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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>Whitmer Group @ ND</title>
<link rel="stylesheet" href="style.css">
</head>
<body>
<div id="wrap">
<div id="header">
<h1>
<a href="index.html">Whitmer Research Group</a>
</h1>
<h2> Soft Materials Modeling and Computation</h2>
<h3>
<a href="http://cbe.nd.edu"> Department of Chemical and Biomolecular Engineering</a>
//
<a href="http://engineering.nd.edu"> College of Engineering </a>
//
<a href="http://www.nd.edu">University of Notre Dame</a>
</h3>
</div>
<div id="menu">
<a href="index.html">Projects</a>
<a href="papers.html">Papers</a>
<a href="positions.html">Positions</a>
<a href="people.html">People</a>
<a href="pictures.html">Pictures</a>
<a href="codes.html">Codes</a>
<a href="community.html">Community</a>
<a href="contact.html">Contact</a>
</div>
<div id="content">
<h2> Publications (<a href="https://scholar.google.com/citations?user=5R_fumEAAAAJ&hl=en">Google Scholar Link</a>)</h2>
<p>
Papers listed below are broken into two sections: Notre Dame (articles submitted after joining the faculty at Notre Dame) and Pre-Notre Dame (articles submitted during undergraduate, graduate, and postdoctoral work).
</p>
<br>
<h2> Notre Dame </h2>
<!--PAPER 58-->
<div class="wrapper">
<div class="a">
[58] Jiacheng Liu, Marvin Diaz-Segura, A Scott Manning, Lingyu Yang, Govinda Devkota, Sunil P. Upadhyay, Jonathan K. Whitmer and Jennifer L. Schaefer.
"<a href="https://doi.org/10.1016/j.electacta.2024.145415">Amphiphilic salts as single-component, solvent-free, lithium electrolytes.</a>"
Electrochimica Acta, <b>511</b>, 145415, 2025.
</div>
<div class="b">
<img src="img/ppr/EA-59.jpg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 57-->
<div class="wrapper">
<div class="a">
[57] Christopher J. Addonizio, Adam S. Braegelman, Connor R. Schmidt, Rachel C. Ollier, Akwasi Ansah Antwi, Bo Su, Mohsen Farshad, Jonathan K. Whitmer and Matthew J. Webber.
"<a href="https://pubs.acs.org/doi/abs/10.1021/acsmacrolett.4c00531">Impact of Guest Orientation in Host-Guest Supramolecular Hydrogels.</a>"
ACS Macro Letters, <b>14</b>, 1, 8-13, 2022.
</div>
<div class="b">
<img src="img/ppr/ACSMacroL-58.jpeg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 56-->
<div class="wrapper">
<div class="a">
[56] Logan Hennes, Chloe Behringer, Mohsen Farshad, Jennifer L. Schaefer and Jonathan K. Whitmer.
"<a href="papers.html">Controlling Electrostatics to Enhance Conductivity in Structured Electrolytes.</a>"
<em>Submitted</em>, 2024.
</div>
<div class="b">
<img src="img/ppr/Submitted-57.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 55-->
<div class="wrapper">
<div class="a">
[55] Andrew V. Marquardt, Mohsen Farshad and Jonathan K. Whitmer.
"<a href="https://pubs.acs.org/doi/abs/10.1021/acs.jctc.3c01186">Calculating Binding Free Energies in Model Host-Guest Systems with Unrestrained Advanced Sampling.</a>"
Journal of Chemical Theory and Computation, <b>20</b>, 9, 3927-3934, 2024.
</div>
<div class="b">
<img src="img/ppr/JCTC-56.jpeg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 54-->
<div class="wrapper">
<div class="a">
[54] Orlando A. Mendible, Jonathan K. Whitmer and Yamil J. Colón.
"<a href="papers.html">Considerations in the use of ML interaction potentials for free energy calculations.</a>"
<em>Submitted</em>, 2024.
</div>
<div class="b">
<img src="img/ppr/Submitted-55.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 53-->
<div class="wrapper">
<div class="a">
[53] Pablo F. Zubieta Rico, Ludwig Schneider, Gustavo R. Pérez-Lemus, Riccardo Alessandri, Siva Dasetty, Trung D. Nguyen, Cintia A. Menéndez, Yiheng Wu, Yezhi Jin, Yinan Xu, Samuel Varner, John A. Parker, Andrew L. Ferguson, Jonathan K. Whitmer and Juan J. de Pablo.
