2014-2008

See also Google Scholar for links to articles and citations.

2014

  1. Kundukad, B., Yan, J., and Doyle, P.S., “Effect of YOYO-1 on the mechanical properties of DNA”, Soft Matter, 10, 9721, 2014. PDF reprint

  1. Zhang, X., Qu, Y., Chen, H., Rouzina, I., Zhang, S., Doyle, P.S., and Yan, J. “Interconversion between three overstretched DNA structures”, JACS, 136, 16073-16080, 2014. PDF reprint
  1. Bong, K.W., Lee, J., and Doyle, P.S. “Stop Flow Lithography in Perfluoropolyether (PFPE) Microfluidic Channels”, Lab Chip, 14, 4680-4687, 2014. PDF reprint
  1. Eral, H.B., O’Mahony, M., Shaw, R., Trout, B.L., Myerson, A.S., and Doyle, P.S.. “Composite Hydrogels Laden with Crystalline Active Pharmaceutical Ingredients of Controlled Size and Loading”, Chemistry of Materials, 26, 6213-6220, 2014. PDF reprint
  1. Renner, C. and Doyle, P.S. “Untying Knotted DNA with Elongational Flows”, ACS Macro Letters, 3, 963–967, 2014. PDF reprint
  1. Dai, L., Renner, C.B., and Doyle, P.S. “Metastable tight knots in semiflexible chains”, Macromolecules, 47 (17), 6135–6140, 2014. PDF reprint
  1. An, H.Z., Eral, H.B., Chen, L., Chen, M.B., and Doyle, P.S. “Synthesis of Colloidal Microgels using Oxygen-controlled Flow Lithography”, Soft Matter, 10, 7595-7605, 2014. PDF reprint
  1. Chew, S.C., Kundukad, B., Seviour, T.W., Van Der Maarel, J., Yang, L., Rice, S.A., Doyle, P.S., and Kjelleberg, S. “Dynamic Remodeling of Microbial Biofilms by Functionally Distinct Exopolysaccharides”, mBio, 5 (4), e01536-14, 2014. PDF reprint
  1. Birjiniuk, A., Billings, N., Nance, E., Hanes, J., Ribbeck, K., and Doyle, P.S. “Single Particle Tracking Reveals Spatial and Dynamic Organization of the E. coli Biofilm Matrix”, New Journal of Physics, 16, 085014, 2014. PDF reprint
  1. Lim, E.J., Ober, T.J., Edd, J.F., Desai, S.P., Neal, D., Bong, K.W., Doyle, P.S., McKinley, G.H., and Toner, M. “Inertio-elastic Focusing of Bioparticles in Microchannels at Ultra-high Throughput”, Nature Communications, 5, 4120. PDF reprint
  1. Renner, C.B., Du, N., and Doyle, P.S., “Enhanced Electrohydrodynamic Collapse of DNA due to Dilute Polymers”, Biomicrofluidics, 8, 034103, 2014. PDF reprint
  1. Uspal, W.E., and Doyle, P.S., “Self-organizing Microfluidic Crystals”, Soft Matter, 10, 5177-5191, 2014. PDF reprint
  1. Lee, J., Bisso, P.W., Srinivas, R.L., Kim, J.J, Swiston, A.J., and Doyle, P.S., “Universal Process-inert Encoding Architecture for Polymer Microparticles”, Nature Materials, 13, 524-529, 2014. PDF reprint
  1. Dai, L., van der Maarel, J., and Doyle, P.S., “Extended de Gennes Regime of DNA Confined in a Nanochannel”, Macromolecules, 47, 2445-2450, 2014. PDF reprint
  1. Helgeson, M.E., Gao, Y., Moran, S.E., Lee, J., Godfrin, M., Tripathi, A., Bose, A., and Doyle, P.S., “Homogeneous percolation versus arrested phase separation in attractively-driven nanoemulsion colloidal gels”, Soft Matter, 10, 3122-33, 2014. PDF reprint
  1. Eral, H., Lopez-Mejias, V., O’Mahony, M., Trout, B., Myerson, A., and Doyle, P.S. “Biocompatible Alginate Microgel Particles as Heteronucleants and Encapsulating Vehicles for Hydrophilic and Hydrophobic Drugs”, Crystal Growth & Design, 14, 2073-2082, 2014. PDF reprint

