Publications

See also Google Scholar for links to articles and citations.

 

 

2017

  1. Gupta, A., Badruddoza, A.Z., and Doyle, P.S.  "A General Route for Nanoemulsion Synthesis using Low Energy Methods at Constant Temperature"  Langmuir, accepted, 2017. pdf reprint
  2. Kundukad, B., Schussman, M., Kaiyuan, Y., Seviour, T., Liang, Y., Rice, S.A., Kjelleberg, S., and Doyle, P.S.  "Mechanistic action of weak acid drugs on biofilms."  Scientific Rep., accepted, 2017.
  3. Klotz, A.R., Narsimhan, V., Soh, B.W., and Doyle, P.S.  "Dynamics of DNA Knots During Chain Relaxation."  Macromolecules,  50, 4074-40822017.  pdf reprint
  4. Lee, H., Gupta, A., Hatton, T.A., and Doyle, P.S..  "Creating isolated liquid compartments using photopatterned obstacles in microfluidics," Phys. Rev. Appl., 7, 044013, 2017.  pdf reprint
  5. Samad, T., Billings, N., Birjiniuk, A., Crouzier, T., Doyle, P.S., and Ribbeck, K.  "Swimming bacteria promote dispersal of non-motile staphylococcal species," ISME Journal, 1-5, 2017.  pdf reprint
  6. Chiu, D.T., deMello, A.J., Di Carlo, D., Doyle, P.S., Hansen, C., Maceiczyk, R.M. and Wootton, R.C.R.  "Small but Perfectly Formed? Successes, Challenges, and Opportunities for Microfluidics in the Chemical and Biological Sciences," Chem, 2, 201-223, 2017.  pdf reprint
  7. Dai, L. and Doyle, P.S.  "Trapping a Knot into Tight Conformations by Intra-Chain Repulsions," Polymers, 9, 57, 2017.  pdf reprint
  8. Chen, L., Wang, K.X., and Doyle, P.S.  "Effect of internal architecture on microgel deformation in microfluidic constrictions," Soft Matter, 13, 1920-1928, 2017.  pdf reprint
  9. Hsiao, L.C., Badruddoza, A.Z.M., Cheng, L.-C., and Doyle, P.S.  "3D Printing of Self-Assembling Thermoresponsive Nanoemulsions into Hierarchical Mesostructured Hydrogels," Soft Matter, 13, 921-929, 2017.  pdf reprint