"<a href="https://www.nature.com/articles/s41524-023-01189-z">PySAGES: flexible, advanced sampling methods accelerated with GPUs.</a>"
npj Computational Materials, <b>10</b>, 35, 2024.
</div>
<div class="b">
<img src="img/ppr/npjCM-54.jpeg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 52-->
<div class="wrapper">
<div class="a">
[52] Ramón González-Pérez, Stephen Adams, Alexander W. Dowling, William A. Phillip and Jonathan K. Whitmer.
"<a href="https://pubs.acs.org/doi/abs/10.1021/acs.jpca.3c00094">Thermodynamics of Li+-Crown Ether Interactions in Aqueous Solvent.</a>"
Journal of Physical Chemistry A, <b>127</b>, 21, 4624-4631, 2023.
</div>
<div class="b">
<img src="img/ppr/JPCA-53.jpg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 51-->
<div class="wrapper">
<div class="a">
[51] Jiale Shi, Fahed Albreiki, Yamil J Colón, Samanvaya Srivastava and Jonathan K Whitmer.
"<a href="https://pubs.acs.org/doi/abs/10.1021/acs.jctc.2c01314">Transfer Learning Facilitates the Prediction of Polymer-Surface Adhesion Strength.</a>"
Journal of Chemical Theory and Computation, <b>19</b>, 14, 4631-4640, 2023.
</div>
<div class="b">
<img src="img/ppr/JCTC-52.jpeg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 50-->
<div class="wrapper">
<div class="a">
[50] Yulu Huang, Weiqiang Wang, Jonathan K Whitmer and Rui Zhang.
"<a href="https://pubs.rsc.org/en/content/articlehtml/2023/sm/d2sm01178f">Structures, thermodynamics and dynamics of topological defects in Gay-Berne nematic liquid crystals.</a>"
Soft Matter, <b>19</b>, 483-496, 2022.
</div>
<div class="b">
<img src="img/ppr/SoftMatt-51.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 49-->
<div class="wrapper">
<div class="a">
[49] Jiale Shi, Michael J Quevillon, Pedro H Amorim Valença and Jonathan K Whitmer.
"<a href="https://pubs.acs.org/doi/abs/10.1021/acsami.2c08891">Predicting Adhesive Free Energies of Polymer–Surface Interactions with Machine Learning.</a>"
ACS Applied Materials & Interfaces, <b>14</b>, 32, 2022.
</div>
<div class="b">
<img src="img/ppr/ACSAMI-50.jpg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 48-->
<div class="wrapper">
<div class="a">
[48] Jiale Shi, Shanghui Huang, François Gygi and Jonathan K Whitmer.
"<a href="https://pubs.acs.org/doi/abs/10.1021/acs.jpca.2c02732">Free-Energy Landscape and Isomerization Rates of Au4 Clusters at Finite Temperatures.</a>"
Journal of Physical Chemistry A, <b>126</b>, 21, 3392-3400, 2022.
</div>
<div class="b">
<img src="img/ppr/JPCA-49.jpg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 47-->
<div class="wrapper">
<div class="a">
[47] Ernesto C Cortés-Morales, Vikramjit S Rathee, Ahmad Ghobadi and Jonathan K Whitmer.
"<a href="https://doi.org/10.1063/5.0065964">A molecular view of plasticization of polyvinyl alcohol.</a>"
Journal of Chemical Physics, <b>155</b>, 174903, 2021.
</div>
<div class="b">
<img src="img/ppr/JCP-48.jpg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 46-->
<div class="wrapper">
<div class="a">
[46] Shanghui Huang, Michael J. Quevillon, Ernesto C. Cortés-Morales and Jonathan K. Whitmer.
"<a href="papers.html">Exploring the Potential of Parallel Biasing in Flat Histogram Methods.</a>"
<em>Submitted</em>, 2021.
</div>
<div class="b">
<img src="img/ppr/Submitted-47.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 45-->
<div class="wrapper">
<div class="a">
[45] Mariana E. Farías-Anguiano, Ernesto C. Cortés-Morales, Jonathan K. Whitmer and Pedro E. Ramírez-González
"<a href="papers.html">Linking dynamics and structure in highly asymmetric ionic liquids.</a>"
<em>Submitted</em>, 2021.
</div>
<div class="b">
<img src="img/ppr/Submitted-46.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 44-->
<div class="wrapper">
<div class="a">
[44] Marco Govoni, Jonathan K. Whitmer, Juan de Pablo, Francois Gygi and Giulia Galli.
