wherein the second entrance is offset from the first entrance by a first amount in a first direction perpendicular to the lines of the grating; and A third entrance to a third receiving region of the plurality of optical waveguides, wherein a first portion of the grating positioned adjacent to the first entrance has a different periodicity than a second portion of the grating positioned adjacent to the third entrance.

34. The integrated device of claim 33, further comprising: a first optical sensor arranged to receive radiation coupled into a first waveguide of the plurality of optical waveguides; as well as A second optical sensor is arranged to receive radiation coupled into a second waveguide of the plurality of optical waveguides.

35. An integrated device according to claim 33 or 34, wherein: The grating includes a plurality of separated grating portions.

36. The integrated device of claim 33, wherein: The lines of the grating include a first dielectric material embedded in a second dielectric material, the second dielectric material having a lower refractive index than the first dielectric material.

37. The integrated device of claim 36, wherein: The first dielectric material is the same material and layer used to form the plurality of optical waveguides.

38. The integrated device of claim 33, wherein: Each waveguide of the plurality of optical waveguides includes a first dielectric material embedded within a second dielectric material, the second dielectric material having a lower refractive index than the first dielectric material.

39. The integrated device of claim 38, wherein: The first dielectric material is nitrogen-rich silicon nitride.

40. The integrated device of claim 33, further comprising a plurality of pixels formed on the substrate, each comprising a reaction chamber and an optical sensor, wherein At least one waveguide is configured to provide excitation radiation to the plurality of reaction chambers.

41. The integrated device of claim 40, wherein: Each reaction chamber is configured to hold a sample for gene sequencing or protein sequencing.

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