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OCF supercomputer

Publications using the Bede Supercomputer

Publications resulting from researchers using the Bede supercomputer

2021 2022 2023 2024

2026

  • B. Thorpe, M.J. Smith, P.J. Hasnip, and N.D. Drummond. Acceleration of the CASINO quantum Monte Carlo software using graphics processing units and OpenACC. Comp. Phys. Comm. 319 (2026) 109900 doi: 10.1016/j.cpc.2025.109900

    2025

  • Yousef Ghaffari Motlagh, Farshid Fathi, John C. Brigham, & Peter K. Jimack. Deep learning for inverse material characterization. Computer Methods in Applied Mechanics and Engineering, 436, 1 March 2025, 117650. https://doi.org/10.1016/j.cma.2024.117650

  • M Burman and A Noy. Atomic description of the reciprocal action between supercoils and melting bubbles on linear DNA.Phys Rev Lett, 134, 038403 https://doi.org/10.1103/PhysRevLett.134.038403.

  • C Grey, SP Niblett, P Kourtis, IB Magdau, G Csyanyi. Transferability of datasets between machine-learned interaction potential algorithms. repository.cam.ac.uk https://www.repository.cam.ac.uk/items/4a6add8b-f5b4-4701-99bc-981952f01530

  • U Dey, EE McCabe, J Íñiguez-González. Prediction of roon temperature electric field reversal of magnetization in the family of A4B3O9 layered oxides. Physical Review Letters https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.134.136801

  • B Lei, H Zhang, D Seipt, A Bonatto, B Qiao Coherent synchrotron radiation by excitation of surface plasmon polariton on near-critical solid microtube surface. arXiv preprint. https://arxiv.org/abs/2507.04561

  • M Rezayani, F Sharif, H Makki Dynamic bonds transform ion transport mechanisms in polymeric covalent adaptable networks. Materials Horizons https://pubs.rsc.org/en/content/articlehtml/2025/mh/d5mh00433k

  • V Velasco-Berrelleza, TE Catley, DE Rollins, ALB Pyne. Imaging and mechanism of DNA-DNA recognition mediated by divalent ions. bioRxiv https://www.biorxiv.org/content/10.1101/2025.09.11.675610.abstract

  • H Yin, S You, J Han, Z Chen. Sequential Joint Dependency Aware Human Pose Estimation with State Space Model Proceedings of the AAAI Conference on Artificial Intelligence https://ojs.aaai.org/index.php/AAAI/article/view/33029

  • WG Poole, ML Samways, D Branduardi. Accelerating fragment-based drug discovery using grand canonical nonequilibrium candidate Monte Carlo. Nature https://www.nature.com/articles/s41467-025-60561-3

  • SM Mousavifard, M Mohseni, H Yahyaei. Water exchangeability between pore volumes: a key mechanism governing water diffusion in highly cross-linked polymer coatings. Progress in Organic Coatings. https://doi.org/10.1016/j.porgcoat.2025.109405

  • R Bryce, C Williams, N Burton. Prediction of Charged Small Molecule Conformations in Solution using a Balanced ML/MM Potential Theoretical and Computational Chemistry https://doi.org/10.26434/chemrxiv-2025-9hps8

  • B Lei, H Zhang, C Bonţoiu, A Bonatto. Leaky surface plasmon-based wakefield acceleration in nanostructured carbon nanotubes. Plasma Physics and Controlled Fusion, Volume 67, Number 6 DOI: 10.1088/1361-6587/ade00a

  • J Morado, K Zinovjev, LO Hedges, DJ Cole, J Michel. Enhancing Electrostatic Embedding for ML/MM Free Energy Calculations. Theoretical and Computational Chemistry https://doi.org/10.26434/chemrxiv-2025-ktjh4

  • Bifeng Lei, Hao Zhang, Cristian Bontoiu, Alexandre Bonatto, Javier Resta-Lopez, Guoxing Xia, Bin Qiao, Carsten Welsch. 100s TeV/m-Level Particle Accelerators Driven by High-density Electron Beams in Micro Structured Carbon Nanotube Forest Channel. New Journal of Physics, Volume 27, August 2025 DOI: 10.1088/1367-2630/adf87d

  • BS Nunes, SP Santos, RP Nunes, C Bonţoiu, et al. Bayesian optimization of laser wakefield acceleration in the self-modulated regime (SM-LWFA) aiming to produce molybdenum-99 via photonuclear reactions. Physics of Plasmas https://doi.org/10.1063/5.0244268

