% Publications of Murat Keçeli — generated from keceli.github.io

@article{2026_grizzi_chemgraph_xanes,
  title = {ChemGraph-XANES: An Agentic Framework for XANES Simulation and Curation},
  author = {Vitor F. Grizzi and Thang Duc Pham and Luke N. Pretzie and Jiayi Xu and Murat Keçeli and Cong Liu},
  journal = {arXiv:2604.16205 (2026)},
  year = {2026},
  eprint = {2604.16205},
  archivePrefix = {arXiv},
  keywords = {XANES, X-ray absorption spectroscopy, agentic AI, retrieval-augmented generation, FDMNES, Parsl, ChemGraph}
}

@article{2026_pham_multiagent_materials_screening,
  title = {Multi-Agent Orchestration for High-Throughput Materials Screening on a Leadership-Class System},
  author = {Thang Duc Pham and Harikrishna Tummalapalli and Fakhrul Hasan Bhuiyan and Álvaro Vázquez-Mayagoitia and Christine Simpson and Riccardo Balin and Venkatram Vishwanath and Murat Keçeli},
  journal = {arXiv:2604.07681 (2026)},
  year = {2026},
  eprint = {2604.07681},
  archivePrefix = {arXiv},
  keywords = {multi-agent systems, LLM agents, high-throughput screening, exascale, Aurora, workflow orchestration, AI for HPC}
}

@article{2026_pham_chemgraph,
  title = {ChemGraph as an agentic framework for computational chemistry workflows},
  author = {Thang D. Pham and Aditya Tanikanti and Murat Keçeli},
  journal = {Communications Chemistry 9, 33 (2026)},
  year = {2026},
  doi = {10.1038/s42004-025-01776-9},
  keywords = {agentic AI, large language models, computational chemistry workflows, machine-learning interatomic potentials, foundation models, automation}
}

@article{2026_roy_llm_hackathon_materials_chemistry,
  title = {From Knowledge to Action: Outcomes of the 2025 Large Language Models (LLM) Hackathon for Applications in Materials Science and Chemistry},
  author = {2025 LLM Hackathon for Applications in Materials Science and Chemistry Participants},
  journal = {arXiv:2605.03205 (2026)},
  year = {2026},
  eprint = {2605.03205},
  archivePrefix = {arXiv},
  keywords = {large language models, hackathon, materials science, chemistry, agentic workflows, community report, self-driving laboratories}
}

@article{2026_smith_petsc_agent_workflows,
  title = {Improving Usability and Productivity of PETSc with Agent-Based Workflows},
  author = {Barry Smith and Hong Zhang and Junchao Zhang and Satish Balay and Le Chen and Murat Keçeli and Lois Curfman McInnes},
  journal = {2026 (preprint/report)},
  year = {2026},
  keywords = {PETSc, LLM agents, retrieval-augmented generation, scientific software usability, numerical solvers, AI for HPC}
}

@article{2026_tummalapalli_ensemblelauncher,
  title = {Overcoming Orchestration Bottlenecks at Exascale: A Decentralized, Policy-Driven Approach for Sim-AI Ensembles},
  author = {Harikrishna Tummalapalli and Christine M. Simpson and Riccardo Balin and Vitali A. Morozov and Thang D. Pham and Murat Keçeli and Thomas D. Uram},
  journal = {arXiv:2607.12211 (2026)},
  year = {2026},
  eprint = {2607.12211},
  archivePrefix = {arXiv},
  keywords = {workflow orchestration, exascale, Aurora, simulation-AI ensembles, decentralized scheduling, HPC}
}

@article{2025_kocabas_mos2_mose2_thermal_conductivity,
  title = {Thermal conductivity limits of MoS2 and MoSe2: Revisiting high-order anharmonic lattice dynamics with machine learning potentials},
  author = {Tuğbey Kocabaş and Murat Keçeli and Tanju Gürel and Milorad V. Milošević and Cem Sevik},
  journal = {Applied Physics Reviews 12, 041424 (2025)},
  year = {2025},
  doi = {10.1063/5.0300627},
  keywords = {thermal conductivity, transition metal dichalcogenides, MoS2, MoSe2, anharmonic lattice dynamics, machine-learning potentials, phonons, 2D materials}
}

