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 for Micro-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.
