de Pablo Group: Publications All

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  1. “Membrane Permeation versus Amyloidogenicity: A Multitechnique Study of Islet Amyloid Polypeptide Interaction with Model Membranes,” Anne Martel, Lucas Antony, Yuri Gerelli, Lionel Porcar, Aaron Fluitt, Kyle Hoffmann, Irena Kiesel, Michel Vivaudou, Giovanna Fragneto, and Juan J. de Pablo. J. Am. Chem. Soc., 139, 137-148, 2017

  2. “ A multi-chain polymer slip-spring model with fluctuating number of entanglements: Density fluctuations, confinement, and phase separation,” A. Ramírez-Hernández, B. L. Peters, L. Schneider, M. Andreev, J. D. Schieber, M. Müller, & J. J. de Pablo. Journal of Chemical Physics, 146, 014903, 2017

  3. “Dynamic structure of active nematic shells,” Rui Zhang, Ye Zhou, Mohammad Rahimi, and Juan J. de Pablo. Nature Communications, 7, 13483, 2016

  4. “Age and structure of a model vapour-deposited glass,” Daniel R. Reid, Ivan Lyubimov, M. D. Ediger & Juan J. de Pablo. Nature Communications, 7, 13062, 2016

  5. “Positioning colloids at the surfaces of cholesteric liquid crystal droplets ,” E. Bukusoglu, X. Wang, Y. Zhou, J. A. Martínez-González, M. Rahimi, Q. Wang, J. J. de Pablo and N. L. Abbott. Soft Matter, 2016

  6. “Structural Transitions in Cholesteric Liquid Crystal Droplets ,” Y. Zhou, E. Bukusoglu, J. A. Martínez-González, M. Rahimi, T. F. Roberts, R. Zhang, X. Wang, N. L. Abbott, and J. J. de Pablo. ACS Nano, 10, 6484–6490, 2016

  7. “Mesoscale structure of chiral nematic shells,” Ye Zhou, Ashley Guo, Rui Zhang, Julio C. Armas-Perez, José A. Martínez-González, Mohammad Rahimi, Monirosadat Sadatia and Juan J. de Pablo. Soft Matter, 2016

  8. “Mechanical Response of DNA–Nanoparticle Crystals to Controlled Deformation,” Joshua Lequieu, Andrés Córdoba, Daniel Hinckley, and Juan J. de Pablo. ACS Cent. Sci., 2, 614-620, 2016

  9. “Tension-Dependent Free Energies of Nucleosome Unwrapping,” Joshua Lequieu, Andrés Córdoba, David C. Schwartz, and Juan J. de Pablo. ACS Cent. Sci., 2, 660-666, 2016

  10. “Photostability Can Be Significantly Modulated by Molecular Packing in Glasses,” Yue Qiu, Lucas W. Antony, Juan J. de Pablo, and M. D. Ediger. J. Am. Chem. Soc., 138, 11282-11289, 2016

  11. “Ordering Transition in Salt-Doped Diblock Copolymers,” Jian Qin and Juan J. de Pablo. Macromolecules , 49, 3630-3638, 2016

  12. “Perspective: Evolutionary design of granular media and block copolymer patterns,” Heinrich M. Jaeger and Juan J. de Pablo. APL Materials, 4, 2016

  13. “A theory of interactions between polarizable dielectric spheres,” Jian Qin, Jiyuan Li, Victor Lee, Heinrich Jaeger, Juan J. de Pablo, and Karl F. Freed. Journal of Colloid and Interface Science, 469, 237-241, 2016

  14. “Turning statistical physics models into materials design engines,” Marc Z. Miskin, Gurdaman Khaira, Juan J. de Pablo, and Heinrich M. Jaeger. PNAS, 113, 34-39, 2016

  15. “Inherent structure energy is a good indicator of molecular mobility in glasses,” Julian Helfferich, Ivan Lyubimov, Daniel Reid, and Juan J. de Pablo. Soft Matter, 12, 5898-5904, 2016

  16. “Anisotropy and probe-medium interactions in the microrheology of nematic fluids,” Andres Cordoba, Tillmann Stieger, Marco G. Mazza, Martin Schoen, and Juan J. de Pablo. Journal of Rheology, 60, 75-95, 2016

  17. “Liquid crystal free energy relaxation by a theoretically informed Monte Carlo method using a finite element quadrature approach,” Julio C. Armas-Perez, Juan P. Hernandez-Ortiz, and Juan J. de Pablo. JCP, 143, 2015

  18. “A multichain polymer slip-spring model with fluctuating number of entanglements for linear and nonlinear rheology,” Abelardo Ramirez-Hernandez, Brandon L. Peters, Marat Andreev, Jay D. Schieber, Juan J. de Pablo. JCP, 143, 2015

  19. “Controlled deformation of vesicles by flexible structured media,” Rui Zhang, Ye Zhou, José A. Martínez-González, Juan P. Hernández-Ortiz, Nicholas L. Abbott, Juan J. de Pablo. Sci. Adv., 2, e1600978 , 2016

  20. “Lattice Boltzmann simulation of asymmetric flow in nematic liquid crystals with finite anchoring,” Rui Zhang, Tyler Roberts, Igor S. Aranson and Juan J. de Pablo. J. Chem. Phys., 144, 084905 , 2016

  21. “Topological defects in liquid crystals as templates for molecular self-assembly,” X. Wang, D. S. Miller, E. Bukusoglu, J. J. de Pablo, and N. L. Abbott. Nature Materials, 15, 106-112, 2016

  22. “Nanoscopic Characterization of DNA within Hydrophobic Pores: Thermodynamics and Kinetics,” F. J.A.L. Cruz, J. J. de Pablo, and J. P. B. Mota. Biochemical Engineering Journal, 104, 41-47, 2015

  23. “Stimuli-Responsive Cubosomes Formed from Blue Phase Liquid Crystals,” E. Bukusoglu, X. Wang, J. A. Martinez-Gonzalez, J. J. de Pablo, and N. L. Abbott. Advanced Materials, 27, 6892–6898, 2015

  24. “Coarse-Grained Ions for Nucleic Acid Modeling,” D. M. Hinckley and J. J de Pablo. Journal of Chemical Theory and Computation, 11, 5436–5446, 2015

  25. “Molecular pathways for defect annihilation in directed self-assembly,” S. Hur, V. Thapar, A. Ramírez-Hernández, G. Khaira, T. Segal-Peretz, P. A. Rincon-Delgadillo, W. Li, M. Müller, P. F. Nealey, and J. J. de Pablo . PNAS, 112, 14144–14149, 2015

  26. “Blue-phase liquid crystal droplets,” J. A. Martínez-González, Y. Zhou, M. Rahimi, E. Bukusoglu, N. L. Abbott, and J. J. de Pablo. PNAS, 112, 13195–13200, 2015

  27. “Liquid Crystal Enabled Early Stage Detection of Beta Amyloid Formation on Lipid Monolayers,” M. Sadati, A. I. Apik, J. C. Armas-Perez, J. Martinez-Gonzalez, J. P. Hernandez-Ortiz, N. L. Abbott, and J. J. de Pablo. Advanced Functional Materials, 25, 6050-6060, 2015

  28. “Orientational anisotropy in simulated vapor-deposited molecular glasses,” I. Lyubimov, L. Antony, D. M. Walters, D. Rodney, M. D. Ediger, and J. J. de Pablo. JCP, 143, 2015

  29. “Fibrillar dimer formation of islet amyloid polypeptides,” C. Chiu and J. J. de Pablo. AIP Advances, 5, 2015

  30. “An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution,” A. M. Fluitt and J. J. de Pablo. Biophysical Journal, 109, 1009-1018, 2015

  31. “Secondary Structure of Rat and Human Amylin across Force Fields,” K. Q. Hoffmann, M. McGovern, C. Chiu, and J. J. de Pablo. PLOS One, 10, 2015

  32. “Theoretically informed Monte Carlo simulation of liquid crystals by sampling of alignment-tensor fields,” J. C. Armas-Perez, A. Londono-Hurtado, O. Guzman, J. P. Hernandez-Ortiz, and J. J. de Pablo. JCP, 143, 2015

  33. “Sculpting bespoke mountains: Determining free energies with basis expansions,” J. K. Whitmer, A. M. Fluitt, L. Antony, J. Qin, M. McGovern, and J. J. de Pablo. JCP, 143, 2015

  34. “Interplay of Surface Energy and Bulk Thermodynamic Forces in Ordered Block Copolymer Droplets,” S. Hur, M. Serdar Onse, A. Ramirez-Hernandez, P. F. Nealey, J. A. Rogers, and J. J. de Pablo. Macromolecules, 48, 4717-4723, 2015

  35. “Self-consistent description of electrokinetic phenomena in particle-based simulations,” J. P. Hernandez-Ortiz and J. J. de Pablo. JCP, 143, 2015

  36. “Nanoparticle self-assembly at the interface of liquid crystal droplets,” M. Rahimi, T. F. Roberts, J. C. Armas-Perez, X. Wang, E. Bukusoglu, N. L. Abbott, and J. J. de Pablo . PNAS, 112, 5297-5302, 2015

  37. “Homeotropic nano-particle assembly on degenerate planar nematic interfaces: films and droplets,” A. Londono-Hurtado, J. C. Armas-Perez, J. P. Hernandez-Ortiz, and J. J. de Pablo. Soft Matter, 11, 5067-5076, 2015

  38. “Characterizing the Three-Dimensional Structure of Block Copolymers via Sequential Infiltration Synthesis and Scanning Transmission Electron Tomography,” Segal-Peretz, T.; Winterstein, J.; Doxastakis, M.; Ramirez-Hernandez, A.; Biswas, M.; Ren, J.; Suh, H.S.; Darling, S.B.; Liddle, J.A.; Elam, J.W.; de Pablo, J.J.; Zaluzec, N.J.; Nealey, P.F.. ACS Nano, 9, 5333–5347, 2015

  39. “Tunable molecular orientation and elevated thermal stability of vapor-deposited organic semiconductors,” S. S. Dalal, D. M. Walters, I. Lyubimov, J. J. de Pablo, and M. D. Ediger. PNAS, 112, 4227-4232, 2015

  40. “Graphoepitaxial Assembly of Cylinder Forming Block Copolymers in Cylindrical Holes,” B. L. Peters, B. Rathsack, M. Somervell, T. Nakano, G. Schmid, and J. J. de Pablo . J. Polym. Sci. Part B Polym. Phys., 53, 430-441, 2015

  41. “ A molecular view of DNA-conjugated nanoparticle association energies,” J. P. Lequieu, D. M. Hinckley, and J. J. de Pablo. Soft Matter, 11, 1919-1929, 2015

  42. “Basis Function Sampling: A New Paradigm for Material Property Computation,” J. K. Whitmer, C. Chiu, A. A. Joshi, and J. J. de Pablo. PRL, 113, 190602, 2014

  43. “Coarse-grained modeling of DNA curvature,” G. S. Freeman, D. M. Hinckley, J. P. Lequieu, J. K. Whitmer, and J. J. de Pablo. JCP, 141, 165103, 2014

  44. “ A molecular view of the role of chirality in charge-driven polypeptide complexation,” K. Q. Hoffmann, S. L. Perry, L. Leon, D. Priftis, M. Tirrell, and J. J. de Pablo. Soft Matter, 11, 1525-1538, 2015

