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publications.html
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<!doctype html>
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<title>Publications</title>
<meta name="description" content="GPU Optimized Monte Carlo (GOMC) is open-source software for simulating many-body molecular systems using the Metropolis Monte Carlo algorithm. Capable of running on single and multi-core architecture.">
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<meta name="author" content="Younes Nejahi">
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<h3 class="center blueText">
<a href="#journal">Journal Publications</a> |
<a href="#refereed">Refereed Conference and Workshop Publications</a> |
<a href="#posters">Posters</a> |
<a href="#technical">Technical Reports</a>
</h3>
<div class="containerFlexible">
<div class="row">
<div class="blueBlock">
<p><a id="journal">Journal Publications</a></p>
</div>
<h3>2021</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Open_Source_Molecular_Modeling.png" alt="Open-Source Molecular Modeling Software Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Open-Source Molecular Modeling Software in Chemical Engineering Focusing on the Molecular Simulation Design Framework
</b>
<br>
<a href="https://aiche.onlinelibrary.wiley.com/doi/10.1002/aic.17206">P. T. Cummings, C. Mc Cabe, C. R. Iacovella, A. Ledeczi, E. Jankowski, A. Jayaraman, J. C. Palmer, E. J. Maginn, S. C. Glotzer, J. A. Anderson, J. I. Siepmann, J. Potoff, R. A. Matsumoto, J. B. Gilmer, R. S. DeFever, R. Singh, B. Crawford. AIChE Journal (2021).</a>
<br>
TRIBUTE TO FOUNDERS: KEITH GUBBINS ISSUE. THERMODYNAMICS AND MOLECULAR‐SCALE PHENOMENA
<br>
</p>
</div>
</div>
<hr>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Update_2_70.jpg" alt="GOMC 2.70 Update Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Update 2.70 to "GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids"
</b>
<br>
<a href="https://www.sciencedirect.com/science/article/pii/S235271102030340X">Y. Nejahi, M. Soroush Barhaghi, G. Schwing, L. Schwiebert, J. Potoff. SoftwareX, 13, 100627 (2021).</a>
<br>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2019</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Effect_of_fluorination.png" alt="Effect of Fluorination Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Effect of fluorination on the partitioning of alcohols.
</b>
<br>
<a href="https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1669837">M. Soroush Barhaghi, C. Luyet, and J. J. Potoff, J. Molecular Physics,117, 3827-3839 (2019).</a>
<br>
This article is part of the <a href="https://www.tandfonline.com/toc/tmph20/117/23-24">Peter Cummings</a> special issue.
<br>
</p>
</div>
</div>
<hr>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Histogram_Free_Reweighting.jpeg" alt="Histogram-Free Reweighting Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Histogram-Free Reweighting with Grand Canonical Monte Carlo: Post-simulation Optimization of Non-bonded Potentials for Phase Equilibrium.
</b>
<br>
<a href="https://pubs.acs.org/doi/abs/10.1021/acs.jced.8b01232">R. A. Messerly, M. Soroush Barhaghi, J. J. Potoff, and Michael R. Shirts, J. chemical & engineering data, 64, 3701-3717 (2019).</a>
<br>
This article is part of the <a href="https://axial.acs.org/chemical-engineering-and-industrial-chemistry/journal-of-chemical-engineering-data-fomms-special-issue">FOMMS</a> special issue.
<br>
</p>
</div>
</div>
<hr>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Prediction_of_phase_equilibria.jpg" alt="Prediction of Phase Equilibria Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Prediction of phase equilibria and Gibbs free energies of transfer using molecular exchange Monte Carlo in the Gibbs ensemble.
</b>
<br>
<a href="https://doi.org/10.1016/j.fluid.2018.12.032">M. Soroush Barhaghi and J. J. Potoff. Fluid Phase Equilibria, 486, 106-118 (2019).</a>
<br>
</p>
</div>
</div>
<hr>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/GPU_Optimized_Monte_Carlo_for_the_simulation_of_phase_equilibria.jpg" alt="GPU Optimized Monte Carlo, Simulation of Phase Equilibria Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids.
</b>
<br>
<a href="https://doi.org/10.1016/j.softx.2018.11.005">Y. Nejahi, M. Soroush Barhaghi, J. Mick, B. Jackman, K. Rushaidat, Y. Li, L. Schwiebert, J. Potoff. SoftwareX, 9, 20-27 (2019).</a>
<br>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2018</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Molecular_Exchange_Monte_Carlo._A_generalized_method.png" alt="Molecular Exchange Monte Carlo Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Molecular Exchange Monte Carlo. A generalized method for identity exchanges in grand canonical Monte Carlo simulations.
