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


    2009

  1. Bong, K.W., Bong, K.T., Pregibon, D.C., and Doyle, P.S., "Hydrodynamic Focusing Lithography", Angew. Chem. Int. Ed., in press.

  2. Yuet, K.P., Hwang, D.K., Haghgooie, R., and Doyle, P.S., "Multifunctional Superparamagnetic Janus Particles", Langmuir, DOI:10.1021/la903348s, 2009. pdf reprint

  3. 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

  4. 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

  5. Haghgooie, R., Toner, M., and Doyle, P.S., "Squishy non-spherical hydrogel microparticles", Macromol. Rapid Commun., DOI:10.1002/marc.200900302, 2009. pdf reprint

  6. Dendukuri, D., and Doyle, P.S., "Microparticle Synthesis Using Microfluidics", Advanced Materials, DOI:10.1002/adma.200803386, 2009. pdf reprint

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

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

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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


    15. 2008

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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

  21. 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

  22. 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

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

  24. 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

  25. 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


    26. 2007

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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
    31. Also featured in Technology Review and MIT Tech Talk.

  31. 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

  32. 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

  33. 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

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

  35. 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

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

  37. 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
    38. Also featured in Chemical Technology.

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

  39. 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

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

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

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

  43. 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


    44. 2006

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

  45. 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

  46. 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

  47. 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

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

  49. 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.

  50. 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

  51. 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


    52. 2005

  52. 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

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

  54. 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

  55. 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

  56. 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

  57. 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

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


    59. 2004

  59. 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

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

  61. 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

  62. 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

  63. 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


    64. 2003

  64. 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


    65. 2002

  65. 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


    66. 2001

  66. 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


    67. 2000

  67. 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

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

  69. 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


    70. 1998

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

  71. 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

  72. 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


    73. 1997

  73. 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

  74. 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