Silicon nanophotonic biosensors
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1 PHOTONICS RESEARCH GROUP Silicon nanophotonic biosensors Peter Bienstman PHOTONICS RESEARCH GROUP 1
2 THE VISION PHOTONICS RESEARCH GROUP 2
3 Deaths by infectious diseases Sheffield University, UK PHOTONICS RESEARCH GROUP 3
4 Public health spending Sheffield University, UK PHOTONICS RESEARCH GROUP 4
5 The problem no access to cheap, reliable diagnostics in developing world Many deaths no access to cheap, reliable diagnostics in developed world Access to expensive diagnostics, though Fewer deaths, but health care costs spiral out of control PHOTONICS RESEARCH GROUP 5
6 The solution: lab-on-a-chip Sample preparation Sensing Read-out equipment PHOTONICS RESEARCH GROUP 6
7 Lab-on-a-chip integrates several functions of medical lab on small chip cheap fast read-out easy to operate small sample volumes many biomolecules detected at once (called multiplexing, multiparameter analysis) PHOTONICS RESEARCH GROUP 7
8 SILICON NANOPHOTONICS PHOTONICS RESEARCH GROUP 8
9 Silicon Photonics: optical chips intel transistor radio discrete elements 1954 pentium nanoelectronics discrete elements 2009 product photonic IC Silicon nano photonic IC 2009 research PHOTONICS RESEARCH GROUP 9
10 Silicon Photonics: Optical Integrated Circuits PHOTONICS RESEARCH GROUP 10
![Normalized tansmission [db] Silicon Photonics: example](/docs-images/81/82677576/images/11-1.jpg "Integrated spectrometer Hair at same scale 250 m 0 0")
11 Normalized tansmission [db] Silicon Photonics: example Integrated spectrometer Hair at same scale 250 m 0 0 FSR=25.3nm 450 nm Transmission [db] Design/fabrication by Ghent University + IMEC wavelength [µm] PHOTONICS RESEARCH GROUP wavelength [nm] 11
12 Nanophotonics biosensing platform Silicon-based Cheap, CMOS mass fabrication Hundreds of ring sensors on single chip Label-free Both proteins and DNA (use case: DNA-based sepsis diagnostics in FP7 Intopsens, IMI Rappid) 12 PHOTONICS RESEARCH GROUP 12
13 INTRODUCTION TO BIOSENSING PHOTONICS RESEARCH GROUP 13
14 Biosensors Detect presence and concentration of DNA Proteins Virus Bacteria Two classes (see later): Labeled: indirect detection of label Label-free: direct detection of biomolecule PHOTONICS RESEARCH GROUP 14
15 Applications Diagnostics Drug development Food safety Environmental monitoring PHOTONICS RESEARCH GROUP 15
16 Desired characteristics Low limit of detection ( sensitivity ) Selective Reproducible Multiplexed / multi-parameter Cheap Portable Fast PHOTONICS RESEARCH GROUP 16
17 Labeled detection detect a molecule by attaching a label to it very sensitive ( mol/l) commercial product (Elisa, DNA arrays,..) PHOTONICS RESEARCH GROUP 17
18 Disadvantages to labeling? PHOTONICS RESEARCH GROUP 18
19 Disadvantages to labeling some labels are very costly only measures final state, no kinetics label can influence properties of biomolecules strong interest in label-free sensors PHOTONICS RESEARCH GROUP 19
20 Label-free sensors detect presence of biomolecules directly focus here: label-free optical biosensors flow with biomolecules matching biomolecule (analyte) biorecognition element (ligand) selective binding causes refractive index change PHOTONICS RESEARCH GROUP 20
21 Index change How to measure the refractive index change? Surface plasmon sensors Dielectric evanescent wave sensors Resonant cavities Mach-Zehnder interferometers Once again, the list is not exhaustive. Also, there are many non-optical techniques (impedimetric, mass, ) PHOTONICS RESEARCH GROUP 21
