Abstract

A grating-coupled porous silicon (PSi) waveguide with an integrated polydimethylsiloxane (PDMS) flow cell is demonstrated as a platform for near real-time detection of chemical and biological molecules. This sensor platform not only allows for quantification of molecular binding events, but also provides a means to improve understanding of diffusion and binding mechanisms in constricted nanoscale geometries. Molecular binding events in the waveguide are monitored by angle-resolved reflectance measurements. Diffusion coefficients and adsorption and desorption rate constants of different sized chemical linkers and nucleic acid molecules are determined based on the rate of change of the measured resonance angle. Experimental results show that the diffusion coefficient in PSi is smaller than that in free solutions, and the PSi morphology slows the molecular adsorption rate constant by a factor of 102–104 compared to that of flat surface interactions. Calculations based on simplified mass balance equations and COMSOL simulations give good agreement with experimental data.

© 2012 OSA

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    [CrossRef] [PubMed]
  4. N. Darwish, D. Caballero, M. Moreno, A. Errachid, and J. Samitier, “Multi-analytic grating coupler biosensor for differential binding analysis,” Sens. Actuators B Chem.144(2), 413–417 (2010).
    [CrossRef]
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    [CrossRef] [PubMed]
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    [CrossRef] [PubMed]
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    [CrossRef]
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    [CrossRef] [PubMed]
  23. H. Matsuyama, M. Teramoto, and K. Suzuki, “Simulation of solute diffusion through porous media,” Sep. Sci. Technol.32(14), 2349–2366 (1997).
    [CrossRef]
  24. D. Mu, Z.-S. Liu, C. Huang, and N. Djilali, “Determination of the effective diffusion coefficient in porous media including Knudsen effects,” Microfluid. Nanofluid.4(3), 257–260 (2008).
    [CrossRef]
  25. K. P. Saripalli, R. J. Serne, P. D. Meyer, and B. P. McGrail, “Prediction of diffusion coefficients in porous media using tortuosity factors based on interfacial areas,” Ground Water40(4), 346–352 (2002).
    [CrossRef] [PubMed]
  26. A. E. Nkodo, J. M. Garnier, B. Tinland, H. J. Ren, C. Desruisseaux, L. C. McCormick, G. Drouin, and G. W. Slater, “Diffusion coefficient of DNA molecules during free solution electrophoresis,” Electrophoresis22(12), 2424–2432 (2001).
    [CrossRef] [PubMed]
  27. J. H. Park and N. R. Aluru, “Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface,” Appl. Phys. Lett.96(12), 123703 (2010).
    [CrossRef] [PubMed]
  28. E. S. Jeng, A. E. Moll, A. C. Roy, J. B. Gastala, and M. S. Strano, “Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes,” Nano Lett.6(3), 371–375 (2006).
    [CrossRef] [PubMed]

2011 (7)

Y. D. Yin and X. S. Zhao, “Kinetics and dynamics of DNA hybridization,” Acc. Chem. Res.44(11), 1172–1181 (2011).
[CrossRef] [PubMed]

V. Goral, Q. Wu, H. Y. Sun, and Y. Fang, “Label-free optical biosensor with microfluidics for sensing ligand-directed functional selectivity on trafficking of thrombin receptor,” FEBS Lett.585(7), 1054–1060 (2011).
[CrossRef] [PubMed]

P. Kozma, A. Hamori, S. Kurunczi, K. Cottier, and R. Horvath, “Grating coupled optical waveguide interferometer for label-free biosensing,” Sens. Actuators B Chem.155(2), 446–450 (2011).
[CrossRef]

T. Claes, W. Bogaerts, and P. Bienstman, “Vernier-cascade label-free biosensor with integrated arrayed waveguide grating for wavelength interrogation with low-cost broadband source,” Opt. Lett.36(17), 3320–3322 (2011).
[CrossRef] [PubMed]

X. Wei and S. M. Weiss, “Guided mode biosensor based on grating coupled porous silicon waveguide,” Opt. Express19(12), 11330–11339 (2011).
[CrossRef] [PubMed]

T. D. Lazzara, I. Mey, C. Steinem, and A. Janshoff, “Benefits and limitations of porous substrates as biosensors for protein adsorption,” Anal. Chem.83(14), 5624–5630 (2011).
[CrossRef] [PubMed]

J. W. Mares and S. M. Weiss, “Diffusion dynamics of small molecules from mesoporous silicon films by real-time optical interferometry,” Appl. Opt.50(27), 5329–5337 (2011).
[CrossRef] [PubMed]

2010 (5)

J. H. Park and N. R. Aluru, “Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface,” Appl. Phys. Lett.96(12), 123703 (2010).
[CrossRef] [PubMed]

J. L. Lawrie, Y. Jiao, and S. M. Weiss, “Size-dependent infiltration and optical detection of nucleic acids in nanoscale pores,” IEEE Trans. NanoTechnol.9(5), 596–602 (2010).
[CrossRef]

A. W. Marczewski, “Analysis of kinetic Langmuir model. Part I: Integrated kinetic Langmuir equation (IKL): a new complete analytical solution of the Langmuir rate equation,” Langmuir26(19), 15229–15238 (2010).
[CrossRef] [PubMed]

H. N. Daghestani and B. W. Day, “Theory and applications of surface plasmon resonance, resonant mirror, resonant waveguide grating, and dual polarization interferometry biosensors,” Sensors (Basel)10(11), 9630–9646 (2010).
[CrossRef] [PubMed]

N. Darwish, D. Caballero, M. Moreno, A. Errachid, and J. Samitier, “Multi-analytic grating coupler biosensor for differential binding analysis,” Sens. Actuators B Chem.144(2), 413–417 (2010).
[CrossRef]

2008 (3)

