Experimental and Computational Design of a Microfluidic Device for Micro-Barcode Based Oligonucleotide Synthesis

美国国家科学基金会-化学运输系统司？微粒多相工艺项目（1415）提案编号：0729771主要研究者：Shaqfeh，Eric隶属机构： 斯坦福大学 提案标题：基于微条形码的寡核苷酸合成微流控装置的实验和计算设计微条形码技术有可能在一个反应容器中实现数十万个生化反应的大规模多路复用。微阵列在二维基底上进行大规模多路复用，通过使基因组范围内的遗传变异和功能研究成为可能，改变了生物医学研究。微条形码颗粒准备将这种能力转化为三维，自由解决方案格式，大大扩展了这种强大技术的可能性。具有0.25至1微米直径和2至10微米长度的棒状金属颗粒（Nanoplex，门洛帕克，CA）可以用编码大约10比特信息的金属条生长。每个微条形码颗粒携带可识别的签名，类似于常规条形码，其用作用于跟踪附接至颗粒表面的分子探针（诸如寡核苷酸）的机制。然后，许多这样的颗粒被混合，与样品反应，并在单个腔室或流体通道中并行检测。我们建议开发一种自动化的粒子流控制，电场对齐，分选和读出技术，适用于并行寡核苷酸合成。我们将构建和展示定制设计的微流体设备，这是第一次，将控制，读取和分类微流体系统中的微条形码颗粒。关键的设备设计和优化，将是广义电动模型的发展，占粒子布朗运动，电泳（包括单极和多极电动效应），水动力，并在有限的几何形状的沉降。这些模型将采用与实验联合开发的新型数值代码进行大规模多粒子模拟。大规模的模拟将使我们能够准确地预测粒子的位置，速度和方向，因为他们通过设备，从而定量预测设备performance.We已经进行了初步的实验中，我们对齐，并随后跟踪的位置和方向的圆柱形颗粒5微米长，直径0.25微米的沉降条件下，在直流和交流电场。除了最初的实验，我们已经开发了模拟工具，以模拟大量的布朗杆在低雷诺数下的沉积与电泳对齐和颗粒诱导的电泳流在周期性系统中，从而确定初始的流动参数制度，我们将最终详细检查。更广泛的研究影响和知识价值，我们的工作包括一个基本的理解，一些悬而未决的问题，直接影响到这些条码阅读器的性能悬挂力学。这些问题包括：（a）棒状聚合物和棒状胶体颗粒悬浮液从稀到半稀的流变学，包括ICEP相互作用;（B）ICEP流动对与纤维悬浮液的同时沉降和平均流动相关的集体现象的影响;（c）剪切诱导扩散对棒状颗粒质心运动的作用;和（d）非局部流中棒悬浮体的集体动力学，即平均流尺度为棒长度量级的流。事实上，尽管这些原理是复杂流体的微流体科学所固有的，但这些非线性物理学的许多组合将首次被研究。此外，通过与斯坦福大学的科学教师暑期研究计划合作，将开发与使用大规模计算设计微流体设备相关的广泛教育影响，作为高中科学教师暑期实习的一个组成部分。这些实习将包括一个或两个标题I学校的教师。一个实习将与研究的实验方面，另一个与计算设计方面。实习将允许教师与PI和研究生密切合作，并组成一个工作组，以了解微流体技术和先进计算作为工程设计工具的应用，然后将实验专业知识，演示和计算机模拟带回课堂。

National Science Foundation - Division of Chemical &Transport Systems ? Particulate & Multiphase Processes Program (1415)Proposal Number: 0729771 Principal Investigators: Shaqfeh, Eric Affiliation: Stanford Proposal Title: Experimental and Computational Design of a Microfluidic Device forMicro-Barcode Based Oligonucleotide Synthesis Micro-barcode technologies have the potential to realize large-scale multiplexing of hundreds of thousands of biochemical reactions in a single reaction vessel. Microarrays, which perform large-scale multiplexing on two-dimensional substrates, have transformed biomedical research by enabling genome wide investigation of genetic variation and function. Micro-barcode particles are poised to translate this capability to a three-dimensional, free-solution format, greatly expanding the possibilities of this powerful technology. Rod-shaped metallic particles with 0.25 to 1 micron diameters and lengths of 2 to 10 microns (Nanoplex, Menlo Park, CA) can be grown with metallic stripes that encode on the order of 10 bits of information. Each micro-barcode particle carries an identifiable signature, analogous to a conventional barcode, that serves as a mechanism for tracking molecular probes, such as oligonucleotides, attached to the particle surface. Many such particles then be mixed, reacted with a sample, and detected in parallel in a single chamber or fluidic channel. We propose to develop an automated particle flow control, electricfield alignment, sorting, and readout technology applicable to massively-parallel oligonucleotide synthesis. We will build and demonstrate custom-designed microfluidic devices, that for the first time, will control, read, and sort micro-barcode particles in microfluidic systems. Critical to the device design and optimization, will be the development of generalized electro-kinetic models that account for particle Brownian motion, electrophoresis (including mono- and multi-pole electrokinetic effects), hydrodynamic forces, and sedimentation in confined geometries. These models will be in the form of large-scale multi-particle simulations using novel numerical codes being developed jointly with the experiments. The large-scale simulations will allow us to accurately predict the location, velocity and orientation of the particles as they travel through the device, and thus quantitatively predict device performance.We have performed preliminary experiments in which we align and subsequently track the positions and orientations of cylindrical particles 5 microns long and 0.25 microns in diameter under settling conditions in both DC and AC electric fields. In additional to the initial experiments, we have already developed simulation tools to model the sedimentation of a large number of Brownian rods at low Reynolds number with electrophoretic alignment and particle-induced electrophoretic flow in periodic systems, thus determining the initial flow parameter regimes that we will ultimately examine in detail. The broader research impact and intellectual merit of our work includes a fundamental understanding of a number of unsolved problems in suspension mechanics which directly bear on the performance of these barcode readers. These issues include developing our understanding of (a) the rheology of rod-like polymer and rod-like colloidal particle suspensions from dilute through semi-dilute including ICEP interactions; (b) the effect of ICEP flow on the collective phenomena associated with the simultaneous sedimentation and mean flow of fiber suspensions; (c) the action of shear-induced diffusion on the center of mass motion of the rod-like particles; and (d) the collective dynamics of rod suspensions in non-local flows, i.e. those in which the mean flow scale is on the order of the length of the rod. Indeed, even though these principles are intrinsic to the science of the microfluidics of complex fluids, many of the combinations of these nonlinear physics will be examined for the first time. Moreover, the broad educational impact associated with using large scale computing for design of microfluidic devices will be developed as an integral part of two summer internships for high school science teachers via a partnership with Stanford's Summer Research Program for Science Teachers. These internships will include faculty at one or two Title I schools. One internship will be associated with the experimental aspects of the research and the other with the computational design aspects. The internships will allow the faculty members to work closely with the PIs and graduate students and form a working group to understand the applications of microfluidic technology and advanced computing as an engineering design tool, and thereafter take experimental expertise, demonstrations and computer simulations back to the classroom.