Biomedical Microdevices

, Volume 10, Issue 2, pp 141–152

Temperature distribution effects on micro-CFPCR performance

  • Pin-Chuan Chen
  • Dimitris E. Nikitopoulos
  • Steven A. Soper
  • Michael C. Murphy


Continuous flow polymerase chain reactors (CFPCRs) are BioMEMS devices that offer unique capabilities for the ultra-fast amplification of target DNA fragments using repeated thermal cycling, typically over the following temperature ranges: 90°C–95°C for denaturation, 50°C–70°C for renaturation, and 70°C–75°C for extension. In CFPCR, DNA cocktail is pumped through the constant temperature zones and reaches thermal equilibrium with the channel walls quickly due to its low thermal capacitance. In previous work, a polycarbonate CFPCR was designed with microchannels 150 μm deep, 50 μm wide, and 1.78 m long—including preheating and post-heating zones, fabricated with LIGA, and demonstrated. The high thermal resistance of the polycarbonate led to a high temperature gradient in the micro-device at steady-state and was partly responsible for the low amplification yield. Several steps were taken to ensure that there were three discrete, uniform temperature zones on the polycarbonate CFPCR device including: reducing the thickness of the CFPCR substrate to decrease thermal capacitance, using copper plates as heating elements to ensure a uniform temperature input, and making grooves between temperature zones to increase the resistance to lateral heat conduction between zones. Finite element analyses (FEA) were used to evaluate the macro temperature distribution in the CFPCR device and the micro temperature distribution along a single microchannel. At steady-state, the simulated CFPCR device had three discrete temperature zones, each with a uniform temperature distribution with a variation of ±0.3°C. An infrared (IR) camera was used to measure the steady-state temperature distribution in the prototype CFPCR and validated the simulation results. The temperature distributions along a microchannel at flow velocities from 0 mm/s to 6 mm/s were used to estimate the resulting temperatures of the DNA reagents in a single microchannel. A 500 bp DNA fragment was generated from a bacteriophage λ-DNA target using 20 cycles of PCR. The amplification efficiencies compared to a commercial thermal cycler were 72.7% (2 mm/s), 44% (3 mm/s), and 29.4% (4 mm/s). The amplification efficiency with the modified CFPCR device increased by 363% at 2 mm/s and 440% at 3 mm/s compared to amplification obtained using a CFPCR device with the same fluidic layout, (Hashimoto et al., Lab Chip 4:638, 2004) strictly due to the improved temperature distribution.


