Kinetic characteristics of continuous flow polymerase chain reaction chip: A numerical investigation

Wang, Shiying; Wang, Wei

doi:10.1007/s11431-010-3096-3

Cited by 6 publications

(5 citation statements)

References 23 publications

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“…The kinetic reactions inside the continuous-flow PCR chip are modeled and the governing equations are presented as follows:

where s is the location along the central line inside the microchannel; v is the speed at the location s ; and [ D ], [ E ], [ S ], [ P ], [ SP ], and [ E·SP ] mean the concentrations of double-stranded DNA molecules, enzyme, single-stranded DNA molecules, single-stranded primer molecules, single-stranded template–primer complexes and single-stranded template–primer–enzyme complexes, respectively. Reaction parameters in the present numerical simulation are listed in Table 1 and values reported in the literature are used [ 18 , 19 , 20 , 21 , 22 , 26 ]. L is the length of a DNA molecule.…”

Section: Theoretical Modeling and Numerical Methodsmentioning

confidence: 99%

“…However, the required thermal fields for PCR and the adequate residence time of each PCR step are not enough to connect with the successful PCR process. To understand the DNA amplification in a unidirectional CFPCR device, Wang and Wang [ 26 ] numerically studied the flowing effects on the DNA amplification with a simplified temperature distribution along the microchannel.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of PCR Kinetics inside a Microfluidic DNA Amplification System

Chen

2018

Micromachines

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In order to analyze the DNA amplification numerically with integration of the DNA kinetics, three-dimensional simulations, including flow and thermal fields, and one-dimensional polymerase chain reaction (PCR) kinetics are presented. The simulated results are compared with experimental data that have been applied to the operation of a continuous-flow PCR device. Microchannels fabricated by Micro Electro-Mechanical Systems (MEMS) technologies are shown. Comprehensive simulations of the flow and thermal fields and experiments measuring temperatures during thermal cycling are presented first. The resultant velocity and temperature profiles from the simulations are introduced to the mathematical models of PCR kinetics. Then kinetic equations are utilized to determine the evolution of the species concentrations inside the DNA mixture along the microchannel. The exponential growth of the double-stranded DNA concentration is investigated numerically with the various operational parameters during PCR. Next a 190-bp segment of Bartonella DNA is amplified to evaluate the PCR performance. The trends of the experimental results and numerical data regarding the DNA amplification are similar. The unique architecture built in this study can be applied to a low-cost portable PCR system in the future.

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“…The kinetic reactions inside the continuous-flow PCR chip are modeled and the governing equations are presented as follows:

Section: Theoretical Modeling and Numerical Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Analysis of PCR Kinetics inside a Microfluidic DNA Amplification System

Chen

2018

Micromachines

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“…Several kinetic models have been developed for the reactions in PCR systems - see for example those of Hunicke-Smith ( 1998 ); Athavale et al. ( 2001 ); Aach and Church ( 2004 ); Wang and Wang ( 2010 ); Papadopoulos et al. ( 2015 ) and Chen and Li ( 2018 ).…”

Section: Problem Specificationmentioning

confidence: 99%

Multi-objective optimisation of polymerase chain reaction continuous flow systems

Zagklavara

Jimack

Kapur

et al. 2022

Biomed Microdevices

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A surrogate-enabled multi-objective optimisation methodology for a continuous flow Polymerase Chain Reaction (CFPCR) systems is presented, which enables the effect of the applied PCR protocol and the channel width in the extension zone on four practical objectives of interest, to be explored. High fidelity, conjugate heat transfer (CHT) simulations are combined with Machine Learning to create accurate surrogate models of DNA amplification efficiency, total residence time, total substrate volume and pressure drop throughout the design space for a practical CFPCR device with sigmoid-shape microfluidic channels. A series of single objective optimisations are carried out which demonstrate that DNA concentration, pressure drop, total residence time and total substrate volume within a single unitcell can be improved by up to $$\sim$$ ∼ 5.7%, $$\sim$$ ∼ 80.5%, $$\sim$$ ∼ 17.8% and $$\sim$$ ∼ 43.2% respectively, for the practical cases considered. The methodology is then extended to a multi-objective problem, where a scientifically-rigorous procedure is needed to allow designers to strike appropriate compromises between the competing objectives. A series of multi-objective optimisation results are presented in the form of a Pareto surface, which show for example how manufacturing and operating cost reductions from device miniaturisation and reduced power consumption can be achieved with minimal impact on DNA amplification efficiency. DNA amplification has been found to be strongly related to the residence time in the extension zone, but not related to the residence times in denaturation and annealing zones.

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“…For instance, they prevent flow bypassing in heat exchangers with parallel flow passages, thus boosting overall heat transfer performance. In practical terms, swirl flow finds applications in various devices that do not involve chemical reactions, such as vortex amplifiers, 2,3 reactors, heat exchangers, cyclone separators, 4 whirlpools, 5 and jet pumps 6 . However, in cases where chemical reactions are involved, swirling devices are extensively used in combustion systems, including industrial furnaces, gas turbines, 7 gasoline and diesel engines, boilers, and heating appliances.…”

Section: Introductionmentioning

confidence: 99%

Thermal hydraulic performance of a tubular heat exchanger with in‐line perforated baffle with shutter type saw tooth turbulator

Rahman

2024

Heat Trans

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This experimental investigation aimed to analyze the impact of a unique design of swirl generator airflow on the performance of a tubular heat exchanger operating with axial flow. To conduct the experiment, we utilized a custom‐built apparatus containing eight sawtooth air deflectors with differing space height ratios (e/h). These deflectors were oriented in a uniform manner (shutter type) and positioned at various inclination angles. Circular baffle plates, housing these deflectors, were equidistantly spaced at different pitch ratios. The arrangement of tubes within the heat exchanger remained constant throughout the study, while the Reynolds number ranged from 16,000 to 30,000. In addition, a consistent heat flux condition was maintained on the surface of the tubes. The research outcomes indicated that incorporating a deflector baffle plate with an inclination angle of 30°, an e/h ratio of 0.4, and a pitch ratio of 1.2 led to an average increase of 1.36 in the thermal enhancement factor when compared to a heat exchanger lacking a baffle plate, tested under similar conditions.

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Kinetic characteristics of continuous flow polymerase chain reaction chip: A numerical investigation

Cited by 6 publications

References 23 publications

Analysis of PCR Kinetics inside a Microfluidic DNA Amplification System

Analysis of PCR Kinetics inside a Microfluidic DNA Amplification System

Multi-objective optimisation of polymerase chain reaction continuous flow systems

Thermal hydraulic performance of a tubular heat exchanger with in‐line perforated baffle with shutter type saw tooth turbulator

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