22 SURFACE PLASMON SENSORS PHOTONICS RESEARCH GROUP 22
23 Plasmons Collective oscillations of electrons in a metal PHOTONICS RESEARCH GROUP 23
24 Surface plasmon Interaction between EM wave (light) and plasmon at an interface EM wave electrons PHOTONICS RESEARCH GROUP 24
25 Magnitude of electric field position magnitude PHOTONICS RESEARCH GROUP 25
26 Dispersion relation ω Determined by upper medium Determined by metal PHOTONICS RESEARCH GROUP 26 k x
27 Coupling from air ω Light in air Light in the plasmon mode k No intersection, no coupling possible! PHOTONICS RESEARCH GROUP 27
28 Coupling from backside ω Light in glass Light in the plasmon mode k Other material at the backside needed to get coupling PHOTONICS RESEARCH GROUP 28
29 In practice: glass prism PHOTONICS RESEARCH GROUP 29
30 Reflection experiment reflection angle angle PHOTONICS RESEARCH GROUP 30
31 Towards a biosensor reflection angle angle PHOTONICS RESEARCH GROUP 31
32 This method: SPR = surface plasmon resonance commercialised by Biacore does not scale well to optical chips limited by losses in metal PHOTONICS RESEARCH GROUP 32
33 DIELECTRIC EVANESCENT WAVE SENSORS PHOTONICS RESEARCH GROUP 33
34 Evanescent wave biosensor Densmore, 2008 PHOTONICS RESEARCH GROUP 34
35 High index or low index contrast? PHOTONICS RESEARCH GROUP 35
36 Influence of mode profile profile should overlap maximally with the adlayer, and not with bulk fluid (noise!) high index contrast is best Low contrast High contrast PHOTONICS RESEARCH GROUP 36
37 Effective index change PHOTONICS RESEARCH GROUP 37
38 Effective index change still needs to be translated into something measurable. Many possibilities: Resonators Interferometers PHOTONICS RESEARCH GROUP 38
39 Intensiteit [A.U.] Golflengte [nm] Verschuiving [nm] Ring resonator biosensor Wavelength shift Time trace binding buffer level resonance wavelength shift [nm] Concentration measurement Wavelength Golflengte [nm] Time avidin concentration [μg/ml] Concentration [ug/ml] PHOTONICS RESEARCH GROUP 39
40 Camera read-out intensity wavelength [nm] PHOTONICS RESEARCH GROUP 40
41 On-line functionalisation and protein detection Protein: 30 kda, 10 nm T. Stakenborg, imec PHOTONICS RESEARCH GROUP 41
42 DNA hybridisation Concentrations down to 100 pm can be detected PHOTONICS RESEARCH GROUP 42
43 Detection of individual beads Streptavidin coated metal bead signal on biotinylated surface Bead diameter = 200nm Discrete bead binding events PHOTONICS RESEARCH GROUP 43
44 Used in many projects RAPP-ID point-of-care tests for lower respiratory tract infection, TB, sepsis joint initiative EU pharmaceutical industries CanDo Detection of free-circulating tumor cells DNA test PHOTONICS RESEARCH GROUP 44
45 FIGURES OF MERIT FOR SENSORS PHOTONICS RESEARCH GROUP 45
46 Towards a better sensor transmission wavelength initial biomolecules transmission Larger shift wavelength More interaction between light and molecules transmission Narrower dips wavelength High demands on read-out system, but filters noise PHOTONICS RESEARCH GROUP 46
47 Increasing the interaction normal waveguide water slot waveguide water ~100nm wide Si Si Si SiO 2 SiO 2 100nm slot width 10 µm First yearly InTopSens Review - Gent, 13/10/09 PHOTONICS RESEARCH GROUP 47
48 wavelength shift [nm] Slot waveguide resonator Avidin biotin sensing: normal ring 87ug/ml slot ring 100ug/ml time [min] T. Claes et al., IEEE Photonics Journal, 2009 PHOTONICS RESEARCH GROUP 48