2016

  1. Gupta, A., Narsimhan, V., Hatton, T.A. and Doyle, P.S..  "Kinetics of Change in Droplet Size during Nanoemulsion Formation," Langmuir, 32, 11551-11559, 2016.  pdf reprint
  2. Dai, L. and Doyle, P.S..  "Effects of intra-chain interactions on the knot size of a polymer," Macromolecules, 49, 7581-7587, 2016.  pdf reprint
  3. Kim, J.J., Bong, K.W., Reategui, E., Irimia, D., and Doyle, P.S..  "Porous microwells for geometry-selective, large-scale microparticle arrays," Nature Materials, 16, 139-146, 2016.  pdf reprint
  4. Eral, H.B., Safai, E.R., Keshavarz, B., Kim, J.J., Lee, J., and Doyle, P.S..  "Governing principles of alginate microparticle synthesis with centrifugal forces," Langmuir, 32, 7198-7209, 2016.  pdf reprint
  5. Kundukad, B., Seviour, T.W., Yang, L., Kjellenberg, S., and Doyle, P.S.  "Mechanical properties of the superficial biofilm layer determine the architecture of biofilm," Soft Matter, 12, 5718-5726, 2016.  pdf reprint
  6. Chew, S.C., Kundukad, B., Teh, W.K., Doyle, P.S., Yang, L., Rice, S.A., and Kjelleberg, S.  "Mechanical signatures of microbial biofilms in micropillar-embedded growth chambers," Soft Matter, 12, 5224-5232, 2016.  pdf reprint
  7. Narsimhan, V., Renner, C.B., and Doyle, P.S.  "Translocation dynamics of knotted polymers under a constant or periodic external field," Soft Matter, 12, 5041-5049, 2016.  pdf reprint
  8. Badruddoza, A.Z.M., Godfrin, P.D., Myerson, A.S., Trout, B.L., and Doyle, P.S.  "Core-shell Composite Hydrogels for Controlled Nanocrystal Formation and Release of Hydrophobic Active Pharmaceutical Ingredients," Adv. Healthcare Mat., 5, 1960-1968, 2016.  pdf reprint
  9. Lee, S.G., Lee, H., Gupta, A., Chang, S., and Doyle, P.S..  "Site-Selective In Situ Grown Calcium Carbonate Micromodels with Tunable Geometry, Porosity, and Wettability," Adv. Func. Mat., 26, 4896-4905, 2016.  pdf reprint
  10. Gupta, A., Eral, H.B., Hatton, T.A., and Doyle, P.S.  "Nanoemulsions: Formation, Properties and Applications," Soft Matter, 12, 2826, 2016.  pdf reprint
  11. Lee, H., Shapiro, S., Chapin, S., and Doyle, P.S.  "Encoded hydrogel microparticles for sensitive and multiplex microRNA detection directly from raw cell lysates," Anal. Chem., 88, 3075-3081, 2016.  pdf reprint
  12. Chen, L., An, H.Z., Haghgooie, R., Shank, A.T., Martel, J.M., Toner, M., and Doyle, P.S.  "Flexible Octopus-shaped Hydrogel Particles for Specific Cell Capture," Small, 12, 2001-2008, 2016.  pdf reprint
  13. Narsimhan, V., Renner, C.B., and Doyle, P.S.  "Jamming of Knots along a Tensioned Chain," ACS Macro Lett., 5, 123-127, 2016.  pdf reprint
  14. Gupta, A., Eral, H.B., Hatton, T.A., and Doyle, P.S.  "Controlling and predicting droplet size of nanoemulsions:  scaling relations with experimental validation," Soft Matter, 12, 1452, 2016.  pdf reprint.
  15. Dai, L., Renner, C.B., and Doyle, P.S.  "The polymer physics of single DNA confined in nanochannels," Adv. Colloid Interface Sci., 232, 80-100, 2016.  pdf reprint

2015

  1. Dai, L., Renner, C.B., Yan, J., and Doyle, P.S.  "Coil-globule transition of a single semiflexible chain in slitlike confinement," Scientific Rep., 5, 18438, 2015.  pdf reprint
  2. Bong, K.W., Kim, J.J., Cho, H., Lim, E., Doyle, P.S., Irimia, D.  "Synthesis of Cell-Adhesive Anisotropic Multifunctional Particles by Stop Flow Lithography and Streptavidin-Biotin Interactions," Langmuir, 31, 13165-13171, 2015.  pdf reprint
  3. Cong, P., Dai, L., Chen, H., van der Maarel, J., Doyle, P.S., and Yan, J.  "Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA," Biophys. J., 109, 2338-2351, 2015.  pdf reprint
  4. Hsiao, L.C. and Doyle, P.S..  "Sequential phase transitions in thermoresponsive nanoemulsions," Soft Matter, 11, 8426-8431, 2015.  pdf reprint.
  5. Chen, L., An, H.Z., and Doyle, P.S..  "Synthesis of non-spherical microcapsules through controlled polyelectrolyte coating of hydrogel templates," Langmuir, 31, 9228-9235.  2015.  pdf reprint.
  6. Lee, H., Lee, S.G., and Doyle, P.S.  "Photopatterned oil-reservoir micromodels with tailored wetting properties," Lab Chip, 15, 3047-3055, 2015. pdf reprint
  7. Le Goff, G.C., Lee, J., Gupta A., Hill, W.A., and Doyle, P.S.  "High-throughput contact flow lithography," Advanced Science, 1500149, 2015. pdf reprint
  8. Dai, L., Renner, C.B., and Doyle, P.S., "Metastable knots in confined semiflexible chains,"  Macromolecules, 48, 2812-2818, 2015.  pdf reprint
  9. Le Goff, G.C., Srinivas, R.L., Hill, W.A., and Doyle, P.S., "Hydrogel microparticles for biosensing," Eur. Polym. J., 2015. pdf reprint
  10. Renner, C.B., and Doyle, P.S., "Stretching Self-Entangled DNA Molecules in Elongational Fields," Soft Matter, 11, 205, 2015.  pdf reprint
  11. Dai, L., Renner, C.B., and Doyle, P.S., "Origin of metastable knots in single flexible chains", Phys. Rev. Lett., 114, 037801, 2015.  pdf reprint
  12. Lee, H., Srinivas, R.L., Gupta, A. and Doyle, P.S.,. "Sensitive and Multiplexed On-chip microRNA Profiling in Oil-Isolated Hydrogel Chambers ", Angew. Chem. In. Ed., 54, 2477-2481, 2015.  pdf reprint
  13. Billings, N., Birjiniuk, A., Samad, T.S., Doyle, P.S., and Ribbeck, K.. "Material properties of biofilms – key methods for understanding permeability and mechanics", Rep. Prog. Phys., 78, 036601, 2015.  pdf reprint

