The Muon Spectroscopy Computational Project

Publications

• Electronic structure calculations for muon spectroscopy
  Electron. Struct. 7 023001, (2025)
  Muon spectroscopy has become a leading tool for the investigation of local magnetic fields in condensed matter physics, finding applications in the study of superconductivity, magnetism, ionic diffusion in battery materials, and numerous other fields. Though the muon yields quantitative information about the material, this can only be fully interpreted if the nature of the muon site and its stability is fully understood. Electronic structure calculations are of paramount importance for providing this understanding, particularly through a group of techniques that has become known as DFT, density functional theory including the presence of the implanted muon. We describe how these electronic structure calculations can be used to underpin muon spectroscopy, and some examples of the science that follows from this, as well as some of the available software tools that are currently being developed.

• Facilitating Reproducibility in Catalysis Research with Managed Workflows and RO-Crates: A Galaxy Case Study
  ChemCatChem(2025)
  Publishing supporting data significantly impacts researchers’ productivity, especially in experiments requiring extensive tracking of data, processing steps, parameters, and outputs. A managed workflow environment, combined with RO-Crates, addresses these data management challenges. Workflows provide an alternative for handling complex data analyses by orchestrating various processing tools. The RO-Crate format, a community-driven proposal for packaging data, provenance, and workflows, facilitates publishing and reproducibility. The Galaxy workflow management system integrates workflows and RO-Crates, enabling the export of analyses, which can be shared and restored by other users. Using Galaxy, we demonstrate how to improve support for reproducibility. We tested our approach by designing an experiment using diverse supporting data from selected papers. In the experiment, we identified specific FAIRness and completeness issues hindering result reproduction, even when authors made significant efforts to document and publish their supporting data. In comparison, the proposed approach supports reproducibility by packaging datasets in RO-Crate format, streamlining the process. The Galaxy RO-Crates, published as supporting materials, enhance data sharing, transparency, and reproducibility, thus supporting the advancement of FAIR research practices in catalysis research.

• Hydrogen Radical Chemistry at High-Symmetry {2Fe2S} Centers Probed Using a Muonium Surrogate
  Inorg. Chem. 64, 10, 5053–5058,(2025)
  In this work, we used muon experiments and theoretical simulations to study redox-active metal hydrides, which are of central importance in the development of novel hydrogen generation catalysts. Direct insight into open-shell hydrides is, however, difficult to obtain. One approach to gain this information is to use muonium (Mu• = μ+ e–) as a surrogate for the hydrogen radical. The chemistry of Mu• is analogous to H•, but Mu• can provide unique information about hyperfine couplings and thus molecular structure. Using this approach, we demonstrated here that the high-symmetry {2Fe2S} systems Fe2(edt)(CO)4L2 (edt = ethane-1,2-dithiolato; L = CO, PMe3, CN–) form bridging radicals directly on the time scale of the muon experiment. We also extend our computational approach to detail all of the possible addition sites in solid state samples.

• Triple Magnetic Stacking in an Iron-Containing Cuprate with Cu–Fe–Cu Magnetic Blocks
  Chem. Mater. 36, 17, 8199–8207, (2024)
  In this work, we performed a combined experimental-theoretical study of the iron-substituted FeSr2YCu2O7.08 cuprate, which displays long-range magnetic ordering below TN ∼ 140 K, involving both Fe3+ cations in the charge reservoir block (CRB) and Cu2+ cations in the CuO2 planes. The magnetic structure comprises antiferromagnetic in-plane coupling within the FeO and the CuO2 layers, but a ferromagnetic coupling along the stacking direction. The observation of this new magnetic structure for a M-1212 type cuprate opened up new possibilities for exploring the interplay between magnetic and superconducting interactions in classical layered cuprates

• Hidden magnetism uncovered in a charge ordered bilayer kagome material ScV₆Sn₆
  Nat Commun 14, 7796, (2023)
  Here, we present the discovery of an unexpected hidden magnetism of the charge order for the recently discovered charge ordered kagome material - ScV₆Sn₆ using advanced muon-spin rotation spectroscopy. An enhancement was observed in the internal field width sensed by the muon ensemble, which takes place within the charge ordered state. Furthermore, the muon spin relaxation rate below the charge ordering temperature is substantially enhanced by applying an external magnetic field. Taken together with the hidden magnetism found in AV₃Sb₅ (A = K, Rb, Cs) and FeGe kagome systems, our results suggest ubiquitous time-reversal symmetry-breaking in charge ordered kagome lattices.

