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Publications using the Bede Supercomputer

Publications resulting from researchers using the Bede supercomputer

2021 2022 2023 2024 2025 2026

2026

  • Arnstein, L., Wetherell, J., Lawrence, R., Hasnip, P.J. and Hodgson, M.J.P. 2026. Addressing hypersensitivity in density functional theory for reliable machine learning. npj Computational Materials volume 12, Article number: 338.
    https://doi.org/10.1038/s41524-026-02191-x
  • Bupathy, A., Hall, D., Smalyukh, I.I., Campos-Villalobos, G., Subert, R. and Dijkstra, M., 2026. From knots to crystals: Machine-learned potentials for self-assembling topological solitons in liquid crystals. Physical Review Research, 8(2), p.023235. doi:10.1103/fbxl-n36k
  • Catley TE, Velasco-Berrelleza V, Rollins DE, Pyne ALB, Noy A. 2026 Imaging and mechanism of DNA–DNA recognition mediated by divalent ions, Nucleic Acids Research, Volume 54, Issue 16 https://doi.org/10.1093/nar/gkag817
  • Nguyen, C.N. and Nguyen, C.V. 2026. Data Distribution Valuation Using Generalized Bayesian Inference, in Proceedings of the 29th International Conference on Artificial Intelligence and Statistics (AISTATS). Available at: https://openreview.net/forum?id=YVokfG01YJ
  • Nguyen, C.N., Ho, L.S.T., Dinh, V.C., Karagiannis, G. and Nguyen, C.V. 2026. A Revisit of Hamiltonian Monte Carlo Efficiency on Bayesian Neural Networks, in Advances in Neural Information Processing Systems.
  • Dang, B., Wu, L., Yang, X., Yuan, Z. and Chen, Z., 2026, March. Segmo: Segment-aligned text to 3d human motion generation. In 2026 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV) (pp. 6946-6955). IEEE. . DOI: 10.48550/arXiv.2512.21237
  • Ellis, E., Mendel, R., Bulpitt, A., Parsa, N., Byrne, M.F. and Ali, S., 2026, April. Self-supervised ultrasound-video segmentation with feature prediction and 3D localised loss. In Medical Imaging 2026: Image Processing (Vol. 13925, pp. 319-326). SPIE. https://doi.org/10.48550/arXiv.2507.18424
  • Han, R., Zhou, K., Chen, S., Atapour-Abarghouei, A. and Shum, H.P.H., 2026. CaFlow: Enhancing long-term action quality assessment with causal counterfactual flow. In: Proceedings of the 2026 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV). Arizona, USA, 14–18 January 2026. Piscataway: IEEE, pp. 8231-8241.
    https://doi.org/10.48550/arXiv.2511.21653
  • Howard, J.A.L., Ambrose, B., Abdelhamid, M.A.S., Frame, L., Alevropoulos-Borrill, A., Ejaz, A., Dresser, L., Dienerowitz, M., Quinn, S.D., Squires, A.H., Noy, A., Craggs, T.D. and Leake, M.C., 2026. The transitional kinetics between open and closed Rep structures can be tuned by salt via two intermediate states. Nucleic Acids Research, 54, p. gkaf1483. 10.1093/nar/gkaf1483
  • Kanagarajan, A. and Wilson, M.R., 2026. A local annealing strategy for equilibrium-like solute insertion into glassy polymer matrices. Soft Matter, 22(30), pp.5033-5042. https://doi.org/10.1039/d6sm00437g
  • Lei B, Xia G, Bonatto A, et al. 2026. Surface Plasmons in Strong Fields and Their Applications to Beam Acceleration. Plasma Science - Current Developments, Applications, and Future Directions. IntechOpen. DOI: 10.5772/intechopen.1013683.
  • Li, R., Chang, Z., Hu, J., Li, J., Atapour-Abarghouei, A. and Shum, H.P.H., 2026. ART: Adaptive Relational Transformer for pedestrian trajectory prediction with temporal-aware relations. In: Proceedings of the 2026 IEEE International Conference on Human-Machine Systems (ICHMS). Singapore, Singapore, 2026. Piscataway: IEEE. https://doi.org/10.1109/ICHMS69701.2026.11602161
  • Morado, J., Zinovjev, K., Hedges, L.O., Michel, J. and Cole, D.J., 2026. Atomic Environment Aware Lennard-Jones Parameterization for Electrostatic Embedding ML/MM Simulations. ChemRxiv. 22. https://doi.org/10.26434/chemrxiv.15004404/v2
  • Nami, M., Guitton‐Spassky, T., Sharif, F., Hanheiser, N., Saudale, R., Gabriel, J., Aarti, Mirzaalipour, A., Hafezi, M., Schade, B. and Singh, A.K., Haag, R., Netz, R.R., and Makki, H. 2026. Predictive Amphiphile Design Enables Control of Self‐Assembled Nanoparticle‐Cell Membrane Interactions. Small, p.e75376. https://doi.org/10.1002/smll.75376
