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Graduate Exam Abstract


Rongjin Yan

Ph.D. Final
July 12, 2011, 1:00pm-4:00pm
Engineering B103
A CMOS COMPATIBLE OPTICAL BIOSENSING SYSTEM BASED ON LOCAL EVANESCENT FIELD SHIFT MECHANISM

Abstract: The need for label-free integrated optical
biosensors has dramatically increased in recent
years. Integrated optical biosensors have many
advantages, including low-cost, and portability.
They can be applied to many fields, including
clinical diagnostics, food safety, environmental
monitoring, and biosecurity applications. One of
the most important applications is point-of-care
diagnosis, which means the disease could be tested
at or near the site of patient care rather than in
a laboratory.

We are exploring the issues of design, modeling
and measurement of a novel chip-scale local
evanescent array coupled (LEAC) biosensor, which
is an ideal platform for point-of-care diagnosis.

Until now, three generations of LEAC samples have
been designed, fabricated and tested. The 1st
generation of LEAC sensor without a buried
detector array was characterized using a
commercial near field scanning optical microscope
(NSOM). The sample was polished and was end-fire
light coupled using single mode fiber. The field
shift mechanism in this proof-to-concept
configuration without buried detector arrays has
been validated with inorganic adlayers[1],
photoresist[2] and different concentrations of CRP
proteins[3]. Mode beating phenomena was predicted
by the beam propagation method (BPM) and was
observed in the NSOM measurement.

A 2nd generation LEAC sensor with a buried
detector array was fabricated using 0.35?m CMOS
process at the Avogo Technologies Inc., Fort
Collins, Colorado. Characterizations with both
single layer patternings, including photoresist as
well as BSA [4] and immunoassay complexes [5] were
done with cooperative efforts from various
research groups. The BPM method was used to study
the LEAC sensor, and the simulation results
demonstrated the sensitivity of the LEAC sensor is
16%/nm, which was proved to match well with the
experimental data [6]. Different
antigen/antibodies, including mouse IgG and Hspx
(a tuberculosis reactive antigen), have been used
to test the immunoassay ability of LEAC sensor
[7].

Many useful data have been collected by using the
2nd generation LEAC chip. However, during the
characterization of the Avago chips, some design
problems were revealed, including incompatibility
with microfluidic integration, restricted
detection region, strong sidewall scattering and
uncoupled light interference from the single mode
fiber. To address these problems, the 3rd
generation LEAC sensor chip with buried detector
arrays was designed to allow real-time monitoring
and compatibility with microfluidic channel
integration. 3rd generation samples have been
fabricated in the CSU cleanroom and the mesa
detector structure has been replaced with the thin
insulator detector structure to solve the problems
encountered during the characterizations. PDMS
microfluidic channels and a multichannel
measurement system consisting of a probe card, a
multiplexing/amplification circuit and a LabVIEW
program have been implemented into the LEAC
system.

In recent years, outbreaks of fast spreading viral
diseases, such as bird flu and H1N1, have drawn a
lot of concern of the point-of-care virus
detection techniques. To test the virus detection
ability of LEAC sensor, 40nm and 200nm polystyrene
nanoparticles were immobilized onto the waveguide,
and the increased scattered light was collected.
Sensitivities of 1%/particle and 0.04%/particle
were observed for 200nm and 40nm particles
respectively.

References:
[1] G. Yuan, M. Stephens, D. Dandy, and K.
Lear, “Direct imaging of transient interference in
a single-mode waveguide using near-field scanning
optical microscopy,” IEEE Photonics Technology
Letters, vol. 17, Nov. 2005, pp. 2382-2384.
[2] G. Yuan, M. Stephens, D.S. Dandy, and K.L.
Lear, “Local Evanescent, Array Coupled (LEAC)
Biosensor Response to Low Index Adlayers,”
Conference on Lasers and Electro-Optics (CLEO),
CThL, 2006.
[3] R. Yan, G. Yuan, M.D. Stephens, X. He,
C.S. Henry, D.S. Dandy, and K.L. Lear, “Evanescent
field response to immunoassay layer thickness on
planar waveguides,” Applied Physics Letters, vol.
93, 2008, pp. 101110-3.
[4] R. Yan, S.P. Mestas, G. Yuan, R.
Safaisini, D.S. Dandy, and K.L. Lear, “Label-free
silicon photonic biosensor system with integrated
detector array,” Lab on a Chip, vol. 9, 2009, pp.
2163-2168.
[5] R. Yan, L. Kingry, R. Slayden, and K.
Lear, “Demonstration of the immunoassay using
local evanescent array coupled biosensor,” SPIE
Photonic West 2010, 2010, 7559-14.
[6] R. Yan, S.P. Mestas, G. Yuan, R.
Safaisini, and K.L. Lear, “Response of Local
Evanescent Array-Coupled Biosensors to Organic
Nanofilms,” Journal of Selected Topics in Quantum
Electronics, vol. 15, 2009, pp. 1469-1477.
[7] R. Yan, N.S. Lynn, L.C. Kingry, Z. Yi, R.A.
Slayden, D.S. Dandy and K.L. Lear, “Waveguide
biosensor with integrated detector array for
tuberculosis testing,” Applied Physics Letters,
vol. 98, 2010, pp. 013702.


