patrick s. doyle
The Doyle Group @MIT
Soft Matter, Microfluidics, Bioassays
patrick s. doyle


Publications of the Doyle Group


    2014

  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, accepted

  2. 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, accepted

  3. 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, accepted

  4. 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, DOI:10.1038/ncomms5120 pdf reprint

  5. Renner, C.B., Du, N., and Doyle, P.S., "Enhanced Electrohydrodynamic Collapse of DNA due to Dilute Polymers", Biomicrofluidics, 8, 034103, 2014. pdf reprint

  6. Uspal, W.E., and Doyle, P.S., "Self-organizing Microfluidic Crystals", Soft Matter, 10, 5177-5191, 2014. pdf reprint

  7. 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

  8. 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

  9. 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

  10. 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

    11. 2013

  11. Srinivas, R., Johnson, S., Doyle, P.S., "Oil-isolated Hydrogel Microstructures for Sensitive Bioassays On-chip", Analytical Chemistry, 86, 12099-12107, 2013. pdf reprint

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. Dai, L., and Doyle, P.S, "Comparisons of a polymer in confinement versus applied force", Macromolecules, 46, 6336-6344, 2013. pdf reprint

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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


    27. 2012

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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


    45. 2011

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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.

  51. 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

  52. 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

  53. Trahan, D.W., and Doyle, P.S., "Simulating the Relaxation of Stretched DNA in Slitlike Confinement", Macromolecules, 44, 382-392, 2011. pdf reprint

  54. Appleyard, D., Chapin, S.C., Srinivas, R., and Doyle, P.S., "Barcoded Hydrogel Microparticles for Protein Detection: Synthesis, Assay, and Scanning", Nat. Protoc., 6, 1761-1774, 2011. pdf reprint

  55. 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

  56. 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

  57. 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

  58. 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

  59. 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


    60. 2010

  60. 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.

  61. 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

  62. 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

  63. Trahan, D.W., and Doyle, P.S., "DNA collisions with a large, conducting post", Macromolecules, 43, 5424-5432, 2010. pdf reprint

  64. 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

  65. Bong, K.W., Chapin, S., and Doyle, P.S., "Magnetic Barcoded Hydrogel Microparticles for Multiplexed Detection", Langmuir, 26, 8008-8014, 2010. pdf reprint

  66. Yuet, K.P., Hwang, D.K., Haghgooie, R., and Doyle, P.S., "Multifunctional Superparamagnetic Janus Particles", Langmuir, 26, 4281-4287, 2010. pdf reprint

  67. 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

  68. Haghgooie, R., Toner, M., and Doyle, P.S., "Squishy non-spherical hydrogel microparticles", Macromol. Rapid Commun., 31, 128-134, 2010. pdf reprint


    69. 2009

  69. 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

  70. 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

  71. Dendukuri, D., and Doyle, P.S., "The Synthesis and Assembly of Polymeric Microparticles Using Microfluidics", Advanced Materials, 21, 1-16, 2009. pdf reprint

  72. Pregibon, D.C., and Doyle, P.S., "Optimization of Encoded Hydrogel Particles for Nucleic Acid Quantification", Anal. Chem., 81, 4873-4881, 2009. pdf reprint

  73. Haghgooie, R., and Doyle, P.S., "Directed self-assembly of field-responsive fluids in confined geometries", Soft Matter, 5, 1192-1197, 2009. pdf reprint

  74. 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

  75. 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.

  76. 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

  77. 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

  78. 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

  79. 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


    80. 2008

  80. 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

  81. 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

  82. 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

  83. 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.

  84. 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

  85. 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

  86. 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

  87. 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

  88. Balducci, A., and Doyle, P.S., "Conformational Preconditioning by Electrophoresis of DNA through a Finite Obstacle Array", Macromolecules, 41, 5485-5492, 2008. pdf reprint

  89. 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

  90. 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


    91. 2007

  91. 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

  92. 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

  93. Kim, J.M. and Doyle, P.S., "Brownian dynamics simulation of a DNA molecule colliding with a small cylindrical post", Macromolecules, 40, 9151-9163, 2007. pdf reprint

  94. Mohan, A. and Doyle, P.S., "Stochastic modeling and simulation of DNA electrophoretic separation in a microfluidic obstacle array", Macromolecules, 40, 8794-8806, 2007. pdf reprint

  95. 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
    96. Also featured in Technology Review and MIT Tech Talk.

  96. Underhill, P.T. and Doyle, P.S., "DNA stretch during electrophoresis due to a step change in mobility", Phys. Rev. E, 76, 011805, 2007. pdf reprint

  97. Savin, T. and Doyle, P.S. "Electrostatically-tuned rate of peptide self-assembly resolved by multiple particle tracking", Soft Matter, 3, 1194-1202, 2007. pdf reprint

  98. 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

  99. Tang, J. and Doyle, P.S., "Electrophoretic stretching of DNA molecules using microscale T-junctions", Appl. Phys. Lett., 90, 224103, 2007. pdf reprint

  100. Hsieh, C.C., Balducci, A., and Doyle, P.S., "An experimental study of DNA rotational relaxation time in nanoslits", Macromolecules, 40, 5196-5205, 2007. pdf reprint

  101. Mohan, A. and Doyle, P.S. "Unraveling of a tethered polymer chain in uniform solvent flow", Macromolecules, 40, 4301-4312, 2007. pdf reprint

  102. Dendukuri, D., Gu, S.S., Pregibon, D.C., Hatton, T.A., and Doyle, P.S., "Stop flow lithography in a microfluidic device", Lab Chip, 7, 818-828, 2007. pdf reprint
    103. Also featured in Chemical Technology.