49 What are we sweeping under the rug here? PHOTONICS RESEARCH GROUP 49
50 Sensitivity vs detection limit Sensitivity: shift of resonance wavelength (in nm) for a given excitation, e.g. Bulk sensitivity: nm / RIU (refractive index unit) Adlayer sensitivity: nm / nm Detection limit: smallest measurable excitation min Detection limit sensitivity Δλ min : smallest distinguishable wavelength shift PHOTONICS RESEARCH GROUP 50
51 What determines Δλ min? precision of measurement equipment noise in the system (thermal, mechanical, ) design of the sensor e.g.: higher Q is better often in conflict with sensitivity quality of data analysis averaging analytical curve fitting Δλ min can get smaller than measurement resolution! PHOTONICS RESEARCH GROUP 51
52 Back to slot waveguide We improved the sensitivity! Translation to detection limit? Normal Slot waveguide waveguide ring sensor ring sensor Sensor resolution Detection limit bulk Detection limit avidin 0.9 pm 4.5 pm 1.3e-5 RIU 1.5e-5 RIU 7 ng/ml 10 ng/ml No improvement of the detection limit Reason: losses in slot waveguide PHOTONICS RESEARCH GROUP 52
53 VERNIER BIOSENSOR PHOTONICS RESEARCH GROUP 53
54 A Vernier-scale (1631) is a well-known method to enhance the accuracy of measurement instruments 2 scales with different period, of which one slides along the other overlap of lines is used to perform the measurement PHOTONICS RESEARCH GROUP 54
55 Vernier ring resonator biosensor Regime 1 Regime 2 PHOTONICS RESEARCH GROUP 55
56 Vernier sensor: implementation PHOTONICS RESEARCH GROUP 56
57 Vernier sensor: sensitivity Huge improvement of sensitivity: 30x PHOTONICS RESEARCH GROUP 57
58 Read-out with a broadband light source and an on-chip spectrum analyzer allows faster and cheaper interrogation tunable laser broadband light source > No need for scanning and synchronization interrogation at frame rate of camera (100Hz to several khz) PHOTONICS RESEARCH GROUP 58
59 We combined the very sensitive Vernier-sensor with an on-chip spectrum analyzer PHOTONICS RESEARCH GROUP 59
60 The sensor signal is divided over multiple wavelength channels, and the envelope is detectable with broadband light PHOTONICS RESEARCH GROUP 60
61 The sensor monitors refractive index changes accurately competitive detection limit ( RIU) with much cheaper source PHOTONICS RESEARCH GROUP 61
62 GOING EVEN CHEAPER PHOTONICS RESEARCH GROUP 62
63 The need 8.8 million new TB cases per year 5000 people dying each day 1/3 of people have latent TB Diagnostic tests exist, but are either expensive or not sensitive enough European project Pocket PHOTONICS RESEARCH GROUP 63
64 The Pocket Transducer Data processing Mach-Zehnder Broad Silicon light nitride source waveguides interferometer + on-chip to spectral use with 850 isolated filter nm light to arm avoid for as reduced very expensive sensitive water tunable transducer absorption laser PHOTONICS RESEARCH GROUP 64
65 Limit of detection for bulk sensing Best LOD so far: 7.2E-7 RIU PHOTONICS RESEARCH GROUP 65
66 Preliminary protein sensing experiment 0,2 wavelength ( ) 0,1 0,0-0, time (s) 500 pg/ml protein Unlabeled! Still room for improvement in soft- and hardware PHOTONICS RESEARCH GROUP 66
67 Disposables and readout equipment PHOTONICS RESEARCH GROUP 67
68 TE/TM BIOSENSOR PHOTONICS RESEARCH GROUP 68
69 Problem We measure total mass and cannot distinguish between: Need way to disentangle thickness and refractive index Aim: study conformational changes PHOTONICS RESEARCH GROUP 69
