Optimization of reaction kinetics on natural convection microfluidic devices by computer simulation


  • Luis C. Olivares-Rueda FCFM-BUAP
  • Claudia Mendoza-Barrera FCFM-BUAP
  • Aldo Y. Tenorio-Barajas FCFM-BUAP
  • Severino Muñoz-Aguirre FCFM-BUAP
  • Marcos Rodríguez-Torres FCFM-BUAP
  • Víctor Altuzar FCFM-BUAP




Computational simulation, methodology, microfluidic natural convection system, PCR


This study presents a novel methodology framework for simulating and optimizing reaction kinetics in natural convection microfluidic devices. The approach involves coupling heat and mass transfer, fluid flow, and chemistry. Visual and regression analyses are performed to evaluate the impact of different operational parameters on reaction speed, aiming to improve microfluidic natural convection systems. The methodology was applied to a practical example of a Polymerase Chain Reaction triangular microfluidic glass device that utilizes natural convection for the required reactions. The findings showed that the fluid flow velocity is significant in determining the reaction speed, which can be controlled by adjusting the temperature cycling differences and the inner diameter of the device. Despite challenges posed by the fluid flow direction, the best reaction times achieved ranged from 18 to 21 minutes. Due to its computational efficiency, the developed methodology allows simulations to be conducted on mid-range computers. Also, the visual and regression analyses offer insights into improving a specific device by measuring the influence of several parameters. Then, the methodology is convenient for selecting the best conditions before developing an experiment.


T. Han et al., Recent advances in detection technologies for COVID-19 (2021), https://doi.org/10.1016/j.talanta.2021.122609

D. Sidransky, Nucleic acid-based methods for the detection of cancer (1997), https://doi.org/10.1126/science.278.5340.1054

J. W. Allen, M. Kenward, and K. D. Dorfman, Coupled flow and reaction during natural convection PCR, Microfluidics and Nanofluidics 6 (2009) 121

N. Agrawal, Y. A. Hassan, and V. M. Ugaz, A PocketSized Convective PCR Thermocycler, Angewandte Chemie 119 (2007) 4394, https://doi.org/10.1002/ange.200700306

C. D. Ahrberg, A. Manz, and B. G. Chung, Polymerase chain reaction in microfluidic devices, Lab on a Chip 16 (2016) 3866

Microfluidics: Applications for analytical purposes in chemistry and biochemistry (2007), https://doi.org/10.1002/elps

Z. Sheidaei, P. Akbarzadeh, and N. Kashaninejad, Advances in numerical approaches for microfluidic cell analysis platforms (2020), https://doi.org/10.1016/j.jsamd.2020.07.008

M. M. A. Bhutta et al., CFD applications in various heat exchangers design: A review (2012), https://doi.org/10.1016/j.applthermaleng.2011.09.001

A. Hassibi, H. Kakavand, and T. H. Lee, A stochastic model and simulation algorithm for polymerase chain reaction (PCR) systems

V. E. Papadopoulos et al., Comparison of continuous-flow and static-chamber micro-PCR devices through a computational study: the potential of flexible polymeric substrates, Microfluidics and Nanofluidics 19 (2015) 867, https://doi.org/10.1007/s10404-015-1613-1

M. Laudon et al., Multi-physics Simulational Analysis of a Novel PCR Micro-Device (Nano Science and Technology Institute, 2007)

A. Priye, Y. A. Hassan, and V. M. Ugaz, Microscale chaotic advection enables robust convective DNA replication, Analytical Chemistry 85 (2013) 10536, https://doi.org/10.1021/ac402611s

S. Raasch and D. Etling, Modeling Deep Ocean Convection: Large Eddy Simulation in Comparison with Laboratory Experiments

J. M. S. Bartlett and D. Stirling, Methods in Molecular Biology TM Methods in Molecular Biology TM PCR Protocols second edition Edited by PCR Protocols

M. A. Innis, PCR protocols: a guide to methods and applications (Academic Press, 1990), p. 482

P. Turnpenny and S. Ellard, Emery’s ELEMENTS of MEDICAL GENETICS, 15th ed. (ELSEVIER, 2017)

Biorender, https://app.biorender.com/

M. Arya et al., Basic principles of real-time quantitative PCR (2005), https://doi.org/10.1586/14737159.5.2.209

Kimbler Microcapsr Capillary Tube — DWK Life Sciences, https://www.dwk.com/na/kimble-microcaps-capillary-tube

H. Bruus, Theoretical microfluidics, vol. 18 (Oxford university press, 2007)

H. D. H. D. Baehr and K. K. Stephan, Heat and mass-transfer (Springer, 2006), p. 688

M. Krishnan et al., Reactions and fluidics in miniaturized natural convection systems, Analytical Chemistry 76 (2004) 6254, https://doi.org/10.1021/ac049323u




How to Cite

L. C. Olivares-Rueda, C. Mendoza-Barrera, A. Y. Tenorio-Barajas, S. Muñoz-Aguirre, M. Rodríguez-Torres, and V. Altuzar, “Optimization of reaction kinetics on natural convection microfluidic devices by computer simulation”, Rev. Mex. Fís., vol. 70, no. 4 Jul-Aug, pp. 041003 1–, Jul. 2024.