Publications

Papers

Peer-reviewed articles, preprints, and reports from 2006 to 2026. Filter by year or topic, or search across titles, authors, and keywords. You can also check the links below for the complete list.

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2026

ChemGraph as an agentic framework for computational chemistry workflows

Thang D. Pham, Aditya Tanikanti, Murat Keçeli

Communications Chemistry 9, 33 (2026)

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2026

ChemGraph-XANES: An Agentic Framework for XANES Simulation and Curation

Vitor F. Grizzi, Thang Duc Pham, Luke N. Pretzie, Jiayi Xu, Murat Keçeli, Cong Liu

RSC Advances 16, 56195–56207 (2026), arXiv:2604.16205

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2026

Data-Driven Discovery of Structure–Reactivity Relationships in Oxidative Addition at Zerovalent Nickel Centers

Sarah N. Elliott, Rosmi Reji, Qingzhi Chen, Xin Zheng, Simah Riaz, Xiaoli Yan, Thang Pham, Eliu Huerta, Ksenija D. Glusac, Murat Keçeli

ChemRxiv preprint (2026)

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2026

From atomistic models to machine learning: Predictive design of nanocarbons under extreme conditions

Xiaoli Yan, Millicent A. Firestone, Murat Keçeli, Santanu Chaudhuri, Eliu Huerta

Carbon 252, 121366 (2026)

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2026

From Knowledge to Action: Outcomes of the 2025 Large Language Models (LLM) Hackathon for Applications in Materials Science and Chemistry

2025 LLM Hackathon for Applications in Materials Science and Chemistry Participants

arXiv:2605.03205 (2026)

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2026

Improving Usability and Productivity of PETSc with Agent-Based Workflows

Barry Smith, Hong Zhang, Junchao Zhang, Satish Balay, Le Chen, Murat Keçeli, Lois Curfman McInnes

PEARC '26: Practice and Experience in Advanced Research Computing (2026)

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2026

Multi-Agent Orchestration for High-Throughput Materials Screening on a Leadership-Class System

Thang Duc Pham, Harikrishna Tummalapalli, Fakhrul Hasan Bhuiyan, Álvaro Vázquez-Mayagoitia, Christine Simpson, Riccardo Balin, Venkatram Vishwanath, Murat Keçeli

arXiv:2604.07681 (2026)

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2026

Overcoming Orchestration Bottlenecks at Exascale: A Decentralized, Policy-Driven Approach for Sim-AI Ensembles

Harikrishna Tummalapalli, Christine M. Simpson, Riccardo Balin, Vitali A. Morozov, Thang D. Pham, Murat Keçeli, Thomas D. Uram

arXiv:2607.12211 (2026)

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2025

AI Assistants to Enhance and Exploit the PETSc Knowledge Base

Barry Smith, Junchao Zhang, Hong Zhang, Lois Curfman McInnes, Murat Keçeli, Archit Vasan, Satish Balay, Toby Isaac, Le Chen, Venkatram Vishwanath

ICPP Workshops '25: Workshop Proceedings of the 54th International Conference on Parallel Processing, 9–17 (2025), arXiv:2506.20608

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2025

AskHPC: A ChatBot for High Performance Computing User Support

Akhilesh Bondapalli, Huihuo Zheng, Oluwaseun T. Ajayi, Murat Keçeli, Haritha Siddabathuni Som, Taylor Childers

SC Workshops '25 (2025)

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2025

EAIRA: Establishing a Methodology for Evaluating AI Models as Scientific Research Assistants

Franck Cappello, Sandeep Madireddy, Robert Underwood, Neil Getty, Nicholas Lee-Ping Chia, Nesar Ramachandra, Josh Nguyen, Murat Keçeli, Tanwi Mallick, Zilinghan Li, Marieme Ngom, Chenhui Zhang, Angel Yanguas-Gil, Evan Antoniuk, Bhavya Kailkhura, Minyang Tian, Yufeng Du, Yuan-Sen Ting, Azton Wells, Bogdan Nicolae, Avinash Maurya, M. Mustafa Rafique, Eliu Huerta, Bo Li, Ian Foster, Rick Stevens

International Journal of High Performance Computing Applications (2026)

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2025

Photochemical CO2 Reduction by a Postsynthetically Modified Zr-MOF

Rosmi Reji, Juan P. Vizuet, Xiaoli Yan, Biki K. Behera, Xin Zheng, Matthew Klenk, Nicholas P. Weingartz, George T. Kostopoulos, Lin X. Chen, Peter Zapol, Neeraj Agarwal, Eliu Huerta, Murat Keçeli, Santanu Chaudhuri, Ksenija D. Glusac

Inorganic Chemistry 64, 18304–18315 (2025)

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2025

Red Teaming for Generative AI, Report on a Copyright-Focused Exercise Completed in an Academic Medical Center

