Patent Application
20200284957
The present application relates to reducing, with an optical absorption filter, unwanted radiation in an integrated device that is used to analyze samples.
In the area of instrumentation that is used for analysis of samples, microfabricated chips may be used to analyze a large number of analytes or specimens (contained within one or more samples) in parallel. In some cases, optical excitation radiation is delivered to a plurality of discrete sites on a chip at which separate analyses are performed. The excitation radiation may excite a specimen at each site, a fluorophore attached to the specimen, or a fluorophore involved in an interaction with the specimen. In response to the excitation, radiation may be emitted from a site that is detected by a sensor. Information obtained from the emitted radiation for a site, or lack of emitted radiation, can be used to determine a characteristic of the specimen at that site.
Apparatus and methods relating to attenuating excitation radiation or other unwanted radiation incident on a sensor in an integrated device (such as a device used for sample analysis) are described. In some embodiments, a semiconductor film of a selected material and crystal morphology is formed in a stack of materials on a substrate and is located between a waveguide and a sensor in a pixel of an integrated device. The semiconductor material and crystal morphology are selected to significantly attenuate excitation radiation while passing more than 75% of radiation emitted from a reaction chamber in the pixel to the sensor. A wavelength-discrimination ratio (also referred to as “rejection ratio” or “extinction ratio”) greater than 100 or more can be obtained for wavelengths that are separated by 40 nm or approximately 40 nm. In some implementations, a multi-layer stack includes layers of absorbing material separated by layers of dielectric material. The stack may include at least three or four layers having different thicknesses. Such stacks can provide rejection ratios greater than 10,000 over a range of incident angles from normal to 80 degrees (or any sub-range within these angles) for wavelengths that are separated by 110 nm or approximately 110 nm.
Some embodiments relate to a multi-layer semiconductor absorber filter comprising a plurality of layers of semiconductor absorbers and a plurality of layers of dielectric material separating the plurality of semiconductor absorbers to form a multi-layer stack, wherein there are at least three different layer thicknesses within the multi-layer stack.
Some embodiments relate to a method of forming a multi-layer semiconductor absorber filter. A method may comprise acts of depositing a plurality of layers of semiconductor absorbers; and depositing a plurality of layers of dielectric material that separate the plurality of semiconductor absorbers to form a multi-layer stack, wherein at least three different layer thicknesses are deposited within the multi-layer stack.
Some embodiments relate to a fluorescence detection assembly, comprising a substrate having an optical detector formed thereon, a reaction chamber arranged to receive a fluorescent molecule, an optical waveguide disposed between the optical detector and the reaction chamber, and an optical absorption filter comprising a layer of semiconductor material and disposed between the optical detector and the reaction chamber.
Some embodiments relate to an optical absorption filter comprising a semiconductor layer formed over non-planar topography on a substrate.
Some embodiments relate to an optical absorption filter comprising a ternary III-V semiconductor formed in an integrated device on a substrate.
Some embodiments relate to a method for forming a fluorescence detection device, the method comprising: forming an optical detector on a substrate; forming a semiconductor optical absorption filter over the optical detector on the substrate; forming an optical waveguide over the optical detector on the substrate; and forming a reaction chamber configured to receive a fluorescent molecule over the optical absorption filter and the optical waveguide.
The foregoing and other aspects, implementations, acts, functionalities, features and, embodiments of the present teachings can be more fully understood from the following description in conjunction with the accompanying drawings.
The skilled artisan will understand that the figures, described herein, are for illustration purposes only. It is to be understood that in some instances various aspects of the invention may be shown exaggerated or enlarged to facilitate an understanding of the invention. In the drawings, like reference characters generally refer to like features, functionally similar and/or structurally similar elements throughout the various figures. The drawings are not necessarily to scale, emphasis instead being placed upon illustrating the principles of the teachings. The drawings are not intended to limit the scope of the present teachings in any way.
The features and advantages of the present invention will become more apparent from the detailed description set forth below when taken in conjunction with the drawings. When describing embodiments in reference to the drawings, directional references (“above,” “below,” “top,” “bottom,” “left,” “right,” “horizontal,” “vertical,” etc.) may be used. Such references are intended merely as an aid to the reader viewing the drawings in a normal orientation. These directional references are not intended to describe a preferred or only orientation of features of an embodied device. A device may be embodied using other orientations.
I. Integrated Device with a Semiconductor Absorber
Instruments for analyzing samples continue to improve and may incorporate microfabricated components (e.g., electronic chips, microfluidic chips) which can help reduce the overall size of the instrument. Samples to be analyzed can include air (e.g., sensing for harmful gaseous leaks, combustion by-products, or toxic chemical components), water or other ingestible liquids, food samples, and biological samples taken from subjects (blood, urine, etc.) In some cases, it is desirable to have portable, hand-held instruments for analyzing samples, so that technicians or medical personnel can easily carry the instrument into the field where service may be performed and a sample needs to be analyzed quickly and accurately. In clinical settings, a desk-top size instrument may be desired for more complex sample analysis such as sequencing of human genes or complete blood count analysis.
In an advanced analytic instrument, such as those described in U.S. Patent Publication No. 2015/0141267 and in U.S. Pat. No. 9,617,594, both of which are incorporated herein by reference, a disposable integrated device (which may be referred to as “chip” and “disposable chip” for brevity) may be used to perform massively parallel sample analyses. The disposable integrated device may comprise a packaged bio-optoelectronic chip on which there can be a large number of pixels having reaction chambers for parallel analyses of one sample or of different samples. For example, the number of pixels having reaction chambers on a bio-optoelectronic chip can 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. In some embodiments, the disposable chip may mount into a receptacle of an advanced analytic instrument and interface with optical and electronic components in the instrument. The disposable chip can be replaced easily by a user for each new sample analysis.
For sample analysis, a sample containing one or more analytes may be deposited over the reaction chamber 1-130. For example, a sample may be disposed in a reservoir or microfluidic channel over the reaction chamber 1-130. In some cases, a sample may be printed as a droplet onto a treated surface that includes the reaction chamber 1-130. During sample analysis, at least one analyte from a sample to be analyzed may enter the reaction chamber 1-130. In some implementations, the analyte itself may fluoresce when excited by excitation radiation delivered from the waveguide 1-115. In some cases, the analyte may carry with it one or more linked fluorescent molecules. In yet other cases, the analyte may quench a fluorophore already present in the reaction chamber 1-130. When the fluorescing entity enters into the reaction chamber and is excited by excitation radiation, the fluorescing entity can emit radiation, at a different wavelength than the excitation radiation, that is in turn detected by the sensor 1-122. The semiconductor absorber 1-135 can preferentially attenuate excitation radiation significantly more than emission radiation from the reaction chamber 1-130.
In further detail, reaction chamber 1-130 may be formed into a transparent or semitransparent layer 1-110. The reaction chamber may have a depth between 50 nm and 1 μm, according to some embodiments. A minimum diameter of the reaction chamber 1-130 may be between 50 nm and 300 nm in some embodiments. If the reaction chamber 1-130 is formed as a zero-mode waveguide, then the minimum diameter may be even less than 50 nm in some cases. If large analytes are to be analyzed, the minimum diameter may be larger than 300 nm. The reaction chamber may be located above the optical waveguide 1-115 such that a bottom of the reaction chamber may be up to 500 nm above a top of the waveguide 1-115. In some cases, the bottom of the reaction chamber 1-130 may be located within the waveguide or on a top surface of the waveguide 1-115. The transparent or semitransparent layer 1-110 can be formed from an oxide or a nitride, according to some embodiments, so that excitation radiation from the optical waveguide 1-115 and emission radiation from the reaction chamber 1-130 will pass through the transparent or semitransparent layer 1-110 without being attenuated by more than 10%, for example.
In some implementations, there can be one or more additional transparent or semitransparent layers 1-137 formed on the substrate 1-105 and located between the substrate and the optical waveguide 1-115. These additional layers may be formed from an oxide or a nitride, and may be of the same type of material as the transparent or semitransparent layer 1-110, in some implementations. The semiconductor absorber 1-135 may be formed within these additional layers 1-137 between the waveguide 1-115 and sensor 1-122. A distance from the bottom of the optical waveguide 1-115 to the sensor 1-122 can be between 500 nm and 10 μm.
