Abstract

The development of microscale analytical techniques has created an increasing demand for reliable and accurate heating at the microscale. Here, we present a novel method for calibrating the temperature of microdroplets using quenched, fluorescently labeled DNA oligomers. Upon melting, the 3′ fluorophore of the reporter oligomer separates from the 5′ quencher of its reverse complement, creating a fluorescent signal recorded as a melting curve. The melting temperature for a given oligomer is determined with a conventional quantitative polymerase chain reaction (qPCR) instrument and used to calibrate the temperature within a microdroplet, with identical buffer concentrations, heated with an infrared laser. Since significant premelt fluorescence prevents the use of a conventional (single-term) sigmoid or logistic function to describe the melting curve, we present a three-term sigmoid model that provides a very good match to the asymmetric fluorescence melting curve with premelting. Using mixtures of three oligomers of different lengths, we fit multiple three-term sigmoids to obtain precise comparison of the microscale and macroscale fluorescence melting curves using “extrapolated two-state” melting temperatures.

© 2014 Optical Society of America

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    [CrossRef]
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    [CrossRef] [PubMed]
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  5. G. Velve Casquillas, C. Fu, M. Le Berre, J. Cramer, S. Meance, A. Plecis, D. Baigl, J.-J. Greffet, Y. Chen, M. Piel, and P. T. Tran, “Fast microfluidic temperature control for high resolution live cell imaging,” Lab Chip11(3), 484–489 (2011).
    [CrossRef] [PubMed]
  6. C. Fang, L. Shao, Y. Zhao, J. Wang, and H. Wu, “A gold nanocrystal/poly(dimethylsiloxane) composite for plasmonic heating on microfluidic chips,” Adv. Mater.24(1), 94–98 (2012).
    [CrossRef] [PubMed]
  7. K. J. Shaw, P. T. Docker, J. V. Yelland, C. E. Dyer, J. Greenman, G. M. Greenway, and S. J. Haswell, “Rapid PCR amplification using a microfluidic device with integrated microwave heating and air impingement cooling,” Lab Chip10(13), 1725–1728 (2010).
    [CrossRef] [PubMed]
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  12. H. Kim, S. Vishniakou, and G. W. Faris, “Petri dish PCR: Laser-heated reactions in nanoliter droplet arrays,” Lab Chip9(9), 1230–1235 (2009).
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    [CrossRef] [PubMed]
  24. A. T. Jonstrup, J. Fredsøe, and A. H. Andersen, “DNA hairpins as temperature switches, thermometers and ionic detectors,” Sensors (Basel)13(5), 5937–5944 (2013).
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  25. Y. You, A. V. Tataurov, and R. Owczarzy, “Measuring thermodynamic details of DNA hybridization using fluorescence,” Biopolymers95(7), 472–486 (2011).
    [CrossRef] [PubMed]
  26. J.-L. Mergny and L. Lacroix, “Analysis of thermal melting curves,” Oligonucleotides13(6), 515–537 (2003).
    [CrossRef] [PubMed]
  27. M. Peyrard, S. Cuesta-López, and G. James, “Nonlinear analysis of the dynamics of DNA breathing,” J. Biol. Phys.35(1), 73–89 (2009).
    [CrossRef] [PubMed]
  28. F. J. Richards, “A flexible growth function for empirical use,” J. Exp. Bot.10(2), 290–301 (1959).
    [CrossRef]
  29. J. H. Ricketts and G. A. Head, “A five-parameter logistic equation for investigating asymmetry of curvature in baroreflex studies,” Am. J. Physiol.277, R441–R454 (1999).
  30. J. SantaLucia., “A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics,” Proc. Natl. Acad. Sci. U.S.A.95(4), 1460–1465 (1998).
    [CrossRef] [PubMed]
  31. L. Movileanu, J. M. Benevides, and G. J. Thomas., “Temperature dependence of the Raman spectrum of DNA. II. Raman signatures of premelting and melting transitions of poly(dA).poly(dT) and comparison with poly(dA-dT).poly(dA-dT),” Biopolymers63(3), 181–194 (2002).
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    [CrossRef] [PubMed]

2013 (2)

J. A. Richardson, T. Morgan, M. Andreou, and T. Brown, “Use of a large Stokes-shift fluorophore to increase the multiplexing capacity of a point-of-care DNA diagnostic device,” Analyst (Lond.)138(13), 3626–3628 (2013).
[CrossRef] [PubMed]

A. T. Jonstrup, J. Fredsøe, and A. H. Andersen, “DNA hairpins as temperature switches, thermometers and ionic detectors,” Sensors (Basel)13(5), 5937–5944 (2013).
[CrossRef] [PubMed]

2012 (2)

C. Fang, L. Shao, Y. Zhao, J. Wang, and H. Wu, “A gold nanocrystal/poly(dimethylsiloxane) composite for plasmonic heating on microfluidic chips,” Adv. Mater.24(1), 94–98 (2012).
[CrossRef] [PubMed]

K. Hettiarachchi, H. Kim, and G. Faris, “Optical manipulation and control of real-time PCR in cell encapsulating microdroplets by IR laser,” Microfluid. Nanofluid.13(6), 967–975 (2012).
[CrossRef]

2011 (4)

G. Velve Casquillas, C. Fu, M. Le Berre, J. Cramer, S. Meance, A. Plecis, D. Baigl, J.-J. Greffet, Y. Chen, M. Piel, and P. T. Tran, “Fast microfluidic temperature control for high resolution live cell imaging,” Lab Chip11(3), 484–489 (2011).
[CrossRef] [PubMed]

