Patrick S. Doyle
Massachusetts Institute of Technology
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Featured researches published by Patrick S. Doyle.
Science | 2007
Daniel C. Pregibon; Mehmet Toner; Patrick S. Doyle
High-throughput screening for genetic analysis, combinatorial chemistry, and clinical diagnostics benefits from multiplexing, which allows for the simultaneous assay of several analytes but necessitates an encoding scheme for molecular identification. Current approaches for multiplexed analysis involve complicated or expensive processes for encoding, functionalizing, or decoding active substrates (particles or surfaces) and often yield a very limited number of analyte-specific codes. We present a method based on continuous-flow lithography that combines particle synthesis and encoding and probe incorporation into a single process to generate multifunctional particles bearing over a million unique codes. By using such particles, we demonstrate a multiplexed, single-fluorescence detection of DNA oligomers with encoded particle libraries that can be scanned rapidly in a flow-through microfluidic channel. Furthermore, we demonstrate with high specificity the same multiplexed detection using individual multiprobe particles.
Lab on a Chip | 2008
Priyadarshi Panda; Shamsher Ali; Edward Lo; Bong Geun Chung; T. Alan Hatton; Ali Khademhosseini; Patrick S. Doyle
Encapsulating cells within hydrogels is important for generating three-dimensional (3D) tissue constructs for drug delivery and tissue engineering. This paper describes, for the first time, the fabrication of large numbers of cell-laden microgel particles using a continuous microfluidic process called stop-flow lithography (SFL). Prepolymer solution containing cells was flowed through a microfluidic device and arrays of individual particles were repeatedly defined using pulses of UV light through a transparency mask. Unlike photolithography, SFL can be used to synthesize microgel particles continuously while maintaining control over particle size, shape and anisotropy. Therefore, SFL may become a useful tool for generating cell-laden microgels for various biomedical applications.
Lab on a Chip | 2007
Dhananjay Dendukuri; Shelley S. Gu; Daniel C. Pregibon; T. Alan Hatton; Patrick S. Doyle
Polymeric particles in custom designed geometries and with tunable chemical anisotropy are expected to enable a variety of new technologies in diverse areas such as photonics, diagnostics and functional materials. We present a simple, high throughput and high resolution microfluidic method to synthesize such polymeric particles. Building off earlier work that we have done on continuous flow lithography (CFL) (D. Dendukuri, D. C. Pregibon, J. Collins, T. A. Hatton, P. S. Doyle, Nat. Mater., 2006, 5, 365-369; ref. 1), we have devised and implemented a new setup that uses compressed air driven flows in preference to syringe pumps to synthesize particles using a technique that we call stop-flow lithography (SFL). A flowing stream of oligomer is stopped before polymerizing an array of particles into it, providing for much improved resolution over particles synthesized in flow. The formed particles are then flushed out at high flow rates before the cycle of stop-polymerize-flow is repeated. The high flow rates enable orders-of-magnitude improvements in particle throughput over CFL. However, the deformation of the PDMS elastomer due to the imposed pressure restricts how quickly the flow can be stopped before each polymerization event. We have developed a simple model that captures the dependence of the time required to stop the flow on geometric parameters such as the height, length and width of the microchannel, as well as on the externally imposed pressure. Further, we show that SFL proves to be superior to CFL even for the synthesis of chemically anisotropic particles with sharp interfaces between distinct sections.
Langmuir | 2010
Kai P. Yuet; Dae Kun Hwang; Ramin Haghgooie; Patrick S. Doyle
In this study, we report the microfluidic-based synthesis of a multifunctional Janus hydrogel particle with anisotropic superparamagnetic properties and chemical composition for the bottom-up assembly of hydrogel superstructures. In a uniform magnetic field, the resulting Janus magnetic particles fabricated in the present method exhibit chainlike or meshlike superstructure forms, the complexity of which can be simply modulated by particle density and composition. This controllable field-driven assembly of the particles can be potentially used as building blocks to construct targeted superstructures for tissue engineering. More importantly, we demonstrated that this method also shows the ability to generate multifunctional Janus particles with great design flexibilities: (a) direct encapsulation and precise spatial distribution of biological substance and (b) selective surface functionalization in a particle. Although these monodisperse particles find immediate use in tissue engineering, their ability to self-assemble with tunable anisotropic configurations makes them an intriguing material for several exciting areas of research such as photonic crystals, novel microelectronic architecture, and sensing.
