PHOTONIC CRYSTAL-BASED SENSOR

Abstract

A sensor for use in biosensing is disclosed. The sensor comprises a photonic crystal waveguide comprising a photonic crystal comprising holes in a layer of dielectric material and a waveguide in the photonic crystal. The sensor comprises at least one strip disposed on the photonic crystal waveguide, spaced apart along, and running across the photonic crystal waveguide so as to form respective strip cavities, each of the at least one strip including a respective layer of material for sensing presence of a respective analyte; and a slot running along the waveguide of the photonic crystal waveguide.

Claims

1. A sensor comprising: a photonic crystal waveguide comprising a photonic crystal comprising holes in a layer of dielectric material and a waveguide in the photonic crystal; at least one strip disposed on the photonic crystal waveguide, spaced apart along, and running across the photonic crystal waveguide so as to form respective strip cavities, each of the at least one strip including a respective layer of material for sensing presence of a respective analyte; and a slot running along the waveguide of the photonic crystal waveguide.

2. The sensor of claim 1, wherein the slot has different widths along the first photonic waveguide.

3. The sensor of claim 1, wherein the photonic crystal waveguide is a first photonic crystal waveguide, the at least one strip comprises a series of strips and the sensor further comprises: a second photonic crystal waveguide running along the first photonic crystal waveguide and arranged such that the strip cavities are coupled to the second photonic crystal waveguide.

4. A sensor comprising: a first photonic crystal waveguide comprising a photonic crystal comprising holes in a layer of dielectric material and a waveguide in the photonic crystal; a series of strips disposed on the first photonic crystal waveguide, spaced apart along, and running across the photonic crystal waveguide so as to form respective strip cavities, each strip including a respective layer of material for sensing presence of a respective analyte; and a second photonic crystal waveguide running along the first photonic crystal waveguide and arranged such that the strip cavities are coupled to the second photonic crystal waveguide.

5. The sensor of claim 4, wherein the first photonic crystal waveguide is an unslotted photonic crystal waveguide.

6. The sensor of claim 3, wherein second photonic crystal waveguide runs along one side of the first photonic crystal waveguide, wherein the first and second photonic crystal waveguides share a common photonic crystal portion.

7. The sensor of claim 3, further comprising: a first coupler arranged at a first end of the second photonic crystal waveguide for coupling light from an external source into the second photonic crystal waveguide; and a second coupler arranged at a second end of the second photonic crystal waveguide for coupling light out of the second photonic crystal waveguide to an external detector.

8. The sensor of claim 7, further comprising: a first transition region interposed between the first coupler and the first end of the second photonic crystal; and a second transition region interposed between the second end of the second photonic crystal and the second coupler.

9. The sensor of claim 1, wherein the waveguide has different widths along the first photonic crystal waveguide.

10. The sensor of claim 1, wherein, on one side of first photonic crystal waveguide, the photonic crystal is broken into at least two section separated by at least one gap.

11. The sensor of claim 1, wherein each strip has a respective thickness of between one and ten monolayers.

12. The sensor of claim 1, wherein each strip has a respective thickness of between 10 and 100 nm.

13. The sensor of claim 12, wherein each strip comprises a first layer for creating a respective cavity and a second layer disposed on

14. A testing device comprising: an array of the sensors of claim 1, the sensors supported on a common substrate; and a microfluidic structure for delivering a fluidic sample to the sensors.

15. A method of forming a sensor, the method comprising: providing a template device, the template device comprising: a photonic crystal waveguide comprising a photonic crystal comprising holes in a layer of dielectric material and a waveguide in the photonic crystal; and a slot running along the waveguide of the photonic crystal waveguide; and printing at least one strip on the photonic crystal waveguide, spaced apart along, and running across the photonic crystal waveguide so as to form respective strip cavities, each strip including a respective layer of material for sensing presence of a respective analyte.

16. A method of using a sensor, the method comprising: exposing a fluid sample to the sensor of claim 1.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0038] Certain embodiments of the present invention will now be described, by way of example, with reference to the accompanying drawings, in which:

[0039] FIG. 1 is a schematic plan view of a first microphotonic device which comprises a hole-based photonic crystal waveguide and a slot (a “slotted photonic crystal waveguide”) and a strip of material running over the photonic crystal forming a strip cavity;

[0040] FIG. 2 is a cross-sectional view of the first microphotonic device shown in FIG. 1 taken along the line A-A′;

[0041] FIG. 3 is a cross-sectional view of the first microphotonic device shown in FIG. 1 taken along the line B-B′;

[0042] FIG. 4 is a schematic plan view of a second microphotonic device which comprises a hole-based photonic crystal waveguide without a slot (an “unslotted photonic waveguide”) and a strip of material running over the photonic crystal forming a strip cavity;

[0043] FIG. 5 is a cross-sectional view of the second microphotonic device shown in FIG. 4 taken along the line C-C′;

[0044] FIG. 6 is a cross-sectional view of the second microphotonic device shown in FIG. 4 taken along the line D-D′;

[0045] FIGS. 7A to 7C illustrate calculated cavity mode distributions for an unslotted photonic waveguide and overlying strips having thicknesses of 10 nm, 20 nm and 30 nm respectively;

[0046] FIG. 8 shows line plots of calculated quality factor Q and mode volumes of a function of strip thickness for the unslotted photonic waveguide shown in FIGS. 7A to 7C;

[0047] FIGS. 9A to 9C illustrate calculated cavity mode distributions for a slotted photonic waveguide and overlying strips having thicknesses of 10 nm, 20 nm and 30 nm respectively;