  45. “Chirality-selected phase behaviour in ionic polypeptide complexes,” S. L. Perry, L. Leon, K. Q. Hoffmann, M. J. Kade, D. Priftis, K. A. Black, D. Wong, R. A. Klein, C. F. Pierce III, K. O. Margossian, J. K. Whitmer, J. Qin, J. J. de Pablo, and M. Tirrell. Nature Communications, 6, 6052, 2015

  46. “Simulation of Defect Reduction in Block Copolymer Thin Films by Solvent Annealing,” S. Hur, G. S. Khaira, A. Ramirez-Hernandez, M. Muller, P. F. Nealey, and J. J. de Pablo. ACS Macro Letters, 4, 11-15, 2015

  47. “The role of hopping on transport above Tc in glycerol,” M. T. Cicerone, D. Averett, and J. J. de Pablo. Journal of Non-Crystalline Solids, 407, 118-125, 2015

  48. “Surface Adsorption in Nonpolarizable Atomic Models,” J. K. Whitmer, A. A. Joshi, R. J. Carlton, N. L. Abbott and J. J. de Pablo. J. Chem. Theory Comput., 10, 5616-5624, 2014

  49. “Defect Removal in the Course of Directed Self-Assembly is Facilitated in the Vicinity of the Order-Disorder Transition,” Li, W.H.; Nealey, P.F.; de Pablo, J.J.; Muller, M.. Physical Review Letters, 113, 8301-8301, 2014

  50. “Reversible Switching of Liquid Crystalline Order Permits Synthesis of Homogeneous Populations of Dipolar Patchy Microparticles,” X. Wang, D. S. Miller, J. J. de Pablo, and N. L. Abbott. Advanced Functional Materials, 24, 6219-6226, 2014

  51. “DNA shape dominates sequence affinity in nucleosome formation ,” Gordon S. Freeman, Joshua P. Lequieu, Daniel M. Hinckley, Jonathan K. Whitmer, and Juan J. de Pablo. Phys. Rev. Lett., in Press, 2014

  52. “Interfacial Tension of Polyelectrolyte Complex Coacervate Phases,” J. Qin, D. Priftis, R. Farina, S. L. Perry, L. Leon, J. Whitmer, K. Hoffmann, M. Tirrell, and J. J. de Pablo . ACS Macro Letters, 3, 565-568, 2014

  53. “Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects,” D. M. Hinckley, J. P. Lequieu, and J. J. de Pablo . JCP , 141, 2014

  54. “Evolutionary Optimization of Directed Self-Assembly of Triblock Copolymers on Chemically Patterned Substrates,” G.S. Khaira, J. Qin, G. P. Grant, S. Xiong, L. Wan, R. Ruiz, H. M. Jaeger, P. F. Nealey, and J. J. de Pablo. ACS Macro Letters, 3, 747-752, 2014

  55. Molecular Engineering Thermodynamics,” Juan J. de Pablo and Jay D. Schieber. Cambridge Series in Chemical Engineering, 2014

    Overview

    Building up gradually from first principles, this unique introduction to modern thermodynamics integrates classical, statistical and molecular approaches, and is especially designed to support students studying chemical and biochemical engineering. In addition to covering traditional problems in engineering thermodynamics in the context of biology and materials chemistry, students are also introduced to the thermodynamics of DNA, proteins, polymers and surfaces. It includes over 80 detailed worked examples, covering a broad range of scenarios such as fuel cell efficiency, DNA/protein binding, semiconductor manufacturing, and polymer foaming, emphasising the practical real-world applications of thermodynamic principles; more than 300 carefully tailored homework problems, designed to stretch and extend students' understanding of key topics, accompanied by an online solution manual for instructors; and all the necessary mathematical background, plus resources summarising commonly used symbols, useful equations of state, microscopic balances for open systems, and links to useful online tools and datasets.

  56. “Free energy landscapes of the encapsulation mechanism of DNA nucleobases onto carbon nanotubes,” Fernando J. A. L. Cruz, Juan J. de Pablo and Jose P. B. Mota. RSC Adv, 4, 1310-1321, 2014

  57. “Measuring liquid crystal elastic constants with free energy perturbations,” Abhijeet A. Joshi, Jonathan K. Whitmer, Orlando Guzman, Nicholas L. Abbott and Juan J. de Pablo. Soft Matter, 10, 882-893, 2014

  58. “Colloid-in-liquid crystal gels formed via spinodal decomposition,” Emre Bukusoglu, Santanu Kumar Pal, Juan J. de Pablo and Nicholas L. Abbott. Soft Matter, 10, 1602-1610, 2014

  59. “Structural motif of polyglutamine amyloid fibrils discerned with mixed-isotope infrared spectroscopy,” Lauren E. Buchanan, Joshua K. Carr, Aaron M. Fluitt, Andrew J. Hoganson, Sean D. Moran, Juan J. de Pablo, James L. Skinner, and Martin T. Zanni. PNAS, 111, 5796-5801, 2014

  60. “The Materials Genome Initiative, the interplay of experiment, theory and computation,” Juan J. de Pablo, Barbara Jones, Cora Lind Kovacs, Vidvuds Ozolins, Arthur P. Ramirez. Current Opinion in Solid State and Materials Science, 18, 99-117, 2014

  61. “Control of Directed Self-Assembly in Block Polymers by Polymeric Topcoats,” Abelardo Ramírez-Hernandez, Hyo Seon Suh, Paul F. Nealey and Juan J. de Pablo. Macromolecules, 47, 3520-3527, 2014

  62. “Molecular modeling of vapor-deposited polymer glasses,” Po-Han Lin, Ivan Lyubimov, Lian Yu, M. D. Ediger, and Juan J. de Pablo. Journal of Chemical Physics, 140, 2014

  63. “Endohedral confinement of a DNA dodecamer onto pristine carbon nanotubes and the stability of the canonical B form,” Fernando J. A. L. Cruz, Juan J. de Pablo, and José P. B. Mota. Journal of Chemical Physics , 140, 2014

  64. “Liquid-Crystal Mediated Nanoparticle Interactions and Gel Formation,” Jonathan K. Whitmer, Abhijeet A. Joshi, Tyler F. Roberts, and Juan J. de Pablo. Journal of Chemical Physics, 141, 194903, 2014

  65. “Block Copolymer Assembly on Nanoscale Patterns of Polymer Brushes Formed by Electrohydrodynamic Jet Printing,” Onses, MS; Ramirez-Hernandez, A; Hur, SM; Sutanto, E; Williamson, L; Alleyne, AG; Nealey, PF; de Pablo, JJ; Rogers, JA. ACS Nano, 8, 6606-6613, 2014

  66. Computational Approaches for the Dynamics of Structure Formation in Self-Assembling Polymeric Materials,” Marcus Mueller and Juan J. de Pablo . Annual Review of Materials , 43, 1-34, 2013

    Overview

    Polymeric materials can assemble into a multitude of intricate nanoscale morphologies whose free energy differs by only a fraction of the thermal energy per molecule. Such small free-energy differences pose a challenge for modeling and simulation but also offer exciting opportunities to direct the assembly of such materials into morphologies that do not correspond to those of equilibrium bulk structures.

  67. Evolutionary pattern design for copolymer directed self-assembly,” Jian Qin, Gurdaman S. Khaira, Yongrui Su, Grant P. Garner, Marc Miskin, Heinrich M. Jaeger, and Juan J. de Pablo . Soft Matter, 9, 11467-11472, 2013

    Overview

    By combining the Cahn-Hilliard equation, which is used to find the equilibrium morphology, and the covariance-matrix evolutionary strategy, which is used to optimize the combined outcome of particular substrate-copolymer combinations, we arrive at an efficient method for design of substrates leading to non-trivial, desirable outcomes.

  68. Evolutionary pattern design for copolymer directed self-assembly,” Jian Qin, Gurdaman S. Khaira, Yongrui Su, Grant P. Garner, Marc Miskin, Heinrich M. Jaeger, and Juan J. de Pablo . Soft Matter, 9, 11467-11472, 2013

    Overview

    By combining the Cahn-Hilliard equation, which is used to find the equilibrium morphology, and the covariance-matrix evolutionary strategy, which is used to optimize the combined outcome of particular substrate-copolymer combinations, we arrive at an efficient method for design of substrates leading to non-trivial, desirable outcomes.

  69. “Revealing the Interfacial Self-Assembly Pathway of Large-Scale, Highly-Ordered, Nanoparticle/Polymer Monolayer Arrays at an Air/Water Interface,” Shisheng Xiong, Darren R. Dunphy, Dan C. Wilkinson, Zhang Jiang, Joseph Strzalka, Jin Wang, Yongrui Su, Juan J. de Pablo, and C. Jeffrey Brinker. Nano Letters, 13, 1041-1046, 2013

  70. Dynamical Simulations of Coarse Grain Polymeric Systems: Rouse and Entangled Dynamics,” Abelardo Ramirez-Hernandez, Francois A. Detcheverry, Brandon L. Peters, Veronica C. Chappa, Kenneth S. Schweizer, Marcus Mueller and Juan J. de Pablo. Macromolecules, 46, 6287-6299, 2013

    Overview

    A particle-based, theoretically informed coarse-grained model for multicomponent polymeric systems is proposed to explore the dynamics of entangled polymeric melts.

  71. Model vapor-deposited glasses: Growth front and composition effects,” Lyubimov, Ivan and Ediger, M. D. and de Pablo, Juan J.. JCP, 139, 14, 2013

    Overview

    In this work, model binary glasses are prepared in a process inspired by physical vapor deposition, in which particles are sequentially added to the free surface of a growing film in molecular dynamics simulations. The resulting glasses are shown to be more stable than those prepared by gradual cooling from the liquid phase. However, it is also shown that the composition of the resulting glass plays a significant role on the physical characteristics of the material. 

  72. Nematic-Field-Driven Positioning of Particles in Liquid Crystal Droplets,” Jonathan K. Whitmer, Xiaoguang Wang, Frederic Mondiot, Daniel S. Miller, Nicholas L. Abbott, and Juan J. de Pablo . PRL, 111, 22, 2013

    Overview

    Here, we explore the interactions of adsorbed particles at the aqueous interface through a combination of experiments and coarse-grained modeling, and demonstrate that surface-active particles, driven by elastic forces in the droplet, readily localize to these defect regions in a programmable manner.

  73. An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization,” Daniel M. Hinckley, Gordon S. Freeman, Jonathan K. Whitmer and Juan J. de Pablo. Journal of Chemical Physics, 139, 144903, 2013

    Overview

    A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. 

  74. Liquid Crystal-Based Emulsions for Synthesis of Spherical and Non-Spherical Particles with Chemical ,” Mondiot, Frederic and Wang, Xiaoguang and de Pablo, Juan J. and Abbott, Nicholas L.. ACS, 135, 9972-9975, 2013

    Overview

    We report the use of liquid crystal (LC)-in-water emulsions for the synthesis of either spherical or non-spherical particles with chemically distinct domains located at the poles of the particles. The approach involves the localization of solid colloids at topological defects that form predictably at surfaces of water-dispersed LC droplets.

  75. A Boundary Correction Algorithm for Metadynamics in Multiple Dimensions,” McGovern, Michael and de Pablo, Juan. Journal of Chemical Physics, 139, 2013

    Overview

    The metadynamics algorithms as originally developed suffer from systematic errors at the corresponding boundaries to specified order parameters. While several approaches have been proposed in the past to correct these errors for unidimensional systems, no method exists to fully correct these errors in multi-dimensional systems at points where multiple boundaries meet. Here we present a correction scheme that circumvents this limitation.

