de Pablo Group: Publications All

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  1. “Fluctuations and phase transitions of uniaxial and biaxial liquid crystals using a theoretically informed Monte Carlo and a Landau free energy density,” Stiven Villada-Gil, Viviana Palacio-Betancur, Julio C Armas-Perez, Juan J. de Pablo, and Juan P Hernandez-Ortiz. Journal of Physics: Condensed Matter, 31, 175101, 2019

  2. “Degenerate conic anchoring and colloidal elastic dipole-hexadecapole transformations,” Ye Zhou, Bohdan Senyuk, Rui Zhang, Ivan I. Smalyukh, and Juan J. de Pablo. Nat. Commun., 10, 1000, 2019

  3. “Thermally reconfigurable Janus droplets with nematic liquid crystalline and isotropic perfluorocarbon oil compartments,” Wang X, Zhou Y, Kim YK, Yang Y, de Pablo, JJ, Abbott. Soft Matter, 2019

  4. “Generalized Navier boundary condition for a volume of fluid approach using a finite-volume method,” Arnout M.P. Boelens, and Juan J. de Pablo. Physics of Fluids, 31, 021203, 2019

  5. “Perfection in Nucleation and Growth of Blue-Phase Single Crystals: Small Free-Energy Required to Self-Assemble at Specific Lattice Orientation,” Xiao Li, Jose A. Martinez-Gonzalez, Kangho Park, Cecilia Yu, Ye Zhou, Juan J. de Pablo, and Paul F. Nealey. ACS Apply. Mater. Interfaces, 11, 9487-9495, 2019

  6. “A pH-Triggered, Self-Assembled, and Bioprintable Hybrid Hydrogel Scaffold for Mesenchymal Stem Cell Based Bone Tissue Engineering,” Chen Zhao, Nader Taheri Qazvini, Monirosadat Sadati, Zongyue Zeng, Shifeng Huang, Ana Losada De La Lastra, Linghuan Zhang, Yixiao Fend, Wei Liu, Bo Huang, Bo Zhang, Zhengyu Dai, Yi Shen, Xi Wang, Wenping Luo, Bo Liu, Yan Lei, Zhenyu Ye, Ling Zhao, Daigui Cao, Lijuan Yand, Xian Chen, Aravind Athiviraham, Michael J. Lee, Jennifer Moriatis Wolf, Russel R. Reid, Matthew Tirrel, Wei Huang, Juan J. de Pablo, and Tong-Chuan He. ACS Apply. Mater. Interfaces., 11, 8749-8762, 2019

  7. “Extracting collective motions underlying nucleosome dynamics via nonlinear manifold learning,” Ashley Z. Guo, Joshua Lequieu, and Juan J. de Pablo. J. Chem. Phys., 150, 054902, 2019

  8. “Sculpting stable structures in pure liquids,” Tadej Emersic, Rui Zhang, Ziga Kos, Simon Copar, Natan Osterman, Juan J. de Pablo, and Uros Tkalec. Sci. Adv., 5, eaav4283, 2019

  9. “Qresp, a tool for curating, discovering and exploring reproducible scientific papers,” Marco Govoni, Milson Munakami, Aditya Tanikanti, Jonathan H. Skone, Hakizumwami B. Runesha, Federico Giberti, Juan de Pablo, and Giulia Galli.

  10. “Pair and many-body interactions between ligated Au nanoparticles,” Christopher Liepold, Alex Smith, Binhua Lin, Juan de Pablo, and Stuart A. Rice. J. Chem. Phys., 150, 044904, 2019

  11. “Anisotropic Vapor-Deposited Glasses: Hybrid Organic Solids,” M.D. Ediger, Juan de Pablo, and Lian Yu. Acc. Chem. Res., 52, 407-414, 2019

  12. “The Free Energy Landscape of Internucleosome Interactions and its Relation to Chromatin Fiber Structure,” Joshua Moller, Joshua Lequieu, and Juan J. de Pablo. ACS Cent. Sci., 5, 341-348, 2019

