Collaborative Research: DNA Amplification in a novel integrated microchip platform with temporal thermal control

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COLLABORATIVE RESEARCH: DNA AMPLIFICATION IN A NOVEL INTEGRATED MICROCHIP PLATFORM WITH TEMPORAL THERMAL CONTROLImplementing precise time and space dependent heating and cooling in a microchip is potentially useful in a wide array of areas including reactions, separation, detection, etc. This project aims to develop such a microchip, and understand the fundamental implications of the temperature changes on fluid flow and heat and mass transfer, while developing a chip that can perform rapid DNA amplification. While microfluidic DNA amplification devices have been fabricated, their use in practical applications is nonexistent due to small throughputs. Here we propose a new paradigm for PCR in a microchannel that is based on temporal temperature cycling. To accomplish this objective, we propose a new chip design for implementing precise and accurate temperature gradients (both spatial and temporal). Furthermore, we propose a synergistic approach that leverages the strengths of both the PI's by combining modeling and experiments to develop a clear understanding of fundamental issues relevant to the proposed device. These issues include contribution of thermal expansion-contraction, and reactions on dispersion and amplification efficiency, and the effect of various design and operating parameters on the fluid-flow and mass transfer in the device. Such an understanding is crucial for designing an optimal microfluidic flow reactor for DNA amplification with a high throughput. The intellectual merit of the program is manifested in the goals of the project that include (i) development of a Smart Thermal Microchip (STM) for precise temperature modulation, (ii) an improved quantitative understanding of transport in microscale systems that are subjected to temporally changing temperatures; (iii) development of a numerical and analytical tools to analyze heat transfer in the Smart Thermal Microchip and to predict the dispersion and amplification of DNA samples using various input parameters such as the channel dimensions, number and frequency of the temperature cycles, dispersion coefficient of the DNA and the initial plug size; (iv) development of a novel idea for continuous and high throughput polymerase chain reaction on a microfluidic chip without an imposed pressure driven flow. The results of this proposal will improve our understanding of mass transfer in systems with reactions and temporal temperature gradients, and in particular lead to a thorough understanding of the transport processes involved in the DNA amplification by polymerase chain reaction on a microchip. These results will lead to a rational design and operation of these chips. The results of this research will have broader impacts in a number of areas. The Smart Thermal Microchip will find applications in other areas related to reactions, separations and detection. Furthermore, the amplification process is an integral part of DNA analysis and the importance of DNA analysis cannot be overstated. It is already important in various areas such as analysis of clinical samples, identification of mutations, detecting cancer, testing safety of genetically modified foods, forensic analysis and applications of DNA analysis are only expected to grow considerably. It is envisioned that the results of this study will enable optimization of amplification devices and additionally lead to development of a novel high throughput device. The educational program couples core skills of thermal and mass transport to reaction kinetics. The research will be integrated with the curriculum development of the Chemical Engineering Department of the University of Florida and of Brown University in the division of engineering and the chemical and biochemical engineering program. The program supports development of new courses in transport processes. The program offers excellent opportunities to new undergraduate laboratories exploring microfluidics. Students also apply their skills in transport phenomena to unveil methods for detecting microbial threats. The program is truly interdisciplinary and invites opportunities for collaborations. Strong ties are promoted between the fundamental engineering research and assay development in biotechnology and nanotechnology industries. Lastly, the research program unites the interests of the two PIs and will foster significant collaborations and exchange of ideas between the two research groups.