70 Conformational analysis to hunt down allosteric inhibitors Primary binding site Allosteric binding site Allosteric binding can be protein-specific There is no high-throughput tool to visualise this PHOTONICS RESEARCH GROUP 70
71 Dual polarisation ring 2 measurements (TE + TM) determine 2 unknowns (d + n) PHOTONICS RESEARCH GROUP 71
72 Design PHOTONICS RESEARCH GROUP 72
73 Measurement PHOTONICS RESEARCH GROUP 73
74 Experiments with dielectric layers Standard deviation of 0.2 RIU and 1.4 nm between ring and ellipsometry measurements PHOTONICS RESEARCH GROUP 74
75 BSA protein conformation in different ph buffers PBS buffer ph7 BSA in PBS ph7 BSA in PBS ph5 BSA in PBS ph7 PBS buffer ph7 PHOTONICS RESEARCH GROUP 75
76 Evolution of thickness and refractive index ph5: Isoelectric point : closer packing ph7 ph5 ph7 PHOTONICS RESEARCH GROUP 76
77 The surface mass can now be determined, showing an irreversible adsorption ph 3 ph 5 ph N No desorption Hydrophilic surface PHOTONICS RESEARCH GROUP 77
78 Acknowledgements UGent Tom Claes Elewout Hallynck Cristina Lerma Arce Sam Werquin Jan-Willem Hoste Daan Martens KULeuven Daan Witters Jeroen Lammertyn imec Wim Van Roy Tim Stakenborg Liesbet Lagae PHOTONICS RESEARCH GROUP 78
79 THROUGH-CHIP FLUIDICS PHOTONICS RESEARCH GROUP 79
80 One of the major issues in biosensors is analyte delivery Pure diffusion is too slow Introducing laminar flow improves delivery time, however Laminar flow velocity near sensor 0 Diffusion-dominated region Problem for low concentrations PHOTONICS RESEARCH GROUP 80
81 Solution: flow-through sensor Droplet containing molecules is applied on a sensor Sensor = membrane with holes (radius >> molecules) By applying under- and overpressure, droplet is pulled or pushed through, along with biomolecules Cycle can be repeated until most biomolecules have bonded in holes PHOTONICS RESEARCH GROUP 81
82 Related ideas Continuous flow through a photonic crystal (still with flow channel) Same concept, different scale, no photonics PamGene (Huang et al, Optics Express, 17(26): ) PHOTONICS RESEARCH GROUP 82
83 What transducer to use? Type Mechanics Photonics Photonic crystal + -- Mach-Zehnder interferometer - ++ Due to a non-uniformity in vapour HF process, we obtained a mechanically robust Mach-Zehnder interferometer PHOTONICS RESEARCH GROUP 83
84 Fabrication in Silicon-on-Insulator Mass-producability of SOI is major advantage for biosensors and should be maintained in fabrication of membranes Substrate can be wet etched anisotropically using KOH Silicon dioxide is removed with vapour HF PHOTONICS RESEARCH GROUP 84
85 Silicon substrate etch using KOH Etching mask: 400 nm PECVD Si 3 N 4 on 400 nm PECVD SiO 2 Lithography is performed on back side using alignment markers on top side We open windows in the nitride/oxide mask using RIE An extra protective coating is applied on the top side due to pinholes in nitride ProTEK (Brewer Science) PHOTONICS RESEARCH GROUP 85
86 Silicon substrate etch using KOH 15 mm (.6 ) 10 mm (.4 ) PHOTONICS RESEARCH GROUP 86
87 Silicon substrate etch using KOH 40 µm 60 µm PHOTONICS RESEARCH GROUP 87
88 Silicon substrate etch using KOH PHOTONICS RESEARCH GROUP 88
89 And finish with a dash of HF ProTEK layer is removed Sample is put in HF solution where top nitride and oxide layers and buried oxide (BOX) layer will be etched PHOTONICS RESEARCH GROUP 89
90 And finish with a dash of HF PHOTONICS RESEARCH GROUP 90
91 Vapour HF is a must PHOTONICS RESEARCH GROUP 91
