biosensing with silicon photonics/menu/... · biosensing with silicon waveguides . the high...
TRANSCRIPT
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KTH – Micro and Nanosystems
RF switch
RF filter Micro fuel cell (www.myfuelcell.se)
Photonic ring resonator biosensors
Lab-on-a-Chip
IR bolometer Silicon microneedles Transdermal drug delivery systems
Polymer microfluidics
IR cameras (www.flir.com)
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Outline
• Why do we need biosensors sensors?
• Biosensor definition.
• The fundamentals of photonic waveguide based biosensing
• Silicon waveguides as biosensors.
• Liquid sample handling for photonic biosensors.
• Reducing temperature sensitivity.
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Why do we need biosensors?
• When intruded by a disease causing virus or bacterium, the body releases biomolecules called antibodies into the blood.
• The antibodies attach selectively to a part of the intruder called the antigen, to label it for attack by the immune system.
• Accurate disease diagnosis requires the measurement of the concentration of these antibodies.
• The concentration is very low (ng/ml), and there are other biomolecules in blood of much higher concentration (mg/ml).
• By fixing an antigen on a biosensor surface, the attachment of antibodies can be measured with high selectivity.
Image from Wikipedia
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More applications of biosensors
• Medical diagnostics
• Drug development
• Explosives and narcotics detection
• Environmental monitoring
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Outline
• Why do we need biosensors sensors?
• Biosensor definition.
• The fundamentals of photonic waveguide based biosensing
• Silicon waveguides as biosensors.
• Liquid sample handling for photonic biosensors.
• Reducing temperature sensitivity.
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Roche Accu-Chek: www.accu-chek.com
What are biosensors?
• In general, biosensors are devices to characterize a chemical quantity: the analyte
• Biosensors can be used to: - Determine analyte
concentration - Study the kinetics of
chemical reactions of the analyte
Some commercial examples:
Attana QCM: www.attana.com Corning EPIC: www.corning.com
Biacore SPR: www.biacore.com
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The formal definition of a biosensor
IUPAC1 definition: “A biosensor is a self-contained
integrated device which is capable of providing selective quantitative analytical information using a biological recognition element which is in direct spatial contact with a transducer element.”
1IUPAC: International Union of Pure and Applied chemistry
[K+] [Antibody]
DNA Antigen Enzyme
QCM SPR EC
[CO2]
Analytes:
Recognition:
Transduction:
For example:
[Virus]
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Analytes
• Biosensors can be used to study: - Ions: K+, Cl-, Ca2+, … - Gasses: CO2, NH3, … - Sugars - Alcohols - Oligonucleotides (short single stranded DNA chains) - Various proteins and peptides: Antibodies, antigens - Viruses - and more …
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Biological recognition elements
• The fundamental idea of biosensing is using the work done by biological evolution to create highly selective biomolecular pairings.
• Using one part of the pair as a recognition element allows selective measurement of the other part.
• The biological recognition system provides selectivity and translates information from the biochemical domain (often an analyte concentration C) into chemical or physical output.
• Biological recognition elements can be: - Oligonucleotides (short single stranded DNA
chains) - Enzymes - Antigens/Antibodies …
Double stranded DNA
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Biological recognition elements
• The biological binding reactions generally work only in water.
• This is a serious limitation for biosensors that are adversely affected by the viscous damping of liquids.
• For example: Resonating micromechanical cantilevers have shown mass detection limits of: - zeptograms (10-21) in vacuum [1] - but nanograms (10-9) in liquid [2]
[2] T. Braun, et al., Nature Nanotechnology 4, 179 (2009) [1] Y. T. Yang, et al., Nano Letters 6, 583 (2006)
Double stranded DNA
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Transducer elements
• The purpose of the transducer is to transform the output from the recognition system to a form suited for data analysis and storage (usually electrical).
• Often the output of the recognition system is a mass change (∆m) or a charge change (∆q).
• Most often these quantities are eventually translated to a frequency change (∆f) or a current change (∆i) of an electrical signal.
