Research

Main research topics

My research sits at the intersection of machine learning, molecular dynamics, and NMR spectroscopy. Working in the group of Dr. Perttu Lantto at the NMR Research Unit, University of Oulu, I develop atomistic models that bridge quantum-mechanical accuracy and the long timescales required to interpret experimental measurements in complex materials.

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Overview
Machine learning interatomic potentials (MLIPs) allow quantum-mechanical accuracy to be achieved at a fraction of the cost of direct DFT calculations, enabling simulations at experimentally relevant timescales and system sizes. My work focuses on training and fine-tuning equivariant GNN potentials for complex inorganic and molecular systems.
Related publications
Local Symmetry Breaking and Two-Stage Phase Transition in RuP Uncovered by a Fine-Tuned Atomistic Foundation Model
ChemRxiv 2026  ·  Preprint
Zakary, O.; Yin, W.; Aryal, N.
DOI: 10.26434/chemrxiv.15001387/v1
Equivariant Neural Networks Reveal How Host–Guest Interactions Shape 129Xe NMR in Porous Liquids
J. Phys. Chem. Lett. 2025, 16, 12095–12103
Zakary, O.; Lantto, P.
DOI: 10.1021/acs.jpclett.5c02846
Machine Learning-Accelerated Path Integral Molecular Dynamics and 13C NMR Simulations Unlock New Insights into Quantum Effects in C60 Fullerene
J. Phys. Chem. A 2026, 130, 2169–2181
Laurila, O.; Jacklin, T.; Zakary, O.; Lantto, P.
DOI: 10.1021/acs.jpca.6c00238
Related software
RuP project
GitHub: data-RuP
Porous liquids project
GitHub: data-Xe_at_CC3_at_TBA
C60 fullerene project
GitHub: data-C60_ML
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Overview
Classical molecular dynamics treats nuclei as point particles, neglecting quantum effects such as zero-point energy and tunneling that are particularly important for light nuclei and at low temperatures. Path integral molecular dynamics (PIMD) addresses this by representing each nucleus as a ring polymer of classical beads, recovering quantum statistical mechanics exactly in the limit of many beads. My work combines PIMD with ML interatomic potentials to make quantum nuclear simulations tractable for large systems.
Related publications
Machine Learning-Accelerated Path Integral Molecular Dynamics and 13C NMR Simulations Unlock New Insights into Quantum Effects in C60 Fullerene
J. Phys. Chem. A 2026, 130, 2169–2181
Laurila, O.; Jacklin, T.; Zakary, O.; Lantto, P.
DOI: 10.1021/acs.jpca.6c00238
Related software
C₆₀ fullerene project
GitHub: data-C60_ML
PIMD GUI for teaching
GitHub: water-pimd-simulations
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Overview
NMR spectroscopy is one of the most powerful probes of local structure and dynamics in materials, but first-principles computation of NMR parameters is expensive, limiting achievable statistical sampling. I develop NMR-ML models that predict NMR parameters for various nuclei at a fraction of the computational cost. A key focus is xenon NMR in porous liquids and carbon nanoporous materials.
Related publications
Equivariant Neural Networks Reveal How Host–Guest Interactions Shape 129Xe NMR in Porous Liquids
J. Phys. Chem. Lett. 2025, 16, 12095–12103
Zakary, O.; Lantto, P.
DOI: 10.1021/acs.jpclett.5c02846
Related software
Porous liquids project
GitHub: data-Xe_at_CC3_at_TBA
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Overview
This part of my research goes back to my PhD period and it deals with the precise structural characterization of disordered inorganic oxyfluorides, making conventional diffraction techniques insufficient for full structural resolution. By combining multi-nuclear solid-state NMR spectroscopy of various nuclei, including 19F, 1H, 23Na, 87Rb, and 93Nb, powder X-ray diffraction, and DFT calculations, I build and validate structural models that capture both the average and the short-range crystal structures. This NMR crystallography strategy has been applied to transition metal oxyfluorides, revealing preferential anion ordering, correlated disorder, and second-order Jahn-Teller distortions that govern the physicochemical properties of these materials.
Related publications
Revealed Preferential Short-Range Anion Ordering in Disordered RbM2O5F (M = Nb, Ta) Pyrochlore-Type Oxyfluorides
Inorg. Chem. 2025, 64, 5764–5777
Zakary, O.; Body, M.; Sarou-Kanian, V.; Charpentier, T.; Legein, C.
DOI: 10.1021/acs.inorgchem.5c00615
Different Magnitudes of Second-Order Jahn-Teller Effect in Isostructural NaMO2F2 (M = Nb, Ta) Oxyfluorides
J. Alloys Compd. 2025, 1010, 177457
Zakary, O.; Body, M.; Sarou-Kanian, V.; Arnaud, B.; Corbel, G.; Legein, C.
DOI: 10.1016/j.jallcom.2024.177457
Structural Modeling of O/F Correlated Disorder in TaOF3 and NbOF3-x(OH)x by Coupling Solid-State NMR and DFT Calculations
Inorg. Chem. 2023, 62, 16627–16640
Zakary, O.; Body, M.; Charpentier, T.; Sarou-Kanian, V.; Legein, C.
DOI: 10.1021/acs.inorgchem.3c02844
Related software
Pyrochlore oxyfluorides project
GitHub: data-RbM2O5F
Ordered oxyfluorides project
GitHub: data-NaMO2F2
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Overview
Deploying ML potentials at scale requires careful integration with HPC infrastructure. I develop and document production-ready workflows for running packages on both AMD ROCm (LUMI) and NVIDIA CUDA (Mahti and Puhti) architectures, resolving compatibility issues between ML libraries, MPI implementations, and GPU backends. These workflows are made publicly available.
Related resources
RuP project
GitHub: data-RuP
MD simulations trajectory slicer
GitHub: TrajSlicer
NMR parameters extraction from VASP output files
GitHub: NMR-VASP
All repositories and workflow documentation
github.com/ozakary

Working with Dr. Perttu Lantto, NMR Research Unit, University of Oulu (NMR-RU UO). Collaborating with Prof. Ville-Veikko Telkki (NMR-RU UO) and Dr. Niraj Aryal (Brookhaven National Laboratory, Upton, New York, USA).

© 2026 Ouail Zakary  ·  ozakary.github.io