One dimensional photonic crystals for enhanced fluorescence based sensing, imaging and assays

1. A method for determining a concentration of a particular analyte comprising:

providing a functionalized substrate for a target optical frequency comprising a one dimensional photonic crystal that is functionalized with a bioactive target molecule that has an affinity for a particular analytic, wherein the one dimensional photonic crystal comprises a plurality of dielectric layers including a plurality of high index of refraction layers alternating with a plurality of low index of refraction layers and the thickness of each layer is within a factor of four of a wavelength of the optical frequency in the layer;

providing a reagent comprising a detection molecule for the particular analyte, wherein the detection molecule includes a fluorophore that fluoresces at the target optical frequency;

determining a calibration curve that relates concentration of the particular analyte to at least one of intensity or direction or polarization of fluorescent emissions at the functionalized substrate in response to incident light for a plurality of known concentrations of the particular analyte mixed with the reagent,

contacting a sample and the reagent to the functionalized substrate;

obtaining measurements of at least one of intensity or direction or polarization of fluorescent emissions at the functionalized substrate in contact with the sample and reagent in response to the incident light; and

determining a concentration of the particular analyte in the sample from the calibration curve and the measurements.

2. A method as recited in claim 1 , wherein the target optical frequency is within a peak in a local radiative density of states (LRDoS) adjacent to a photonic band gap of the one dimensional photonic crystal.

3. A method as recited in claim 1 , wherein obtaining measurements further comprises directing the incident light to impinge on the sample without passing through the one dimensional photonic crystal.

4. A method as recited in claim 3 , wherein obtaining measurements further comprises directing the incident light normal to the plurality of dielectric layers in the one dimensional photonic crystal.

5. A method as recited in claim 3 , wherein obtaining measurements further comprises directing the incident light polarized parallel to the plurality of dielectric layers in the one dimensional photonic crystal.

6. A method as recited in claim 1 , wherein obtaining measurements further comprises directing the incident light to impinge on a surface of the one dimensional photonic crystal opposite the sample at an angle of minimum external reflection.

7. A method as recited in claim 6 , wherein obtaining measurements further comprises directing the incident light polarized parallel to the plurality of dielectric layers in the one dimensional photonic crystal.

8. A method as recited in claim 1 , wherein the angle of minimum external reflection depends on an index of refraction of a solution of the sample and the reagent.

9. A method as recited in claim 1 , further comprising determining an angle of an emission intensity maximum independent of a direction of the incident light.

10. A method as recited in claim 9 , wherein obtaining measurements further comprises collecting fluorescent emissions in a collection cone that includes the angle of the emission intensity maximum.

11. A method as recited in claim 9 , wherein the angle of an emission intensity maximum is associated with a Bloch surface wave coupled emission (BWCE).

12. A method as recited in claim 9 , wherein the angle of an emission intensity maximum is associated with a Bragg grating coupled emission (BGCE).

13. A method as recited in claim 1 , wherein the functionalized substrate further comprises a glass prism abutting a surface of the one dimensional photonic crystal opposite a surface that the sample contacts.

14. A method as recited in claim 1 , wherein:

the substrate includes a top layer that comprises silica or alumina;

the plurality of low index of refraction layers comprises SiO 2 ; and

the plurality of high index of refraction layers comprises Si 3 N 4 .

15. A method as recited in claim 1 , wherein a distance from the fluorophore to the one dimensional photonic crystal, when the detection molecule is bound to the bioactive target molecule, is less than a wavelength of the target optical frequency in the sample.

16. A method as recited in claim 1 , wherein obtaining measurements further comprises directing the incident light with a wavelength of 580 nanometers in air to impinge on a surface of the one dimensional photonic crystal opposite the sample at an angle of 45.2 degrees from normal.

17. A functionalized substrate for a target optical frequency comprising a one dimensional photonic crystal that is functionalized with a bioactive target molecule that has an affinity for a particular analyte, wherein

the one dimensional photonic crystal comprises a plurality of dielectric layers including a plurality of high index of refraction layers alternating with a plurality of low index of refraction layers, and

the thickness of each layer is within a factor of four of a wavelength of the optical frequency in the layer,

wherein the target optical frequency is within a peak in a local radiative density of states (LRDoS) adjacent to a photonic band gap of the one dimensional photonic crystal.

18. A functionalized substrate as recited in claim 17 , further comprising a glass prism abutting a surface of the one dimensional photonic crystal opposite a functionalized surface with the bioactive target molecule.

19. A functionalized substrate as recited in claim 18 , wherein:

the substrate includes a top layer that comprises silica or alumina;

the plurality of low index of refraction layers comprises SiO 2 ; and

the plurality of high index of refraction layers comprises Si 3 N 4 .