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

  2. Zhang, X., Qu, Y., Chen, H., Rouzina, I., Zhang, S., Doyle, P.S., and Yan, J. "Interconversion between three overstretched DNA structures", JACS136, 16073-16080, 2014.  pdf reprint
  3. Bong, K.W., Lee, J., and Doyle, P.S. "Stop Flow Lithography in Perfluoropolyether (PFPE) Microfluidic Channels", Lab Chip14, 4680-4687, 2014.  pdf reprint
  4. 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
  5. Renner, C. and Doyle, P.S. "Untying Knotted DNA with Elongational Flows", ACS Macro Letters, 3, 963–967, 2014. pdf reprint
  6. Dai, L., Renner, C.B., and Doyle, P.S. "Metastable tight knots in semiflexible chains", Macromolecules,  47 (17), 6135–6140, 2014. pdf reprint

  7. 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

  8. Chew, S.C., Kundukad, B., Seviour, T.W., Van Der Maarel, J., Yang, L., Rice, S.A., Doyle, P., and Kjelleberg, S. "Dynamic Remodeling of Microbial Biofilms by Functionally Distinct Exopolysaccharides", mBio, 5 (4),  e01536-14, 2014. pdf reprint
  9. 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
  10. 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
  11. Renner, C.B., Du, N., and Doyle, P.S., "Enhanced Electrohydrodynamic Collapse of DNA due to Dilute Polymers", Biomicrofluidics8, 034103, 2014. pdf reprint
  12. Uspal, W.E., and Doyle, P.S., "Self-organizing Microfluidic Crystals", Soft Matter10, 5177-5191, 2014. pdf reprint
  13. 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 Materials13, 524-529, 2014. pdf reprint
  14. Dai, L., van der Maarel, J., and Doyle, P.S., "Extended de Gennes Regime of DNA Confined in a Nanochannel", Macromolecules47, 2445-2450, 2014. pdf reprint
  15. 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 Matter10, 3122-33, 2014. pdf reprint
  16. 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 & Design14, 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 Chemistry86, 12099-12107, 2013. pdf reprint
  2. Tree, D.R., Muralidhar, A., Doyle, P.S., and Dorfman, K.D., "Is DNA a Good Model Polymer?", Macromolecules46, 8369-8382, 2013. pdf reprint
  3. An, H., Safai, E., Eral, H.B., and Doyle, P.S., "Synthesis of biomimetic oxygen-carrying compartmentalized microparticles using flow lithography", Lab Chip13, 4765-4774, 2013. pdf reprint
  4. 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
  5. 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
  6. 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 Matter9, 9593-9601, 2013. pdf reprint
  7. Dai, L., and Doyle, P.S, "Comparisons of a polymer in confinement versus applied force", Macromolecules46, 6336-6344, 2013. pdf reprint
  8. Rahman, M., Barikbin, Z., Badruddoza, A.Z., Doyle, P.S., and Khan, S., "Monodisperse Polymeric Ionic Liquid Microgel Beads with Multiple Chemically Switchable Functionalities", Langmuir29, 9535-9543, 2013. pdf reprint
  9. 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 ONE8, e69528, 2013. pdf reprint
  10. 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 ONE8, e66648, 2013. pdf reprint
  11. 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
  12. 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 Chip13, 2821-2826, 2013. pdf reprint
  13. 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
  14. 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
  15. 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
  16. 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 Matter9, 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
  2. 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
  3. 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
  4. Uspal, W.E., and Doyle, P.S., "Collective dynamics of small clusters of particles flowing in a quasi-two-dimensional microchannel", Soft Matter8, 10676-10686, 2012. pdf reprint
  5. 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
  6. Rich, J.P., Doyle, P.S., McKinley, G.H., "Magnetorheology in an aging, yield stress matrix fluid", Rheol. Acta51, 579-593, 2012. pdf reprint
  7. 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
  8. 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
  9. 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
  10. 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
  11. An, H., Helgeson, M.E., and Doyle, P.S, "Nanoemulsion Composite Microgels for Orthogonal Encapsulation and Release",Advanced Materials24, 3838-3844, 2012. pdf reprint
  12. 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. B116, 3031-3036, 2012. pdf reprint
  13. Rich, J.P., McKinley, G.H., and Doyle, P.S., "Arrested Chain Growth During Magnetic Directed Particle Assembly in Yield Stress Matrix Fluids", Langmuir28, 3683-3689, 2012. pdf reprint
  14. 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
  15. Uspal, W.E., and Doyle, P.S., "Scattering and nonlinear bound states of hydrodynamically coupled particles in a narrow channel", Phys. Rev. E85, 016325, 2012. pdf reprint
  16. 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 Matter8, 2972-2982, 2012. pdf reprint
  17. 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
