Molecular film growth monitoring via reflection microscopy on periodically patterned substrates

I. Archontas; A. Salapatas; K. Misiakos

doi:10.1364/OE.21.004215

Molecular film growth monitoring via reflection microscopy on periodically patterned substrates

I. Archontas, A. Salapatas, and K. Misiakos

Optics Express
Vol. 21,
Issue 4,
pp. 4215-4227
(2013)
•https://doi.org/10.1364/OE.21.004215

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I. Archontas, A. Salapatas, and K. Misiakos, "Molecular film growth monitoring via reflection microscopy on periodically patterned substrates," Opt. Express 21, 4215-4227 (2013)

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Related Topics
Table of Contents Category
- Thin Films
Optics & Photonics Topics
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The topics in this list come from the OSA Optics and Photonics Topics applied to this article.
Previously assigned OCIS codes
- Image processing (100.0100)
- Image analysis (100.2960)
- Optical sensing and sensors (280.4788)
- Thin films, optical properties (310.6860)

About this Article
History
- Original Manuscript: October 23, 2012
- Manuscript Accepted: January 9, 2013
- Published: February 12, 2013
Virtual Issues
Virtual Journal for Biomedical Optics Vol. 8, Iss. 3

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Open Access

Abstract

An optical method is presented for in the situ monitoring of biomolecular films via reflection microscopy on patterned substrates. The method is based on measuring the reflection coefficient of a composite consisting of a substrate, a patterned optical layer, the thin film to be monitored and the cover medium. The optical layer is patterned so that an array of squares is surrounded by the bare substrate. The reflectance difference between the optical layer squares and the bare substrate is the observable, whose fractional changes reveal the thickness of the film through a simple analytical expression. The periodic image is recorded by a digital microscope, and through Fourier transform techniques, the normalized differential reflectance of the patterned optical composite is calculated as the contrast factor of two dimensional bit map. The method is demonstrated by measuring a protein binding assay inside a microfluidic module placed under a microscope.

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References

View by:
Article Order
|
Year
|
Author
|
Publication

A. P. F. Turner, “Biochemistry. Biosensors--sense and sensitivity,” Science 290(5495), 1315–1317 (2000).
[Crossref] [PubMed]
X. W. Guo, “Surface plasmon resonance based biosensor technique: a review,” J Biophotonics 5(7), 483–501 (2012).
[Crossref] [PubMed]
S. Herranz, M. Bockova, M. D. Marazuela, J. Homola, and M. C. Moreno-Bondi, “Surface plasmon resonance biosensor for parallelized detection of protein biomarkers in diluted blood plasma,” Anal. Bioanal. Chem. 398(6), 2625–2634 (2010).
[Crossref] [PubMed]
M. S. Luchansky and R. C. Bailey, “Silicon photonic microring resonators for quantitative cytokine detection and T-cell secretion analysis,” Anal. Chem. 82(5), 1975–1981 (2010).
[Crossref] [PubMed]
A. Brecht, G. Gauglitz, and J. Polster, “Interferometric immunoassay in a FIA-system - a sensitive and rapid approach in label-free immunosensing,” Biosens. Bioelectron. 8(7-8), 387–392 (1993).
[Crossref]
X. Zhu, J. P. Landry, Y. S. Sun, J. P. Gregg, K. S. Lam, and X. Guo, “Oblique-incidence reflectivity difference microscope for label-free high-throughput detection of biochemical reactions in a microarray format,” Appl. Opt. 46(10), 1890–1895 (2007).
[Crossref] [PubMed]
J. Y. Wang, J. Dai, L. P. He, Y. Sun, H. B. Lu, K. J. Jin, and G. Z. Yang, “Label-free and real-time detections of the interactions of swine IgG with goat anti-swine IgG by oblique-incidence reflectivity difference technique,” J. Appl. Phys. 112(6), 064702 (2012).
[Crossref]
O. S. Heavens, Optical Properties of Thin Solid Films (Dover Publications, 1991) Chap.4.
M. Zavali, P. S. Petrou, S. E. Kakabakos, M. Kitsara, I. Raptis, K. Beltsios, and K. Misiakos, “Label-free kinetic study of biomolecular interactions by white light reflectance spectroscopy,” Micro & Nano Lett. 1(2), 94–98 (2006).
[Crossref]
S. Busse, V. Scheumann, B. Menges, and S. Mittler, “Sensitivity studies for specific binding reactions using the biotin/streptavidin system by evanescent optical methods,” Biosens. Bioelectron. 17(8), 704–710 (2002).
[Crossref] [PubMed]
P. Ihalainen and J. Peltonen, “Immobilization of streptavidin onto biotin-functionalized Langmuir-Schaefer binary monolayers chemisorbed on gold,” Sens. Actuat. B 102(2), 207–218 (2004).
[Crossref]
M. Zavali, “Direct Study of biomolecular interactions through white light reflection spectroscopy” Senior Thesis, University of Ioannina, Greece, (2006).