[0048] FIG. 10 shows line plots of calculated quality factor Q and mode volumes as a function of strip thickness for the slotted photonic waveguide shown in FIGS. 9A to 9C;

[0049] FIG. 11A shows a line plot of resonant wavelength as a function of refractive index of material used in a 10 nm-thick strip for a slotted photonic crystal waveguide;

[0050] FIG. 11B shows a line plot of resonant wavelength as a function of refractive index of material used in a 10 nm-thick strip for an unslotted photonic crystal waveguide;

[0051] FIG. 11C shows a line plot of resonant wavelength as a function of refractive index of aqueous solution lying over a slotted photonic crystal waveguide having a 10 nm-thick strip of material;

[0052] FIG. 12 is a schematic plan view of a multiplexed biosensor which integrates a slotted photonic crystal waveguide, three strip cavities disposed at different positions along the waveguide comprising different bio-probe molecules and having different corresponding resonances;

[0053] FIG. 13 is a schematic cross-sectional view taken along the line G-G′ in FIG. 12 showing a layer of bio-probe molecules before and after attachment of target molecules and showing a shift Δλ in resonant wavelength λ;

[0054] FIG. 14 is a dispersion diagram of a slotted photonic crystal waveguide having a waveguide width w=1.2a (where a is the photonic lattice constant) showing mode profile of first, second and third bands A, B and D at k=0.5 and of an unslotted photonic waveguide crystal having a waveguide with of w=0.9 a showing a mode profile of a fourth band C;

[0055] FIGS. 15A to 15C illustrate calculated cavity mode distributions for slotted photonic waveguides each having a strip thickness of 10 nm and having slot widths of 100 nm, 80 nm and 60 nm respectively;

[0056] FIG. 16 shows line plots of calculated quality factor Q and mode volumes of a function of slot width for the slotted photonic waveguides shown FIGS. 15A to 15C;

[0057] FIG. 17 is a schematic block diagram of a device comprising an optical splitter, a plurality of multiple multiplexed biosensors having strip cavities, an integrated microfluidic device for presenting analytes to the biosensors, and optical output;

[0058] FIG. 18 is a schematic diagram illustrating an arrangement of optical splitter, microfluidic device and biosensors;

[0059] FIG. 19A is a fluorescence signal obtained from a sample comprising a silicon substrate having a surface silicon dioxide layer on which single-strand DNA is printed with an electrohydrodynamic inkjet printer forming an array of sub-5 μm microdots;

[0060] FIG. 19B is a fluorescence signal obtained from a sample comprising a silicon substrate having a surface silicon dioxide layer on which hybridized-strand DNA is printed with an electrohydrodynamic inkjet printer forming an array of sub-5 μm microdots;

[0061] FIG. 20 is a schematic plan view of a multiplexed biosensor which integrates an unslotted photonic crystal waveguide, three strip cavities disposed at different positions along the waveguide comprising different bio-probe molecules and having different corresponding resonances;

[0062] FIG. 21 is a schematic cross-sectional view taken along the line H-H′ in FIG. 20 showing a layer of bio-probe molecules before and after attachment of target molecules and showing a shift Δλ in resonant wavelength λ; and

[0063] FIG. 22 is a dispersion diagram of an unslotted photonic crystal waveguide with width w between 0.97 a and 1.0 a (where a is the photonic lattice constant).

DETAILED DESCRIPTION OF THE INVENTION

[0064] In the following like parts are denoted by like reference numbers.

[0065] Devices and methods herein described can be used in applications involving detection of biological molecules (or “biomolecules”), for example DNA, RNA and proteins such as antibodies and enzymes, without the need for fluorescent labels. The devices and methods herein described involve creating one or more cavities by depositing localised layers (or “strips”) of bio-probes or bio-polymer on the surface of a photonic crystal template and arranging for each cavity to a specific resonance wavelength to form a multiplexed biosensor.

[0066] A photonic crystal template (or simply a “photonic crystal”) herein described comprises of a triangular lattice of etched holes in an inorganic, non-toxic material layer with a sufficiently high refractive index, preferably greater than 2, such as silicon or silicon nitride. The lattice spacing a is usually on the order of the emission wavelength of a cavity, for example, between 300 nm and 600 nm. The lattice spacing a depends on the refractive index of the template material and whether biosensor cavities emit in the visible or near-infrared part of the spectra. The hole size ∅ (i.e., hole diameter) is usually between a half and three-quarters of the lattice spacing a, and is preferably about 0.6 a. For example, the hole size ∅ may be between 150 nm and 450 nm. The lattice pattern can be defined by using deep UV or E-beam lithography and transferred to the inorganic material by reactive ion etching. The thickness of the photonic crystal template is typically half the lattice spacing, for example, between 100 nm and 200 nm. The photonic crystal template provides vertical confinement to an optical mode similar to a conventional optical waveguide. Bottom cladding, under the photonic crystal template, is preferably provided by an oxide layer, such as silicon dioxide. The bottom cladding may, however, be air, formed by a suspended photonic crystal membrane. Upper cladding, above the photonic crystal, is preferably provided by air. Upper cladding may, however, be provided by a layer of silicon dioxide. In that case, the thickness of the silicon dioxide layer is kept sufficiently small, typically below 100 nm, to allow effective sensing of biomolecules on the photonic crystal surface. The refractive index of the claddings should be smaller than that of the photonic crystal template.

[0067] Referring to FIGS. 1 to 3, a first microphotonic device 1 is shown.