  18. 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
  2. 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
  3. Suh, S.K., Bong, K.W., Hatton, T.A., and Doyle, P.S., "Using Stop-Flow Lithography to Produce Opaque Microparticles: Synthesis and Modeling", Langmuir27, 13813-13819, 2011. pdf reprint
  4. Panda, P., Bong, K.W., Hatton, T.A., and Doyle, P.S., "Branched Networks By Directed Assembly of Shape Anisotropic Magnetic Particles.", Langmuir27, 13428-13435, 2011. pdf reprint
  5. Tang, J., Du, N., and Doyle, P.S., "Compression and self-entanglement of single DNA molecules under uniform electric field",Proc. Natl. Acad. Sci.108, 16153-16158, 2011. pdf reprint
  6. 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.
  7. Rich, J.P., Lammerding, J., McKinley, G.H., and Doyle, P.S., "Nonlinear microrheology of an aging, yield stress fluid using magnetic tweezers", Soft Matter7, 9933-9943, 2011. pdf reprint
  8. 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
  9. Trahan, D.W., and Doyle, P.S., "Simulating the Relaxation of Stretched DNA in Slitlike Confinement", Macromolecules44, 382-392, 2011. pdf reprint
  10. 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
  11. 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
  12. 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
  13. Bong, K.W., Chapin, S.C., Pregibon, D.C., Baah, D., Floyd-Smith, T.M., and Doyle, P.S., "Compressed-air flow system", Lab Chip11, 743-747, 2011. pdf preprint
  14. 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
  15. 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.
  2. Tang, J., Levy, S., Trahan, D., Jones, J., Craighead, H., and Doyle, P.S., "Revisiting the Conformational Dynamics of DNA in Slitlike Confinement", Macromolecules43, 7368-7377, 2010. pdf reprint
  3. 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", Langmuir26, 13436-13441, 2010. pdf reprint
  4. Trahan, D.W., and Doyle, P.S., "DNA collisions with a large, conducting post", Macromolecules43, 5424-5432, 2010. pdf reprint
  5. 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
  6. Bong, K.W., Chapin, S., and Doyle, P.S., "Magnetic Barcoded Hydrogel Microparticles for Multiplexed Detection", Langmuir,26, 8008-8014, 2010. pdf reprint
  7. Yuet, K.P., Hwang, D.K., Haghgooie, R., and Doyle, P.S., "Multifunctional Superparamagnetic Janus Particles", Langmuir26, 4281-4287, 2010. pdf reprint
  8. 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
  9. 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
  2. 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
  3. Dendukuri, D., and Doyle, P.S., "The Synthesis and Assembly of Polymeric Microparticles Using Microfluidics", Advanced Materials21, 1-16, 2009. pdf reprint
  4. Pregibon, D.C., and Doyle, P.S., "Optimization of Encoded Hydrogel Particles for Nucleic Acid Quantification", Anal. Chem.,81, 4873-4881, 2009. pdf reprint
  5. Haghgooie, R., and Doyle, P.S., "Directed self-assembly of field-responsive fluids in confined geometries", Soft Matter5, 1192-1197, 2009. pdf reprint
  6. Panda, P., Yuet, K.P., Hatton, T.A., and Doyle, P.S., "Tuning Curvature in Flow Lithography: A New Class of Concave/Convex Particles", Langmuir25, 5986-5992, 2009. pdf reprint
  7. Bong, K.W., Pregibon, D.C., and Doyle, P.S., "Lock release lithography for 3D and composite microparticles", Lab Chip9, 863-866, 2009. pdf reprintFeatured in Chemical Technology and the Lab Chip inside cover.
  8. 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
  9. Attia, R., Pregibon, D.C., Doyle, P.S., Viovy, J.-L., and Bartolo, D., "Soft microflow sensors", Lab Chip9, 1213-1218, 2009.pdf reprint
  10. Trahan, D.W. and Doyle, P.S., "Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning", Biomicrofluidics3, 012803, 2009. pdf reprint
  11. 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 Chip9, 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",Macromolecules41, 9914-9918, 2008. pdf reprint
  2. 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
  3. 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", Macromolecules41, 8547-8556, 2008. pdf reprint
  4. 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 Materials20 4734-4739, 2008. pdf reprint. Featured on the cover page.
  5. 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", Langmuir24, 12483-12488, 2008. pdf reprint
  6. 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
  7. 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
  8. Hwang, D.K., Dendukuri, D., and Doyle, P.S., "Microfluidic-based synthesis of non-spherical magnetic hydrogel particles", Lab Chip8 1640-1647, 2008. pdf reprint
  9. Balducci, A., and Doyle, P.S., "Conformational Preconditioning by Electrophoresis of DNA through a Finite Obstacle Array",Macromolecules41, 5485-5492, 2008. pdf reprint
  10. 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 Chip8, 1056-1061, 2008. pdf reprint
  11. Hsieh, C.-C., Balducci, A., and Doyle, P.S., "Ionic effects on the equilibrium dynamics of DNA confined in nanoslits", Nano Letters8, 1683-1688, 2008. pdf reprint