• Complete biosensors can thus be described by their transduction chains. For example: ∆C ∆q ∆i or ∆C ∆m ∆f
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Classification of biosensors
Analyte Recognition Transduction
Ions Enzymes Electrochemical
Dissolved gasses Vapors
Enzymes Antibodies Receptor proteins
Electrochemical Piezoelectric Optical
Substrates (molecules upon which enzymes act)
Enzymes Membrane receptors Whole cells Plant or animal tissue
Electrochemical Piezoelectric Optical Calorimetric
Antibody/Antigen Virus
Antigen/Antibody Electrochemical Piezoelectric Optical Surface plasmon
Various proteins Receptor proteins Electrochemical Piezoelectric Optical Surface plasmon
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Outline
• Why do we need biosensors sensors?
• Biosensor definition.
• The fundamentals of photonic waveguide based biosensing
• Silicon waveguides as biosensors.
• Liquid sample handling for photonic biosensors.
• Reducing temperature sensitivity.
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Interaction of light and matter: Wavelength change (refractive index)
λ0 Speed of light in vacuum: c Wavelength in vacuum:
λ0 = c/f
In water light slows down to vꞌ Wavelength in water:
λꞌ = vꞌ/f = λ0/nw
Wavelength in a biomolecule solution: λꞌꞌ = λ0/ns < λꞌ
λꞌꞌ ns
λꞌ nw
n is the material's refractive index
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Waveguides for light control, by microfabrication
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Guided wave propagation
Electric field (Ey) of the light wave in the A-A’ cross-section
Core
Bottom cladding
Liquid sample
Evanescent field
Evanescent field
ns
nc
nb
neff =f(nb, ns, nc)
Effective refractive index of waveguide λ = λ0/neff
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Evanescent field based biosensing with photonic waveguides
• Cross section along guide
• Electric field of the propagating light wave
• Biomolecule binding
Increased wg. effective index:
Δλ/λ = Δne/ne
Core
Bottom cladding
Liquid sample
Antigens
Strength of evanescent field
Anti- bodies
Y
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Photonic waveguide circuits for Δλ read out
Image from: http://www.comsol.com/wave-optics-module
• The transduction chain of a photonic biosensor is:
∆C ∆m ∆n ∆λ
• We need to read out ∆λ. • Lithography enables
fabrication of functional photonic circuits.
• The directional coupler permits nearly lossless splitting and combining of light. Directional
coupler
Overlapping evanescent fields
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Ring resonators for Δλ read out Light in at free space
wavelength λ0
Transmitted light to detector
Off resonance
λ0
• Off resonance Most of light transmitted
• On resonance Light coupled to ring Transmission minimum
• Surface binding ne increase Resonace wavel. increase: Δλ0
Integer Surface binding mλ’0/n’e = 2πR
λ0
mλ0/ne = 2πR On resonance
λ’0
fixed
Transmitted light to detector
m = 10 New trans- mission spectrum of ring
Light in
Light out
R=70 µm Directional
coupler
Ring resonator
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Ring resonator sensing fundamentals
Input Pass
𝑄 =𝜆Δ𝜆
Quality factor
𝑆𝑉 =𝜕𝜆𝜕𝑛
Volume sensitivity
𝑆𝑆 =𝜕𝜆𝜕𝜎
Surface sensitivity
The Q limits the achievable
sensor resolution.
Resonance wavelength shift per refractive index unit
change of top cladding.
Resonance wavelength shift for surface density change
of surface coating.
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An example ring resonator biosensor chip
Light in
Optical sensor array
Light out
Ring resonator transducer
Antigen-Antibody pair 1 µm
750 µm
70 µm
Biosensor cartridge
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C. F. Carlborg, K. B. Gylfason, et al., "A packaged optical slot-waveguide ring resonator sensor array for multiplex label-free assays in labs-on-chips," Lab Chip, vol. 10, pp. 281-290, Feb. 2010.
