Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 31819
Simulation and Design of the Geometric Characteristics of the Oscillatory Thermal Cycler

Authors: Tse-Yu Hsieh, Jyh-Jian Chen


Since polymerase chain reaction (PCR) has been invented, it has emerged as a powerful tool in genetic analysis. The PCR products are closely linked with thermal cycles. Therefore, to reduce the reaction time and make temperature distribution uniform in the reaction chamber, a novel oscillatory thermal cycler is designed. The sample is placed in a fixed chamber, and three constant isothermal zones are established and lined in the system. The sample is oscillated and contacted with three different isothermal zones to complete thermal cycles. This study presents the design of the geometric characteristics of the chamber. The commercial software CFD-ACE+TM is utilized to investigate the influences of various materials, heating times, chamber volumes, and moving speed of the chamber on the temperature distributions inside the chamber. The chamber moves at a specific velocity and the boundary conditions with time variations are related to the moving speed. Whereas the chamber moves, the boundary is specified at the conditions of the convection or the uniform temperature. The user subroutines compiled by the FORTRAN language are used to make the numerical results realistically. Results show that the reaction chamber with a rectangular prism is heated on six faces; the effects of various moving speeds of the chamber on the temperature distributions are examined. Regarding to the temperature profiles and the standard deviation of the temperature at the Y-cut cross section, the non-uniform temperature inside chamber is found as the moving speed is larger than 0.01 m/s. By reducing the heating faces to four, the standard deviation of the temperature of the reaction chamber is under 1.4×10-3K with the range of velocities between 0.0001 m/s and 1 m/s. The nature convective boundary conditions are set at all boundaries while the chamber moves between two heaters, the effects of various moving velocities of the chamber on the temperature distributions are negligible at the assigned time duration.

Keywords: Polymerase chain reaction, oscillatory thermal cycler, standard deviation of temperature, nature convective.

Digital Object Identifier (DOI):

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1420


[1] K. Mullis, F. Ferre, R. A. (Eds.), Gibbs, The Polymerase Chain Reaction, Springer, 1994.
[2] S. H. Kim, J. Noh, M. K. Jeon, K. W. Kim, L. P. Lee, and S. I. Woo, "Micro-Raman Thermometry for Measuring the Temperature Distribution inside the Microchannel of a Polymerase Chain Reaction Chip," Micromechanics and Microengineering, Vol. 16, pp. 526-530, 2006.
[3] M. A. Northrup, M. T. Ching, R. M. White, and R. T. Wltson, "DNA Amplification in a Microfabricated Reaction Chamber," 7th International Conference of Solid-State Sensors and Actuators, Transducers -93, pp. 924-926, 1993.
[4] M. U. Kopp, A. J. D., Mello, and A. Manz, "Chemical Amplification: Continuous-Flow PCR on a Chip," Science, Vol. 280, pp. 1046-1048, 1998.
[5] Q. Zhang, W. Wang, H. Zhang, and Y. Wang, "Temperature Analysis of Continuous-Flow Micro-PCR Based on FEA," Sensors and Actuators B, Vol. 82, pp.75-81, 2002.
[6] C. F. Chou, R. Changrani, P. Roberts, D. Sadler, J. Burdon, F. Zenhausern, S. Lin, A. Mulholland, N. Swami, and R. Terbrueggen, "A Miniaturized Cyclic PCR Device-Modeling and Experiments," Microelectronic Engineering, Vol. 61-62, pp. 921-925, 2002.
[7] M. Bu, T. Melvin, G. Ensell, J. S. Wilkinson, and A. G. R. Evans, "Design and Theoretical Evaluation of a Novel Microfluidic Device to Be Used for PCR," Journal of Micromecanics Microengineering, Vol. 13, pp. S125-S130, 2003.
[8] M. Hashimoto, P. C. Chen, M. W. Mitchell, D. E. Nikitopoulos, S. A. Soper, and M. C. Murphy, "Rapid PCR in a Continuous Flow Device," Lab on a Chip, Vol. 4, pp. 638-645, 2004.
[9] S. R. Joung, C. J. Kang, and Y. S. Kim, "Series DNA Amplification Using the Continuous-Flow Polymerase Chain Reaction Chip," Japanese Journal of Applied Physic, Vol. 47, pp. 1342-1345, 2008.
[10] J. Xiaoyu, N. Zhiqiang, C. Wenyuan, and Z. Weiping, "Polydimethylsiloxane (PDMS)-Based Spiral Channel PCR Chip," in Proc. 4th Electronics Letters Conf. Vol. 41, No. 16, 2005.
[11] N. C. Tsai, and C. Y. Sue, "Thermal Control of Micro Reverse Transcription-Polymerase Chain Reaction Systems," Sensors and Actuators A, Vol. 136, pp. 178-183, 2007.
[12] T. Nakayama, Y. Kurosawa, S. Furui, K. Kerman, M. Kobayashi, S. R. Raao, Y. Yonezawa, K. Nakano, A. Hino, S. Yamamura, Y. Takamura, and E. Tamiya, "Circumventing Air Bubbles in Microfluidic Systems and Quantitative Continuous-Flow PCR Applications," Analytical and Bioanalytical Chemistry, Vol. 386, pp. 1327-1333, 2006.
[13] C. Gartner, R. Klemm, and H. Becker, "Methods and Instruments for Continuous-Flow PCR on a Chip," Proc. of SPIE, Vol. 6465, pp. 646502-1-646502-8, 2007.
[14] N. Crews, C. Wittwer, and B. Gale, "Continuous-Flow Thermal Gradient PCR," Biomed Microdevices, Vol. 10, pp. 187-195, 2008.
[15] D. S. Lee, and C. S. Chen, "Development of a Temperature Sensor Array Chip and a Chip-Based Real-Time PCR Machine for DNA Amplification Efficiency-Based Quantification," Biosensors and Bioelectronics, Vol. 23, pp. 971-979, 2008.