</b>
<br>
<a href="https://aip.scitation.org/doi/abs/10.1063/1.5025184">M. Soroush Barhaghi, K. Torabi, Y. Nejahi, L. Schwiebert, and J. J. Potoff. J. Chem. Phys. 149, 072318 (2018)</a>
<br>
Part of the <a href="https://aip.scitation.org/doi/10.1063/1.5049669">Special Topic issue on Enhanced Sampling for Molecular Systems.</a>
<br>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2017</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Optimized_Mie_Potentials.png" alt="Optimized Mie Potentials, Application to Branched Alkanes">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Optimized Mie Potentials for Phase Equilibria: Application to Branched Alkanes.
</b>
<br>
<a href="https://pubs.acs.org/doi/10.1021/acs.jced.6b01036">M. Soroush Barhaghi, J. R. Mick and J. J. Potoff. Molec. Phys. 115, 1378-1388 (2017).</a>
<br>
</p>
</div>
</div>
<hr>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Optimized_Mie_Potentials_Application_to_Alkynes..png" alt="Optimized Mie Potentials, Application to Alkynes Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Optimized Mie Potentials for Phase Equilibria: Application to Alkynes.
</b>
<br>
<a href="https://www.tandfonline.com/doi/abs/10.1080/00268976.2017.1297862">M. Soroush Barhaghi, J. R. Mick and J. J. Potoff. Molec. Phys. 115, 1378-1388 (2017).</a>
<br>
<a href="https://www.tandfonline.com/doi/full/10.1080/00268976.2017.1323713">Special Issue of Molecular Physics in Honor of Professor Johann Fischer.</a>
<br>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2016</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Improving_performance_of_GPU_code.png" alt="Improving Performance of GPU Code Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Improving performance of GPU code using novel features of the NVIDIA kepler architecture.
</b>
<br>
<a href="http://onlinelibrary.wiley.com/doi/10.1002/cpe.3744/abstract;jsessionid=186D449D786613CE0BC8B6A20049043F.f02t02">Y. Li, L. Schwiebert, E. Hailat, J. Mick, and J. J. Potoff. Concurrency and Computation Practice and Experience, 28, 3586-3605 (2016).</a>
<br>
</p>
</div>
</div>
<hr>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Prediction_of_radon_222_phase.png" alt="Prediction of Radon-222 Phase Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Prediction of radon-222 phase behavior from Monte Carlo simulation.
</b>
<br>
<a href="http://pubs.acs.org/doi/abs/10.1021/acs.jced.5b01002">J. R. Mick, M. Soroush Barhaghi, and J. J. Potoff. J. Chem. Eng. Data 61, 1625-1631 (2016).</a>
<br>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2015</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Optimized_Mie_potentials_for_phase_equilibria_Application_to_noble_gases.png" alt="Optimized Mie Potentials for Phase Equilibria, Application to Noble Gasses">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Optimized Mie potentials for phase equilibria: Application to noble gases and their mixtures with n-alkanes.
</b>
<br>
<a href="http://aip.scitation.org/doi/abs/10.1063/1.4930138">J. Mick, M. Soroush Barhaghi, B. Jackman, K. Rushaidat, L. Schwiebert and J. Potoff. The Journal of Chemical Physics, 143, 114504 (2015).</a>
<br>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2014</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Mie_potentials_for_phase_equilibria_application_to_alkenes.png" alt="Mie Potentials for Phase Equilibria, Application to Alkenes">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Mie potentials for phase equilibria: application to alkenes.
</b>
<br>
<a href="http://pubs.acs.org/doi/abs/10.1021/je500202q">J. J. Potoff and G Kamath. J. Chem. Eng. Data 59, 3144-3150 (2014).</a>
<br>
<a href="https://pubs.acs.org/doi/10.1021/je500852y">Modeling and Simulation of Real Systems special issue.</a>
<br>
</p>
</div>
</div>
<hr>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Parallel_Monte_Carlo_Simulation_for_Canonical_Ensemble.png" alt="Parallel Monte Carlo Simulation for Canonical Ensemble">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Parallel Monte Carlo Simulation for Canonical Ensemble on the graphics processing unit.
</b>
<br>
<a href="http://www.tandfonline.com/doi/abs/10.1080/17445760.2013.833617">E. Hailat, V. Russo, J. Mick, K. Rushaidat, L. Schwiebert, and J. Potoff. International Journal of Parallel, Emergent, and Distributed Systems, 29(4), 379-400 (2014).</a>
<br>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2013</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/GPU_accelerated_Gibbs_ensemble_Monte_Carlo.png" alt="GPU-Accelerated Gibbs Ensemble Monte Carlo Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
GPU-accelerated Gibbs ensemble Monte Carlo simulations of Lennard-Jonesium.