• Magnetic structure and crystal field states of Pr₂Pd₃Ge₅: μSR and neutron scattering investigations
  Phys.Rev.B 107,104412, (2023)
  In this work, we present the results of muon spin relaxation (μSR), powder neutron diffraction, and inelastic neutron scattering investigations on polycrystalline Pr₂Pd₃Ge₅. The material exhibits dual antiferromagnetic transitions, confirmed by heat capacity measurements. Our findings reveal a canted antiferromagnetic structure of ordered Pr³⁺ moments. The internal field calculations at muon stopping sites predicted by DFT calculation are in good agreement with experimental observations. In the paramagnetic state, 3 crystal electric field excitations were identified arising from the crystal electric field split J=4 ground state of Pr³⁺.

• MuSpinSim: spin dynamics calculations for muon science
  J. Phys.: Conf. Ser. 2462 012017, (2023)
  In this work, we present muspinsim: an open-source python package to simulate the spin dynamics of a system of a muon along with other spins such as electrons and atomic nuclei. All of its utilities to facilitate µSR experiments are also detailed.

• Low-temperature magnetic crossover in the topological kagome magnet TbMn₆Sn₆
  Communications Physics volume 5, Article number: 107, (2022)
  Here, we explore magnetic correlations in the recently identified topological kagome system TbMn₆Sn₆ using muon spin rotation, combined with local field analysis and neutron diffraction. Our studies identify an out-of-plane ferrimagnetic structure with slow magnetic fluctuations which exhibit a critical slowing down below T^*_C1 ≃ 120 K and finally freeze into static patches with ideal out-of-plane order below T_C1 ≃ 20 K.

• Observation of a molecular muonium polaron and its application to probing magnetic and electronic states
  Phys.Rev.B 104,064429, (2021)
  Here, we give evidence for the detection of a muonium state that propagates in a molecular semiconductor lattice via thermally activated dynamics: a muonium polaron.

• MuDirac: A Dirac equation solver for elemental analysis with muonic X‐rays
  X-Ray Spectrometry,1–17, (2020)
  In this work, we present MuDirac: a new open‐source software for the integration of the radial Dirac equation developed specifically for muonic atoms. The software can be used to predict frequencies and transitions probabilities between levels of the muonic atom, which are useful for the interpretation of muonic X‐ray spectra in elemental analysis.

• Computational prediction of muon stopping sites: A novel take on the unperturbed electrostatic potential method
  The Journal of Chemical Physics, 153, 044111, (2020)
  In this work, we present a software implementation of the Unperturbed Electrostatic Potential (UEP) Method: an approach used for finding the muon stopping site in crystalline materials. The UEP method requires only one DFT calculation, necessary to compute the electronic density of the host material.

• A Muon Spectroscopic and Computational Study of the Microscopic Electronic Structure in Thermoelectric Hybrid Silicon Nanostructures
  J. Phys. Chem. C, 124, 18, 9656–9664, (2020)
  Phenylacetylene-capped silicon nanoparticles have attracted interest as a novel thermoelectric material. In this paper, we report a combined muon spectroscopic (μSR) and computational study of this material in solution to investigate the microscopic electronic structure of this system.

• Comparison between Density Functional Theory and Density Functional Tight Binding approaches for finding the muon stopping site in organic molecular crystals
  The Journal of Chemical Physics, 150, 154301, (2019)
  Expanding on our previous use of AIRSS to find the muon stopping site, this paper focuses on its application to organic molecules and shows how the tight binding software DFTB+, combined with the 3ob-3-1 parameter set, can produce satisfying results for it in a fraction of the time required by DFT simulations.

• Computational Prediction of Muon Stopping Sites Using AIRSS
  The Journal of Chemical Physics, 148, 134114, (2018)
  The stopping site of the muon in a muon-spin relaxation experiment (µ+SR) is generally unknown and there are few techniques that can be used to determine the muon stopping site. In this work, we propose a purely theoretical method that can be used to predict muon stopping sites in crystalline materials using only computer simulations.

• Exploring the Temperature Dependent Solid-State ALC Spectrum of the C₆H₆Mu^• Radical with Ab-Initio Simulation Techniques
  JPS Conf. Proc. 21, 011036, (2018)
  In this work, we used a number of different computational techniques to study the temperature dependence of the Avoided Level Crossing spectrum of crystalline benzene.