2012 (2)

X. W. Guo, “Surface plasmon resonance based biosensor technique: a review,” J Biophotonics 5(7), 483–501 (2012).
[Crossref] [PubMed]

J. Y. Wang, J. Dai, L. P. He, Y. Sun, H. B. Lu, K. J. Jin, and G. Z. Yang, “Label-free and real-time detections of the interactions of swine IgG with goat anti-swine IgG by oblique-incidence reflectivity difference technique,” J. Appl. Phys. 112(6), 064702 (2012).
[Crossref]

2010 (2)

S. Herranz, M. Bockova, M. D. Marazuela, J. Homola, and M. C. Moreno-Bondi, “Surface plasmon resonance biosensor for parallelized detection of protein biomarkers in diluted blood plasma,” Anal. Bioanal. Chem. 398(6), 2625–2634 (2010).
[Crossref] [PubMed]

M. S. Luchansky and R. C. Bailey, “Silicon photonic microring resonators for quantitative cytokine detection and T-cell secretion analysis,” Anal. Chem. 82(5), 1975–1981 (2010).
[Crossref] [PubMed]

2007 (1)

X. Zhu, J. P. Landry, Y. S. Sun, J. P. Gregg, K. S. Lam, and X. Guo, “Oblique-incidence reflectivity difference microscope for label-free high-throughput detection of biochemical reactions in a microarray format,” Appl. Opt. 46(10), 1890–1895 (2007).
[Crossref] [PubMed]

2006 (1)

M. Zavali, P. S. Petrou, S. E. Kakabakos, M. Kitsara, I. Raptis, K. Beltsios, and K. Misiakos, “Label-free kinetic study of biomolecular interactions by white light reflectance spectroscopy,” Micro & Nano Lett. 1(2), 94–98 (2006).
[Crossref]

2004 (1)

P. Ihalainen and J. Peltonen, “Immobilization of streptavidin onto biotin-functionalized Langmuir-Schaefer binary monolayers chemisorbed on gold,” Sens. Actuat. B 102(2), 207–218 (2004).
[Crossref]

2002 (1)

S. Busse, V. Scheumann, B. Menges, and S. Mittler, “Sensitivity studies for specific binding reactions using the biotin/streptavidin system by evanescent optical methods,” Biosens. Bioelectron. 17(8), 704–710 (2002).
[Crossref] [PubMed]

2000 (1)

A. P. F. Turner, “Biochemistry. Biosensors--sense and sensitivity,” Science 290(5495), 1315–1317 (2000).
[Crossref] [PubMed]

1993 (1)

A. Brecht, G. Gauglitz, and J. Polster, “Interferometric immunoassay in a FIA-system - a sensitive and rapid approach in label-free immunosensing,” Biosens. Bioelectron. 8(7-8), 387–392 (1993).
[Crossref]

Bailey, R. C.

Beltsios, K.

Bockova, M.

Brecht, A.

Busse, S.

Dai, J.

Gauglitz, G.

Gregg, J. P.

Guo, X.

Guo, X. W.

X. W. Guo, “Surface plasmon resonance based biosensor technique: a review,” J Biophotonics 5(7), 483–501 (2012).
[Crossref] [PubMed]

He, L. P.