  13. “Origin of Anisotropic Molecular Packing in Vapor-Deposited Alq3 Glasses,” Kushal Bagchi, Nicholas E. Jackson, Ankit Gujral, Chengbin Juang, Michael F. Toney, Lian Yu, Juan J. de Pablo, and M.D. Ediger. J. Phys. Chem. Lett., 10, 164-170, 2019

  14. “Graph-Based Approach to Systematic Molecular Coarse-Graining,” Michael A. Webb, Jean-Yves Delannoy, and Juan J. de Pablo. J. Chem. Theory Comput., 15, 1199-1208, 2019

  15. “Tenfold increase in the photostability of an azobenzene guest in vapor-deposited glass mixtures,” Yue Qiu, Lucas W. Antony, John M. Torkelson, Juan J. de Pablo, and M.D. Ediger. J. Chem. Phys., 149, 204503, 2018

  16. “Nanocrystalline Oligo(ethylene sulfide)-b-poly(ethylene glycol) Micelles: Structure and Stability,” Emre Sevgen, Moshe Dolejsi, Paul F. Nealey, Jeffrey A. Hubbell, and Juan J. de Pablo. Macromolecules, 51, 9538-9546, 2018

  17. “Structural Correlations and Percolation in Twisted Perylene Diimides Using a Simple Anisotropic Coarse-Grained Model,” Alec S. Bowen, Nicholas E. Jackson, Daniel R. Reid, and Juan J. de Pablo. J. Chem. Theory Comput., 14, 6495-6504, 2018

  18. “Effect of temperature on the structure and dynamics of triblock polyelectrolyte gels,” Anand Rahalkar, Guangmin Wei, Ryan Nieuwendaal, Vivek M. Prabhu, Samanvaya Srivastava, Adam E. Levi, Juan J. de Pablo, Matthew V. Tirrell. J. Chem. Phys., 149, 163310, 2018

  19. “Amphiphile-Induced Phase Transition of Liquid Crystals at Aqueous Interfaces,” Hadi Ramezani-Dakhel, Mohammad Rahimi, Joel Pendery, Young-Ki Kim, Sankaran Thayumanavan, Benoit Roux, Nichoals L. Abbott, and Juan J. de Pablo. ACS Appl. Mater. Interfaces, 10, 37618-37624, 2018

  20. “Tunable structure and dynamics of active liquid crystals,” Nitin Kumar, Rui Zhang, Juan J. de Pablo, and Margaret L. Gardel. Sci. Adv., 4, eaat7779, 2018

  21. “Defect Annihilation Pathways in Directed Assembly of Lamellar Block Copolymer Thin Films,” Su-Mi Hur, Vikram Thapar, Abelardo Ramirez-Hernandez, Paul F. Nealey, and Juan J. de Pablo. ACS Nano, 12, 9974-9981, 2018

  22. “Complex Coacervation in Polyelectrolytes from a Coarse-Grained Model,” Marat Andreev, Vivek M. Prabhu, Jack F. Douglas, Matthew Tirrell, and Juan J. de Pablo. Macromolecules, 51, 6716-6723, 2018

  23. “Layered nested Markov chain Monte Carlo,” Nicholas E. Jackson, Michael A. Webb, and Juan J. de Pablo. J. Chem. Phys., 149, 072326, 2018

  24. “Oligomers as Triggers for Responsive Liquid Crystals,” Young-Ki Kim, Krishna R. Raghupathi, Joel S. Pendery, Piyachai Khomein, Uma Sridhar, Juan J. de Pablo, S. Thayumanavan, and Nicholas L. Abbott. Langmuir, 34, 10092-10101, 2018

  25. “Aggregation and Solubility of a Model Conjugated Donor-Acceptor Polymer,” Daniel R. Reid, Nicholas E. Jackson, Alexander J. Bourque, Chad R. Snyder, Ronald L. Jones, and Juan J. de Pablo. J. Phys. Chem. Lett., 9, 4802-4807, 2018

  26. “Simulations of splashing high and low viscosity droplets,” Arnout M.P. Boelens, and Juan J. de Pablo. Physics of Fluids, 30, 072106, 2018