James Wen, Sahil Nalawade, Zhiwei Liang, Catherine Bielick, Marisa Ferrara Boston, Alexander Chowdhury, Adele Collin, Luigi De Angelis, Jacob Ellen, Heather Frase, Rodrigo R. Gameiro, Juan Manuel Gutierrez, Pooja Kadam, Murat Keçeli, Srikanth Krishnamurthy, Anne Kwok, Yanan Lance Lu, Heather Mattie, Liam G. McCoy, Katherine Miller, Allison C. Morgan, Marlene Louisa Moerig, Trang Nguyen, Alexander Owen-Post, Alex D. Ruiz, Sreekar Reddy Puchala, Soujanya Samineni, Takeshi Tohyama, Varun Ullanat, Carmine Valenza, Camilo Velez, Pengcheng Wang, Anna Wuest, Yuxiang Zhou, Yingde Zhu, Jason M. Johnson, Naomi Lenane, Jennifer Willcox, Francis J. Vitiello, Leo Anthony G. Celi, Renato Umeton

2025

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2025

Thermal conductivity limits of MoS2 and MoSe2: Revisiting high-order anharmonic lattice dynamics with machine learning potentials

Tuğbey Kocabaş, Murat Keçeli, Tanju Gürel, Milorad V. Milošević, Cem Sevik

Applied Physics Reviews 12, 041424 (2025)

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2024

Intro to HPC Bootcamp: Engaging New Communities Through Energy Justice Projects

Mary Ann Leung, Katharine Cahill, Rebecca Hartman-Baker, Paige Kinsley, Lois Curfman McInnes, Suzanne Parete-Koon, Sreeranjani Ramprakash, Subil Abraham, Lacy Beach Barrier, Gladys Chen, Lizanne DeStefano, Scott Feister, Sam Foreman, Daniel Fulton, Lipi Gupta, Yun He, Anjuli Jain Figueroa, Murat Keçeli, Talia Capozzoli Kessler, Kellen Leland, Charles Lively, Keisha Moore, Wilbur Ouma, Michael Sandoval, Rollin Thomas, Álvaro Vázquez-Mayagoitia

Journal of Computational Science Education 15, 49–56 (2024)

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2023

Gaussian approximation potentials for accurate thermal properties of two-dimensional materials

Tuğbey Kocabaş, Murat Keçeli, Álvaro Vázquez-Mayagoitia, Cem Sevik

Nanoscale 15, 8772 (2023)

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2023

High-Accuracy Heats of Formation for Alkane Oxidation: From Small to Large via the Automated CBH-ANL Method

Sarah N. Elliott, Murat Keçeli, Manik K. Ghosh, Kieran P. Somers, Henry J. Curran, Stephen J. Klippenstein

J. Phys. Chem. A 127, 1512–1531 (2023)

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2023

PluginPlay: Enabling Exascale Scientific Software One Module at a Time

Ryan M. Richard, Kristopher Keipert, Jonathan Waldrop, Murat Keçeli, David Williams-Young, Raymond Bair, Jeffery Boschen, Zachery Crandall, Kevin Gasperich, Quazi Ishtiaque Mahmud, Ajay Panyala, Edward Valeev, Hubertus van Dam, Wibe de Jong, Theresa L. Windus

J. Chem. Phys. (2023)

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2023

Systematically derived thermodynamic properties for alkane oxidation

Sarah N. Elliott, Kevin B. Moore III, Andreas V. Copan, Yuri Georgievskii, Murat Keçeli, Kieran P. Somers, Manik K. Ghosh, Henry J. Curran, Stephen J. Klippenstein

Combustion and Flame 257, 112487 (2023)

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2021

Automated theoretical chemical kinetics: Predicting the kinetics for the initial stages of pyrolysis

Sarah N. Elliott, Kevin B. Moore III, Andreas V. Copan, Murat Keçeli, Carlo Cavallotti, Yuri Georgievskii, Henry F. Schaefer III, Stephen J. Klippenstein

Proceedings of the Combustion Institute 38, 375–384 (2021)

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2021

Computation of the Thermal Expansion Coefficient of Graphene with Gaussian Approximation Potentials

İlker Demiroğlu, Yenal Karaaslan, Tuğbey Kocabaş, Murat Keçeli, Álvaro Vázquez-Mayagoitia, Cem Sevik

J. Phys. Chem. C 125, 14409–14415 (2021)

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2021

Exploring the anharmonic vibrational structure of carbon dioxide trimers

Jesus Ruiz, Kyle Misa, Arabi Seshappan, Murat Keçeli, Olaseni Sode

J. Chem. Phys. 154, 144302 (2021)

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2021

From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape

Karol Kowalski, Raymond Bair, Nicholas P. Bauman, Jeffery S. Boschen, Eric J. Bylaska, Jeff Daily, Wibe A. de Jong, Thom Dunning Jr., Niranjan Govind, Robert J. Harrison, Murat Keçeli, Kristopher Keipert, Sriram Krishnamoorthy, Suraj Kumar, Erdal Mutlu, Bruce Palmer, Ajay Panyala, Bo Peng, Ryan M. Richard, T. P. Straatsma, Peter Sushko, Edward F. Valeev, Marat Valiev, Hubertus J. J. van Dam, Jonathan M. Waldrop, David B. Williams-Young, Chao Yang, Marcin Zalewski, Theresa L. Windus