  • Robert Welch, Charles Laughton, Oliver Henrich, Tom Burnley, Daniel Cole, Alan Real, Sarah Harris, James Gebbie-Rayet. Engineering Supercomputing Platforms for Biomolecular Applications. arXiv preprint https://doi.org/10.48550/arXiv.2506.15585

  • Abouzied M. A. Nasar, Benedict D. Rogers, Georgios Fourtakas, Scott T. Kay, Matthieu Schaller. Task-parallelism in SWIFT for heterogeneous compute architectures arXiv preprint https://doi.org/10.48550/arXiv.2505.14538

  • Elliot W. Chan, Mark C. Leake, Agnes Noy. HU Searches and Binds Specific DNA via a Multistep Process Combining Weak Electrostatic Binding, Protein Reorientation, and DNA Flexibility. JACS Au, 2025 - ACS Publications https://pubs.acs.org/doi/full/10.1021/jacsau.5c00800

  • Lantra, Zaman. OP-PIC - an unstructured-mesh particle-in-cell domain specific language. wrap.warwick.ac.uk. https://wrap.warwick.ac.uk/194362/

  • Samuel P. Niblett, Panagiotis KourtisIoan-Bogdan Magdău, Clare P. Grey, Gábor Csányi. Transferability of Data Sets between Machine-Learned Interatomic Potential Algorithms. Journal of Chemical Theory and Computation, Vol 21/Issue 12. https://pubs.acs.org/doi/full/10.1021/acs.jctc.5c00272

  • Fei Jiang, Zhonghua Zheng, Hugh Coe, Robert M. Healy, Laurent Poulain, Valérie Gros, Hao Zhang, Weijun Li, Dantong Liu, Matthew West, David Topping, Nicole Riemer. Integrating Simulations and Observations: A Foundation Model for Estimating the Aerosol Mixing State Index. ACS ES&T AirVol 2/Issue 5 https://pubs.acs.org/doi/full/10.1021/acsestair.4c00329

  • Amirhossein Gooranorimi, Seyyed Mohammad Mousavifard, Mohsen Mohseni, Hossein Yahyaei, Hesam Makki. Effective Cross-Link Density as a Metric for Structure–Property Relationships in Complex Polymer Networks: Insights from Acrylic Melamine Systems. ACS Applied Polymer Materials, Vol 7/Issue 14. https://pubs.acs.org/doi/full/10.1021/acsapm.5c01155

    2024

  • JW Shepherd, S Guilbaud, Z Zhou, J Howard, M Burman, C Schaefer, A Kerrigan, C Steele-King, A Noy, and MC Leake. Correlating fluorescence microscopy, optical, and magnetic tweezers to study single chiram biopolymers such as DNA. Nature Communications, 15, 2748 https://www.nature.com/articles/s41467-024-47126-6

  • Gardasevic and A. Noy. The impact of sequence periodicity on DNA elasticity: investigating the origin of A-tract’s curvature.Nanoscale, 16, 18410 – 18420. https://doi.org/10.1039/D4NR02571G

  • Azam Nesabi, Jas Kalayan, Sara Al-Rawashdeh, Mohammad A. Ghattas & Richard A. Bryce. Molecular dynamics simulations as a guide for modulating small molecule aggregation. Journal of Computer-Aided Molecular Design https://link.springer.com/article/10.1007/s10822-024-00557-1

  • Jeremiah P. Tidey, Urmimala Dey, Ana M. Sanchez, Wei-Tin Chen, Bo-Hao Chen, Yu-Chun Chuang, Maria T. Fernandez-Diaz, Nicholas C. Bristowe, Richard Beanland & Mark S. Senn. Structural origins of dielectric anomalies in the filled tetragonal tungsten bronze Sr2NaNb5O15 Communications Materials https://www.nature.com/articles/s43246-024-00508-1

  • Jing Li, Carlos Amador, and Mark R. Wilson. Computational predictions of interfacial tension, surface tension, and surfactant adsorption isotherms. Phys. Chem. Chem. Phys., 2024, 26, 12107-12120. https://doi.org/10.1039/D3CP06170A

