Microfluidic device with optical detector, microfluidic system comprsining the microfluidic device and method

Abstract

The disclosed approach may include an example microfluidic device (150) that can be integrated directly into a microfluidic system. The device (150) includes a fluid chamber (154) with a transparent wall (158) through which excitation light can be emitted. One or more apertures (114) can be used to isolate excitation light (156) from an optical detector (164) by providing a direct path for emission light from the fluid chamber (154) to reach the optical detector (164) but not a direct path for the excitation light (156). The fluid chamber (154) includes walls to suppress the excitation light (156) as it reflects within the fluid chamber (154). The microfluidic device (150; 500) can be integrated with one or more heating elements (512) for nucleic acid amplification or other biological processes. The microfluidic device (150; 500) may be configured to detect multiple excitable molecules inside a single fluidic chamber (154; 502). The microfluidic device (150; 500) can be lens-less, or otherwise have reduced component count and lower cost, as compared to conventional microfluidic devices.

Description

MICROFLUIDIC DEVICE WITH OPTICAL DETECTOR, MICROFLUIDIC SYSTEM COMPRSINING THE MICROFLUIDIC DEVICE AND METHODBACKGROUND

[0001] Microfluidic devices manipulate small volumes of fluids (e.g., down to femtoliters) using small channels (e.g., on a scale ranging from a few to hundreds of microns). Such devices may be used in systems that process low volumes of fluids that can include biomolecules and chemicals.SUMMARY OF EXAMPLE EMBODIMENTS OF THE DISCLOSURE

[0002] As an overview of example aspects to be further detailed below, in various embodiments, a microfluidic device includes a fluid chamber capable of holding a fluid, such as a fluid comprising a biological sample. The chamber includes a transparent wall and one or more reflective walls. A light source is included with the microfluidic device to emit an excitation light into the fluid chamber through the transparent wall. The light source can be or can comprise a light emitting diode (LED) light, a non-LED light, and / or a laser. The light source may be an excitation light source, and the excitation light can cause emission light to be emitted by excited molecules in the fluid chamber. The microfluidic device comprises one or more apertures and an optical detector positioned to detect an emission light via the one or more apertures. The emission light may be emission light from one or more excitable molecules that are excited by excitation light from the light source. The excitation light would have a shorter wavelength (higher frequency) than the emission light because not all of the energy of the excitation light is converted to emission light emitted by the excited excitable molecules.

[0003] The microfluidic device may be configured such that the excitation light entering the chamber does not have a direct path to the optical detector, whereas the emission light from within the fluid chamber has a direct path to the optical detector via the one or more apertures. The excitation light may enter the fluid chamber along a first axis, and each of the one or more apertures may extend along a second axis that is substantially orthogonal to the first axis. Each aperture of the one or more apertures may have an opening sized between 10pm and 1mm. The one or more apertures may be holes etched into a silicon substrate. At least one of the one or more apertures may have a sloped sidewall. The microfluidic device may have a filter configured to filter out wavelengths of light corresponding to the excitation light. For example, the filter may be a high-pass filter configured to allow light with wavelengths above a threshold to pass to the optical detector.The threshold may fall within a first range of wavelengths corresponding to the emission light (e.g., light with a higher wavelength than the excitation light) to be detected using the optical detector, but above a second range of wavelengths corresponding to the excitation light (e.g., light with a lower wavelength than the emission light)

[0004] The one or more apertures may be multiple apertures configured as an array of apertures. The microfluidic device may include a first array with a first plurality of apertures. The microfluidic device may also include one or more additional apertures separate from the first array of apertures. The one or more additional apertures may also be multiple apertures configured as an array of apertures. The microfluidic device may include a second array with a second plurality of apertures oriented to allow light from the first plurality of apertures to travel through the second plurality of apertures. The first array may be made of (or may comprise) different materials than the second array. In some embodiments, the microfluidic device may include an air gap between the first array and the second array. The light source may be positioned between 5 mm and 10 mm from a center of the one or more apertures.

[0005] One or more heating elements may be incorporated to heat fluids in the fluid chamber. The one or more apertures may be etched in a silicon substrate, and one or more heating elements may be embedded in the silicon substrate. The microfluidic device may be incorporated into a microfluidic system (e.g., as an optical subsystem of the microfluidic system). The microfluidic system may additionally or alternatively include one or more heating elements. The fluid chamber of the microfluidic device may be a first chamber (e.g., a reaction chamber in which one or more reactions occur, or a non-reactive chamber in which no reactions occur but fluids can be optically evaluated) one or more fluids are. The microfluidic system may include one or more additional chambers fluidly connected with the first chamber (e.g., via one or more fluidic channels).

[0006] An example method includes emitting an excitation light into a fluid chamber. The excitation light is emitted from a light source that may be an LED, non-LED, or laser light source. The excitation light may be an excitation light directed into a fluid chamber comprising one or more excitable molecules. The excitation light is emitted through a transparent wall of the fluid chamber. The example method includes detecting an emission light emitted from within the chamber. The emission light may be emission light emitted by one or more excitable molecules as a result of the excitation light. The emission light may be detected after the emission light passes through one or more apertures. The emissionlight may be provided a direct path, via the one or more apertures, to an optical detector used to detect the emission light. The excitation light may not be provided a direct path to the optical detector. The chamber may be provided with one or more surfaces that attenuate or suppress the excitation light as the excitation light reflects off the surfaces of the chamber.BRIEF DESCRIPTION OF THE DRAWINGS

[0007] FIG. 1 A depicts an example microfluidic device according to various embodiments of the disclosure. FIG. IB depicts an example microfluidic device in operation according to various embodiments of the disclosure.

[0008] FIG. 2 depicts an example aperture array according to various embodiments of the disclosure.

[0009] FIGs. 3 A and 3B depict microscopic images of example apertures of aperture arrays according to various embodiments of the disclosure.

[0010] FIGs. 4A and 4B depict stacked aperture arrays according to various embodiments of the disclosure.

[0011] FIG. 5 depicts integration of heating element(s) in a microfluidic device according to various embodiments of the disclosure.

[0012] FIG. 6 provides an illustrative microfluidic system with components and devices that may be incorporated according to various embodiments of the disclosure.

[0013] Fig. 7 provides an illustrative process for using example microfluidic devices and systems disclosed herein according to various embodiments of the disclosure.

[0014] The foregoing and other features of the present disclosure will become apparent from the following description and appended claims, taken in conjunction with the accompanying drawings. Understanding that these drawings depict only several embodiments in accordance with the disclosure and are, therefore, not to be considered limiting of its scope, the disclosure will be described with additional specificity and detail through use of the accompanying drawings.DETAILED DESCRIPTION

[0015] In the following detailed description, reference is made to the accompanying drawings, which form a part hereof. In the drawings, similar symbols typically identifysimilar components, unless context dictates otherwise. The illustrative embodiments described in the detailed description, drawings, and claims are not meant to be limiting. Other embodiments may be utilized, and other changes may be made, without departing from the spirit or scope of the subject matter presented here. It will be readily understood that the aspects of the present disclosure, as generally described herein, and illustrated in the figures, may be arranged, substituted, combined, and designed in a wide variety of different configurations, all of which are explicitly contemplated and make part of this disclosure.

[0016] Various applications may require reliable detection of particular light (e.g., from one light source) when, in the same environment, there may be one or more light sources emitting light that is not of interest. The light emitted by one object may provide useful information, but one or more other objects might be emitting light nearby (e.g., stray light, background light, etc.), making it difficult to capture that useful information using an optical detector that measures the amount of light reaching the optical detector. This can be a particular challenge when the desired light to be quantified is significantly less concentrated than other light that is more concentrated. Light concentration is herein used synonymously with light intensity, both of which refer to relative number of photons of light, such that high-concentration (or high-intensity) light has more photons relative to low concentration (or low-intensity) light, and conversely, low-concentration (or low-intensity) light has fewer photons relative to high-concentration (or high-intensity) light. The signal from the less concentrated light may be difficult to distinguish from the more concentrated light, with readings caused by the less-concentrated light potentially falling within the margin of error of the optical detector when the optical detector is receiving both the high- concentration light and the low-concentration light.