2013

  1. Srinivas, R.L., Johnson, S., Doyle, P.S., “Oil-isolated Hydrogel Microstructures for Sensitive Bioassays On-chip”, Analytical Chemistry, 86, 12099-12107, 2013. PDF reprint
  1. Tree, D.R., Muralidhar, A., Doyle, P.S., and Dorfman, K.D., “Is DNA a Good Model Polymer?”, Macromolecules, 46, 8369-8382, 2013. PDF reprint
  1. An, H., Safai, E., Eral, H.B., and Doyle, P.S., “Synthesis of biomimetic oxygen-carrying compartmentalized microparticles using flow lithography”, Lab Chip, 13, 4765-4774, 2013. PDF reprint
  1. Uspal, W.E., Eral, H.B., and Doyle, P.S., “Engineering particle trajectories in microfluidic flows using particle shape”, Nat. Commun., 4, 2666, 2013. PDF reprint
  1. Zhang, C., Hernandez-Garcia, A., Jiang, K., Gong, Z., Guttula, D., Ng, S.Y., Malar, P.P., van Kan, J.A., Dai, L., Doyle, P.S., de Vries, R., and an der Maarel, J.R.C., “Amplified Stretch of Bottlebrush-Coated DNA in Nanofluidic Channels”, Nucleic Acids Res., 41, e189, 2013. PDF reprint
  1. Zhang, C., Guttula, D., Liu, F., Malar, P.P., Ng, S.Y., Dai, L., Doyle, P.S., van Kan, J.A., and van der Maarel, J.R.C., “Effect of H-NS on the elongation and compaction of single DNA molecules in a nanospace”, Soft Matter, 9, 9593-9601, 2013. PDF reprint
  1. Dai, L., and Doyle, P.S, “Comparisons of a polymer in confinement versus applied force”, Macromolecules, 46, 6336-6344, 2013. PDF reprint
  1. Rahman, M., Barikbin, Z., Badruddoza, A.Z., Doyle, P.S., and Khan, S., “Monodisperse Polymeric Ionic Liquid Microgel Beads with Multiple Chemically Switchable Functionalities”, Langmuir, 29, 9535-9543, 2013. PDF reprint
  1. Critchfield, A.S., Yao, G., Jaishankar, A., Friedlander, R.S., Lieleg, O., Doyle, P.S., McKinley, G., House, M., and Ribbeck, K., “Cervical Mucus Properties Stratify Risk for Preterm Birth”, PLOS ONE, 8, e69528, 2013. PDF reprint
  1. Yeo, S., Choi, S., Dien, V., Sow-Peh, Y., Qi, G., Hatton, T.A., Doyle, P.S., and Thio, B.J., “Use of magnetically responsive tea waste to remove lead in waters under environmentally relevant conditions”, PLOS ONE, 8, e66648, 2013. PDF reprint
  1. Kundukad, B., Cong, P., van der Maarel, J.R.C., and Doyle, P.S., “Time-dependent bending rigidity and helical twist of DNA by rearrangement of bound HU protein”, Nucleic Acids Res., 41, 8280-8288, 2013. PDF reprint
  1. Zhang, C., Jiang, K., Liu, F., Doyle, P.S., van Kan, J.A., and van der Maarel, J.R.C., “A Nanofluidic Device for Single Molecule Studies with In Situ Control of Environmental Solution Conditions”, Lab Chip, 13, 2821-2826, 2013. PDF reprint
  1. Dai, L., Tree, D.R., van der Maarel, J.R.C., Dorfman, K.D., and Doyle, P.S., “Revisiting blob theory for DNA diffusivity in slitlike confinement”, Phys. Rev. Lett., 110, 168105, 2013. PDF reprint
  1. Zhang, X., Chen, H., Le, S., Rouzina, I., Doyle, P.S., and Yan, J., “Revealing the Competition between Peeled-ssDNA, Melting Bubbles and S-DNA during DNA Overstretching by Single-Molecule Calorimetry”, Proc. Natl. Acad. Sci., 110, 3859-3864, 2013. PDF reprint
  1. Jones, J.J., van der Maarel, J.R.C., and Doyle, P.S., “Intrachain dynamics of large dsDNA confined to slit-like channels”, Phys. Rev. Lett., 110, 068101, 2013. PDF reprint
  1. Kim, Y.S., Kundukad, B., Allahverdi, A., Nordenskiöld, L., Doyle, P.S., and van der Maarel, J.R.C., “Gelation of the genome by topoisomerase II targeting anticancer agents”, Soft Matter, 9, 1656-1663, 2013. PDF reprint