  • Nasar, A.M., Rogers, B.D., Fourtakas, G., Ivkovic, M., Weinzierl, T., Kay, S.T. and Schaller, M., 2026. Task-parallelism in SWIFT for heterogeneous compute architectures. RAS Techniques and Instruments, 5, p.rzag008. https://doi.org/10.1093/rasti/rzag008
  • Nguyen, C.N. and Nguyen, C.V., 2026. Data Distribution Valuation Using Generalized Bayesian Inference. arXiv preprint arXiv:2604.05993.
    https://doi.org/10.48550/arXiv.2604.05993
  • Ouyang, M., Augarde, C.E., Coombs, W.M., Petalas, A., Knappett, J., Brown, M. and Alagha, A., 2026. A reduced order model framework suitable for geotechnical problems. Acta Geotechnica, pp.1-16. https://doi.org/10.1007/s11440-026-03221-0
  • Ouyang, M., Augarde, C.E., Coombs, W.M., Petalas, A., Knappett, J., Brown, M. and Alagha, A., 2026. Data-driven reduced order models for multidimensional data. In: UK Association for Computational Mechanics Conference (UKACM). Liverpool, UK, 9–10 April 2026.
  • Ouyang, M., Petalas, A., Coombs, W.M., Augarde, C.E., Alagha, A., Knappett, J. and Brown, M., 2026. Reduced Order Models for geotechnical predictions. In: Proceedings of the 21st International Conference on Soil Mechanics and Geotechnical Engineering (ICSMGE 2026). Vienna, Austria, 14–19 June 2026. Open Access: International Society for Soil Mechanics and Geotechnical Engineering (ISSMGE), pp. 1339–1342.
  • Parthasarathy, D., Ramakrishnan, S., Tsang, G., Patnaik, A.V., Hardy, S.M.C., Vanderlinden, W., Howard, J., Bylett, B., Law, J.R., Leake, M.C., Noy, A. and Michieletto, D., 2026. The Integration Host Factor is a pH-responsive protein that switches from DNA bending to DNA bridging in acidic biofilm-like conditions. https://arxiv.org/abs/2603.03466
  • Sjökvist, R., Xie, Y., Aslam, Z., Brown, A.P., Bristowe, N.C., Senn, M.S. and Beanland, R., 2026. Microscopic structure of stacking faults in Sr 2 NaNb 5 O 15. Physical Review Materials, 10(6), p.064404. https://doi.org/10.1103/snjy-yzgq
  • Stylianidis, E., Koutsogiannis, P., Lione, A., Risch, F., Hechler, L., Stolichnov, I., Íñiguez-González, J., Pardo, J.A., Bristowe, N.C., Magén, C. and Zubko, P., 2026. Alternative origins of polarity in compressively strained SrTiO3-RENiO3 capacitors. arXiv preprint arXiv:2605.29499. https://doi.org/10.48550/arXiv.2605.29499
  • Svahn, V., Magdau, I.B., Niblett, S.P., Csányi, G., Hermansson, K. and Kullgren, J., 2026. Limitations of Cluster-Trained MLIPs for Liquid Density and Diffusivity. Journal of Chemical Theory and Computation, 22(7), pp.3660-3671. https://doi.org/10.1021/acs.jctc.5c02043
  • The Ascona B-DNA Consortium, 2026. hexABC: Seeking the physical code of DNA. Nature Communications, 17, p. 8169. https://www.nature.com/articles/s41467-026-74390-5
  • Thorpe B., Smith M.J., Hasnip P.J., and Drummond N.D. 2026. Acceleration of the CASINO quantum Monte Carlo software using graphics processing units and OpenACC. Comp. Phys. Comm. 319 109900 doi: 10.1016/j.cpc.2025.109900
  • Williams, C.D., Burton, N.A. and Bryce, R.A., 2026. Prediction of Charged Small Molecule Conformations in Solution Using a Balanced ML/MM Potential. Journal of Chemical Information and Modeling, 66(4), pp.2094-2109. https://doi.org/10.1021/acs.jcim.5c02706
  • Williams, P., Durham, B., Smith, M., Hasnip, P. and Tamerus, A., 2026, October. OpenMP for GPU Data Management in CASTEP. In International Workshop on OpenMP (pp. 131-144). Cham: Springer Nature Switzerland.
  • Wilson, M.R. and Oganesyan, V.S., 2026. EPR-refined atomistic molecular dynamics delivers predictive spectroscopy in self-organized soft matter systems. Cell Reports Physical Science, 7(6). https://doi.org/10.1016/j.xcrp.2026.103332
  • Wu, L., Chen, Z. and Lan, J., 2026. Hoi-dyn: Learning interaction dynamics for human-object motion diffusion. Advances in Neural Information Processing Systems, 38, pp.90795-90825. 10.52202/085713-3037
  • Yang, Z., 2026. Bio-inspired reinforcement learning: Algorithm development and its application to visual search (Doctoral dissertation, University of Leeds). https://etheses.whiterose.ac.uk/id/eprint/37748/