  27. “Early-stage human islet amyloid polypeptide aggregation: Mechanisms behind dimer formation,” Ashley Z. Guo, Aaron M. Fluitt, and Juan J. de Pablo. J. Chem. Phys., 149, 025101, 2018

  28. “Evolutionary strategy for inverse charge measurements of dielectric particles,” Xikai Jiang, Jiyuan Li, Victor Lee, Heinrich M Jaeger, Olle G. Heinonen, Juan J. de Pablo. J. Chem. Phys., 148, 234302, 2018

  29. “Adaptive enhanced sampling by force-biasing using neural networks,” Ashley Z. Guo, Emre Sevgen, Hythem Sidky, Jonathan K. Whitmer, Jeffrey A. Hubbell, and Juan J. de Pablo. J. Chem. Phys., 148, 134108, 2018

  30. “Influence of Ion Solvation on the Properties of Electrolyte Solutions,” Marat Andreev, Juan J. de Pablo, Alexandros Chremos, and Jack F. Douglas. J. Phys. Chem. B, 122, 4029-4034, 2018

  31. “Mechanisms of Directed Self-Assembly in Cylindrical Hole Confinements,” Cody T. Bezik, Grant P. Garner, and Juan J. de Pablo. Macromolecules, 51, 2418-2427, 2018

  32. “Intra-molecular Charge Transfer and Electronic Delocalization in Non-fullerene Organic Solar Cells,” Qinghe Wu, Donglin Zhao, Matthew B. Goldey, Alexander S. Filatov, Valerii Sharapov, Yamil J. Colon, Zhengxu Cai, Wei Chen, Juan de Pablo, Giulia Galli, Luping Yu. ACS Apply. Mater. Interfaces, 10, 10043-10052, 2018

  33. “Thickness dependence of forming single crystal by liquid-crystalline blue phase on chemically patterned surface,” Xiao Li, Jose A. Martinez-Gonzalez, Juan J. de Pablo, Paul Nealey. Emerging Liquid Crystal Technologies XIII, 1055514, 2018

  34. “Human Islet Amyloid Polypeptide: Identifying Early-Stage Aggregation Mechanisms through Molecular Simulation,” AZ Guo, JJ de Pablo. Biophysical Journal, 114, 2018

  35. “A Computational and Experimental Study of Crystallization-Driven Self-Assembly and Micelle Formation in Poly(Ethylene Glycol)-B-Oligo(Ethylene Sulfide),” ES Sevgen, JJ de Pablo, JA Hubbell. Biophysical Journal, 114, 2018

  36. “Optimizing self-consistent field theory block copolymer models with X-ray metrology,” Adam F. Hannon, Daniel F. Sunday, Alec Bowen, Gurdaman Khaira, Jiaxing Ren, Paul F. Nealey, Juan J. de Pablo, R. Joseph Kline. Mol. Syst. Des. Eng., 3, 376-389, 2018

  37. Topological Effects in Isolated Poly[n]catenanes: Molecular Dynamics Simulations and Rouse Mode Analysis,” P.M. Rauscher, S.J. Rowan, JJ de Pablo. ACS Macro Letters, 7, 938-943, 2018

    Overview

    Molecular dynamics simulations of isolated poly[n]catenanes have been conducted, along with a Rouse mode analysis. At large length scales poly[n]catenanes do not relax much slower than isolated linear polymers and are less strongly impacted by increased segmental stiffness.

  38. “Multivalent counterions diminish the lubricity of polyelectrolyte brushes,” J. Yu, N. E. Jackson, X. Xu, Y. Morgenstern, Y. Kaufman, M. Ruths, J. J. de Pablo, M. Tirrell. Science , 360, 1434-1438, 2018

  39. Hierarchical Coupling of First Principles Molecular Dynamics with Advanced Sampling Methods,” Emre Sevgen, Federico Giberti, Hythem Sidky, Jonathan Whitmer, Giulia Galli, Francois Gygi, and Juan de Pablo. J. Chem. Theory Comput., 14, 6, 2018

  40. “Phase Behavior and Salt Partitioning in Polyelectrolyte Complex Coacervates,” L. Li, S. Srivastava, M. Andreev, A. Marciel, J.de Pablo, M. V. Tirrell. Macromolecules, 51, 2988–2995, 2018