  76. Effect of Proline Mutations on the Monomer Conformations of Amylin,” Chiu, Chi-cheng; Singh, Sadanand and de Pablo, Juan J.. Biophysical Journal, 105, 1227-1235, 2013

    Overview

     In this work, we use molecular simulations and bias-exchange metadynamics to investigate the effect of proline substitutions on the conformation of the hIAPP monomer. Our results demonstrate that hIAPP can adopt various beta-sheet conformations, some of which have been reported in experiments. 

  77. “Ultrastable glasses from in silico vapour deposition,” Sadanand Singh, M. D. Ediger, and Juan J. de Pablo. Nature Materials, 2013, 12, 139-144

  78. “Theoretically informed entangled polymer simulations: linear and non-linear rheology of melts,” Abelardo Ramírez-Hernández, Marcus Müller, and Juan J. de Pablo. Soft Matter, 9, 2030-203644, 2013

  79. “Modeling the polydomain-monodomain transition of liquid crystal elastomers,” Jonathan K. Whitmer, Tyler F. Roberts, Raj Shekhar, Nicholas L. Abbott, and Juan J. de Pablo. Phy. Rev. E, 87, 020502, 2013

  80. “Chemical Patterns for Directed Self-Assembly of Lamellae-Forming Block Copolymers with Density Multiplication of Features,” Chi-Chun Liu, Abelardo Ramírez-Hernández, Eungnak Han, Gordon S. W. Craig, Yasuhiko Tada, Hiroshi Yoshida, Huiman Kang, Shengxiang Ji, Padma Gopalan, Juan J. de Pablo, and Paul F. Nealey. Macromolecules, 46, 1415-1424, 2013

  81. “Revealing the Interfacial Self-Assembly Pathway of Large-Scale, Highly-Ordered, Nanoparticle/Polymer Monolayer Arrays at an Air/Water Interface,” Shisheng Xiong, Darren R. Dunphy, Dan C. Wilkinson, Zhang Jiang, Joseph Strzalka, Jin Wang, Yongrui Su, Juan J. de Pablo, and C. Jeffrey Brinker. Nano Letters, 13, 1041-1046, 2013

  82. “α-helix to β-hairpin transition of human amylin monomer,” Sadanand Singh, Chi-cheng Chiu, Allam S. Reddy, and Juan J. de Pablo. J. Chem. Phys. , 138, 155101, 2013

  83. “Liquid-crystal mediated nanoparticle interactions and gel formation ,” Jonathan K. Whitmer, Abhijeet A. Joshi, Tyler F. Roberts, and Juan J. de Pablo. J. Chem. Phys. , 138, 194903, 2013

  84. “Topcoat Approaches for Directed Self-Assembly of Strongly Segregating Block Copolymer Thin Films,” Yoshida, Hiroshi and Suh, Hyo Seon and Ramirez-Hernandez, Abelardo and Lee, Jeong In and Aida, Kouhei and Wan, Lei and Ishida, Yoshihito and Tada, Yasuhiko and Ruiz, Ricardo and de Pablo, Juan and Nealey, Paul F.. Photopolymer Science and Technology, 26, 55-58, 2013

  85. “Liquid crystal mediated interactions between nanoparticles in a nematic phase,” Vivek Tomar, Tyler F Roberts, Nicholas Lawrence Abbott, Juan Pablo Hernandez-Ortiz, and Juan J. de Pablo. Langmuir, 28(14), 6124-6131, 2012

  86. “Free energy of defects in ordered assemblies of block copolymer domains,” Umang Nagpal, Marcus Müller, Paul F. Nealey, and Juan J. de Pablo. ACS Macro Letters, 1 (3), 418-422, 2012

  87. “Liquid crystal nanodroplets, and the balance between bulk and interfacial interactions,” S. I. Hernandez, J. A. Moreno-Razo, A. Ramirez-Hernandez, E. Diaz-Herrera, J. P. Hernandez-Ortiz, and J. J. de Pablo. Soft Matter, 8(5), 1443-1450, 2012

  88. “An immersed boundary method for Brownian dynamics simulation of polymers in complex geometries: Application to DNA flowing through a nanoslit with embedded nanopits,” Yu Zhang, Juan J. de Pablo, and Michael D. Graham. Journal of Chemical Physics, 136(1), 2012

  89. “Dynamics and Deformation Response of Rod-Containing Nanocomposites,” Gregory N. Toepperwein, Robert A. Riggleman, and Juan J. de Pablo. Macromolecules, 45(1), 543-554, 2012

  90. “Morphology of Lamellae-Forming Block Copolymer Films between Two Orthogonal Chemically Nanopatterned Striped Surfaces,” Guoliang Liu, Abelardo Ramirez-Hernandez, Hiroshi Yoshida, Kim Nygard, Dillip K. Satapathy, Oliver Bunk, Juan J. de Pablo, and Paul F. Nealey. Physical Review Letters, 108(6), 2012

  91. “Modulation of Wnt/beta-catenin signaling in human embryonic stem cells using a 3-D microwell array,” Samira M. Azarin, Xiaojun Lian, Elise A. Larson, Heidi M. Popelka, Juan J. de Pablo, and Sean P. Palecek. Biomaterials, 33(7), 2041-2049, 2012

  92. “Symmetric diblock copolymers confined by two nanopatterned surfaces,” Abelardo Ramírez-Hernández, Guoliang Liu, Paul F. Nealey, and Juan J. de Pablo. Macromolecules, 45(5), 2588-2596, 2012

  93. “Parallel β-Sheet Vibrational Couplings Revealed by 2D IR Spectroscopy of an Isotopically Labeled Macro- cycle: Quantitative Benchmark for the Interpretation of Amyloid and Protein Infrared Spectra,” Ann Marie Woys, Aaron M. Almeida, Lu Wang, Chi-Cheng Chiu, Michael McGovern, Juan J. de Pablo, James L. Skinner, Samuel H.Gellman, and Martin T. Zanni. J. Am. Chem. Soc., 134, 19118-19128, 2012

  94. “Efficient Free Energy Calculation of Biomolecules from Diffusion-Biased Molecular Dynamics,” Sadanand Singh, Chi-Cheng Chiu, and Juan J. de Pablo. J. Chem. Theory. Comp., 8, 4657-4662, 8

  95. “Heterogeneous Segmental Dynamics during Creep and Constant Strain Rate Deformations of Rod-Containing Polymer Nanocomposites ,” Gregory N. Toepperwein, Kenneth S. Schweizer, Robert A. Riggleman, and Juan J. de Pablo. Macromolecules, 45, 8467-8481, 2012

  96. “Nonequilibrium Simulations of Lamellae Forming Block Copolymers under Steady Shear: A Comparison of Dissipative Particle Dynamics and Brownian Dynamics,” Brandon L. Peters, Abelardo Ramírez-Hernández, Darin Q. Pike, Marcus Müller, and Juan J. de Pablo. Macromolecules, 45, 8109-8116, 2012

  97. “Isotropic-nematic phase transition in the Lebwohl-Lasher model from density of states simulations,” Raj Shekhar, Jonathan K. Whitmer, Rohit Malshe, J. A. Moreno-Razo, Tyler F. Roberts, and Juan J. de Pablo. J. Chem. Phys., 136, 234503, 2012

  98. “Directed Assembly of Non-equilibrium ABA Triblock Copolymer Morphologies on Nanopatterned Substrates,” Shengxiang Ji, Umang Nagpal, Guoliang Liu, Sean P. Delcambre, Marcus Müller, Juan J. de Pablo, and Paul F. Nealey. ACS Nano, 6, 5440-5448, 2012

  99. “Nonbulk Complex Structures in Thin Films of Symmetric Block Copolymers on Chemically Nanopatterned Surfaces,” Guoliang Liu, Fran ̧cois Detcheverry, Abelardo Ramírez-Hernández, Hiroshi Yoshida, Yasuhiko Tada, Juan J. de Pablo, and Paul F. Nealey. Macromolecules, 45, 3986-3992, 2012

  100. “Liquid-crystal-mediated self-assembly at nanodroplet interfaces,” J. A. Moreno-Razo, E. J. Sambriski, N. L. Abbott, J. P. Hernández-Ortiz, and J. J. de Pablo. Nature, 485, 86-89, 2012

  101. “Two-dimensional infrared spectroscopy reveals the complex behaviour of an amyloid fibril inhibitor,” Chris T. Middleton, Peter Marek, Ping Cao, Chi-cheng Chiu, Sadanand Singh, Ann Marie Woys, Juan J. de Pablo, Daniel P. Raleigh, and Martin T. Zanni. Nature Chemistry, 4, 355-360, 2012

  102. “Dimerization of Helical β-Peptides in Solution,” Michael McGovern, Nicholas Abbott, and Juan J. de Pablo. Biophysical Journal, 102, 1435-1442, 2012

  103. “Effects of 3D microwell culture on growth kinetics and metabolism of human embryonic stem cells,” Samira M. Azarin, Elise A. Larson, Janice M. Almódovar-Cruz, Juan J. de Pablo, and Sean P. Palecek. Biotechnology and Applied Biochemistry, 59, 88-96, 2012

  104. “Density of States-Based Molecular Simulations,” Sadanand Singh, Manan Chopra, and Juan J. de Pablo. Annu. Rev. Chem. Biomol. Eng., 3, 369-394, 2012

  105. “Morphological transitions in liquid crystal nanodroplets,” V. Tomar, S. I. Hernández, N. L. Abbott, J. P. Hernández-Ortiz, and J. J. de Pablo. Soft Matter, 8, 8679-8689, 2012

  106. “Fast relaxation and elasticity-related properties of trehalose-glycerol mixtures,” Devin Averett, Marcus T. Cicerone, Jack F. Douglas, and Juan J. de Pablo. Soft Matter, 8, 4936-4945, 2012

  107. “Evolution of fivefold local symmetry during crystal nucleation and growth in dense hard-sphere packings,” Nikos Ch. Karayiannis, Rohit Malshe, Martin Kröger, Juan J. de Pablo, and Manuel Laso. Soft Matter, 8, 844-858, 2012

  108. “Polymer-solid contacts described by soft, coarse-grained models,” Marcus Mueller, Birger Steinmueller, Kostas Ch. Daoulas, Abelardo Ramirez-Hernandez, and Juan J. de Pablo. Physical Chemistry Chemical Physics, 13(22), 10491-10502, 2011

  109. “Effect of trehalose on the interaction of alzheimer's a beta-peptide and anionic lipid monolayers,” Aslin Izmitli, Carolina Schebor, Michael P. McGovern, Allam S. Reddy, Nicholas L. Abbott, and Juan J. de Pablo. Biochimica et Biophysica Acta-Biomembranes, 1808(1), 26-33, 2011

  110. “Coarse-grained simulations of macromolecules: From dna to nanocomposites,” Juan J. de Pablo. SR Leone, PS Cremer, JT Groves, and MA Johnson, editors. Annual Review of Physical Chemistry, 62, 555-574, 2011

  111. “Study of volume phase transitions in polymeric nanogels by theoretically informed coarse-grained simulations,” Prateek K. Jha, Jos W. Zwanikken, Francois A. Detcheverry, Juan J. de Pablo, and Monica Olvera de la Cruz. Soft Matter, 7(13), 5965-5975, 2011