Y. T. Atalay, S. Vermeir, D. Witters, N. Vergauwe, B. Verbruggen, P. Verboven, B. M. Nicolaï, and J. Lammertyn, “Microfluidic analytical systems for food analysis,” Trends Food Sci. Technol.22(7), 386–404 (2011).
[CrossRef]

Y. You, A. V. Tataurov, and R. Owczarzy, “Measuring thermodynamic details of DNA hybridization using fluorescence,” Biopolymers95(7), 472–486 (2011).
[CrossRef] [PubMed]

M. A. Bennet, P. R. Richardson, J. Arlt, A. McCarthy, G. S. Buller, and A. C. Jones, “Optically trapped microsensors for microfluidic temperature measurement by fluorescence lifetime imaging microscopy,” Lab Chip11(22), 3821–3828 (2011).
[CrossRef] [PubMed]

2010 (4)

D. Wlodkowic and J. M. Cooper, “Tumors on chips: Oncology meets microfluidics,” Curr. Opin. Chem. Biol.14(5), 556–567 (2010).
[CrossRef] [PubMed]

G. B. Salieb-Beugelaar, G. Simone, A. Arora, A. Philippi, and A. Manz, “Latest developments in microfluidic cell biology and analysis systems,” Anal. Chem.82(12), 4848–4864 (2010).
[CrossRef] [PubMed]

K. J. Shaw, P. T. Docker, J. V. Yelland, C. E. Dyer, J. Greenman, G. M. Greenway, and S. J. Haswell, “Rapid PCR amplification using a microfluidic device with integrated microwave heating and air impingement cooling,” Lab Chip10(13), 1725–1728 (2010).
[CrossRef] [PubMed]

E. M. Graham, K. Iwai, S. Uchiyama, A. P. de Silva, S. W. Magennis, and A. C. Jones, “Quantitative mapping of aqueous microfluidic temperature with sub-degree resolution using fluorescence lifetime imaging microscopy,” Lab Chip10(10), 1267–1273 (2010).
[CrossRef] [PubMed]

2009 (4)

H. Kim, S. Dixit, C. J. Green, and G. W. Faris, “Nanodroplet real-time PCR system with laser assisted heating,” Opt. Express17(1), 218–227 (2009).
[CrossRef] [PubMed]

H. Kim, S. Vishniakou, and G. W. Faris, “Petri dish PCR: Laser-heated reactions in nanoliter droplet arrays,” Lab Chip9(9), 1230–1235 (2009).
[CrossRef] [PubMed]

B. Selva, J. Marchalot, and M.-C. Jullien, “An optimized resistor pattern for temperature gradient control in microfluidics,” J. Micromech. Microeng.19(6), 065002 (2009).
[CrossRef]

M. Peyrard, S. Cuesta-López, and G. James, “Nonlinear analysis of the dynamics of DNA breathing,” J. Biol. Phys.35(1), 73–89 (2009).
[CrossRef] [PubMed]

2008 (1)

H. Terazono, A. Hattori, H. Takei, K. Takeda, and K. Yasuda, “Development of 1480 nm photothermal high-speed real-time polymerase chain reaction system for rapid nucleotide recognition,” Jpn. J. Appl. Phys.47(6), 5212–5216 (2008).
[CrossRef]

2007 (3)

H. Reinhardt, P. S. Dittrich, A. Manz, and J. Franzke, “micro-Hotplate enhanced optical heating by infrared light for single cell treatment,” Lab Chip7(11), 1509–1514 (2007).
[CrossRef] [PubMed]

S. Mondal and V. Venkataraman, “Novel fluorescence detection technique for non-contact temperature sensing in microchip PCR,” J. Biochem. Biophys. Methods70(5), 773–777 (2007).
[CrossRef] [PubMed]

J. Jung, L. Chen, S. Lee, S. Kim, G. H. Seong, J. Choo, E. K. Lee, C.-H. Oh, and S. Lee, “Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel,” Anal. Bioanal. Chem.387(8), 2609–2615 (2007).
[CrossRef] [PubMed]

2006 (1)

J. Jung and A. Van Orden, “A three-state mechanism for DNA hairpin folding characterized by multiparameter fluorescence fluctuation spectroscopy,” J. Am. Chem. Soc.128(4), 1240–1249 (2006).
[CrossRef] [PubMed]

2003 (1)

J.-L. Mergny and L. Lacroix, “Analysis of thermal melting curves,” Oligonucleotides13(6), 515–537 (2003).
[CrossRef] [PubMed]

2002 (2)

S. A. E. Marras, F. R. Kramer, and S. Tyagi, “Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes,” Nucleic Acids Res.30(21), 122e (2002).
[CrossRef] [PubMed]

L. Movileanu, J. M. Benevides, and G. J. Thomas., “Temperature dependence of the Raman spectrum of DNA. II. Raman signatures of premelting and melting transitions of poly(dA).poly(dT) and comparison with poly(dA-dT).poly(dA-dT),” Biopolymers63(3), 181–194 (2002).
[CrossRef] [PubMed]

2001 (1)

D. Ross, M. Gaitan, and L. E. Locascio, “Temperature measurement in microfluidic systems using a temperature-dependent fluorescent dye,” Anal. Chem.73(17), 4117–4123 (2001).
[CrossRef] [PubMed]

2000 (1)

A. F. R. Hühmer and J. P. Landers, “Noncontact infrared-mediated thermocycling for effective polymerase chain reaction amplification of DNA in nanoliter volumes,” Anal. Chem.72(21), 5507–5512 (2000).
[CrossRef] [PubMed]

1999 (1)

J. H. Ricketts and G. A. Head, “A five-parameter logistic equation for investigating asymmetry of curvature in baroreflex studies,” Am. J. Physiol.277, R441–R454 (1999).