2021 2022 2023 2024 2025 2026

2025

  • AlMutair, L., Atwell, E. and Ravikumar, N., 2025, January. Unlocking Clinical Narrative Text for Secondary Clinical Usage. In Proceedings of Eighth International Conference on Information System Design and Intelligent Applications (pp. 381-395). Singapore: Springer Nature Singapore. https://doi.org/10.1007/978-981-96-9242-2_28
  • Bryce R., Williams C, Burton N.2025. 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
  • Burman M. and Noy A. 2025. 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.
  • Chan, E.W., Leake, M.C., Noy, A. 2025. HU Searches and Binds Specific DNA via a Multistep Process Combining Weak Electrostatic Binding, Protein Reorientation, and DNA Flexibility. JACS Au, ACS Publications https://pubs.acs.org/doi/full/10.1021/jacsau.5c00800
  • Davoudinia, S., Imani, R., Tafazzoli-Shadpour, M., Fani, N. and Makki, H., 2025. Tunable DNA binding on graphene oxide via polyethyleneimine topology and density: mechanistic insights for nonviral gene delivery. Nanoscale, 17(48), pp.27911-27922. https://doi.org/10.1039/d5nr03441h
  • Dey, U., McCabe, E.E., Íñiguez-González, J. and Bristowe, N.C., 2025. Prediction of room temperature electric field reversal of magnetization in the family of A 4 B 3 O 9 layered oxides. Physical Review Letters, 134(13), p.136801. https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.134.136801
  • Gooranorimi, A., Mousavifard, S.M., Mohseni, M., Yahyaei, H. and Makki, H., 2025. Effective cross-link density as a metric for structure–property relationships in complex polymer networks: insights from acrylic melamine systems. ACS applied polymer materials, 7(14), p.9034. 10.1021/acsapm.5c01155
  • Han, R., Zhou, K., Amir Atapour-Abarghouei, A., Liang, X. and Shum, H.P.H., 2025. FineCausal: A causal-based framework for interpretable fine-grained action quality assessment. In: Proceedings of the 2025 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW). Nashville, USA, 15–20 June 2025. Piscataway: IEEE, pp. 6017-6026.
  • Ilyes B., et al. A foundation model for atomistic materials chemistry.2025 The Journal of Chemical Physics 163 (18). DOI: 10.1063/5.0297006
  • Jiang, F., Zheng, Z., Coe, H., Healy, R.M., Poulain, L., Gros, V., Zhang, H., Li, W., Liu, D., West, M. and Topping, D., 2025. Integrating simulations and observations: a foundation model for estimating the aerosol mixing state index. ACS ES&T Air, 2(5), pp.877-890. https://pubs.acs.org/doi/full/10.1021/acsestair.4c00329
  • Li, R., Katsigiannis, S., Kim, T.-K. and Shum, H.P.H., 2025. BP-SGCN: Behavioral pseudo-label informed sparse graph convolution network for pedestrian and heterogeneous trajectory prediction. IEEE Transactions on Neural Networks and Learning Systems, 36(8), pp. 14566-14580
  • Li, R., Qiao, T., Katsigiannis, S., Zhu, Z. and Shum, H.P.H., 2025. Unified spatial-temporal edge-enhanced graph networks for pedestrian trajectory prediction. IEEE Transactions on Circuits and Systems for Video Technology, 35(7), pp. 7047-7060.
  • Kovács D.P., Moore J.H., Browning N.J., Batatia I., Horton J.T, Pu Y, Kapil V., Witt W.C., Magdău I-B., Cole D.J., Csányi G. 2025. MACE-OFF: Short-Range Transferable Machine Learning Force Fields for Organic Molecules. Journal American Chemical Society 147 (21): 17598–17611. DOI: 10.1021/jacs.4c07099
  • Lantra, Z., 2025. OP-PIC-an unstructured-mesh particle-in-cell domain specific language (Doctoral dissertation, University of Warwick). https://wrap.warwick.ac.uk/194362/
  • Lei, B., Zhang, H., Bonţoiu, C., Bonatto, A., Martín-Luna, P., Liu, B., Resta López, J., Xia, G. and Welsch, C., 2025. Leaky surface plasmon-based wakefield acceleration in nanostructured carbon nanotubes. Plasma Physics and Controlled Fusion, 67(6), p.065036. DOI 10.1088/1361-6587/ade00a