2007

  1. Balducci, A., Hsieh, C.-C., and Doyle, P.S., "Relaxation of stretched DNA in slit-like confinement", Phys. Rev. Lett.99, 238102, 2007. pdf reprint
  2. Mohan, A. and Doyle, P.S., "Effect of disorder on DNA electrophoresis in a microfluidic array of obstacles", Phys. Rev. E,76(4), 040903, 2007. pdf reprint
  3. Kim, J.M. and Doyle, P.S., "Brownian dynamics simulation of a DNA molecule colliding with a small cylindrical post",Macromolecules40, 9151-9163, 2007. pdf reprint
  4. Mohan, A. and Doyle, P.S., "Stochastic modeling and simulation of DNA electrophoretic separation in a microfluidic obstacle array", Macromolecules40, 8794-8806, 2007. pdf reprint
  5. Jang, J., Dendukuri, D., Hatton, T.A., Thomas, E.L., and Doyle, P.S., "A route to three-dimensional structures in a microfluidic device: Stop flow interference lithography", Angew. Chem. Int. Ed.46, 9027-9031, 2007. pdf reprint
    Also featured in Technology Review and MIT Tech Talk.  
  6. Underhill, P.T. and Doyle, P.S., "DNA stretch during electrophoresis due to a step change in mobility", Phys. Rev. E76, 011805, 2007. pdf reprint
  7. Savin, T. and Doyle, P.S. "Electrostatically-tuned rate of peptide self-assembly resolved by multiple particle tracking", Soft Matter3, 1194-1202, 2007. pdf reprint
  8. Underhill, P.T. and Doyle, P.S., "Accuracy of Bead-Spring Chains in Strong Flow", J. Non-Newt. Fluid Mech.145, 109-123, 2007. pdf reprint
  9. Tang, J. and Doyle, P.S., "Electrophoretic stretching of DNA molecules using microscale T-junctions", Appl. Phys. Lett.90, 224103, 2007. pdf reprint
  10. Hsieh, C.C., Balducci, A., and Doyle, P.S., "An experimental study of DNA rotational relaxation time in nanoslits",Macromolecules40, 5196-5205, 2007. pdf reprint
  11. Mohan, A. and Doyle, P.S. "Unraveling of a tethered polymer chain in uniform solvent flow", Macromolecules40, 4301-4312, 2007. pdf reprint
  12. Dendukuri, D., Gu, S.S., Pregibon, D.C., Hatton, T.A., and Doyle, P.S., "Stop flow lithography in a microfluidic device", Lab Chip7, 818-828, 2007. pdf reprint
    Also featured in Chemical Technology.  
  13. Savin, T. and Doyle, P.S. "Statistical and sampling issues when using multiple particle tracking", Phys. Rev. E76, 021501, 2007. pdf reprint
  14. Haghgooie, R. and Doyle, P.S. "Transition from 2D to 3D behavior in the self-assembly of magnetorheological fluids confined in thin-slits", Phys. Rev. E75, 061406, 2007. pdf reprint
  15. Dendukuri, D., Hatton, T.A., and Doyle, P.S. "Synthesis and self-assembly of amphiphilic polymeric microparticles",Langmuir23, 4669-4674, 2007. pdf reprint
  16. Pregibon, D.C., Toner M., and Doyle, P.S. "Multifunctional encoded particles for high-throughput biomolecule analysis",Science315, 1393-1396, 2007. pdf reprint
    Also featured in Nature Chemical BiologyNature MethodsTechnology Review, and the MIT Homepage
  17. Haghgooie, R. and Doyle, P.S. "MR fluid structure in quasi-2D", Euro. Phys. Lett.77, 18002, 2007. pdf reprint
  18. Kim, J.M. and Doyle, P.S. "Design and numerical simulation of a DNA electrophoretic stretching device", Lab Chip7(2), 213-225, 2007. pdf reprint