[0017] In certain life science applications, for example, excitation light may be directed at a biological sample that includes excitable molecules. As used herein, excitable molecules are molecules that emit emission light upon excitation by excitation light. Example excitable molecules include luminescent particles that can be fluorescent or phosphorescent. The excitation light is emitted so as to reach locations in which an excitable molecule may be located (e.g., to reach all parts of a chamber holding the biological sample). However, only a fraction of the excitation light hits excitable molecules to induce the excitable molecules to emit light (e.g., to luminesce). This could result in, for example, an environment in which more than 90%, 95%, 99%, or 99.9% of the light (e.g., more than 90% of the photons in the chamber) is excitation light, and less than 10%, 5%, 1%, or 0.1%of the light (e.g., fewer than 10% of the photons in the chamber), respectively, is emission light, depending on how many excitable molecules are present in the biological sample. While the excitation light is needed to excite molecules, the excitation light itself generally does not provide information like the emission light provides information. But the excitation light is nonetheless present at the same time and in the same chamber as the emission light, and the excitation light is more prevalent than the emission light. Prior approaches would add additional optical components such as discrete excitation and emission filters, mirrors, beam splitters, and lenses to direct and gather light . These systems are large and expensive and suffer from various disadvantages. For example, confocal optical systems that rely on beam splitting mirrors reduce the power of light that reaches the photodetector. Embodiments of the disclosed approach thus enable devices and systems with reduced component count and lower cost. In space-constrained microfluidic environments, for example, adding components can mean there is less room for samples to be received and for tests to be run, potentially reducing efficiency.

[0018] Various embodiments of the disclosed approach provide a microfluidic device that isolates emission light from excitation light, reducing the amount of the excitation light that reaches an optical detector in the first place, relative to the amount of the emission light that reaches the optical detector. As further discussed below, excitation light reaching the optical detector can be reduced through, for example, one or more apertures configured to receive more of the emission light relative to the excitation light. The apertures may be holes positioned to provide a direct path for the emission light to reach the optical detector, without providing excitation light a direct path to the optical detector. Because the emission light is emitted in all directions, some of the emission light will be able to travel through the apertures and reach the optical detector. For each aperture, light may be received at an entry point (i.e., a first end where the light can enter the aperture) and travel to an exit point (i.e., a second end where the light leaves the aperture). One or more optical detectors may be placed at the exit points of the one or more apertures to detect the light that reaches and travels through the apertures.

[0019] The excitation light may enter the fluid chamber from a first direction along a first axis, such that the excitation light reflects off the walls of the chamber, and each of the plurality of apertures may extend along a second axis that is not in a direction in which the excitation light will travel as it bounces off the walls. For example, the second axis may make an angle between 80 degrees and 100 degrees with respect to the first axis, or may besubstantially orthogonal to (i.e., may make a 90 degree angle with respect to) the first axis. As used herein, “substantially”, “approximately”, “about” and similar terms generally allow for a deviation of plus or minus 10% from values provided. In some embodiments, the angle between the first and second axes is between 85 and 95 degrees, between 86 and 94 degrees, between 87 and 93 degrees, between 88 and 92 degrees, between 89 and 91 degrees, between 89.5 and 90.5 degrees, between 89.6 and 90.4 degrees, between 89.7 and 90.3 degrees, between 89.8 and 90.2 degrees, or between 89.9 and 90.1 degrees. The amount of the unwanted excitation light able to reach the optical detector can also be reduced through, for example, attenuation by having surfaces that absorb and suppress a fraction of the excitation light each time the excitation light reflects off of the walls.

[0020] In some embodiments, the disclosed microfluidic device can be incorporated into a microfluidic system (e.g., as an optical component or optical subsystem of the microfluidic system). The microfluidic system may include multiple chambers and channels that are used to perform one or more operations, such as by allowing reagents and / or reactants to react or interact with each other for various biological processes. Example reagents and / or reactants include buffers (e.g., lysis buffers), gels, dyes, nucleic acids, enzymes, antibodies, a polymerase chain reaction (PCR) mastermix (with, e.g., nucleic acid polymerase(s), such as deoxyribonucleic acid (DNA) polymerase or ribonucleic acid (RNA) polymerase, deoxynucleotide triphosphates (dNTPs), magnesium dichloride (MgCh), etc. The microfluidic device may include a fluid chamber that receives, from other chambers of the microfluidic system, fluids to be evaluated optically. In some embodiments, the microfluidic device is a lens-less microfluidic device that can be integrated directly into the microfluidic system. In some example embodiments, the system also has only a single dichroic filter instead of two or more, which is the number conventionally used for detection of emission light, thereby reducing costs.

[0021] The disclosed microfluidic device can provide a fluid chamber that can receive fluids and, through optical detection functionality described herein, evaluate the status of fluids and / or the progress of reactions in the fluid chamber of the microfluidic device. The microfluidic system may, for example, perform nucleic acid amplification, and the microfluidic device integrated into the microfluidic system can optically evaluate one or more steps in the nucleic acid amplification. With respect to nucleic acid amplification, for example, emission light may indicate the presence of certain nucleic acids.

[0022] In some examples, the microfluidic system as described herein can be used in a multiplex nucleic acid amplification system, such as, for example, a multiplex PCR system. Such a microfluidic system would be designed to identify different target nucleic acids. Each target nucleic acid would be associated with or correspond to a different excitable molecule. Thus, in some examples, multiple microfluidic devices, each comprising an optical detector as defined herein, would be used in the microfluidic system comprising heating element(s). The microfluidic system with heating element(s) might be able to amplify different nucleic acids of interest, each nucleic acid being associated with or corresponding to different excitable molecules and identified with specific microfluidic devices with optical detectors. In other words, each microfluidic device would be able to identify a specific excitation light from the fluidic chamber, and said specific excitation light would be associated with or correspond to a target nuclide acid of intertest and be detected and eventually analyzed accordingly.

[0023] The microfluidic device may also include a filter (e.g., a dichroic filter or other color filter), also referred to as an excitation filter, to selectively restrict light with wavelengths falling in a range corresponding to the excitation light from reaching the optical detector, but allow light with wavelengths falling in a second range corresponding to the emission light to reach the optical detector. In operation, the chamber can include a substantially higher concentration of excitation light from a light source, and a substantially lower concentration of emission light from excited molecules, but the disclosed approach enables effective detection of the lower concentration light without the cost and complexity of the additional optical components employed by prior approaches.

[0024] In another aspect, the disclosed approach includes a method of emitting an excitation light into a fluid chamber that includes excitable molecules. The excitation light may be emitted by a light source into the fluid chamber through a transparent wall of the fluid chamber. The fluid chamber may one or more reflective walls, and the walls may be configured to attenuate the light reflecting from the walls. Light emitted by the excitable molecules as a result of the excitation light may travel through one or more apertures to reach one or more optical detectors.

[0025] Referring initially to Fig. 1 A, an example microfluidic device 100 includes a fluid chamber 102 and a light source 104. The chamber 102 includes a transparent wall 106, and reflective walls 108, 110, and 112. The microfluidic device 100 includes one or more apertures 114 and one or more optical detectors 116. In Fig. 1 A, the microfluidic device100 can include a single aperture 118, or as represented by the dotted lines, microfluidic device 100 can include more than one aperture, such as two or three apertures (e.g., apertures 120 and / or 122) as shown in Fig. 1 A, or more than three apertures (not shown in Fig. 1 A). The one or more apertures 114 is referred to as an aperture array if the one or more apertures 114 includes more than one aperture.