2012

  1. Choi, N.W., Kim, J., Chapin, S.C., Duong, T., Donohue, E., Pandey, P., Broom, W., Hill, W., and Doyle, P.S., “Multiplexed detection of mRNA using porosity-tuned hydrogel microparticles”, Anal. Chem., 84, 9370-9378, 2012. PDF reprint
  1. Leith, J.S., Tafvizi, A., Huang, F., Uspal, W.E., Doyle, P.S., Fersht, A.R., Mirny, L.A., and van Oijen, A.M., “Sequence-dependent sliding kinetics of p53”, Proc. Natl. Acad. Sci., 109, 16552-16557, 2012. PDF reprint
  1. Dai, L., Ng, S., Doyle, P.S., and van der Maarel, J., “Conformation model of back-folding and looping of a single DNA molecule confined inside a nanochannel”, ACS Macro Lett., 1, 1046-1050, 2012. PDF reprint
  1. Uspal, W.E., and Doyle, P.S., “Collective dynamics of small clusters of particles flowing in a quasi-two-dimensional microchannel”, Soft Matter, 8, 10676-10686, 2012. PDF reprint
  1. Dai, L., van der Maarel, J., and Doyle, P.S., “Effect of nanoslit confinement on the knotting probability of circular DNA”, ACS Macro Lett., 1, 732-736, 2012. PDF reprint
  1. Rich, J.P., Doyle, P.S., McKinley, G.H., “Magnetorheology in an aging, yield stress matrix fluid”, Rheol. Acta, 51, 579-593, 2012. PDF reprint
  1. Suh, S.K., Yuet, K., Hwang, D.K., Bong, K.W., Doyle, P.S., and Hatton, T.A., “Synthesis of Non-spherical Superparamagnetic Particles: In-situ Co-precipitation of Magnetic Nanoparticles in Microgels Prepared by Stop-Flow-Lithography”, J. Am. Chem. Soc., 134, 7337-7343, 2012. PDF reprint
  1. Suh, S.K., Chapin, S.C., Hatton, T.A., and Doyle, P.S., “Synthesis of magnetic hydrogel microparticles for bioassays and tweezer manipulation in microwells”, Microfluid. Nanofluid., 13, 665-674, 2012. PDF reprint
  1. Bong, K.W., Xu, J., Kim, J.-H., Chapin, S.C., Strano, M.S., Gleason, K.K., and Doyle, P.S., “Non-polydimethylsiloxane devices for Oxygen-Free Flow Lithography”, Nat. Commun., 3, 805, 2012. PDF reprint
  1. Zhang, X., Chen, H., Fu, H., Doyle, P.S., and Yan, J., “Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements”, Proc. Natl. Acad. Sci., 109, 8103-8108, 2012. PDF reprint
  1. An, H., Helgeson, M.E., and Doyle, P.S, “Nanoemulsion Composite Microgels for Orthogonal Encapsulation and Release”,Advanced Materials, 24, 3838-3844, 2012. PDF reprint
  1. Zhang, C., Gong, Z., Guttula, D., Malar, P., van Kan, J., Doyle, P.S., and van der Maarel, J., “Nanofluidic Compaction of DNA by Like-Charge Protein”, J. Phys. Chem. B, 116, 3031-3036, 2012. PDF reprint
  1. Rich, J.P., McKinley, G.H., and Doyle, P.S., “Arrested Chain Growth During Magnetic Directed Particle Assembly in Yield Stress Matrix Fluids”, Langmuir, 28, 3683-3689, 2012. PDF reprint
  1. Helgeson, M.E., Moran, S., An, H., and Doyle, P.S., “Mesoporous organohydrogels from thermogelling photocrosslinkable nanoemulsions”, Nat. Mater., 11, 344-352, 2012. PDF reprint
  1. Uspal, W.E., and Doyle, P.S., “Scattering and nonlinear bound states of hydrodynamically coupled particles in a narrow channel”, Phys. Rev. E, 85, 016325, 2012. PDF reprint
  1. Dai, L., Jones, J.J., van der Maarel, J.R.C., and Doyle, P.S., “A Systematic Study of DNA Conformation in Slitlike Confinement”, Soft Matter, 8, 2972-2982, 2012. PDF reprint
  1. Diao, Y., Whaley, K.E., Helgeson, M.E., Woldeyes, M.A., Doyle, P.S., Myerson, A.S., Hatton, T.A., and Trout, B.L., “Gel-induced selective crystallization of polymorphs”, J. Am. Chem. Soc., 134, 673-684, 2012. PDF reprint
  1. Diao, Y., Helgeson, M., Siam, Z., Doyle, P.S., Myerson, A., Hatton, T.A., and Trout, B., “Nucleation under Soft Confinement: Role of Polymer-Solute Interactions”, Cryst. Growth Des., 12, 508-517, 2012. PDF reprint