"<a href="https://www.nature.com/articles/s41524-021-00501-z">Code interoperability extends the scope of quantum simulations.</a>"
npj Computational Materials, <b>7</b>, 32, 2021.
</div>
<div class="b">
<img src="img/ppr/npjCM-45.jpeg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 43-->
<div class="wrapper">
<div class="a">
[43] Shanghui Huang, Michael J. Quevillon, Soren Kyhl and Jonathan K. Whitmer.
"<a href="https://pubs.aip.org/aip/jcp/article/152/13/134901/198141">Surveying the free energy landscape of clusters of attractive colloidal spheres.</a>"
Journal of Chemical Physics, <b>152</b>, 134901, 2020.
</div>
<div class="b">
<img src="img/ppr/JCP-44.jpg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 42-->
<div class="wrapper">
<div class="a">
[42] Anne C. Leonhard and Jonathan K. Whitmer.
"<a href="https://doi.org/10.1021/acs.jctc.9b00348">Accurate Determination of Cavitand Binding Free Energies via Unrestrained Advanced Sampling</a>"
Journal of Chemical Theory and Computation, <b>15</b>, 11, 5761-5768, 2019.
</div>
<div class="b">
<img src="img/ppr/Submitted-42.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 41-->
<div class="wrapper">
<div class="a">
[41] Jiale Shi, Hythem Sidky and Jonathan K. Whitmer.
"<a href="https://pubs.rsc.org/en/content/articlelanding/2019/sm/c9sm01395d/unauth">Novel elastic response in twist-bend nematic models.</a>"
Soft Mattter, <b>15</b>, 8219-8226, 2019.
</div>
<div class="b">
<img src="img/ppr/Submitted-41.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 40-->
<div class="wrapper">
<div class="a">
[40] Michael Quevillon and Jonathan K. Whitmer.
"<a href="papers.html">Replica Exchange Simualtions of the Crystal--Smectic-A Transition in Ionic Liquid Crystals</a>",
<em>Submitted</em>, 2019.
</div>
<div class="b">
<img src="img/ppr/Submitted-40.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 39-->
<div class="wrapper">
<div class="a">
[39] Hythem Sidky, Jiale Shi and Jonathan K. Whitmer.
"<a href="https://pubs.rsc.org/en/content/articlehtml/2020/me/c9me00065h">Automated determination of <em>n</em>-cyanobiphenyl and n-cyanobiphenyl binary mixtures elastic constants in the nematic phase from molecular simulation.</a>"
Molecular Systems Design & Engineering, <b>5</b>, 1131-1136, 2020.
</div>
<div class="b">
<img src="img/ppr/Submitted-39.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 38-->
<div class="wrapper">
<div class="a">
[38] Vikramjit S. Rathee, Benjamin J. Sikora, Hythem Sidky and Jonathan K. Whitmer.
"<a href="papers.html">Explicit Ion Effects on the Charge and Conformation of Weak Polyelectrolytes.</a>"
Polymers, <b>11</b>, 183, 2019.
</div>
<div class="b">
<img src="img/ppr/Polymers-38.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 37-->
<div class="wrapper">
<div class="a">
[37] Ming Han, Jonathan K. Whitmer and Erik Luijten.
"<a href="papers.html">Dynamics and Structure of Colloidal Aggregates Under Microchannel Flow.</a>"
Soft Matter, <b>15</b>, 744-751 2019.
</div>
<div class="b">
<img src="img/ppr/SoftMatt-37.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 36-->
<div class="wrapper">
<div class="a">
[36] Mark J. Summe, Sushree Jagriti Sahoo, Jonathan K. Whitmer and William A. Phillip.
"<a href="papers.html">Salt Permeation mechanisms in ink-jet printed charge mosaic membranes.</a>"
Molecular Systems Design & Engineering <b>3</b>, 959-969, 2018.
</div>
<div class="b">
<img src="img/ppr/MSDE-36.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 35-->
<div class="wrapper">
<div class="a">
[35] Vikramjit S. Rathee, Hythem Sidky, Benjamin J. Sikora and Jonathan K. Whitmer.
"<a href="papers.html">Role of associative charging in the entropy-energy balance of polyelectrolyte complexes.</a>"
Journal of the American Chemical Society, <b>140</b>, 15319-15328, 2018.