In various embodiments, the substrate 1-105 may comprise a semiconductor substrate, such as silicon (Si). However, other semiconductor materials may be used in some embodiments. The sensor 1-122 may comprise a semiconductor photodiode that is patterned and formed on the substrate 1-105. The sensor 1-122 may connect to other complementary metal-oxide-semiconductor (CMOS) circuitry on the substrate via interconnects 1-170.
Another example of structure that may be included at a pixel of an integrated device is shown in
In some implementations, a process of etching of the reaction chamber may begin with opening an aperture in the one or more light-blocking layers that will become a top of the reaction chamber 1-230. The light-blocking layers 1-250 may be formed from one or more metal layers. In some cases, the light-blocking layers 1-250 may include a semiconductor and/or oxide layer. The light-blocking layers 1-250 may reduce or prevent excitation radiation from the optical waveguide 1-115 from travelling into a sample above the reaction chamber 1-230 and exciting analytes within the sample. Additionally, the light-blocking layers 1-250 can prevent external radiation from above the reaction chamber to pass through to the sensor 1-122. Emission from outside the reaction chamber can contribute to unwanted background radiation and signal noise.
In some embodiments, one or more iris layers 1-240 may be formed above the sensor 1-122. An iris layer 1-240 may include an opening 1-242 to allow emission from the reaction chamber 1-230 to pass through to the sensor 1-122, while blocking emission or radiation from other directions (e.g., from adjacent pixels or from scattered excitation radiation). For example, the iris layer 1-240 may be formed from a light-blocking material that can block scattered excitation radiation at wide angles of incidence from striking the sensor 1-122 and contributing to background noise.
In some cases, an iris layer 1-240 may be formed from a conductive material and provide a potential reference plane or grounding plane for circuitry formed on or above the substrate 1-105. According to some implementations, a via or hole 1-237 may be formed in the semiconductor absorber 1-235 (and capping layers, if present, that contact the semiconductor absorbing layer) so that a vertical conductive interconnect or via 1-260 may connect to the iris layer 1-240 without contacting the semiconductor absorber 1-235, which may be conductive. In some cases, the semiconductor absorber 1-235 may be used as a potential reference plane or grounding plane for circuitry formed on or above the substrate 1-105, and a vertical interconnect may connect to the semiconductor absorber 1-235 and may not connect to the iris layer 1-240. In some cases, the hole 1-237 may include electrically insulating material (e.g., an oxide) that prevents electrical contact between a conductive via 1-260 and the semiconductor absorbing layer 1-235. In some implementations, the semiconductor absorbing layer 1-235 may have high resistivity and the hole 1-237 may be filled with conductive material to provide an electrical connection through the semiconductor absorbing layer. In embodiments, there may be additional electronic components, such as storage and read-out electronics 1-224 formed with the sensor on the substrate 1-105 at each pixel. The read-out electronics may be used to control signal acquisition and to read out stored charges at each sensor 1-122, for example. In some embodiments, a hole 1-237 in the semiconductor absorber 1-235 (and capping layers) can facilitate electrical connection through the semiconductor layer, e.g., connection of an integrated circuit to an external circuit, via wire bonding, flip-chip bonding, or other methods.
In some cases, there may be multiple layers of semiconducting absorbing material, as depicted in
By using multiple layers of semiconductor absorbing material 1-336 as depicted in
Further details of a semiconductor absorber 2-135 are shown in
The type of semiconductor material used for the semiconductor absorbing layer 2-210 can be selected or tailored to provide a desired absorption for the excitation radiation and transmission for radiation emitted from the reaction chamber 1-230. For example, a semiconductor material may be selected or tailored to have a bandgap, such that excitation radiation having photon energies greater than the bandgap will be mostly absorbed by the semiconductor material and fluorophore emission from the reaction chamber 1-230 having photon energies less than the bandgap will be mostly transmitted by the semiconductor material. In embodiments, the bandgap is chosen or tailored such that the transition between wavelengths that are absorbed and wavelengths that are transmitted lies between excitation radiation provided by the optical waveguide 1-115 and fluorescence emission emitted from the reaction chamber 1-230. The bandgap of a semiconductor absorbing layer 2-210 may be tailored by changing the composition of a semiconductor (e.g., changing the stoichiometric ratio of In and Ga in InxGa1-xN where x ranges in value according to 0<x<1).
An example transmission curve for a semiconductor absorbing layer 2-210 formed from ZnTe is shown in
The inventors have recognized and appreciated that the abruptness of the filter cut-off and ratio of transmitted radiation at wavelengths longer than the cut-off to absorbed radiation at wavelengths shorter than the cut-off depends on thickness of the semiconductor absorbing layer(s) 2-210, number of semiconductor absorbing layers, crystal quality of the semiconductor absorbing layer(s), and separation of excitation and emission characteristic wavelengths and that each of these parameters can be modified to some extent. The thickness of a semiconductor absorbing layer 2-210 can be controlled by adjusting the length of a deposition time for the semiconductor absorbing material, for example.
In some implementations, a type of deposition process may be selected (e.g., metal-organic chemical vapor deposition, molecular beam epitaxy, or physical vapor deposition) to improve crystal quality of the semiconductor absorbing layer 2-210. In some cases, a seed layer of a different material may be deposited first on an underlying layer to improve the crystal quality of a subsequently deposited semiconductor absorbing layer 2-210. In some implementations, a post-deposition anneal step can be carried out to improve the crystal quality of a semiconductor absorbing layer 2-210. In some embodiments, a semiconductor absorbing layer 2-210 may have an average crystal grain size, as measured in the plane of the layer, that is no smaller than 20 nm. In some cases, the average crystal grain size is no smaller than 50 nm. In some cases, the average crystal grain size is no smaller than 100 nm. In some cases, the average crystal grain size is no smaller than 500 nm. In some cases, the average crystal grain size is between 40 nm and 100 nm. In some cases, the average crystal grain size is between 100 nm and 500 nm. In some cases, the average crystal grain size is between 100 nm and 1 μm. In some cases, the average crystal grain size is between 1 μm and 3 μm. In some cases, the average crystal grain size is between 2 μm and 5 μm. In some cases, the average crystal grain size is between 5 μm and 10 μm. According to some implementations, the semiconductor absorbing layer 2-210 may have larger crystal grain sizes or may be essentially single crystal. For example, the semiconductor absorbing layer 2-210 may be delaminated and transferred from a single-crystal wafer as grown using a handle wafer, and deposited by bonding to an underlying layer on the substrate 1-105.
In some implementations, the semiconductor absorbing layer 2-210 may have a particular crystalline morphology, such as fibrous, cylindrical, or pancake. A fibrous morphology may exhibit fiber-like or tall columnar crystals oriented vertically in the semiconductor absorbing layer 2-210. An example of fibrous crystals is shown in the transmission-electron microscope image of
In some cases, a semiconductor absorbing layer 2-210 may be formed from amorphous semiconductor material. For example, any of the semiconductor materials described herein may be deposited as amorphous material by sputtering, e-beam evaporation, or a chemical vapor deposition process, such as plasma-enhanced chemical vapor deposition (PECVD). Example amorphous semiconductor materials include, but are not limited to, amorphous silicon, amorphous silicon carbide, amorphous silicon nitride, amorphous silicon oxide, amorphous ZnTe, amorphous InGaN, and alloys thereof. In some implementations, an amorphous semiconductor material or alloy may be hydrogenated (e.g., amorphous hydrogenated silicon, amorphous hydrogenated silicon carbide, etc.) In some implementations, nitrogen may be added to an amorphous semiconductor material or alloy during deposition, e.g., during a chemical vapor deposition process. In some cases, nitrogen and/or other element(s) can be added to a material during deposition, such as amorphous silicon, to tune the refractive index n and extinction coefficient k to values desired for transmitting and blocking wavelengths of interest. In some embodiments, a deposited amorphous semiconductor material may include nanocrystals or microcrystals distributed throughout the amorphous semiconductor material. An amorphous semiconductor absorbing layer 2-210 may be used in any of the semiconductor absorber structures described herein. In practice, an amorphous semiconductor absorbing layer 2-210 may be easier and less costly to fabricate on a substrate with existing foundry tools and processes. In some cases, deposition of an amorphous semiconductor or other material may be achieved at lower temperatures (e.g., less than 500° C.) that are compatible with a CMOS process, for example. Although an amorphous semiconductor material may not provide a band-edge that is as abrupt as a polycrystalline or crystalline semiconductor material of the same type, the band-edge may be sufficient when there is a large difference in characteristic excitation and emission wavelengths. However, some microfabrication processes may enable polycrystalline or crystalline semiconductor materials to be used in a way that is compatible with CMOS structures.