1998 (3)

J. SantaLucia., “A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics,” Proc. Natl. Acad. Sci. U.S.A.95(4), 1460–1465 (1998).
[CrossRef] [PubMed]

J. Coppeta and C. Rogers, “Dual emission laser induced fluorescence for direct planar scalar behavior measurements,” Exp. Fluids25(1), 1–15 (1998).
[CrossRef]

R. P. Oda, M. A. Strausbauch, A. F. R. Huhmer, N. Borson, S. R. Jurrens, J. Craighead, P. J. Wettstein, B. Eckloff, B. Kline, and J. P. Landers, “Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA,” Anal. Chem.70(20), 4361–4368 (1998).
[CrossRef] [PubMed]

1959 (1)

F. J. Richards, “A flexible growth function for empirical use,” J. Exp. Bot.10(2), 290–301 (1959).
[CrossRef]

Andersen, A. H.

A. T. Jonstrup, J. Fredsøe, and A. H. Andersen, “DNA hairpins as temperature switches, thermometers and ionic detectors,” Sensors (Basel)13(5), 5937–5944 (2013).
[CrossRef] [PubMed]

Andreou, M.

J. A. Richardson, T. Morgan, M. Andreou, and T. Brown, “Use of a large Stokes-shift fluorophore to increase the multiplexing capacity of a point-of-care DNA diagnostic device,” Analyst (Lond.)138(13), 3626–3628 (2013).
[CrossRef] [PubMed]

Arlt, J.

M. A. Bennet, P. R. Richardson, J. Arlt, A. McCarthy, G. S. Buller, and A. C. Jones, “Optically trapped microsensors for microfluidic temperature measurement by fluorescence lifetime imaging microscopy,” Lab Chip11(22), 3821–3828 (2011).
[CrossRef] [PubMed]

Arora, A.

G. B. Salieb-Beugelaar, G. Simone, A. Arora, A. Philippi, and A. Manz, “Latest developments in microfluidic cell biology and analysis systems,” Anal. Chem.82(12), 4848–4864 (2010).
[CrossRef] [PubMed]

Atalay, Y. T.

Y. T. Atalay, S. Vermeir, D. Witters, N. Vergauwe, B. Verbruggen, P. Verboven, B. M. Nicolaï, and J. Lammertyn, “Microfluidic analytical systems for food analysis,” Trends Food Sci. Technol.22(7), 386–404 (2011).
[CrossRef]

Baigl, D.

G. Velve Casquillas, C. Fu, M. Le Berre, J. Cramer, S. Meance, A. Plecis, D. Baigl, J.-J. Greffet, Y. Chen, M. Piel, and P. T. Tran, “Fast microfluidic temperature control for high resolution live cell imaging,” Lab Chip11(3), 484–489 (2011).
[CrossRef] [PubMed]

Benevides, J. M.

L. Movileanu, J. M. Benevides, and G. J. Thomas., “Temperature dependence of the Raman spectrum of DNA. II. Raman signatures of premelting and melting transitions of poly(dA).poly(dT) and comparison with poly(dA-dT).poly(dA-dT),” Biopolymers63(3), 181–194 (2002).
[CrossRef] [PubMed]

Bennet, M. A.

M. A. Bennet, P. R. Richardson, J. Arlt, A. McCarthy, G. S. Buller, and A. C. Jones, “Optically trapped microsensors for microfluidic temperature measurement by fluorescence lifetime imaging microscopy,” Lab Chip11(22), 3821–3828 (2011).
[CrossRef] [PubMed]

Borson, N.

R. P. Oda, M. A. Strausbauch, A. F. R. Huhmer, N. Borson, S. R. Jurrens, J. Craighead, P. J. Wettstein, B. Eckloff, B. Kline, and J. P. Landers, “Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA,” Anal. Chem.70(20), 4361–4368 (1998).
[CrossRef] [PubMed]

Brown, T.

J. A. Richardson, T. Morgan, M. Andreou, and T. Brown, “Use of a large Stokes-shift fluorophore to increase the multiplexing capacity of a point-of-care DNA diagnostic device,” Analyst (Lond.)138(13), 3626–3628 (2013).
[CrossRef] [PubMed]

Buller, G. S.

M. A. Bennet, P. R. Richardson, J. Arlt, A. McCarthy, G. S. Buller, and A. C. Jones, “Optically trapped microsensors for microfluidic temperature measurement by fluorescence lifetime imaging microscopy,” Lab Chip11(22), 3821–3828 (2011).
[CrossRef] [PubMed]

Chen, L.

J. Jung, L. Chen, S. Lee, S. Kim, G. H. Seong, J. Choo, E. K. Lee, C.-H. Oh, and S. Lee, “Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel,” Anal. Bioanal. Chem.387(8), 2609–2615 (2007).
[CrossRef] [PubMed]

Chen, Y.