</div>
<div class="b">
<img src="img/ppr/JACS-35.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 34-->
<div class="wrapper">
<div class="a">
[34] Emre Sevgen, Federico Giberti, Hythem Sidky, Jonathan K. Whitmer, Giulia Galli, Francois Gygi and Juan J. de Pablo.
"<a href="https://pubs.acs.org/doi/abs/10.1021/acs.jctc.8b00192">Hierarchical Coupling of First-Principles Molecular Dynamics with Advanced Sampling Methods</a>",
The Journal of Chemical Theory and Computation, <em>Accepted</em> (2018).
</div>
<div class="b">
<img src="img/ppr/JCTC-34.jpg" style="width:100%"/>
</div>
</div>
<!--PAPER 33-->
<div class="wrapper">
<div class="a">
[33] Ashley Guo, Emre Sevgen, Hythem Sidky, Jonathan K. Whitmer and Juan J. de Pablo.
"<a href="https://aip.scitation.org/doi/full/10.1063/1.5020733"> Adaptive enhanced sampling by force-biasing using neural networks</a>",
The Journal of Chemical Physics, <b>148</b>, 134108 (2018).
</div>
<div class="b">
<img src="img/ppr/JCP-33.jpg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 32-->
<div class="wrapper">
<div class="a">
[32] Vikramjit S. Rathee, Aristotle J. Zervoudakis and Jonathan K. Whitmer. "<a href="https://aip.scitation.org/doi/10.1063/1.5017941">Weak Polyelectrolyte Complexation Driven by Associative Charging</a>",
The Journal of Chemical Physics, <b>148</b>, 114901 (2018).
</div>
<div class="b">
<img src="img/ppr/JCP-32.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 31-->
<div class="wrapper">
<div class="a">
[31] Hythem Sidky, Juan J. de Pablo and Jonathan K. Whitmer
"<a href="https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.107801"><em>In Silico</em> Measurement of Elastic Moduli of Nematic Liquid Crystals</a>",
Physical Review Letters, <b>120</b>, 107801 (2018).
</div>
<div class="b">
<img src="img/ppr/PRL-31.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 30-->
<div class="wrapper">
<div class="a">
[30] Hythem Sidky and Jonathan K. Whitmer. "<a href="https://aip.scitation.org/doi/10.1063/1.5018708">Learning Free Energy Landscapes Using Artificial Neural Networks.</a>"
The Journal of Chemical Physics, <b>148</b>, 104111 (2018).
</div>
<div class="b">
<img src="img/ppr/JCP-30.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 29-->
<div class="wrapper">
<div class="a">
[29] Hythem Sidky, Yamil J. Colon, Benjamin J. Sikora, Cody Bezik, Federico Giberti, Weiwei Chu, Federico
Giberti, Ashley Z. Guo, Joshua Lequieu, Jiyuan Li, Joshua Moller, Michael Quevillon, Mohammad Rahimi,
Hadi Ramezani-Dakhel, Vikramjit S. Rathee, Daniel R. Reid, Emre Sevgen, Vikram Thapar, Michael Webb,
Xikai Jiang, Jonathan K. Whitmer, and Juan J. de Pablo
"<a href="https://aip.scitation.org/doi/full/10.1063/1.5008853">SSAGES: Software Suite for Advanced General Ensemble Simulations.</a>",
The Journal of Chemical Physics, <b>148</b>, 044104 (2018).
</div>
<div class="b">
<img src="img/ppr/JCP-29.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 28-->
<div class="wrapper">
<div class="a">
[28] Michael Quevillon and Jonathan K. Whitmer. "<a href="papers.html">Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations.</a>",
Materials, <b>11</b>, 64 (2018).
</div>
<div class="b">
<img src="img/ppr/Materials-28.png" style="width:100%"/>
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<!--PAPER 27-->
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[27] Vikramjit S. Rathee, Benjamin Sikora, Hythem Sidky and Jonathan K. Whitmer.
"<a href="http://iopscience.iop.org/article/10.1088/2053-1591/aaa049">Simulating the Thermodynamics of Charging in Weak Polyelectrolytes: The Debye-Huckel Limit.</a>",
Materials Research Express, <b>5</b>, 014010 (2018). <em> Invited Article and Award Winner, Emerging Investigators in Materials Science 2017-2018 issue.</em>
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<img src="img/ppr/MRX-27.png" style="width:100%"/>
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<br>
<!--PAPER 26-->
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[26] Hythem Sidky and Jonathan K. Whitmer. "<a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b03113">The Emergent Nematic Phase in Ionic Chromonic Liquid Crystals.</a>" <em>The Journal of Physical Chemistry B</em> <b>121</b>, 6691-6698.