An advantage of an absorbing layer, such as a semiconductor absorbing layer 2-210, is that it can have a higher angular tolerance than other types of wavelength filters, such as multilayer dielectric filters. In a dielectric filter, the layers each absorb negligible amounts of radiation (e.g., less than one percent of incident radiation). For example, a multilayer dielectric filter (such as a distributed Bragg reflector) with thickness of about 2 microns can provide a rejection ratio Rr of approximately 800 at normal incidence. The rejection ratio Rr is a ratio of transmitted intensity at an emission wavelength (572 nm for an example structure) to transmitted intensity at an excitation wavelength (532 nm for the example structure). At 30 degrees angle of incidence, the rejection ratio Rr drops to 110. In contrast, a 2.0-micron-thick, ZnTe semiconductor absorbing layer 2-210 provides a rejection ratio Rr of exceeding 800 at all angles of incidence. Accordingly, a micron-scale, thin film, absorbing layer or semiconductor absorbing layer 2-210 can outperform a micron-scale, thin film, multilayer dielectric filter in terms of angular tolerance, and additionally be compatible with widely available CMOS processing equipment. For example, a semiconductor absorbing layer 2-210 may comprise one or a few layers that may not have as tight dimensional tolerances required for a multilayer dielectric filter.
According to some embodiments, a semiconductor absorbing layer 2-210 may be formed from InGaN which can provide tunability of the bandgap over a broad range. For example, by varying the ratio of concentrations of In and Ga, the bandgap can be tuned from 0.8 eV to 3.4 eV, covering the entire visible wavelength range. InGaN can be grown epitaxially as single crystal material on a crystalline substrate, or may be deposited in polycrystalline form by various chemical and physical deposition methods, including metallorganic chemical vapor deposition (MOCVD), molecular beam epitaxy (MBE), sputtering, reactive sputtering, and other established methods. In some implementations, a bandgap may be tuned by alloying or otherwise combining a binary semiconductor with a third group II and/or group VI element. Some example resulting ZnTe semiconductor compositions include, but are not limited to, ZnTeO and CdZnTe.
Modelling of single-crystal InGaN suggests that a rejection ratio Rr (572 nm/532 nm) greater than 3000 can be obtained for a layer thickness of 1.5 microns. In some embodiments, a semiconductor absorber 2-135 may comprise a semiconductor absorbing layer 2-210 formed from InGaN. A thickness of the absorbing layer may be between 200 nm and 3 microns, and a rejection ratio Rr for the layer may be between 20 and 100,000. An example curve of rejection ratio Rr calculated for single-crystal InGaN as a function of layer thickness is plotted in
In some embodiments, one or more capping layers 2-220 may be formed adjacent to the semiconductor absorbing layer 2-210. In some cases, there may be one capping layer 2-220 on one side of the semiconductor absorbing layer 2-210. In other cases there may be a capping layer on each side of the semiconductor absorbing layer 2-210, for example top and bottom sides. A capping layer 2-220 may comprise at least one thin layer between 20 nm and 100 nm thick, according to some embodiments, though thicker layers may be used in some cases. In some implementations, a capping layer 2-220 on one side of the semiconductor absorbing layer 2-210 may comprise plural layers of different materials. Example materials that can be used for the capping layer 2-220 include, but are not limited to, silicon nitride, aluminum oxide, titanium oxide, hafnium oxide, and tantalum oxide.
One or more capping layers 2-220 may be included to prevent diffusion of the semiconductor absorbing layer 2-210 into adjacent material or to prevent release of the semiconductor absorbing material into an environment. In some implementations, a capping layer 2-220 may additionally or alternatively provide improved adhesion to an immediately adjacent layer than would be provided by the semiconductor absorbing layer 2-210 alone. In some implementations, one or more capping layers 2-220 can reduce or induce stresses in the semiconductor absorbing layer 2-210 and/or improve crystallinity of the semiconductor absorbing layer 2-210. In some cases, a capping layer 2-220 may reduce stress from the semiconductor absorbing layer 2-210 in the assembly by providing a compensating type of stress (e.g., tensile stress if the semiconductor absorbing layer has compressive stress).
Additionally or alternatively, in some embodiments, a capping layer may be formed to reduce optical reflections from the semiconductor absorbing layer 2-210. In some cases, the semiconductor absorbing layer 2-210 may have a significantly different index of refraction than the adjacent layers, which can cause an appreciable amount of reflected radiation from the interface between the semiconductor absorbing layer 2-210 and an adjacent layer. In this regard, one or more capping layers 2-220 may formed as anti-reflection coating(s) for the semiconductor absorbing layer 2-210, and reduce optical reflections one or more wavelengths over a range of wavelengths. For example, a capping layer 2-220 may reduce reflection of emission radiation from the reaction chamber 1-230 and/or of excitation radiation. For a semiconductor absorbing layer 2-210 formed from ZnTe and having adjacent silicon oxide layers, the reflections at 532 nm and 572 nm can be approximately 14% and 10%, respectively. Adding a capping layer 2-220 of silicon nitride, 63 nm thick, can reduce these reflections to less than 1%. According to some embodiments, an oxide or nitride capping layer formed adjacent to the semiconductor absorbing layer reduces optical reflection from the semiconductor absorbing layer for a visible wavelength between 500 nm and 750 nm compared to a case where the oxide or nitride capping layer is not present. A thickness of the oxide or nitride capping layer can be chosen to reduce the optical reflection for the desired wavelength.
According to some implementations, a semiconductor absorbing layer 2-210 may be incorporated by itself, or with one or more capping layers 2-220, into a stack that includes one or more dielectric layers having different optical properties than the semiconductor absorbing layer 2-210, as depicted in
The inventors have further recognized and appreciated that emission radiation may be shifted to a longer wavelength using Dexter energy transfer (DET) and/or Førster resonant energy transfer (FRET) processes. As an example, there may be two fluorophores associated with an analyte or specimen. A first of the two fluorophores may be excited more efficiently by excitation radiation delivered to a reaction chamber than the second fluorophore. The second fluorophore may be attached with a chemical linker so that it is in close proximity (e.g., less than 10 nm) from the first fluorophore. As such, emission energy from the first fluorophore may transfer from the first fluorophore to the second fluorophore and excite the second fluorophore so that it emits radiation at a longer characteristic wavelength than the first fluorophore and is detected by a sensor 1-122. As an example, the first fluorophore may emit with a characteristic wavelength that is within the yellow region of the optical spectrum, and the second fluorophore may emit with a characteristic wavelength that is red-shifted, e.g., within the yellow-red or red region of the optical spectrum. The energy transfer from the first fluorophore to the second fluorophore may be a non-radiative DET or FRET process in some cases. The energy transfer and shift of emission radiation to a longer characteristic wavelength results in an effective Stokes shift that is larger than a Stokes shift for a single fluorophore. Such an increased effective Stokes shift may move the emission radiation farther from the band-edge of a semiconductor absorber to a location where absorption of the emission wavelength by the semiconductor absorber is less than it would be for the first fluorophore.
In general, it is desirable to use a fluorophore with a large separation between excitation wavelength and emission wavelength. For a single electronic transition in a fluorophore, this separation is referred to as the “Stokes shift.” In some embodiments, multiple fluorophores may be used as described above in a FRET or DET approach to achieve a larger separation between excitation wavelength and emission wavelength. This larger separation between excitation wavelength and emission wavelength resulting from the use of multiple fluorophores is referred to herein as an “effective Stokes shift.”
