Skip to main content

Trinity College Dublin, The University of Dublin

Trinity Menu Trinity Search

You are here Postgraduate Research > Research Groups > Ultramicroscopy Group > Publications


Below is a list of recent publications with links to the publisher's websites. Many are also available from Google Scholar or ResearchGate. Most of this list is also available at: ORCID iD


Refereed Journal Articles

  • "Using Your Beam Efficiently: Reducing Electron Dose in the STEM via Flyback Compensation", Tiarnan Mullarky, Jonathan J. P. Peters, Clive Downing & Lewys Jones, Microscopy and Microanalysis (2022). DOI:10.1017/S1431927621013908.
  • "Ferroelectric incommensurate spin crystals", Dorin Rusu, Jonathan J. P. Peters et al., Nature, 602 (2022). DOI:10.1038/s41586-021-04260-1.


Book Chapter

  • "Scanning Transmission Electron Microscopy: Advanced Characterization Methods for Materials Science Applications", Edited by Alina Bruma, CRC Press (2021). ISBN:9780367197360.

Refereed Journal Articles

  • "Unlocking the Origin of Compositional Fluctuations in InGaN Light Emitting Diodes", Tara Mishra et al., Physical Review Materials, 5 (2021). DOI:10.1103/PhysRevMaterials.5.024605.
  • "A Fast Frozen Phonon Algorithm Using Mixed Static Potentials", Jonathan J. P. Peters, Ultramicroscopy, 229 (2021). DOI:10.1016/j.ultramic.2021.113364.
  • "Increasing Spatial Fidelity and SNR of 4D-STEM using Multi-frame Data Fusion", Colum M. O'Leary et al., Microscopy and Microanalysis, 1-11 (2021). DOI:10.1017/S1431927621012587.
  • "Prismatic 2.0–Simulation software for scanning and high resolution transmission electron microscopy (STEM and HRTEM)", Luis Rangel DaCosta et al., Micron, 151 (2021). DOI:10.1016/j.micron.2021.103141.


Refereed Journal Articles

  • "Development of a Practicable Digital Pulse Read-out for Dark-field STEM", Tiarnan Mullarkey, Clive Downing & Lewys Jones, Microscopy and Microanalysis (2020). DOI:10.1017/S1431927620024721.
  • "Towards data-driven next-generation transmission electron microscopy", Spurgeon et al., Nature Materials (2020). DOI:10.1038/s41563-020-00833-z.
  • "Measuring Dynamic Structural Changes of Nanoparticles at the Atomic Scale Using Scanning Transmission Electron Microscopy", De Backer et al., Physical Review Letters 124 10 (2020). DOI:10.1103/PhysRevLett.124.106105.
  • "Synthesis of tungsten ditelluride thin films and highly crystalline nanobelts from pre-deposited reactants", Mc Manus et al., Tungsten (2020). DOI:10.1007/s42864-020-00056-4.

Conference Proceedings

  • "Retaining Precision at Low-Dose and High-Speed STEM Imaging Conditions", Tiarnan Mullarkey, Clive Downing & Lewys Jones, Microscopy & Microanalysis (2020). DOI:10.1017/S1431927620023351.
  • "Probing the Dynamics of Topologically Protected Charged Ferroelectric Domain Walls with the Electron Beam at the Atomic Scale", Michele Conroy et al., Microscopy & Microanalysis (2020). DOI:10.1017/S1431927620023594.
  • "Comparison of Ptychography vs. Center-of-Mass Analysis of Registered 4D-STEM Series", Benedikt Haas et al., Microscopy & Microanalysis (2020). DOI:10.1017/S1431927620019765.
  • "3D Atomic Scale Quantification of Nanostructures and their Dynamics Using Model-based STEM", Sandra Van Aert et al., Microscopy & Microanalysis (2020). DOI:10.1017/S1431927620022163.
  • "Focused-probe STEM Ptychography: Developments and Opportunities", Colum O'Leary et al., Microscopy & Microanalysis (2020). DOI:10.1017/S1431927620014762.