X. Wei, C. Kang, M. Liscidini, G. Rong, S. T. Retterer, M. Patrini, J. E. Sipe, and S. M. Weiss, “Grating couplers on porous silicon planar waveguides for sensing applications,” J. Appl. Phys.104(12), 123113 (2008).
[CrossRef]

Z. A. Lai, Y. L. Wang, N. Allbritton, G. P. Li, and M. Bachman, “Label-free biosensor by protein grating coupler on planar optical waveguides,” Opt. Lett.33(15), 1735–1737 (2008).
[CrossRef] [PubMed]

D. Mu, Z.-S. Liu, C. Huang, and N. Djilali, “Determination of the effective diffusion coefficient in porous media including Knudsen effects,” Microfluid. Nanofluid.4(3), 257–260 (2008).
[CrossRef]

2007 (2)

N. Kim, I. S. Park, and W. Y. Kim, “Salmonella detection with a direct-binding optical grating coupler immunosensor,” Sens. Actuators B Chem.121(2), 606–615 (2007).
[CrossRef]

K. Schmitt, B. Schirmer, C. Hoffmann, A. Brandenburg, and P. Meyrueis, “Interferometric biosensor based on planar optical waveguide sensor chips for label-free detection of surface bound bioreactions,” Biosens. Bioelectron.22(11), 2591–2597 (2007).
[CrossRef] [PubMed]

2006 (3)

J. N. Yih, Y. M. Chu, Y. C. Mao, W. H. Wang, F. C. Chien, C. Y. Lin, K. L. Lee, P. K. Wei, and S. J. Chen, “Optical waveguide biosensors constructed with subwavelength gratings,” Appl. Opt.45(9), 1938–1942 (2006).
[CrossRef] [PubMed]

Y. Gao, L. K. Wolf, and R. M. Georgiadis, “Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison,” Nucleic Acids Res.34(11), 3370–3377 (2006).
[CrossRef] [PubMed]

E. S. Jeng, A. E. Moll, A. C. Roy, J. B. Gastala, and M. S. Strano, “Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes,” Nano Lett.6(3), 371–375 (2006).
[CrossRef] [PubMed]

2005 (1)

H. K. Wu, B. Huang, and R. N. Zare, “Construction of microfluidic chips using polydimethylsiloxane for adhesive bonding,” Lab Chip5(12), 1393–1398 (2005).
[CrossRef] [PubMed]

2002 (3)

J. C. McDonald and G. M. Whitesides, “Poly(dimethylsiloxane) as a material for fabricating microfluidic devices,” Acc. Chem. Res.35(7), 491–499 (2002).
[CrossRef] [PubMed]

J. Vörös, J. J. Ramsden, G. Csúcs, I. Szendro, S. M. De Paul, M. Textor, and N. D. Spencer, “Optical grating coupler biosensors,” Biomaterials23(17), 3699–3710 (2002).
[CrossRef] [PubMed]

K. P. Saripalli, R. J. Serne, P. D. Meyer, and B. P. McGrail, “Prediction of diffusion coefficients in porous media using tortuosity factors based on interfacial areas,” Ground Water40(4), 346–352 (2002).
[CrossRef] [PubMed]

2001 (2)

A. E. Nkodo, J. M. Garnier, B. Tinland, H. J. Ren, C. Desruisseaux, L. C. McCormick, G. Drouin, and G. W. Slater, “Diffusion coefficient of DNA molecules during free solution electrophoresis,” Electrophoresis22(12), 2424–2432 (2001).
[CrossRef] [PubMed]

G. M. Whitesides, E. Ostuni, S. Takayama, X. Jiang, and D. E. Ingber, “Soft lithography in biology and biochemistry,” Annu. Rev. Biomed. Eng.3(1), 335–373 (2001).
[CrossRef] [PubMed]

1997 (1)

H. Matsuyama, M. Teramoto, and K. Suzuki, “Simulation of solute diffusion through porous media,” Sep. Sci. Technol.32(14), 2349–2366 (1997).
[CrossRef]

1994 (1)

J. J. Ramsden, S. Y. Li, J. E. Prenosil, and E. Heinzle, “Kinetics of adhesion and spreading of animal cells,” Biotechnol. Bioeng.43(10), 939–945 (1994).
[CrossRef] [PubMed]

Allbritton, N.

Aluru, N. R.

J. H. Park and N. R. Aluru, “Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface,” Appl. Phys. Lett.96(12), 123703 (2010).
[CrossRef] [PubMed]

Bachman, M.

Bienstman, P.

Bogaerts, W.

Brandenburg, A.

K. Schmitt, B. Schirmer, C. Hoffmann, A. Brandenburg, and P. Meyrueis, “Interferometric biosensor based on planar optical waveguide sensor chips for label-free detection of surface bound bioreactions,” Biosens. Bioelectron.22(11), 2591–2597 (2007).
[CrossRef] [PubMed]

Caballero, D.

N. Darwish, D. Caballero, M. Moreno, A. Errachid, and J. Samitier, “Multi-analytic grating coupler biosensor for differential binding analysis,” Sens. Actuators B Chem.144(2), 413–417 (2010).
[CrossRef]

Chen, S. J.

Chien, F. C.

Chu, Y. M.

Claes, T.

Cottier, K.

P. Kozma, A. Hamori, S. Kurunczi, K. Cottier, and R. Horvath, “Grating coupled optical waveguide interferometer for label-free biosensing,” Sens. Actuators B Chem.155(2), 446–450 (2011).
[CrossRef]

Csúcs, G.

J. Vörös, J. J. Ramsden, G. Csúcs, I. Szendro, S. M. De Paul, M. Textor, and N. D. Spencer, “Optical grating coupler biosensors,” Biomaterials23(17), 3699–3710 (2002).
[CrossRef] [PubMed]

Daghestani, H. N.

