patrick s. doyle
Dynamics of Biopolymers and Complex Fluids
Professor Patrick S. Doyle
Department of Chemical Engineering
MIT
patrick s. doyle


Publications of the Doyle Group


    2012

  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, in press.

  2. Rich, J.P., McKinley, G.H., and Doyle, P.S., "Arrested Chain Growth During Magnetic Directed Particle Assembly in Yield Stress Matrix Fluids", Langmuir, in press.

  3. Helgeson, M.E., Moran, S., An, H., and Doyle, P.S., "Mesoporous organohydrogels from thermogelling photocrosslinkable nanoemulsions", Nat. Mater., in press.

  4. 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

  5. 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, DOI:10.1039/C2SM07322F, 2012. pdf reprint

  6. Diao, Y., Whlaey, 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

  7. 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


    8. 2011

  8. 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

  9. 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

  10. 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

  11. 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

  12. Tang, J., Du, N., and Doyle, P.S., "Compression and self-entanglement of single DNA molecules under uniform electric field", Proc. Natl. Acad. Sci., DOI:10.1073/pnas.1105547108, 2011. pdf reprint

  13. 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.

  14. 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

  15. 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

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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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


    23. 2010

  23. 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.

  24. 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

  25. 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

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

  27. 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

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

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

  30. 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

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


    32. 2009

  32. 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

  33. 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

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

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

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

  37. 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

  38. 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.

  39. 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

  40. 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

  41. 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

  42. 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


    43. 2008

  43. 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

  44. 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

  45. 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

  46. 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.

  47. 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

  48. 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

  49. 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

  50. 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

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

  52. 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

  53. 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


    54. 2007

  54. 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

  55. 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

  56. 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

  57. 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

  58. 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
    59. Also featured in Technology Review and MIT Tech Talk.

  59. 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

  60. 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

  61. 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

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

  63. 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

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

  65. 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
    66. Also featured in Chemical Technology.

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

  67. 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

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

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

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

  71. 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


    72. 2006

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

  73. 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

  74. 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

  75. 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

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

  77. 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.

  78. 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

  79. 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


    80. 2005

  80. 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

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

  82. 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

  83. 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

  84. 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

  85. 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

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


    87. 2004

  87. 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

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

  89. 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

  90. 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

  91. 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


    92. 2003

  92. 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


    93. 2002

  93. 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


    94. 2001

  94. 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


    95. 2000

  95. 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

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

  97. 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


    98. 1998

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

  99. 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

  100. 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


    101. 1997

  101. 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

  102. 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