G. Velve Casquillas, C. Fu, M. Le Berre, J. Cramer, S. Meance, A. Plecis, D. Baigl, J.-J. Greffet, Y. Chen, M. Piel, and P. T. Tran, “Fast microfluidic temperature control for high resolution live cell imaging,” Lab Chip11(3), 484–489 (2011).
[CrossRef] [PubMed]

Choo, J.

J. Jung, L. Chen, S. Lee, S. Kim, G. H. Seong, J. Choo, E. K. Lee, C.-H. Oh, and S. Lee, “Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel,” Anal. Bioanal. Chem.387(8), 2609–2615 (2007).
[CrossRef] [PubMed]

Cooper, J. M.

D. Wlodkowic and J. M. Cooper, “Tumors on chips: Oncology meets microfluidics,” Curr. Opin. Chem. Biol.14(5), 556–567 (2010).
[CrossRef] [PubMed]

Coppeta, J.

J. Coppeta and C. Rogers, “Dual emission laser induced fluorescence for direct planar scalar behavior measurements,” Exp. Fluids25(1), 1–15 (1998).
[CrossRef]

Craighead, J.

R. P. Oda, M. A. Strausbauch, A. F. R. Huhmer, N. Borson, S. R. Jurrens, J. Craighead, P. J. Wettstein, B. Eckloff, B. Kline, and J. P. Landers, “Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA,” Anal. Chem.70(20), 4361–4368 (1998).
[CrossRef] [PubMed]

Cramer, J.

G. Velve Casquillas, C. Fu, M. Le Berre, J. Cramer, S. Meance, A. Plecis, D. Baigl, J.-J. Greffet, Y. Chen, M. Piel, and P. T. Tran, “Fast microfluidic temperature control for high resolution live cell imaging,” Lab Chip11(3), 484–489 (2011).
[CrossRef] [PubMed]

Cuesta-López, S.

M. Peyrard, S. Cuesta-López, and G. James, “Nonlinear analysis of the dynamics of DNA breathing,” J. Biol. Phys.35(1), 73–89 (2009).
[CrossRef] [PubMed]

de Silva, A. P.

E. M. Graham, K. Iwai, S. Uchiyama, A. P. de Silva, S. W. Magennis, and A. C. Jones, “Quantitative mapping of aqueous microfluidic temperature with sub-degree resolution using fluorescence lifetime imaging microscopy,” Lab Chip10(10), 1267–1273 (2010).
[CrossRef] [PubMed]

Dittrich, P. S.

H. Reinhardt, P. S. Dittrich, A. Manz, and J. Franzke, “micro-Hotplate enhanced optical heating by infrared light for single cell treatment,” Lab Chip7(11), 1509–1514 (2007).
[CrossRef] [PubMed]

Dixit, S.

Docker, P. T.

K. J. Shaw, P. T. Docker, J. V. Yelland, C. E. Dyer, J. Greenman, G. M. Greenway, and S. J. Haswell, “Rapid PCR amplification using a microfluidic device with integrated microwave heating and air impingement cooling,” Lab Chip10(13), 1725–1728 (2010).
[CrossRef] [PubMed]

Dyer, C. E.

K. J. Shaw, P. T. Docker, J. V. Yelland, C. E. Dyer, J. Greenman, G. M. Greenway, and S. J. Haswell, “Rapid PCR amplification using a microfluidic device with integrated microwave heating and air impingement cooling,” Lab Chip10(13), 1725–1728 (2010).
[CrossRef] [PubMed]

Eckloff, B.

R. P. Oda, M. A. Strausbauch, A. F. R. Huhmer, N. Borson, S. R. Jurrens, J. Craighead, P. J. Wettstein, B. Eckloff, B. Kline, and J. P. Landers, “Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA,” Anal. Chem.70(20), 4361–4368 (1998).
[CrossRef] [PubMed]

Fang, C.

C. Fang, L. Shao, Y. Zhao, J. Wang, and H. Wu, “A gold nanocrystal/poly(dimethylsiloxane) composite for plasmonic heating on microfluidic chips,” Adv. Mater.24(1), 94–98 (2012).
[CrossRef] [PubMed]

Faris, G.

K. Hettiarachchi, H. Kim, and G. Faris, “Optical manipulation and control of real-time PCR in cell encapsulating microdroplets by IR laser,” Microfluid. Nanofluid.13(6), 967–975 (2012).
[CrossRef]

Faris, G. W.

H. Kim, S. Dixit, C. J. Green, and G. W. Faris, “Nanodroplet real-time PCR system with laser assisted heating,” Opt. Express17(1), 218–227 (2009).
[CrossRef] [PubMed]

H. Kim, S. Vishniakou, and G. W. Faris, “Petri dish PCR: Laser-heated reactions in nanoliter droplet arrays,” Lab Chip9(9), 1230–1235 (2009).
[CrossRef] [PubMed]

Franzke, J.

H. Reinhardt, P. S. Dittrich, A. Manz, and J. Franzke, “micro-Hotplate enhanced optical heating by infrared light for single cell treatment,” Lab Chip7(11), 1509–1514 (2007).
[CrossRef] [PubMed]

Fredsøe, J.

A. T. Jonstrup, J. Fredsøe, and A. H. Andersen, “DNA hairpins as temperature switches, thermometers and ionic detectors,” Sensors (Basel)13(5), 5937–5944 (2013).
[CrossRef] [PubMed]

Fu, C.