H. N. Daghestani and B. W. Day, “Theory and applications of surface plasmon resonance, resonant mirror, resonant waveguide grating, and dual polarization interferometry biosensors,” Sensors (Basel)10(11), 9630–9646 (2010).
[CrossRef] [PubMed]

Darwish, N.

N. Darwish, D. Caballero, M. Moreno, A. Errachid, and J. Samitier, “Multi-analytic grating coupler biosensor for differential binding analysis,” Sens. Actuators B Chem.144(2), 413–417 (2010).
[CrossRef]

Day, B. W.

H. N. Daghestani and B. W. Day, “Theory and applications of surface plasmon resonance, resonant mirror, resonant waveguide grating, and dual polarization interferometry biosensors,” Sensors (Basel)10(11), 9630–9646 (2010).
[CrossRef] [PubMed]

De Paul, S. M.

J. Vörös, J. J. Ramsden, G. Csúcs, I. Szendro, S. M. De Paul, M. Textor, and N. D. Spencer, “Optical grating coupler biosensors,” Biomaterials23(17), 3699–3710 (2002).
[CrossRef] [PubMed]

Desruisseaux, C.

A. E. Nkodo, J. M. Garnier, B. Tinland, H. J. Ren, C. Desruisseaux, L. C. McCormick, G. Drouin, and G. W. Slater, “Diffusion coefficient of DNA molecules during free solution electrophoresis,” Electrophoresis22(12), 2424–2432 (2001).
[CrossRef] [PubMed]

Djilali, N.

D. Mu, Z.-S. Liu, C. Huang, and N. Djilali, “Determination of the effective diffusion coefficient in porous media including Knudsen effects,” Microfluid. Nanofluid.4(3), 257–260 (2008).
[CrossRef]

Drouin, G.

A. E. Nkodo, J. M. Garnier, B. Tinland, H. J. Ren, C. Desruisseaux, L. C. McCormick, G. Drouin, and G. W. Slater, “Diffusion coefficient of DNA molecules during free solution electrophoresis,” Electrophoresis22(12), 2424–2432 (2001).
[CrossRef] [PubMed]

Errachid, A.

N. Darwish, D. Caballero, M. Moreno, A. Errachid, and J. Samitier, “Multi-analytic grating coupler biosensor for differential binding analysis,” Sens. Actuators B Chem.144(2), 413–417 (2010).
[CrossRef]

Fang, Y.

V. Goral, Q. Wu, H. Y. Sun, and Y. Fang, “Label-free optical biosensor with microfluidics for sensing ligand-directed functional selectivity on trafficking of thrombin receptor,” FEBS Lett.585(7), 1054–1060 (2011).
[CrossRef] [PubMed]

Gao, Y.

Y. Gao, L. K. Wolf, and R. M. Georgiadis, “Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison,” Nucleic Acids Res.34(11), 3370–3377 (2006).
[CrossRef] [PubMed]

Garnier, J. M.

A. E. Nkodo, J. M. Garnier, B. Tinland, H. J. Ren, C. Desruisseaux, L. C. McCormick, G. Drouin, and G. W. Slater, “Diffusion coefficient of DNA molecules during free solution electrophoresis,” Electrophoresis22(12), 2424–2432 (2001).
[CrossRef] [PubMed]

Gastala, J. B.

E. S. Jeng, A. E. Moll, A. C. Roy, J. B. Gastala, and M. S. Strano, “Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes,” Nano Lett.6(3), 371–375 (2006).
[CrossRef] [PubMed]

Georgiadis, R. M.

Y. Gao, L. K. Wolf, and R. M. Georgiadis, “Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison,” Nucleic Acids Res.34(11), 3370–3377 (2006).
[CrossRef] [PubMed]

Goral, V.

V. Goral, Q. Wu, H. Y. Sun, and Y. Fang, “Label-free optical biosensor with microfluidics for sensing ligand-directed functional selectivity on trafficking of thrombin receptor,” FEBS Lett.585(7), 1054–1060 (2011).
[CrossRef] [PubMed]

Hamori, A.

P. Kozma, A. Hamori, S. Kurunczi, K. Cottier, and R. Horvath, “Grating coupled optical waveguide interferometer for label-free biosensing,” Sens. Actuators B Chem.155(2), 446–450 (2011).
[CrossRef]

Heinzle, E.

J. J. Ramsden, S. Y. Li, J. E. Prenosil, and E. Heinzle, “Kinetics of adhesion and spreading of animal cells,” Biotechnol. Bioeng.43(10), 939–945 (1994).
[CrossRef] [PubMed]

Hoffmann, C.

K. Schmitt, B. Schirmer, C. Hoffmann, A. Brandenburg, and P. Meyrueis, “Interferometric biosensor based on planar optical waveguide sensor chips for label-free detection of surface bound bioreactions,” Biosens. Bioelectron.22(11), 2591–2597 (2007).
[CrossRef] [PubMed]

Horvath, R.

P. Kozma, A. Hamori, S. Kurunczi, K. Cottier, and R. Horvath, “Grating coupled optical waveguide interferometer for label-free biosensing,” Sens. Actuators B Chem.155(2), 446–450 (2011).
[CrossRef]

Huang, B.

H. K. Wu, B. Huang, and R. N. Zare, “Construction of microfluidic chips using polydimethylsiloxane for adhesive bonding,” Lab Chip5(12), 1393–1398 (2005).
[CrossRef] [PubMed]

Huang, C.

D. Mu, Z.-S. Liu, C. Huang, and N. Djilali, “Determination of the effective diffusion coefficient in porous media including Knudsen effects,” Microfluid. Nanofluid.4(3), 257–260 (2008).
[CrossRef]

Ingber, D. E.