[0068] The microphotonic device 1 can be formed on a substrate 2 and comprises a bottom cladding layer 3 having first and second opposite faces 4, 5 and a patterned layer 6 (or “photonic crystal template”) having first and second opposite face 7, 8 (hereinafter referred to as “upper and lower faces” or “upper and lower surfaces”) disposed on the first face 4 of the bottom cladding layer 3.

[0069] The photonic crystal template 6 comprises a two-dimensional, hole-based photonic crystal waveguide 9 comprising a photonic crystal 10 formed by a lattice of holes 11 (or “air-holes”) in a layer 12 of dielectric material (also referred to as the “slab” or “body”), and a waveguide 13 in the photonic crystal 10 formed by defects in the lattice (i.e., the absences of holes 11), and an elongate slot 14 running along the middle of the waveguide 13. Herein, the photonic crystal waveguide 9 and slot 14 is referred to as a slotted waveguide 6. The slot 14 is rectangular with parallel long sides 16. As will be explained in more detail later, the slot 14 can be tapered (i.e., with straight, non-parallel long sides). A rectangular layer 18 of biomolecules runs transversely across the photonic crystal template 6 on the upper surface 7 of the photonic crystal template 6. A strip cavity 19 is formed where the biomolecular layer 18 intersects with the slotted photonic crystal waveguide 6.

[0070] The lattice spacing a is between 300 nm and 600 nm. The hole diameter ∅ is between a half to three-quarters of the lattice spacing a, for example, about two-thirds of the lattice spacing a. The dielectric material is silicon or silicon nitride and has a thickness t of between about 180 and 360 nm. The bottom cladding layer 3 may comprise a dielectric material, such as silicon dioxide. The layer 18 of biomolecules can be formed by depositing (or “printing”) a solution (not shown) containing biomolecules using high-resolution electrohydrodynamic inkjet printing, for example, as described in EP 3 333 605 A1 which is incorporated herein by reference.

[0071] Referring to FIGS. 4 to 6, a second microphotonic device 21 is shown.

[0072] The second microphotonic device 21 is similar to the first microphotonic device 1 (FIG. 1) hereinbefore described except that it does not have an elongate slot running along the middle of the waveguide 13. Herein, the photonic crystal waveguide 29 without a slot is referred to as a “non-slotted photonic crystal waveguide” or an “unslotted photonic crystal waveguide”.

[0073] As will be explained in more detail hereinafter, non-slotted photonic crystal waveguides are generally less suited to creating cavities using ultra-thin layers of organic material, such as a mono-layer of biomolecules, whereas a slotted photonic crystal waveguide 6 (FIG. 1) are better suited, exhibiting considerably better performance. As will also be explained in more detail hereinafter, non-slotted photonic crystal waveguides, however, may be used if thick layers of organic material are employed.

[0074] Performance of optical sensors may be evaluated via their sensitivity to a change in the refractive index of the local environment. For a biosensor, an index change can be caused by the binding of a target molecule to a probe molecule attached to the surface of the sensor. If the sensor consists of an optical cavity, an index change Δn results in a change of in cavity resonance wavelength Δλ which can be detected by, for example, a spectrometer. The shift is proportional to the amount of target molecules binding to the sensor. Thus, the sensor can be used to identify a particular molecule and to determine its concentration. For optical sensors, the sensitivity S is defined by S=Δλ/Δn in units of nm per Refractive Index Unit, nm/RIU. The ability to resolve a shift depends on the linewidth δλ of the resonance and is expressed by FoM=S/δλ, where FoM is the Figure of Merit. The linewidth is linked to the quality factor Q of the cavity via the relation Q=λ/δλ and thus FoM=SQ/λ.

[0075] A numerical study is used to investigate creation of a cavity using a strip with refractive index 1.5 on top of a silicon photonic crystal template in an aqueous (water) environment defining the top cladding. The photonic crystal template bottom cladding is silicon dioxide. The refractive index of the strip is chosen to match that of a layer of single-strand DNA (ssDNA), which in this example is the probe layer. The water top cladding simulates the sensor properties when encased by microfluidics to deliver the target analytes. Refractive indices of 1.3 for water, 1.45 for silicon dioxide and 3.5 for silicon are used. In this example, a strip having a width of 4.75 a is used, where a is the lattice spacing. This corresponds to a strip having a width w.sub.t of 1.75 μm for a lattice spacing a of 370 nm and targeted cavity resonance wavelength around 1.3 μm. A strip width w.sub.t of between 1 and 5 μm can be used to create the cavity.

[0076] Referring to FIGS. 7A, 7B and 7C, first, second and third cavity mode distributions 31.sub.1, 31.sub.2, 31.sub.3 for an unslotted photonic waveguide 29 are shown.

[0077] The cavity mode distributions 31.sub.1, 31.sub.2, 31.sub.3 are created by respective strips 18.sub.1, 18.sub.2, 18.sub.3 on a non-slotted photonic crystal waveguide template 29 (i.e., the same unslotted photonic waveguide) with a top water cladding and a strip thickness t.sub.s.

[0078] For the first cavity mode distribution 31.sub.1, a first strip 18.sub.1 has a thickness is of 10 nm. For the second cavity mode distribution 31.sub.2, a second strip 18.sub.2 has a thickness is of 20 nm. For the third cavity mode distribution 31.sub.3, a third strip 18.sub.3 has a thickness is of 30 nm.

[0079] Referring also to FIG. 8, line plots 32, 33 of calculated quality factor Q and mode volumes of a function of strip thickness are shown for the unslotted photonic waveguides 29.