2011

  1. Srinivas, R.L., Chapin, S.C., and Doyle, P.S., “Aptamer Functionalized Microgel Particles for Protein Detection”, Anal. Chem.,83, 9138-9145, 2011. PDF reprint
  1. Jones, J.J., Van Der Maarel, J.R.C., and Doyle, P.S., “Effect of nanochannel geometry on DNA structure in the presence of macromolecular crowding agent”, Nano Lett., 11, 5047-5053, 2011. PDF reprint
  1. Suh, S.K., Bong, K.W., Hatton, T.A., and Doyle, P.S., “Using Stop-Flow Lithography to Produce Opaque Microparticles: Synthesis and Modeling”, Langmuir, 27, 13813-13819, 2011. PDF reprint
  1. Panda, P., Bong, K.W., Hatton, T.A., and Doyle, P.S., “Branched Networks By Directed Assembly of Shape Anisotropic Magnetic Particles.”, Langmuir, 27, 13428-13435, 2011. PDF reprint
  1. Tang, J., Du, N., and Doyle, P.S., “Compression and self-entanglement of single DNA molecules under uniform electric field”, PNAS, 108, 16153-16158, 2011. PDF reprint
  1. Chapin, S.C., and Doyle, P.S., “Ultrasensitive Multiplexed MicroRNA Quantification on Encoded Gel Microparticles Using Rolling Circle Amplification”, Anal. Chem., 83, 7179-7185, 2011. PDF reprint. Featured in Chemical & Engineering News and on the MIT front page.
  1. Rich, J.P., Lammerding, J., McKinley, G.H., and Doyle, P.S., “Nonlinear microrheology of an aging, yield stress fluid using magnetic tweezers”, Soft Matter, 7, 9933-9943, 2011. PDF reprint
  1. Zhang, H., DeConinck, A.J., Slimmer, S.C., Doyle, P.S., Lewis, J.A., and Nuzzo, R.G., “Genotyping by Alkaline Dehybridization Using Graphically Encoded Particles”, Chem.-Eur. J., 17, 2867-2873, 2011. PDF reprint
  1. Trahan, D.W., and Doyle, P.S., “Simulating the Relaxation of Stretched DNA in Slitlike Confinement”, Macromolecules, 44, 382-392, 2011. PDF reprint
  1. Appleyard, D., Chapin, S.C., Srinivas, R.L., and Doyle, P.S., “Barcoded Hydrogel Microparticles for Protein Detection: Synthesis, Assay, and Scanning”, Nat. Protoc., 6, 1761-1774, 2011. PDF reprint
  1. Diao, Y., Helgeson, M.E., Myerson, A.S., Hatton, T.A., Doyle, P.S., and Trout, B.L., “Controlled Nucleation from Solution Using Polymer Microgels”, J. Am. Chem. Soc., 133, 3756-3759, 2011. PDF reprint
  1. Rich, J.P., McKinley, G., and Doyle, P.S., “Size dependence of microprobe dynamics during gelation of a discotic colloidal clay”, J. Rheol., 55, 273-299, 2011. PDF reprint
  1. Bong, K.W., Chapin, S.C., Pregibon, D.C., Baah, D., Floyd-Smith, T.M., and Doyle, P.S., “Compressed-air flow system”, Lab Chip, 11, 743-747, 2011. pdf preprint
  1. Chapin, S.C., Pregibon, D., and Doyle, P.S., “Rapid microRNA Profiling on Encoded Gel Microparticles”, Angew. Chem. Int. Ed., 50, 2289-2293, 2011. PDF reprint
  2. Helgeson, M., Chapin, S.C., and Doyle, P.S., “Hydrogel microparticles from lithographic processes: novel materials for fundamental and applied colloid science”, Curr. Opin. Colloid Interface Sci., 16, 106-117, 2011. PDF reprint