Refereed Journal Articles

  • “Interstitial Boron Atoms in Palladium Lattice of Industrial Type of Nano-catalyst: Properties and Structural Modifications“, Chen et al., Journal of the American Chemical Society 141 50 (2019). DOI:10.1021/jacs.9b06120.
  • “Prospect for detecting magnetism of a single impurity atom using electron magnetic chiral dichroism“, Devendra Negi et al., Physical Review B 100 (2019). DOI:10.1103/PhysRevB.100.104434.
  • “Self-Assembly of Atomically Thin Chiral Copper Heterostructures Templated by Black Phosphorus“, Hannah Nerl et al., Advanced Functional Materials, 1903120 (2019). DOI:10.1002/adfm.201903120.
  • “Control of knock-on damage for 3D atomic scale quantification of nanostructures: Making every electron count in scanning transmission electron microscopy“, Sandra Van Aert, Annick De Backer, Lewys Jones, Gerardo T. Martinez, Armand Béché, and Peter D. Nellist, Physical Review Letters, 122 (2019), DOI:10.1103/PhysRevLett.122.066101.
  • “Targeted T1 MRI contrast enhancement with extraordinarily small CoFe2O4 nanoparticles“, Dominique Piché et al., ACS Applied Materials & Interfaces, 11 7 (2019). DOI: 10.1021/acsami.8b17162.

Conference Proceedings

  • “Investigating Ferroelectric Domain and Domain Wall Dynamics at Atomic Resolution by TEM/STEM in situ Heating and Biasing“, Michele Conroy et al., Microscopy and Microanalysis (S2) (2019). DOI:10.1017/S1431927619010146.
  • “Quantification of 3D Atomic Structures and Their Dynamics by Atom-Counting from an ADF STEM Image“, Annick De Backer et al., Microscopy and Microanalysis (S2) (2019). DOI:10.1017/S1431927619009772.


Refereed Journal Articles

  • “Managing dose-, damage- and data-rates in multi-frame spectrum-imaging“, Lewys Jones, Aakash Varambhia, Richard Beanland, Demie Kepaptsoglou, Ian Griffiths, Akimitsu Ishizuka, Feridoon Azough, Robert Freer, Kazuo Ishizuka, David Cherns, Quentin M. Ramasse, Sergio Lozano-Perez, and Peter D. Nellist, Microscopy, 67 (2018), DOI:10.1093/jmicro/dfx125.
  • “Maximising the resolving power of the scanning tunneling microscope“, Lewys Jones, Shuqiu Wang, Xiao Hu, Shams ur Rahman and Martin R. Castell, Advanced Structural and Chemical Imaging, 4:7 (2018), DOI:10.1186/s40679-018-0056-7.
  • “Proposal for a three-dimensional magnetic measurement method with nanometer spatial resolution“, Devendra Negi, Lewys Jones, Juan-Carlos Idrobo, and Jan Rusz, Physical Review B, 98:17 (2018), DOI:10.1103/PhysRevB.98.174409.
  • “An optical configuration for fastidious STEM detector calibration and the effect of the objective-lens prefield“, Lewys Jones, Aakash Varambhia, Hidetaka Sawada, and Peter D. Nellist, Journal of Microscopy, 270:2 (2018), DOI:10.1111/jmi.12672.
  • “Direct Observation of High Densities of Antisite Defects in Ag2ZnSnSe4“, David Cherns, Ian Griffiths, Lewys Jones, Douglas Bishop, Michael Lloyd and Brian McCandless, ACS Applied Energy Materials, 1:11 (2018), DOI:10.1021/acsaem.8b01274.
  • “Determining EDS and EELS partial cross-sections from multiple calibration standards to accurately quantify bi-metallic nanoparticles using STEM“, Aakash Varambhia, Lewys Jones, Andrew London, Dogan Ozkaya, Peter D. Nellist, Sergio Lozano-Perez, Micron, (in press), DOI:10.1016/j.micron.2018.06.015.
  • “Ideal vs real: Simulated annealing of experimentally derived and geometric platinum nanoparticles“, Tom Ellaby, Jolyon Aarons, Aakash Varambhia, Lewys Jones, Peter Nellist, Doğan Özkaya, Misbah Sarwar, David Thompsett and Chris-Kriton Skylaris, Journal of Physics: Condensed Matter, 30:15 (2018), DOI:10.1088/1361-648X/aab251.
  • “Subsampled STEM-Ptychography“, Andrew Stevens, Hao Yang, Weituo Hao, Lewys Jones, Colin Ophus, Peter D. Nellist and Nigel D. Browning, Applied Physics Letters 113:3 (2018), DOI:10.1063/1.5040496.