  112. “Effects of anchoring strength on the diffusivity of nanoparticles in model liquid-crystalline fluids,” J. A. Moreno-Razo, E. J. Sambriski, G. M. Koenig, E. Diaz-Herrera, N. L. Abbott, and J. J. de Pablo. Soft Matter, 7(15), 6828-6835, 2011

  113. “Influence of nanorod inclusions on structure and primitive path network of polymer nanocomposites at equilibrium and under deformation,” Gregory N. Toepperwein, Nikos Ch. Karayiannis, Robert A. Riggleman, Martin Kroeger, and Juan J. de Pablo. Macromolecules, 44(4), 1034-1045, 2011

  114. “Modeling flows of confined nematic liquid crystals,” Juan P. Hernandez-Ortiz, Brian T. Gettelfinger, Jose Moreno-Razo, and Juan J. de Pablo. Journal of Chemical Physics, 134(13), 134905, 2011

  115. “A molecular view of vapor deposited glasses,” Sadanand Singh and Juan J. de Pablo. Journal of Chemical Physics, 134, 194903, 2011

  116. “Numerical determination of the translocation rate of particles through a pore,” Stephanie Geier, Juan Pablo Hernandez-Ortiz, and Juan Jose de Pablo. Chemie Ingenieur Technik, 83, 900-906, 2011

  117. “Endotoxin-induced structural transformations in liquid crystalline droplets,” I-Hsin Lin, Daniel S. Miller, Paul J. Bertics, Christopher J. Murphy, Juan J. de Pablo, and Nicholas L. Abbott. Science, 332, 1297-1300, 2011

  118. “Molecular origins of dna flexibility: Sequence effects on conformational and mechanical properties,” Vanessa Ortiz and Juan J. de Pablo. Physical Review Letters, 106, 238107, 2011

  119. “Fivefold symmetry as an inhibitor to hard-sphere crystallization,” Nikos Ch. Karayiannis, Rohit Malshe, Juan J. de Pablo, and Manuel Laso. Physical Review E, 83, 061505,

  120. “Pattern dimensions and feature shapes of ternary blends of block copolymer and low molecular weight homopolymers directed to assemble on chemically nanopatterned surfaces,” Umang Nagpal, Huiman Kang, Gordon S. W. Craig, Paul F. Nealey, and Juan J. de Pablo. ACS Nano, 5, 5673-5682, 2011

  121. “Cavitation and crazing in rod-containing nanocomposites,” Gregory N. Toepperwein and Juan J. de Pablo. Macromolecules, 44, 5498-5509, 2011

  122. “Morphologies of linear triblock copolymers from monte carlo simulations,” Umang Nagpal, Francois A. Detcheverry, Paul F. Nealey, and Juan J. de Pablo. Macromolecules, 44, 5490-5497, 2011

  123. “Three-dimensional directed assembly of block copolymers together with two-dimensional square and rectangular nanolithography,” Shengxiang Ji, Umang Nagpal, Wen Liao, Chi-Chun Liu, Juan J. de Pablo, and Paul F. Nealey. Advanced Materials, 23, 3692+, 2011

  124. “2dir spectroscopy of human amylin fibrils reflects stable beta-sheet structure,” Lu Wang, Chris T. Middleton, Sadanand Singh, Allam S. Reddy, Ann M. Woys, David B. Strasfeld, Peter Marek, Daniel P. Raleigh, Juan J. de Pablo, Martin T. Zanni, and James L. Skinner. The American Chemical Society, 133, 16062-16071, 2011

  125. “Monte-carlo simulation of ternary blends of block copolymers and homopolymers,” Darin Q. Pike, Marcus Mueller, and Juan J. de Pablo. Journal of Chemical Physics, 135, 114904, 2011

  126. “A coarse-grain three-site-per-nucleotide model for dna with explicit ions,” Gordon S. Freeman, Daniel M. Hinckley, and Juan J. de Pablo. Journal of Chemical Physics, 135, 165104, 2011

  127. “Flux tempered metadynamics,” Sadanand Singh, Chi-cheng Chiu, and Juan J. de Pablo. Journal of Statistical Physics, 145, 932-945, 2011

  128. “Electrostatic control of nanoscale phase behavior of polyelectrolyte networks,” Prateek K. Jha, Jos W. Zwanikken, Juan J. de Pablo, and Monica Olvera de la Cruz. Current Opinion in Solid State & Materials Science, 15, 271-276, 2011

  129. “Heterogeneous dynamics during deformation of a polymer glass,” Robert A. Riggleman, Hau-Nan Lee, Mark D. Ediger, and Juan J. de Pablo. Soft Matter, 6, 287-291, 2010

  130. “Antiplastization and the elastic properties of glass-forming polymer liquids,” Robert A. Riggleman, Jack F. Douglas, and Juan J. de Pablo. Soft Matter, 6, 292-304, 2010

  131. “Human embryonic stem cell-derived keratinocytes exhibit an epidermal transcription program and undergo epithelial morphogenesis in engineered tissue contacts,” Christian M. Metallo, Samira M. Azarin, Laurel E. Moses, Lin Ji, Juan J. de Pablo, and Sean P. Palecek. Tissue Engineering Part A, 16, 212-223, 2010

  132. “Simulations of theoretically informed coarse grain models polymeric systems,” Francois A. Detcheverry, Darin Q. Pike, Paul F. Nealey, Marcus Meuller, and Juan J. de Pablo. Faraday Discussions, 144, 111-125, 2010

  133. “Solution structures of rat amylin peptide: Simulation, theory, and experiment,” Allam S. Reddy, Lu Wang, Yu-Shan Lin, Yun Ling, Manan Chopra, Martin T. Zanni, James L. Skinner, and Juan J. de Pablo. Biophysical Journal, 98, 443-451, 2010

  134. “The microwell control of embryiod body size in order to regulate cardiac differentiation of human embryoid stem cells,” Jeffry C. Mohr, Jianhua Zhang, Samira M. Azarin, Andrew G. Soerens, Juan J. de Pablo, James A. Thomson, Gary E. Lyons, Sean P. Palacek, and Timothy J. Kamp. Biomaterials, 31, 1885-1893, 2010

  135. “Remediation of line edge roughness in chemical nanopatterns by the directed assembly of overlying block copolymer films,” Mark P. Stoykovich, Kostas Ch. Daoulas, Marcus Mueller, Huiman Kang, Juan J. de Pablo, and Paul F. Nealey. Macromolecules, 43, 2334-2342, 2010

  136. “Flow induced deformation of defects around nanoparticles and nanodroplets suspended in liquid crystals,” Brian T. Gettelfinger, Jose Antonio Moreno-Razo, Gary M. Koenig, Jr., Juan P. Hernandez-Ortiz, Nicholas L. Abbott, and Juan J. de Pablo. Soft Matter, 6, 896-901, 2010

  137. “2D IR line shapes probe ovispirin peptide conformation and depth in lipd bilayers,” Ann Marie Woys, Yu-Shan Lin, Allam S. Reddy, Wei Xiong, Juan J. de Pablo, James L. Skinner, and Martin T. Zanni. Journal of the American Chemical Society, 132, 2832-2838, 2010

  138. “GNNQQNY - Investigation of early steps during Amyloid formation,” Allam S. Reddy, Manan Chopra, and Juan J. de Pablo. Biophysical Journal, 98, 1038-1045, 2010

  139. “GNNQQNY - Investigation of early steps during Amyloid formation,” Allam S. Reddy, Manan Chopra, and Juan J. de Pablo. Biophysical Journal, 98, 1038-1045, 2010

  140. “Interpolation in the directed assembly of block copolymers on nanopatterned substrates: simulation and experiments,” Francois A. Detcheverry, Guoliang Liu, Pual F. Nealey, and Juan J. de Pablo. Macromolecules, 43, 3446-3454, 2010

  141. “Cross sectional imaging of block copolymer thin films on chemically patterned surfaces,” Guoliang Liu, Huiman Kang, Gordon S. W. Craig, Francois Detcheverry, Juan J. de Pablo, Paul F. Nealey, Yasuhiko Tada, and Hiroshi Yoshida. Journal of Photopolymer Science and Technology, 23, 149-154, 2010

  142. “Directed assembly of a cylinder-forming diblock copolymer: topographic and chemical patterns,” Francois A. Detcheverry, Paul F. Nealey, Marcus Meuller, and Juan J. de Pablo. Macromolecules, 43, 6495-9504, 2010

  143. “Mechanical properties of antiplasticized polymer nanostructures,” Sean P. Delcambe, Robert A. Riggleman, Juan J. de Pablo, and Paul F. Nealey. Soft Matter, 6, 2475-2483, 2010

  144. “Stable and metastable states of human amylin in solution,” Allam S. Reddy, Lu Wang, Sadanand Singh, Yun L. Ling, Lauren Buchanan, Martin T. Zanni, James L. Skinner, and Juan J. de Pablo. Biophysical Journal, 99, 2208-2216, 2010

  145. “Numerical simulation of gaussian chains near hard surfaces,” Abelardo Ramirez-Hernandez, Francois Detcheverry, and Juan J. de Pablo. Journal of Chemical Physics, 133, 064905, 2010

  146. “Graphoepitaxial assembly of assymetric ternary blends of block copolymers and homopolymers,” Karl O. Stuen, Francois A. Detcheverry, Gordon S. W. Craig, Carla S. Thomas, Richard A. Farrell, Michael A. Morris, Juan J. de Pablo, and Paul F. Nealey. Nanotechnology, 21, 495301, 2010

  147. “Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways,” Edward J. Sambriski, Vanessa Ortiz, and Juan J. de Pablo. Journal of Physics-Condensed Matter, 21, 034105, 2009

  148. “Surface activity of amphiphilic helical beta-peptides from molecular dynamics simulation,” Clark A. Miller, Nicholas L. Abbott, and Juan J. de Pablo. Langmuir, 25, 2811-2823, 2009

  149. “A mesoscale model of DNA and its renaturation,” Edward J. Sambriski, David C. Schwartz, and Juan J. de Pablo. Biophysical Journal, 95, 1675-1690, 2009

  150. “Molecular propulsion: chemical sensing and chemotaxis of DNA driven by DNA polymerase,” Hua Yu, Kyubong Jo, Kristy L. Kounovsky, Juan J. de Pablo, and David C. Schwartz. Journal of the American Chemical Society, 131, 5722, 2009

  151. “Monte carlo simulation of coarse grain polymeric systems,” Francois A. Detcheverry, Darin Q. Pike, Paul F. Nealey, Marcus Meuller, and Juan J. de Pablo. Physical Review Letters, 102, 197801, 2009

  152. “Dynamics of a glassy polymer nanocomposite during active deformation,” Robert A. Riggleman, Gregory N. Toepperwein, George J. Papakonstantopoulos, and Juan J. de Pablo. Macromolecules, 42, 3632-3640, 2009

  153. “Association of helical beta-peptides and their aggregation behavior from the potential of mean force in explicit solvent,” Clark A. Miller, Samuel H. Gellman, Nicholas L. Abbott, and Juan J. de Pablo. Biophysical Journal, 96, 4349-4362, 2009

  154. “Tethered DNA dynamics in shear flow,” Yu Zhang, Aleksander Donev, Todd Weisgraber, Berni J. Alder, Michael D. Graham, and Juan J. de Pablo. Journal of Chemical Physics, 130, 234902, 2009

  155. “Deformation-induced mobility in polymer glasses during multistep creep experiments and simulations,” Hau-Nan Lee, Robert A. Riggleman, Juan J. de Pablo, and Mark D. Ediger. Macromolecules, 42, 4328-4336, 2009