  41. “Dynamic actuation of glassy polymersomes through isomerization of a single azobenzene unit at the block copolymer interface,” Mijanur Rahaman Molla, Poornima Rangadurai, Lucas Antony, Subramani Swaminathan, Juan J. de Pablo & S. Thayumanavan. Nature Chemistry, 2018

  42. “Ion Distribution in Microphase-Separated Copolymers with Periodic Dielectric Permittivity ,” Weiwei Chu, Jian Qin, Juan J. de Pablo. Macromolecules, 51, 1986-1991, 2018

  43. “A Detailed Examination of the Topological Constraints of Lamellae-Forming Block Copolymers ,” Abelardo Ramírez-Hernández, Brandon L. Peters, Ludwig Schneider, Marat Andreev, Jay D. Schieber, Marcus Müller, Martin Kröger, Juan J. de Pablo. Macromolecules, 51, 2110-2124, 2018

  44. “In Silico Measurement of Elastic Moduli of Nematic Liquid Crystals ,” Hythem Sidky, Juan J. de Pablo, Jonathan K. Whitmer. Phys. Rev. Lett., 120, 2018

  45. “Role of translational entropy in spatially inhomogeneous, coarse-grained models ,” Marcel Langenberg, Nicholas E. Jackson, Juan J. de Pablo, Marcus Müller. The Journal of Chemical Physics, 148, 2018

  46. “Drop splashing is independent of substrate wetting ,” Andrzej Latka, Arnout M. P. Boelens, Sidney R. Nagel, Juan J. de Pablo. Physics of Fluids, 30, 2018

  47. “Low-temperature anomalies of a vapor deposited glass ,” Beatriz Seoane, Daniel R. Reid, Juan J. de Pablo, and Francesco Zamponi. Phys. Rev. Materials, 2, 2018

  48. “SSAGES: Software Suite for Advanced General Ensemble Simulations ,” Hythem Sidky, Yamil J. Colón, Julian Helfferich, Benjamin J. Sikora, Cody Bezik, Weiwei Chu, Federico Giberti, Ashley Z. Guo, Xikai Jiang, Joshua Lequieu, Jiyuan Li, Joshua Moller, Michael J. Quevillon, Mohammad Rahimi, Hadi Ramezani-Dakhel, Vikramjit S. Rathee, Daniel R. Reid, Emre Sevgen, Vikram Thapar, Michael A. Webb, Jonathan K. Whitmer, and Juan J. de Pablo. the Journal of Chemical Physics, 148, 2018

  49. “Interplay of structure, elasticity, and dynamics in actin-based nematic materials ,” Rui Zhang, Nitin Kumar, Jennifer L. Ross, Margaret L. Gardel and Juan J. de Pablo. PNAS, 115, E124-E133, 2018

  50. “Water Flux Induced Reorientation of Liquid Crystals ,” Hadi Ramezani-Dakhel, Monirosadat Sadati, Rui Zhang, Mohammad Rahimi, Khia Kurtenbach, Benoît Roux, and Juan J. de Pablo. ACS Cent. Sci., 3, 1345-1349, 2017

  51. “Electrostatic confinement and manipulation of DNA molecules for genome analysis ,” Kristy L. Kounovsky-Shafer, Juan P. Hernandez-Ortiz, Konstantinos Potamousis, Gene Tsvid, Michael Place, Prabu Ravindran, Kyubong Jo, Shiguo Zhou, Theo Odijk, Juan J. de Pablo and David C. Schwartz. PNAS, 114, 13400-13405, 2017

  52. “Multivalent ions induce lateral structural inhomogeneities in polyelectrolyte brushes ,” Jing Yu, Nicholas E. Jackson, Xin Xu, Blair K. Brettmann, Marina Ruths, Juan J. de Pablo, Matthew Tirrell. Science Advances , 3, 2017

  53. “Design of surface patterns with optimized thermodynamic driving forces for the directed self-assembly of block copolymers in lithographic applications ,” Grant P. Garner, Paulina Rincon Delgadillo, Roel Gronheid, Paul F. Nealey, and Juan J. de Pablo. Mol. Syst. Des. Eng., 2017, 567-580, 2017