Conference Proceedings

  • “The MTF & DQE of Annular Dark Field STEM: Implications for Low-dose Imaging and Compressed Sensing“, Lewys Jones, Clive Downing, Microscopy and Microanalysis, 24:(S1) (2018), DOI:10.1017/S143192761800288X.
  • “Towards Nanometer-Scale Three-Dimensional Magnetic Studies with Atomic Size Electron Vortex Beams“, Jan Rusz, Devendra Negi, Lewys Jones, Juan-Carlos Idrobo, Microscopy and Microanalysis, 24:(S1) (2018), DOI:10.1017/S1431927618005081.
  • “Exploring the Limits of Focused-Probe STEM Ptychography“, Peter D. Nellist, Gerardo Martinez, Colmn O’Leary, Lewys Jones, Microscopy and Microanalysis, 24:(S1) (2018), DOI:10.1017/S1431927618001447.


Refereed Journal Articles

  • “Predicting the oxygen binding properties of platinum nanoparticle ensembles by combining high-precision electron microscopy & DFT”,Jolyon Aarons, Lewys Jones, Aakash Varambhia, Katherine E. MacArthur, Dogan Ozkaya, Misbah Sarwar, Chris-Kriton Skylaris, Peter D. Nellist, Nano Letters, 17(7) (2017), DOI:10.1021/acs.nanolett.6b04799.
  • “Three-dimensional atomic models from a single projection using Z-contrast imaging: verification by electron tomography and opportunities”, Annick De Backer, Lewys Jones, Ivan Lobato, Thomas Altantzis, Bart Goris, Peter D. Nellist, Sara Bals, and
    Sandra Van Aert, Nanoscale, 9 (2017), DOI:10.1039/c7nr02656k.
  • “Optimising Multi-frame ADF-STEM for High-precision Atomic-resolution Strain Mapping”, Lewys Jones, Sigurd Wenner, Magnus Nord, Per Harald Ninive, Ole Martin Løvvik, Randi Holmestad and Peter D. Nellist, Ultramicroscopy, 179 (2017), DOI:10.1016/j.ultramic.2017.04.007.
  • “Atomic-resolution chemical mapping of ordered precipitates in Al alloys using energy-dispersive X-ray spectroscopy”, Sigurd Wenner, Lewys Jones, Calin D. Marioara, Randi Holmestad, Micron, 96 (2017), DOI: 10.1016/j.micron.2017.02.007.
  • “Hybrid statistics-simulations based method for atom-counting from ADF STEM images”, Annelies De wael, Annick De Backer, Lewys Jones, Peter D. Nellist, Sandra Van Aert, Ultramicroscopy 177 (2017), DOI:10.1016/j.ultramic.2017.01.010.
  • “Route to achieving perfect B-site ordering in double perovskite thin films”, Josée E Kleibeuker, Eun-Mi Choi, Edward D Jones, Tse-Min Yu, Bianca Sala, Belinda A MacLaren, Demie Kepaptsoglou, David Hernandez-Maldonado, Quentin M Ramasse, Lewys Jones, Juri Barthel, Ian MacLaren and Judith L MacManus-Driscoll, NPG Asia Materials, 9 (2017), DOI:10.1038/am.2017.113.
  • “Electrochemical CO Oxidation at Platinum on Carbon Studied Through Analysis of Anomalous In Situ IR Spectra”, Ian McPherson, Philip Ash, Lewys Jones, Aakash Varambhia, Robert Jacobs, and Kylie Vincent, Journal of Physical Chemistry C (in press), DOI:10.1021/acs.jpcc.7b02166.
  • “3D Elemental Mapping with Nanometer Scale Depth Resolution via Electron Optical Sectioning”, Timothy Pennycook, Hao Yang, Lewys Jones, Mariona Cabero, Alberto Rivera-Calzada, Carlos Leon, Maria Varela, Jacobo Santamaria, Peter D. Nellist, Ultramicroscopy 174 (2017), DOI:10.1016/j.ultramic.2016.12.002.
  • “Electron ptychographic phase imaging of light elements in crystalline materials using Wigner distribution deconvolution”, Hao Yang, Ian MacLaren, Lewys Jones, Gerardo Martinez, Martin Simson, Martin Huth, Henning Ryll, Heike Soltau, Ryusuke Sagawa, Yukihito Kondo, Colin Ophus, Peter Ercius, Lei Jin, Andras Kovacs & Peter D. Nellist, Ultramicroscopy, 180 (2017) DOI:10.1016/j.ultramic.2017.02.006.