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<img src="img/ppr/JPCB-26.png" style="width:60%"/>
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<!--PAPER 25-->
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<div class="a">
[25] Hythem Sidky, Alan C. Liddell Jr., Dhagash Mehta, Jonathan D. Hauenstein and Jonathan K. Whitmer. "<a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b03113">Algebraic Geometric Method for Calculating Phase Equilibria from Fundamental Equation of State.</a>" <em>Industrial & Engineering Chemistry Research</em> <b>55</b>, 11363-11370.
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<img src="img/ppr/IEC-25.png" style="width:60%"/>
</div>
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<br>
<!--PAPER 24-->
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<div class="a">
[24] Vikramjit Singh Rathee, Siyi Qu, William A. Phillip and Jonathan K. Whitmer. "<a href="https://doi.org/10.1039/C6ME00045B">A coarse-grained thermodynamic model for the predictive engineering of valence-selective membranes.</a>" <em>Molecular Systems Design & Engineering</em> <b>1</b>, 301-312.
</div>
<div class="b">
<img src="img/ppr/MSDE-24.png" style="width:100%"/>
</div>
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<br>
<!--PAPER 23-->
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<div class="a">
[23] Hythem Sidky and Jonathan K. Whitmer. "<a href="http://dx.doi.org/10.1080/02678292.2016.1201869">Elastic properties of common Gay–Berne nematogens from density of states (DOS) simulations.</a>" <em>Liquid Crystals</em> <b>43</b>, 2285-2299. Invited Article.
</div>
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<img src="img/ppr/LiqCryst-23.png" style="width:100%"/>
</div>
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<br>
<!--PAPER 22-->
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<div class="a">
[22] Hythem Sidky, Dhagash Mehta and Jonathan K. Whitmer. "<a href="http://dx.doi.org/10.1002/aic.15319">Reliable mixture critical point computation using polynomial homotopy continuation.</a>" <em>AIChE Journal</em> <b>62</b>, 4497-4507.
</div>
<div class="b">
<img src="img/ppr/AIChEJ-22.png" style="width:60%"/>
</div>
</div>
<br>
<!--PAPER 21-->
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<div class="a">
[21] Hythem Sidky and Jonathan K. Whitmer. "<a href="https://doi.org/10.1039/C5SM03107A">Elastic response and phase behavior in binary liquid crystal mixtures.</a>" <em>Soft Matter</em> <b>12</b>, 4489-4498.
</div>
<div class="b">
<img src="img/ppr/SoftMatt-21.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 21-->
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<div class="a">
[20] Whitmer, Jonathan K., Aaron M. Fluitt, Lucas Antony, Jian Qin, Michael McGovern, and Juan J. de Pablo. <a href="http://aip.scitation.org/doi/abs/10.1063/1.4927147">"Sculpting bespoke mountains: Determining free energies with basis expansions."</a> <em>The Journal of Chemical Physics</em> <b>143</b>, 044101 (2015).
</div>
<div class="b">
<img src="img/ppr/JCP-20.png" style="width:80%"/>
</div>
</div>
<br>
<h2> Pre-Notre Dame </h2>
<!--PAPER 19-->
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[19] Sarah L. Perry, Lorraine Leon, Kyle Q. Hoffmann, Matthew J. Kade, Dimitrios Priftis, Katie A. Black, Derek Wong, Ryan
A. Klein, Charles F. Pierce III, Khatcher O. Margossian, Jonathan K. Whitmer, Jian Qin, Juan J. de Pablo and Matthew Tirrell. <a href="http://www.nature.com/articles/ncomms7052">"Chirality-selected phase behaviour in ionic polypeptide complexes."</a> Nature Communications <b>6</b>, 6052 (2015).
</div>
<div class="b">
<img src="img/ppr/NatComm-19.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 18-->
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<div class="a">
[18] Gordon S. Freeman, Daniel M. Hinckley, Joshua Lequieu, Jonathan
K. Whitmer and Juan J. de
Pablo. <a href="http://dx.doi.org/10.1063/1.4897649">"Coarse-grained Modeling of DNA Curvature."</a> The Journal of Chemical Physics <b>141</b>, 165103 (2014).