92 Pressure needed to pull a droplet through? Initial equilibrium We provide a hydrophilic material, surface tension does the rest (hydrophobic pressure of over 4 bar required) Creating a flow Membrane can be modelled as parallel channels Using COMSOL, the flow rate in function of the pressure can be calculated 10 kpa: MZI = 2.7 µl/s; PhC = 0.01 µl/s PHOTONICS RESEARCH GROUP 92
93 Through-chip flow PHOTONICS RESEARCH GROUP 93
94 Measurement set-up PHOTONICS RESEARCH GROUP 94
95 Applying pressure PHOTONICS RESEARCH GROUP 95
96 Proof-of-principle: BSA (0.625 mg/ml) Flow-through at least 3 times faster than in the case of no pumping PHOTONICS RESEARCH GROUP 96
97 Novel format: integration with reaction tubes PHOTONICS RESEARCH GROUP 97
98 Ring resonator biosensors b) Fluid flows through the perforations Perforations through the chip PHOTONICS RESEARCH GROUP 98
99 INTEGRATION WITH DIGITAL MICROFLUIDICS PHOTONICS RESEARCH GROUP 99
100 Microfluidics used in Silicon Photonics PDMS microchannels fabrication Packaging Tubing connections Leaks Bad adhesion PHOTONICS RESEARCH GROUP 100
101 MeBioS Biosensors KU Leuven PHOTONICS RESEARCH GROUP 101
102 Electrowetting-on-dielectric A potential is applied between a conducting liquid and an electrode modifying the surface tension hydrophobic hydrophilic Charge accumulates at the solid-liquid interface, leading to a change in contact angle PHOTONICS RESEARCH GROUP 102
103 Digital Microfluidics Tape spacer Aluminium layer pattern by standard photolithographic techniques. MeBioS Biosensors KU Leuven PHOTONICS RESEARCH GROUP 103
104 Combining both technologies Array of ring resonators SOI SOI Teflon coating PHOTONICS RESEARCH GROUP 104
105 Optical setup IR Camera Tunable laser ~1550nm Measuring Collimator through the Si substrate PHOTONICS RESEARCH GROUP 105
106 PHOTONICS RESEARCH GROUP Sensors area PHOTONICS RESEARCH GROUP 106
107 Resonance wavelength shift vs. Time Measured in water and two different salt solution concentrations Water Salt 1 Water Salt 2 PHOTONICS RESEARCH GROUP 107
108 Results Resonance wavelength shift vs. Refractive Index Unit Y=77*x-1e +002 PHOTONICS RESEARCH GROUP 108
109 CHIP-ON-FIBRE PHOTONICS RESEARCH GROUP 109
110 DESING: SENSOR ON FIBER Development of a fiber probe sensor for use as a biosensor It is transferred from the silicon-on-insulator chip onto the fiber facet. PHOTONICS RESEARCH GROUP 110
111 DESIGN: SENSOR ON FIBER PHOTONICS RESEARCH GROUP 111
112 FABRICATION SOI: 220nm Si 2µm SiO 2 750µm Si Dry etching: 2µm SiO 2 layer thinned down to 700nm PHOTONICS RESEARCH GROUP 112
113 FABRICATION Wax Si Wafer PHOTONICS RESEARCH GROUP 113
114 FABRICATION Si substrate removed 1. Mechanical grinding 2. Dry etching 3. Wet etching PHOTONICS RESEARCH GROUP 114
115 FABRICATION PHOTONICS RESEARCH GROUP 115
116 FABRICATION PHOTONICS RESEARCH GROUP 116
117 FABRICATION 2010 PHOTONICS RESEARCH GROUP 117
118 Wavelength Shift (nm) No degradation of sensitivity compared to normal ring resonators Bulk sensing experiments: Sensitivity for refractive index change in aqueous ethanol solutions x Measurements Fitting 1.2 ~70 nm/riu Refractive Index Unit (RIU) PHOTONICS RESEARCH GROUP 118
119 Acknowledgements UGent Tom Claes Elewout Hallynck Cristina Lerma Arce Sam Werquin Jan-Willem Hoste Daan Martens KULeuven Daan Witters Jeroen Lammertyn imec Wim Van Roy Tim Stakenborg Liesbet Lagae PHOTONICS RESEARCH GROUP 119
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