[0026] The one or more optical detectors 116 can include optical detector 124, which can be configured to detect light from one or more of the apertures 114. For example, microfluidic device 100 may have an optical detector for each aperture, at a 1 : 1 ratio, such that there is a separate optical detector for each aperture. In various embodiments, fewer than one optical detector may be incorporated for each aperture, such that a single optical detector detects light from two or more apertures. In some embodiments, a single optical detector 124 may be used (e.g., enlarged as represented by the dotted lines) so as to capture the light traveling through all apertures (here, apertures 118, 120, and 122). In other embodiments, microfluidic device 100 can include a first optical detector for a first subset of apertures (e.g., one or more of the apertures 114) and a second optical detector for a second subset of apertures (e.g., one or more other apertures 114). Example optical detectors 164 include photodiodes, avalanche photodiodes, metal-semiconductor-metal (MSM) photodetectors, phototransistors, charge-coupled devices (CCDs), complementary metal-oxide-semiconductor (CMOS) image sensors, and / or photomultiplier tubes (PMTs).

[0027] Fig. IB depicts an example microfluidic device 150 in operation (e.g., integrated into a microfluidic system). The microfluidic device 150 of Fig. IB includes one or more light sources 152 configured to emit excitation light 156 into a fluid chamber 154. The one or more light sources 152 may be LEDs, non-LEDs, and / or lasers, that emit excitation light into the fluid chamber 154 with excitable molecules 170 therein (depicted as black circles, which are not to scale). The excitation light 156 emitted by light source 152 travels through a transparent wall 158 and can excite excitable molecules 170 that collide with the excitation light 156. The excitable molecules absorb excitation light, and emit a fraction of the energy from the excitation light as lower-energy emission light (which has a higher wavelength than the excitation light). Excitation light may have wavelengths in a range from 300nm to 700nm, depending on which excitable molecules to be excited, and emission light may range from 450nm to 850nm, depending on which excitable molecules have been excited. In example embodiments, a light source may have a power range from about ImW to about 2mW, whereas the light emitted by excited molecules might have a power rangefrom about IpW to about lOnW. Example excitable molecules include fluorophores such as: fluorescein amidites (FAM), which has an excitation wavelength range of 450nm to 490nm and an emission wavelength range of 510nm to 530nm; hexachloro-fluorescein (HEX), which has an excitation wavelength range of 515nm to 535nm and an emission wavelength range of 560nm to 580nm; sulforhodamine 101 acid chloride (Texas Red), which has an excitation wavelength range of 560nm to 590nm and an emission wavelength range of 610nm to 650nm; cyanine-5 (Cy5), which has an excitation wavelength range of 620nm to 650nm and an emission wavelength range of 675nm to 690nm; and Quasar™ 705 (or other Quasar™ dyes), which has an excitation wavelength range of 672nm to 684nm and an emission wavelength range of 705nm to 730nm.

[0028] Microfluidic device 150 includes an aperture array 160 (i.e., a plurality of apertures) to isolate excitation light source from an optical detector 164. Each aperture may have an opening that is wide enough to allow a detectable amount of the emission light to pass through the aperture, but not so wide that a significant amount of excitation light can also travel through the aperture and reach the optical detector 164. Each of the apertures of the aperture array 160 may have, for example, a diameter that is between about 10pm and about 1.5mm. In various embodiments, each aperture may have a diameter of about 50pm to 1475pm, 100pm to 1450pm, 150pm to 1425pm, 200pm to 1400pm, 250pm to 1375pm, 300pm to 1350pm, 350pm to 1300pm, 400pm to 1275pm, 450pm to 1250pm, 500pm to 1225pm, 550pm to 1200pm, 600pm to 1175pm, 650pm to 1150pm, 700pm to 1125pm, 725pm to 1100pm, 750pm to 1075pm, 775pm to 1050pm, 750pm to 1025pm, 775pm to 1000pm, 800pm to 975pm, 825pm to 950pm, 850pm to 900pm, 850pm to 950pm, 850pm to 1000pm, 850pm to 1050pm, 850pm to 1100pm, 850pm to 1150pm, 850pm to 1200pm, 850pm to 1250pm, 850pm to 1300pm, 850pm to 1350pm, 850pm to 1400pm, 850pm to 1450pm, or 850pm to 1500pm. In some embodiments, the diameter of some apertures can be, or can slope to, substantially 850pm or greater, as further discussed below.

[0029] The aperture array 160 may include a plurality of holes etched into a substrate, such as a silicon substrate. The substrate in which one or more apertures are incorporated that can be (or can comprise) silicon, aluminum, and / or other machinable metals. Silicon may also be selected, for example, for being micro-machinable using standard semiconductor processing methods (e.g., a Bosch plasma etch process), but other materials can be selected (e.g., aluminum, copper, or other metals) if they can be machined to include the one or more apertures with desired diameters. For example, an array of micro-drilledapertures in a polished aluminum mirror can be used to lower costs. The substrate in which apertures are formed may have a thickness (from top to bottom as depicted in Figs. 1 A and IB) ranging between approximately 100pm to approximately 3mm.

[0030] In Fig. 1A, the fluid chamber 154 may have walls with characteristics configured to reduce the amount of excitation light reaching the detector relative to the amount of emission light. For example, the fluid chamber 154 may have a wall 166 (at the “top” in the orientation of Fig. 1 A) that is mirrored or otherwise reflective to reflect light back into the fluid chamber 154 so that the excitation light has more opportunity to excite excitable molecules and / or so that emission light is more likely to enter the apertures in the aperture arrays. The walls may be polished to enhance smoothness (e.g., to reduce peaks and valleys on a microscopic level at the surface of the walls) so as to reduce scattering of excitation light, as scattered excitation light is more likely to enter the apertures. Smoothness is also desirable fluidically, because “sharp” points could be nucleation sites that might cause unintended or undesirable bubbles in the fluid. The material(s) of the walls of the fluid chamber 154 may be selected for their ability to suppress or attenuate undesirable light (e.g., excitation light) as the light bounces around (e.g., reflects off the walls of the fluid chamber 154). Silicon, for example, advantageously suppresses light by 40% to 60% each time the light is reflected, helping reduce the potential excitation light that could reach the optical detector. The walls can also be clear or mirrored glass, with metal film sputtered thereon. The walls may have material that is black to better block excitation light.

[0031] The microfluidic device 150 can be configured to detect multiple wavelengths (corresponding to different excitable molecules) inside a single fluidic chamber 154, such as a first excitable molecule within a first wavelength range, and in the same chamber, a second excitable molecule within a second wavelength range. Because different excitable molecules may be excited by different wavelengths of excitation light, different excitation lights may be required, such as by employing multiple light sources or by employing a light source able to emit excitation light at multiple wavelengths. The disclosed microfluidic device 150 is scalable such that additional excitation light sources and wavelength-specific optical detectors may be added to enable multiplex detection of multiple types of excitable molecules. Such multiplexing may be well suited for reusable systems in which different reactions may be performed in the fluid chamber, and having multiple optical detectors provides a capability of detecting a variety of different wavelengths of emission light for a variety of different reactions to be performed in the fluid chamber.

