Simulation and Design of the Geometric Characteristics of the Oscillatory Thermal Cycler
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.
[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.
[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.
@article{"International Journal of Chemical, Materials and Biomolecular Sciences:59537", author = "Tse-Yu Hsieh and Jyh-Jian Chen", title = "Simulation and Design of the Geometric Characteristics of the Oscillatory Thermal Cycler", abstract = "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.", volume = "3", number = "5", pages = "264-9", }