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Layout of sensor array optical circuit
Grating coupling
Waveguide
Ring-resonator
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Waveguide cross-section
Sample
Bottom cladding
Waveguide
Δσp Y Y Y Y
Y Y Y nb
nc
ns Δns ΔσpΔλ
Surface sensing
Volume sensing ΔnsΔλ
Time average of optical power through cross section (TM, λ=1310 nm)
Y Y Y Y Y
Y Y
Y Y
Increased light-analyte interaction
Waveguide
Evanescent wave
A-A’
(TE, λ=1310 nm)
Slot waveguide Strip waveguide
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Volume refractive index measurement of ethanol and methanol dilutions
Limit of detection: noise level / sensitivity = 5 x 10-6 RIU
State of the art refractometers: 10-8 RIU
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Selective surface bio-coating by spotting
Spotting jets
Chip spotted
with BSA
Spotts
Biological recognition components
Ring
Bus
Coupler
Precipitated salt crystals on surface
Spotting robot
Spotted Not spotted
Sensor M5 Sensor M6
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Biosensing
(the antibody)
(the antigen)
C. F. Carlborg, K. B. Gylfason, et al. “A packaged optical slot-waveguide ring resonator sensor array for multiplex label-free assays in labs-on-chips,” Lab on a Chip, vol. 10, pp. 281-290, 2010.
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Outline
• Why do we need biosensors sensors?
• Biosensor definition.
• The fundamentals of photonic waveguide based biosensing
• Silicon waveguides as biosensors.
• Liquid sample handling for photonic biosensors.
• Reducing temperature sensitivity.
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Biosensing with silicon waveguides
The high refractive index of silicon waveguides provide two benefits for sensing:
1. Rings can be made very small without reducing Q by bending loss,
2. The evanescent electric field at the silicon surface is very high, yielding high sensitivity for surface sensing.
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Biosensing with silicon waveguides
K. De Vos, et al., "Silicon-on-Insulator microring resonator for sensitive and label-free biosensing," Optics Express, vol. 15, no. 12, pp. 7610-7615, 2007.
Label-free detection limit of a few hundred molecules.
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Multiplexing
K. De Vos, et al., "Multiplexed antibody detection with an array of Silicon-on-Insulator microring resonators," Photonics Journal, IEEE, vol. 1, no. 4, pp. 225-235, Oct. 2009.
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Signal enhancement
M. S. Luchansky, et al., "Sensitive on-chip detection of a protein biomarker in human serum and plasma over an extended dynamic range using silicon photonic microring resonators and sub-micron beads," Lab Chip, vol. 11, pp. 2042-2044, 2011.
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Outline
• Why do we need biosensors sensors?
• Biosensor definition.
• The fundamentals of photonic waveguide based biosensing
• Silicon waveguides as biosensors.
• Liquid sample handling for photonic biosensors.
• Reducing temperature sensitivity.
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Challenge: Cost-efficient microfluidic integration
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Challenge: Cost-efficient microfluidic integration
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• Minimize wafer footprint of microfluidics • Bonding compatible with biofunctionalization • Extendable to wafer scale
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OSTE
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Off-Stoichiometric Thiol-Ene (OSTE) polymer technology enables new solutions for Lab-on-a Chip
Tailor-made mechanical properties
Patternable wettability
Injection molding
Photolithography
Bonding to Si
Compatible with biofunctionalization
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OSTE: photolithography
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Photolithography enables footprint efficient vias
A-A’
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Bonding compatible with biofunctionalized surfaces
OSTE: bonding
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C.F. Carlborg et al. MicroTAS 2011
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Fabrication: concept
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Fabrication: process
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BONDING
DEVELOPMENT
30 s in Butyl acetate 13 s
CURING
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A biophotonic sensor with microfabricated sample handling system Light
in Light out 75 µm
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A biophotonic sensor example: Refractive index sensing
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Refractive index sensitivity
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S=50 nm/RIU
C. Errando-Herranz, K. B. Gylfason, et al., Opt. Express, vol. 21, pp. 21293-21298, Sep. 2013.
Carlos
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Outline
• Why do we need biosensors sensors?