@article{2025_cappello_eaira,
  title = {EAIRA: Establishing a Methodology for Evaluating AI Models as Scientific Research Assistants},
  author = {Franck Cappello and Sandeep Madireddy and Robert Underwood and Neil Getty and Nicholas Lee-Ping Chia and Nesar Ramachandra and Josh Nguyen and Murat Keçeli and Tanwi Mallick and Zilinghan Li and Marieme Ngom and Chenhui Zhang and Angel Yanguas-Gil and Evan Antoniuk and Bhavya Kailkhura and Minyang Tian and Yufeng Du and Yuan-Sen Ting and Azton Wells and Bogdan Nicolae and Avinash Maurya and M. Mustafa Rafique and Eliu Huerta and Bo Li and Ian Foster and Rick Stevens},
  journal = {preprint (2025)},
  year = {2025},
  keywords = {AI evaluation, large language models, scientific research assistants, benchmarks, methodology, AI for science}
}

@article{2025_bondapalli_askhpc,
  title = {AskHPC: A ChatBot for High Performance Computing User Support},
  author = {Akhilesh Bondapalli and Huihuo Zheng and Oluwaseun T. Ajayi and Murat Keçeli and Haritha Siddabathuni Som and Taylor Childers},
  journal = {SC Workshops '25 (2025)},
  year = {2025},
  doi = {10.1145/3731599.3767433},
  keywords = {HPC user support, chatbot, retrieval-augmented generation, large language models, documentation, ALCF}
}

@article{2025_reji_zr_mof_co2_photoreduction,
  title = {Photochemical CO2 Reduction by a Postsynthetically Modified Zr-MOF},
  author = {Rosmi Reji and Juan P. Vizuet and Xiaoli Yan and Biki K. Behera and Xin Zheng and Matthew Klenk and Nicholas P. Weingartz and George T. Kostopoulos and Lin X. Chen and Peter Zapol and Neeraj Agarwal and Eliu Huerta and Murat Keçeli and Santanu Chaudhuri and Ksenija D. Glusac},
  journal = {Inorganic Chemistry 64, 18304–18315 (2025)},
  year = {2025},
  keywords = {metal-organic frameworks, CO2 reduction, photocatalysis, MOF-808, ruthenium complexes, DFT, X-ray absorption spectroscopy}
}

@article{2025_smith_petsc_ai_assistants,
  title = {AI Assistants to Enhance and Exploit the PETSc Knowledge Base},
  author = {Barry Smith and Junchao Zhang and Hong Zhang and Lois Curfman McInnes and Murat Keçeli and Archit Vasan and Satish Balay and Toby Isaac and Le Chen and Venkatram Vishwanath},
  journal = {arXiv:2506.20608 (2025)},
  year = {2025},
  eprint = {2506.20608},
  archivePrefix = {arXiv},
  keywords = {PETSc, knowledge base, retrieval-augmented generation, chatbots, scientific software, LLM assistants}
}

@article{2025_wen_red_teaming_generative_ai_copyright,
  title = {Red Teaming for Generative AI, Report on a Copyright-Focused Exercise Completed in an Academic Medical Center},
  author = {James Wen and Sahil Nalawade and Zhiwei Liang and Catherine Bielick and Marisa Ferrara Boston and Alexander Chowdhury and Adele Collin and Luigi De Angelis and Jacob Ellen and Heather Frase and Rodrigo R. Gameiro and Juan Manuel Gutierrez and Pooja Kadam and Murat Keçeli and Srikanth Krishnamurthy and Anne Kwok and Yanan Lance Lu and Heather Mattie and Liam G. McCoy and Katherine Miller and Allison C. Morgan and Marlene Louisa Moerig and Trang Nguyen and Alexander Owen-Post and Alex D. Ruiz and Sreekar Reddy Puchala and Soujanya Samineni and Takeshi Tohyama and Varun Ullanat and Carmine Valenza and Camilo Velez and Pengcheng Wang and Anna Wuest and Yuxiang Zhou and Yingde Zhu and Jason M. Johnson and Naomi Lenane and Jennifer Willcox and Francis J. Vitiello and Leo Anthony G. Celi and Renato Umeton},
  journal = {2025},
  year = {2025},
  keywords = {red teaming, generative AI, copyright compliance, AI safety, academic medical center, responsible AI}
}

@article{2024_leung_intro_hpc_bootcamp,
  title = {Intro to HPC Bootcamp: Engaging New Communities Through Energy Justice Projects},
  author = {Mary Ann Leung and Katharine Cahill and Rebecca Hartman-Baker and Paige Kinsley and Lois Curfman McInnes and Suzanne Parete-Koon and Sreeranjani Ramprakash and Subil Abraham and Lacy Beach Barrier and Gladys Chen and Lizanne DeStefano and Scott Feister and Sam Foreman and Daniel Fulton and Lipi Gupta and Yun He and Anjuli Jain Figueroa and Murat Keçeli and Talia Capozzoli Kessler and Kellen Leland and Charles Lively and Keisha Moore and Wilbur Ouma and Michael Sandoval and Rollin Thomas and Álvaro Vázquez-Mayagoitia},
  journal = {Journal of Computational Science Education (2024)},
  year = {2024},
  keywords = {HPC education, workforce development, energy justice, broadening participation, DOE, outreach}
}