  54. “Directly Observing Micelle Fusion and Growth in Solution by Liquid-Cell Transmission Electron Microscopy ,” Lucas R. Parent, Evangelos Bakalis, Abelardo Ramírez-Hernández, Jacquelin K. Kammeyer, Chiwoo Park, Juan de Pablo, Francesco Zerbetto, Joseph P. Patterson, Nathan C. Gianneschi. J. Am. Chem. Soc., 139, 17140-17151, 2017

  55. “Spherical nematic shells with a prolate ellipsoidal core ,” Monirosadat Sadati, Ye Zhou, Drew Melchert, Ashley Guo, Jose A. Martinez-Gonzalez, Tyler F. Roberts, Rui Zhang, Juan J. de Pablo. Soft Matter, 13, 7465-7472, 2017

  56. “Sharp Morphological Transitions from Nanoscale Mixed-Anchoring Patterns in Confined Nematic Liquid Crystals ,” Julio C. Armas-Pérez, Xiao Li, José A. Martínez-González, Coleman Smith, J. P. Hernández-Ortiz, Paul F. Nealey, Juan J. de Pablo. Langmuir, 33, 12516-12524, 2017

  57. “Derivation of Multiple Covarying Material and Process Parameters Using Physics-Based Modeling of X-ray Data ,” Gurdaman Khaira, Manolis Doxastakis, Alec Bowen, Jiaxing Ren, Hyo Seon Suh, Tamar Segal-Peretz, Xuanxuan Chen, Chun Zhou, Adam F. Hannon, Nicola J. Ferrier, Venkatram Vishwanath, Daniel F. Sunday, Roel Gronheid, R. Joseph Kline, Juan J. de Pablo, Paul F. Nealey. Macromolecules, 50, 7783, 7793

  58. “Polymer Informatics: Opportunities and Challenges,” Debra J. Audus and Juan J. de Pablo. ACS Macro Lett., 6, 1078-1082, 2017

  59. “Coarse-Grained Model of the Dynamics of Electrolyte Solutions ,” Marat Andreev, Alexandros Chremos, Juan de Pablo, Jack F. Douglas. J. Phys. Chem. B, 121, 8195-8202, 2017

  60. “Influence of Molecular Shape on the Thermal Stability and Molecular Orientation of Vapor-Deposited Organic Semiconductors ,” Diane M. Walters, Lucas Antony, Juan J. de Pablo, Mark D. Ediger. J. Phys. Chem. Lett., 8, 3380-3386, 2017

  61. “Visualization and Simulation of the Transfer Process of Index-Matched Silica Microparticle Inks for Gravure Printing,” Arnout M. P. Boelens, Juan J. de Pablo, Sooman Lim, Lorraine Francis, Bok Y. Ahn, Jennifer A. Lewis. AIChE Journal, 63, 1419-1429, 2017

  62. “Gel phase formation in dilute triblock copolyelectrolyte complexes,” Samanvaya Srivastava, Marat Andreev, Adam E. Levi, David J. Goldfeld, Jun Mao, William T. Heller, Vivek M. Prabhu, Juan J. de Pablo, Matthew V. Tirrell. Nature Communications, 8, 2017

  63. “Light-activated helical inversion in cholesteric liquid crystal microdroplets,” Piotr Sleczkowski, Ye Zhou, Supitchaya Iamsaard, Juan J. de Pablo, Nathalie Katsonis and Emmanuelle Lacaze. PNAS, 201720742, 2018

  64. “Auxetic metamaterials from disordered networks,” Daniel R. Reid, Nidhi Pashine, Justin M. Wozniak, Heinrich M. Jaeger, Andrea J. Liu, Sidney R. Nagel and Juan J. de Pablo. PNAS, 115, 2018

  65. Planarity and multiple components promote organic photovoltaic efficiency by improving electronic transport ,” M. Goldey, D. Reid, J. J. de Pablo, G. Galli. Phys. Chem. Chem. Phys., 18, 31388, 2016