[0032] In example embodiments, a silicon aperture array can also perform the function of a heating element. Silicon has excellent heat transfer properties and can be heated using either substrate heaters or surface heating elements between the aperture array. The system can be designed to detect more than one fluorophore, as additional fluorophores can be detected by including excitation, hole arrays, and the

[0033] In example embodiments, the microfluidic device 150 may include one or more filters to filter out wavelengths of light corresponding to excitation light, while allowing for wavelengths of light corresponding to emission light to pass. Additionally, films or coatings may be added around the fluid chamber 154 on the interior or exterior surfaces to either enhance reflection of excitation and emissive light back to the fluid chamber 154 or to enhance absorption of undesirable scattered light that may reach the optical detectors. Black carbon paint or anodized coatings may be added, for example, to enhance light absorption, whereas aluminum may be sputtered to enhance reflection. Multiple stacked Si die, and angled hole walls can improve light isolation, as further discussed below.

[0034] The light source 152 may be positioned relative to the fluid chamber 154 such that the excitation light 156 entering the fluid chamber 154 does not have a direct path through the apertures of the aperture array 160, but instead tends to reflect off the walls of the fluid chamber 154. The light source may be positioned far enough away from the transparent wall such that the light entering the chamber does not have a direct path through the apertures to the optical detector (e.g., such that the excitation light reflects off the walls and a certain percentage is attenuated with each reflection), without being so far away that the light source needs to be unnecessarily powerful (and thus costlier) to be able to provide sufficient light to excite particles in the fluid chamber 154. In various embodiments, the light source may be positioned, for example, between about 5mm and about 10mm from a center of the light source and a center of an aperture (if only one aperture) or an aperture array (if a plurality of apertures). In various embodiments, the light source may be positioned, for example, between 5.1mm and 9.75mm, between 5.2mm and 9.5mm, between 5.3mm and 9.25mm, between 5.4mm and 9mm, between 5.5mm and 8.75mm, between 5.6mm and 8.5mm, between 5.7mm and 8.25mm, between 5.8mm and 8mm, between 5.9mm and 7.75mm, between 6mm and 7.5mm, between 6mm and 7.25mm, between 6mm and 7mm, between 6mm and 6.75mm, between 6mm and 6.5mm, between 6mm and 8mm, between 6mm and 8.5mm, between 6mm and 9mm, between 6mm and 9.5mm, or between 6mm and 10mm from the center of the aperture or aperture array. Incertain embodiments, the light source may be spaced such that there is at least approximately 6mm between the light source and the aperture or aperture arrays.

[0035] The emission light from excited molecules is emitted in all directions, and a portion of the emission light enters the apertures of the aperture array 160 to reach the optical detector 164. Some of the emission light has a straight path to the optical detector 164, while some of the emission light reflects within the apertures while traveling in the direction of the optical detector 164. In some embodiments, the diameters are not uniform, such that the apertures in an array have different diameters. The diameter may be varied depending on position of the aperture in the chamber 15 to make it more likely that emission light enter the apertures than light from the excitation light source. For example, if an aperture is less likely to receive light from the excitation light source based on its position (e.g., distance from the light source), then the aperture’s diameter can be increased to allow the aperture to receive more light (which is more likely to be from excited molecules). In certain embodiments, where multiple arrays are employed, the diameters of apertures in different arrays may be different from each other. For example, the diameters of apertures in a second array may be larger than the diameters of apertures in a first array if the second array is less likely to receive unwanted light from the excitation light source.

[0036] In example embodiments, the fluidic chamber containing the excitable molecules is designed to efficiently isolate the excitation light source from the optical detector. A light source is directed into the fluidic chamber through a transparent side wall, and the excitation light is reflected inside the smooth reflective walls of the chamber to efficiently excite the excitable molecules. Walls may be polished reduce peaks and valleys at the surface of the walls so as to increase smoothness and thereby reduce scattering of excitation light, as scattered excitation light is more likely to enter the apertures and reach the optical detectors. Smoothness is also desirable for fluidically because peaks and valleys could become nucleation sites that cause bubbles in the fluid. The emission light (which has lower energy and lower photon count relative to the excitation light) has a direct line of sight path through a series of apertures etched in a silicon substrate to an excitation filter and optical detector. None of the excitation light from the LED has a direct path to the detector unless potentially it is scattered. Silicon is 40% to 60% reflective to visible light so with every reflection this light is attenuated by about 50% on average as it bounces off the side walls.

[0037] It is noted that a dichroic filter for the excitation light (which may be referred to as an excitation filter) may be selected because of its sharp cutoff for wavelengths, allowing itmore precisely filter out, for example, stray excitation light. A filter may be useful especially because the wavelength of the light from the excitation source may fall within a range of wavelengths (called a band) which can get close to the range of wavelengths of emitted light. In some embodiments, if a laser is used as a light source, the excitation light would have a narrower spectrum, and an excitation filter may not be needed to filter the excitation light.

[0038] Multiple optical detectors may be employed to detect multiple frequencies of light from different excitable molecules. Fig. 2 depicts a side view of an example array of apertures. In the version of Fig. 2, an aperture array is etched with sloped side walls. Example dimensions include about 10pm to about 1mm at the top (wl) and the same or wider width (w2) at the bottom between about 10pm and about 1mm. The light which reflects off the walls of the apertures may be angled to a certain degree 0 depending on the slope. The angle may range between about zero degrees and about 10 degrees, or between about 3 degrees and about 7 degrees, or between about 5 and about 6 degrees. In example embodiments, the angle is substantially 5.5 degrees. If, for example, there is an angle 9 between the vertical and the aperture side wall as depicted in Fig. 2, the light which reflects off aperture walls will be angled 9 degrees closer to perpendicular (the normal) to the surface of the filter, which can improve filter response. The values for wl and w2 depend on the angle 9. For example, if 9 is zero, such that there is no slope, wl = w2. Depending on angle 9, wl might be, for example, between about 700pm and about 800pm and w2 might be between about 800pm and 900pm. Fig. 3 A depicts a scanning electron microscope (SEM) image of a 50pm diameter hole etched through silicon, and Fig. 3B illustrates scallop features on hole walls that are about 0.4pm each.

[0039] The microfluidic device can include multiple aperture arrays, each array having a plurality of apertures. The arrays can be stacked, with the apertures oriented to allow light from the first plurality of apertures to travel through the second plurality of apertures. Fig. 4A depicts example embodiments that include stacked aperture arrays 400 for additional light reduction. In the version depicted in Fig. 4A, aperture arrays 402 and 404, each formed in silicon substrate, provide additional thickness. Each aperture array may be any suitable thickness as discussed above, between about 100pm to about 3mm, such as about 200pm thickness for a first aperture array 402 and about 680pm thickness for a second aperture array 404, as non-limiting examples. The aperture arrays 402 and 404 may have the same thickness as each other, as shown in Fig. 4A, or may have different thicknesses asshown in Fig. 4B. The arrays may be, or may comprise, different materials for additional light reduction. Silicon, for example, has greater heat transfer, but tends to be more expensive, so silicon can be used as the “top” aperture array closest to fluid chamber 452 for optimization, where a more cost-effective material may be used for the remainder of the arrays (such as aluminum, or other metals that can be machined to have holes of the desired sizes).

[0040] In some embodiments, materials (e.g., metals) used for apertures that are positioned closer to (or adjacent to) the fluid chamber (i.e., that would be closer to the fluid in the fluid chamber, such as the apertures of the arrays 402 and 460 that are on top in Figs. 4A and 4B, respectively) are highly reflective to maximize an amount of excitation light that is reflected at the shallow angles inside the fluid. In some embodiments, materials (e.g., metals) that are readily machinable and can be highly polished (e.g., aluminum) can be selected for being lower in manufacturing cost than harder metals (e.g., stainless steel). Regarding dimensions, in some embodiments, it is desirable to have the fluid chamber configured such that it is conducive to fluid flowing into and out of the fluid chamber without trapping air bubbles. For example, reducing the number of sharp angles inside the fluid chamber and / or avoiding comers helps reduce fluid eddies or areas in which bubbles can form. Also, materials selected for the fluid chamber may be selected for being biocompatible, or at least not incompatible with the reactions or other processes that are to be performed in the fluid chamber. For example, certain plastics and adhesives that may inhibit PCR may be avoided if PCR is to be performed in the fluid chamber, while other materials that are inert and non-inhibitory of PCR may be selected. Moreover, materials may be selected for being able to withstand other conditions during the reactions or other processes that are to be performed in the fluid chamber, such as being able to withstand PCR temperatures of about 100 degrees Celsius without distortion.