@article{2023_elliott_alkane_oxidation_thermodynamics,
  title = {Systematically derived thermodynamic properties for alkane oxidation},
  author = {Sarah N. Elliott and Kevin B. Moore III and Andreas V. Copan and Yuri Georgievskii and Murat Keçeli and Kieran P. Somers and Manik K. Ghosh and Henry J. Curran and Stephen J. Klippenstein},
  journal = {Combustion and Flame 257, 112487 (2023)},
  year = {2023},
  keywords = {thermochemistry, combustion mechanisms, alkane oxidation, AutoMech, automated quantum chemistry, thermodynamic properties}
}

@article{2023_elliott_cbh_anl_heats_of_formation,
  title = {High-Accuracy Heats of Formation for Alkane Oxidation: From Small to Large via the Automated CBH-ANL Method},
  author = {Sarah N. Elliott and Murat Keçeli and Manik K. Ghosh and Kieran P. Somers and Henry J. Curran and Stephen J. Klippenstein},
  journal = {J. Phys. Chem. A 127, 1512–1531 (2023)},
  year = {2023},
  keywords = {thermochemistry, heats of formation, CBH-ANL, connectivity-based hierarchy, combustion, alkane oxidation, automation, high-accuracy quantum chemistry}
}

@article{2023_kocabas_gap_2d_thermal_properties,
  title = {Gaussian approximation potentials for accurate thermal properties of two-dimensional materials},
  author = {Tuğbey Kocabaş and Murat Keçeli and Álvaro Vázquez-Mayagoitia and Cem Sevik},
  journal = {Nanoscale 15, 8772 (2023)},
  year = {2023},
  doi = {10.1039/d3nr00399j},
  keywords = {Gaussian approximation potentials, machine-learning interatomic potentials, 2D materials, thermal properties, phonons, graphene, h-BN, molecular dynamics}
}

@article{2023_richard_pluginplay,
  title = {PluginPlay: Enabling Exascale Scientific Software One Module at a Time},
  author = {Ryan M. Richard and Kristopher Keipert and Jonathan Waldrop and Murat Keçeli and David Williams-Young and Raymond Bair and Jeffery Boschen and Zachery Crandall and Kevin Gasperich and Quazi Ishtiaque Mahmud and Ajay Panyala and Edward Valeev and Hubertus van Dam and Wibe de Jong and Theresa L. Windus},
  journal = {J. Chem. Phys. (2023)},
  year = {2023},
  doi = {10.1063/5.0147903},
  keywords = {scientific software engineering, modular frameworks, exascale, NWChemEx, plugins, software sustainability}
}

@article{2021_demiroglu_graphene_thermal_expansion_gap,
  title = {Computation of the Thermal Expansion Coefficient of Graphene with Gaussian Approximation Potentials},
  author = {İlker Demiroğlu and Yenal Karaaslan and Tuğbey Kocabaş and Murat Keçeli and Álvaro Vázquez-Mayagoitia and Cem Sevik},
  journal = {J. Phys. Chem. C 125, 14409–14415 (2021)},
  year = {2021},
  keywords = {graphene, thermal expansion, Gaussian approximation potentials, machine-learning potentials, molecular dynamics, 2D materials}
}

@article{2021_elliott_automech_pyrolysis_kinetics,
  title = {Automated theoretical chemical kinetics: Predicting the kinetics for the initial stages of pyrolysis},
  author = {Sarah N. Elliott and Kevin B. Moore III and Andreas V. Copan and Murat Keçeli and Carlo Cavallotti and Yuri Georgievskii and Henry F. Schaefer III and Stephen J. Klippenstein},
  journal = {Proceedings of the Combustion Institute 38, 375–384 (2021)},
  year = {2021},
  keywords = {AutoMech, automated kinetics, transition state theory, master equation, pyrolysis, combustion chemistry}
}

@article{2021_ruiz_co2_trimer_anharmonic,
  title = {Exploring the anharmonic vibrational structure of carbon dioxide trimers},
  author = {Jesus Ruiz and Kyle Misa and Arabi Seshappan and Murat Keçeli and Olaseni Sode},
  journal = {J. Chem. Phys. 154, 144302 (2021)},
  year = {2021},
  doi = {10.1063/5.0039793},
  keywords = {anharmonic vibrations, CO2 clusters, vibrational configuration interaction, VSCF, VMP2, many-body potential, van der Waals complexes}
}