G. Velve Casquillas, C. Fu, M. Le Berre, J. Cramer, S. Meance, A. Plecis, D. Baigl, J.-J. Greffet, Y. Chen, M. Piel, and P. T. Tran, “Fast microfluidic temperature control for high resolution live cell imaging,” Lab Chip11(3), 484–489 (2011).
[CrossRef] [PubMed]

Gaitan, M.

D. Ross, M. Gaitan, and L. E. Locascio, “Temperature measurement in microfluidic systems using a temperature-dependent fluorescent dye,” Anal. Chem.73(17), 4117–4123 (2001).
[CrossRef] [PubMed]

Graham, E. M.

E. M. Graham, K. Iwai, S. Uchiyama, A. P. de Silva, S. W. Magennis, and A. C. Jones, “Quantitative mapping of aqueous microfluidic temperature with sub-degree resolution using fluorescence lifetime imaging microscopy,” Lab Chip10(10), 1267–1273 (2010).
[CrossRef] [PubMed]

Green, C. J.

Greenman, J.

K. J. Shaw, P. T. Docker, J. V. Yelland, C. E. Dyer, J. Greenman, G. M. Greenway, and S. J. Haswell, “Rapid PCR amplification using a microfluidic device with integrated microwave heating and air impingement cooling,” Lab Chip10(13), 1725–1728 (2010).
[CrossRef] [PubMed]

Greenway, G. M.

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G. Velve Casquillas, C. Fu, M. Le Berre, J. Cramer, S. Meance, A. Plecis, D. Baigl, J.-J. Greffet, Y. Chen, M. Piel, and P. T. Tran, “Fast microfluidic temperature control for high resolution live cell imaging,” Lab Chip11(3), 484–489 (2011).
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K. J. Shaw, P. T. Docker, J. V. Yelland, C. E. Dyer, J. Greenman, G. M. Greenway, and S. J. Haswell, “Rapid PCR amplification using a microfluidic device with integrated microwave heating and air impingement cooling,” Lab Chip10(13), 1725–1728 (2010).
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H. Terazono, A. Hattori, H. Takei, K. Takeda, and K. Yasuda, “Development of 1480 nm photothermal high-speed real-time polymerase chain reaction system for rapid nucleotide recognition,” Jpn. J. Appl. Phys.47(6), 5212–5216 (2008).
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K. Hettiarachchi, H. Kim, and G. Faris, “Optical manipulation and control of real-time PCR in cell encapsulating microdroplets by IR laser,” Microfluid. Nanofluid.13(6), 967–975 (2012).
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R. P. Oda, M. A. Strausbauch, A. F. R. Huhmer, N. Borson, S. R. Jurrens, J. Craighead, P. J. Wettstein, B. Eckloff, B. Kline, and J. P. Landers, “Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA,” Anal. Chem.70(20), 4361–4368 (1998).
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K. Hettiarachchi, H. Kim, and G. Faris, “Optical manipulation and control of real-time PCR in cell encapsulating microdroplets by IR laser,” Microfluid. Nanofluid.13(6), 967–975 (2012).
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R. P. Oda, M. A. Strausbauch, A. F. R. Huhmer, N. Borson, S. R. Jurrens, J. Craighead, P. J. Wettstein, B. Eckloff, B. Kline, and J. P. Landers, “Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA,” Anal. Chem.70(20), 4361–4368 (1998).
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A. F. R. Hühmer and J. P. Landers, “Noncontact infrared-mediated thermocycling for effective polymerase chain reaction amplification of DNA in nanoliter volumes,” Anal. Chem.72(21), 5507–5512 (2000).
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G. Velve Casquillas, C. Fu, M. Le Berre, J. Cramer, S. Meance, A. Plecis, D. Baigl, J.-J. Greffet, Y. Chen, M. Piel, and P. T. Tran, “Fast microfluidic temperature control for high resolution live cell imaging,” Lab Chip11(3), 484–489 (2011).
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J. Jung, L. Chen, S. Lee, S. Kim, G. H. Seong, J. Choo, E. K. Lee, C.-H. Oh, and S. Lee, “Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel,” Anal. Bioanal. Chem.387(8), 2609–2615 (2007).
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J. Jung, L. Chen, S. Lee, S. Kim, G. H. Seong, J. Choo, E. K. Lee, C.-H. Oh, and S. Lee, “Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel,” Anal. Bioanal. Chem.387(8), 2609–2615 (2007).
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J. Jung, L. Chen, S. Lee, S. Kim, G. H. Seong, J. Choo, E. K. Lee, C.-H. Oh, and S. Lee, “Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel,” Anal. Bioanal. Chem.387(8), 2609–2615 (2007).
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D. Ross, M. Gaitan, and L. E. Locascio, “Temperature measurement in microfluidic systems using a temperature-dependent fluorescent dye,” Anal. Chem.73(17), 4117–4123 (2001).
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E. M. Graham, K. Iwai, S. Uchiyama, A. P. de Silva, S. W. Magennis, and A. C. Jones, “Quantitative mapping of aqueous microfluidic temperature with sub-degree resolution using fluorescence lifetime imaging microscopy,” Lab Chip10(10), 1267–1273 (2010).
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G. Velve Casquillas, C. Fu, M. Le Berre, J. Cramer, S. Meance, A. Plecis, D. Baigl, J.-J. Greffet, Y. Chen, M. Piel, and P. T. Tran, “Fast microfluidic temperature control for high resolution live cell imaging,” Lab Chip11(3), 484–489 (2011).
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J.-L. Mergny and L. Lacroix, “Analysis of thermal melting curves,” Oligonucleotides13(6), 515–537 (2003).
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Y. T. Atalay, S. Vermeir, D. Witters, N. Vergauwe, B. Verbruggen, P. Verboven, B. M. Nicolaï, and J. Lammertyn, “Microfluidic analytical systems for food analysis,” Trends Food Sci. Technol.22(7), 386–404 (2011).
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J. Jung, L. Chen, S. Lee, S. Kim, G. H. Seong, J. Choo, E. K. Lee, C.-H. Oh, and S. Lee, “Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel,” Anal. Bioanal. Chem.387(8), 2609–2615 (2007).
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Y. You, A. V. Tataurov, and R. Owczarzy, “Measuring thermodynamic details of DNA hybridization using fluorescence,” Biopolymers95(7), 472–486 (2011).
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M. Peyrard, S. Cuesta-López, and G. James, “Nonlinear analysis of the dynamics of DNA breathing,” J. Biol. Phys.35(1), 73–89 (2009).
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G. B. Salieb-Beugelaar, G. Simone, A. Arora, A. Philippi, and A. Manz, “Latest developments in microfluidic cell biology and analysis systems,” Anal. Chem.82(12), 4848–4864 (2010).
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G. Velve Casquillas, C. Fu, M. Le Berre, J. Cramer, S. Meance, A. Plecis, D. Baigl, J.-J. Greffet, Y. Chen, M. Piel, and P. T. Tran, “Fast microfluidic temperature control for high resolution live cell imaging,” Lab Chip11(3), 484–489 (2011).
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G. Velve Casquillas, C. Fu, M. Le Berre, J. Cramer, S. Meance, A. Plecis, D. Baigl, J.-J. Greffet, Y. Chen, M. Piel, and P. T. Tran, “Fast microfluidic temperature control for high resolution live cell imaging,” Lab Chip11(3), 484–489 (2011).
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H. Reinhardt, P. S. Dittrich, A. Manz, and J. Franzke, “micro-Hotplate enhanced optical heating by infrared light for single cell treatment,” Lab Chip7(11), 1509–1514 (2007).
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M. A. Bennet, P. R. Richardson, J. Arlt, A. McCarthy, G. S. Buller, and A. C. Jones, “Optically trapped microsensors for microfluidic temperature measurement by fluorescence lifetime imaging microscopy,” Lab Chip11(22), 3821–3828 (2011).
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J. H. Ricketts and G. A. Head, “A five-parameter logistic equation for investigating asymmetry of curvature in baroreflex studies,” Am. J. Physiol.277, R441–R454 (1999).