G. M. Whitesides, E. Ostuni, S. Takayama, X. Jiang, and D. E. Ingber, “Soft lithography in biology and biochemistry,” Annu. Rev. Biomed. Eng.3(1), 335–373 (2001).
[CrossRef] [PubMed]

Janshoff, A.

T. D. Lazzara, I. Mey, C. Steinem, and A. Janshoff, “Benefits and limitations of porous substrates as biosensors for protein adsorption,” Anal. Chem.83(14), 5624–5630 (2011).
[CrossRef] [PubMed]

Jeng, E. S.

E. S. Jeng, A. E. Moll, A. C. Roy, J. B. Gastala, and M. S. Strano, “Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes,” Nano Lett.6(3), 371–375 (2006).
[CrossRef] [PubMed]

Jiang, X.

G. M. Whitesides, E. Ostuni, S. Takayama, X. Jiang, and D. E. Ingber, “Soft lithography in biology and biochemistry,” Annu. Rev. Biomed. Eng.3(1), 335–373 (2001).
[CrossRef] [PubMed]

Jiao, Y.

J. L. Lawrie, Y. Jiao, and S. M. Weiss, “Size-dependent infiltration and optical detection of nucleic acids in nanoscale pores,” IEEE Trans. NanoTechnol.9(5), 596–602 (2010).
[CrossRef]

Kang, C.

X. Wei, C. Kang, M. Liscidini, G. Rong, S. T. Retterer, M. Patrini, J. E. Sipe, and S. M. Weiss, “Grating couplers on porous silicon planar waveguides for sensing applications,” J. Appl. Phys.104(12), 123113 (2008).
[CrossRef]

Kim, N.

N. Kim, I. S. Park, and W. Y. Kim, “Salmonella detection with a direct-binding optical grating coupler immunosensor,” Sens. Actuators B Chem.121(2), 606–615 (2007).
[CrossRef]

Kim, W. Y.

N. Kim, I. S. Park, and W. Y. Kim, “Salmonella detection with a direct-binding optical grating coupler immunosensor,” Sens. Actuators B Chem.121(2), 606–615 (2007).
[CrossRef]

Kozma, P.

P. Kozma, A. Hamori, S. Kurunczi, K. Cottier, and R. Horvath, “Grating coupled optical waveguide interferometer for label-free biosensing,” Sens. Actuators B Chem.155(2), 446–450 (2011).
[CrossRef]

Kurunczi, S.

P. Kozma, A. Hamori, S. Kurunczi, K. Cottier, and R. Horvath, “Grating coupled optical waveguide interferometer for label-free biosensing,” Sens. Actuators B Chem.155(2), 446–450 (2011).
[CrossRef]

Lai, Z. A.

Lawrie, J. L.

J. L. Lawrie, Y. Jiao, and S. M. Weiss, “Size-dependent infiltration and optical detection of nucleic acids in nanoscale pores,” IEEE Trans. NanoTechnol.9(5), 596–602 (2010).
[CrossRef]

Lazzara, T. D.

T. D. Lazzara, I. Mey, C. Steinem, and A. Janshoff, “Benefits and limitations of porous substrates as biosensors for protein adsorption,” Anal. Chem.83(14), 5624–5630 (2011).
[CrossRef] [PubMed]

Lee, K. L.

Li, G. P.

Li, S. Y.

J. J. Ramsden, S. Y. Li, J. E. Prenosil, and E. Heinzle, “Kinetics of adhesion and spreading of animal cells,” Biotechnol. Bioeng.43(10), 939–945 (1994).
[CrossRef] [PubMed]

Lin, C. Y.

Liscidini, M.

X. Wei, C. Kang, M. Liscidini, G. Rong, S. T. Retterer, M. Patrini, J. E. Sipe, and S. M. Weiss, “Grating couplers on porous silicon planar waveguides for sensing applications,” J. Appl. Phys.104(12), 123113 (2008).
[CrossRef]

Liu, Z.-S.

D. Mu, Z.-S. Liu, C. Huang, and N. Djilali, “Determination of the effective diffusion coefficient in porous media including Knudsen effects,” Microfluid. Nanofluid.4(3), 257–260 (2008).
[CrossRef]

Mao, Y. C.

Marczewski, A. W.

A. W. Marczewski, “Analysis of kinetic Langmuir model. Part I: Integrated kinetic Langmuir equation (IKL): a new complete analytical solution of the Langmuir rate equation,” Langmuir26(19), 15229–15238 (2010).
[CrossRef] [PubMed]

Mares, J. W.

Matsuyama, H.

H. Matsuyama, M. Teramoto, and K. Suzuki, “Simulation of solute diffusion through porous media,” Sep. Sci. Technol.32(14), 2349–2366 (1997).
[CrossRef]

McCormick, L. C.

A. E. Nkodo, J. M. Garnier, B. Tinland, H. J. Ren, C. Desruisseaux, L. C. McCormick, G. Drouin, and G. W. Slater, “Diffusion coefficient of DNA molecules during free solution electrophoresis,” Electrophoresis22(12), 2424–2432 (2001).
[CrossRef] [PubMed]

McDonald, J. C.

J. C. McDonald and G. M. Whitesides, “Poly(dimethylsiloxane) as a material for fabricating microfluidic devices,” Acc. Chem. Res.35(7), 491–499 (2002).
[CrossRef] [PubMed]

McGrail, B. P.

K. P. Saripalli, R. J. Serne, P. D. Meyer, and B. P. McGrail, “Prediction of diffusion coefficients in porous media using tortuosity factors based on interfacial areas,” Ground Water40(4), 346–352 (2002).
[CrossRef] [PubMed]

Mey, I.

T. D. Lazzara, I. Mey, C. Steinem, and A. Janshoff, “Benefits and limitations of porous substrates as biosensors for protein adsorption,” Anal. Chem.83(14), 5624–5630 (2011).
[CrossRef] [PubMed]

Meyer, P. D.