@article{2021_kowalski_nwchem_to_nwchemex,
  title = {From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape},
  author = {Karol Kowalski and Raymond Bair and Nicholas P. Bauman and Jeffery S. Boschen and Eric J. Bylaska and Jeff Daily and Wibe A. de Jong and Thom Dunning Jr. and Niranjan Govind and Robert J. Harrison and Murat Keçeli and Kristopher Keipert and Sriram Krishnamoorthy and Suraj Kumar and Erdal Mutlu and Bruce Palmer and Ajay Panyala and Bo Peng and Ryan M. Richard and T. P. Straatsma and Peter Sushko and Edward F. Valeev and Marat Valiev and Hubertus J. J. van Dam and Jonathan M. Waldrop and David B. Williams-Young and Chao Yang and Marcin Zalewski and Theresa L. Windus},
  journal = {Chemical Reviews (2021)},
  year = {2021},
  doi = {10.1021/acs.chemrev.0c00998},
  keywords = {NWChem, NWChemEx, exascale computing, computational chemistry software, review, co-design, GPUs}
}

@article{2020_yu_elsi,
  title = {ELSI — An open infrastructure for electronic structure solvers},
  author = {Victor Wen-zhe Yu and Carmen Campos and William Dawson and Alberto García and Ville Havu and Ben Hourahine and William P. Huhn and Mathias Jacquelin and Weile Jia and Murat Keçeli and Raul Laasner and Yingzhou Li and Lin Lin and Jianfeng Lu and Jonathan Moussa and Jose E. Roman and Álvaro Vázquez-Mayagoitia and Chao Yang and Volker Blum},
  journal = {Computer Physics Communications 256, 107459 (2020)},
  year = {2020},
  keywords = {electronic structure, eigensolvers, ELSI, Kohn-Sham, SLEPc, density matrix solvers, HPC software infrastructure}
}

@article{2019_fletcher_valence_vsvb,
  title = {VALENCE: A Massively Parallel Implementation of the Variational Subspace Valence Bond Method},
  author = {Graham D. Fletcher and Colleen Bertoni and Murat Keçeli and Michael D'Mello},
  journal = {J. Comput. Chem. (2019)},
  year = {2019},
  keywords = {valence bond theory, VSVB, nonorthogonal orbitals, parallel electronic structure, open-source software, HPC}
}

@article{2019_keceli_butane_thermochemistry,
  title = {Automated Computational Thermochemistry for Butane Oxidation: A Prelude to Predictive Automated Combustion Kinetics},
  author = {Murat Keçeli and Sarah N. Elliott and Yi-Pei Li and Matthew S. Johnson and Carlo Cavallotti and Yuri Georgievskii and William H. Green and Matteo Pelucchi and Justin M. Wozniak and Ahren W. Jasper and Stephen J. Klippenstein},
  journal = {Proceedings of the Combustion Institute 37 (2019)},
  year = {2019},
  keywords = {automated thermochemistry, combustion, butane oxidation, conformer sampling, anharmonic corrections, high-performance computing, workflow automation}
}

@article{2019_maystrovsky_co2_dimer_anharmonic,
  title = {Understanding the anharmonic vibrational structure of the carbon dioxide dimer},
  author = {Samuel Maystrovsky and Murat Keçeli and Olaseni Sode},
  journal = {J. Chem. Phys. 150, 144302 (2019)},
  year = {2019},
  doi = {10.1063/1.5089460},
  keywords = {anharmonic vibrations, CO2 dimer, vibrational configuration interaction, many-body potential, van der Waals complexes, quartic force field}
}

@article{2018_keceli_siesta_sips,
  title = {SIESTA-SIPs: Massively Parallel Spectrum-Slicing Eigensolver for an Ab Initio Molecular Dynamics Package},
  author = {Murat Keçeli and Fabiano Corsetti and Carmen Campos and Jose E. Roman and Hong Zhang and Álvaro Vázquez-Mayagoitia and Peter Zapol and Albert F. Wagner},
  journal = {J. Comput. Chem. (2018)},
  year = {2018},
  keywords = {eigensolvers, spectrum slicing, SIESTA, SLEPc, PETSc, density functional theory, parallel scalability, ab initio molecular dynamics}
}