Adviser: Kevin L. Lear
Co-Adviser: N/A
Non-ECE Member: David S. Dandy, Department of Chemical and Biological Engineering
Member 3: V Chandrasekar, Electrical and Computer Engineering
Addional Members: Branislav Notaros, Electrical and Computer Engineering

Publications:
Journal papers [1] R. Yan, N.S. Lynn, L.C. Kingry, Z. Yi, R.A. Slayden, D.S. Dandy and K.L. Lear, “Waveguide biosensor with integrated detector array for tuberculosis testing,” Applied Physics Letters, vol. 98, pp. 013702, 2010.
[2] R. Yan, S.P. Mestas, G. Yuan, R. Safaisini, D.S. Dandy, and K.L. Lear, “Label-free silicon photonic biosensor system with integrated detector array,” Lab on a Chip, Featured on the front cover, vol. 9, pp. 2163-2168, 2009.
[3] R. Yan, S.P. Mestas, G. Yuan, R. Safaisini, and K.L. Lear, “Response of Local Evanescent Array-Coupled Biosensors to Organic Nanofilms,” IEEE Journal of Selected Topics in Quantum Electronics, vol. 15, pp. 1469-1477, 2009.
[4] R. Yan, G. Yuan, M.D. Stephens, X. He, C.S. Henry, D.S. Dandy, and K.L. Lear, “Evanescent field response to immunoassay layer thickness on planar waveguides,” Applied Physics Letters, vol. 93, pp. 101110-3, 2008.
Conference Papers:
[1] David S. Dandy, N. Scott Lynn, Luke C. Kingry, Rongjin Yan, and Kevin L. Lear, “Label Free Detection of Virus-Like Particles”, MicroTAS, 2011
[2] Z. Yi, R. Yan, R. Safaisini, K. Lear, “Optimization of waveguide thickness for local evanescent field shift detection,” SPIE Photonic West 2011, 7888-21, 2011
[3] K. Lear, R. Yan, D. Dandy, N. Lynn, R. Slayden, L. Kingry, “A novel evanescent field biosensor with an integrated photodetector array (invited),” SPIE Photonic West 2011, 7888-5, 2011
[4] R. Yan, S. Lynn, L. Kingry, R. Slayden, D. Dandy and K. Lear, “Demonstration of nanoparticle detection using a local evanescent array coupled biosensor,” The 23rd Annual Meeting of the IEEE Photonics Society, TuN2, 2010
[5] R. Yan, S. Lynn, L. Kingry, D. Dandy, R. Slayden, and K. Lear , “Waveguide biosensor with integrated photodetector array for tuberculosis serology ,” The Conference on Lasers and Electro-Optics (CLEO) 2010, AMC5, 2010.
[6] R. Yan, S. Lynn, L. Kingry, R. Slayden, D. Dandy, and K. Lear, “An optical waveguide array biosensor for serology,” Biomedical Sciences Instrumentation, vol. 46, pp. 45-50, 2010.
[7] R. Yan, L. Kingry, R. Slayden, and K. Lear , “Demonstration of the immunoassay using local evanescent array coupled biosensor ,” SPIE Photonic West 2010, pp. 7559-14, 2010.
[8] K. Lear and R. Yan, “A photonic biosensor system on a CMOS chip (Invited),” SPIE Photonic West 2010, pp. 7606-11, 2010.
[9] R. Yan, S. Mestas, Guangwei Yuan, and K. Lear, “High sensitivity local evanescent array coupled biosensors with nanometer BSA film,” The Conference on Lasers and Electro-Optics (CLEO) 2009, CTuCC5, 2009.
[10] R. Yan, G. Yuan , S. Mestas, R. Safaisini, and K. Lear, “Demonstration of local evanescent array coupled biosensors with organic nanofilms,” The 21th Annual Meeting of the IEEE Lasers and Electro-Optics Society (LEOS), pp. 240-241, 2008
[11] R. Yan, G. Yuan, R. Pownall, and K. Lear, “A novel low-loss y-type splitter with adjustable branching ratio,” The 20th Annual Meeting of the IEEE Lasers and Electro-Optics Society (LEOS), pp. 543-544, 2007.
[12] R. Yan, G. Yuan, R. Pownall, and K.L. Lear, “Waveguide Characterization Using Shear Force Scanning Optical Microscopy,” 2007 American Physical Society Annual Meeting, L38.00015, 2007.
[13] G. Yuan, R. Yan, M. Stephens, D. Dandy, and K. Lear, “Evanescent field response to small patterned features on a planar waveguide biosensor,” 2007 American Physical Society Annual Meeting, J41.00006, 2007.
[14] K. Lear, G. Yuan, M. Stephens, X. He, R. Pownall, R. Yan, P. Nikkel, C. Henry, T. Chen, and D. Dandy, “A waveguide biosensors local evanescent field response to an immunoassay complex,” 2007 Digest of the IEEE/LEOS Summer Topical Meetings, pp. 97-98, 2007.


Program of Study:
EE672
EE536
EE525
EE504
EE680
EE799
EE799
EE799