[0080] Reasonably high Q cavity can be created in all cases, but as the strip thickness t.sub.s is reduced, the mode volume increases significantly due to mode leaking out of the photonic crystal waveguide 13.sub.1, 13.sub.2, 13.sub.3, resulting in a strong decrease in the value of Q. Given that a strip made from a monolayer of bio-probes, such as DNA molecules, has a thickness of between 2 or 3 nm to 10 nm, this strip-cavity configuration (i.e., using an unslotted photonic waveguide) does not perform sufficiently well when immersed in water and, thus, tends to be unsuited for use with microfluidics.

[0081] Referring to FIGS. 9A, 9B and 9C, fourth, fifth and sixth cavity mode distributions 31.sub.4, 31.sub.5, 31.sub.6 for a slotted photonic waveguide template 9 are shown. In this case, the width w.sub.s of the slots 14.sub.1, 14.sub.2, 14.sub.3 is 100 nm.

[0082] Referring also to FIG. 10, line plots 34, 35 of calculated quality factor Q and mode volumes of a function of strip thickness are shown for the slotted photonic waveguide 9.

[0083] The cavity mode distributions 31.sub.4, 31.sub.5, 31.sub.6 and the line plots 34, 35 show that a cavity with a high Q and small mode volume can be created by a strip covering the surface of the slotted photonic waveguide 9. The optical mode is the strongest in the air-slot 14 as opposed to inside the photonic crystal material 12 (FIGS. 7A to 7C) for the non-slotted photonic crystal waveguide 29 (FIGS. 7A to 7C) thereby increasing optical field overlap with the target analytes and increasing amplified sensitivity due to a smaller mode volume of the cavity. Unlike the non-slotted strip photonic crystal waveguide cavity 29 (FIGS. 7A to 7C), the value of Q for the slotted photonic crystal waveguide 9 strongly increases in an aqueous environment, thus making this configuration well suited for integration with microfluidics. Furthermore, the value of Q also strongly increases as the thickness of the strip decreases, indicating suitability for use with ultrathin strip layers.

[0084] Referring to FIGS. 11A, 11B and 11C, line plots 36, 37, 38 of resonant wavelength as a function of refractive index are shown. FIG. 11A shows a line plot of resonant wavelength as a function of refractive index of material used in a 10 nm-thick strip for a slotted photonic crystal waveguide. FIG. 11B shows a line plot of resonant wavelength as a function of refractive index of material used in a 10 nm-thick strip for an unslotted photonic crystal waveguide. FIG. 11C shows a line plot of resonant wavelength as a function of refractive index of aqueous solution lying over a slotted photonic crystal waveguide having a 10 nm-thick strip of material.

[0085] FIGS. 11A, 11B and 11C show a comparison of sensitivity for slotted and non-slotted strip photonic crystal waveguide cavities. The slotted strip photonic crystal waveguide cavities in FIG. 11C has a top water cladding.

[0086] In particular, FIGS. 11A and 11B show, for slotted and non-slotted strip photonic crystal waveguide cavities, a change in resonance for changes in the refractive index of the strip having a thickness of 10 nm. A change in refractive index can be produced by hybridization of ssDNA strands attached to a sensor surface to target complementary strand DNA (cDNA) brought by a microfluidic circuit (not shown). The results show that a slotted strip photonic crystal waveguide cavity is about six times more sensitive than a non-slotted photonic crystal waveguide cavity and that, as a result, the Figure of Merit FoM is about ten times greater thereby demonstrating superior performance for even thin strips.

[0087] Comparison of the performance of biosensors is usually based on their sensitivity to a change of the refractive index of the medium surrounding the sensor, and not just a thin strip layer, as described above.

[0088] Referring to FIG. 11C, change of the resonance wavelength of the slotted strip photonic crystal waveguide cavity with a change in the refractive index of water cladding is shown. The slotted strip photonic crystal waveguide cavity exhibits a FoM of 4,200. By comparison, a slotted waveguide cavity described in C. Caër, Serna-Otálvaro, W. Zhang, X. Le Roux, E. Cassan: “Liquid sensor based on high-Q slot photonic crystal cavity in silicon-on-insulator configuration”, Optical Letters, volume 39, page 5792 (2014) exhibited a FoM of 3,700. Thus, this shows that a similarly high-performing cavity can be obtained by surface deposition of a strip of organic material.

First Multiplexed Biosensor 50

[0089] Referring to FIGS. 12 and 13, a first multiplexed biosensor 50 is shown.

[0090] The first multiplexed biosensor 50 comprises a first part 51 comprising a slotted photonic waveguide 52. The slotted photonic waveguide 52 has a similar structure to slotted photonic crystal waveguide 9 (FIG. 1) hereinbefore described. The slotted photonic crystal waveguide 52 comprises a photonic crystal 53 comprising air-holes 54 in a dielectric material layer 55 which is supported on a cladding layer 56 which in turn can be supported on a substrate (not shown) and a waveguide 57 in the photonic crystal 53, and a gently-tapered elongate slot 58 running along the middle of the waveguide 57. The first part 51 also includes a series of overlying strips 59.sub.1, 59.sub.2, 59.sub.3 of respective biomolecular material spaced apart along the length of the slotted photonic waveguide 52 forming respective cavities 60.sub.1, 60.sub.2, 60.sub.3 in a similar way to that hereinbefore described.