2006

  1. Randall, G.C. and Doyle, P.S. "Collision of a DNA polymer with a small obstacle", Macromolecules39(22), 7734-7745, 2006.pdf reprint
  2. Balducci, A., Mao, P., Han, J. and Doyle, P.S. "Double-Stranded DNA Diffusion in Slit-like Nanochannels", Macromolecules,39(18), 6273-6281, 2006. pdf reprint
  3. Kim, J.M. and Doyle, P.S. "A Brownian dynamics-finite element method for simulating DNA electrophoresis in non-homogeneous electric fields", J. Chem. Phys.125(7), 074906, 2006. pdf reprint
  4. Underhill, P.T. and Doyle, P.S. "Alternative spring force law for bead-spring chain models of the worm-like chain", J. Rheol.,50(4), 513-529, 2006. pdf reprint
  5. Pregibon, D.C., Toner, M., and Doyle, P.S. "Magnetically and Biologically Active Bead-Patterned Hydrogels", Langmuir22, 5122-5128, 2006.pdf reprint
  6. Dendukuri, D., Pregibon, D.C., Collins, J., Hatton, T.A. and Doyle, P.S. "Continuous Flow Lithography for High-Throughput Microparticle Synthesis", Nat. Mater.5, 365-369, May 2006.pdf reprint Also featured in Technology ReviewNature,Analytical Chemistry, and Lab on a Chip.
  7. Randall, G.C., Schultz K.M., and Doyle, P.S. "Methods to Electrophoretically Stretch DNA: Microcontractions, Gels, and Hybrid Gel-Microcontraction Devices", Lab Chip6(4), 516-525, 2006.pdf reprint
  8. Haghgooie, R., Li, C., and Doyle, P.S. "Experimental study of structure and dynamics in a monolayer of paramagnetic colloids confined by parallel hard walls", Langmuir22, 3601-3605, 2006. pdf reprint

2005

  1. Underhill, P.T. and Doyle, P.S. "Development of bead-spring polymer models using the constant extension ensemble", J. Rheol. , 49(5), 963-987, 2005.pdf reprint
  2. Randall, G.C. and Doyle, P.S. "Permeation driven flow in in poly(dimethylsiloxane) microfluidic devices", PNAS 102(31), 10813-10818, 2005.pdf reprint
  3. Haghgooie, R. and Doyle, P.S. "Structure and dynamics of repulsive magnetorheological colloids in two-dimensional channels", Phys. Rev. E, 72(1), 011405, 2005.pdf reprint
  4. Dendukuri, D., Tsoi, K., Hatton, T.A., and Doyle, P.S. "Controlled Synthesis of Non-Spherical Microparticles Using Microfluidics", Langmuir21, 2113-2116, 2005.pdf reprint
  5. Savin, T. and Doyle, P.S. "Role of a finite exposure time on measuring an elastic modulus using microrheology", Phys. Rev. E71, 041106, 2005.pdf reprint
  6. Randall, G.C. and Doyle, P.S. "DNA Deformation in Electric Fields: DNA Driven Past a Cylindrical Obstruction",Macromolecules38, 2410-2418, 2005.pdf reprint
  7. Savin, T. and Doyle, P.S. "Static and dynamic errors in particle tracking microrheology", Biophys. J.88, 623-638, 2005.pdf reprint