K. P. Saripalli, R. J. Serne, P. D. Meyer, and B. P. McGrail, “Prediction of diffusion coefficients in porous media using tortuosity factors based on interfacial areas,” Ground Water40(4), 346–352 (2002).
[CrossRef] [PubMed]

Meyrueis, P.

K. Schmitt, B. Schirmer, C. Hoffmann, A. Brandenburg, and P. Meyrueis, “Interferometric biosensor based on planar optical waveguide sensor chips for label-free detection of surface bound bioreactions,” Biosens. Bioelectron.22(11), 2591–2597 (2007).
[CrossRef] [PubMed]

Moll, A. E.

E. S. Jeng, A. E. Moll, A. C. Roy, J. B. Gastala, and M. S. Strano, “Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes,” Nano Lett.6(3), 371–375 (2006).
[CrossRef] [PubMed]

Moreno, M.

N. Darwish, D. Caballero, M. Moreno, A. Errachid, and J. Samitier, “Multi-analytic grating coupler biosensor for differential binding analysis,” Sens. Actuators B Chem.144(2), 413–417 (2010).
[CrossRef]

Mu, D.

D. Mu, Z.-S. Liu, C. Huang, and N. Djilali, “Determination of the effective diffusion coefficient in porous media including Knudsen effects,” Microfluid. Nanofluid.4(3), 257–260 (2008).
[CrossRef]

Nkodo, A. E.

A. E. Nkodo, J. M. Garnier, B. Tinland, H. J. Ren, C. Desruisseaux, L. C. McCormick, G. Drouin, and G. W. Slater, “Diffusion coefficient of DNA molecules during free solution electrophoresis,” Electrophoresis22(12), 2424–2432 (2001).
[CrossRef] [PubMed]

Ostuni, E.

G. M. Whitesides, E. Ostuni, S. Takayama, X. Jiang, and D. E. Ingber, “Soft lithography in biology and biochemistry,” Annu. Rev. Biomed. Eng.3(1), 335–373 (2001).
[CrossRef] [PubMed]

Park, I. S.

N. Kim, I. S. Park, and W. Y. Kim, “Salmonella detection with a direct-binding optical grating coupler immunosensor,” Sens. Actuators B Chem.121(2), 606–615 (2007).
[CrossRef]

Park, J. H.

J. H. Park and N. R. Aluru, “Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface,” Appl. Phys. Lett.96(12), 123703 (2010).
[CrossRef] [PubMed]

Patrini, M.

X. Wei, C. Kang, M. Liscidini, G. Rong, S. T. Retterer, M. Patrini, J. E. Sipe, and S. M. Weiss, “Grating couplers on porous silicon planar waveguides for sensing applications,” J. Appl. Phys.104(12), 123113 (2008).
[CrossRef]

Prenosil, J. E.

J. J. Ramsden, S. Y. Li, J. E. Prenosil, and E. Heinzle, “Kinetics of adhesion and spreading of animal cells,” Biotechnol. Bioeng.43(10), 939–945 (1994).
[CrossRef] [PubMed]

Ramsden, J. J.

J. Vörös, J. J. Ramsden, G. Csúcs, I. Szendro, S. M. De Paul, M. Textor, and N. D. Spencer, “Optical grating coupler biosensors,” Biomaterials23(17), 3699–3710 (2002).
[CrossRef] [PubMed]

J. J. Ramsden, S. Y. Li, J. E. Prenosil, and E. Heinzle, “Kinetics of adhesion and spreading of animal cells,” Biotechnol. Bioeng.43(10), 939–945 (1994).
[CrossRef] [PubMed]

Ren, H. J.

A. E. Nkodo, J. M. Garnier, B. Tinland, H. J. Ren, C. Desruisseaux, L. C. McCormick, G. Drouin, and G. W. Slater, “Diffusion coefficient of DNA molecules during free solution electrophoresis,” Electrophoresis22(12), 2424–2432 (2001).
[CrossRef] [PubMed]

Retterer, S. T.

X. Wei, C. Kang, M. Liscidini, G. Rong, S. T. Retterer, M. Patrini, J. E. Sipe, and S. M. Weiss, “Grating couplers on porous silicon planar waveguides for sensing applications,” J. Appl. Phys.104(12), 123113 (2008).
[CrossRef]

Rong, G.

X. Wei, C. Kang, M. Liscidini, G. Rong, S. T. Retterer, M. Patrini, J. E. Sipe, and S. M. Weiss, “Grating couplers on porous silicon planar waveguides for sensing applications,” J. Appl. Phys.104(12), 123113 (2008).
[CrossRef]

Roy, A. C.

E. S. Jeng, A. E. Moll, A. C. Roy, J. B. Gastala, and M. S. Strano, “Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes,” Nano Lett.6(3), 371–375 (2006).
[CrossRef] [PubMed]

Samitier, J.

N. Darwish, D. Caballero, M. Moreno, A. Errachid, and J. Samitier, “Multi-analytic grating coupler biosensor for differential binding analysis,” Sens. Actuators B Chem.144(2), 413–417 (2010).
[CrossRef]

Saripalli, K. P.

K. P. Saripalli, R. J. Serne, P. D. Meyer, and B. P. McGrail, “Prediction of diffusion coefficients in porous media using tortuosity factors based on interfacial areas,” Ground Water40(4), 346–352 (2002).
[CrossRef] [PubMed]

Schirmer, B.

K. Schmitt, B. Schirmer, C. Hoffmann, A. Brandenburg, and P. Meyrueis, “Interferometric biosensor based on planar optical waveguide sensor chips for label-free detection of surface bound bioreactions,” Biosens. Bioelectron.22(11), 2591–2597 (2007).
[CrossRef] [PubMed]

Schmitt, K.