@article{2018_sarikurt_mxene_thermal_thermoelectric,
  title = {The influence of surface functionalization on thermal transport and thermoelectric properties of MXene monolayers},
  author = {Sevil Sarikurt and Deniz Çakır and Murat Keçeli and Cem Sevik},
  journal = {Nanoscale 10, 8859 (2018)},
  year = {2018},
  doi = {10.1039/c7nr09144c},
  keywords = {MXenes, thermoelectrics, lattice thermal conductivity, Seebeck coefficient, 2D materials, phonon Boltzmann transport, first principles}
}

@article{2016_keceli_sips_eigensolver_dftb,
  title = {Shift-and-Invert Parallel Spectral Transformation Eigensolver: Massively Parallel Performance for Density-Functional Based Tight-Binding},
  author = {Murat Keçeli and Hong Zhang and Peter Zapol and David A. Dixon and Albert F. Wagner},
  journal = {J. Comput. Chem. (2016)},
  year = {2016},
  keywords = {eigensolvers, spectrum slicing, SLEPc, DFTB, tight-binding, carbon nanotubes, massively parallel, sparse linear algebra}
}

@article{2012_hirata_extensivity_crystals,
  title = {Extensivity of Energy and Electronic and Vibrational Structure Methods for Crystals},
  author = {So Hirata and Murat Keçeli and Yu-ya Ohnishi and Olaseni Sode and Kiyoshi Yagi},
  journal = {Annual Review of Physical Chemistry 63, 131–153 (2012)},
  year = {2012},
  keywords = {size extensivity, size consistency, many-body theory, crystals, diagrammatic methods, vibrational structure theory, review}
}

@article{2010_hirata_anharmonic_lattice_vibrations,
  title = {First-principles theories for anharmonic lattice vibrations},
  author = {So Hirata and Murat Keçeli and Kiyoshi Yagi},
  journal = {J. Chem. Phys. 133, 034109 (2010)},
  year = {2010},
  keywords = {anharmonic lattice vibrations, vibrational self-consistent field, vibrational coupled cluster, quartic force field, phonons, size extensivity, periodic systems}
}

@article{2010_keceli_fast_ccsd_extended_systems,
  title = {Fast coupled-cluster singles and doubles for extended systems: Application to the anharmonic vibrational frequencies of polyethylene in the Γ approximation},
  author = {Murat Keçeli and So Hirata},
  journal = {Physical Review B 82, 115107 (2010)},
  year = {2010},
  keywords = {coupled cluster, periodic systems, Brillouin-zone sampling, polyethylene, anharmonic vibrations, electron correlation, polymers}
}

@article{2009_keceli_anharmonic_combustion_species,
  title = {Anharmonic vibrational frequencies and vibrationally-averaged structures of key species in hydrocarbon combustion: HCO+, HCO, HNO, HOO, HOO−, CH3+, and CH3},
  author = {Murat Keçeli and Toru Shiozaki and Kiyoshi Yagi and So Hirata},
  journal = {Molecular Physics 107, 1283–1301 (2009)},
  year = {2009},
  keywords = {anharmonic vibrational frequencies, combustion intermediates, radicals, coupled cluster, quartic force field, vibrationally averaged structures, spectroscopy}
}

@article{2009_sode_solid_hf_coupled_cluster,
  title = {Coupled-Cluster and Many-Body Perturbation Study of Energies, Structures, and Phonon Dispersions of Solid Hydrogen Fluoride},
  author = {Olaseni Sode and Murat Keçeli and So Hirata and Kiyoshi Yagi},
  journal = {International Journal of Quantum Chemistry 109, 1928–1939 (2009)},
  year = {2009},
  doi = {10.1002/qua.22022},
  keywords = {molecular crystals, solid hydrogen fluoride, coupled cluster, many-body expansion, phonon dispersion, anharmonic vibrations, hydrogen bonding}
}

@article{2007_keceli_nonlinear_optics_ansatz_bec,
  title = {Ansatz from nonlinear optics applied to trapped Bose–Einstein condensates},
  author = {Murat Keçeli and F. Ö. Ilday and M. Ö. Oktel},
  journal = {Physical Review A (2007)},
  year = {2007},
  keywords = {Bose-Einstein condensates, Gross-Pitaevskii equation, variational ansatz, nonlinear optics, similariton, ultracold atoms}
}

@article{2006_keceli_tkachenko_modes_two_component_bec,
  title = {Tkachenko modes and structural phase transitions of the vortex lattice of a two-component Bose–Einstein condensate},
  author = {M. Keçeli and M. Ö. Oktel},
  journal = {Physical Review A (2006)},
  year = {2006},
  keywords = {Bose-Einstein condensates, vortex lattices, Tkachenko modes, quantum Hall regime, elastic constants, structural phase transitions, ultracold atoms}
}