  66. “Interplay of Structure, Elasticity and Dynamics in Actin-Based Nematic Materials,” Rui Zhang, Nitin Kumar, Jennifer L. Ross, Margaret L. Gardel, and Juan J. de Pablo. Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1713832115, 2017

  67. “Electrostatic confinement and manipulation of DNA molecules for genome analysis,” Kristy L. Kounovsky-Shafer, Juan P. Hernandez-Ortiz, Konstantinos Potamousis, Gene Tsvid, Michael Place, Prabu Ravindran, Kyubong Jo, Shiguo Zhou, Theo Odijk, Juan J. de Pablo, and David C. Schwartz. Proceedings of the National Academy of Sciences , doi: 10.1073/pnas.1711069114, 2017

  68. “Poly[n]catenanes: Synthesis of molecular interlocked chains,” Qiong Wu, Phillip M. Rauscher, Xiaolong Lang, Rudy J. Wojtecki, Juan J. de Pablo, Michael J. A. Hore, Stuart J. Rowan. Science, 30 Nov, 2017

  69. “In silico evidence for sequence-dependent nucleosome sliding,” Joshua Lequieu, David C. Schwartz, and Juan J. de Pablo. Proc. Natl. Acad. Sci., doi: 10.1073/pnas.1705685114, 2017

  70. “Spherical nematic shells with a prolate ellipsoidal core,” Monirosadat Sadati, Ye Zhou, Drew Melchert, Ashley Guo, Jose A. Martinez-Gonzalez, Tyler F. Roberts, Rui Zhang, and Juan J. de Pablo. Soft Matter, DOI: 10.1039/C7SM01403A, 2017

  71. “Mesoscale martensitic transformation in single crystals of topological defects,” Xiao Li, José A. Martínez-González, Juan P. Hernández-Ortiz, Abelardo Ramírez-Hernández, Ye Zhou, Monirosadat Sadati, Rui Zhang, Paul F. Nealey, and Juan J. de Pablo. Proc. Natl. Acad. Sci., 114, 10011–10016, 2017

  72. “Parallel O(N) Stokes’ solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries,” Xujun Zhao, Jiyuan Li, Xikai Jiang, Dmitry Karpeev, Olle Heinonen, Barry Smith, Juan P. Hernandez-Ortiz, and Juan J. de Pablo. J. Chem. Phys., 146, 244114, 2017

  73. “Patterned surface anchoring of nematic droplets at miscible liquid–liquid interfaces,” Xiaoguang Wang, Ye Zhou, Young-Ki Kim, Daniel S. Miller, Rui Zhang, Jose A. Martinez-Gonzalez, Emre Bukusoglu, Bo Zhang, Thaddeus M. Brown, Juan J. de Pablo and Nicholas L. Abbott. Soft Matter, 2017

  74. “Educating local radial basis functions using the highest gradient of interest in three dimensional geometries ,” Viviana Palacio‐Betancur, Stiven Villada‐Gil, Juan J. de Pablo, and Juan P. Hernández‐Ortiz. Int. J. Numer. Meth. Engng , 110, 603-617, 2017

  75. “Segregation of liquid crystal mixtures in topological defects,” Mohammad Rahimi, Hadi Ramezani-Dakhel, Rui Zhang, Abelardo Ramirez-Hernandez, Nicholas L. Abbott, and Juan J. de Pablo. Nature Communications, 8, 2017

  76. “A Molecular View of the Dynamics of dsDNA Packing Inside Viral Capsids in the Presence of Ions,” Andrés Córdoba, Daniel M. Hinckley, Joshua Lequieu, and Juan J. de Pablo. Biophysical Journal, 112, 1302-1315, 2017

  77. “Visualization and simulation of the transfer process of index-matched silica microparticle inks for gravure printing,” Arnout M. P. Boelens, Juan J. de Pablo, Sooman Lim, Lorraine Francis, Bok Y. Ahn, Jennifer A. Lewis. AIChE Journal , 63, 1419-1429, 2017

