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Juan J. de Pablo
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Journal Articles

The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle

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Rikkert J. Nap, Paola Carillo Gonzalez, Aria E. Coraor, Ranya K. A. Virk, Juan J. de Pablo, Vadim Backman, Igal Szleifer
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 235101 (2024)
https://doi.org/10.1063/5.0241529
Published: December 2024
View article titled, The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle
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Journal Articles

Dynamics of poly[n]catenane melts

Editor’s Pick
Phillip M. Rauscher, Kenneth S. Schweizer, Stuart J. Rowan, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 152, 214901 (2020)
https://doi.org/10.1063/5.0007573
Published: June 2020
View article titled, Dynamics of poly[<em>n</em>]catenane melts
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Includes: Supplementary data
Journal Articles

Structure and dynamics of hydrodynamically interacting finite-size Brownian particles in a spherical cavity: Spheres and cylinders

Jiyuan Li, Xikai Jiang, Abhinendra Singh, Olle G. Heinonen, Juan P. Hernández-Ortiz, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 152, 204109 (2020)
https://doi.org/10.1063/1.5139431
Published: May 2020
View article titled, Structure and dynamics of hydrodynamically interacting finite-size Brownian particles in a spherical cavity: Spheres and cylinders
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Journal Articles

Shape induced segregation and anomalous particle transport under spherical confinement

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Abhinendra Singh, Jiyuan Li (李冀圆), Xikai Jiang (蒋玺恺), Juan P. Hernández-Ortiz, Heinrich M. Jaeger, Juan J. de Pablo
Journal: Physics of Fluids
Physics of Fluids 32, 053307 (2020)
https://doi.org/10.1063/5.0002906
Published: May 2020
View article titled, Shape induced segregation and anomalous particle transport under spherical confinement
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Journal Articles

Ultrathin initiated chemical vapor deposition polymer interfacial energy control for directed self-assembly hole-shrink applications

Editor’s Pick
Moshe Dolejsi, Priya Moni, Cody T. Bezik, Chun Zhou, Juan J. de Pablo, Karen K. Gleason, Paul F. Nealey
Journal: Journal of Vacuum Science & Technology B
J. Vac. Sci. Technol. B 37, 061804 (2019)
https://doi.org/10.1116/1.5121541
Published: October 2019
View article titled, Ultrathin initiated chemical vapor deposition polymer interfacial energy control for directed self-assembly hole-shrink applications
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Journal Articles

1CPN: A coarse-grained multi-scale model of chromatin

Joshua Lequieu, Andrés Córdoba, Joshua Moller, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 215102 (2019)
https://doi.org/10.1063/1.5092976
Published: June 2019
View article titled, 1CPN: A coarse-grained multi-scale model of chromatin
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Includes: Supplementary data
Journal Articles

Free energy of metal-organic framework self-assembly

Yamil J. Colón, Ashley Z. Guo, Lucas W. Antony, Kyle Q. Hoffmann, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 104502 (2019)
https://doi.org/10.1063/1.5063588
Published: March 2019
View article titled, Free energy of metal-organic framework self-assembly
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Includes: Supplementary data
Journal Articles

Extracting collective motions underlying nucleosome dynamics via nonlinear manifold learning

Ashley Z. Guo, Joshua Lequieu, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 054902 (2019)
https://doi.org/10.1063/1.5063851
Published: February 2019
View article titled, Extracting collective motions underlying nucleosome dynamics via nonlinear manifold learning
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Journal Articles

Generalised Navier boundary condition for a volume of fluid approach using a finite-volume method

Editor’s Pick
Arnout M. P. Boelens, Juan J. de Pablo
Journal: Physics of Fluids
Physics of Fluids 31, 021203 (2019)
https://doi.org/10.1063/1.5055036
Published: December 2018
View article titled, Generalised Navier boundary condition for a volume of fluid approach using a finite-volume method
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Journal Articles

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, M. D. Ediger
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 204503 (2018)
https://doi.org/10.1063/1.5052003
Published: November 2018
View article titled, Tenfold increase in the photostability of an azobenzene guest in vapor-deposited glass mixtures
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Includes: Supplementary data
Journal Articles

Simulations of splashing high and low viscosity droplets

Arnout M. P. Boelens, Juan J. de Pablo
Journal: Physics of Fluids
Physics of Fluids 30, 072106 (2018)
https://doi.org/10.1063/1.5036519
Published: July 2018
View article titled, Simulations of splashing high and low viscosity droplets
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Journal Articles

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
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 163310 (2018)
https://doi.org/10.1063/1.5035083
Published: July 2018
View article titled, Effect of temperature on the structure and dynamics of triblock polyelectrolyte gels
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Includes: Supplementary data
Journal Articles

Early-stage human islet amyloid polypeptide aggregation: Mechanisms behind dimer formation

Ashley Z. Guo, Aaron M. Fluitt, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 025101 (2018)
https://doi.org/10.1063/1.5033458
Published: July 2018
View article titled, Early-stage human islet amyloid polypeptide aggregation: Mechanisms behind dimer formation
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Journal Articles

Layered nested Markov chain Monte Carlo

Nicholas E. Jackson, Michael A. Webb, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 072326 (2018)
https://doi.org/10.1063/1.5030531
Published: June 2018
View article titled, Layered nested Markov chain Monte Carlo
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Includes: Supplementary data
Journal Articles

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
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 234302 (2018)
https://doi.org/10.1063/1.5027435
Published: June 2018
View article titled, Evolutionary strategy for inverse charge measurements of dielectric particles
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Includes: Supplementary data
Journal Articles

Adaptive enhanced sampling by force-biasing using neural networks

Ashley Z. Guo, Emre Sevgen, Hythem Sidky, Jonathan K. Whitmer, Jeffrey A. Hubbell, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 134108 (2018)
https://doi.org/10.1063/1.5020733
Published: April 2018
View article titled, Adaptive enhanced sampling by force-biasing using neural networks
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Journal Articles

Role of translational entropy in spatially inhomogeneous, coarse-grained models

Marcel Langenberg, Nicholas E. Jackson, Juan J. de Pablo, Marcus Müller
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 094112 (2018)
https://doi.org/10.1063/1.5018178
Published: March 2018
View article titled, Role of translational entropy in spatially inhomogeneous, coarse-grained models
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Journal Articles

Drop splashing is independent of substrate wetting

Andrzej Latka, Arnout M. P. Boelens, Sidney R. Nagel, Juan J. de Pablo
Journal: Physics of Fluids
Physics of Fluids 30, 022105 (2018)
https://doi.org/10.1063/1.5012529
Published: February 2018
View article titled, Drop splashing is independent of substrate wetting
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Journal Articles

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, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 044104 (2018)
https://doi.org/10.1063/1.5008853
Published: January 2018
View article titled, SSAGES: Software Suite for Advanced General Ensemble Simulations
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Journal Articles

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, Juan J. de Pablo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 146, 244114 (2017)
https://doi.org/10.1063/1.4989545
Published: June 2017
View article titled, Parallel <em>O</em>(<em>N</em>) Stokes’ solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries
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