[0041] Fig. 4B depicts a stack 450 with aperture arrays 460 and 462 below fluid chamber 452. In some examples, aperture array 460 may, for example, be formed in a silicon substrate and aperture array 462 may be formed in a substrate that is silicon, aluminum, or other machinable metals. In certain embodiments, aperture array 460 may be silicon, and aperture array 462 may aluminum. In example embodiments, aperture array 460 may integrate one or more heating elements to heat the fluid chamber 452. Between aperture array 460 and aperture array 462 there may be a thermal break 454 to reduce the amount of heat that reaches aperture array 462. For example, the thermal break 454 may be an air gapto, for example, reduce conductive heat transfer between arrays. In other examples, a thermal break 454 may include a vacuum gap instead of (or in addition to) an air gap, and / or one or more layers of one or more insulating materials that reduce heat transfer between aperture arrays. Fig. 4B also depicts a filter 456 (e.g., a dichroic filter) and an optical detector 458 for the light that exits the aperture array 462.

[0042] Fig. 5 depicts an example microfluidic device 500, with a substrate 510 (e.g., a silicon substrate) in which an aperture array is formed, can integrate one or more heating elements 512 to heat the contents of a fluid chamber 502 to promote various processes or reactions, such as, for example, nucleic acid amplification, such as polymerase chain reaction (PCR) or loop-mediated isothermal amplification (LAMP), and / or peptide competition assay (PCA). As depicted in Fig. 5, a heater 512 embedded in a substrate 508 is situated on one side of a fluid chamber 502, and additional heaters 512 are situated on another side of the fluid chamber 502. Heater elements 512 can be semiconductor-based heaters embedded in the silicon, or a surface heater such a serpentine resistive traces (e.g., thin film) interwoven through substrate 510 in which the aperture array is formed. Microfluidic device 500 also includes a filter 504 and an optical detector 506. The filter 504 and optical detector 506 can be separate components as depicted in Fig. 5, or they can be integrated into one component of the microfluidic device 500.

[0043] Example microfluidic devices discussed herein can have a relatively small form factor and low component count. Utilizing an aperture array in a silicon substrate, for example, enables the integration of heaters, thermal sensing, and control functions into the same device. Smart silicon with active logic, heaters, and temperature sensors can be used to provide extremely fast and accurate thermal control.

[0044] Fig. 6 depicts an example system 600 that may incorporate one or more microfluidic devices as disclosed herein. A controller 602 can be connected and configured so as to be able to control different components of system 600 individually and separately depending on the functions to be performed by system 600. System 600 includes an input (“In”) through which fluids (e.g., a sample) can be provided, and an outlet (“Out”) through which wastes or other fluids can be ejected. Fluids can initially be received in a fluidic network which includes sub-systems 604A, 604B, and 604C as well as microfluidic devices 620 and 650 as depicted in Fig. 6. This fluidic network includes fluid chambers and channels through which fluids can be transported, stored, and modified as the fluids are processed by system 600. The network includes chambers 606, channels 608, and pumpsand / or valves 610 (depicted by a circle with an “X”) that are used to hold, move, and manipulate fluids.

[0045] Initially, fluids from the system inlet (“In”) are received at sub-system 104 A, and the fluids can proceed to sub-system 604B and / or subsystem 604C via channels 608 before the fluids reach the system outlet (“Out”). In the fluidic network, the fluids can undergo various process steps such as heating, lysing, and mixing to perform, for example, nucleic acid amplification and other processes. Transport of fluids can be controlled, for example, via various pumps and / or valves 610.

[0046] System 600 as depicted in Fig. 6 includes a first microfluidic device with a first fluid chamber 620 and a second microfluidic device with a second fluid chamber 650, and fluids can be evaluated as discussed above at one or both of these microfluidic devices. In other embodiments there can be fewer than two, or more than two, microfluidic devices 620 / 650 in one system 600. The first microfluidic device includes one or more excitation light sources 622, a first aperture array (Al), a second aperture array (A2), and a third aperture array (A3), each array including a plurality of apertures (not individually shown). The second microfluidic device includes one or more excitation light sources 652, a fourth aperture array (A4), and a fifth aperture array (A5), each array including a plurality of apertures (not individually shown). The aperture arrays Al - A5 can detect the same wavelength range (e.g., corresponding to the same excitable molecules) or multiple wavelength ranges (e.g., corresponding to multiple excitable molecules). For example, Al might have photodetectors configured to detect wavelengths emitted by FAM, A2 might have photodetectors configured to detect wavelengths emitted by HEX, A3 might have photodetectors configured to detect wavelengths emitted by Texas Red, A4 might have photodetectors configured to detect wavelengths emitted by Cy5, and A5 might have photodetectors configured to detect wavelengths emitted by Quasar™ 705. In another example, Al, A2, and A3 may be configured to detect wavelengths corresponding to a first excitable molecule, and A4 and A5 may be configured to detect wavelengths corresponding to a second excitable molecule. Any arrangement, combination, or configuration of aperture arrays, optical detectors, and light sources may be employed as deemed suitable for the functionalities to be provided by system 600.

[0047] In various embodiments, multiple microfluidic devices with optical detection functionality may be incorporated into a single microfluidic system 600 to evaluate multiple fluids at the same time or through one or more passes through fluidic network (e.g., fluids atdifferent points along a sequence of steps in a biological reaction, or multiple samples). In some embodiments, multiple microfluidic devices may be configured to detect the same emission light from an excitable molecule. In various embodiments, a single microfluidic device may be configured to detect emission light from multiple types of excitable molecules inside a single fluidic chamber, each emission light having a different wavelength. Because different excitable molecules (e.g., FAM, HEX, Texas Red, Cy5, or Quasar) may be excited by light having different wavelengths, such a microfluidic device may integrate multiple excitation light sources (or one excitation light source capable of emitting light at more than one wavelength) and multiple photodetectors, each photodetector configured to detect light at one of the wavelengths corresponding to one of the types of excitable molecules detectable by the microfluidic device. In Fig. 6, if multiple light sources are to be incorporated for microfluidic device 620, the additional light sources may be positioned “behind” the light source 622 as illustrated in Fig. 6 (such that the additional light sources may be positioned along an axis extending into the page).

[0048] In some embodiments, multiple excitable molecules may be excited by the same wavelength of excitation light (or the same range of wavelengths of excitation light). However, the efficiency of the excitation of different excitable molecules can vary for different wavelengths of excitation light. For example, even though an excitable molecule may be excitable using excitation light at multiple different wavelengths, there may be one wavelength (an excitation maximum) at which a maximum amount of emission light will be emitted by the excited molecule (an emission maximum), such that there can be an ideal wavelength at which the excitable molecule’s emission light will be maximal. Similarly, even though two excitable molecules can be excitable by one wavelength of excitation light, one of the excitable molecules may be more efficiently excited using the excitation light than the other excitable molecule.