  • Arohi Jain, Samuel R. Yoffe, Bernhard Ersfeld, George K. Holt, Devki Nandan Gupta, & Dino A. Jaroszynski. The effect of laser pulse evolution on down-ramp injection in laser wakefield accelerators. Scientific Reports volume 14, Article number: 19127. https://www.nature.com/articles/s41598-024-69049-4

  • Zaman Lantra, Steven A. Wright, Gihan R. Mudalige. OP-PIC - an Unstructured-Mesh Particle-in-Cell DSL for Developing Nuclear Fusion Simulations. ICPP '24: Proceedings of the 53rd International Conference on Parallel Processing https://doi.org/10.1145/3673038.3673130

  • Tuong Do; Binh X. Nguyen; Quang D. Tran; Hien Nguyen; Erman Tjiputra; Te-Chuan Chiu. Reducing Non-IID Effects in Federated Autonomous Driving with Contrastive Divergence Loss. 2024 IEEE International Conference on Robotics and Automation (ICRA). https://doi.org/10.1109/ICRA57147.2024.10611202

  • Eghbal Rahimikia & Felix Drinkall Re(Visiting) Large Language Models in Finance.SRRNhttps://dx.doi.org/10.2139/ssrn.4963618

  • Broad, Andrew. Can Attention-Inspired Artificial Intelligence Provide a Diagnostic Understanding of Colorectal Cancer Imaging Data? Integrated PhD and Master's thesis, University of Leeds. https://etheses.whiterose.ac.uk/id/oai_id/oai:etheses.whiterose.ac.uk:35698

  • Aniculaesei C., Ha T., Yoffe S., Labun L., Milton S., McCary E., Spinks M.M., Quevedo H.J., Labun O.Z., Sain R., Hannasch A., Zgadzaj R., Pagano I., Franco-Altamirano J.A., Ringuette M.L., Gaul E., Luedtke S.V., Tiwari G., Ersfeld B., Brunetti E., Ruhl H., Ditmire T., Bruce S., Donovan M.E., Downer M.C., Jaroszynski D.A., Hegelich B.M. The acceleration of a high-charge electron bunch to 10 GeV in a 10-cm nanoparticle-assisted wakefield accelerator (2024). Matter and Radiation at Extremes, 9 (1) doi: 1063/5.0161687

  • Bryce, Richard, Irfan Alibay, Philip Biggin, and Sondos Musleh. "Analysis of protein-glycan recognition using absolute binding free energies." (2024).Theoretical and Computational Chemistryhttps://doi.org/10.1021/acs.jcim.4c01088

  • Do T, Nguyen BX, Tran QD, Nguyen H, Tjiputra E, Chiu TC, Nguyen A. Reducing Non-IID Effects in Federated Autonomous Driving with Contrastive Divergence Loss. In 2024 IEEE International Conference on Robotics and Automation (ICRA) 2024 May 13 (pp. 2190-2196). IEEE.

  • Li, L., Ismail, K. N., Shum, H. P., & Breckon, T. P. (2024). DurLAR: A High-fidelity 128-channel LiDAR Dataset with Panoramic Ambient and Reflectivity Imagery for Multi-modal Autonomous Driving Applications. ArXiv. doi: 10.1109/3DV53792.2021.00130

  • Musleh S, Alibay I, Biggin PC, Bryce RA. Analysis of Glycan Recognition by Concanavalin A Using Absolute Binding Free Energy Calculations. Journal of Chemical Information and Modeling, Vol 64/Issue 20https://doi.org/10.1021/acs.jcim.4c01088

  • Pollak H, Degiacomi MT, Erastova V. Modeling Realistic Clay Systems with ClayCode. Journal of Chemical Theory and Computation. 2024 Oct 15;20(21):9606-17. https://pubs.acs.org/doi/10.1021/acs.jctc.4c00987

  • Tidey, Jeremiah P., Urmimala Dey, Ana M. Sanchez, Wei-Tin Chen, Bo-Hao Chen, Yu-Chun Chuang, Maria T. Fernandez-Diaz, Nicholas C. Bristowe, Richard Beanland, and Mark S. Senn. Structural origins of dielectric anomalies in the filled tetragonal tungsten bronze Sr2NaNb5O15. Communications Materials 5, no. 1 (2024): 71.

  • Zhao, Rixin, Haitao Xue, Shuangfang Lu, H. Chris Greenwell, and Valentina Erastova. Revealing crucial effects of reservoir environment and hydrocarbon fractions on fluid behaviour in kaolinite pores." Chemical Engineering Journal 489 (2024): 151362.