• Biosensor definition.
• The fundamentals of photonic waveguide based biosensing
• Silicon waveguides as biosensors.
• Liquid sample handling for photonic biosensors.
• Reducing temperature sensitivity.
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Temperature sensitivity
• For practical biosensing we need to reach a detection limit of 10-6 RIU.
• Water has a thermo optic co-efficient of κH2O = -1.1 × 10-4 RIU/K. Waveguide based biosensors
normally need temperature control.
(SPR-BIAcore T100)
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Athermal waveguides
Athermal waveguide If we can make
Cross-section Thermo-optic coefficients
κ = ∂n/∂T
Optical power (TE mode, λ = 1550 nm)
Strip waveguide
Slot waveguide
A-A’
n = 3.5
n = 1.3
n = 1.5
K. B. Gylfason, et al. “On-chip temperature compensation in an integrated slot-waveguide ring resonator sensor array,” Optics Express, vol. 18, pp. 3226-3237, 2010.
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Athermal slot-waveguide design
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Zero-contour
A
A Wrail=180 nm
B B: Wrail = 215 nm
C
C: Wrail = 240 nm
Wslot=120 nm
A: Wrail = 180 nm
Athermal design
Temperature dependence of effective index Calculated with COMSOL Multiphysics® FEM mode solver
h = 220 nm
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Mach-Zehnder Interferometer
Evaluation circuit
Lower cladding (SiO2)
Slot-waveguide (Si)
150 nm
Top view
K. B. Gylfason, A. Romero, et al., "Reducing the temperature sensitivity of SOI waveguide-based biosensors,“ Proc. SPIE, vol. 8431, pp. 84 310F-84 310F-15, May 2012. http://dx.doi.org/10.1117/12.922263
Albert
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Summary
• By fixing a receptor to a photonic sensor surface, antibodies can be measured with high selectivity.
• Biomolecules binding within the evanescent field of a sensing waveguide shorten the wavelength of light in the guide.
• Slot waveguides are good bulk sensors, marginal benefit for surface sensing.
• However, silicon slot waveguides enable athermal photonic biosensors.
• Cost-efficient microfluidic integration on silicon sensors challenging: OSTE
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Outlook
• Silicon waveguide based photonic transducers already good enough for many practical applications.
• However, benefits over existing biosensors is not clear enough yet to make an impact.
• Improvements in microfluidics integration (pumping, filtering etc.) necessary to leverage the benefits of CMOS fabrication.
• Unique features for future exploration: - Low absolute mass detection limit. - Spatial resolution by sensor arrays.
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Further reading
• W. Bogaerts, et al., "Silicon microring resonators," Laser & Photon. Rev., vol. 6, pp. 47-73, 2012. http://dx.doi.org/10.1002/lpor.201100017 A review of ring resonators.
• C. Errando-Herranz, K. B. Gylfason et al., "Integration of microfluidics with grating coupled silicon photonic sensors by one-step combined photopatterning and molding of OSTE," Opt. Express, vol. 21, pp. 21 293-21 298, 2013. http://dx.doi.org/10.1364/oe.21.021293
• K. B. Gylfason, et al., "Reducing the temperature sensitivity of SOI waveguide-based biosensors," Proceedings of SPIE, vol. 8431, pp. 84 310F, 2012. http://dx.doi.org/10.1117/12.922263
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Apodized through-etched grating couplers for single lithography circuits
M. Antelius, K. B. Gylfason, and H. Sohlström, "An apodized SOI waveguide-to-fiber surface grating coupler for single lithography silicon photonics, " Opt. Express, vol. 19, no. 4, pp. 3592-3598, Feb. 2011.
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Grating design
Periodic grating optimization
Apodization
BOX thickness dependence
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Field profile in grating cross-section
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Implementation and experiments