Selected Presentations

• Developing sustainable software tools for large-scale facilities using the Galaxy platform
  Presentation at the 2025 Psi-K conference, Laussane, Switzerland, 25-28 August 2025.

• Managing materials science workflows with Galaxy at STFC
  Presentation at Galaxy and Bioconductor Community Conference 2025 (GBCC2025), Cold Spring Harbor, 23–26 June 2025.

• Galaxy for X-Rays
  Presentation at the 2024 NoBugs event, Grenoble, France. 23-27 September 2024.

• The Galaxy Platform: Applications to Catalysis Workflows
  Presentation at the 2024 Galaxy Conference, June 24-29, 2024, Brno, Czech Republic.

• SONAR 1: First Workshop on SOftware for NegAtive-muon Research
  Presentation at the SONAR 1: First Workshop on SOftware for NegAtive-muon Research.

• DAPHNE4NFDI Task Area 3 seminars
  Presentation given for one of DAPHNE4NFDI Task Area 3 seminars.

• Finding the Muon Stopping Site: pymuon-suite in​ Galaxy​
  Muon User Meeting 2023: celebrating the work of Pabitra Biswas. 11-12 September, 2023, The Queens College, Oxford, UK.

• Applications to Catalysis Workflows​
  European Galaxy Days (EGD). 4-6 October, 2023, Freiburg, Germany.

• Galaxy workflow tools for processing and analysis of catalysis data (Short Lecture)​
  Presentation to the Catalysis Hub. 2 November, 2023, Harwell, UK.

• Galaxy workflow tools for processing and analysis of catalysis data (Flash Pitch)
  Presentation to the Catalysis Hub. 2 November, 2023, Harwell, UK.

• Computational Techniques to Support Muon Science: the Muon Spectroscopy Computational Project at ISIS
  Japan Proton Accelerator Research Complex (J-PARC). 4 August, 2023.

• Computing Simulations for Large Scale Experiments: the Case of Muons​
  Presentation to the Catalysis Hub. 18 July, 2023, Harwell, UK.

• Galaxy and Scientific Communities: How to Incorporate New Ones, Uplift Engaged Ones and Maintain Mature Ones​
  THE PASC23 CONFERENCE 2023. 26-28 June, 2023.

• Muon Galaxy – an open web platform for computational muon science
  NOBUGS 2022. 19-22 September, 2022.

• Muon Galaxy: Facilitating FAIR data analysis in muon science
  RSECon 2022. 6-8 September, 2022.

• MuSpinSim: spin dynamics calculations for muon science
  15th International Conference on Muon Spin Rotation, Relaxation and Resonance. 28 August - 2 September, 2022.

• Muon Galaxy: Extending Galaxy for Muon Science
  Galaxy Community Conference 2021 (Virtual Edition). 28 June - 10 July, 2021.

• Scientific Computing for Muons: the Muon Spectroscopy Computational Project
  Muon Jamboree! (Virtual Edition). 13-16 December, 2021.

• The Ada Lovelace Project on Muon Spectroscopy
  2020 Edition Muon Site Calculation Meeting (Virtual Edition). 4 September, 2020.

• Computer Simulations for Interpreting μSR Experiments
  International Advanced School on Muon Spectroscopy. 15-22 August 2019, Rutherford Appleton Laboratory, Harwell, UK.

• Computer Simulations for Interpreting μSR Experiments
  The 2018 ISIS Muon Spectroscopy Training School. 22 March 2018, Rutherford Appleton Laboratory, Harwell, UK.

• CalcALC: a user tool for predicting and interpreting ALC and QLCR spectra
  Muon Spectroscopy User Meeting: Future Developments and Site Calculations. 17 July 2018, The Cosener’s House, Abingdon, UK.

• Computer Simulations for Interpreting µSR Experiments: Beyond DFT
  Muon Spectroscopy User Meeting: Future Developments and Site Calculations. 17 July 2018, The Cosener’s House, Abingdon, UK.

• Computational Prediction of Muon Stopping Sites in Silicon
  The 14th International Conference on Muon Spin Rotation, Relaxation and Resonance. 30 June 2017, Sapporo, Japan.

Lecture Events

• Using the Galaxy Platform in Large Scale Experiments

• SONAR 1: First Workshop on SOftware for NegAtive-muon Research
  Event organised in conjunction with the ISIS Neutron Source and Technion Israel.

• Finding the muon stopping site with pymuon-suite in Galaxy
  Lecture give at the 2024 ISIS Muon Training School.

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