The results plotted in
In some cases, maintaining only a high rejection of excitation radiation at large non-normal angles of incidence can be sufficient for increasing pixel density. For example, in
Another example of a multi-layer semiconductor absorber filter 2-600 is depicted in
Although the example filter depicted in
In many conventional multi-layer dielectric filters, the layers in the filter stack are quarter-wavelength layers and a same thickness for each material is used throughout the stack, such that the stack has a very regular, repeating structure (e.g., t1, t2, t1, t2, t1, t2, t1, t2) where t1 is a thickness of a first dielectric material in the stack and t2 is a thickness of a second dielectric material in the stack. For a multi-layer semiconductor absorber filter 2-600, the inventors have found that layer thicknesses other than quarter-wavelength and non-uniform thicknesses can improve the filter characteristics. For example, the layers of semiconductor absorbers 2-630 may all have a same thickness ta and the layers of dielectric material 2-620 can have different thicknesses that are greater than a quarter wavelength. Improvements can also be obtained when thicknesses of absorbing layers are greater than quarter-wavelength and not a multiple of quarter-wavelength. In some cases, there may be at least three or four different thicknesses of layers within the stack. For example, thickness t1 can differ from thickness t2, and both thicknesses can differ from thickness t3, as depicted in the illustration of
According to some embodiments, thicknesses of the semiconductor absorbers 2-630 can be between 20 nm and 300 nm in a multi-layer semiconductor absorber filter. Thicknesses of the layers of dielectric material 2-620 can be between 40 nm and 300 nm. In some cases, the semiconductor absorbers 2-630 can be formed from doped or alloyed amorphous silicon or other semiconductor materials described above. An advantage of using amorphous silicon is that it can be deposited at temperatures that are low enough to be compatible with other CMOS processes (such as processes to form back-end metallization). In some implementations, nitrogen can be used as a dopant or additive, although other dopants or additives (e.g., carbon, phosphorous, germanium, arsenic, etc.) may be used in some absorbers. For the case of nitrogen-doped amorphous silicon, an amount of nitrogen added during deposition of amorphous silicon may be between 0 and 40 atomic percent. This range of doping levels can produce a range of refractive index values between 2.6 and 4.3 and a range of extinction coefficient values between 0.01 and 0.5. Other dopants, semiconductor materials, and doping ranges can be used in other embodiments to obtain different refractive index and extinction coefficient values for a particular wavelength range (e.g., green, blue, or ultraviolet wavelengths or infrared wavelengths).
The filter design, for the results illustrated in
Further details of angular dependence are shown in
It may be appreciated that the performance of the filter can differ depending upon the materials surrounding the filter (e.g., located above and below the filter when integrated into a substrate, such as depicted in
A multi-layer absorber filter may be formed by sequential timed depositions of absorbing material and dielectric material. The depositions may be timed to achieve desired thicknesses for each layer. Chemical vapor deposition processes may be used. A preferred method of deposition is plasma enhanced chemical vapor deposition (PECVD). The number of absorbing layers deposited can be fewer than 20 in some embodiments, fewer than 10 in some embodiments, and yet fewer than 5 in some embodiments. According to some embodiments, the absorbing layers may be located at regions in an integrated stack that include portions of one or more peaks of electric field within the stack for the excitation radiation. In some cases, the absorbing layers may be located away from peaks in the electric field for emission radiation.
Although the semiconductor absorber 1-235 is shown as a planar layer in
Topography in a semiconductor absorber 3-135 may be included to relieve in-plane stress in the semiconductor absorber 3-135. In some cases, a semiconductor absorbing material may accumulate in-plane stress as a result of the deposition process. Such stress, if severe enough, can cause warping of the substrate and in some cases cracking and/or delamination of the semiconductor layer. The topography may allow the stress to be relieved and prevent warping, cracking, and delamination. In some embodiments, there may be one or more topographical features in a region of a semiconductor absorber 3-135 that is between the reaction chamber 1-230 and a corresponding sensor 1-122. In some cases, there may be no topography between a reaction chamber 1-230 and a sensor 1-122, and the topography may be in adjacent regions within or between pixels. In some implementations, topographical features in a semiconductor absorber 3-135 may be separated by distances greater than 500 microns (e.g., up to 1 millimeter or more), and in some cases the topographical features may be located outside a pixel region and are sufficient to relieve stress for the pixel region.
Topography in the semiconductor absorber 3-135 may provide additional improvements, in some cases. For example, topography may increase overall absorption of the filter, since longer paths through the absorber will be presented to some incident radiation. Additionally crystallinity of the deposited semiconductor absorbing layer may be improved by the topography (e.g., by inducing or relieving film stress), leading to more abrupt filter cut-off and better rejection ratios.
In some cases, a semiconductor absorber 3-135 that includes topography may be etched back after deposition to form one or more insulated vias 3-210 through the semiconductor absorber, as illustrated in
In some implementations, there may be no vertical interconnects within a pixel. Instead, a hole may be opened through a semiconductor absorber 1-235, 3-135 and within an insulated via 3-210, so that a wire bond may be made to a contact pad below the semiconductor absorber 3-135. The wire bond may be located outside a pixel region, for example. A hole for a wire bond may be opened by patterning photoresist or a hard mask and etching the semiconductor absorber in an exposed region that is not covered by the photoresist or hard mask. The etched semiconductor absorber may or may not have topographical structure prior to the etching.
Structure associated with an example method for forming a semiconductor absorber 3-135 having topography and a single insulated via 3-310 are illustrated in
In a subsequent step of the process, an etching step may be performed to etch away regions of the first layer 3-110 that are not covered by the first patterned resist 3-410 and second patterned resist 3-420. In some cases, a preliminary etch may be carried out to etch away portions of the first patterned resist 3-410 that are not covered by the second patterned resist 3-420. The etching may produce etch cavities 3-430 having cavity walls 3-435, as illustrated in
In a subsequent process step, the second patterned resist 3-420 is removed leaving the first patterned resist 3-410. Then, a second etching step may be carried out to further etch the first layer 3-110, as depicted in
After etching topography into the first layer 3-110, the first patterned resist 3-410 can be removed from the first layer 3-110 and the surface of the layer cleaned in preparation for deposition of the semiconductor absorber 3-135. One or more layers of the semiconductor absorber 3-135 may then be deposited over the topography of the first layer 3-110. In some cases, the deposition may be conformal, such that the conformal layers have a uniform thickness (to within 10%) on horizontal and inclined surfaces of the first layer 3-110 as measured normal to the contacting surface. The semiconductor absorber 3-135 may be deposited, for example, by a plasma deposition process or atomic layer deposition process or any other suitable deposition process. Other example deposition processes that may be used to deposit one or more layers of the semiconductor absorber 3-135 include, but are not limited to, sputtering, molecular beam epitaxy, pulsed laser deposition, closed space sublimation, electron-beam evaporation, vapor deposition, chemical vapor deposition, plasma enhanced chemical vapor deposition, electrodeposition, and metal-organic chemical-vapor deposition. In some implementations, where the semiconductor absorber 1-235 is planar, the semiconductor absorber may be deposited by wafer transfer. In some implementations, where the semiconductor absorber 3-135 has topography, the semiconductor absorber and one or more adjacent layers may be deposited by wafer transfer. In some cases the semiconductor absorber layer 3-135 may be annealed after deposition to improve crystallinity of the semiconductor absorber. Subsequently, a second layer 3-312 may be deposited over the semiconductor absorber 3-135 yielding structure as shown in
Chemical mechanical polishing (CMP) may then be used to planarize the structure as shown in
Example structure 4-100 for a disposable chip is shown in
The disposable chip structure 4-100 may further include walls 4-120 that are formed around a pixel region on the bio-optoelectronic chip 4-110. The walls 4-120 may be part of a plastic or ceramic casing that supports the bio-optoelectronic chip 4-110. The walls 4-120 may form at least one reservoir 4-130 into which at least one sample may be placed and come into direct contact with reaction chambers 1-130 on the surface of the bio-optoelectronic chip 4-110. The walls 4-120 may prevent the sample in the reservoir 4-130 from flowing into a region containing the optical port 4-150 and grating coupler, for example. In some embodiments, the disposable chip structure 4-100 may further include electrical contacts on an exterior surface of the disposable chip and interconnects within the package, so that electrical connections can be made between circuitry on the bio-optoelectronic chip 4-110 and circuitry in an instrument into which the disposable chip is mounted.