Chemical Reviews (2021)

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2020

ELSI — An open infrastructure for electronic structure solvers

Victor Wen-zhe Yu, Carmen Campos, William Dawson, Alberto García, Ville Havu, Ben Hourahine, William P. Huhn, Mathias Jacquelin, Weile Jia, Murat Keçeli, Raul Laasner, Yingzhou Li, Lin Lin, Jianfeng Lu, Jonathan Moussa, Jose E. Roman, Álvaro Vázquez-Mayagoitia, Chao Yang, Volker Blum

Computer Physics Communications 256, 107459 (2020)

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2019

Automated Computational Thermochemistry for Butane Oxidation: A Prelude to Predictive Automated Combustion Kinetics

Murat Keçeli, Sarah N. Elliott, Yi-Pei Li, Matthew S. Johnson, Carlo Cavallotti, Yuri Georgievskii, William H. Green, Matteo Pelucchi, Justin M. Wozniak, Ahren W. Jasper, Stephen J. Klippenstein

Proceedings of the Combustion Institute 37, 363–371 (2019)

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2019

Understanding the anharmonic vibrational structure of the carbon dioxide dimer

Samuel Maystrovsky, Murat Keçeli, Olaseni Sode

J. Chem. Phys. 150, 144302 (2019)

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2019

VALENCE: A Massively Parallel Implementation of the Variational Subspace Valence Bond Method

Graham D. Fletcher, Colleen Bertoni, Murat Keçeli, Michael D'Mello

J. Comput. Chem. 40, 1664–1673 (2019)

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2018

SIESTA-SIPs: Massively Parallel Spectrum-Slicing Eigensolver for an Ab Initio Molecular Dynamics Package

Murat Keçeli, Fabiano Corsetti, Carmen Campos, Jose E. Roman, Hong Zhang, Álvaro Vázquez-Mayagoitia, Peter Zapol, Albert F. Wagner

J. Comput. Chem. 39, 1806–1814 (2018)

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2018

The influence of surface functionalization on thermal transport and thermoelectric properties of MXene monolayers

Sevil Sarikurt, Deniz Çakır, Murat Keçeli, Cem Sevik

Nanoscale 10, 8859 (2018)

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2016

Shift-and-Invert Parallel Spectral Transformation Eigensolver: Massively Parallel Performance for Density-Functional Based Tight-Binding

Murat Keçeli, Hong Zhang, Peter Zapol, David A. Dixon, Albert F. Wagner

J. Comput. Chem. 37, 448–459 (2016)

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2012

Extensivity of Energy and Electronic and Vibrational Structure Methods for Crystals

So Hirata, Murat Keçeli, Yu-ya Ohnishi, Olaseni Sode, Kiyoshi Yagi

Annual Review of Physical Chemistry 63, 131–153 (2012)

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2010

Fast coupled-cluster singles and doubles for extended systems: Application to the anharmonic vibrational frequencies of polyethylene in the Γ approximation

Murat Keçeli, So Hirata

Physical Review B 82, 115107 (2010)

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2010

First-principles theories for anharmonic lattice vibrations

So Hirata, Murat Keçeli, Kiyoshi Yagi

J. Chem. Phys. 133, 034109 (2010)

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2009

Anharmonic vibrational frequencies and vibrationally-averaged structures of key species in hydrocarbon combustion: HCO+, HCO, HNO, HOO, HOO−, CH3+, and CH3

Murat Keçeli, Toru Shiozaki, Kiyoshi Yagi, So Hirata

Molecular Physics 107, 1283–1301 (2009)

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2009

Coupled-Cluster and Many-Body Perturbation Study of Energies, Structures, and Phonon Dispersions of Solid Hydrogen Fluoride

Olaseni Sode, Murat Keçeli, So Hirata, Kiyoshi Yagi

International Journal of Quantum Chemistry 109, 1928–1939 (2009)

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2007

Ansatz from nonlinear optics applied to trapped Bose–Einstein condensates

Murat Keçeli, F. Ö. Ilday, M. Ö. Oktel

Physical Review A 75, 035601 (2007)

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2006

Tkachenko modes and structural phase transitions of the vortex lattice of a two-component Bose–Einstein condensate

M. Keçeli, M. Ö. Oktel

Physical Review A 73, 023611 (2006)

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Supplementary materials are attached to their parent papers. Author-accepted PDFs are provided for personal, non-commercial use; please cite the published version.