Apparatus for single-molecule detection

1. A single molecule detection apparatus, comprising:

a) a waveguide comprising:

a core layer; and

a first cladding layer made of a dielectric material, wherein

at least one nanowell is formed in at least the first cladding layer, and

an upper opening of the at least one nanowell is larger than a bottom of the at least one nanowell;

b) a first opaque protection layer arranged over the first cladding layer without extending into the at least one nanowell;

c) a second opaque protection layer arranged below the waveguide, the second opaque protection layer having a nanostructured metal pattern; and

d) at least one light detector.

2. The detection apparatus of claim 1 , further comprising a light source.

3. The detection apparatus of claim 2 , further comprising a light coupler.

4. The detection apparatus of claim 1 , wherein an effective excitation zone is formed near the bottom of the at least one nanowell by a light field induced from a light wave propagating along the core layer.

5. The detection apparatus of claim 1 , wherein the at least one nanowell and the detector are arranged at opposite sides of the waveguide.

6. The detection apparatus of claim 1 , wherein the light detector generates a signal based on a detected light.

7. The detection apparatus of claim 1 , wherein the waveguide is a planar waveguide further comprising a second cladding layer, the first cladding layer and the second cladding layer being arranged at opposite sides of the core layer.

8. The detection apparatus of claim 1 , wherein the at least one nanowell extends through partial thickness of the first cladding layer.

9. The detection apparatus of claim 1 , wherein the at least one nanowell extends through full thickness of the first cladding layer.

10. The detection apparatus of claim 1 , wherein the at least one nanowell extends through full thickness of the first cladding layer and partial thickness of the core layer.

11. The detection apparatus of claim 7 , wherein the at least one nanowell extends through full thickness of the first cladding layer and full thickness of the core layer.

12. The detection apparatus of claim 1 , wherein the light detector comprises a set of optical sensors.

13. The detection apparatus of claim 1 , further comprising a plurality of nanowells forming a nanowell array.

14. The detection apparatus of claim 13 , further comprising a plurality of light detectors forming a detector array, each light detector in the detector array corresponding to at least one nanowell in the nanowell array.

15. The detection apparatus of claim 1 , wherein the core layer has a higher refractive index than the first cladding layer.

16. The detection apparatus of claim 7 , wherein the core layer has a higher refractive index than the first and second cladding layers.

17. The detection apparatus of claim 1 , wherein the core layer is made from a material chosen from at least one of Si x Ti 1−x O 2 , TiO 2 , Ta 2 O 5 , Nb 2 O 5 , HfO 2 , Al 2 O 3 , ZrO 2 , ZnS, SiN x , AlN x , TiN x , PC, PMMA, or Su8.

18. The detection apparatus of claim 1 , wherein the first cladding layer is made from a material chosen from at least one of SiO 2 , MgF 2 , CaF 2 , Al 2 O 3 , PMMA, Su8, or polycarbonate.

19. The detection apparatus of claim 7 , wherein the first cladding layer and the second cladding layer are made from a material chosen from at least one of SiO 2 , MgF 2 , CaF 2 , Al 2 O 3 , PMMA, Su8, or polycarbonate.

20. The detection apparatus of claim 1 , wherein the first opaque protection layer is made from a material chosen from at least one of Al, Ti, Ni, Cr, Au, Ag, Cu, Pt, Pd, or an alloy of any two or more thereof.

21. The detection apparatus of claim 1 , wherein the second opaque protection layer is made from a material chosen from Al, Ti, Ni, Cr, Au, Ag, Cu, Pt, Pd, or an alloy of any two or more thereof.

22. The detection apparatus of claim 1 , wherein an optical filter is arranged between the waveguide and the light detector.

23. The detection apparatus of claim 7 , wherein an optical filter is arranged between the second cladding layer and the light detector.

24. The detection apparatus of claim 1 , wherein an optical filter is arranged between the second opaque protection layer and the light detector.

25. The detection apparatus of claim 7 , wherein the second cladding layer also serves as an optical filter.

26. The detection apparatus of claim 1 , further comprising a cover over the at least one nanowell.

27. The detection apparatus of claim 1 , wherein at least a first surface of the at least one nanowell has different surface property than at least a second surface of the at least one nanowell.

28. The detection apparatus of claim 1 , wherein a sidewall surface of the at least one nanowell is hydrophilic, the sidewall surface comprising a material chosen from silicon, silica, metal, or metal oxide.

29. The detection apparatus of claim 1 , wherein a bottom surface of the at least one nanowell is hydrophobic.

30. The detection apparatus of claim 29 ,

wherein the bottom surface of the at least one nanowell is formed from a silicate or a metal with a hydrophilic property modified, by R1 x -Si(O—R2) 4−x or a polymer with a functional group, to hydrophobic, and

wherein

R1 is a hydrophobic group chosen from alkyl chain —(CH 2 ) n —CH 3 and R2 is C n H 2n+1 , and

the functional group is chosen from —COOH, —PO 3 H 2 , —SH, or NH 2 .