2004

  1. Chen, Y.-L, Graham, M.D., de Pablo, J.J., Randall, G.C., Gupta, M. and Doyle, P.S. "Conformation and Dynamics of Single DNA in Parallel-Plate Slit Microchannels", Phys. Rev. E70, 060901 (R) 2004.pdf reprint
  2. Haghgooie, R. and Doyle, P.S. "Structural analysis of a dipole system in two-dimensional channels", Phys. Rev. E70, 061408, 2004.pdf reprint
  3. Doyle, P.S. and Underhill, P.T. "Brownian dynamics simulations of polymers and soft matter", In S. Yip, (ed.), Handbook of Materials Modeling, 2005, Springer, 2619-2630 pdf preprint
  4. Underhill, P.T. and Doyle, P.S. "On the Coarse-graining of Polymers into Bead-Spring Chains", J. Non-Newt. Fluid Mech.,122(1),3-31, 2004 pdf reprint
  5. Randall, G.C. and Doyle, P.S. "Electrophoretic collision of a DNA molecule with an insulating post", Phys. Rev. Lett.93(5), 058102, 2004. pdf reprint

2003

  1. Wagner, C., Amarouchene, Y., Doyle P.S., Bonn, D., "Turbulent-drag reduction of polyelectrolyte solutions: Relation with the elongational viscosity", Europhys. Lett.64(6), 823-829, 2003. pdf reprint

2002

  1. Doyle, P.S., Bibette, J., Bancaud, A., Viovy, J.L., "Self-Assembled Magnetic Matrices for DNA Separation in Lab on a Chip",Science , 295, 2237, 2002. pdf reprint

2001

  1. Ladoux, B., Quivy, J.P., Doyle, P.S., , Almouzni, G., Viovy, J.L., "Direct imaging of single-molecules: from dynamics of single DNA chain to the study of complex DNA-protein intereactions", Science Progress , 84, 267-290, 2001. pdf reprint

2000

  1. Ladoux, B., Quivy, J.P., Doyle, P.S., du Roure, O., Almouzni, G., Viovy, J.L., "Fast Kinetics of Chromatin Assembly Revealed by Single-Molecule Videomicroscopy and Scanning Force Microscopy", PNAS , 97, 14251-14256, 2000. pdf reprint
  2. Ladoux, B. and Doyle, P.S., "Stretching Tethered DNA Chains in Shear Flow", Europhysics Lett. , 52, 511-517, 2000. pdf reprint
  3. Doyle, P.S., Ladoux, B., Viovy, J.L., "Dynamics of a Tethered Polymer in Shear Flow", Phys. Rev. Lett. , 84, 4769-4772, 2000. pdf reprint

1998

  1. Doyle, P.S., Shaqfeh, E.S.G., Gast, A.P., "Rheology of Polymer Brushes: A Brownian Dynamics Study", Macromolecules , 31, 5468-5474, 1998. pdf reprint
  2. Doyle, P.S., Shaqfeh, E.S.G., McKinley, G.H., Spiegelberg, S.H., "Relaxation of Dilute Polymer Solutions Following Extensional Flow", Journal of Non-Newtonian Fluid Mechanics, 76, 79-110, 1998. pdf reprint
  3. Doyle, P.S., Shaqfeh, E.S.G., "Dynamic Simulation of Freely-Draining, Flexible Bead-Rod Chains: Start-Up of Extensional and Shear Flow", Journal of Non-Newtonian Fluid Mechanics, 76, 43-78, 1998. pdf reprint

1997

  1. Doyle, P.S., Shaqfeh, E.S.G., Gast, A.P. "Rheology of "Wet" Polymer Brushes via Brownian Dynamics Simulation: Steady vs. Oscillatory Shear", Physical Review Letters, 78, 1182-1185, 1997. pdf reprint
  2. Doyle, P.S., Shaqfeh, E.S.G., Gast, A.P. "Dynamic Simulation of Freely Draining Flexible Polymers in Steady Linear Flows",Journal of Fluid Mechanics, 334, 251-291, 1997. pdf reprint