</div>
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<img src="img/ppr/JCP-18.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 17-->
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<div class="a">
[17] Jonathan K. Whitmer, Abhijeet A. Joshi, Rebecca J. Carlton,
Nicholas L. Abbott and Juan J. de Pablo. <a href="http://dx.doi.org/10.1021/ct5005406">"Surface
Adsorption in Non-Polarizable Atomic Models."</a> Journal
Chemical Theory and Computation <b>10</b>, 5616 (2014).
</div>
<div class="b">
<img src="img/ppr/JCTC-17.jpg" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 16-->
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<div class="a">
[16] Jonathan K. Whitmer, Chi-cheng Chiu, Abhijeet A. Joshi and
Juan J. de
Pablo. <a href="http://dx.doi.org/10.1103/PhysRevLett.113.190602">"Basis
Function Sampling: A New Paradigm for Material Property
Computation."</a> Physical Review Letters <b>113</b>, 190602 (2014).
</div>
<div class="b">
<img src="img/ppr/PRL-16.png" style="width:75%"/>
</div>
</div>
<br>
<!--PAPER 15-->
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<div class="a">
[15] Gordon S. Freeman, Daniel M. Hinckley, Joshua Lequieu,
Jonathan K. Whitmer and Juan J. de
Pablo. <a href="http://dx.doi.org/10.1103/PhysRevLett.113.168101">"DNA
Shape Dominates Sequence Affinity in Nucleosome Formation."</a> Physical Review Letters <b>113</b>, 168101 (2014).
</div>
<div class="b">
<img src="img/ppr/PRL-15.png" style="width:75%"/>
</div>
</div>
<br>
<!--PAPER 14-->
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<div class="a">
[14] Jian Qin, Dmitris Priftis, Robert Farina, Sarah Perry,
Jonathan K. Whitmer, Kyle Hoffmann, Matthew Tirrell and Juan J. de Pablo. <a href="http://dx.doi.org/10.1021/mz500190w">"Interfacial
Tension of Polyelectrolyte Complex Coacervate Phases."</a> ACS
Macro Letters <b>3</b>, 565 (2014).
</div>
<div class="b">
<img src="img/ppr/MacroLett-14.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 13-->
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<div class="a">
[13] Shan Jiang, Jing Yan, Jonathan K. Whitmer, Stephen A. Anthony,
Erik Luijten and Steve
Granick. <a href="http://dx.doi.org/10.1103/PhysRevLett.112.218301">"Orientationally
Glassy Crystals of Janus Spheres."</a> Physical Review Letters <b>112</b>, 218301 (2014).
</div>
<div class="b">
<img src="img/ppr/PRL-13.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 12-->
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<div class="a">
[12] Abhijeet A. Joshi, Jonathan K. Whitmer, Orlando Guzman and
Juan J. de
Pablo. <a href="http://dx.doi.org/10.1039/C3SM51919H">"Measuring
Liquid Crystal Elastic Constants with Free Energy
Perturbations."</a> Soft Matter <b>10</b>, 882 (2014).
</div>
<div class="b">
<img src="img/ppr/SoftMatt-12.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 11-->
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<div class="a">
[11] Jonathan K. Whitmer, Xiaoguang Wang, Frederic Mondio, Daniel S. Miller, Nicholas L. Abbott and Juan J. de Pablo. <a href="http://dx.doi.org/10.1103/PhysRevLett.111.227801">"Nematic-field-driven positioning of particles in liquid crystal droplets."</a> Physical Review Letters <b>111</b>, 227801 (2013).
</div>
<div class="b">
<img src="img/ppr/PRL-11.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 10-->
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<div class="a">
[10] Daniel M. Hinckley, Gordon S. Freeman, Jonathan K. Whitmer and Juan J. de Pablo. <a href="http://dx.doi.org/10.1063/1.4822042">"An Experimentally Informed Coarse-Grained 3-Site-Per-Nucleotide Model of DNA: Structure, Thermodynamics and Dynamics of Hybridization."</a> The Journal of Chemical Physics <b>139</b>, 144903 (2013).
</div>
<div class="b">
<img src="img/ppr/JCP-10.png" style="width:80%"/>
</div>
</div>
<br>
<!--PAPER 9-->
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<div class="a">
[9] Jonathan K. Whitmer, Abhijeet A. Joshi, Tyler F. Roberts and Juan J. de Pablo <a href="http://dx.doi.org/10.1063/1.4802774">"Liquid-Crystal Mediated Nanoparticle Interactions and Gel Formation."</a> The Journal of Chemical Physics <b>138</b>, 194903 (2013).