Herranz, S.

Homola, J.

Ihalainen, P.

Jin, K. J.

Kakabakos, S. E.

Kitsara, M.

Lam, K. S.

Landry, J. P.

Lu, H. B.

Luchansky, M. S.

Marazuela, M. D.

Menges, B.

Misiakos, K.

Mittler, S.

Moreno-Bondi, M. C.

Peltonen, J.

Petrou, P. S.

Polster, J.

Raptis, I.

Scheumann, V.

Sun, Y.

Sun, Y. S.

Turner, A. P. F.

A. P. F. Turner, “Biochemistry. Biosensors--sense and sensitivity,” Science 290(5495), 1315–1317 (2000).
[Crossref] [PubMed]

Wang, J. Y.

Yang, G. Z.

Zavali, M.

Zhu, X.

Anal. Bioanal. Chem. (1)

Anal. Chem. (1)

Appl. Opt. (1)

Biosens. Bioelectron. (2)

J Biophotonics (1)

X. W. Guo, “Surface plasmon resonance based biosensor technique: a review,” J Biophotonics 5(7), 483–501 (2012).
[Crossref] [PubMed]

J. Appl. Phys. (1)

Micro & Nano Lett. (1)

Science (1)

A. P. F. Turner, “Biochemistry. Biosensors--sense and sensitivity,” Science 290(5495), 1315–1317 (2000).
[Crossref] [PubMed]

Sens. Actuat. B (1)

Other (2)

M. Zavali, “Direct Study of biomolecular interactions through white light reflection spectroscopy” Senior Thesis, University of Ioannina, Greece, (2006).

O. S. Heavens, Optical Properties of Thin Solid Films (Dover Publications, 1991) Chap.4.

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Fig. 1 Schematic diagram of the thin film to be monitored and the optical layer sandwiched between the cover medium and the substrate.

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Fig. 2 Exact differential reflectance sensitivity at d₂ = d_2m as a function of the optical layer refractive index and for two different substrates, silicon (dash-dotted) and quartz (dotted). The solid line is the approximate expression in Eq. (16). The two sets of curves correspond to n₁ = 1.4 and 1.45, respectively. Here, n₀ = 1.34, optical length δ_2m = 3π/4 and λ₀ = 450 nm.

Download Full Size | PPT Slide | PDF

Fig. 3 Plot of cos(2δ_m) in Eq. (10) as a function of n₂ for the silicon and the quartz substrate.

Download Full Size | PPT Slide | PDF

Fig. 4 Differential reflectance sensitivity for monochromatic light at 450 nm (solid line) compared to the averaged sensitivity defined as

(Δ R (d_{1}, d_{2}_{m}) - Δ R (0, d_{2}_{m})) / (d_{1} Δ R (0, d_{2}_{m}))

with d₁ = 1nm and ΔR calculated by averaging R(d₁,d_2m), R(d₁,0) and R(0,d_2m) from (1) over the spectral range 425-475nm. Here, n₀ = 1.34 and δ_2m≈3π/4.

Download Full Size | PPT Slide | PDF

Fig. 5 The squares are the silicon oxide square islands surrounded by bare silicon. The island side is 10 μm and the pitch 20 μm.

Download Full Size | PPT Slide | PDF

Fig. 6 Schematic cross section and photograph of the opto-fluidic structure. In (a) the objective light is focused on the oxide pattern within the fluidic structure. The Al plate seals the structure by applying pressure on the quartz cover against the PDMS gasket and the underlying silicon wafer. The shaded area is the assay buffer solution on top of the SiO2 squares (shown out of scale). In (b) the gasket is illustrated sandwiched between the quartz cover (shown as a disk) and the silicon wafer below. In the gasket the four diamond shaped bioreaction fluidic chambers are connected to the reagent supply tubing. Also shown is the top Al plate with the optical window and two of the clamping screws.