Journal of Fluid Mechanics | 1997
Patrick S. Doyle; Eric S. G. Shaqfeh; Alice P. Gast
We present a study of the rheological and optical behaviour of Kramers bead{rod chains in dilute solution using stochastic computer simulations. We consider two model linear flows, steady shear and uniaxial extensional flow, in which we calculate the non-Newtonian Brownian and viscous stress contribution of the polymers, their birefringence and a stress-optic coecient. We have developed a computer algorithm to dierentiate the Brownian from the viscous stress contributions which also avoids the order (t) 1=2 noise associated with the Brownian forces. The strain or shear rate is made dimensionless with a molecular relaxation time determined by simulated relaxation of the birefringence and stress after a strong flow is applied. The characteristic long relaxation time obtained from the birefringence and stress are equivalent and shown to scale with N 2 where N is the number of beads in the chain. For small shear or extension rates the viscous contribution to the eective viscosity is constant and scales as N. We obtain an analytic expression which explains the scaling and magnitude of this viscous contribution. In uniaxial extensional flow we nd an increase in the extensional viscosity with the dimensionless flow strength up to a plateau value. Moreover, the Brownian stress also reaches a plateau and we develop an analytic expression which shows that the Brownian stress in an aligned bead{rod chain scales as N 3 . Using scaling arguments we show that the Brownian stress dominates in steady uniaxial extensional flow until large Wi ,Wi 0:06N 2 , where Wi is the chain Weissenberg number. In shear flow the viscosity decays as Wi 1= 2 and the rst normal stress as Wi 4= 3 at moderate Wi. We demonstrate that these scalings can be understood through a quasi-steady balance of shear forces with Brownian forces. For small Wi (in shear and uniaxial extensional flow) and for long times (in stress relaxation) the stress-optic law is found to be valid. We show that the rheology of the bead{rod chain can be qualitatively described by an equivalent FENE dumbbell for small Wi .
Journal of Non-newtonian Fluid Mechanics | 1998
Patrick S. Doyle; Eric S. G. Shaqfeh; Gareth H. McKinley; Stephen H. Spiegelberg
Abstract The relaxation of dilute polymer solutions following stretch in uniaxial extensional flow is investigated via Brownian dynamic simulations of a flexible freely-draining bead-rod chain. The bead-rod chain simulations are compared to Brownian dynamic simulations of a FENE dumbbell and numerical calculations of a FENE-PM chain. A universal relaxation curve for the stress decay from steady-state is found by shifting the results to lie on the curve described by the relaxation of an initially straight chain. For all the models investigated, the initial rapid decay of the polymer stress decreases at a rate which scales for large Weissenberg number, Wi as Wi 2 . Our universal curve is in good qualitative and in some cases quantitative agreement with the available experimental data: it is particularly good in predicting decay after stretch at the largest strains. We find hysteresis in comparing the stress versus birefringence during the startup of flow and subsequent relaxation for the bead-rod chain and FENE dumbbell, but not for the FENE-PM chain. The hysteresis in the latter model is lost in the preaveraging of the nonlinear terms. The bead-rod model also displays a configuration hysteresis. The hysteresis observed in these models is in qualitative agreement with recent experiments involving polystyrene-based Boger fluids.
Angewandte Chemie | 2011
Stephen C. Chapin; David C. Appleyard; Daniel C. Pregibon; Patrick S. Doyle
MicroRNAs (miRNAs) are short non-coding RNAs that mediate protein translation and are known to be dysregulated in diseases including diabetes, Alzheimer’s, and cancer.[1–3] With greater stability and predictive value than mRNA, this relatively small class of biomolecules has become increasingly important in determining disease diagnosis and prognosis. However, the sequence homology, wide range of abundance, and common secondary structures of miRNAs have complicated efforts to develop accurate, unbiased quantification techniques.[4,5] Applications in the discovery and clinical fields require high-throughput processing, large coding libraries for multiplexed analysis, and the flexibility to develop custom assays. Microarray approaches provide high sensitivity and multiplexing capacity, but their low-throughput, complexity, and fixed design make them less than ideal for use in a clinical setting.[6,7] PCR-based strategies suffer from similar throughput issues, yet offer highly sensitive and specific detection for genome-wide miRNA expression profiling.[8] Alternative bead-based systems provide a high sample throughput, but with reduced sensitivity,[9] dynamic range, and multiplexing capacities (luminexcorp.com). miRNA profiling by deep sequencing is emerging as a powerful tool for small RNA analysis; however, the high cost of implementation and need for large amounts of input RNA currently limit its utility.[10] The ideal system for miRNA quantification would offer the detection performance of array and PCR-based methods, the throughput of bead-based systems, and improved reproducibility with a user-friendly workflow.