2010

  1. Appleyard, D., Chapin, S.C., and Doyle, P.S., “Multiplexed Protein Quantification with Barcoded Hydrogel Microparticles”,Anal. Chem., 83, 193-199, 2010. PDF reprint. Featured in Chemical & Engineering News and NIBIB e-advances.
  1. Tang, J., Levy, S., Trahan, D., Jones, J., Craighead, H., and Doyle, P.S., “Revisiting the Conformational Dynamics of DNA in Slitlike Confinement”, Macromolecules, 43, 7368-7377, 2010. PDF reprint
  1. Lewis, C., Lin, Y., Yang, C., Manocchi, A., Yuet, K.P., Doyle, P.S., and Yi, H., “Microfluidic Fabrication of Hydrogel Microparticles Containing Functionalized Viral Nanotemplates”, Langmuir, 26, 13436-13441, 2010. PDF reprint
  1. Trahan, D.W., and Doyle, P.S., “DNA collisions with a large, conducting post”, Macromolecules, 43, 5424-5432, 2010. PDF reprint
  1. Tang, J., Trahan, D.W., and Doyle, P.S., “Coil-Stretch Transition of DNA Molecules in Slitlike Confinement”, Macromolecules,43, 3081-3089, 2010. PDF reprint
  1. Bong, K.W., Chapin, S., and Doyle, P.S., “Magnetic Barcoded Hydrogel Microparticles for Multiplexed Detection”, Langmuir,26, 8008-8014, 2010. PDF reprint
  1. Yuet, K.P., Hwang, D.K., Haghgooie, R., and Doyle, P.S., “Multifunctional Superparamagnetic Janus Particles”, Langmuir, 26, 4281-4287, 2010. PDF reprint
  1. Bong, K.W., Bong, K.T., Pregibon, D.C., and Doyle, P.S., “Hydrodynamic Focusing Lithography”, Angew. Chem. Int. Ed., 49, 87-90, 2010. PDF reprint
  1. Haghgooie, R., Toner, M., and Doyle, P.S., “Squishy non-spherical hydrogel microparticles”, Macromol. Rapid Commun., 31, 128-134, 2010. PDF reprint

2009

  1. Panda, P., Yuet, K.P., Dendukuri, D., Hatton, T.A., and Doyle, P.S., “Temporal Response of an Initially Deflected PDMS Channel”, New J. Phys., 11, 115001, 2009. PDF reprint
  1. Chapin, S., Pregibon, D.C., and Doyle, P.S., “High-throughput flow alignment of barcoded hydrogel microparticles”, Lab Chip,9, 3100-3109, 2009. PDF reprint
  1. Dendukuri, D., and Doyle, P.S., “The Synthesis and Assembly of Polymeric Microparticles Using Microfluidics”, Advanced Materials, 21, 1-16, 2009. PDF reprint
  1. Pregibon, D.C., and Doyle, P.S., “Optimization of Encoded Hydrogel Particles for Nucleic Acid Quantification”, Anal. Chem.,81, 4873-4881, 2009. PDF reprint
  1. Haghgooie, R., and Doyle, P.S., “Directed self-assembly of field-responsive fluids in confined geometries”, Soft Matter, 5, 1192-1197, 2009. PDF reprint
  1. Panda, P., Yuet, K.P., Hatton, T.A., and Doyle, P.S., “Tuning Curvature in Flow Lithography: A New Class of Concave/Convex Particles”, Langmuir, 25, 5986-5992, 2009. PDF reprint
  1. Bong, K.W., Pregibon, D.C., and Doyle, P.S., “Lock release lithography for 3D and composite microparticles”, Lab Chip, 9, 863-866, 2009. PDF reprint. Featured in Chemical Technology and the Lab Chip inside cover.
  1. Hwang, D.K., Oakey, J., Toner, M., Arthur, J., Anseth, K., Lee, S., Zeiger, A., Van Vliet, K., and Doyle, P.S., “Stop-Flow Lithography for the Production of Shape-Evolving Degradable Microgel Particles”, J. Am. Chem. Soc., 131, 4499-4504, 2009.PDF reprint
  1. Attia, R., Pregibon, D.C., Doyle, P.S., Viovy, J.-L., and Bartolo, D., “Soft microflow sensors”, Lab Chip, 9, 1213-1218, 2009. PDF reprint
  1. Trahan, D.W. and Doyle, P.S., “Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning”, Biomicrofluidics, 3, 012803, 2009. PDF reprint
  1. Im, S.G., Bong, K.W, Lee, C.-H., Doyle, P.S., and Gleason, K., “A Conformal Nano-adhesive via Initiated Chemical Vapor Deposition for Microfluidic Devices”, Lab Chip, 9, 411-416, 2009. PDF reprint