K. Schmitt, B. Schirmer, C. Hoffmann, A. Brandenburg, and P. Meyrueis, “Interferometric biosensor based on planar optical waveguide sensor chips for label-free detection of surface bound bioreactions,” Biosens. Bioelectron.22(11), 2591–2597 (2007).
[CrossRef] [PubMed]

Serne, R. J.

K. P. Saripalli, R. J. Serne, P. D. Meyer, and B. P. McGrail, “Prediction of diffusion coefficients in porous media using tortuosity factors based on interfacial areas,” Ground Water40(4), 346–352 (2002).
[CrossRef] [PubMed]

Sipe, J. E.

X. Wei, C. Kang, M. Liscidini, G. Rong, S. T. Retterer, M. Patrini, J. E. Sipe, and S. M. Weiss, “Grating couplers on porous silicon planar waveguides for sensing applications,” J. Appl. Phys.104(12), 123113 (2008).
[CrossRef]

Slater, G. W.

A. E. Nkodo, J. M. Garnier, B. Tinland, H. J. Ren, C. Desruisseaux, L. C. McCormick, G. Drouin, and G. W. Slater, “Diffusion coefficient of DNA molecules during free solution electrophoresis,” Electrophoresis22(12), 2424–2432 (2001).
[CrossRef] [PubMed]

Spencer, N. D.

J. Vörös, J. J. Ramsden, G. Csúcs, I. Szendro, S. M. De Paul, M. Textor, and N. D. Spencer, “Optical grating coupler biosensors,” Biomaterials23(17), 3699–3710 (2002).
[CrossRef] [PubMed]

Steinem, C.

T. D. Lazzara, I. Mey, C. Steinem, and A. Janshoff, “Benefits and limitations of porous substrates as biosensors for protein adsorption,” Anal. Chem.83(14), 5624–5630 (2011).
[CrossRef] [PubMed]

Strano, M. S.

E. S. Jeng, A. E. Moll, A. C. Roy, J. B. Gastala, and M. S. Strano, “Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes,” Nano Lett.6(3), 371–375 (2006).
[CrossRef] [PubMed]

Sun, H. Y.

V. Goral, Q. Wu, H. Y. Sun, and Y. Fang, “Label-free optical biosensor with microfluidics for sensing ligand-directed functional selectivity on trafficking of thrombin receptor,” FEBS Lett.585(7), 1054–1060 (2011).
[CrossRef] [PubMed]

Suzuki, K.

H. Matsuyama, M. Teramoto, and K. Suzuki, “Simulation of solute diffusion through porous media,” Sep. Sci. Technol.32(14), 2349–2366 (1997).
[CrossRef]

Szendro, I.

J. Vörös, J. J. Ramsden, G. Csúcs, I. Szendro, S. M. De Paul, M. Textor, and N. D. Spencer, “Optical grating coupler biosensors,” Biomaterials23(17), 3699–3710 (2002).
[CrossRef] [PubMed]

Takayama, S.

G. M. Whitesides, E. Ostuni, S. Takayama, X. Jiang, and D. E. Ingber, “Soft lithography in biology and biochemistry,” Annu. Rev. Biomed. Eng.3(1), 335–373 (2001).
[CrossRef] [PubMed]

Teramoto, M.

H. Matsuyama, M. Teramoto, and K. Suzuki, “Simulation of solute diffusion through porous media,” Sep. Sci. Technol.32(14), 2349–2366 (1997).
[CrossRef]

Textor, M.

J. Vörös, J. J. Ramsden, G. Csúcs, I. Szendro, S. M. De Paul, M. Textor, and N. D. Spencer, “Optical grating coupler biosensors,” Biomaterials23(17), 3699–3710 (2002).
[CrossRef] [PubMed]

Tinland, B.

A. E. Nkodo, J. M. Garnier, B. Tinland, H. J. Ren, C. Desruisseaux, L. C. McCormick, G. Drouin, and G. W. Slater, “Diffusion coefficient of DNA molecules during free solution electrophoresis,” Electrophoresis22(12), 2424–2432 (2001).
[CrossRef] [PubMed]

Vörös, J.

J. Vörös, J. J. Ramsden, G. Csúcs, I. Szendro, S. M. De Paul, M. Textor, and N. D. Spencer, “Optical grating coupler biosensors,” Biomaterials23(17), 3699–3710 (2002).
[CrossRef] [PubMed]

Wang, W. H.

Wang, Y. L.

Wei, P. K.

Wei, X.

X. Wei and S. M. Weiss, “Guided mode biosensor based on grating coupled porous silicon waveguide,” Opt. Express19(12), 11330–11339 (2011).
[CrossRef] [PubMed]

X. Wei, C. Kang, M. Liscidini, G. Rong, S. T. Retterer, M. Patrini, J. E. Sipe, and S. M. Weiss, “Grating couplers on porous silicon planar waveguides for sensing applications,” J. Appl. Phys.104(12), 123113 (2008).
[CrossRef]

Weiss, S. M.

X. Wei and S. M. Weiss, “Guided mode biosensor based on grating coupled porous silicon waveguide,” Opt. Express19(12), 11330–11339 (2011).
[CrossRef] [PubMed]

J. W. Mares and S. M. Weiss, “Diffusion dynamics of small molecules from mesoporous silicon films by real-time optical interferometry,” Appl. Opt.50(27), 5329–5337 (2011).
[CrossRef] [PubMed]

J. L. Lawrie, Y. Jiao, and S. M. Weiss, “Size-dependent infiltration and optical detection of nucleic acids in nanoscale pores,” IEEE Trans. NanoTechnol.9(5), 596–602 (2010).
[CrossRef]

X. Wei, C. Kang, M. Liscidini, G. Rong, S. T. Retterer, M. Patrini, J. E. Sipe, and S. M. Weiss, “Grating couplers on porous silicon planar waveguides for sensing applications,” J. Appl. Phys.104(12), 123113 (2008).
[CrossRef]

Whitesides, G. M.