[0091] The multiplexed biosensor 50 comprises a second part 61 comprising an unslotted photonic waveguide 62. The unslotted photonic waveguide 62 has a similar structure to unslotted photonic crystal waveguide 29 (FIG. 3) hereinbefore described. The unslotted photonic crystal waveguide 62 comprises a photonic crystal 63 formed by air holes 54 in the dielectric material 55 and a waveguide 64 in the photonic crystal 63. The unslotted photonic crystal waveguide 62 does not have an elongate slot. The second part 61 of the biosensor does not have overlying strips of material and does not have any cavities.

[0092] The slotted and unslotted photonic waveguides 52, 62 run side by side and share a common photonic crystal portion 65, for example, by virtue of holes 54.

[0093] The unslotted photonic waveguide 62 is interposed between first and second light-couplers 66, 67 in the form of gratings which, in this case, comprise multiple, concentric, half-ring-shaped slots 68. Light passes between a coupler 66, 67 and an end of the unslotted photonic waveguide 62 through transition regions 69, 70 comprising short, unslotted photonic waveguide sections. Air holes 54 in the transition regions 69, 70 are shown shaded to aid clarity.

[0094] In this configuration, light 71 which is guided through the unslotted photonic waveguide 62 is side-coupled into the slotted photonic waveguide 52 and the strip cavities 60.sub.1, 60.sub.2, 60.sub.3. Each cavity 60.sub.1, 60.sub.2, 60.sub.3 has a respective, different resonance λ.sub.1, λ.sub.2, λ.sub.3. Coupling into the cavities 60.sub.1, 60.sub.2, 60.sub.3 results in sharp dips 72.sub.1, 72.sub.2, 72.sub.3 in the transmission spectra of the waveguide 62, each dip 72.sub.1, 72.sub.2, 72.sub.3 corresponding to a cavity resonance λ1, λ2, λ3.

[0095] Thus, all the cavities 60.sub.1, 60.sub.2, 60.sub.3 can be simultaneously monitored through the unslotted photonic waveguide 62.

[0096] Light 75 from a single mode TE polarized fibre (not shown) can couple into the first light coupler 66. Examples of suitable gratings are described in A. Faraon, I. Fushman, D. Englund, N. Stoltz, P. Petroff, J. Vuckovic: “Dipole induced transparency in waveguide coupled photonic crystal cavities”, Optical Express, volume 16, pages 12154 to 12162 (2008) and Y. Zou, S. Chakravarty, D. N. Kwong, W. C. Lai, X. Xu, X. Lin, A. Hosseini, R. T. Chen: “Cavity-Waveguide Coupling Engineered High Sensitivity Silicon Photonic Crystal Microcavity Biosensors With High Yield” IEEE Journal of Selected Topics in Quantum Electronics, volume 20, Art no. 6900710 (2014) which provides a 50 nm bandwidth. This light-coupling arrangement tends to require less stringent alignment than a fibre-contacting arrangement.

[0097] The transition regions 69, 70 comprise etched air-holes 54 of gradually increasing size ∅.sub.T1, ∅.sub.T2, . . . , ∅.sub.TN, i.e., increasing in size between the coupler 66, 67 and the unslotted photonic waveguide 62. This can improve coupling into and out of the unslotted photonic waveguide 62, as well as reducing Fabry Perot back reflections.

[0098] Coupling between the unslotted photonic waveguide 62 and slotted photonic waveguide 52 is permitted by matched mode symmetry. In this example, the waveguide 64 in the unslotted photonic waveguide 62 has a width of 0.9 a and the waveguide 57 in the slotted waveguide 52 has a width of 1.2 a wide (where a is the lattice spacing).

[0099] A cavity 60.sub.1, 60.sub.2, 60.sub.3 created from a strip 59.sub.1, 59.sub.2, 59.sub.3 has a resonance frequency corresponding to the bottom of the slotted photonic waveguide 52.

[0100] Referring also to FIG. 14, first, second, third and fourth dispersion bands A, B, C and D for a slotted photonic crystal waveguide are shown for a waveguide width 1.2 a. In this example, only band D is of interest due to mode symmetry. When a strip is patterned on this waveguide, a cavity is created with resonance frequency spectrally close to the bottom of the fourth dispersion band D (also called “band edge”) located at k=0.50. The cavity is “pulled” from the band edge and, thus, has the same mode symmetry. The frequency is slightly smaller (in other words, the wavelength is slightly larger), than that that corresponding to the band edge of fourth dispersion band D. For instance, suppose the band edge corresponds to a wavelength of 1,300 nm, then the cavity would be typically between 1,300 nm and 1,310 nm, depending on strip index and thickness.

[0101] Referring also to FIG. 14, the cavity 60.sub.1, 60.sub.2, 60.sub.3 can couple to the unslotted photonic waveguide 62 provided the frequency of the cavity 60.sub.1, 60.sub.2, 60.sub.3 intersects the band 82 of the waveguide 62. The widths W.sub.S, W.sub.US of the waveguides 57, 64 can be adjusted to adjust the matching frequency region.

[0102] The second and third dispersion bands B, C correspond to the unslotted waveguide whose mode profile has same symmetry as slotted waveguide band D and, therefore, the same symmetry as the cavity of the slotted waveguide. Modes from third band C cannot couple to band B because of mismatched symmetry. To couple the unslotted waveguide to the cavity, the resonance frequency of the cavity should be within the frequency range 82 spanned by the second and third frequencies around the third band C (shown shaded region). Thus, the waveguide width for the slotted and unslotted waveguides should satisfy these conditions. A slotted waveguide should be wider than an unslotted waveguide. Here, for a slotted waveguide width 1.2 a, the unslotted waveguide width matching these conditions is about 0.9 a.