  156. “Entanglement network in nanoparticle reinforced polymers,” Robert A. Riggleman, Greggory Toepperwein, George J. Papakonstantopoulos, Jean-Louis Barrat, and Juan J. de Pablo. Journal of Chemical Physics, 130, 244903, 2009

  157. “Single nanoparticle tracking reveals influence of chemical functionality of nanoparticles on local ordering of liquid crystals and nanoparticle diffusion coefficients,” Gary M. Koenig, Rizal Ong, Angel D. Cortes, J. Antonio Moreno-Razo, Juan J. de Pablo, and Nicholas L. Abbott. Nano Letters, 9, 2794-2801, 2009

  158. “Fluorinated quaternary ammonium salts as dissolution aids for polar polymers in environmentally benign supercritical carbon dioxide,” Manabu Tanaka, Abhinav Rastogi, Gregory N. Toepperwein, Robert A. Riggleman, Nelson M. Felix, Juan J. de Pablo, and Christopher K. Ober. Chemistry of Materials, 21, 3125-3135, 2009

  159. “Theoretically informed coarse grain simulations of polymeric systems,” Darin Q. Pike, Francois A. Detcheverry, Marcus Meuller, and Juan J. de Pablo. Journal of Chemical Physics, 131, 084903, 2009

  160. “Effect of trehalose on amyloid beta (29-40)-membrane interaction,” Allam S. Reddy, Aslin Izmitli, and Juan J. de Pablo. Journal of Chemical Physics, 131, 085101, 2009

  161. “Elongation and migration of single DNA molecules in microchannels using oscillatory shear flows,” Kyubong Jo, Yeng-Long Chen, Juan J. de Pablo, and David C. Schwartz. Lab on a Chip, 9, 2348-2355, 2009

  162. “Characterization of adsorbate-induced ordering transitions of liquid crystals within monodisperse droplets,” Jugal K. Gupta, Jacob S. Zimmerman, Juan J. de Pablo, Frank Caruso, and Nicholas L. Abbott. Langmuir, 25, 9016-9024, 2009

  163. “Nonlinear effects on the nanophase segregation of polyelectrolyte gels,” Prateek K. Jha, Francisco J. Solis, Juan J. de Pablo, and Monica Olvera de la Cruz. Macromolecules, 42, 6284-6289, 2009

  164. “Multiple free energy minima in systems of confined tethered polymers-toward soft nanomechanical bistable elements,” Yu Zhang, Juan J. de Pablo, and Michael D. Graham. Soft Matter, 5, 3694-3700, 2009

  165. “Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis,” Edward J. Sambriski, David C. Schwartz, and Juan J. de Pablo. Proceedings of the National Academy of Sciences, 106, 18125-18130, 2009

  166. “Swelling and collapse of polyelectrolyte gels in equilibrium with monovalent and divalent electrolyte solutions,” De-Wei Yin, Monica Olvera de la Cruz, and Juan J. de Pablo. Journal of Chemical Physics, 131, 194907, 2009

  167. “Theoretically informed coarse grain simulations of block copolymer melts: method and applications,” Francois A. Detcheverry, Darin Q. Pike, Umang Nagpal, Paul Nealey, and Juan J. de Pablo. Soft Matter, 5, 4858-4865, 2009

  168. “Characterization of the reversible interaction of pairs of nanoparticles dispersed in nematic liquid crystals,” Gary M. Koenig, Juan J. de Pablo, and Nicholas L. Abbott. Langmuir, 25, 13318-13321, 2009

  169. “TGF-beta/Activin/Nodal Pathway in Inhibition of Human Embryonic Stem Cell Differentiation by Mechanical Strain,” Somen Saha, Lin Ji, Juan J. de Pablo, and Sean Palecek. Biophysical Journal, 94, 4123–4133,

  170. “Engineering Tissue from Human Embryonic Stem Cells,” Christian M. Metallo, Samira M. Azarin, Lin Ji, Juan J. de Pablo, and Sean P. Palecek. Journal of Cellular and Molecular Medicine, 12, 709-729, 2008

  171. “The response of human embryonic stem cell-derived endothelial cells to shear stress,” Christian M. Metallo, Maxim A. Vodyanik, Juan J. de Pablo, Igor I. Slukvin, and Sean P. Palecek. Biotechnology and Bioengineering, 100, 830-837, 2008

  172. “Folding of Polyglutamine Chains,” Manan Chopra, Allam Santosh Reddy, Vanessa Ortiz, and Juan J. de Pablo. Biophysical Journal, 94, 2797, 2008

  173. “Directed Copolymer Assembly on Chemical Substrate Patterns: A Phenomenological and Single-Chain-in-Mean-Field Simulations Study of the Influence of Roughness in the Substrate Pattern,” Kostas Ch. Daoulas, Marcus Müller, Mark P. Stoykovich, Huiman Kang, Juan J. de Pablo, and Paul F. Nealey. Langmuir, 24, 1284-1295, 2008

  174. “The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores,” Aslin Izmitli, David C. Schwartz, Michael D. Graham, and Juan J. de Pablo. Journal of Chemical Physics, 128, 085102, 2008

  175. “Monte Carlo simulation of a coarse grain polymer nanocomposite model,” F. A. Detcheverry, K. Daoulas, H. Kang, M. Muller, P. F. Nealey, J. J. de Pablo. Macromolecules, 41, 4989-5001, 2008

  176. “Retinoic acid and bone morphogenetic protein signaling synergize to efficiently direct epithelial differentiation of human embryonic stem cells,” Christian M. Metallo, Lin Ji, Juan J. de Pablo, and Sean P. Palecek. Stem Cells, 26, 372-380, 2008

  177. “An Entropic Perspective of Protein Stability on Surfaces,” Thomas A. Knotts IV, Nitin Rathore, and Juan J. de Pablo. Biophysical Journal, 94, 4473–4483, 2008

  178. “Molecular pasticity of polymeric glasses in the elastic regime,” George J. Papakonstantopoulos, Robert A. Riggleman, Jean-Louis Barrat, and Juan J. de Pablo. Physical Review E, 77, 041502, 2008

  179. “Rapid directed assembly of block copolymer films at elevated temperature,” Adam M. Welander, Huiman Kang, Karl O. Stuen, Harun H. Solak, Marcus Meuller, Juan J. de Pablo, and Paul F. Nealey. Macromolecules, 41, 2759-2761, 2008

  180. “Hierarchical assembly of nanoparticle superstructures from block copolymer-nanoparticle composites,” Huiman Kang, Francois A. Detcheverry, Andrew N. Mangham, Mark P. Stoykovich, Kostas Ch. Daoulas, Robert J. Hamers, Marcus Meuller, Juan J. de Pablo, and Paul F. Nealey. Physical Review Letters, 100, 148303, 2008

  181. “Antiplasticization and local elastic constants in trehalose and glycerol mixtures,” Robert A. Riggleman, and Juan J. de Pablo. Journal of Chemical Physics, 128, 224504, 2008

  182. “Nonlinear creep in a polymer glass,” Robert A. Riggleman, Kenneth S. Schweizer, and Juan J. de Pablo. Macromolecules, 41, 4969-4977, 2008

  183. “The effect of the water/methane interface on methane hydrate cages: The potential of mean force and cage lifetimes,” Ethan A. Mastny, Clark A. Miller, and Juan J. de Pablo. Journal of Chemical Physics, 129, 034701, 2008

  184. “Utilizing localized surface plasmon resonances to probe the nanoscopic origins of adsorbate-driven ordering transitions of liquid crystals in contact with chemically functionalized gold nanodots,” Gary M. Koenig, Brian T. Gettelfinger, Juan J. de Pablo, and Nicholas L. Abbott. Nano Letters, 8, 2362-2368, 2008

  185. “Density multiplication and improved lithography by directed block copolymer assembly,” Ricardo Ruiz, Huiman Kang, Francois A. Detcheverry, Eleizabeth Dobisz, Dan S. Kercher, Thomas R. Albrecht, Juan J. de Pablo, and Paul F. Nealey. Science, 231, 936-939, 2008

  186. “vConcentration distributions during flow of confined flowing polymer solutions at finite concentration: slit and grooved channel,” uan P. Hernandez-Ortiz, Hongbo Ma, Juan J. de Pablo, Michael D. Graham. Korea-Australia Rheology Journal, 20, 143-152, 2008

  187. “Secondary relaxations in supercooled and glassy sucrose-borate aqueous solutions,” M. Paula Longinotti, Horacio R. Corti, and Juan J. de Pablo. Carbohydrate Research, 242, 2650-2656, 2008

  188. “Molecular Simulation of the Swelling of Polyelectrolyte Gels by Monovalent and Divalent Counterions,” De-Wei Yin, Ferenc Horkay, Jack F. Douglas, and Juan J. de Pablo. Journal of Chemical Physics, 129, 154902, 2008

  189. “In situ characterization of block copolymer ordering on chemically nanopatterned surfaces by time-resolved small angle x-ray scattering,” Karl O. Stuen, Charles Liu, Adam M. Welander, G. Liu, Juan J. de Pablo, Paul F. Nealey, D. K. Satapathy, K. Nygard, O. Bunk, H. H. Solak, and J. F. van der Veen. Journal of Vacuum Science & Technology B, 26, 2504-2508, 2008

  190. “Ordering of Solid Microparticles at Liquid Crystal-Water Interfaces,” I-Hsin Lin, Gary M. Koenig Jr., Juan J. de Pablo, and Nicholas L. Abbott. Journal of Physical Chemistry B, 112, 16552-16558, 2008

  191. “A Molecular View of Melting in Anhydrous Phospholipidic Membranes,” Emmanouil Doxastakis, Victoria García Sakai, Satoshi Ohtake, Janna K. Maranas, and Juan J. de Pablo. Biophysical Journal, 92, 147-161, 2007

  192. “ Dimensions and shapes of block copolymer domains assembled on lithographically defined chemically patterned substrates,” E. W. Edwards, M. Muller, M. P. Stoykovich, H. H. Solak, J. J. de Pablo, P. F. Nealey. Macromolecules, 40, 90-96, 2007

  193. “Engineering the Stem Cell Microenvironment,” Christian M. Metallo, Jeffrey C. Mohr, Christopher J. Detzel, Juan J. de Pablo, Bernard J. Van Wie, and Sean P. Palecek. Biotechnology Progress, 23, 18-23, 2007

  194. “A Single-Molecule Barcoding System Using Nanoslits for DNA Analysis,” Kyubong Jo, Dalia M. Dhingra, Theo Odijk, Juan J. de Pablo, Michael D. Graham, Rod Runnheim, Daniel K. Forest, and David C. Schwartz. Proceedings of the National Academy of Sciences of the United States of America, 104, 2673-2678, 2007

  195. “A Coarse Grain Model for DNA,” Thomas A. Knotts IV, Nitin Rathore, David C. Schwartz, and Juan J. de Pablo. Journal of Chemical Physics, 126, 084901, 2007

  196. “Calculation of Local Mechanical Properties of Filled Polymers,” George J. Papakonstantopoulos, Emmanouil Doxastakis, Paul F. Nealey, Jean-Louis Barrat, and Juan J. de Pablo. Physical Review E, 75, 031803, 2007

  197. “Improved density of states Monte Carlo method based on recycling of rejected states,” Manan Chopra and Juan J. de Pablo. Journal of Chemical Physics, 124, 114102, 2006