20. A functionalized substrate for a target optical frequency comprising a one dimensional photonic crystal that is functionalized with a bioactive target molecule that has an affinity for a particular analyte, wherein

the one dimensional photonic crystal comprises a plurality of dielectric layers including a plurality of high index of refraction layers alternating with a plurality of low index of refraction layers;

the thickness of each layer is within a factor of four of a wavelength of the optical frequency in the layer; and

for emissions from a fluorophore bound to the target molecule and excited by incident light, there is an emission intensity maximum centered at an angle independent of the direction of the incident light.

21. A fluorescence affinity assay kit for determining the quantity of a particular analyte, comprising:

a one dimensional photonic crystal comprising a plurality of dielectric layers including a plurality of high index of refraction layers alternating with a plurality of low index of refraction layers, wherein the thickness of each layer is within a factor of four of a wavelength of the optical frequency in the layer;

a solution comprising a bioactive target molecule that has affinity for a particular analyte, wherein the target molecule includes a ligand for affixing to the one dimensional photonic crystal to form a functionalized surface; and

a reagent comprising at least one plurality of substantively identical detection molecules, wherein the detection molecule comprises a fluorophore, and the detection molecule has affinity for the particular analyte.

22. A fluorescence affinity assay kit as recited in claim 21 , wherein for emissions from a fluorophore bound to the target molecule on the one dimensional photonic crystal and excited by incident light, there is an emission intensity maximum centered at an angle independent of the direction of the incident light.

23. A fluorescence affinity assay kit as recited in claim 21 , wherein the target optical frequency is within a peak in a local radiative density of states (LRDoS) adjacent to a photonic band gap of the one dimensional photonic crystal.

24. A fluorescence affinity assay kit as recited in claim 21 , further comprising a glass prism abutting a surface of the one dimensional photonic crystal opposite the functionalized surface.

25. A fluorescence affinity assay kit as recited in claim 21 , wherein:

the substrate includes a top layer that comprises silica or alumina;

the plurality of low index of refraction layers comprises SiO 2 ; and

the plurality of high index of refraction layers comprises Si 3 N 4 .

26. A system comprising:

a source of incident light,

a functionalized substrate that is to be placed in contact with a mixture of a sample and a reagent, wherein

the functionalized substrate comprises a one dimensional photonic crystal for a target optical frequency and a bioactive target molecule that has an affinity for a particular analyte,

the one dimensional photonic crystal comprises a plurality of dielectric layers including a plurality of high index of refraction layers alternating with a plurality of low index of refraction layers, and

the thickness of each layer is within a factor of four of a wavelength of the target optical frequency in the layer; and

the reagent comprises a detection molecule for the particular analyte wherein the detection molecule includes a fluorophore that fluoresces at the target optical frequency;

an optical coupler that directs incident light onto the functionalized substrate; and

a detector that measure fluorescent emissions from the functionalized substrate.

27. A system as recited in claim 26 , wherein the target optical frequency is within a peak in a local radiative density of states (LRDoS) adjacent to a photonic band gap of the one dimensional photonic crystal.

28. A system as recited in claim 26 , wherein the detector that collects fluorescent emissions in a collection cone that includes an angle of an emission intensity maximum that is independent of a direction of the incident light impinging on the substrate.

29. A system as recited in claim 28 , wherein the angle of an emission intensity maximum is associated with a Bloch surface wave coupled emission (BWCE).

30. A system as recited in claim 28 , wherein the angle of an emission intensity maximum is associated with a Bragg grating coupled emission (BGCE).

31. A system as recited in claim 26 , the functionalized substrate further comprising a glass prism abutting a surface of the one dimensional photonic crystal opposite a functionalized surface with the bioactive target molecule.

32. A system as recited in claim 31 , wherein the optical coupler directs the incident light to impinge on a surface of the one dimensional photonic crystal through the glass prism.

33. A system as recited in claim 32 , wherein the optical coupler further comprises a polarizer that polarizes the incident light in a direction parallel to the plurality of dielectric layers.

34. A system as recited in claim 26 , further comprising:

at least one processor; and

at least one memory including one or more sequences of instructions,

the at least one memory, and the one or more sequences of instructions and the at least one processor, cause the apparatus to perform at least the following,

determining a calibration curve that relates concentration of a particular analyte to at least one of intensity or direction or polarization of fluorescent emissions at the functionalized substrate in response to the incident light for a plurality of known concentrations of the particular analyte mixed with the reagent; and

determining a concentration of the particular analyte in a sample directly from the calibration curve and measurements of at least one of intensity or direction or polarization of fluorescent emissions at the functionalized substrate in contact with the sample and reagent in response to the incident light.