</b>
<br>
<a href="http://www.sciencedirect.com/science/article/pii/S0010465513002270">J. R. Mick, E. Hailat, V. Russo, K. Rushaidat, L. Schwiebert, and J. J. Potoff. Computer Physics Communications, 184(12), 2662-2669 (2013).</a>
<br>
</p>
</div>
</div>
</div>
<div class="row">
<div class="blueBlock">
<p><a id="refereed">Refereed Conference and Workshop Publications</a></p>
</div>
<h3>2015</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Evaluation_of_Hybrid_Parallel_Cell_List.png" alt="Evaluation of Hybrid Parallel Cell List Algorithms Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Evaluation of Hybrid Parallel Cell List Algorithms For Monte Carlo Simulation.
</b>
<br>
<a href="http://ieeexplore.ieee.org/document/7336443/">K. Rushaidat, L. Schwiebert, B. Jackman, J. Mick, and J. Potoff. In Proceedings of The 7th IEEE International Workshop on Multicore and Multithreaded Architectures and Algorithms (M2A2 2015), New York, NY, August 2015.</a>
<br>
</p>
</div>
</div>
<hr>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Efficient_Parallel_Cell_List_Algorithms.png" alt="Efficient Parallel Cell List Algorithms Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Efficient Parallel Cell List Algorithms for Monte Carlo Simulations.
</b>
<br>
<a href="https://dl.acm.org/citation.cfm?id=2874986&preflayout=flat">K. Rushaidat, L. Schwiebert, B. Jackman, J. Mick, and J. Potoff. <i>In Proceedings of 2015 The Summer Simulation Multi-Conference</i> (SummerSim'15), Chicago, IL, July 2015.</a>
<br>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2013</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/GPU_based_Monte_Carlo_simulation_Gibbs_Ensemble.png" alt="GPU-Based Monte Carlo for Gibbs Ensemble Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
GPU-based Monte Carlo simulation for the Gibbs Ensemble.
</b>
<br>
<a href="https://dl.acm.org/citation.cfm?id=2499978">E. Hailat, K. Rushaidat, L. Schwiebert, J. R. Mick, and J. J. Potoff. High Performance Computing Symposium, April 2013.</a>
<br>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2012</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/GPU_Accelerated_Configurational_Bias_Monte_Carlo.png" alt="GPU Accelerated COnfigurational Bias Monte Carlo Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
GPU Accelerated Configurational Bias Monte Carlo Simulations of Linear Alkanes.
</b>
<br>
J. Mick, K. Rushaidat, E. Hailat, V. Russo, L. Schwiebert, and J. Potoff. AIChE Annual Meeting, paper no. 283711, October 2012.
<br>
</p>
</div>
</div>
<hr>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Optimization_Lennard_Jones_Particle.png" alt="Optimization of Lennard-Jones Particle Graphic">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
Optimization of a Lennard-Jones Particle Monte Carlo GPU Code.
</b>
<br>
<a href="http://www.sciencedirect.com/science/article/pii/S0010465513002270">J. Mick, E. Hailat, Y. Li, K. Rushaidat, L. Schwiebert, and J. Potoff. AIChE Annual Meeting, paper no. 283934, October 2012.</a>
<br>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2011</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/GPU_Accelerated_Monte_Carlo_Simulations_In_the_Gibbs_and_Canonical_Ensembles.png" alt="GPU Accellerated Monte Carlo, Gibbs and Canonical Ensembles">
</div>
<div class="column">
<p class="paragraphBlock">
<b>
GPU Accelerated Monte Carlo Simulations In the Gibbs and Canonical Ensembles.