2008

  1. Balducci, A.G., Tang, J., and Doyle, P.S., “Electrophoretic Stretching of DNA Molecules in Cross-slot Nanoslit Channels”,Macromolecules, 41, 9914-9918, 2008. PDF reprint
  1. Im, S.G., Bong, K.W, Kim, B.-S., Baxamusa, S., Hammond, P., Doyle, P.S., and Gleason, K., “Patterning Nanodomains with Orthogonal Functionalities: Solventless Synthesis of Self-Sorting Surfaces”, J. Am. Chem. Soc., 130, 14424-14425, 2008. PDF reprint
  1. Dendukuri, D., Panda, P., Haghgooie, R., Kim, J.M., Hatton, T.A., and Doyle, P.S., “Modeling of Oxygen-Inhibited Free Radical Photopolymerization in a PDMS Microfluidic Device”, Macromolecules, 41, 8547-8556, 2008. PDF reprint
  1. Shepherd, R.F., Panda, P., Bao, Z., Sandhage, K.H., Hatton, T.A., Lewis, J.A., and Doyle, P.S., “Stop-flow lithography of colloidal, glass, and silicon microcomponents”, Advanced Materials, 20 4734-4739, 2008. PDF reprint. Featured on the cover page.
  1. Tan, W.S., Lewis, C., Horelik, N., Pregibon, D., Doyle, P.S., and Yi, H., “Hierarchical Assembly of Viral Nanotemplates with Encoded Microparticles via Nucleic Acid Hybridization”, Langmuir, 24, 12483-12488, 2008. PDF reprint
  1. Hsieh, C.-C., and Doyle, P.S., “Studying Confined Polymers Using Single-Molecule DNA Experiments”, Korea-Aust. Rheol. J., 20, 127-142, 2008. PDF reprint
  1. Savin, T., Spicer, P., and Doyle, P.S., “A Rational Approach to Noise Discrimination in Video Microscopy Particle Tracking”,Appl. Phys. Lett., 93, 024102, 2008. PDF reprint
  1. Hwang, D.K., Dendukuri, D., and Doyle, P.S., “Microfluidic-based synthesis of non-spherical magnetic hydrogel particles”, Lab Chip, 8 1640-1647, 2008. PDF reprint
  1. Balducci, A., and Doyle, P.S., “Conformational Preconditioning by Electrophoresis of DNA through a Finite Obstacle Array”,Macromolecules, 41, 5485-5492, 2008. PDF reprint
  1. Panda, P., Ali, S., Lo, E., Chung, B.G., Hatton, T.A., Khademhosseini, A., and Doyle, P.S., “Stop-Flow Lithography to Generate Cell-Laden Microgel Particles”, Lab Chip, 8, 1056-1061, 2008. PDF reprint
  1. Hsieh, C.-C., Balducci, A., and Doyle, P.S., “Ionic effects on the equilibrium dynamics of DNA confined in nanoslits”, Nano Letters, 8, 1683-1688, 2008. PDF reprint