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

在微芯片中实现精确的时间和空间相关加热和冷却，在包括反应、分离、检测等在内的广泛领域具有潜在的用途。本项目旨在开发这样的微芯片，并了解温度变化对流体流动和传热传质的基本含义，同时开发一种可以进行快速DNA扩增的芯片。虽然微流控DNA扩增装置已经被制造出来，但由于其通量小，其在实际应用中的应用尚不存在。在这里，我们提出了一种基于时间温度循环的微通道PCR新范式。为了实现这一目标，我们提出了一种新的芯片设计，用于实现精确和精确的温度梯度（空间和时间）。此外，我们提出了一种协同方法，通过结合建模和实验来利用PI的优势，以清楚地了解与所提议设备相关的基本问题。这些问题包括热膨胀-收缩的贡献，对扩散和放大效率的影响，以及各种设计和操作参数对装置内流体流动和传质的影响。这种理解对于设计最佳的高通量DNA扩增微流控反应器至关重要。该计划的智力价值体现在项目的目标中，包括(i)开发用于精确温度调制的智能热微芯片（STM）， （ii）改进对受时间变化温度影响的微尺度系统中传输的定量理解；（iii）开发一种数值和分析工具来分析智能热芯片中的热传递，并使用各种输入参数（如通道尺寸、温度循环的数量和频率、DNA的分散系数和初始插头尺寸）预测DNA样品的分散和扩增；（iv）在微流控芯片上开发连续和高通量聚合酶链反应的新想法，而无需施加压力驱动流。本研究的结果将提高我们对具有反应和时间温度梯度系统的传质的理解，特别是对微芯片上聚合酶链反应扩增DNA的传递过程的深入理解。这些结果将有助于这些芯片的合理设计和操作。这项研究的结果将在许多领域产生更广泛的影响。智能热芯片将在与反应、分离和检测相关的其他领域找到应用。此外，扩增过程是DNA分析的一个组成部分，DNA分析的重要性怎么强调都不为过。它已经在临床样本分析、突变鉴定、癌症检测、转基因食品安全性测试、法医分析和DNA分析应用等各个领域发挥了重要作用，预计只会大幅增长。预计本研究的结果将使放大设备的优化，并导致一种新的高通量设备的开发。教育计划将热和质量传递的核心技能与反应动力学相结合。该研究将与佛罗里达大学化学工程系和布朗大学工程系以及化学与生物化学工程项目的课程开发相结合。该计划支持开发运输过程中的新课程。该计划为探索微流体的新本科实验室提供了极好的机会。学生还将运用他们在运输现象方面的技能来揭示检测微生物威胁的方法。该计划是真正的跨学科，并邀请合作的机会。生物技术和纳米技术行业的基础工程研究和分析开发之间的紧密联系得到了促进。最后，该研究项目联合了两个pi的利益，并将促进两个研究小组之间的重要合作和思想交流。

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.