  103. Savin, T. and Doyle, P.S. "Statistical and sampling issues when using multiple particle tracking", Phys. Rev. E, 76, 021501, 2007. pdf reprint

  104. 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. E, 75, 061406, 2007. pdf reprint

  105. Dendukuri, D., Hatton, T.A., and Doyle, P.S. "Synthesis and self-assembly of amphiphilic polymeric microparticles", Langmuir, 23, 4669-4674, 2007. pdf reprint

  106. Pregibon, D.C., Toner M., and Doyle, P.S. "Multifunctional encoded particles for high-throughput biomolecule analysis", Science, 315, 1393-1396, 2007. pdf reprint
    107. Also featured in Nature Chemical Biology, Nature Methods, Technology Review, and the MIT Homepage.

  107. Haghgooie, R. and Doyle, P.S. "MR fluid structure in quasi-2D", Euro. Phys. Lett., 77, 18002, 2007. pdf reprint

  108. Kim, J.M. and Doyle, P.S. "Design and numerical simulation of a DNA electrophoretic stretching device", Lab Chip, 7(2), 213-225, 2007. pdf reprint


    109. 2006

  109. Randall, G.C. and Doyle, P.S. "Collision of a DNA polymer with a small obstacle", Macromolecules, 39(22), 7734-7745, 2006. pdf reprint

  110. 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

  111. 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

  112. 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

  113. Pregibon, D.C., Toner, M., and Doyle, P.S. "Magnetically and Biologically Active Bead-Patterned Hydrogels", Langmuir, 22, 5122-5128, 2006.pdf reprint

  114. 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 Review, Nature, Analytical Chemistry, and Lab on a Chip.

  115. Randall, G.C., Schultz K.M., and Doyle, P.S. "Methods to Electrophoretically Stretch DNA: Microcontractions, Gels, and Hybrid Gel-Microcontraction Devices", Lab Chip, 6(4), 516-525, 2006.pdf reprint

  116. 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", Langmuir, 22, 3601-3605, 2006. pdf reprint


    117. 2005

  117. 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

  118. Randall, G.C. and Doyle, P.S. "Permeation driven flow in in poly(dimethylsiloxane) microfluidic devices", PNAS , 102(31), 10813-10818, 2005.pdf reprint

  119. 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

  120. Dendukuri, D., Tsoi, K., Hatton, T.A., and Doyle, P.S. "Controlled Synthesis of Non-Spherical Microparticles Using Microfluidics", Langmuir, 21, 2113-2116, 2005.pdf reprint

  121. Savin, T. and Doyle, P.S. "Role of a finite exposure time on measuring an elastic modulus using microrheology", Phys. Rev. E, 71, 041106, 2005.pdf reprint

  122. Randall, G.C. and Doyle, P.S. "DNA Deformation in Electric Fields: DNA Driven Past a Cylindrical Obstruction", Macromolecules, 38, 2410-2418, 2005.pdf reprint

  123. Savin, T. and Doyle, P.S. "Static and dynamic errors in particle tracking microrheology", Biophys. J., 88, 623-638, 2005.pdf reprint


    124. 2004

  124. 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. E, 70, 060901 (R) 2004.pdf reprint

  125. Haghgooie, R. and Doyle, P.S. "Structural analysis of a dipole system in two-dimensional channels", Phys. Rev. E, 70, 061408, 2004.pdf reprint

  126. 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

  127. 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

  128. 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


    129. 2003

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


    130. 2002

  130. Doyle, P.S., Bibette, J., Bancaud, A., Viovy, J.L., "Self-Assembled Magnetic Matrices for DNA Separation in Lab on a Chip", Science , 295, 227, 2002. pdf reprint


    131. 2001

  131. 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


    132. 2000

  132. 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

  133. Ladoux, B. and Doyle, P.S., "Stretching Tethered DNA Chains in Shear Flow", Europhysics Lett. , 52, 511-517, 2000. pdf reprint

  134. 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


    135. 1998

  135. Doyle, P.S., Shaqfeh, E.S., Gast, A.P., "Rheology of Polymer Brushes: A Brownian Dynamics Study", Macromolecules , 31 5468-5474, 1998. pdf reprint

  136. Doyle, P.S., Shaqfeh, E.S., 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

  137. Doyle, P.S., Shaqfeh, E.S., "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


    138. 1997

  138. Doyle, P.S., Shaqfeh, E.S., 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

  139. Doyle, P.S., Shaqfeh, E.S., Gast, A.P. "Dynamic Simulation of Freely Draining Flexible Polymers in Steady Linear Flows", Journal of Fluid Mechanics, 334, 251-291, 1997. pdf reprint