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D. Ross, M. Gaitan, and L. E. Locascio, “Temperature measurement in microfluidic systems using a temperature-dependent fluorescent dye,” Anal. Chem.73(17), 4117–4123 (2001).
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G. B. Salieb-Beugelaar, G. Simone, A. Arora, A. Philippi, and A. Manz, “Latest developments in microfluidic cell biology and analysis systems,” Anal. Chem.82(12), 4848–4864 (2010).
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B. Selva, J. Marchalot, and M.-C. Jullien, “An optimized resistor pattern for temperature gradient control in microfluidics,” J. Micromech. Microeng.19(6), 065002 (2009).
[CrossRef]

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J. Jung, L. Chen, S. Lee, S. Kim, G. H. Seong, J. Choo, E. K. Lee, C.-H. Oh, and S. Lee, “Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel,” Anal. Bioanal. Chem.387(8), 2609–2615 (2007).
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C. Fang, L. Shao, Y. Zhao, J. Wang, and H. Wu, “A gold nanocrystal/poly(dimethylsiloxane) composite for plasmonic heating on microfluidic chips,” Adv. Mater.24(1), 94–98 (2012).
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K. J. Shaw, P. T. Docker, J. V. Yelland, C. E. Dyer, J. Greenman, G. M. Greenway, and S. J. Haswell, “Rapid PCR amplification using a microfluidic device with integrated microwave heating and air impingement cooling,” Lab Chip10(13), 1725–1728 (2010).
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G. B. Salieb-Beugelaar, G. Simone, A. Arora, A. Philippi, and A. Manz, “Latest developments in microfluidic cell biology and analysis systems,” Anal. Chem.82(12), 4848–4864 (2010).
[CrossRef] [PubMed]

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R. P. Oda, M. A. Strausbauch, A. F. R. Huhmer, N. Borson, S. R. Jurrens, J. Craighead, P. J. Wettstein, B. Eckloff, B. Kline, and J. P. Landers, “Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA,” Anal. Chem.70(20), 4361–4368 (1998).
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H. Terazono, A. Hattori, H. Takei, K. Takeda, and K. Yasuda, “Development of 1480 nm photothermal high-speed real-time polymerase chain reaction system for rapid nucleotide recognition,” Jpn. J. Appl. Phys.47(6), 5212–5216 (2008).
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H. Terazono, A. Hattori, H. Takei, K. Takeda, and K. Yasuda, “Development of 1480 nm photothermal high-speed real-time polymerase chain reaction system for rapid nucleotide recognition,” Jpn. J. Appl. Phys.47(6), 5212–5216 (2008).
[CrossRef]