[0049] For example, fluorophores HEX and ROX (carboxy-X-rhodamine) may both be excitable using excitation light having a wavelength of about 550nm, with both of them having about a 40% efficiency at the 550nm wavelength. However, if excited at 533nm, HEX would be about 100% efficient and ROX would be about 34% efficient. HEX may have a peak excitation wavelength at 533nm (with a corresponding peak emission wavelength of 559nm), and ROX may have a peak excitation wavelength at 578nm (with a corresponding peak emission wavelength at of 604nm).

[0050] In various embodiments, emission light signals may be maximized by exciting excitable molecules at their excitation maximum wavelengths and tuning optical detectors to detect at wavelengths corresponding to emission maximums. As a result of an excitable molecule’s excitability using multiple different wavelengths (even though one wavelength may be the molecule’s peak excitation wavelength), fewer excitation light sources may be employed (depending on which excitable molecules are to be detected) because even a single wavelength can potentially excite multiple different excitable molecules (even though efficiency may vary for the different excitable molecules).

[0051] In Fig. 6, a set of heating / cooling elements 112 allow for selective heating / cooling of fluids at different locations and at different times. Cooling can be active (e.g., fans or endothermic reactions) or passive (e.g., heat sink). Heating elements may be configured to raise the temperature of components of the network, or fluids therein, up to 100 degrees Celsius. The heating elements may, in some embodiments, be capable of raising the temperature in components of system 600 above 100 degrees (e.g., 120 degrees or 160 degrees) to, for example, sterilize the fluidic network. In Fig. 6, microfluidic device 620 includes two separate heating elements 612, or one heating element and one cooling element, whereas microfluidic device 650 includes one lengthier heating / cooling element 612.

[0052] As illustrated in Fig. 6, the pumps / valves 610, heating / cooling elements 612, light sources 622, 652, and / or combinations thereof, can be individually interfaced with and / or controlled through controller 602. For example, depending on the reactions to be performed, at suitable points in time, one or more heaters, one or more pumps, and / or one or more light sources may be activated or deactivated, and signals from one or more aperture arrays may be obtained. Various sensors (not depicted in Fig. 6), such as for temperature, pH, viscosity, pressure, etc., can be placed at suitable locations in system 600. Each sensor may be individually connected to the controller 602 so that sensors can be instructed to take readings, and various readings can be received by the controller 602.

[0053] Referring to Fig. 7, an example process 700 is depicted. At 705, components of a microfluidic system (e.g., system 600 in Fig. 6) may be controlled (e.g., by controller 602) to prepare and / or position fluids through the fluidic network such that some fluids of interest are in a first chamber (e.g., first fluid chamber 620). During this step, the controller may be activating and deactivating, for example, heating elements, pumps, valves, etc. At 710, the controller may use one or more light sources to emit one or more wavelengths ofexcitation light (e.g., from one or more light sources 622) into the first fluid chamber, and at 715, the controller (e.g., controller 602) may detect light emitted by one or more types of excited molecules at one or more wavelengths using photodetectors of aperture arrays of the first microfluidic device (e.g., Al, A2, and / or A3).

[0054] At 720, the microfluidic system may be controlled (e.g., by controller 602) to prepare and / or position fluids through the fluidic network such that some fluids of interest are in a second fluid chamber (e.g., fluid chamber 650) of a second microfluidic device. During this step, the controller may also activate and / or deactivate, for example, heating elements, pumps, valves, etc. At 725, the controller may emit one or more wavelengths of excitation light (e.g., from one or more light sources 652) into the second fluid chamber, and at 730, the controller may detect light emitted by one or more types of excited molecules at one or more wavelengths using photodetectors of aperture arrays (e.g., A4 and / or A5) of the second microfluidic device.

[0055] The steps taken using system 600 may be or may include, for example, preparation steps for nucleic acid amplification or other processes. Reagents may include, for example, components of a mastermix that includes nucleotides, primers, etc. Once a sample is obtained from a patient, the sample may be purified (e.g., a nasal swab may be processed to remove undesired elements of the sample), and the resulting sample may be processed to capture desired particles such as, for examples, nucleic acids and flush out other residuals not needed for the process.

[0056] Based on what light was detected, a controller (e.g., controller 602 or another computing device) can determine what excitable molecules were present in particular chambers at different times. The excitable molecules might be indicative of a reaction occurring or progressing, a material being contained the fluids, target molecule of interest, such as a specific target nucleic acid, etc. In some embodiments, for example, one sample can be used to run multiple tests by determining whether different excitable molecules are detectable.

[0057] The disclosure has been described above with reference to the various examples. However, it is to be understood that various modifications may be made in form and detail without departing from the scope of the disclosure as defined by the appended claims and their equivalents.

[0058] The various illustrative logical blocks, circuits, modules, routines, and algorithm steps described in connection with the embodiments disclosed herein can be implemented as electronic hardware, or combinations of electronic hardware and computer software. To clearly illustrate this interchangeability, various illustrative components, blocks, modules, and steps have been described above generally in terms of their functionality. Whether such functionality is implemented as hardware, or as software that runs on hardware, depends upon the particular application and design constraints imposed on the overall system. The described functionality can be implemented in varying ways for each particular application, but such implementation decisions should not be interpreted as causing a departure from the scope of the disclosure.

[0059] Moreover, the various illustrative logical blocks and modules described in connection with the embodiments disclosed herein can be implemented or performed by a machine, such as a general purpose processor device, a digital signal processor (DSP), an application specific integrated circuit (ASIC), a field programmable gate array (FPGA) or other programmable logic device, discrete gate or transistor logic, discrete hardware components, or any combination thereof designed to perform the functions described herein. A control processor can synthesize a model for an FPGA. For example, the control processor can synthesize a model for logical programmable gates to implement a tensor array and / or a pixel array. The control channel can synthesize a model to connect the tensor array and / or pixel array on an FPGA, a reconfigurable chip and / or die, and / or the like. A general purpose processor device can be a microprocessor, but in the alternative, the processor device can be a controller, microcontroller, or state machine, combinations of the same, or the like. A processor device can include electrical circuitry configured to process computer-executable instructions. In another embodiment, a processor device includes an FPGA or other programmable device that performs logic operations without processing computer-executable instructions. A processor device can also be implemented as a combination of computing devices, e.g., a combination of a DSP and a microprocessor, a plurality of microprocessors, one or more microprocessors in conjunction with a DSP core, or any other such configuration. Although described herein primarily with respect to digital technology, a processor device may also include primarily analog components. For example, some or all of the algorithms described herein may be implemented in analog circuitry or mixed analog and digital circuitry. A computing environment can include any type of computer system, including, but not limited to, a computer system based on amicroprocessor, a mainframe computer, a digital signal processor, a portable computing device, a device controller, or a computational engine within an appliance, to name a few.

[0060] The elements of a method, process, routine, or algorithm described in connection with the embodiments disclosed herein can be embodied directly in hardware, in a software module executed by a processor device, or in a combination of the two. A software module can reside in RAM memory, flash memory, ROM memory, EPROM memory, EEPROM memory, registers, hard disk, a removable disk, a CD-ROM, or any other form of a non- transitory computer-readable storage medium. An example storage medium can be coupled to the processor device such that the processor device can read information from, and write information to, the storage medium. In the alternative, the storage medium can be integral to the processor device. The processor device and the storage medium can reside in an ASIC. The ASIC can reside in a user terminal. In the alternative, the processor device and the storage medium can reside as discrete components in a user terminal.

[0061] Conditional language used herein, such as, among others, "can," "could," "might," "may," “e.g.,” and the like, unless specifically stated otherwise, or otherwise understood within the context as used, is generally intended to convey that certain embodiments include, while other embodiments do not include, certain features, elements and / or steps. Thus, such conditional language is not generally intended to imply that features, elements and / or steps are in any way required for one or more embodiments or that one or more embodiments necessarily include logic for deciding, with or without other input or prompting, whether these features, elements and / or steps are included or are to be performed in any particular embodiment. The terms “comprising,” “including,” “having,” and the like are synonymous and are used inclusively, in an open-ended fashion, and do not exclude additional elements, features, acts, operations, and so forth. Also, the term “or” is used in its inclusive sense (and not in its exclusive sense) so that when used, for example, to connect a list of elements, the term “or” means one, some, or all of the elements in the list.

