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Biosensing with silicon photonics

Kristinn B. Gylfason KTH Micro and Nanosystems kristinn.gylfason@ee.kth.se

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)

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.

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

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.

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.

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

Waveguides for light control, by microfabrication

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

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

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

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

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.

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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

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

OSTE: photolithography

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Photolithography enables footprint efficient vias

A-A’

Bonding compatible with biofunctionalized surfaces

OSTE: bonding

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C.F. Carlborg et al. MicroTAS 2011

Fabrication: concept

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Fabrication: process

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BONDING

DEVELOPMENT

30 s in Butyl acetate 13 s

CURING

A biophotonic sensor with microfabricated sample handling system Light

in Light out 75 µm

A biophotonic sensor example: Refractive index sensing

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

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.

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.

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

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

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

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.

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

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.

Grating design

Periodic grating optimization

Apodization

BOX thickness dependence

Field profile in grating cross-section

Implementation and experiments