  78. “Molecular Structure of Canonical Liquid Crystal Interfaces,” Monirosadat Sadati, Hadi Ramezani-Dakhel, Wei Bu, Emre Sevgen, Zhu Liang, Cem Erol, Mohammad Rahimi, Nader Taheri Qazvini, Binhua Lin, Nicholas L. Abbott, Benoı̂t Roux, Mark L. Schlossman, and Juan J. de Pablo. J. Am. Chem. Soc., 139, 3841-3850, 2017

  79. “Demixing by a Nematic Mean Field: Coarse-Grained Simulations of Liquid Crystalline Polymers,” Abelardo Ramírez-Hernández, Su-Mi Hur, Julio C. Armas-Pérez, Monica Olvera de la Cruz, and Juan J. de Pablo . Polymers, 9, 2017

  80. “Comparing Solvophobic and Multivalent Induced Collapse in Polyelectrolyte Brushes,” Nicholas E. Jackson, Blair K. Brettmann, Venkatram Vishwanath, Matthew Tirrell, and Juan J. de Pablo. ACS Macro Lett., 6, 155-160, 2017

  81. “Understanding Atomic-Scale Behavior of Liquid Crystals at Aqueous Interfaces,” Hadi Ramezani-Dakhel, Monirosadat Sadati, Mohammad Rahimi, Abelardo Ramirez-Hernandez, Benoît Roux, and Juan J. de Pablo. J. Chem. Theory Comput., 13, 237-244, 2017

  82. “Directed self-assembly of liquid crystalline blue-phases into ideal single-crystals ,” Jose A. Martínez-González, Xiao Li, Monirosadat Sadati, Ye Zhou, Rui Zhang, Paul F. Nealey & Juan J. de Pablo. Nature Communications, 8, 2017

  83. “Directed Self-Assembly of Colloidal Particles onto Nematic Liquid Crystalline Defects Engineered by Chemically Patterned Surfaces,” Xiao Li, Julio C. Armas-Pérez, Juan P. Hernández-Ortiz, Christopher G. Arges, Xiaoying Liu, José A. Martínez-González, Leonidas E. Ocola, Camille Bishop, Helou Xie, Juan J. de Pablo, and Paul F. Nealey . ACS Nano, 11, 6492–6501, 2017

  84. “Influence of Vapor Deposition on Structural and Charge Transport Properties of Ethylbenzene Films,” Lucas W. Antony, Nicholas E. Jackson, Ivan Lyubimov, Venkatram Vishwanath, Mark D. Ediger, and Juan J. de Pablo. ACS Cent. Sci., 3, 415-424, 2017

  85. “Molecular Structure of Canonical Liquid Crystal Interfaces,” M. Sadati, H. Ramezani-Dakhel, W. Bu, E. Sevgen, Z. Liang, C. Erol, M. Rahimi, N. Taheri Qazvini, B. Lin, N. L. Abbott, B. Roux, M. L. Schlossman, and J. J. de Pablo. J. Am. Chem. Soc., 139, 3841, 2017

  86. “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

  87. “ 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

  88. “An O(N) and parallel approach to integral problems by a kernel-independent fast multipole method: Application to polarization and magnetization of interacting particles,” Xikai Jiang, Jiyuan Li, Xujun Zhao, Jian Qin, Dmitry Karpeev, Juan Hernandez-Ortiz, Juan J. de Pablo, and Olle Heinonen. J. Chem. Phys., 145, 064307, 2016

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

  90. “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

  91. “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

  92. “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

  93. “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

  94. “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

  95. “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

  96. “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

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

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

  99. “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

  100. “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

  101. “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

  102. “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

  103. “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

  104. “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

  105. “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

  106. “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

  107. “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

  108. “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

  109. “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

  110. “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

  111. “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

  112. “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

  113. “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

  114. “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

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

  116. “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

  117. “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

  118. “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

  119. “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

  120. “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

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

  122. “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

  123. “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

  124. “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

  125. “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

  126. “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

  127. “ 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

  128. “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

  129. “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

  130. “ 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

  131. “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

  132. “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

  133. “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

  134. “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

  135. “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

  136. “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

  137. “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

  138. “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

  139. “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

  140. “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

  141. 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.