In some embodiments, a semiconductor absorber 2-135 may be integrated at each pixel in a disposable chip structure like that shown in
According to some implementations, a rejection ratio Rr for a semiconductor absorber 2-135 integrated into an assembly can have a value between 10 and 100. In some implementations, the rejection ratio Rr can have a value between 100 and 500. In some cases, the rejection ratio Rr can have a value between 500 and 1000. In some implementations, the rejection ratio Rr can have a value between 1000 and 2000. In some implementations, the rejection ratio Rr can have a value between 2000 and 5000. An advantage of a semiconductor absorber is that the rejection ratio Rr can be selected more easily than for a multi-layer filter by selecting the thickness of the semiconductor absorbing layer, as can be seen from
II. Example Bioanalytic Application
An example bioanalytic application is described in which an integrated semiconductor absorber 1-135 can be used to improve detection of radiation emitted from reaction chambers on a disposable chip that is used in an advanced analytical instrument. For example, a semiconductor absorber 1-135 can significantly reduce excitation radiation incident on the sensor 1-122 and thereby reduce detected background noise appreciably that might otherwise overwhelm emitted radiation from the reaction chamber 1-130. In some cases, as explained in connection with
When mounted in a receptacle of the instrument, the disposable chip can be in optical and electronic communication with optical and electronic apparatus within the advanced analytic instrument. The instrument may include hardware for an external interface, so that data from the chip can be communicated to an external network. In embodiments, the term “optical” may refer to ultra-violet, visible, near-infrared, and short-wavelength infrared spectral bands. Although various types of analyses can be performed on various samples, the following explanation describes genetic sequencing. However, the invention is not limited to instruments configured for genetic sequencing.
In overview and referring to
In some cases, the analytic instrument 5-100 is configured to receive a removable, packaged, bio-optoelectronic or optoelectronic chip 5-140 (also referred to as a “disposable chip”). The disposable chip can include a bio-optoelectronic chip 4-110, as depicted in
In some embodiments and referring to
According to some embodiments, the pulsed optical source 5-108 comprises a compact mode-locked laser module 5-110. The mode-locked laser can comprise a gain medium 5-105 (which can be solid-state material in some embodiments), an output coupler 5-111, and a laser-cavity end mirror 5-119. The mode-locked laser's optical cavity can be bound by the output coupler 5-111 and end mirror 5-119. An optical axis 5-125 of the laser cavity can 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 for an optical pulse to make a round-trip within the laser cavity).
In some embodiments, there can be additional optical elements (not shown in
When the laser 5-110 is mode locked, an intracavity pulse 5-120 can circulate between the end mirror 5-119 and the output coupler 5-111, and a portion of the intracavity pulse can be transmitted through the output coupler 5-111 as an output pulse 5-122. Accordingly, a train of output pulses 5-122, as depicted in the graph of
The output pulses 5-122 can be separated by regular intervals T. For example, T can be determined by a round-trip travel time between the output coupler 5-111 and cavity end mirror 5-119. According to some embodiments, the pulse-separation interval T can be between about 1 ns and about 30 ns. In some cases, the pulse-separation interval T can be between about 5 ns and about 20 ns, corresponding to a laser-cavity length (an approximate length of the optical axis 5-125 within the laser cavity) between about 0.7 meter and about 3 meters. In embodiments, the pulse-separation interval corresponds to a round trip travel time in the laser cavity, so that a cavity length of 3 meters (round-trip distance of 6 meters) provides a pulse-separation interval T of approximately 20 ns.
According to some embodiments, a 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, fluorescent emission characteristics, and the speed of data-handling circuitry for reading data from the chip 5-140. In embodiments, different fluorophores can be distinguished by their different fluorescent decay rates or characteristic lifetimes. Accordingly, there needs to be a sufficient pulse-separation interval T to collect adequate statistics for the selected fluorophores to distinguish between their different decay rates. Additionally, if the pulse-separation interval T is too short, the data handling circuitry cannot keep up with the large amount of data being collected by the large number of reaction chambers. Pulse-separation interval T between about 5 ns and about 20 ns is suitable for fluorophores that have decay rates up to about 2 ns and for handling data from between about 60,000 and 10,000,000 reaction chambers.
According to some implementations, a beam-steering module 5-150 can receive output pulses from the pulsed optical source 5-108 and is configured to adjust at least the position and incident angles of the optical pulses onto an optical coupler (e.g., grating coupler) of the chip 5-140. In some cases, the output pulses 5-122 from the pulsed optical source 5-108 can be operated on by a beam-steering module 5-150 to additionally or alternatively change a beam shape and/or beam rotation at an optical coupler on the chip 5-140. In some implementations, the beam-steering module 5-150 can further provide focusing and/or polarization adjustments of the beam of output pulses onto the optical coupler. One example of a beam-steering module is described in U.S. patent application Ser. No. 15/161,088 titled “Pulsed Laser and Bioanalytic System,” filed May 20, 2016, which is incorporated herein by reference. Another example of a beam-steering module is described in a separate U.S. Patent Application No. 62/435,679, filed Dec. 16, 2016 and titled “Compact Beam Shaping and Steering Assembly,” which is incorporated herein by reference.
Referring to
Each waveguide 5-312 can include a tapered portion 5-315 below the reaction chambers 5-330 to equalize optical power coupled to the reaction chambers along the waveguide. The reducing taper can force more optical energy outside the waveguide's core, increasing coupling to the reaction chambers and compensating for optical losses along the waveguide, including losses for radiation coupling into the reaction chambers. A second grating coupler 5-317 can be located at an end of each waveguide to direct optical energy to an integrated photodiode 5-324. The integrated photodiode can detect an amount of power coupled down a waveguide and provide a detected signal to feedback circuitry that controls the beam-steering module 5-150, for example.
The reaction chambers 5-330 or reaction chambers 5-330 can be aligned with the tapered portion 5-315 of the waveguide and recessed in a tub 5-340. There can be photodetectors 5-322 located on the semiconductor substrate 5-305 for each reaction chamber 5-330. In some embodiments, a semiconductor absorber (shown in
There can be a plurality of rows of waveguides, reaction chambers, and time-binning photodetectors on the chip 5-140. For example, there can be 128 rows, each having 512 reaction chambers, for a total of 65,536 reaction chambers in some implementations. Other implementations may include fewer or more reaction chambers, and may include other layout configurations. Optical power from the pulsed optical source 5-108 can be distributed to the multiple waveguides via one or more star couplers or multi-mode interference couplers, or by any other means, located between an optical coupler 5-310 to the chip 5-140 and the plurality of waveguides 5-312.
A non-limiting example of a biological reaction taking place in a reaction chamber 5-330 is depicted in
When a labeled nucleotide or nucleotide analog 5-610 is incorporated into a growing strand of complementary nucleic acid, as depicted in
According to some embodiments, an advanced analytic instrument 5-100 that is configured to analyze samples based on fluorescent emission characteristics can detect differences in fluorescent lifetimes and/or intensities between different fluorescent molecules, and/or differences between lifetimes and/or intensities of the same fluorescent molecules in different environments. By way of explanation,
A second fluorescent molecule may have a decay profile pB(t) that is exponential, but has a measurably different lifetime τ2, as depicted for curve B in
Differences in fluorescent emission lifetimes can be used to discern between the presence or absence of different fluorescent molecules and/or to discern between different environments or conditions to which a fluorescent molecule is subjected. In some cases, discerning fluorescent molecules based on lifetime (rather than emission wavelength, for example) can simplify aspects of an analytical instrument 5-100. As an example, wavelength-discriminating optics (such as wavelength filters, dedicated detectors for each wavelength, dedicated pulsed optical sources at different wavelengths, and/or diffractive optics) can be reduced in number or eliminated when discerning fluorescent molecules based on lifetime. In some cases, a single pulsed optical source operating at a single characteristic wavelength can be used to excite different fluorescent molecules that emit within a same wavelength region of the optical spectrum but have measurably different lifetimes. An analytic system that uses a single pulsed optical source, rather than multiple sources operating at different wavelengths, to excite and discern different fluorescent molecules emitting in a same wavelength region can be less complex to operate and maintain, more compact, and can be manufactured at lower cost.
Although analytic systems based on fluorescent lifetime analysis can have certain benefits, the amount of information obtained by an analytic system and/or detection accuracy can be increased by allowing for additional detection techniques. For example, some analytic systems 5-160 can additionally be configured to discern one or more properties of a specimen based on fluorescent wavelength and/or fluorescent intensity.