Download Full Size | PPT Slide | PDF

Fig. 7 Digital images of the patterned wafer (a,b) and Fourier transform (c). The digital image as a 2x2 array before (a) and after the reaction (b) with 20 nM streptavidin for 4000 seconds. In (b) the contrast is visibly lower than in (a). Two dimensional Fourier transform of the microscope image (c). The position of the sharp peak corresponds to the number of square islands in the X and Y direction.

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Fig. 8 Experimental results for three streptavidin concentrations: 20 nM, 10 nM and 5nM. The signal plotted is the peak in the Fourier transform domain normalized by its value at 0 time. The analyte is introduced after the first 120 shots (vertical arrow). Every shot takes 4 seconds. In the 5 nM plot, the straight line segment between shots 713 and 787 is an extrapolation of missing data due to air bubbles.

Download Full Size | PPT Slide | PDF

Equations (17)

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R (d_{1}, d_{2}) = \frac{r_{1}^{2} r_{2}^{2} r_{3}^{2} + r_{1}^{2} + r_{2}^{2} + r_{3}^{2} + F (δ_{1}, δ_{2})}{1 + r_{1}^{2} r_{2}^{2} + r_{2}^{2} r_{3}^{2} + r_{1}^{2} r_{3}^{2} + F (δ_{1}, δ_{2})}

δ_{i} = \frac{2 π n_{i} d_{i}}{λ_{0}}

r_{i} = \frac{(n_{i - 1} - n_{i})}{(n_{i - 1} + n_{i})}

\begin{array}{l} F (δ_{1}, δ_{2}) = 2 r_{1} r_{2} [r_{3}^{2} + 1] \cos (2 δ_{1}) + 2 r_{3} r_{2} [r_{1}^{2} + 1] \cos (2 δ_{2}) + \\ 2 r_{3} r_{1} \cos (2 δ_{1} + 2 δ_{2}) + 2 r_{2}^{2} r_{3} r_{1} \cos (2 δ_{1} - 2 δ_{2}) ​ \end{array}

\partial R / \partial d_{1} = (2 π n_{1} / λ_{0}) \frac{\partial F (δ_{1}, δ_{2})}{\partial δ_{1}} \frac{(1 - r_{1}^{2}) (1 - r_{2}^{2}) (1 - r_{3}^{2})}{{[1 + r_{1}^{2} r_{2}^{2} + r_{2}^{2} r_{3}^{2} + r_{1}^{2} r_{3}^{2} + F (δ_{1}, δ_{2})]}^{2}}

\partial R / \partial d_{1} = - 4 (2 π n_{1} / λ_{0}) r_{1} r_{3} \sin (2 δ_{2}) \frac{(1 - r_{1}^{2}) (1 - r_{2}^{4}) (1 - r_{3}^{2})}{{[1 + F R (r_{1}, r_{2}, r_{3}) + C R (r_{1}, r_{2}, r_{3}) \cos (2 δ_{2})]}^{2}}

F R (r_{1}, r_{2}, r_{3}) = r_{1}^{2} r_{2}^{2} + r_{2}^{2} r_{3}^{2} + r_{1}^{2} r_{3}^{2} + 2 r_{1} r_{2} (r_{3}^{2} + 1)

C R (r_{1}, r_{2}, r_{3}) = 2 r_{3} (r_{1} + r_{2}) (1 + r_{1} r_{2})

\partial R (d_{1}, 0) / \partial d_{1} = 0

\begin{array}{l} \frac{\partial (\partial R / \partial d_{1})}{\partial d_{2}} = 0 \to \\ \cos (2 δ_{2 m}) = \frac{1 + F R (r_{1}, r_{2}^{}, r_{3}) - \sqrt{{(1 + F R (r_{1}, r_{2}, r_{3}))}^{2} + 8 C R {(r_{1}, r_{2}, r_{3})}^{2}}}{2 C R (r_{1}, r_{2}^{}, r_{3})} \end{array}

\partial R (d_{1}, d_{2}_{m}) / \partial d_{1}_{} \approx \pm 4 (2 π n_{1} / λ_{0}) r_{1} r_{3} (1 - r_{3}^{2})