J. C. McDonald and G. M. Whitesides, “Poly(dimethylsiloxane) as a material for fabricating microfluidic devices,” Acc. Chem. Res.35(7), 491–499 (2002).
[CrossRef] [PubMed]

G. M. Whitesides, E. Ostuni, S. Takayama, X. Jiang, and D. E. Ingber, “Soft lithography in biology and biochemistry,” Annu. Rev. Biomed. Eng.3(1), 335–373 (2001).
[CrossRef] [PubMed]

Wolf, L. K.

Y. Gao, L. K. Wolf, and R. M. Georgiadis, “Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison,” Nucleic Acids Res.34(11), 3370–3377 (2006).
[CrossRef] [PubMed]

Wu, H. K.

H. K. Wu, B. Huang, and R. N. Zare, “Construction of microfluidic chips using polydimethylsiloxane for adhesive bonding,” Lab Chip5(12), 1393–1398 (2005).
[CrossRef] [PubMed]

Wu, Q.

V. Goral, Q. Wu, H. Y. Sun, and Y. Fang, “Label-free optical biosensor with microfluidics for sensing ligand-directed functional selectivity on trafficking of thrombin receptor,” FEBS Lett.585(7), 1054–1060 (2011).
[CrossRef] [PubMed]

Yih, J. N.

Yin, Y. D.

Y. D. Yin and X. S. Zhao, “Kinetics and dynamics of DNA hybridization,” Acc. Chem. Res.44(11), 1172–1181 (2011).
[CrossRef] [PubMed]

Zare, R. N.

H. K. Wu, B. Huang, and R. N. Zare, “Construction of microfluidic chips using polydimethylsiloxane for adhesive bonding,” Lab Chip5(12), 1393–1398 (2005).
[CrossRef] [PubMed]

Zhao, X. S.

Y. D. Yin and X. S. Zhao, “Kinetics and dynamics of DNA hybridization,” Acc. Chem. Res.44(11), 1172–1181 (2011).
[CrossRef] [PubMed]

Acc. Chem. Res. (2)

Y. D. Yin and X. S. Zhao, “Kinetics and dynamics of DNA hybridization,” Acc. Chem. Res.44(11), 1172–1181 (2011).
[CrossRef] [PubMed]

J. C. McDonald and G. M. Whitesides, “Poly(dimethylsiloxane) as a material for fabricating microfluidic devices,” Acc. Chem. Res.35(7), 491–499 (2002).
[CrossRef] [PubMed]

Anal. Chem. (1)

T. D. Lazzara, I. Mey, C. Steinem, and A. Janshoff, “Benefits and limitations of porous substrates as biosensors for protein adsorption,” Anal. Chem.83(14), 5624–5630 (2011).
[CrossRef] [PubMed]

Annu. Rev. Biomed. Eng. (1)

G. M. Whitesides, E. Ostuni, S. Takayama, X. Jiang, and D. E. Ingber, “Soft lithography in biology and biochemistry,” Annu. Rev. Biomed. Eng.3(1), 335–373 (2001).
[CrossRef] [PubMed]

Appl. Opt. (2)

Appl. Phys. Lett. (1)

J. H. Park and N. R. Aluru, “Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface,” Appl. Phys. Lett.96(12), 123703 (2010).
[CrossRef] [PubMed]

Biomaterials (1)

J. Vörös, J. J. Ramsden, G. Csúcs, I. Szendro, S. M. De Paul, M. Textor, and N. D. Spencer, “Optical grating coupler biosensors,” Biomaterials23(17), 3699–3710 (2002).
[CrossRef] [PubMed]

Biosens. Bioelectron. (1)

K. Schmitt, B. Schirmer, C. Hoffmann, A. Brandenburg, and P. Meyrueis, “Interferometric biosensor based on planar optical waveguide sensor chips for label-free detection of surface bound bioreactions,” Biosens. Bioelectron.22(11), 2591–2597 (2007).
[CrossRef] [PubMed]

Biotechnol. Bioeng. (1)

J. J. Ramsden, S. Y. Li, J. E. Prenosil, and E. Heinzle, “Kinetics of adhesion and spreading of animal cells,” Biotechnol. Bioeng.43(10), 939–945 (1994).
[CrossRef] [PubMed]

Electrophoresis (1)

A. E. Nkodo, J. M. Garnier, B. Tinland, H. J. Ren, C. Desruisseaux, L. C. McCormick, G. Drouin, and G. W. Slater, “Diffusion coefficient of DNA molecules during free solution electrophoresis,” Electrophoresis22(12), 2424–2432 (2001).
[CrossRef] [PubMed]

FEBS Lett. (1)

V. Goral, Q. Wu, H. Y. Sun, and Y. Fang, “Label-free optical biosensor with microfluidics for sensing ligand-directed functional selectivity on trafficking of thrombin receptor,” FEBS Lett.585(7), 1054–1060 (2011).
[CrossRef] [PubMed]

Ground Water (1)

K. P. Saripalli, R. J. Serne, P. D. Meyer, and B. P. McGrail, “Prediction of diffusion coefficients in porous media using tortuosity factors based on interfacial areas,” Ground Water40(4), 346–352 (2002).
[CrossRef] [PubMed]

IEEE Trans. NanoTechnol. (1)

J. L. Lawrie, Y. Jiao, and S. M. Weiss, “Size-dependent infiltration and optical detection of nucleic acids in nanoscale pores,” IEEE Trans. NanoTechnol.9(5), 596–602 (2010).
[CrossRef]