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Y. You, A. V. Tataurov, and R. Owczarzy, “Measuring thermodynamic details of DNA hybridization using fluorescence,” Biopolymers95(7), 472–486 (2011).
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H. Terazono, A. Hattori, H. Takei, K. Takeda, and K. Yasuda, “Development of 1480 nm photothermal high-speed real-time polymerase chain reaction system for rapid nucleotide recognition,” Jpn. J. Appl. Phys.47(6), 5212–5216 (2008).
[CrossRef]

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L. Movileanu, J. M. Benevides, and G. J. Thomas., “Temperature dependence of the Raman spectrum of DNA. II. Raman signatures of premelting and melting transitions of poly(dA).poly(dT) and comparison with poly(dA-dT).poly(dA-dT),” Biopolymers63(3), 181–194 (2002).
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G. Velve Casquillas, C. Fu, M. Le Berre, J. Cramer, S. Meance, A. Plecis, D. Baigl, J.-J. Greffet, Y. Chen, M. Piel, and P. T. Tran, “Fast microfluidic temperature control for high resolution live cell imaging,” Lab Chip11(3), 484–489 (2011).
[CrossRef] [PubMed]

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S. A. E. Marras, F. R. Kramer, and S. Tyagi, “Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes,” Nucleic Acids Res.30(21), 122e (2002).
[CrossRef] [PubMed]

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E. M. Graham, K. Iwai, S. Uchiyama, A. P. de Silva, S. W. Magennis, and A. C. Jones, “Quantitative mapping of aqueous microfluidic temperature with sub-degree resolution using fluorescence lifetime imaging microscopy,” Lab Chip10(10), 1267–1273 (2010).
[CrossRef] [PubMed]

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J. Jung and A. Van Orden, “A three-state mechanism for DNA hairpin folding characterized by multiparameter fluorescence fluctuation spectroscopy,” J. Am. Chem. Soc.128(4), 1240–1249 (2006).
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S. Mondal and V. Venkataraman, “Novel fluorescence detection technique for non-contact temperature sensing in microchip PCR,” J. Biochem. Biophys. Methods70(5), 773–777 (2007).
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Y. T. Atalay, S. Vermeir, D. Witters, N. Vergauwe, B. Verbruggen, P. Verboven, B. M. Nicolaï, and J. Lammertyn, “Microfluidic analytical systems for food analysis,” Trends Food Sci. Technol.22(7), 386–404 (2011).
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Y. T. Atalay, S. Vermeir, D. Witters, N. Vergauwe, B. Verbruggen, P. Verboven, B. M. Nicolaï, and J. Lammertyn, “Microfluidic analytical systems for food analysis,” Trends Food Sci. Technol.22(7), 386–404 (2011).
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Y. T. Atalay, S. Vermeir, D. Witters, N. Vergauwe, B. Verbruggen, P. Verboven, B. M. Nicolaï, and J. Lammertyn, “Microfluidic analytical systems for food analysis,” Trends Food Sci. Technol.22(7), 386–404 (2011).
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Y. T. Atalay, S. Vermeir, D. Witters, N. Vergauwe, B. Verbruggen, P. Verboven, B. M. Nicolaï, and J. Lammertyn, “Microfluidic analytical systems for food analysis,” Trends Food Sci. Technol.22(7), 386–404 (2011).
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H. Kim, S. Vishniakou, and G. W. Faris, “Petri dish PCR: Laser-heated reactions in nanoliter droplet arrays,” Lab Chip9(9), 1230–1235 (2009).
[CrossRef] [PubMed]

Wang, J.

C. Fang, L. Shao, Y. Zhao, J. Wang, and H. Wu, “A gold nanocrystal/poly(dimethylsiloxane) composite for plasmonic heating on microfluidic chips,” Adv. Mater.24(1), 94–98 (2012).
[CrossRef] [PubMed]

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R. P. Oda, M. A. Strausbauch, A. F. R. Huhmer, N. Borson, S. R. Jurrens, J. Craighead, P. J. Wettstein, B. Eckloff, B. Kline, and J. P. Landers, “Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA,” Anal. Chem.70(20), 4361–4368 (1998).
[CrossRef] [PubMed]

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Y. T. Atalay, S. Vermeir, D. Witters, N. Vergauwe, B. Verbruggen, P. Verboven, B. M. Nicolaï, and J. Lammertyn, “Microfluidic analytical systems for food analysis,” Trends Food Sci. Technol.22(7), 386–404 (2011).
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C. Fang, L. Shao, Y. Zhao, J. Wang, and H. Wu, “A gold nanocrystal/poly(dimethylsiloxane) composite for plasmonic heating on microfluidic chips,” Adv. Mater.24(1), 94–98 (2012).
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H. Terazono, A. Hattori, H. Takei, K. Takeda, and K. Yasuda, “Development of 1480 nm photothermal high-speed real-time polymerase chain reaction system for rapid nucleotide recognition,” Jpn. J. Appl. Phys.47(6), 5212–5216 (2008).
[CrossRef]

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K. J. Shaw, P. T. Docker, J. V. Yelland, C. E. Dyer, J. Greenman, G. M. Greenway, and S. J. Haswell, “Rapid PCR amplification using a microfluidic device with integrated microwave heating and air impingement cooling,” Lab Chip10(13), 1725–1728 (2010).
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Y. You, A. V. Tataurov, and R. Owczarzy, “Measuring thermodynamic details of DNA hybridization using fluorescence,” Biopolymers95(7), 472–486 (2011).
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C. Fang, L. Shao, Y. Zhao, J. Wang, and H. Wu, “A gold nanocrystal/poly(dimethylsiloxane) composite for plasmonic heating on microfluidic chips,” Adv. Mater.24(1), 94–98 (2012).
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Adv. Mater. (1)

C. Fang, L. Shao, Y. Zhao, J. Wang, and H. Wu, “A gold nanocrystal/poly(dimethylsiloxane) composite for plasmonic heating on microfluidic chips,” Adv. Mater.24(1), 94–98 (2012).
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Figures (8)

Fig. 1
Fig. 1

Instrument schematic for microdroplet heating with an infrared diode laser and imaging of sample fluorescence.