Δ R (d_{1}, d_{2}_{m}) = R (d_{1}, 0) - R (d_{1}, d_{2}_{m})

\begin{array}{l} \partial Δ R (d_{1}, d_{2}_{m}) / \partial d_{1} = 4 (2 π n_{1} / λ_{0}) r_{1} r_{3} \sin (2 δ_{2 m}) \times \\ \frac{(1 - r_{1}^{2}) (1 - r_{2}^{4}) (1 - r_{3}^{2})}{[1 + r_{1}^{2} r_{2}^{2} + r_{2}^{2} r_{3}^{2} + r_{1}^{2} r_{3}^{2} + 2 r_{1} r_{2} (r_{3}^{2} + 1)) + 2 r_{3} (r_{1} + r_{2}) (1 + r_{1} r_{2}) \cos (2 δ_{2 m})]^{2}} \end{array}

Δ R_{0} = R (0, 0) - R (0, d_{2 m}) = \frac{{(r_{1, 2} + r_{3})}^{2}}{{(r_{1, 2} r_{3} + 1)}^{2}} - \frac{r_{1, 2}^{2} + r_{3}^{2} + 2 r_{3} r_{1, 2} \cos (2 δ_{2 m})}{1 + r_{1, 2}^{2} r_{3}^{2} + 2 r_{3} r_{1, 2} \cos (2 δ_{2 m})}

r_{1, 2} = \frac{n_{0} - n_{2}}{n_{0} + n_{2}}

\frac{\partial Δ R (d_{1}, d_{2}_{m}) / \partial d_{1}}{Δ R_{0}} \approx \pm \frac{2 (2 π n_{1} / λ_{0}) r_{1}}{r_{1, 2}} = \pm (4 π n_{1} / λ_{0}) \frac{n_{0} - n_{1}}{n_{0} + n_{1}} \frac{n_{0} + n_{2}}{n_{0} - n_{2}}

\begin{array}{l} \frac{Δ R (d_{1}, d_{2}_{m}) - Δ R (0, d_{2}_{m})}{Δ R_{0}} = \frac{Δ R (d_{1}, d_{2}_{m}) - Δ R_{0}}{Δ R_{0}} \approx \pm 2 \frac{2 π n_{1}}{λ_{0}} \frac{n_{0} - n_{1}}{n_{0} + n_{1}} \frac{n_{0} + n_{2}}{n_{0} - n_{2}} d_{1} \to \\ d_{1} ≃ | \frac{Δ R (d_{1}, d_{2}_{m}) - Δ R_{0}}{Δ R_{0}} \frac{λ_{0}}{4 π n_{1}} \frac{n_{0} + n_{1}}{n_{0} - n_{1}} \frac{n_{0} - n_{2}}{n_{0} + n_{2}} | \end{array}

Abstract

References

2012 (2)

2010 (2)

2007 (1)

2006 (1)

2004 (1)

2002 (1)

2000 (1)

1993 (1)

Bailey, R. C.

Beltsios, K.

Bockova, M.

Brecht, A.

Busse, S.

Dai, J.

Gauglitz, G.

Gregg, J. P.

Guo, X.

Guo, X. W.

He, L. P.

Herranz, S.

Homola, J.

Ihalainen, P.

Jin, K. J.

Kakabakos, S. E.

Kitsara, M.

Lam, K. S.

Landry, J. P.

Lu, H. B.

Luchansky, M. S.

Marazuela, M. D.

Menges, B.

Misiakos, K.

Mittler, S.

Moreno-Bondi, M. C.

Peltonen, J.

Petrou, P. S.

Polster, J.

Raptis, I.

Scheumann, V.

Sun, Y.

Sun, Y. S.

Turner, A. P. F.

Wang, J. Y.

Yang, G. Z.

Zavali, M.

Zhu, X.

Anal. Bioanal. Chem. (1)

Anal. Chem. (1)

Appl. Opt. (1)

Biosens. Bioelectron. (2)

J Biophotonics (1)

J. Appl. Phys. (1)

Micro & Nano Lett. (1)

Science (1)

Sens. Actuat. B (1)

Other (2)

Cited By

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Equations (17)

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