  198. “Simulation of Nonlinear Shear Rheology of Dilute Salt-Free Polyelectrolyte Solutions,” Christopher G. Stoltz, Juan J. de Pablo, and Michael D. Graham. Journal of Chemical Physics, 126, 124906, 2007

  199. “Fast Computation of Many-Particle Hydrodynamic and Electrostatic Interactions in a Confined Geometry,” Juan P. Hernández-Ortiz, Juan J. de Pablo, and Michael D. Graham. Physical Review Letters, 98, 140602, 2007

  200. “Tuning Polymer Melt Fragility with Antiplasticizer Additives,” Robert A. Riggleman, Jack F. Douglas, and Juan J. de Pablo. Journal of Chemical Physics, 126, 234903, 2007

  201. “Characterization of the potential energy landscape of an antiplasticized polymer,” Robert A. Riggleman, Jack F. Douglas, and Juan J. de Pablo. Physical Review E, 76, 011504, 2007

  202. “Melting line of the Lennard-Jones system, infinite size, and full potential,” Ethan A. Mastny and Juan J. de Pablo. Journal of Chemical Physics, 127, 104504, 2007

  203. “Directed self-assembly of block copolymers for nanolithography: Fabrication of isolated features and essential integrated circuit geometries,” M. P. Stoykovich, H. Kang, K. Daoulas, G. Liu, C.-C. Liu, J. J. de Pablo, M. Muller, P. F. Nealey. ACS Nano, 1, 168-175, 2007

  204. “Nanoparticles in nematic liquid crystals: Interactions with nanochannels,” Francisco R. Hung, Brian T. Gettelfinger, Gary M. Koenig, Jr., Nicholas L. Abbott, and Juan J. de Pablo. Journal of Chemical Physics, 127, 124702, 2007

  205. “Free Volume and Finite-Size Effects in a Polymer Glass Under Stress,” Robert A. Riggleman, Hau-Nan Lee, Mark D. Ediger, and Juan J. de Pablo. Physical Review Letters, 99, 215501, 2007

  206. “Morphology of multi-component polymer systems: single chain in mean field simulation studies,” K. C. Daoulas, M. Muller, J. J. de Pablo, P. F. Nealey, G. D. Smith. Soft Matter, 2, 573-583, 2006

  207. “Directed assembly of copolymer materials on patterned substrates: Balance of simple symmetries in complex structures,” K. C. Daoulas, M. Muller, M. P. Stoykovich, Y. J. Papakonstantopoulos, J. J. de Pablo, P. F. Nealey, S. M. Park, H. H. Solak. Journal of Polymer Science Part B: Polymer Physics, 44, 2589-2604, 2006

  208. “Fabrication of Complex Three-Dimensional Nanostructures from Self-Assembling Block Copolymer Materials on Two-Dimensional Chemically Patterned Templates with Mismatched Symmetry,” Kostas Ch. Daoulas, Marcus Müller, Mark P. Stoykovich, Sang-Min Park, Yioryos, J. Papakonstantopoulos, Juan J. de Pablo, Paul F. Nealey, and Harun H. Solak. Physical Review Letters, 96, 036104, 2006

  209. “Effects of trehalose on the phase behavior of DPPC-cholesterol unilamellar vesicles,” Satoshi Ohtake, Carolina Schebor, and Juan J. de Pablo. Biochimica et Biophysica Acta-Biomembranes, 1758, 65-73, 2006

  210. “Confinement Effects on the Thrmodynamics of Protein Folding: Monte Carlo Simulations,” Nitin Rathore, Thomas A. Knotts IV, and Juan J. de Pablo. Biophysical Journal, 90, 1767-1773, 2006

  211. “Concentration dependence of shear and extensional rheology of polymer solutions: Brownian dynamics simulations,” Christopher G. Stoltz, Juan J. de Pablo, and Michael D. Graham. Journal of Rheology, 50, 137-167, 2006

  212. “Order-parameter-based Monte Carlo simulation of crystallization,” Manan Chopra, Marcus Müller, and Juan J. de Pablo. Journal of Chemical Physics, 124, 134102, 2006

  213. “Ethylene and 1-hexene sorption in LLDPE under typical gas-phase reactor conditions: Experiments,” Antonin Novak, Marek Bobak, Juraj Kosek, Brian J. Banaszak, Dennis Lo, Tomy Widya, W. Harmon Ray, and Juan J. de Pablo. Journal of Applied Polymer Science, 100, 1124-1136, 2006

  214. “Cross-Stream Migration of Flexible Molecules in a Nanochannel,” Rajesh Khare, Michael D. Graham, and Juan J. de Pablo. Physical Review Letters, 96, 224505, 2006

  215. “Anisotropic Nanoparticles Immersed in a Nematic Liquid Crystal: Defect Structures and Potentials of Mean Force,” Francisco R. Hung, Orlando Guzmán, Brian T. Gettelfinger, Nicholas L. Abbott, and Juan J. de Pablo. Physical Review E, 74, 011711, 2006

  216. “Influence of Confinement on the Fragility of Antiplasticized and Pure Polymer Films,” Robert A. Riggleman, Kenji Yoshimoto, Jack F. Douglas, and Juan J. de Pablo. Physical Review Letters, 97, 045502, 2006

  217. “Simulation Techniques for Calculating Free Energies,” Marcus Müller and Juan J. de Pablo In Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology, Volume 1, edited by Mauro Ferrario, Giovanni Ciccotti, and Kurt Binder. Lecture Notes in Physics, 703, 67-126, 2006

  218. “NlogN Method for Hydrodynamic Interactions of Confined Polymer Systems: Brownian Dynamics,” Juan P. Hernández-Ortiz, Juan J. de Pablo, and Michael D. Graham. Journal of Chemical Physics, 125, 164906, 2006

  219. “Thermodynamic Stability of beta-Peptide Helices and the Role of Cyclic Residues,” Nitin Rathore, Samuel H. Gellman, and Juan J. de Pablo. Biophysical Journal, 91, 3425-3435, 2006

  220. “Cross-Stream-Line Migration in Confined Flowing Polymer Solutions: Theory and Simulation,” Juan P. Hernández-Ortiz, Hongbo Ma, Juan J. de Pablo, and Michael D. Graham. Physics of Fluids, 18, 123101, 2006

  221. “Optimal allocation of replicas in parallel tempering simulations,” Nitin Rathore, Manan Chopra, and Juan J. de Pablo. Journal of Chemical Physics, 122, 024111, 2005

  222. “Slow dynamics of thin nematic films in the presence of adsorbed nanoparticles,” Sylvain Grollau, Orlando Guzmán, Nicholas L. Abbott, and Juan J. de Pablo. Journal of Chemical Physics, 122, 024703, 2005

  223. “Defect structures and three-body potential of the mean force for nanoparticles in a nematic host,” Orlando Guzmán, Nicholas L. Abbott, and Juan J. de Pablo. Journal of Polymer Science B, 43, 1033-1040, 2005

  224. “Direct calculation of solid-liquid equilibria from density-of-states Monte Carlo simulations,” Ethan A. Mastny and Juan J. de Pablo. Journal of Chemical Physics, 122, 124109, 2005

  225. “Local dynamic mechanical properties in model free-standing polymer thin films,” Kenji Yoshimoto, Tushar S. Jain, Paul F. Nealey, and Juan J. de Pablo. Journal of Chemical Physics, 122, 144712, 2005

  226. “Role of local structure on motions on the potential energy landscape for a model supercooled polymer,” Tushar S. Jain and Juan J. de Pablo. Journal of Chemical Physics, 122, 174515, 2005

  227. “Quenched disorder in a liquid-crystal biosensor: Adsorbed nanoparticles at confining walls,” Orlando Guzmán, Nicholas. L. Abbott, and Juan J. de Pablo. Journal of Chemical Physics, 122, 184711, 2005

  228. “Statistical calculation of elastic moduli for atomistic models,” Kenji Yoshimoto, George J. Papakonstantopoulos, James F. Lutsko, and Juan J. de Pablo. Physical Review B, 71, 184108, 2005

  229. “Platelet cryopreservation using a trehalose and phosphate formulation,” Ying Nie, Juan J. de Pablo, and Sean P. Palecek. Biotechnology and Bioengineering, 92, 79-90, 2005

  230. “Directed Assembly of Block Copolymer Blends into Nonregular Device-Oriented Structures,” Mark P. Stoykovich, Marcus Müller, Sang Ouk Kim, Harun H. Solak, Erik W. Edwards, Juan J. de Pablo, and Paul F. Nealey. Science, 308, 1442-1446, 2005

  231. “Isothermal stress and elasticity tensors for ions and point dipoles using Ewald summations,” Kevin Van Workum, Kenji Yoshimoto, Juan J. de Pablo, and Jack F. Douglas. Physical Review E, 71, 061102, 2005

  232. “Influence of Surfactant Tail Branching and Organization on the Orientation of Liquid Crystals at Aqueous-Liquid Crystal Interfaces,” Nathan A. Lockwood, Juan J. de Pablo, and Nicholas L. Abbott. Langmuir, 21, 6805-6814, 2005

  233. “Potential of mean force between two nanometer-scale particles in a polymer solution,” Manolis Doxastakis, Yeng-Long Chen, and Juan J. de Pablo. Journal of Chemical Physics, 123, 034901, 2005

  234. “Phase behavior of freeze-dried phospholipid-cholesterol mixtures stabilized with trehalose,” Satoshi Ohtake, Carolina Schebor, Sean P. Palecek, and Juan J. de Pablo. Biochimica et Biophysica Acta-Biomembranes, 1713, 57-64, 2005

  235. “Local mechanical properties of polymeric nanocomposites,” George J. Papakonstantopoulos, Kenji Yoshimoto, Manolis Doxastakis, Paul F. Nealey, and Juan J. de Pablo. Physical Review E, 72, 031801, 2005

  236. “Molecular Dynamics Simulation of Discontinuous Volume Phase Transitions in Highly-Charged Crosslinked Polyelectrolyte Networks with Explicit Counterions in Good Solvent,” De-Wei Yin, Qiliang Yan, and Juan J. de Pablo. Journal of Chemical Physics, 123, 174909, 2005

  237. “Modulating Membrane Properties: The Effect of Trehalose and Cholesterol on a Phospholipid Bilayer,” Emmanouil Doxastakis, Amadeu K. Sum, and Juan J. de Pablo. Journal of Physical Chemistry B, 109, 24173-24181, 2005

  238. “Mechanism and kinetics of ordering in diblock copolymer thin films on chemically nanopatterned substrates,” E. W. Edwards, M. P. Stoykovich, M. Muller, H. H. Solak, J. J. De Pablo, P. F. Nealey. Journal of Polymer Science Part B: Polymer Physics, 43, 3444, 2005

  239. “Modelling of Polymer Glasses: Molecular Dynamics,” Kevin Van Workum, Thomas R. Böhme, and Juan J. de Pablo. Encyclopedia of Materials: Science and Technology, Elsevier, 2004. ISBN 0-08-043152-6

  240. “Monte Carlo molecular simulation of the hydration of Na-montmorillonite at reservoir conditions,” L. de Pablo, M. L. Chávez, Amadeu K. Sum, and Juan J. de Pablo. Journal of Chemical Physics, 120, 939-946, 2004

  241. “Effect of sugar-phosphate mixtures on the stability of DPPC membranes in dehydrated systems,” Satoshi Ohtake, Carolina Schebor, Sean P. Palecek, and Juan J. de Pablo. Cryobiology, 48, 81-89, 2004