[0103] Referring in particular to FIGS. 12 and 13, a strip 59.sub.1, 59.sub.2, 59.sub.3 of bio-probes is patterned across the slotted photonic waveguide 52 to create a cavity 60.sub.1, 60.sub.2, 60.sub.3.

[0104] Each strip 59.sub.1, 59.sub.2, 59.sub.3 has a length L. Each strip 59.sub.1, 59.sub.2, 59.sub.3 is sufficiently long that it crosses over the slot 58. Each strip 59.sub.1, 59.sub.2, 59.sub.3 can extend, on its far side (i.e., the side furthest from the unslotted photonic waveguide 62), beyond the edge 77 of the slotted photonic crystal waveguide 52. The strip 59.sub.1, 59.sub.2, 59.sub.3 does not extend over the waveguide 64 of the unslotted photonic crystal waveguide 62 and so does not form any additional cavities.

[0105] The slot 58 has different widths w.sub.c at different positions along the waveguide 52 to provide strip cavities 60.sub.1, 60.sub.2, 60.sub.3 with different resonance wavelengths λ1, λ2, λ3. In this case, this is achieved by smoothly tapering the slot 58. However, a slot 58 having steps in width (which may or may not vary monotonically along its length) may be used.

[0106] Referring to FIGS. 15A, 15B, 15C and 16, a numerical simulation demonstrates that the Q value of the cavity can be kept high across a range of slot widths w.sub.c, in this case, between 60 nm and 100 nm. The variation in slot width w.sub.c translates into a variation in cavity resonance of about 50 nm. The cavities are arranged to have distinguishable resonances to avoid mutual coupling. The minimum spectral spacing between each cavity is governed by a maximum resonance shift Δλ.sub.max due to binding of the probe cavity to a target analyte. For this example, a slotted photonic waveguide with slot width between 60 nm and 100 nm can support about 50 cavities for Δλ.sub.max=1 nm. Thus, each slotted photonic waveguide can be used for simultaneously sensing or detecting up to 50 different target molecules.

[0107] For a spacing of about 1 μm between the edges of each strip cavity and a strip width of 1.75 μm, then the length of the slotted photonic waveguide needs to be about 140 μm to accommodate 50 cavities.

[0108] Referring to FIG. 17, a testing device 100 is shown which includes an array of biosensors 50 supported on a common substrate 101 and a microfluidic device 102 for bringing target analytes to the bio-probes strip cavities.

[0109] Referring also to FIG. 18, a microfluidic channel 103 of the microfluidic device 102 can run across the slotted photonic crystal waveguide. The width of the channel 103 corresponds to the length of the slotted photonic crystal waveguide. This can allow a densely-packed array of cavities to be incorporated into one testing device 100. Thus, many waveguides can be served per microchannel thereby enhancing multiplexing capabilities.

[0110] The testing device 100 includes a common coupler 66 and light received via the common coupler 66 is delivered to each biosensor 50 via a network of optical splitters 104.

[0111] Before using a biosensor, a protocol is followed which generally includes activating the photonic crystal surface to enable bio-probes to bind to the surface of the photonic crystal, depositing the bio-probes to form strips on a slotted photonic crystal waveguide, incubating, washing, blocking non-specific binding, incorporating microfluidic channels on the photonic crystal waveguide to bring the target analytes, incubating and performing a final wash.

[0112] A protocol for binding a target cDNA to a ssDNA probe (hybridization) anchored on a silicon (Si), silicon dioxide (SiO.sub.2) or silicon nitride (Si.sub.xN.sub.y)sample will now be described.

[0113] The sample surface is activated by oxygen plasma treatment or by exposure to a piranha solution to create OH groups. The OH groups enable covalent binding of silane groups, such as APTES ((3-Aminopropyl)trimethoxysilane) or GPTS ((3-Glycidyloxypropyl)trimethoxysilane) and formation of a self-assembled monolayer (SAM) either via liquid or gas phase.

[0114] The sample is washed with toluene, ethanol, acetone (all with >95% purity), dried with nitrogen and stored in a low humidity environment, for example, an argon- or nitrogen-filled storage cabinet.

[0115] Following this treatment, ssDNA strands in water can covalently bind to the SAM surface and left to incubate overnight in a sealed container (not shown) under a relatively high humidity.

[0116] Following incubation, the sample is washed in a PBS buffer with ultrasonic bath to remove unbound bio-probes (i.e., ssDNA) and left in ultrapure water for 5 minutes to block all OH groups left on the surface.

[0117] Prior to hybridization, the sample with ssDNA is immersed in a buffer containing Tris-Cl, NaCl, EDTA, Tween-20 and BSA for 30 minutes to prevent electrostatic binding of the target cDNA strand. Binding of the cDNA to ssDNA involves a buffer containing Tris-Cl, NaCl, EDTA, Tween-20 and the cDNA strands heated to about 90° C. before adding the sample with the bound ssDNA. Following incubation, the non-hybridized DNA can be removed with a buffer containing NaCl, trisodium citrate and SDS.

[0118] The bio-probe strips can be patterned with feature size smaller than 5 μm. Such resolution can be achieved via printing, preferably with electrohydrodynamic inkjet printing. Modified AFM tips, however, could also be used.

[0119] Referring to FIG. 19A and 19B, arrays of single-strand DNA and hybridized DNA microdots 110′, 110 are respectively shown.