Journal of the American Chemical Society | 2009
Dae Kun Hwang; John Oakey; Mehmet Toner; Jeffrey A. Arthur; Kristi S. Anseth; Sunyoung Lee; Adam S. Zeiger; Krystyn J. Van Vliet; Patrick S. Doyle
Microgel particles capable of bulk degradation have been synthesized from a solution of diacrylated triblock copolymer composed of poly(ethylene glycol) and poly(lactic acid) in a microfluidic device using stop-flow lithography (SFL). It has been previously demonstrated that SFL can be used to fabricate particles with precise control over particle size and shape. Here, we have fabricated hydrogel particles of varying size and shape and examined their mass-loss and swelling behavior histologically and mechanically. We report that these features, as well as degradation behavior of the hydrogel particles may be tailored with SFL. By reducing the applied UV dose during fabrication, hydrogel particles can be made to exhibit a distinct deviation from the classical erosion profiles of bulk-degrading hydrogels. At higher UV doses, a saturation in cross-linking density occurs and bulk-degrading behavior is observed. Finally, we synthesized multifunctional composite particles, providing unique features not found in homogeneous hydrogels.
Analytical Chemistry | 2011
David C. Appleyard; Stephen C. Chapin; Patrick S. Doyle
We demonstrate the use of graphically encoded hydrogel microparticles for the sensitive and high-throughput multiplexed detection of clinically relevant protein panels in complex media. Combining established antibody capture techniques with advances in both microfluidic synthesis and analysis, we detected 1-8 pg/mL amounts of three cytokines (interleuken-2, interleuken-4, and tumor necrosis factor alpha) in single and multiplexed assays without the need for filtration or blocking agents. A range of hydrogel porosities was investigated to ensure rapid diffusion of targets and reagents into the particle as well as to maintain the structural integrity of particles during rinsing procedures and high-velocity microfluidic scanning. Covalent incorporation of capture antibodies using a heterobifunctional poly(ethylene glycol) linker enabled one-step synthesis and functionalization of particles using only small amounts of valuable reagents. In addition to the use of three separate types of single-probe particles, the flexibility of the stop-flow lithography (SFL) method was leveraged to spatially segregate the three probes for the aforementioned target set on an individual encoded particle, thereby demonstrating the feasibility of single-particle diagnostic panels. This study establishes the gel-particle platform as a versatile tool for the efficient quantification of protein targets and significantly advances efforts to extend the advantages of both hydrogel substrates and particle-based arrays to the field of clinical proteomics.
Nature Protocols | 2011
David C. Appleyard; Stephen C. Chapin; Rathi L. Srinivas; Patrick S. Doyle
This protocol describes the core methodology for the fabrication of bar-coded hydrogel microparticles, the capture and labeling of protein targets and the rapid microfluidic scanning of particles for multiplexed detection. Multifunctional hydrogel particles made from poly(ethylene glycol) serve as a sensitive, nonfouling and bio-inert suspension array for the multiplexed measurement of proteins. Each particle type bears a distinctive graphical code consisting of unpolymerized holes in the wafer structure of the microparticle; this code serves to identify the antibody probe covalently incorporated throughout a separate probe region of the particle. The protocol for protein detection can be separated into three steps: (i) synthesis of particles via microfluidic flow lithography at a rate of 16,000 particles per hour; (ii) a 3–4-h assay in which protein targets are captured and labeled within particles using an antibody sandwich technique; and (iii) a flow scanning procedure to detect bar codes and quantify corresponding targets at rates of 25 particles per s. By using the techniques described, single- or multiple-probe particles can be reproducibly synthesized and used in customizable multiplexed panels to measure protein targets over a three-log range and at concentrations as low as 1 pg ml−1.