  142. “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

  143. “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

  144. “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

  145. “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

  146. “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

  147. “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

  148. “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

  149. “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

  150. “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

  151. “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

  152. 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.

  153. 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.

  154. 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.

  155. “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

  156. 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.

  157. 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. 

  158. 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.

  159. 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. 

  160. 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.

  161. 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.

  162. 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. 

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

  164. “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

  165. “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

  166. “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

  167. “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

  168. “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

  169. “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

  170. “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

  171. “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

  172. “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

  173. “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

  174. “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

  175. “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

  176. “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

  177. “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

  178. “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

  179. “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

  180. “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

  181. “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

  182. “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

  183. “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

  184. “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

  185. “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

  186. “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

  187. “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

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

  189. “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

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

  191. “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

  192. “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

  193. “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

  194. “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

  195. “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

  196. “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

  197. “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

  198. “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

  199. “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

  200. “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

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

  202. “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

  203. “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

  204. “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

  205. “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,

  206. “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

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

  208. “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

  209. “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

  210. “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

  211. “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

  212. “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

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

  214. “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

  215. “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

  216. “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

  217. “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

  218. “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

  219. “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

  220. “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

  221. “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

  222. “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

  223. “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

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

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

  226. “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

  227. “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

  228. “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

  229. “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

  230. “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

  231. “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

  232. “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

  233. “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

  234. “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

  235. “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

  236. “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

  237. “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

  238. “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

  239. “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

  240. “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

  241. “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

  242. “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

  243. “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

  244. “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

  245. “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

  246. “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

  247. “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

  248. “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

  249. “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

  250. “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

  251. “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

  252. “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

  253. “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

  254. “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

  255. “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,

  256. “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

  257. “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

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

  259. “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

  260. “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

  261. “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

  262. “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

  263. “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

  264. “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

  265. “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

  266. “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

  267. “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

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

  269. “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

  270. “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

  271. “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

  272. “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

  273. “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

  274. “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

  275. “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

  276. “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

  277. “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

  278. “ 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

  279. “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

  280. “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

  281. “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

  282. “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

  283. “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

  284. “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

  285. “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

  286. “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

  287. “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

  288. “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

  289. “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

  290. “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

  291. “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

  292. “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

  293. “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

  294. “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

  295. “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

  296. “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

  297. “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

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

  299. “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

  300. “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

  301. “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

  302. “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

  303. “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

  304. “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

  305. “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

  306. “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

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

  308. “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

  309. “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

  310. “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

  311. “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

  312. “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

  313. “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

  314. “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

  315. “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

  316. “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

  317. “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

  318. “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

  319. “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

  320. “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

  321. “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

  322. “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

  323. “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

  324. “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

  325. “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

  326. “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

  327. “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

  328. “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

  329. “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

  330. “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

  331. “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

  332. “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

  333. “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

  334. “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

  335. “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

  336. “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

  337. “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

  338. “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

  339. “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

  340. “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

  341. “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

  342. “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

  343. “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

  344. “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

  345. “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

  346. “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

  347. “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

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

  349. “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

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

  351. “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

  352. “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

  353. “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

  354. “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

  355. “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

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

  357. “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

  358. “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

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

  360. “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

  361. “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

  362. “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

  363. “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

  364. “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

  365. “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

  366. “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

  367. “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

  368. “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

  369. “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

  370. “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

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

  372. “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

  373. “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

  374. “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

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

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

  377. “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

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

  379. “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

  380. “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

  381. “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

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

  383. “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

  384. “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

  385. “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

  386. “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

  387. “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

  388. “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

  389. “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

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

  391. “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

  392. “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

  393. “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

  394. “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

  395. “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

  396. “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

  397. “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

  398. “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

  399. “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

  400. “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

  401. “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

  402. “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

  403. “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

  404. “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

  405. “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

  406. “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

  407. “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

  408. “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

  409. “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

  410. “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

  411. “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

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

  413. “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

  414. “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

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

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

  417. “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

  418. “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

  419. “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

  420. “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

  421. “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

  422. “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

  423. “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

  424. “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

  425. “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

  426. “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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