Coupled flow and reaction during natural convection PCR

Joshua W. Allen, Martin Kenward, Kevin D. Dorfman

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


Polymerase chain reaction (PCR) in a microfluidic Rayleigh-Benard convection cell represents a promising route towards portable PCR for point-of-care uses. In the present contribution, the coupled fluid mechanics and heat transport processes are solved numerically for a 2-D flow cell. The resultant velocity and temperature fields serve as the inputs to a convection-diffusion-reaction model for the DNA amplification, wherein the reaction kinetics are modeled by Gaussian distributions around the conventional bulk PCR reaction temperatures. These evolution equations are integrated to determine the exponential growth rate of the double-stranded DNA concentration. The predicted doubling time is approximately 10-25 s, increasing with the Péclet number. This effect is attributed to low velocity, slow kinetics "dead zones" located at the center of the reactor. The latter observation provides an alternative rationalization for the use of loop-based natural convection PCR systems.

Original languageEnglish (US)
Pages (from-to)121-130
Number of pages10
JournalMicrofluidics and Nanofluidics
Issue number1
StatePublished - 2009

Bibliographical note

Funding Information:
Acknowledgments JWA acknowledges the support of the Minnesota Bioinformatics Summer Institute. This work was supported by a Career Development Award from the Human Frontier Science Program and the Camille and Henry Dreyfus New Faculty Award Program. This work was carried out in part using computing resources at the University of Minnesota Supercomputing Institute.


  • DNA
  • Modeling
  • Natural convection
  • Polymerase chain reaction
  • Rayleigh-Benard cell


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