[0120] The hybridized DNA microdots 110 are formed following the protocol hereinbefore described. ssDNA dots 110′ about 3 μm in diameter are printed with an electrohydrodynamic inkjet printer (not shown) on a silicon substrate (not shown) having a thin (50 nm) capping layer 111 of silicon dioxide (SiO.sub.2). The SiO.sub.2 layer 111 helps to avoid destructive optical interference and quenching by the silicon substrate when exciting the fluorescent label attached to the DNA.

[0121] The bio-ink (not shown) consists of ssDNA strands in water with 10% glycerol to avoid drying-induced clogging of the printer nozzle. Inkjet-printed ssDNA strands are hybridized with their cDNA strands in Eppendorf tubes (not shown) and the fluorescent signal measured with a confocal microscope (not shown). Integration with the label-free photonic crystal biosensor involves incorporating microfluidic channels made from, for example, PDMS to deliver the target analytes (cDNA). Reference is made to M. G. Scullion, A. Di Falco, T. F. Krauss: “Slotted photonic crystal cavities with integrated microfluidics for biosensing applications”, Biosensors and Bioelectronics, volume 27, issue 1, pages 101-105 (2011).

[0122] The movement of fluid within these channels enables separation of bound and unbound molecules to the bio-probe strip. Specific binding results in a shift of the resonance wavelength of the strip cavity which can be monitored by the light transmitted through the non-slotted photonic crystal waveguide. PDMS maintains mechanical stability for up to 200° C. Thus, the heated cDNA solution can be directly injected through the microchannel and left to incubate with the printed ssDNA bio-probes, typically for a few hours, before washing the surface with injected ultra-pure water. ssDNA is used as the bio-probe material. However, aptamers, antibodies and other proteins could also be used.

Second Multiplexed Biosensor 150

[0123] Referring to FIGS. 20 and 21, a second multiplexed biosensor 150 is shown.

[0124] The second multiplexed biosensor 150 is similar to the first multiplexed biosensor 50 (FIG. 12) hereinbefore described. In particular, the second multiplexed biosensor 150 has a second part 161 which is substantially the same as the second part 61 (FIG. 12) of the first multiplexed biosensor 50 (FIG. 12), although the width of the waveguide differs.

[0125] The second multiplexed biosensor 150 has a first part 151 which differs from the first part 51 (FIG. 12) of the first multiplexed biosensor 50 (FIG. 12) in four ways.

[0126] First, the first part 151 has an unslotted photonic waveguide 152, although a slot may be used.

[0127] Secondly and thirdly, the unslotted photonic crystal waveguide 152 comprises a photonic crystal 153 comprising first and second parts 178.sub.1, 178.sub.2 either side of variable-width waveguide 157.sub.1, 157.sub.2, 157.sub.3 and the first side 178.sub.1 is non-continuous, instead broken into discrete sections 179.sub.1, 179.sub.2, 179.sub.3 separated by gaps 180.sub.1, 180.sub.2. Waveguide width, W.sub.A1, W.sub.A2, W.sub.A3 is defined by centre-to-centre distance of the air-holes 154, for example, having values between 0.98 and 1.0 a.

[0128] Coupling between modes of the waveguides follows the same principle as hereinbefore described in relation to modes of slotted and unslotted waveguides. In this case, the frequency range 182 spanned by the waveguide without the strip is highlighted. FIG. 22 shows bands for waveguide width between 1 and 0.97 a for the strip waveguide. Strip cavities are still spectrally close to the band edge of these bands. Thus, the cavities will couple to the waveguide for widths between 1 and 0.97 a.

[0129] In the case of slotted cavities, no gaps and no discrete sections are needed because lattice symmetry is preserved between cavities. In this case, transition from one cavity to the next cannot be done without breaking the lattice symmetry due to the change in waveguide width. Preservation of symmetry is usually preferred to avoid additional reflections and losses. In addition, air gaps prevent potential coupling between different waveguide modes. A gap length of a few lattices (for instance 5 lattices) is usually sufficient.

[0130] Fourthly, the overlying strips 171.sub.1, 171.sub.2, 171.sub.3 of biocompatible material are thicker than a monolayer (for example, greater than or equal to 10 nm) and less than or equal to 100 nm. Keeping the strip thickness below 100 nm can help to preserve the sensor surface sensitivity and the high Q of strip cavities.

[0131] Each strip 171.sub.1, 171.sub.2, 171.sub.3 is a bi-layer which comprises a base layer 172.sub.1 of a respective bio-compatible material which is solution-processable, which is transparent at the cavity resonance wavelength, and which is able to immobilize bio-probes 159.sub.1. Bio-compatible materials can be of a type which can be cleaned from the sample surface 173 (i.e., surface 173 of layer 155) and printed again to immobilize fresh probes 159.sub.1 thereby providing a re-usable biosensor. For example, polydopamine is a bio-compatible material which is transparent in the near-infrared, which can be inkjet-printed, and which can be used to immobilize proteins, as well as thiol or amine-containing molecules.

[0132] Polydopamine can be removed from silicon or silicon dioxide substrate using acetone thereby providing a re-usable photonic crystal biosensor. Other bio-compatible and transparent materials include chitosan for the immobilization of amino groups or enzymes and cellulose for the immobilization of antibodies and enzymes.

[0133] The thickness of the base layer can be adjusted by the concentration of the bio-compatible material in solution which, in for polydopamine, is a Tris-buffer. It can also be adjusted according to the number of printer passes.

[0134] Employing thicker strips allows unslotted photonic crystal waveguides to be used. This can help make the device easier to fabricate and avoid the need to infiltrate a slot.