  242. “Shear-induced migration in flowing polymer solutions: Simulation of long-chain DNA in microchannels,” Richard M. Jendrejack, David C. Schwartz, Juan J. de Pablo, and Michael D. Graham. Journal of Chemical Physics, 120, 2513-2529, 2004

  243. “Molecular simulation of the reversible mechanical unfolding of proteins,” Nitin Rathore, Qiliang Yan, and Juan J. de Pablo. Journal of Chemical Physics, 120, 5781-5788, 2004

  244. “Polymer-particle mixtures: depletion and packing effects,” Manolis Doxastakis, Yeng-Long Chen, Orlando Guzmán, and Juan J. de Pablo. Journal of Chemical Physics, 120, 9335-9342, 2004

  245. “Influence of confinement on the vibrational density of states and the Boson peak in a polymer glass,” Tushar S. Jain and Juan J. de Pablo. Journal of Chemical Physics, 120, 9371-9375, 2004

  246. “Potential of mean force between a spherical particle suspended in a nematic liquid crystal and a substrate: Sphere size effects,” Evelina B. Kim and Juan J. de Pablo. Physical Review E, 69, 061703, 2004

  247. “Simulation of Vapor-Liquid Phase Equilibria of Primary Alcohols and Alcohol-Alkane Mixtures,” Rajesh Khare, Amadeu K. Sum, Shyamal K. Nath, and Juan J. de Pablo. Journal of Physical Chemistry B, 108, 10071-10076, 1004

  248. “Density-of-States Monte Carlo Simulation of a Binary Glass,” Qiliang Yan, Tushar S. Jain, and Juan J. de Pablo. Physical Review Letters, 92, 235701, 2004

  249. “Simulation of the effects of chain architecture on the sorption of ethylene in polyethylene,” Brian J. Banaszak, Roland Faller, and Juan J. de Pablo. Journal of Chemical Physics, 120, 11304-11315, 2004

  250. “Interactions between spherical colloids mediated by a liquid crystal: a molecular simulation and mesoscale study,” Evelina B. Kim, Orlando Guzmán, Sylvain Grollau, Nicholas L. Abbott, and Juan J. de Pablo. Journal of Chemical Physics, 121, 1949-1961, 2004

  251. “A two-dimensional model of the deformation of photoresist structures using elastoplastic polymer properties,” Kenji Yoshimoto, Mark P. Stoykovich, Heidi B. Cao, Juan J. de Pablo, Paul F. Nealey, and Walter J. Drugan. Journal of Applied Physics, 96, 1857-1865, 2004

  252. “Effect of pH, counter ion, and phosphate concentration on the glass transition temperature of freeze-dried sugar-phosphate mixtures,” Satoshi Ohtake, Carolina Schebor, Sean P. Palecek, and Juan J. de Pablo. Pharmaceutical Research, 21, 1615-1621, 2004

  253. “Effect of pH, counter ion, and phosphate concentration on the glass transition temperature of freeze-dried sugar-phosphate mixtures,” Satoshi Ohtake, Carolina Schebor, Sean P. Palecek, and Juan J. de Pablo. Pharmaceutical Research, 21, 1615-1621, 2004

  254. “A microfluidic system for large DNA molecule arrays,” Eileen T. Dimalanta, Alex Lim, Rod Runnheim, Casey Lamers, Chris Churas, Daniel K. Forrest, Juan J. de Pablo, Michael D. Graham, Susan N. Coppersmith, Steve Goldstein, and David C. Schwartz. Analytical Chemistry, 76, 5293-5301, 2004

  255. “Mechanical heterogeneities in model polymer glasses at small length scales,” Kenji Yoshimoto, Tushar S. Jain, Kevin Van Workum, Paul F. Nealey, Juan J. de Pablo. Physical Review Letters, 93, 175501, 2004

  256. “Monte Carlo Molecular Simulation of the Hydration of K-Montmorillonite at 353 K and 625 bar,” M. de Lourde Chávez-García, Liberto de Pablo-Galán, and Juan J. de Pablo. Langmuir, 20, 10764-10770, 2004

  257. “Conformation and dynamics of single DNA molecules in parallel-plate slit microchannels,” Yeng-Long Chen, Michael D. Graham, Juan J. de Pablo, Greg C. Randall, Malancha Gupta, and Patrick S. Doyle. Physical Review E, 70, 060901, 2004

  258. “Spherical particle immersed in a nematic liquid crystal: Effects of confinement on the director field configurations,” Sylvain Grollau, Nicholas L. Abbott, and Juan J. de Pablo. Physical Review E, 67, 011702, 2003

  259. “Improved simulation method for the calculation of the elastic constants of crystalline and amorphous systems using strain fluctuations,” Kevin Van Workum and Juan J. de Pablo. Physical Review E, 67, 011505, 2003

  260. “Fast calculation of the density of states of a fluid by Monte Carlo simulations,” Qiliang Yan and Juan J. de Pablo. Physical Review Letters, 90, 035701, 2003

  261. “An effective-colloid pair potential for Lennard-Jones colloid-polymer mixtures,” Orlando Guzmán and Juan J. de Pablo. Journal of Chemical Physics, 118, 2392-2397, 2003

  262. “Calculation of interfacial tension from density of states,” Tushar S. Jain and Juan J. de Pablo. ournal of Chemical Physics, 118, 4226-4229, 2003

  263. “Density of states simulations of proteins,” Nitin Rathore, Thomas A. Knotts IV, and Juan J. de Pablo. Journal of Chemical Physics, 118, 4285-4290, 2003

  264. “Local elastic constants in thin films of an fcc crystal,” Kevin Van Workum and Juan J. de Pablo. Physical Review E, 67, 031601, 2003

  265. “Dynamic interaction between suspended particles and defects in a nematic liquid crystal,” Sylvain Grollau, Nicholas L. Abbott, and Juan J. de Pablo. Physical Review E, 67, 051703, 2003

  266. “Behavior of single nanoparticle/homopolymer chain in ordered structures of diblock copolymers,” Qiang Wang, Paul F. Nealey, and Juan J. de Pablo. Journal of Chemical Physics, 118, 11278-11285, 2003

  267. “Effect of confinement of DNA dynamics in microfluidic devices,” Richard M. Jendrejack, David C. Schwarz, Michael D. Graham, and Juan J. de Pablo. Journal of Chemical Physics, 119, 1165-1173, 2003

  268. “DNA Dynamics in a Microchannel,” Richard M. Jendrejack, Eileen T. Dimalanta, David C. Schwartz, Michael D. Graham, and Juan J. de Pablo. Physical Review Letters, 91, 038102, 2003

  269. “Monte Carlo simulations and dynamic field theory for syspended particles in liquid crystalline systems,” Sylvain Grollau, Evelina B. Kim, Orlando Guzmán, Nicholas L. Abbott, and Juan J. de Pablo. Journal of Chemical Physics, 119, 2444-2455, 2003

  270. “A new double-rebridging technique for linear polyethylene,” Brian J. Banaszak and Juan J. de Pablo. Journal of Chemical Physics, 119, 2456-2462, 2003

  271. “Epitaxial self-assembly of block copolymers on lithographically defined nanopatterned substrates,” Sang Ouk Kim, Harun H. Solak, Mark P. Stoykovich, Nicola J. Ferrier, Juan J. de Pablo, and Paul F. Nealey. Nature, 424, 411-414, 2003

  272. “Simulations of the morphology of cylinder-forming asymmetric diblock copolymer thin films on nanopatterned substrates,” Q. Wang, P. F. Nealey, J. J. de Pablo. Macromolecules, 36, 1731, 2003

  273. “Density of states of a binary Lennard-Jones glass,” Roland Faller and Juan J. de Pablo. Journal of Chemical Physics, 119, 4405-4408, 2003

  274. “Effect of annealing on freeze-dried Lactobacillus acidophilus,” Nancy Ekdawi-Sever, L. A. Goentoro, and Juan J. de Pablo. Journal of Food Science, 68, 2504-2511, 2003

  275. “Molecular Simulation Study of Phospholipid Bilayers and Insights of the Interactions with Disaccharides,” Amadeu K. Sum, Roland Faller, and Juan J. de Pablo. Biophysical Journal, 85, 2830-2844, 2003

  276. “Molecular Simulation Study on the Influence of Dimethylsulfoxide on the Structure of Phospholipid Bilayers,” Amadeu K. Sum and Juan J. de Pablo. Biophysical Journal, 85, 3636-3645, 2003

  277. “Configurational temperature density of states simulations of proteins,” Nitin Rathore, Thomas A. Knotts IV, and Juan J. de Pablo. Biophysical Journal, 85, 3964-3968, 2003

  278. “Defect Structure around Two Colloids in a Liquid Crystal,” Orlando Guzmán, Evelina B. Kim, Sylvain Grollau, Nicholas L. Abbott, and Juan J. de Pablo. Physical Review Letters, 91, 235507, 2003

  279. “A method for multiscale simulation of flowing complex fluids,” Richard M. Jendrejack, Juan J. de Pablo and Michael D. Graham. Journal of Non-Newtonian Fluid Mechanics, 108, 123-142, 2002

  280. “Potential of mean force between a spherical particle suspended in a nematic liquid crystal and a substrate,” Evelina B. Kim, Roland Faller, Qiliang Yan, Nicholas L. Abbott, and Juan J. de Pablo. Journal of Chemical Physics, 117, 7781-7787, 2002

  281. “Evidence for size-dependent mechanical properties from simulations of nanoscopic polymeric structures,” Thomas R. Böhme and Juan J. de Pablo. Journal of Chemical Physics, 116, 9939-9951, 2002

  282. “Density-of-states Monte Carlo method for simulation of fluids,” Qiliang Yan, Roland Faller, and Juan J. de Pablo. Journal of Chemical Physics, 116, 8745-8749, 2002

  283. “Segmental dynamics in a blend of alkanes: Nuclear magnetic resonance experiments and molecular dynamics simulation,” Joanne Budzien, Colleen Raphael, Mark D. Ediger, and Juan J. de Pablo. Journal of Chemical Physics, 116, 8209-8217, 2002

  284. “Stochastic simulations of DNA in flow: Dynamics and the effects of hydrodynamic interactions,” Richard M. Jendrejack, Juan J. de Pablo, and Michael D. Graham. Journal of Chemical Physics, 116, 7752-7759, 2002

  285. “Structure and mobility of cyclohexane as a solvent for trans-polyisoprene,” Roland Faller. Physical Chemistry Chemical Physics, 4, 2269-2272, 2002

  286. “Lamellar structures of symmetric diblock copolymers: Comparisons between lattice Monte Carlo simulations and self-consistent mean-field calculations,” Q. Wang, P. F. Nealey, J. J. de Pablo. Macromolecules, 35, 9563, 2002

  287. “A biased Monte Carlo technique for calculation of the density of states of polymer films,” Tushar S. Jain and Juan J. de Pablo. Journal of Chemical Physics, 116, 7238-7243, 2002

  288. “Monte Carlo simulations of proteins through a random walk in energy space,” Nitin Rathore and Juan J. de Pablo. Journal of Chemical Physics, 116, 7225-7230, 2002

  289. “Multicanonical parallel tempering,” Roland Faller, Qiliang Yan, and Juan J. de Pablo. Journal of Chemical Physics, 116, 5419-5423, 2002

  290. “Phase equilibria of charge-, size-, and shape-asymmetric model electrolytes,” Qiliang Yan and Juan J. de Pablo. Physical Review Letters, 88, 095504, 2002