    2023

  • Alexandridis K.P., Luo S., Nguyen A., Deng J., Zafeiriou S. Inverse Image Frequency for Long-Tailed Image Recognition (2023). IEEE Transactions on Image Processing, 32, pp. 5721 - 5736 doi: 10.1109/TIP.2023.3321461

  • Horton J.T., Boothroyd S., Behara P.K., Mobley D.L., Cole D.J. A transferable double exponential potential for condensed phase simulations of small molecules (2023). Digital Discovery, 2 (4), pp. 1178 - 1187 doi: 1039/d3dd00070b

  • Keepfer, N., Flynn, T., Parker, N. and Billam, T., 2023. SuperVortexNet: Reconstructing Superfluid Vortex Filaments Using Deep Learning. arXiv preprint arXiv:2312.14815.

  • Lin Y., Whitehouse P.L., Valentine A.P., Woodroffe S.A. GEORGIA: A Graph Neural Network Based EmulatOR for Glacial Isostatic Adjustment (2023). Geophysical Research Letters, 50 (18) doi: 1029/2023GL103672

  • Tang H., Li H., Prakaash D., Pedebos C., Qiu X., Sauer D.B., Khalid S., Duerr K., Robinson C.V. The solute carrier SPNS2 recruits PI(4,5)P2 to synergistically regulate transport of sphingosine-1-phosphate (2023). Molecular Cell, 83 (15), pp. 2739 - 2752.e5 doi: 1016/j.molcel.2023.06.033

  • Wilson M.R. & Yu G. Computer Simulations of a Twist Bend Nematic (NTB): A Coarse-Grained Simulation of the Phase Behaviour of the Liquid Crystal Dimer CB7CB (2023). Crystals, 13 (3), art. no. 502 doi: 3390/cryst13030502

  • Zuzic L., Marzinek J.K., Anand G.S., Warwicker J., Bond P.J. A pH-dependent cluster of charges in a conserved cryptic pocket on flaviviral envelopes (2023). eLife, 12, art. no. e82447 doi: 10.7554/eLife.82447

  • Walls, N. Essays on Academic Innovation & Labour Markets. Doctoral Thesis, University of Durham. https://etheses.dur.ac.uk/15139/

  • El Sayed, Sherihan E.A.  Treatment of inflammation: Novel inhibitors of the inflammasome Doctoral Thesis, Univeristy of Manchester. View thesis on ProQuest

    2022

  • Alexandridis K.P., Deng J., Nguyen A., Luo S. Long-Tailed Instance Segmentation Using Gumbel Optimized Loss (2022). Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 13670 LNCS, pp. 353 - 369 doi: 1007/978-3-031-20080-9_21

  • Almushyti M., Li F.W.B. STIT: Spatio-Temporal Interaction Transformers for Human-Object Interaction Recognition in Videos (2022). Proceedings - International Conference on Pattern Recognition, 2022-August, pp. 3287 - 3294 doi: 1109/ICPR56361.2022.9956030

  • Almushyti M., Li F.W.B. Distillation of human–object interaction contexts for action recognition (2022). Computer Animation and Virtual Worlds, 33 (5) doi: 10.1002/cav.2107

  • Bieniek M.K., Cree B., Pirie R., Horton J.T., Tatum N.J., Cole D.J. An open-source molecular builder and free energy preparation workflow (2022). Communications Chemistry, 5 (1) doi: 10.1038/s42004-022-00754-9

  • El-Sayed S., Freeman S., Bryce R.A. A Selective Review and Virtual Screening Analysis of Natural Product Inhibitors of the NLRP3 Inflammasome (2022). Molecules, 27 (19) doi: 3390/molecules27196213

  • El-Sayed S., Freeman S., Bryce R.A. Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation (2022). Protein Science, 31 (10) doi: 1002/pro.4420

  • Godson L., Alemi N., Nsengimana J., Cook G.P., Clarke E.L., Treanor D., Bishop D.T., Newton-Bishop J., Gooya A. Weakly-supervised learning for image-based classification of primary melanomas into genomic immune subgroups (2022). Proceedings of Machine Learning Research, 172, pp. 423 - 440

  • Gupta D.N., Yoffe S.R., Jain A., Ersfeld B., Jaroszynski D.A. Propagation of intense laser pulses in plasma with a prepared phase-space distribution (2022). Scientific Reports, 12 (1) doi: 1038/s41598-022-24664-x