Referring again to
For a single molecule or a small number of molecules, however, the emission of fluorescent photons occurs according to the statistics of curve B in
Examples of a time-binning photodetector 5-322 are described in U.S. patent application Ser. No. 14/821,656, filed Aug. 7, 2015, titled “Integrated Device for Temporal Binning of Received Photons” and in U.S. patent application Ser. No. 15/852,571, filed Dec. 22, 2017, titled “Integrated Photodetector with Direct Binning Pixel,” which are both incorporated herein by reference in their entirety. For explanation purposes, a non-limiting embodiment of a time-binning photodetector is depicted in
In operation, a portion of an excitation pulse 5-122 from a pulsed optical source 5-108 (e.g., a mode-locked laser) is delivered to a reaction chamber 5-330 over the time-binning photodetector 5-322. Initially, some excitation radiation photons 5-901 may arrive at the photon-absorption/carrier-generation region 5-902 and produce carriers (shown as light-shaded circles). There can also be some fluorescent emission photons 5-903 that arrive with the excitation radiation photons 5-901 and produce corresponding carriers (shown as dark-shaded circles). Initially, the number of carriers produced by the excitation radiation can be too large compared to the number of carriers produced by the fluorescent emission. The initial carriers produced during a time interval |te−t1| can be rejected by gating them into a carrier-discharge channel 5-906 with a first electrode 5-920, for example.
At a later times mostly fluorescent emission photons 5-903 arrive at the photon-absorption/carrier-generation region 5-902 and produce carriers (indicated a dark-shaded circles) that provide useful and detectable signal that is representative of fluorescent emission from the reaction chamber 5-330. According to some detection methods, a second electrode 5-921 and third electrode 5-923 can be gated at a later time to direct carriers produced at a later time (e.g., during a second time interval |t1−t2|) to a first carrier-storage bin 5-908a. Subsequently, a fourth electrode 5-922 and fifth electrode 5-924 can be gated at a later time (e.g., during a third time interval |t2−t3|) to direct carriers to a second carrier-storage bin 5-908b. Charge accumulation can continue in this manner after excitation pulses for a large number of excitation pulses to accumulate an appreciable number of carriers and signal level in each carrier-storage bin 5-908a, 5-908b. At a later time, the signal can be read out from the bins. In some implementations, the time intervals corresponding to each storage bin are at the sub-nanosecond time scale, though longer time scales can be used in some embodiments (e.g., in embodiments where fluorophores have longer decay times).
The process of generating and time-binning carriers after an excitation event (e.g., excitation pulse from a pulsed optical source) can occur once after a single excitation pulse or be repeated multiple times after multiple excitation pulses during a single charge-accumulation cycle for the time-binning photodetector 5-322. After charge accumulation is complete, carriers can be read out of the storage bins via the read-out channel 5-910. For example, an appropriate biasing sequence can be applied to electrodes 5-923, 5-924 and at least to electrode 5-940 to remove carriers from the storage bins 5-908a, 5-908b. The charge accumulation and read-out processes can occur in a massively parallel operation on the chip 5-140 resulting in frames of data.
Although the described example in connection with
Regardless of how charge accumulation is carried out for different time intervals after excitation, signals that are read out can provide a histogram of bins that are representative of the fluorescent emission decay characteristics, for example. An example process is illustrated in
In some implementations, only a single photon may be emitted from a fluorophore following an excitation event, as depicted in
In some implementations, there may not be a fluorescent photon emitted and/or detected after each excitation pulse received at a reaction chamber 5-330. In some cases, there can be as few as one fluorescent photon that is detected at a reaction chamber for every 10,000 excitation pulses delivered to the reaction chamber. One advantage of implementing a mode-locked laser 5-110 as the pulsed excitation source 5-108 is that a mode-locked laser can produce short optical pulses having high intensity and quick turn-off times at high pulse-repetition rates (e.g., between 50 MHz and 250 MHz). With such high pulse-repetition rates, the number of excitation pulses within a 10 millisecond charge-accumulation interval can be 50,000 to 250,000, so that detectable signal can be accumulated.
After a large number of excitation events and carrier accumulations, the carrier-storage bins of the time-binning 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 a reaction chamber. The signal values for each bin can depend upon the decay rate of the fluorophore. For example and referring again to
To further aid in understanding the signal analysis, the accumulated, multi-bin values can be plotted as a histogram, as depicted in
In some implementations, fluorescent intensity can be used additionally or alternatively to distinguish between different fluorophores. For example, some fluorophores may emit at significantly different intensities or have a significant difference in their probabilities of excitation (e.g., at least a difference of about 35%) even though their decay rates may be similar. By referencing binned signals (bins 5-3) to measured excitation energy and/or other acquired signals, it can be possible to distinguish different fluorophores based on intensity levels.
In some embodiments, different numbers of fluorophores of the same type can be linked to different nucleotides or nucleotide analogs, so that the nucleotides can be identified based on fluorophore intensity. For example, two fluorophores can be linked to a first nucleotide (e.g., “C”) or nucleotide analog and four or more fluorophores can be linked to a second nucleotide (e.g., “T”) or nucleotide analog. Because of the different numbers of fluorophores, there may be different excitation and fluorophore emission probabilities associated with the different nucleotides. For example, there may be more emission events for the “T” nucleotide or nucleotide analog during a signal accumulation interval, so that the apparent intensity of the bins is significantly higher than for the “C” nucleotide or nucleotide analog.
Distinguishing nucleotides or any other biological or chemical specimens based on fluorophore decay rates and/or fluorophore intensities enables a simplification of the optical excitation and detection systems in an analytical instrument 5-100. For example, optical excitation can be performed with a single-wavelength source (e.g., a source producing one characteristic wavelength rather than multiple sources or a source operating at multiple different characteristic wavelengths). Additionally, wavelength-discriminating optics and filters may not be needed in the detection system to distinguish between fluorophores of different wavelengths. Also, a single photodetector can be used for each reaction chamber to detect emission from different fluorophores.
The phrase “characteristic wavelength” or “wavelength” is used to refer to a central or predominant wavelength within a limited bandwidth of radiation (e.g., a central or peak wavelength within a 20 nm bandwidth output by a pulsed optical source). In some cases, “characteristic wavelength” or “wavelength” may be used to refer to a peak wavelength within a total bandwidth of radiation output by a source.
Fluorophores having emission wavelengths in a range between about 560 nm and about 900 nm can provide adequate amounts of fluorescence to be detected by a time-binning photodetector (which can be fabricated on a silicon wafer using CMOS processes). These fluorophores can be linked to biological molecules of interest, such as nucleotides or nucleotide analogs for genetic sequencing applications. Fluorescent emission in this wavelength range can be detected with higher responsivity in a silicon-based photodetector than fluorescence at longer wavelengths. Additionally, fluorophores and associated linkers in this wavelength range may not interfere with incorporation of the nucleotides or nucleotide analogs into growing strands of DNA. In some implementations, fluorophores having emission wavelengths in a range between about 560 nm and about 660 nm can be optically excited with a single-wavelength source. An example fluorophore in this range is Alexa Fluor 647, available from Thermo Fisher Scientific Inc. of Waltham, Mass.
Excitation energy at shorter wavelengths (e.g., between about 500 nm and about 650 nm) may be used to excite fluorophores that emit at wavelengths between about 560 nm and about 900 nm. In some embodiments, the time-binning photodetectors can efficiently detect longer-wavelength emission from the reaction chambers, e.g., by incorporating other materials, such as Ge, into the photodetectors' active regions.
Embodiments of absorbing filters and related methods are possible in various configurations as described further below. Example device configurations include combinations of configurations (1) through (8) as described below.
(1) A multi-layer absorber filter comprising: a plurality of layers of absorbers, such as semiconductor absorbers; and a plurality of layers of dielectric material separating the plurality of absorbers to form a multi-layer stack, wherein there are at least three different layer thicknesses within the multi-layer stack. The absorbers may be semiconductor absorbers.
(2) The filter of configuration (1), wherein the plurality of layers of dielectric material include at least two different thicknesses.
(3) The filter of configuration 1 or 2, wherein the plurality of layers of absorbers include at least two different thicknesses.
(4) The filter of any one of configurations (1) through (3), wherein there are at least four different layer thicknesses within the stack.
(5) The filter of any one of configurations (1) through (4), wherein some of the thicknesses within the stack do not correspond to a quarter-wavelength of radiation for which the filter is designed to block.
(6) The filter of any one of configurations (1) through (5), wherein at least two of the three different layer thicknesses differ by more than 50%.
(7) The filter of any one of configurations (1) through (6), wherein the layers of absorbers comprise doped silicon.
(8) The filter of any one of configurations (1) through (7), wherein thicknesses of the layers of absorbers are between 20 nm and 300 nm.
Methods for making an absorber filter can include various processes. Example methods include combinations of processes (9) through (13) as described below. These processes may be used, at least in part, to make an absorbing filter of the configurations listed above.