Conference Proceedings

  • “From High-precision Imaging to High-performance Computing: Leveraging ADF-STEM Atom-counting and DFT for Catalyst Nano-metrology”, Lewys Jones, Jolyon Aarons, Aakash Varambhia, Katherine E. MacArthur, Dogan Ozkaya, Misbah Sarwar, Chris-Kriton Skylaris, Peter D. Nellist, Microscopy and Microanalysis, 23(S1) (2017), DOI:10.1017/S1431927617010066.
  • “Mapping the Chemistry Within, and the Strain Around, Al-alloy Precipitates at Atomic Resolution by Multi-frame Scanning Transmission Electron Microscopy”, Lewys Jones, Sigurd Wenner, Magnus Nord, Per Harald Ninive, Ole Martin Løvvik, Calin D. Marioara, Randi Holmestad and Peter D. Nellist, Microscopy and Microanalysis23(S1) (2017), DOI:10.1017/S1431927617002604.
  • “Quantitative STEM of Catalyst Nanoparticles using ADF Imaging with Simultaneous EDS and EELS Spectroscopy”, Aakash M Varambhia, Lewys Jones, Annick De Backer, Sandra Van Aert, Dogan Ozkaya, Sergio Lozano-Perez, Peter D Nellist, Microscopy and Microanalysis23(S1) (2017), DOI:10.1017/S1431927617010108.
  • “Measuring the Cation and Oxygen Atomic Column Displacement at Picometer Precision”, Yi Wang, Lewys Jones, Benjamin Berkels, Wilfried Sigle and Peter A. van Aken, Microscopy and Microanalysis23(S1) (2017), DOI:10.1017/S1431927617008728.
  • “Towards a Direct Visualization of Charge Transfer in Monolayer Hexagonal Boron Nitride using a Fast Pixelated Detector in the Scanning Transmission Electron Microscope”, G.T. Martinez, T. J. Pennycook, T.C. Naginey, L. Jones, H. Yang, J.R. Yates, R.J. Nicholls, M. Huth, M. Simson, H. Soltau, L. Struder, Y. Kondo, R. Sagawa and P.D. Nellist. Microscopy and Microanalysis23(S1) (2017), DOI:10.1017/S1431927617002860.
  • “Development of Fast Pixelated STEM Detector and its Applications using 4-Dimensional Dataset”, Ryusuke Sagawa, Hao Yang, Lewys Jones, Martin Simson, Martin Huth, Heike Soltau, Peter D. Nellist and Yukihito Kondo, DOI:10.1017/S1431927617000940.