[0062] While the above detailed description has shown, described, and pointed out novel features as applied to various embodiments, it can be understood that various omissions, substitutions, and changes in the form and details of the devices or algorithms illustrated can be made without departing from the spirit of the disclosure. As can be recognized, certain embodiments described herein can be embodied within a form that does not provide all of the features and benefits set forth herein, as some features can be used or practiced separately from others.

[0063] The herein described subject matter sometimes illustrates different components contained within, or connected with, different other components. It is to be understood that such depicted architectures are merely examples, and that in fact many other architectures can be implemented which achieve the same functionality. In a conceptual sense, any arrangement of components to achieve the same functionality is effectively "associated" such that the desired functionality is achieved. Hence, any two components herein combined to achieve a particular functionality can be seen as "associated with" each other such that the desired functionality is achieved, irrespective of architectures or intermedial components. Likewise, any two components so associated can also be viewed as being "operably connected," or "operably coupled," to each other to achieve the desired functionality, and any two components capable of being so associated can also be viewed as being "operably couplable," to each other to achieve the desired functionality. Specific examples of operably couplable include but are not limited to physically mateable and / or physically interacting components and / or wirelessly interactable and / or wirelessly interacting components and / or logically interacting and / or logically interactable components.

[0064] As utilized herein, the terms “approximately,” “about,” “substantially”, and similar terms are intended to have a broad meaning in harmony with the common and accepted usage by those of ordinary skill in the art to which the subject matter of this disclosure pertains. These terms are intended to allow a description of certain features described and claimed without restricting the scope of these features to the precise numerical ranges provided. Accordingly, these terms should be interpreted as indicating that insubstantial or inconsequential modifications or alterations of the subject matter described and claimed are considered to be within the scope of the disclosure as recited in the appended claims. By default the terms “approximately,” “about,” “substantially”, and similar terms can indicate that a plus or minus 10% deviation from a value is allowed, such that, for example, a value that is substantially equal to 10 units may vary from 9 units to 11 units. With respect to the use of terms such as substantially any plural and / or singular terms herein, those having skill in the art can translate from the plural to the singular and / or from the singular to the plural as is appropriate to the context and / or application. The various singular / plural permutations may be expressly set forth herein for sake of clarity.

[0065] It will be understood by those within the art that, in general, terms used herein, and especially in the appended claims (e.g., bodies of the appended claims) are generallyintended as "open" terms (e.g., the term "including" should be interpreted as "including but not limited to," the term "having" should be interpreted as "having at least," the term "includes" should be interpreted as "includes but is not limited to," etc.). It will be further understood by those within the art that if a specific number of an introduced claim recitation is intended, such an intent will be explicitly recited in the claim, and in the absence of such recitation no such intent is present. For example, as an aid to understanding, the following appended claims may contain usage of the introductory phrases "at least one" and "one or more" to introduce claim recitations. However, the use of such phrases should not be construed to imply that the introduction of a claim recitation by the indefinite articles "a" or "an" limits any particular claim containing such introduced claim recitation to containing only one such recitation, even when the same claim includes the introductory phrases "one or more" or "at least one" and indefinite articles such as "a" or "an" (e.g., "a" and / or "an" should typically be interpreted to mean "at least one" or "one or more"); the same holds true for the use of definite articles used to introduce claim recitations. In addition, even if a specific number of an introduced claim recitation is explicitly recited, those skilled in the art will recognize that such recitation should typically be interpreted to mean at least the recited number (e.g., the bare recitation of "two recitations," without other modifiers, typically means at least two recitations, or two or more recitations). Furthermore, in those instances where a convention analogous to "at least one of A, B, and C, etc." is used, in general such a construction is intended in the sense one having skill in the art would understand the convention (e.g., "a system having at least one of A, B, and C" would include but not be limited to systems that have A alone, B alone, C alone, A and B together, A and C together, B and C together, and / or A, B, and C together, etc.). In those instances, where a convention analogous to "at least one of A, B, or C, etc." is used, in general such a construction is intended in the sense one having skill in the art would understand the convention (e.g., "a system having at least one of A, B, or C" would include but not be limited to systems that have A alone, B alone, C alone, A and B together, A and C together, B and C together, and / or A, B, and C together, etc.). It will be further understood by those within the art that virtually any disjunctive word and / or phrase presenting two or more alternative terms, whether in the description, claims, or drawings, should be understood to contemplate the possibilities of including one of the terms, either of the terms, or both terms. For example, the phrase "A or B" will be understood to include the possibilities of "A" or "B" or "A and B." Further, unless otherwise noted, the use of the words “approximate,” “about,” “around,” “substantially,” etc., mean plus or minus ten percent.

[0066] It should be noted that the terms “exemplary,” “example,” “potential,” and variations thereof, as used herein to describe various embodiments, are intended to indicate that such embodiments are possible examples, representations, or illustrations of possible embodiments (and such terms are not intended to connote that such embodiments are necessarily extraordinary or superlative examples).

[0067] The term “coupled” and variations thereof, as used herein, means the joining of two members directly or indirectly to one another. Such joining may be stationary (e.g., permanent or fixed) or moveable (e.g., removable or releasable). Such joining may be achieved with the two members coupled directly to each other, with the two members coupled to each other using a separate intervening member and any additional intermediate members coupled with one another, or with the two members coupled to each other using an intervening member that is integrally formed as a single unitary body with one of the two members. If “coupled” or variations thereof are modified by an additional term (e.g., directly coupled), the generic definition of “coupled” provided above is modified by the plain language meaning of the additional term (e.g., “directly coupled” means the joining of two members without any separate intervening member), resulting in a narrower definition than the generic definition of “coupled” provided above. Such coupling may be mechanical, electrical, or fluidic.

[0068] The term “or,” as used herein, is used in its inclusive sense (and not in its exclusive sense) so that when used to connect a list of elements, the term “or” means one, some, or all of the elements in the list. Conjunctive language such as the phrase “at least one of X, Y, and Z,” unless specifically stated otherwise, is understood to convey that an element may be either X, Y, Z; X and Y; X and Z; Y and Z; or X, Y, and Z (i.e., any combination of X, Y, and Z). Thus, such conjunctive language is not generally intended to imply that certain embodiments require at least one of X, at least one of Y, and at least one of Z to each be present, unless otherwise indicated.

[0069] References herein to the positions of elements (e.g., “top,” “bottom,” “above,” “below,” “up,” “down”) may merely be used to describe the orientation of various elements as arranged in the Figures. It should be noted that the orientation of various elements may differ according to other potential embodiments, and that such variations are intended to be encompassed by the present disclosure.

[0070] The embodiments described herein have been described with reference to drawings. The drawings illustrate certain details of specific embodiments that implement the systems, methods and programs described herein. However, describing the embodiments with drawings should not be construed as imposing on the disclosure any limitations that may be present in the drawings.

[0071] It is important to note that the construction and arrangement of the devices, assemblies, and steps as shown in the various exemplary embodiments is illustrative only. Additionally, any element disclosed in one embodiment may be incorporated or utilized with any other embodiment disclosed herein. Although only one example of an element from one embodiment that can be incorporated or utilized in another embodiment has been described above, it should be appreciated that other elements of the various embodiments may be incorporated or utilized with any of the other embodiments disclosed herein.