(9) A method of forming a multi-layer absorber filter, the method comprising: depositing a plurality of layers of absorbers; and depositing a plurality of layers of dielectric material that separate the plurality of absorbers to form a multi-layer stack, wherein at least three different layer thicknesses are deposited within the multi-layer stack.
(10) The method of (9), wherein depositing the plurality of layers of absorbers comprises depositing at least two different thicknesses of absorbers that differ by at least 20%.
(11) The method of (9) or (10), wherein depositing the plurality of layers of absorbers comprises depositing layers of absorbers that are not quarter-wavelength thick.
(12) The method of any one of (9) through (11), wherein depositing the plurality of layers of dielectric material comprises depositing at least two different thicknesses of dielectric material that differ by at least 20%.
(13) The method of any one of (9) through (12), wherein depositing the plurality of layers of dielectric material comprises depositing layers of dielectric material that are not quarter-wavelength thick.
Embodiments of absorbing filters can be included in fluorescence detection assemblies. Examples of such embodiments are listed in configurations (14) through (42).
(14) A fluorescence detection assembly, comprising: a substrate having an optical detector formed thereon; a reaction chamber arranged to receive a fluorescent molecule; an optical waveguide disposed between the optical detector and the reaction chamber; and an optical absorption filter comprising a semiconductor absorbing layer disposed between the optical detector and the reaction chamber.
(15) The assembly of configuration (14), further comprising: an iris layer having an opening between the reaction chamber and the optical detector; a first capping layer contacting a first side of the semiconductor absorbing layer; a hole passing through the first capping layer and semiconductor absorbing layer; and a conductive interconnect extending through the hole.
(16) The assembly of configuration (14) or (15), further comprising at least one dielectric layer arranged in a stack with the semiconductor absorbing layer to form an absorptive-interference filter, wherein a rejection ratio for the stack is greater than a rejection ratio for the semiconductor absorbing layer alone.
(17) The assembly of any one of configurations (14) through (16), further comprising at least one dielectric layer arranged in a stack with the semiconductor absorbing layer and at least one additional semiconductor absorbing layer to form an absorptive-interference filter, wherein a rejection ratio for the stack is greater than a rejection ratio for the semiconductor absorbing layer alone.
(18) The assembly of any one of configurations (14) through (17), wherein the semiconductor absorbing layer comprises a bandgap sufficient to absorb excitation radiation of a first wavelength directed at the reaction chamber and to transmit emission radiation of a second wavelength from the reaction chamber.
(19) The assembly of configuration (18), wherein the first wavelength corresponds to the green region of the visible electromagnetic spectrum, and the second wavelength corresponds to the yellow region or red region of the visible electromagnetic spectrum.
(20) The assembly of configuration (19), wherein the first wavelength is in a range from 515 nanometers (nm) to 540 nm and the second wavelength is in a range from 620 nm to 650 nm.
(21) The assembly of configuration (19), wherein the first wavelength is approximately 532 nm and the second wavelength is approximately 572 nanometers.
(22) The assembly of configuration (18), wherein the bandgap is in a range from 2.2 eV to 2.3 eV.
(23) The assembly of any one of configurations (14) through (22), wherein the semiconductor absorbing layer comprises a binary II-VI semiconductor.
(24) The assembly of configuration (23), wherein the semiconductor absorbing layer is zinc telluride.
(25) The assembly of configuration (23), wherein the semiconductor absorbing layer is alloyed with a third element from group II or group VI.
(26) The assembly of any one of configurations (14) through (22), wherein the semiconductor absorbing layer comprises a ternary III-V semiconductor.
(27) The assembly of configuration (26), wherein the semiconductor absorbing layer is indium gallium nitride.
(28) The assembly of any one of configurations (14) through (27), wherein the semiconductor absorbing layer is amorphous.
(29) The assembly of any one of configurations (14) through (27), wherein the semiconductor absorbing layer is polycrystalline.
(30) The assembly of any one of configurations (14) through (27), wherein the semiconductor absorbing layer has an average crystal grain size no smaller than 20 nm.
(31) The assembly of any one of configurations (14) through (27), wherein the semiconductor absorbing layer is essentially single crystal.
(32) The assembly of any one of configurations (14) through (31), further comprising a first capping layer contacting the semiconductor absorbing layer.
(33) The assembly of configuration (32), wherein the capping layer prevents diffusion of an element from the semiconductor absorbing layer.
(34) The assembly of configuration (32) or (33), wherein the capping layer comprises a refractory metal oxide with thickness from 5 nm to 200 nm.
(35) The assembly of configuration (34), wherein the refractory metal oxide comprises tantalum oxide, titanium oxide, or hafnium oxide.
(36) The assembly of any one of configurations (32) through (35), wherein the capping layer reduces optical reflection from the semiconductor absorbing layer for a visible wavelength between 500 nm and 750 nm.
(37) The assembly of any one of configurations (32) through (36), wherein the capping layer provides increased adhesion of the semiconductor absorbing layer in the assembly.
(38) The assembly of any one of configurations (32) through (37), wherein the capping layer reduces in-plane stress from the semiconductor absorbing layer in the assembly.
(39) The assembly of any one of configurations (14) through (38), further comprising an opening formed through the optical absorption filter and an electrically-conductive connection extending through the opening.
(40) The assembly of any one of configurations (14) through (39), wherein the optical absorption filter is formed over non-planar topography.
(41) The assembly of configuration (40), further comprising an opening formed through the optical absorption filter and an electrically-conductive connection extending through the opening.
(42) The assembly of configuration (41), wherein the opening is located at a planarized interface between the optical absorption filter and an adjacent layer and at which the semiconductor absorbing layer has been removed.
Additional embodiments of an optical absorption filter are described in configurations (43) through (54).
(43) An optical absorption filter comprising a semiconductor absorbing layer formed over non-planar topography on a substrate.
(44) The optical absorption filter of configuration (43), wherein at least a portion of the semiconductor absorbing layer has been removed by planarization.
(45) The optical absorption filter of configuration (44), further comprising an electrically-conductive, connection extending through an opening formed by a removed portion of the semiconductor absorbing layer.
(46) The optical absorption filter of any one of configurations (43) through (45), wherein the semiconductor absorbing layer has a uniform thickness to within 10% and conforms to the non-planar topography.
(47) The optical absorption filter of configuration (46), wherein portions of the semiconductor absorbing layer extend essentially orthogonal to a plane of the substrate.
(48) An optical absorption filter comprising a ternary III-V semiconductor absorbing layer formed in an integrated device on a substrate.
(49) The optical absorption filter of configuration (48), wherein the ternary III-V semiconductor absorbing layer is single crystal.
(50) The optical absorption filter of configuration (48) or (49), wherein the ternary III-V semiconductor absorbing layer is indium-gallium nitride.
(51) The optical absorption filter of any one of configurations (48) through (50), wherein the integrated device includes an optical detector and a reaction chamber located on opposite sides of the optical absorption filter.
(52) The optical absorption filter of configuration (51), wherein the integrated device further includes an optical waveguide located on a same side of the optical absorption filter as the reaction chamber.
(53) The optical absorption filter of any one of configurations (48) through (50), wherein the integrated device includes an optical detector and an optical waveguide located on opposite sides of the optical absorption filter.
(54) The optical absorption filter of any one of configurations (48) through (53), further comprising an anti-reflection layer formed adjacent to the semiconductor absorbing layer that is configured to reduce optical reflection from the semiconductor absorbing layer for a visible wavelength between 500 nm and 750 nm.
Various methods for forming a fluorescence detection device are possible. Example methods include combinations of processes (55) through (58) as described below. These processes may be used, at least in part, to make a fluorescence detection device of the configurations listed above.
(55) A method for forming fluorescence detection device, the method comprising: forming an optical detector on a substrate; forming a semiconductor optical absorption filter over the optical detector on the substrate; forming an optical waveguide over the optical detector on the substrate; and forming a reaction chamber configured to receive a fluorescent molecule over the optical absorption filter and the optical waveguide.
(56) The method of (55), wherein forming the semiconductor optical absorption filter comprises depositing a semiconductor absorbing layer conformally over non-planar topography.
(57) The method of (55) or (56), further comprising forming an oxide or nitride capping layer in contact with the semiconductor absorbing layer to prevent diffusion of an element from the semiconductor absorbing layer.