Fig. 2
Fig. 2

Three-state equilibrium that describes the melting process of a static-quenched DNA oligomer pair. The premelt fluorescence we observe is accounted for by the existence of an intermediate state FQ* in which distance-based fluorescence resonance energy transfer (FRET) quenching is in effect.

Fig. 3
Fig. 3

Experimental data and theoretical fits for fluorescence melting curves. The same data are displayed in two parameterizations: normalized (dimensionless) fluorescence f versus temperature T in (a); and as an Arrhenius plot or ln(κ) versus 1/T in (b). Solid lines show five replicates of experimental data with a different color for each of the three oligos. Dotted lines show the three single-term κ or f for each oligo, labeled m (melt), p (premelt), or t (transition), appearing as straight lines on the Arrhenius plot (b) and sigmoids in (a). For clarity, κt is not displayed in (a). Dashed lines show the two-term calculations κ(2) = κm + κp, and f(2) in (b) and (a), respectively, demonstrating good fits to the experimental data in the high- and low-temperature regions, but poor agreement in the transition region. The three-term calculations κ(3) = κm + κp + κt and f(3) precisely overlap the data (not shown for clarity; see Fig. 4 for examples). Two points at T = Tm are shown: upward pointing triangles at κm = 1 or fm = 1/2 (which define Tm) and downward pointing triangles on κ(3) or f(3) at the same temperature. For comparison between the parameterizations κ or f and T or 1/T, the other parameterizations are shown on the opposing axes (right and top axes). While full experimental data sets are shown in (a), in (b) we only show data values for f < 0.995 to minimize the noise that would obscure part of the linear fits.

Fig. 4
Fig. 4

Fitting of three-term (f(3), a-c) and two-term (f(2), d-f) versions of the model to fluorescence melting curves of the 20-mer (a, d), 27-mer (b, e), and 47-mer (c, f) oligomer pairs. The f(2) fit experiences significant deviation from the data in the premelt and melting regions for the 27- and 47-mer data. This deviation is largely absent when the f(3) fit is applied. To minimize systematic effects from fluctuations in the saturated region (f ~1), fits were performed only up to a maximum temperature given by fm = 0.995 plus 5 degrees. The same experimental data has been presented in Fig. 3 as f and κ calculated using the A and B determined by the f(3) fits.

Fig. 5
Fig. 5

Fluorescent melting curves of Oligos 20(a), 27(b), and 47(c) in a microdroplet heated by an infrared laser. Single-oligo premelt model fit is applied using parameters of Table 3 and similar results are obtained as from application to the macroscale melting curves. Note that discrepancies in fit become larger with the oligomer length. The temperature axis at the top of each graph is calculated from the calibration curve in Fig. 7.

Fig. 6
Fig. 6

Fluorescent melting curves of samples containing all three oligo quenched pairs, both at the macroscale (a) and in microdroplets (b). Three-oligo premelt model fit is applied. The temperature axis in (b) is calculated from the calibration curve in Fig. 7.

Fig. 7
Fig. 7

Calibration curve for heating a microdroplet with an infrared laser. A linear relationship (black) is obtained when oligomer melting laser voltages are plotted against oligomer melting temperatures (blue). The regression line is interpolated to obtain a laser power corresponding to 60 °C and extrapolated to obtain a laser power corresponding to 95 °C (red).

Fig. 8
Fig. 8

Real-time qPCR amplification curves for macroscale (a, b) and microdroplet instrument (c, d) reactions. Effective ranges for the microdroplet around the calibration are explored and compared to the range of a qPCR instrument. The calibration curve for this experiment gives approximately a 1 °C / 0.66 mW slope.

Tables (3)

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Table 1 DNA Oligomer Sequences

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Table 2 Pseudoequilibrium Constants κ and Associated Sigmoid Curves f

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Table 3 Three-Term κ Fit Parameters

Equations (12)

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K 1 = [F][Q] [FQ]
K 2 = [F Q * ] [FQ]
K 3 = [F][Q] [F Q * ]
κ= [F]+[F Q * ] [FQ] = K 1 [Q] + K 2 .
f= [F]+[F Q * ] [F]+[F Q * ]+[FQ] = κ 1+κ = 1 1+1/κ .
κ= f 1f .
κ m (T)= κ m ( T o )exp[ D m ( 1 T o 1 T ) ] equalforhighT K 1 [Q] = [F] [FQ]
κ p (T)= κ p ( T o )exp[ D p ( 1 T o 1 T ) ] equalforlowT K 2 = [F Q * ] [FQ] .
κ m ( T m )=1.
A+B f (3) =A+ B 1+ 1 e D m ( 1 T m 1 T ) + κ p ( T m ) e D p ( 1 T m 1 T ) + κ t ( T m ) e D t ( 1 T m 1 T )
T= T a +αP
A+ f 20 B 20 + f 27 B 27 + f 47 B 47 .

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