  • Hancox Z., Relton S.D. Temporal Graph-Based CNNs (TG-CNNs) for Online Course Dropout Prediction (2022). Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 13515 LNAI, pp. 357 - 367 doi: 1007/978-3-031-16564-1_34

  • Horton J.T., Boothroyd S., Wagner J., Mitchell J.A., Gokey T., Dotson D.L., Behara P.K., Ramaswamy V.K., Mackey M., Chodera J.D., Anwar J., Mobley D.L., Cole D.J. Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale (2022). Journal of Chemical Information and Modeling, 62 (22), pp. 5622 - 5633 doi: 1021/acs.jcim.2c01153

  • Huang G., Bors A.G. Busy-Quiet Video Disentangling for Video Classification (2022). Proceedings - 2022 IEEE/CVF Winter Conference on Applications of Computer Vision, WACV 2022, pp. 756 - 765 doi: 1109/WACV51458.2022.00083

  • McKinney, Alex F., and Chris G. Willcocks. Megapixel Image Generation with Step-Unrolled Denoising Autoencoders. arXiv preprint arXiv:2206.12351 (2022).

  • O'Connor J., Domínguez J.M., Rogers B.D., Lind S.J., Stansby P.K. Eulerian incompressible smoothed particle hydrodynamics on multiple GPUs (2022). Computer Physics Communications, 273 doi: 1016/j.cpc.2021.108263

  • Ringrose C., Horton J.T., Wang L.-P., Cole D.J . Exploration and validation of force field design protocols through QM-to-MM mapping (2022). Physical Chemistry Chemical Physics, 24 (28), pp. 17014 - 17027 doi: 1039/d2cp02864f

  • Matthew Smith, Arjen Tamerus, & Phil Hasnip. Portable Acceleration of Materials Modeling Software: CASTEP, GPUs, and OpenACC. Computing in Science & Engineering, Volume: 24 Issue: 1 https://doi.org/10.1109/MCSE.2022.3141714

  • Wilson M.R., Yu G., Potter T.D., Walker M., Gray S.J., Li J., Boyd N.J. Molecular Simulation Approaches to the Study of Thermotropic and Lyotropic Liquid Crystals (2022). Crystals, 12 (5) doi: 3390/cryst12050685

  • Yu G., Wilson M.R. All-atom simulations of bent liquid crystal dimers: the twist-bend nematic phase and insights into conformational chirality (2022). Soft Matter, 18 (15), pp. 3087 - 3096 doi: 1039/d2sm00291d

    2021

  • DN Gupta, SR Yoffe, A Jain, B Ersfeld, DA Jaroszynski. Plasma guiding using a chaperone pre-pulse for stable wakefield generation. Preprint https://doi.org/10.21203/rs.3.rs-679840/v2

  • Hudson G.T., Moubayed N.A. Ask me in your own words: paraphrasing for multitask question answering (2021). PeerJ Computer Science, 7, pp. 1 - 16 doi: 10.7717/PEERJ-CS.759

  • Li, Li, Khalid N. Ismail, Hubert PH Shum, and Toby P. Breckon. Durlar: A high-fidelity 128-channel lidar dataset with panoramic ambient and reflectivity imagery for multi-modal autonomous driving applications. In 2021 International Conference on 3D Vision (3DV), pp. 1227-1237. IEEE, 2021.

  • Yang L., Horton J.T., Payne M.C., Penfold T.J., Cole D.J. Modeling Molecular Emitters in Organic Light-Emitting Diodes with the Quantum Mechanical Bespoke Force Field (2021). Journal of Chemical Theory and Computation, 17 (8), pp. 5021 - 5033 doi: 1021/acs.jctc.1c00135

  • Yoffe S.R., Ersfeld B., Gupta D.N., Jain A., Tooley M.P., Holt G.K., Jaroszynski D.A. Controlling the group velocity of an intense laser pulse using a pre-pulse (2021). Proceedings of SPIE - The International Society for Optical Engineering, 11778 doi: 1117/12.2595294

  • Zhu J., Kelly T. Seamless Satellite-image Synthesis (2021). Computer Graphics Forum, 40 (7), pp. 193 - 204 doi: 1111/cgf.14413

  • Zuzic, L. A Simulation Approach to Cryptic Pocket Discovery in Viral Envelopes. PhD thesis, University of Manchester ProQuest

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