(58) The method of (57), further comprising forming the oxide or nitride capping layer adjacent to the semiconductor absorbing layer with a thickness that reduces optical reflection from the semiconductor absorbing layer for a visible wavelength between 500 nm and 750 nm compared to a case where the oxide or nitride capping layer is not present.
Various methods for improving signal-to-noise ratio for an optical detector are possible. Example methods include combinations of processes (59) through (66) as described below.
(59) A method of improving signal-to-noise for an optical detector, the method comprising: delivering, with an optical waveguide, excitation radiation to a reaction chamber, wherein the optical waveguide and reaction chamber are integrated on a substrate; passing emission radiation from the reaction chamber through an optical absorption filter comprising a semiconductor absorbing layer; detecting emission radiation that has passed through the semiconductor absorbing layer with an optical detector; and attenuating, with the semiconductor absorbing layer, excitation radiation travelling toward the optical detector.
(60) The method of (59), further comprising attenuating, with the semiconductor absorbing layer, the excitation radiation travelling toward the optical detector between 10 times and 100 times more than attenuating the emission radiation that has passed through the semiconductor absorbing layer.
(61) The method of (59), further comprising attenuating, with the semiconductor absorbing layer, the excitation radiation travelling toward the optical detector between 100 times and 1000 times more than attenuating the emission radiation that has passed through the semiconductor absorbing layer.
(62) The method of (59), further comprising attenuating, with the semiconductor absorbing layer, the excitation radiation travelling toward the optical detector between 1000 times and 3000 times more than attenuating the emission radiation that has passed through the semiconductor absorbing layer.
(63) The method of any one of (59) through (62), wherein the excitation radiation has a first characteristic wavelength in a range from 500 nm to 540 nm and the emission radiation has a second characteristic wavelength between 560 nm and 690 nm.
(64) The method of any one of (59) through (63), further comprising passing the emission radiation through a first capping layer that contacts the semiconductor absorbing layer.
(65) The method of (64), further comprising reducing a reflection of the emission radiation from the semiconductor absorbing layer with the first capping layer.
(66) The method of any one of (59) through (65), wherein the first capping layer comprises a refractory metal oxide with thickness from 5 nm to 200 nm.
(67) The method of any one of (59) through (66), further comprising reducing, with the capping layer, in-plane stress from the semiconductor absorbing layer.
Having thus described several aspects of several embodiments of system architecture for an advanced analytic system 5-100, it is to be appreciated that various alterations, modifications, and improvements will readily occur to those skilled in the art. Such alterations, modifications, and improvements are intended to be part of this disclosure, and are intended to be within the spirit and scope of the invention. While the present teachings have been described in conjunction with various embodiments and examples, it is not intended that the present teachings be limited to such embodiments or examples. On the contrary, the present teachings encompass various alternatives, modifications, and equivalents, as will be appreciated by those of skill in the art.
While various inventive embodiments have been described and illustrated, those of ordinary skill in the art will readily envision a variety of other means and/or structures for performing the function and/or obtaining the results and/or one or more of the advantages described, and each of such variations and/or modifications is deemed to be within the scope of the inventive embodiments described. More generally, those skilled in the art will readily appreciate that all parameters, dimensions, materials, and configurations described are meant to be examples and that the actual parameters, dimensions, materials, and/or configurations will depend upon the specific application or applications for which the inventive teachings is/are used. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific inventive embodiments described. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, inventive embodiments may be practiced otherwise than as specifically described and claimed. Inventive embodiments of the present disclosure may be directed to each individual feature, system, system upgrade, and/or method described. In addition, any combination of two or more such features, systems, and/or methods, if such features, systems, system upgrade, and/or methods are not mutually inconsistent, is included within the inventive scope of the present disclosure.
Further, though some advantages of the present invention may be indicated, it should be appreciated that not every embodiment of the invention will include every described advantage. Some embodiments may not implement any features described as advantageous. Accordingly, the foregoing description and drawings are by way of example only.
All literature and similar material cited in this application, including, but not limited to, patents, patent applications, articles, books, treatises, and web pages, regardless of the format of such literature and similar materials, are expressly incorporated by reference in their entirety. In the event that one or more of the incorporated literature and similar materials differs from or contradicts this application, including but not limited to defined terms, term usage, described techniques, or the like, this application controls.
The section headings used are for organizational purposes only and are not to be construed as limiting the subject matter described in any way.
Also, the technology described may be embodied as a method, of which at least one example has been provided. The acts performed as part of the method may be ordered in any suitable way. Accordingly, embodiments may be constructed in which acts are performed in an order different than illustrated, which may include performing some acts simultaneously, even though shown as sequential acts in illustrative embodiments.
All definitions, as defined and used, should be understood to control over dictionary definitions, definitions in documents incorporated by reference, and/or ordinary meanings of the defined terms.
Numerical values and ranges may be described in the specification and claims as approximate or exact values or ranges. For example, in some cases the terms “about,” “approximately,” and “substantially” may be used in reference to a value. Such references are intended to encompass the referenced value as well as plus and minus reasonable variations of the value. For example, a phrase “between about 10 and about 20” is intended to mean “between exactly 10 and exactly 20” in some embodiments, as well as “between 10±δ1 and 20±δ2” in some embodiments. The amount of variation δ1, δ2 for a value may be less than 5% of the value in some embodiments, less than 10% of the value in some embodiments, and yet less than 20% of the value in some embodiments. In embodiments where a large range of values is given, e.g., a range including two or more orders of magnitude, the amount of variation δ1, δ2 for a value could be as high as 50%. For example, if an operable range extends from 2 to 200, “approximately 80” may encompass values between 40 and 120 and the range may be as large as between 1 and 300. When exact values are intended, the term “exactly” is used, e.g., “between exactly 2 and exactly 200.”
The term “adjacent” may refer to two elements arranged within close proximity to one another (e.g., within a distance that is less than about one-fifth of a transverse or vertical dimension of a 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 immediately adjacent to one another with no intervening structures or elements.
The indefinite articles “a” and “an,” as used in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean “at least one.”
The phrase “and/or,” as used in the specification and in the claims, should be understood to mean “either or both” of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Multiple elements listed with “and/or” should be construed in the same fashion, i.e., “one or more” of the elements so conjoined. Other elements may optionally be present other than the elements specifically identified by the “and/or” clause, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, a reference to “A and/or B”, when used in conjunction with open-ended language such as “comprising” can refer, in one embodiment, to A only (optionally including elements other than B); in another embodiment, to B only (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc.
As used in the specification and in the claims, “or” should be understood to have the same meaning as “and/or” as defined above. For example, when separating items in a list, “or” or “and/or” shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as “only one of” or “exactly one of,” or, when used in the claims, “consisting of,” will refer to the inclusion of exactly one element of a number or list of elements. In general, the term “or” as used shall only be interpreted as indicating exclusive alternatives (i.e. “one or the other but not both”) when preceded by terms of exclusivity, such as “either,” “one of,” “only one of,” or “exactly one of.” “Consisting essentially of,” when used in the claims, shall have its ordinary meaning as used in the field of patent law.
As used in the specification and in the claims, the phrase “at least one,” in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements. This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase “at least one” refers, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, “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”) can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another embodiment, to at least one, optionally including more than one, B, with no A present (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); etc.
In the claims, as well as in the specification above, all transitional phrases such as “comprising,” “including,” “carrying,” “having,” “containing,” “involving,” “holding,” “composed of,” and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases “consisting of” and “consisting essentially of” shall be closed or semi-closed transitional phrases, respectively.
The claims should not be read as limited to the described order or elements unless stated to that effect. It should be understood that various changes in form and detail may be made by one of ordinary skill in the art without departing from the spirit and scope of the appended claims. All embodiments that come within the spirit and scope of the following claims and equivalents thereto are claimed.
This application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Application Ser. No. 62/813,997, entitled “SEMICONDUCTOR OPTICAL ABSORPTION FILTER FOR AN INTEGRATED DEVICE” filed Mar. 5, 2019 and to U.S. Provisional Application Ser. No. 62/831,237, entitled “SEMICONDUCTOR OPTICAL ABSORPTION FILTER FOR AN INTEGRATED DEVICE” filed Apr. 9, 2019, each of which is herein incorporated by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| 62831237 | Apr 2019 | US | |
| 62813997 | Mar 2019 | US |