PCR Continuous flow PCR Micro PCR Thermal management Finite element simulation 


  1. ANSYS CFD FLOTRAN Analysis Guide, SAS Ip, Inc., 3rd, (1997)Google Scholar
  2. Y.D. Bejat, M.S. Thesis, Louisiana State University, Baton Rouge, LA, (2001).Google Scholar
  3. Y. Bejat, X. Liu, D.E. Nikitopoulos, M.C. Murphy, M.W. Mitchell, S.A. Soper, A Continuous Flow Polymerization Chain Reaction (CFPCR) Micro-Chip, Bulletin of the American Physical Society, 55th Annual Meeting of the APS Division of Fluid Dynamics, Dallas TX, 47, 10, 15 (November 24–26, 2002)Google Scholar
  4. T.D. Boone, Z.H. Fan, H.H. Hooper, A.J. Ricco, H. Tan, S.J. Williams, Anal. Chem. 74, 78A (Feb. 2002)CrossRefGoogle Scholar
  5. M. Bu, T. Melvin, G. Ensell, J.S. Wilkinson, A.G.R. Evans, J. Micromech. Microeng. 13, 125 (2003)CrossRefGoogle Scholar
  6. A.M. Chaudhari, T.M. Woudenberg, M. Albin, K.E. Goodson, JMEMS 7(4), 345 (1998)Google Scholar
  7. J. Chen, M. Wabuyele, H. Chen, D. Patterson, M. Hupert, H. Shadpour, D.E. Nikitopoulos, S.A. Soper, Anal. Chem. 77, 658 (2005)CrossRefGoogle Scholar
  8. P.C. Chen, D.E. Nikitopoulos, S.A. Soper, M.C Murphy, InterPACK2007, Paper # IPACK2007-33330 (ASME, Vancouver, 2007)Google Scholar
  9. J. Chiou, P. Matsudaira, A. Sonin, D. Enrlich, Anal. Chem. 73, 2018 (2001)CrossRefGoogle Scholar
  10. M. Curcio, J. Roeraade, Anal. Chem. 75(1), 1 (2003)CrossRefGoogle Scholar
  11. J.H. Daniel, S. Iqbal, R.B. Millington, D.F. Moore, C.R. Lowe, D.L. Leslie, M.A. Lee, M.J. Pearce, Sens. Actuators A 71, 81 (1998)CrossRefGoogle Scholar
  12. K.L. Davis, K.K.K. Liu, M. Lanan, M.D. Morris, Anal. Chem. 65, 293 (1993)CrossRefGoogle Scholar
  13. J. El-Ali, I.R. Perch-Nielsen, C.R. Poulsen, D.D. Bang, P. Telleman, A. Wolff, Sens. Actuators A 110, 3 (2004)CrossRefGoogle Scholar
  14. O. Geschke, H. Klank, P. Telleman, Microsystem Engineering of Lab-on-a-chip Devices (WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, 2004), Chap 5Google Scholar
  15. B.C. Giordano, J. Ferrance, S. Swedberg, A.F.R. Huhmer, J.P. Landers, Anal. Biochem. 291, 124 (2001)CrossRefGoogle Scholar
  16. Q. Hao, J. Micromech. Microeng. 14, 914 (2004)CrossRefGoogle Scholar
  17. M. Hashimoto, P.C. Chen, M.W. Mitchell, D.E. Nikitopoulos, S.A. Soper, M.C Murphy, Lab Chip 4, 638 (2004)CrossRefGoogle Scholar
  18. A. Iles, R. Fortt, A.J. de Mello, Lab Chip 5, 540 (2005)CrossRefGoogle Scholar
  19. F.P. Incropera, D.P. Dewitt, Fundamentals of Heat and Mass Transfer, 5th edn. (Wiley, Danvers, 2001), AppendixGoogle Scholar
  20. M.A. Innis, K.B. Myambo, D.H. Gelfand, M.A.D. Brow, PNAS. USA 85, 9436 (1988)CrossRefGoogle Scholar
  21. M.U. Kopp, A.J. DeMello, A. Manz, Science 280(5366), 1046 (1998)CrossRefGoogle Scholar
  22. K.K. Lee, K. Liu, K.L. Davis, M.D. Morris, Anal. Chem. 66, 3744 (1994)CrossRefGoogle Scholar
  23. S. Li, D.Y. Fozdar, M.F. Ali, H. Li, D. Shao, D.M. Vykoukal, J. Vykoukal, P.N. Floriano, M. Olsen, J.T. McDevitt, P.R.C. Gascoyne, S. Chen, JMEMS 15(1), 223 (2006)Google Scholar
  24. C.S. Liao, G.B. Lee, J.J. Wu, C.C. Chang, T.M. Hsien, F.C. Huang, C.H. Luo, Biosens. Bioelectron. 20, 1341 (2005)CrossRefGoogle Scholar
  25. Y.C. Lin, C.C. Yang, M.Y. Huang, Sens. Actuators B 71, 127 (2000)CrossRefGoogle Scholar
  26. M.W. Mitchell, M.S. Thesis, LSU, December 2002.Google Scholar
  27. K.B. Mullis, F. A. Faloona, Methods Enzymol. 155, 335 (1987)CrossRefGoogle Scholar
  28. H. Nagai, Y. Murakami, Y. Morita, K. Yokoyama, E. Tamiya, Anal. Chem. 73, 1043 (2001)CrossRefGoogle Scholar
  29. J. Noh, S.W. Sung, M.K. Jeon, S.H Kim, L.P. Lee, S.I. Woo, Sens. Actuators A 122, 196 (2005)CrossRefGoogle Scholar
  30. P.J. Obeid, T.K. Christopoulos, Anal. Chim. Acta 494, 1 (2003)CrossRefGoogle Scholar
  31. D. Ross, M. Gaitan, L.E. Locascio, Anal. Chem. 73, 4117 (2001)CrossRefGoogle Scholar
  32. D.J. Sadler, R. Changrani, P. Robers, C.F. Chou, F. Zenhausern, IEEE Trans. Compon. Packag. Technol. 26(2), 309 (2003)CrossRefGoogle Scholar
  33. S.D. Senturia, Microsystem Design (Springer Science + Business Media, New York, 2001), Chap. 22Google Scholar
  34. Y.S. Shin, K. Cho, S.H. Lim, S. Chung, S.J. Park, C. Chung, D.C. Han, J.K. Chang, J. Micromech. Microeng. 13, 768 (2003)CrossRefGoogle Scholar
  35. S.A. Soper, S.M. Ford, S. Qi, R.L. McCarley, K. Kelly, M.C. Murphy, Anal. Chem. 643A (Oct. 2000)Google Scholar
  36. S.C. Terry, J.H. Jerman, J.B. Angell, IEEE Trans. Electron Devices 26, 1880 (1979)CrossRefGoogle Scholar
  37. W. Wang, Z.X. Li, R. Luo, S.H. Lu, A.D. Xu, Y.J. Yang, J. Micromech. Microeng. 15, 1369 (2005)CrossRefGoogle Scholar
  38. D.S. Yoon, Y.S. Lee, Y. Lee, H.J. Cho, S.W. Sung; K.W. Oh, J. Cha, G. Lim, J. Micromech. Microeng. 12, 813 (2002)CrossRefGoogle Scholar
  39. M. Yuan, R. Pal, M.A. Burns, J. Micromech. Microeng. 15, 221 (2005)CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Pin-Chuan Chen
    • 1
    • 3
  • Dimitris E. Nikitopoulos
    • 1
    • 3
  • Steven A. Soper
    • 1
    • 2
  • Michael C. Murphy
    • 1
    • 3
  1. 1.Center for Bio-Modular Multi-Scale SystemsLouisiana State UniversityBaton RougeUSA
  2. 2.Department of ChemistryLouisiana State UniversityBaton RougeUSA
  3. 3.Department of Mechanical EngineeringLouisiana State UniversityBaton RougeUSA

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