  291. “Effect of charge, size, and shape-asymmetry on the phase behaviour of model electrolytes,” Qiliang Yan and Juan J. de Pablo. Journal of Chemical Physics, 116, 2967-2972, 2002

  292. “Constant pressure hybrid Molecular Dynamics-Monte Carlo simulations,” Roland Faller and Juan J. de Pablo. Journal of Chemical Physics, 116, 55-59, 2002

  293. “Monte Carlo Simulation of Free-Standing Polymer Films near the Glass Transition Temperature,” Tushar S. Jain and Juan J. de Pablo. Macromolecules, 35, 2167-2176, 2002

  294. “Phase equilibria and clustering in size-asymmetric primitive model electrolytes,” Qiliang Yan and Juan J. de Pablo. Journal of Chemical Physics, 114, 1727-1731, 2001

  295. “A new united atom force field for alpha-olefins,” Shyamal K. Nath, Brian J. Banaszak, and Juan J. de Pablo. Journal of Chemical Physics, 114, 3612-3616, 2001

  296. “Phase equilibria of size-asymmetric primitive model electrolytes,” Qiliang Yan and Juan J. de Pablo. Physical Review Letters, 86, 2054-2057, 2001

  297. “Simulation of ternary mixtures of ethylene, 1-hexene, and polyethylene,” Shyamal K. Nath, Brian J. Banaszak, and Juan J. de Pablo. Macromolecules, 34, 7841-7848, 2001

  298. “Dependence of the glass transition temperature of polymer films on interfacial energy and thickness,” D. S. Fryer, R. D. Peters, E. J. Kim, J. E. Tomaszewski, J. J. de Pablo, P. F. Nealey, C. C. White, W. L. Wu. Macromolecules, 34, 5627, 2001

  299. “Extraordinary elevation of the glass transition temperature of thin polymer films grafted to silicon oxide substrates,” Ranjeet S. Tate, David S. Fryer, Silvia Pasqualini, Martha F. Montague, Juan J. de Pablo, and Paul F. Nealey. Journal of Chemical Physics, 115, 9982-9990, 2001

  300. “Monte Carlo simulations of asymmetric diblock copolymer thin films confined between two homogeneous surfaces,” Q. Wang, P. F. Nealey, J. J. de Pablo. Macromolecules, 34, 3458, 2001

  301. “Aqueous-based photoresist drying using supercritical carbon dioxide to prevent pattern collapse,” D. L. Goldfarb, J. J. de Pablo, P. F. Nealey, J. P. Simons, W. M. Moreau, M. Angelopoulos. Journal of Vacuum Science and Technology B, 19, 600, 2001

  302. “Molecular simulation of ultrathin polymeric films near the glass transition,” J. Andres Torres, Paul F. Nealey, and Juan J. de Pablo. Physical Review Letters, 85, 3221-3224, 2000

  303. “Hydrodynamic interactions in long chain polymers: Application of the Chebyshev polynomial approximation in stochastic simulations,” Richard M. Jendrejack, Michael D. Graham, and Juan J. de Pablo. Journal of Chemical Physics, 113, 2894-2900, 2000

  304. “Hyperparallel tempering Monte Carlo simulation of polymeric systems,” Qiliang Yan and Juan J. de Pablo. Journal of Chemical Physics, 113, 1276-1282, 2000

  305. “Symmetric diblock copolymer thin films confined between homogeneous and patterned surfaces: Simulations and theory,” Qiang Wang, Shyamal K. Nath, Michael D. Graham, Paul F. Nealey, and Juan J. de Pablo. Journal of Chemical Physics, 112, 9996-10010, 2000

  306. “Thermodynamic and transport properties of nitrogen and butane mixtures,” J. L. Rivera, J. Alejandre, Shyamal K. Nath, and Juan J. de Pablo. Molecular Physics, 98, 43-55, 2000

  307. “Monte Carlo simulations of diblock copolymer thin films confined between two homogeneous surfaces,” Qiang Wang, Qiliang Yan, Paul F. Nealey, and Juan J. de Pablo. Journal of Chemical Physics, 112, 450-464, 2000

  308. “Critical behavior of lattice polymers studied by Monte Carlo simulations,” Qiliang Yan and Juan J. de Pablo. Journal of Chemical Physics, 113, 5954--5957, 2000

  309. “Simulation of swelling of model polymeric gels by subcritical and supercritical solvents,” Fernando A. Escobedo and Juan J. de Pablo. Journal of Chemical Physics, 110, 1290-1298, 1999

  310. “Simulation of phase transitions in fluids,” Juan J. de Pablo, Qiliang Yan, and Fernando A. Escobedo. Annual Review of Physical Chemistry, 50, 377-411, 1999

  311. “Density functional theory of molecular structure for thin diblock copolymer films on chemically heterogeneous surfaces,” S. K. Nath, P. F. Nealey, J. J. de Pablo. Journal of Chemical Physics, 110, 7483-7490, 1999

  312. “Hyper-parallel tempering Monte Carlo: Application to the Lennard-Jones fluid and the restricted primitive model,” Qiliang Yan and Juan J. de Pablo. Journal of Chemical Physics, 111, 9509-9516, 1999

  313. “Simulation of phase equilibria for polymer-supercritical solvent mixtures,” Dmitry G. Gromov, Juan J. de Pablo, Gabriel Luna-Bárcenas, Isaac C. Sanchez, and Keith P. Johnston. Journal of Chemical Physics, 108, 4647-4653, 1998

  314. “On the simulation of vapor-liquid equilibria for alkanes,” Shyamal K. Nath, Fernando A. Escobedo, and Juan J. de Pablo. Journal of Chemical Physics, 108, 9905-9911, 1998

  315. “Simulation of vapor-liquid equilibria for alkane mixtures,” Shyamal K. Nath, Fernando A. Escobedo, Juan J. de Pablo, and Issarin Patramai. Industrial & Engineering Chemistry Research, 37, 3195-3202, 1998

  316. “Simulation of structure and interaction forces for surfaces coated with grafted chains in a compressible solvent,” J. Carson Meredith, Isaac C. Sanchez, Keith P. Johnston, and Juan J. de Pablo. Journal of Chemical Physics, 109, 6424-6434, 1998

  317. “Phase equilibria in binary polymer blends: Integral equation approach,” Dmitry G. Gromov and Juan J. de Pablo. Journal of Chemical Physics, 109, 10042-10052, 1998

  318. “Relationship between polymer chain conformation and phase boundaries in a supercritical fluid,” Gabriel Luna-Bárcenas, J. Carson Meredith, Isaac C. Sanchez, Keith P. Johnston, Dmitry G. Gromov, and Juan J. de Pablo. Journal of Chemical Physics, 107, 10782-10792, 1997

  319. “Monte Carlo simulation of athermal mesogenic chains: Pure systems, mixtures, and constrained environments,” Fernando A. Escobedo and Juan J. de Pablo. Journal of Chemical Physics, 106, 9858-9868, 1997

  320. “On the calculation of transport properties of polymer melts from nonequilibrium molecular dynamics,” Zhengfang Xu, Rajesh Khare, Juan J. de Pablo, and Sangtae Kim. Journal of Chemical Physics, 106, 8285-8286, 1997

  321. “Thermophysical properties of trehalose and its concentrated aqueous solutions,” Danforth P. Miller, Juan J. de Pablo, and Horacio Corti. Pharmaceutical Research, 14, 578-590, 1997

  322. “Combined Brownian Dynamics and Spectral Simulation of the Recovery of Polymeric Fluids after Shear Flow,” Todd W. Bell, G. H. Nyland, Juan J. de Pablo, and Michael D. Graham. Macromolecules, 30, 1806-1812, 1997

  323. “Pseudo-ensemble simulations and Gibbs-Duhem integrations for polymers,” Fernando A. Escobedo and Juan J. de Pablo. Journal of Chemical Physics, 106, 2911-2923, 1997

  324. “Monte Carlo simulation of polymer chain collapse in an athermal solvent,” Jason K. C. Suen, Fernando A. Escobedo, and Juan J. de Pablo. Journal of Chemical Physics, 106, 1288-1290, 1997

  325. “Simulation and theory of the swelling of athermal gels,” Fernando A. Escobedo and Juan J. de Pablo. Journal of Chemical Physics, 106, 793-810, 1997

  326. “Chemical potential and dimensions of chain molecules in athermal environments,” Fernando A. Escobedo and Juan J. de Pablo. Molecular Physics, 89, 1733-1754, 1996

  327. “Comment on 'The effect of charged impurities on a glass transition in a polar medium,” Danforth P. Miller, Juan J. de Pablo, and Horacio R. Corti. Journal of Chemical Physics, 105, 8979-8980, 1996

  328. “Expanded grand canonical and Gibbs ensemble Monte Carlo simulation of polymers,” Fernando A. Escobedo and Juan J. de Pablo. Journal of Chemical Physics, 105, 4391-4394, 1996

  329. “Monte Carlo simulation of branched and crosslinked polymers,” Fernando A. Escobedo and Juan J. de Pablo. Journal of Chemical Physics, 104, 4788-4801, 1996

  330. “Simulation and prediction of vapour-liquid equilibria for chain molecules,” Fernando A. Escobedo and Juan J. de Pablo. Molecular Physics, 87, 347-366, 1996

  331. “Structure of binary polymer blends: Multiple time step hybrid Monte Carlo simulations and self-consistent integral-equation theory,” Dmitry G. Gromov and Juan J. de Pablo. Journal of Chemical Physics, 103, 8247-8256, 1995

  332. “Comment on the accuracy of Wertheim's theory of associating fluids,” Erich A. Müller, Keith E. Gubbins, Dimitrios M. Tsangaris, and Juan J. de Pablo. Journal of Chemical Physics, 103, 3868-3869, 1995

  333. “Monte Carlo simulation of the chemical potential of polymers in an expanded ensemble,” Fernando A. Escobedo and Juan J. de Pablo. Journal of Chemical Physics, 103, 2703-2710, 1995

  334. “Chemical potential and equations of state of hard core chain molecules,” Fernando A. Escobedo and Juan J. de Pablo. Journal of Chemical Physics, 103, 1946-1956, 1995

  335. “Transport properties of polymer melts from nonequilibrium molecular dynamics,” Zhengfang Xu, Juan J. de Pablo, and Sangtae Kim. Journal of Chemical Physics, 102, 5836-5844, 1995

  336. “Extended continuum configurational bias Monte Carlo methods for simulation of flexible molecules,” Fernando A. Escobedo and Juan J. de Pablo. Journal of Chemical Physics, 102, 2636-2652, 1995

  337. “The recovery of polymer melts after shear and elongational flows,” Ulrik Borgbjerg, Juan J. de Pablo, and Hans Christian Öttinger. Journal of Chemical Physics , 101, 7144-7153, 1994

  338. “The effect of solvation on the conformation of freely jointed repulsive trimers,” Christopher J. Grayce and Juan J. de Pablo. Journal of Chemical Physics , 101, 6013-6023, 1994

  339. “Anisotropic friction and excluded volume effects in freely jointed bead-rod polymer chain models,” Zhengfang Xu, Sangtae Kim, and Juan J. de Pablo. Journal of Chemical Physics , 101, 5293-5304, 1994

  340. “Bond-bias simulation of phase equilibria for strongly associating fluids,” Dimitrios M. Tsangaris and Juan J. de Pablo. Journal of Chemical Physics, 101, 1477-1489, 1994

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