</div>
<div class="b">
<img src="img/ppr/JCP-9.png" style="width:80%"/>
</div>
</div>
<br>
<!--PAPER 8-->
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<div class="a">
[8] Jonathan K. Whitmer, Raj Shekhar, Tyler F. Roberts, Nicholas L. Abbott and Juan J. de Pablo <a href="http://dx.doi.org/10.1103/PhysRevE.87.020502">"Modeling the Polydomain-Monodomain Transition of Liquid Crystal Elastomers."</a> Physical Review E <b>87</b>, 020502(R) (2013).
</div>
<div class="b">
<img src="img/ppr/PRE-8.png" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 7-->
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<div class="a">
[7] Raj Shekhar, Jonathan K. Whgitmer, Rohit Malshe, Jose Antonio Moreno Razo, Tyler F. Roberts and Juan J. de Pablo <a href="http://dx.doi.org/10.1063/1.4722209">"Isotropic Nematic Phase Transition in the Lebwohl-Lasher Model from Density of States Simulation."</a> The Journal of Chemical Physics<b>136</b>, 234503 (2012).
</div>
<div class="b">
<img src="img/ppr/JCP-7.png" style="width:70%"/>
</div>
</div>
<br>
<!--PAPER 6-->
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<div class="a">
[6] Jonathan K. Whitmer and Erik Luijten. <a href="http://dx.doi.org/10.1021/jp111388m">"Influence of Hydrodynamics on Cluster Formation in Colloid-Polymer Mixtures."</a> The Journal of Physical Chemistry B<b>115</b>, 7294 (2011).
</div>
<div class="b">
<img src="img/ppr/JPCB-6.gif" style="width:100%"/>
</div>
</div>
<br>
<!--PAPER 5-->
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<div class="a">
[5] Qian Chen, Erich Diesel, Jonathan K. Whitmer, Sung-Chul Bae, Erik Luijten and Steve Granick. <a href="http://dx.doi.org/10.1021/jp111388m">"Triblock Colloidal Spheres for Directed Self-Assembly"</a> Journal of the American Chemical Society <b>113</b>, 7725 (2011).
</div>
<div class="b">
<img src="img/ppr/JACS-5.png" style="width:80%"/>
</div>
</div>
<br>
<!--PAPER 4-->
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<div class="a">
[4] Qian Chen, Jonathan K. Whitmer, Shan Jiang, Sung-Chul Bae, Erik Luijten and Steve Granick. <a href="http://dx.doi.org/10.1126/science.1197451">"Supracolloidal Reaction Kinetics of Janus Spheres"</a> Science <b>331</b>, 199 (2011).
</div>
<div class="b">
<img src="img/ppr/Science-4.png" style="width:80%"/>
</div>
</div>
<br>
<!--PAPER 3-->
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<div class="a">
[3] Jonathan K. Whitmer and Erik Luijten. <a href="http://dx.doi.org/10.1063/1.3525923">"Sedimentation of Aggregating Colloids."</a> The Journal of Chemical Physics <b>134</b>, 034510 (2011).
</div>
<div class="b">
<img src="img/ppr/JCP-3.png" style="width:80%"/>
</div>
</div>
<br>
<!--PAPER 2-->
<div class="wrapper">
<div class="a">
[2] Jonathan K. Whitmer and Erik Luijten. <a href="http://dx.doi.org/10.1088/0953-8984/22/10/104106">"Fluid-Solid Boundary Conditions for Multiparticle Collision Dynamics."</a> Journal of Physics: Condensed Matter <b>22</b>, 104106 (2010).
</div>
<div class="b">
<img src="img/ppr/JPCM-2.png" style="width:80%"/>
</div>
</div>
<br>
<!--PAPER 1-->
<div class="wrapper">
<div class="a">
[1] Jonathan K. Whitmer, Sergei B. Kiselev and Bruce M. Law. <a href="http://dx.doi.org/10.1063/1.2128705">"Adsorption at the Liquid-Vapor Interface of a Binary Liquid Mixture"</a> The Journal of Chemical Physics <b>123</b>, 204720 (2005).
</div>
<div class="b">
<img src="img/ppr/JCP-1.png" style="width:50%"/>
</div>
</div>
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