[0072] The foregoing description of embodiments has been presented for purposes of illustration and description. It is not intended to be exhaustive or to limit the disclosure to the precise form disclosed, and modifications and variations are possible in light of the above teachings or may be acquired from this disclosure. The embodiments were chosen and described in order to explain the principals of the disclosure and its practical application to enable one skilled in the art to utilize the various embodiments and with various modifications as are suited to the particular use contemplated. Other substitutions, modifications, changes and omissions may be made in the design, operating conditions and arrangement of the embodiments without departing from the scope of the present disclosure as expressed in the appended claims.

[0073] Sample implementations are disclosed below, in order to represent illustrative examples, which may be further modified, combined, constrained, etc. according to the entirety of this disclosure.

[0074] Example AA: A microfluidic device comprising: a fluid chamber comprising a transparent wall and a reflective wall; a light source to emit an excitation light into the fluid chamber through the transparent wall; one or more apertures; and an optical detector positioned to detect an emission light via the one or more apertures.

[0075] Example AB: The microfluidic device of Example AA, wherein the microfluidic device is configured such that the excitation light does not have a direct path to the opticaldetector, and such that the emission light from within the fluid chamber has a direct path to the optical detector via the one or more apertures.

[0076] Example AC: The microfluidic device of either AA or AB, wherein the one or more apertures are holes etched into a silicon die.

[0077] Example AD: The microfluidic device any of AA - AC, wherein each of the one or more apertures has an opening sized between 10pm and 1mm.

[0078] Example AE: The microfluidic device any of AA - AD, wherein each of the one or more apertures has a sloped sidewall.

[0079] Example AF: The microfluidic device any of AA - AE, wherein the excitation light has a shorter wavelength than the emission light.

[0080] Example AG: The microfluidic device any of AA - AF, wherein the excitation light has wavelengths falling in a first range, and wherein the microfluidic device further comprises a filter configured to filter out wavelengths in the first range.

[0081] Example AH: The microfluidic device any of AA - AG, wherein the excitation light enters the fluid chamber along a first axis, and each of the one or more apertures extends along a second axis that is substantially orthogonal to the first axis.

[0082] Example AE The microfluidic device any of AA - AH, wherein the one or more apertures is a first plurality of apertures formed in a first array, and wherein the microfluidic device further comprises a second array with a second plurality of apertures oriented to allow light from the first plurality of apertures to travel through the second plurality of apertures.

[0083] Example AJ: The microfluidic device of Al, further comprising an air gap separating the first array from the second array.

[0084] Example AK: The microfluidic device any of AA - AJ, wherein the light source is positioned between 5mm and 10mm from a center of the one or more apertures.

[0085] Example AL: The microfluidic device any of AA - AK, further comprising one or more heating elements to heat the fluid chamber.

[0086] Example AM: The microfluidic device of any of AA - AL, wherein the transparent wall, the reflective wall, and the one or more apertures are formed in one or more dies.

[0087] Example AN: The microfluidic device of AM, wherein the one or more dies comprise silicon.

[0088] Example AO: The microfluidic device of AL, wherein the one or more apertures are etched in a silicon die.

[0089] Example AP: The microfluidic device of AO, wherein the heating element(s) is / are embedded in the silicon die.

[0090] Example AQ: The microfluidic device of any of AA - AP, comprising a high-pass filter configured to allow light with wavelengths above a threshold to pass to the optical detector.

[0091] Example AR: The microfluidic device of any of AA - AQ, wherein the one or more apertures is a first plurality of apertures formed in a first array, wherein the microfluidic device further comprises a second array with a second plurality of apertures oriented to allow light from the first plurality of apertures to travel through the second plurality of apertures, and wherein the first array has a material composition that differs from the second array.

[0092] Example AS: The microfluidic device of AR, wherein the first array is a silicon array and the second array is a metallic array.

[0093] Example AT: The microfluidic device of either AR or AS, wherein the second array comprises aluminum.

[0094] Example BA: A microfluidic system comprising any of the microfluidic devices of Examples AA - AT, and a heating element.

[0095] Example BB: The microfluidic system of BA, wherein the fluid chamber of the microfluidic device is a reaction chamber.

[0096] Example BC: The microfluidic system of either BA or BB, wherein the microfluidic system further comprises one or more additional chambers fluidly connected with the fluid chamber of the microfluidic device.

[0097] Example CA: A method comprising: emitting, from a light source, an excitation light into a fluid chamber comprising one or more excitable molecules, wherein the excitation light is emitted through a transparent wall of the fluid chamber, and wherein the fluid chamber further comprises a reflective wall; and detecting, via one or more apertures, a light emitted by the one or more excitable molecules as a result of the excitation light.

[0098] Example DA: A method comprising: emitting, from a light source, excitation light into a fluid chamber, wherein the excitation light is emitted through a transparent wall of the fluid chamber, and wherein the fluid chamber further comprises a reflective wall; and detecting, via one or more apertures, an emission light originating within the chamber.

[0099] Example DB: The method of Example DA, wherein the chamber comprises excitable molecules, and the emission light is emitted by the excitable molecules as a result of the excitation light.

[0100] Example EA: A device and / or system configured to perform any of the above methods.

Claims

WHAT IS CLAIMED:

1. A microfluidic device comprising: a. a fluid chamber comprising a transparent wall and a reflective wall; b. a light source to emit an excitation light into the fluid chamber through the transparent wall; c. one or more apertures; and d. an optical detector positioned to detect an emission light via the one or more apertures.

2. The microfluidic device of claim 1, wherein the microfluidic device is configured such that the excitation light does not have a direct path to the optical detector, and such that the emission light from within the fluid chamber has a direct path to the optical detector via the one or more apertures.

3. The microfluidic device of claim 1, wherein the transparent wall, the reflective wall, and the one or more apertures are formed in one or more silicon dies.

4. The microfluidic device of claim 1, wherein each aperture of the one or more apertures has an opening sized between 10pm and 1mm.

5. The microfluidic device of claim 1, wherein at least one of the one or more apertures has a sloped sidewall.

6. The microfluidic device of claim 1, wherein the excitation light has wavelengths falling in a first range, wherein the emission light has wavelengths falling in a second range, and wherein the microfluidic device further comprises a filter configured to filter out wavelengths in the first range.

7. The microfluidic device of claim 1, wherein the excitation light enters the fluid chamber along a first axis, and each of the one or more apertures extends along a second axis that is substantially orthogonal to the first axis.

8. The microfluidic device of claim 1, wherein the one or more apertures is a first plurality of apertures formed in a first array, and wherein the microfluidic device furthercomprises a second array with a second plurality of apertures oriented to allow light from the first plurality of apertures to travel through the second plurality of apertures.

9. The microfluidic device of claim 8, further comprising an air gap separating the first array from the second array.

10. The microfluidic device of claim 1, wherein the light source is positioned between 5 mm and 10 mm from a center of the one or more apertures.

11. The microfluidic device of claim 1, further comprising one or more heating elements to heat the fluid chamber.

12. The microfluidic device of claim 11, wherein the one or more apertures are etched in a silicon die, and wherein the heating element(s) is / are embedded in the silicon die.

13. A microfluidic system comprising the microfluidic device of claim 1 and one or more heating elements, wherein the fluid chamber is a reaction chamber, and wherein the microfluidic system further comprises one or more additional chambers fluidly connected with the fluid chamber.

14. A method comprising: a. emitting, from a light source, an excitation light into a fluid chamber, wherein the excitation light is emitted through a transparent wall of the fluid chamber, and wherein the fluid chamber further comprises a reflective wall; and b. detecting, via one or more apertures, an emission light originating within the chamber.

15. The method of claim 14, wherein the chamber comprises excitable molecules, and the emission light is emitted by the excitable molecules as a result of the excitation light.

Images