</b>
<br>
J. Mick, J. Potoff, E. Hailat, V. Russo, and L. Schwiebert. AIChE Annual Meeting, October 2011.
<br>
</p>
</div>
</div>
</div>
<div class="row">
<div class="blueBlock">
<p><a id="posters">Posters</a></p>
</div>
<h3>2017</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Development_of_The_Parallel_Monte_Carlo_Simulation_Engine_GOMC.png" alt="Development of the Parallel Monte Carlo Simulation Engine Poster">
</div>
<div class="column">
<p class="paragraphBlock">
Mohammad S. Barhaghi, Jason Mick, Kamel Rushaidat, Runxuan Jiang, Brock Jackman, Yuanzhe Li, Younes Nejahi, Loren Schwiebert, and Jeffrey Potoff,
<a href="images/publications/Development_of_The_Parallel_Monte_Carlo_Simulation_Engine_GOMC.png">"Development of The Parallel Monte Carlo Simulation Engine GOMC". AIChE Annual Meeting October 2017.</a>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2015</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Development_of_a_GPU_Accelerated_Gibbs_Ensemble_Monte_Carlo_Simulation_Engine.png" alt="Development of a GPU Accelerated Gibbs Ensemble Monte Carlo Poster">
</div>
<div class="column">
<p class="paragraphBlock">
Mohammad S. Barhaghi, Jason Mick, Kamel Rushaidat, Brock Jackman, Yuanzhe Li, Younes Nejahi, Loren Schwiebert, and Jeffrey Potoff,
<a href="images/publications/Development_of_a_GPU_Accelerated_Gibbs_Ensemble_Monte_Carlo_Simulation_Engine.png">"Development of a GPU Accelerated Gibbs Ensemble Monte Carlo Simulation Engine". AIChE Annual Meeting October 2015.</a>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2013</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/A_Massively_Parallel_Implementation_for_the_Grand_Canonical_Monte_Carlo_Simulation.png" alt="A Massively Parallel Grand Canonical Monte Carlo Poster">
</div>
<div class="column">
<p class="paragraphBlock">
E. Hailat, J. Mick, K. Rushaidat, L. Schwiebert, and J. Potoff,
<a href="images/publications/A_Massively_Parallel_Implementation_for_the_Grand_Canonical_Monte_Carlo_Simulation.png">"A Massively Parallel Implementation for the Grand Canonical Monte Carlo Simulation," Wayne State University Graduate Exhibition, March 2013.</a>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2012</h3>
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<div class="column">
<img class="publicationImage" src="images/publications/GPU_Monte_Carlo_Developments_Biased_Gibbs_Ensemble_Alkane_Simulations_and_Architectural_Optimizations.png" alt="GPU Monte Carlo Developments: Biased Gibbs Ensemble Poster">
</div>
<div class="column">
<p class="paragraphBlock">
J. Mick, K. Rushaidat, E. Hailat, Y. Li, V. Russo, L. Schwiebert, and J. Potoff,
<a href="images/publications/GPU_Monte_Carlo_Developments_Biased_Gibbs_Ensemble_Alkane_Simulations_and_Architectural_Optimizations.png">"GPU Monte Carlo Developments: Biased Gibbs Ensemble Alkane Simulations and Architectural Optimizations," AIChE Annual Meeting, October 2012.</a>
</p>
</div>
</div>
<hr>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/GPU_Based_Monte_Carlo_Simulations_for_Canonical_and_Gibbs_Ensembles.png" alt="GPU-Based Monte Carlo, Canonical Gibbs Ensembles Poster">
</div>
<div class="column">
<p class="paragraphBlock">
E. Hailat, V. Russo, J. Mick, K. Rushaidat, L. Schwiebert, and J. Potoff,
<a href="images/publications/GPU_Based_Monte_Carlo_Simulations_for_Canonical_and_Gibbs_Ensembles.png">"GPU-Based Monte Carlo Simulations for Canonical and Gibbs Ensembles," 2012 GPU Technology Conference (GTC), May 2012.</a>
</p>
</div>
</div>
<hr class="siteBlue">
<h3>2011</h3>
<div class="row">
<div class="column">
<img class="publicationImage" src="images/publications/Accelerating_Simulations_in_the_Gibbs_and_Canonical_Ensembles_with_GPUs.png" alt="Accelerating Simulations in the Gibbs and Canonical Ensembles Poster">
</div>
<div class="column">
<p class="paragraphBlock">
J. Mick, E. Hailat, V. Russo, K. Rushaidat,L. Schwiebert, and J. Potoff,
<a href="images/publications/Accelerating_Simulations_in_the_Gibbs_and_Canonical_Ensembles_with_GPUs.png">"Accelerating Simulations in the Gibbs and Canonical Ensembles with GPUs," AIChE Annual Meeting, October 2011.</a>
</p>
</div>
</div>
</div>
<div class="row">
<div class="blueBlock">
<p><a id="technical">Technical Reports</a></p>
</div>
<h3>2014</h3>
<p class="paragraphBlock">
L. Schwiebert, E. Hailat, K. Rushaidat, J. Mick, and J. Potoff,
<a href="https://arxiv.org/abs/1408.3764">"An Efficient Cell List Implementation for Monte Carlo Simulation on GPUs," arXiv.org, August 2014</a>.
</p>
</div>
</div>
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