J. Appl. Phys. (1)

X. Wei, C. Kang, M. Liscidini, G. Rong, S. T. Retterer, M. Patrini, J. E. Sipe, and S. M. Weiss, “Grating couplers on porous silicon planar waveguides for sensing applications,” J. Appl. Phys.104(12), 123113 (2008).
[CrossRef]

Lab Chip (1)

H. K. Wu, B. Huang, and R. N. Zare, “Construction of microfluidic chips using polydimethylsiloxane for adhesive bonding,” Lab Chip5(12), 1393–1398 (2005).
[CrossRef] [PubMed]

Langmuir (1)

A. W. Marczewski, “Analysis of kinetic Langmuir model. Part I: Integrated kinetic Langmuir equation (IKL): a new complete analytical solution of the Langmuir rate equation,” Langmuir26(19), 15229–15238 (2010).
[CrossRef] [PubMed]

Microfluid. Nanofluid. (1)

D. Mu, Z.-S. Liu, C. Huang, and N. Djilali, “Determination of the effective diffusion coefficient in porous media including Knudsen effects,” Microfluid. Nanofluid.4(3), 257–260 (2008).
[CrossRef]

Nano Lett. (1)

E. S. Jeng, A. E. Moll, A. C. Roy, J. B. Gastala, and M. S. Strano, “Detection of DNA hybridization using the near-infrared band-gap fluorescence of single-walled carbon nanotubes,” Nano Lett.6(3), 371–375 (2006).
[CrossRef] [PubMed]

Nucleic Acids Res. (1)

Y. Gao, L. K. Wolf, and R. M. Georgiadis, “Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison,” Nucleic Acids Res.34(11), 3370–3377 (2006).
[CrossRef] [PubMed]

Opt. Express (1)

Opt. Lett. (2)

Sens. Actuators B Chem. (3)

P. Kozma, A. Hamori, S. Kurunczi, K. Cottier, and R. Horvath, “Grating coupled optical waveguide interferometer for label-free biosensing,” Sens. Actuators B Chem.155(2), 446–450 (2011).
[CrossRef]

N. Darwish, D. Caballero, M. Moreno, A. Errachid, and J. Samitier, “Multi-analytic grating coupler biosensor for differential binding analysis,” Sens. Actuators B Chem.144(2), 413–417 (2010).
[CrossRef]

N. Kim, I. S. Park, and W. Y. Kim, “Salmonella detection with a direct-binding optical grating coupler immunosensor,” Sens. Actuators B Chem.121(2), 606–615 (2007).
[CrossRef]

Sensors (Basel) (1)

H. N. Daghestani and B. W. Day, “Theory and applications of surface plasmon resonance, resonant mirror, resonant waveguide grating, and dual polarization interferometry biosensors,” Sensors (Basel)10(11), 9630–9646 (2010).
[CrossRef] [PubMed]

Sep. Sci. Technol. (1)

H. Matsuyama, M. Teramoto, and K. Suzuki, “Simulation of solute diffusion through porous media,” Sep. Sci. Technol.32(14), 2349–2366 (1997).
[CrossRef]

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Figures (6)

Fig. 1
Fig. 1

Design of the PDMS flow cell integrated biosensor. (a) A schematic of the two components: the bottom is the PSi (light grey round area) with grating couplers (orange rectangular area); the top is the PDMS flow cell. (b) A picture of the fabricated device. (c) PSi waveguide integrated with the flow cell geometry used for Eqs. (2)(7). (d) A single pore cross-section geometry (axially symmetric) used for finite element simulations with COMSOL.

Fig. 2
Fig. 2

(a) Resonance angle shifts during the injections of DI water, 1%, 2%, 3%, 5%, 7.5% and 10% NaCl solutions. The blue circles are experimental data, and the red lines are the average value of each concentration and drawn as visual guides. (b) The relation between NaCl concentrations and resonance angle shifts with a linear fit shown. The typical variation in the resonance angle shift for each data point is ± 0.005°.

Fig. 3
Fig. 3

Resonance angle shift during the 3-APTES and Sulfo-SMCC attachments at room temperature. Blues circles are experimental data, and the fitted curve is shown for visual guidance. The gap between two curves (35–45 min) is for the 3-APTES annealing process.

Fig. 4
Fig. 4

Resonance angle shift during exposure to probe DNA, mismatch PNA, and antisense PNA, performed at 37°C. Blues circles are experimental data and the fitted curve is shown for visual guidance.

Fig. 5
Fig. 5

(a) Resonance angle shifts of integrated PSi waveguide biosensor during the injection of 3-APTES. The fitted curve is shown for visual guidance. (b) Time dependent change of 3-APTES surface coverage upon binding to a flat silicon surface.

Fig. 6
Fig. 6

Experimental (blue circle) and COMSOL simulated (red line) normalized resonance angle changes during (a) 3-APTES, (b) Sulfo-SMCC, (c) probe DNA and (d) antisense PNA binding in the PSi waveguide.

Tables (1)

Tables Icon

Table 1 Diffusion coefficient, adsorption and desorption rate constants of 3-APTES, Sulfo-SMCC, probe DNA and antisense PNA in PSi

Equations (7)

Equations on this page are rendered with MathJax. Learn more.

n eff = n c sinθ+m λ 0 Λ
c(y,t) t =D 2 c(y,t) y 2 ,0yb
at t=0,c= c b  for all 0yb,
for all t,c( y= b 2 )= c b ,
at y=0, dΓ(t) dt =D c(0,t) y = k ad c(0,t)( Γ max Γ(t)) k des Γ(t),
Γ(t)=2 c b Dt π S inlet S PSi
Γ(t)= Γ max k ad c b k ad c b + k des { 1exp[ ( k ad c b + k des )t ] } S inlet S PSi

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