31. The detection apparatus of claim 29 ,

wherein the bottom surface of the at least one nanowell is formed from a metal oxide with a hydrophilic property modified, by R1 x -Si(O—R2) 4−x , or a polymer with a functional group, to hydrophobic, and

wherein

R1 is a hydrophobic group chosen from alkyl chain —(CH 2 ) n —CH3 and R2 is C n H 2n+1 , and

the functional group is chosen from —COOH, —PO 3 H 2 , —SH, or NH 2 .

32. The detection apparatus of claim 1 , wherein a bottom of the at least one nanowell has a different surface property from that of a sidewall surface of the at least one nanowell.

33. The detection apparatus of claim 27 , wherein the surface property comprises hydrophobicity, functional group, functional group density, material density, or conductivity.

34. The detection apparatus of claim 32 , wherein the surface property comprises hydrophobicity, functional group, functional group density, material density, or conductivity.

35. The detection apparatus of claim 3 , wherein the light coupler is a grating coupler located over the core layer, in the core layer, or beneath the core layer.

36. The detection apparatus of claim 3 , wherein the light coupler is a prism coupler.

37. The detection apparatus of claim 3 , wherein the light coupler is a side coupler.

38. The detection apparatus of claim 3 , wherein the light coupler is an absorbing-emitting coupler, which absorbs an incident light emitted from the light source and emits an excitation light.

39. The detection apparatus of claim 38 , wherein the absorbing-emitting coupler comprises a photoluminescent material having a Stokes shift greater than or equal to 30 nm.

40. The detection apparatus of claim 39 , wherein the photoluminescent material is doped in a polymer.

41. The detection apparatus of claim 39 , wherein the photoluminescent material comprises a photoluminescent dye, the photoluminescent dye comprising anthracene, coumarin, pyrene, stilbene, porphyrin, perylene, Alq3, eosin, Bodipy dye, fluorescein, rhodamine, polymethine dye, DCM, or its derivative.

42. The detection apparatus of claim 39 , wherein the photoluminescent material comprises a photoluminescent polymer, the photoluminescent polymer comprising PPV or its derivative.

43. The detection apparatus of claim 39 , wherein the photoluminescent material comprises an inorganic compound, the inorganic compound comprising quantum dot, alumina oxide, or zinc oxide.

44. The detection apparatus of claim 3 , wherein the light coupler is a co-directional coupler.

45. The detection apparatus of claim 2 , wherein the light source is a laser, a laser diode, an LED, an OLED, a QLED, a fiber light source, or an arc discharge fluorescent lamp.

46. The detection apparatus of claim 1 , wherein the first cladding layer has a refractive index approximately equal to that of a sample solution.

47. The detection apparatus of claim 1 , wherein the first cladding layer has a refractive index larger than that of a sample solution.

48. The detection apparatus of claim 1 , wherein a size of a bottom of the at least one nanowell is smaller than a wavelength of an excitation light in the core layer, smaller than one-half of the wavelength, smaller than one-quarter of the wavelength, or smaller than one-eighth of the wavelength.

49. The detection apparatus of claim 1 , wherein the light detector is an optical sensor chosen from a CCD, a CMOS optical sensor, a photoconductive type optical sensor, a photovoltaic type optical sensor, an APD, a p-n photodiode, a p-i-n photodiode, or a multi-junction photodiode.

50. The detection apparatus of claim 1 , wherein the light detector is a set of optical sensors chosen from CCDs, CMOS optical sensors, photoconductive type optical sensors, photovoltaic type optical sensors, APDs, p-n photodiodes, p-i-n photodiodes, or multi-junction photodiodes.

51. The detection apparatus of claim 50 , wherein the optical sensors in one set have different sensitive wavelength bands.

52. A method of detecting a single molecule, comprising:

emitting, by a light source, an incident light;

coupling, by a coupler, the incident light into a waveguide, forming an excitation light in the waveguide;

forming, by the excitation light and at least one nanowell formed in at least a cladding layer of the waveguide, an effective excitation zone, the cladding layer being formed of a dielectric material, a first opaque protection layer being arranged over the cladding layer without extending into the at least one nanowell, a second opaque protection layer arranged below the waveguide, the second opaque protection layer having a nanostructured metal pattern, and an upper opening of the at least one nanowell being larger than a bottom of the at least one nanowell;

locating a single molecule object in the effective excitation zone; and

exciting, by the excitation light, the single molecule object in the effective excitation zone, to cause the single molecule object to emit a light to be detected by a light detector.