[0135] Referring still to FIGS. 20 and 21, the second multiplexed biosensor 150 includes the photonic waveguide 152 and strips 171.sub.1, 171.sub.2, 171.sub.3 which form strip cavities 160.sub.1, 160.sub.2, 160.sub.3.

[0136] Similar to the first multiplexed biosensor 50 (FIG. 12), in the second multiplexed biosensor 150, the photonic waveguide 152 is side-coupled to the photonic crystal waveguide 162 which used for monitoring transmission spectra.

[0137] The unslotted photonic waveguide 162 has a similar structure to unslotted photonic crystal waveguide 29 (FIG. 3) hereinbefore described and exhibits mode cavities of a type shown in FIGS. 7A to 7C. The unslotted photonic crystal waveguide 162 comprises a photonic crystal 163 formed by air holes 154 in the dielectric material 155 and a waveguide 164 in the photonic crystal 163. The unslotted photonic crystal waveguide 162 does not have an elongate slot. The second part 161 of the biosensor does not have overlying strips of material and does not have any cavities.

[0138] Referring also to FIG. 22, the widths W.sub.A1, W.sub.A2, W.sub.A3 of photonic crystal waveguide 152 should be smaller, but similar to, the width W.sub.B of photonic crystal waveguide 162 to allow coupling of photonic crystal waveguide 162 to the strip cavity of photonic crystal waveguide 152.

[0139] FIG. 22 shows a dispersion diagram a non-slotted photonic waveguide having a width w between 0.97 a and 1.0 a. A photonic waveguide having a width 1.0 a can couple to a strip cavity mode provided the photonic waveguide width of the cavity is between 0.98 a and 1.0 a (which is highlighted). If the photonic waveguide width of the cavity is between 0.97 a, then the photonic waveguide does not couple into a strip cavity mode.

[0140] In the second multiplexed biosensor 150, strips 171.sub.1, 171.sub.2, 171.sub.3 with different thicknesses provide cavities with different resonant wavelengths allowing multiplexing. Larger variations of resonance wavelength can be achieved by geometric variation of the photonic crystal waveguide 152, such as a reduction in width W.sub.A in different parts of the waveguide, i.e., W.sub.A1≠W.sub.A2≠W.sub.A3.

[0141] The second multiplexed biosensor 150 can be prepared in two ways.

[0142] In one approach, bio-compatible materials (such as polydopamine) are deposited to form strips 172.sub.1 on the photonic crystal waveguide via high-resolution inkjet printing, then bio-probes 159.sub.2 (such as thiol and amine modified probes) are deposited on the biocompatible material strips 172.sub.1 with the same printer. This is followed by incubation, washing, blocking of non-specific binding, incorporation of microfluidic channels on the photonic crystal waveguide to bring target analytes, incubate and a final wash.

[0143] In another approach, modified bio-compatible materials (such as modified polydopamine), which contains functional groups suitable for bio-probe binding, is chemically synthesised, and is directly deposited onto the photonic crystal template followed by printing of the bio-probe 159.sub.2.

[0144] In a variation of the first and second devices, the resonance wavelengths of the printed strip cavities can be first measured with the bio-probes only. The sample is then immersed in a solution containing all target molecules. Alternatively, a solution containing all target molecules is printed directly on the bio-probes with the same inkjet printer. Following incubation and washing, analytes having no affinity with a bio-probe are removed and the strongly-bound ones result in a shift of the cavity resonance which can be detected as end-point reading. This approach does not require microfluidics. Thus, the device is simpler, but does not allow continuous monitoring of the binding process during the incubation time.

Uses

[0145] Devices herein described allow detection and quantification of biomolecules on a silicon-based photonic chip. Pathogens, such as virus antigens, and specific enzymes secreted by cancerous cells can be detected. Due to the inert nature of silicon, blood samples and corrosive solutions, such as urine, can be analysed.

[0146] More generally, the devices can be used to detect, chemical species (i.e., they do not necessarily need to be biochemical species). Strips of printed polymers or probe molecules can bind to chemical species (which may be presented as a gas or liquid). The polymers or probe molecules can react to a change in environmental conditions, such as temperature, humidity, pressure, or pH of liquids.

[0147] Thin (<100 nm) printed polymers or probe molecules can be dissolved by the presence of particular chemical species in small concentrations. Provided these species do not react with the photonic crystal substrate, suppression of a cavity resonance can indicate the presence of a particular chemical and its concentration by the rate at which the resonance peak is suppressed. The possibility to sense the presence of a target molecule by monitoring both the spectral shift and intensity of the cavity resonance is a feature of a strip cavity which is not available to cavities fabricated in an inorganic photonic crystal template. In other words, it cannot be obtained by a cavity made using e-beam lithography, for instance, since e-beam-defined cavities are embedded (or “permanently formed”) in the photonic crystal template and, thus, cannot be dissolved.

Modifications

[0148] It will be appreciated that various modifications may be made to the embodiments hereinbefore described. Such modifications may involve equivalent and other features which are already known in the design, manufacture and use of photonic biosensors and component parts thereof and which may be used instead of or in addition to features already described herein. Features of one embodiment may be replaced or supplemented by features of another embodiment.

[0149] Although claims have been formulated in this application to particular combinations of features, it should be understood that the scope of the disclosure of the present invention also includes any novel features or any novel combination of features disclosed herein either explicitly or implicitly or any generalization thereof, whether or not it relates to the same invention as presently claimed in any claim and whether or not it mitigates any or all of the same technical problems as does the present invention. The applicants hereby give notice that new claims may be formulated to such features and/or combinations of such features during the prosecution of the present application or of any further application derived therefrom.