  • Lei, B., Zhang, H., Bonţoiu, C., Bonatto, A., Resta-López, J., Xia, G., Qiao, B. and Welsch, C., 2025. 100 s tev/m-level particle accelerators driven by high-density electron beams in micro structured carbon nanotube forest channel. New Journal of Physics, 27(8), p.084301. DOI: 10.1088/1367-2630/adf87d
  • Lei, B., Zhang, H., Seipt, D., Bonatto, A., Qiao, B., Resta-López, J., Xia, G. and Welsch, C., 2025. Coherent synchrotron radiation by excitation of surface plasmon polariton on near-critical solid microtube surface. Physical review letters, 135(20), p.205001. DOI: 10.1103/cnym-16hc
  • Mirzaalipoor, A., Nami, M., Sharif, F., Ghermezcheshme, H., Netz, R.N. and Makki, H., 2025. Parameter Optimization for Accurate Coarse-Grained Modeling of Perfluorocarbon Phase Behavior. https://doi:10.26434/chemrxiv-2025-8h3d3
  • Moat, G.J., Gaudet-Trafit, M., Paul, J, Bacardit, J., Ben Hamid S, & Poirier C. 2025. The MacqD deep-learning-based model for automatic detection of socially housed laboratory macaques. Sci Rep 15, 11883. https://doi.org/10.1038/s41598-025-95180-x
  • Morado J., Zinovjev K., Hedges L.O., Cole D.J., Michel J.2025. Enhancing Electrostatic Embedding for ML/MM Free Energy Calculations. J. Chem. Theory Comput. 21 (22): 11805–11819. https://doi.org/10.1021/acs.jctc.5c01464
  • Motlagh GM, Fathi F, Brigham JC, & Jimack PK. 2025 Deep learning for inverse material characterization. Computer Methods in Applied Mechanics and Engineering, 436, 117650. https://doi.org/10.1016/j.cma.2024.117650
  • Mousavifard, S.M., Mohseni, M., Yahyaei, H. and Makki, H., 2025. Water exchangeability between pore volumes: a key mechanism governing water diffusion in highly cross-linked polymer coatings. Progress in Organic Coatings, 207, p.109405. https://doi.org/10.1016/j.porgcoat.2025.109405
  • Niblett, S.P., Kourtis, P., Magdau, I.B., Grey, C.P. and Csányi, G., 2025. Transferability of data sets between machine-learned interatomic potential algorithms. Journal of Chemical Theory and Computation, 21(12), pp.6096-6112. https://pubs.acs.org/doi/full/10.1021/acs.jctc.5c00272
  • Nunes, B.S., Santos, S.P.D., Nunes, R.P., Bonţoiu, C., Alva-Sánchez, M.S., Samad, R.E., Vieira, N.D., Xia, G., Resta-López, J. and Bonatto, A., 2025. Bayesian optimization of laser wakefield acceleration in the self-modulated regime (SM-LWFA) aiming to produce molybdenum-99 via photonuclear reactions. Physics of Plasmas, 32(3). doi: 10.1063/5.0244268
  • Ouyang, M., Petalas, A., Coombs, W.M. and Augarde, C.E., 2025. Developing efficient data-driven predictive tools for geotechnics. In: 18th International Conference on Computational Plasticity (COMPLAS 2025). Barcelona, Spain, 2–5 September 2025.
  • Petitjean, A., Plehn, T., Spinner, J. and Köthe, U., 2025. Economical Jet Taggers--Equivariant, Slim, and Quantized. arXiv preprint arXiv:2512.17011. https://doi.org/10.48550/arXiv.2512.17011
  • Poole, W.G., Samways, M.L., Branduardi, D., Taylor, R.D., Verdonk, M.L. and Essex, J.W., 2025. Accelerating fragment-based drug discovery using grand canonical nonequilibrium candidate Monte Carlo. Nature Communications, 16(1), p.6198. https://www.nature.com/articles/s41467-025-60561-3
  • Rahimikia, E., Ni, H. and Wang, W., 2025. Re (visiting) time series foundation models in finance. SSRN. doi: 10.2139/ssrn.5770562
  • Rezayani, M., Sharif, F. and Makki, H., 2025. Dynamic bonds transform ion transport mechanisms in polymeric covalent adaptable networks. Materials Horizons, 12(22), pp.9643-9652. https://pubs.rsc.org/en/content/articlehtml/2025/mh/d5mh00433k
  • Welch, R., Laughton, C., Henrich, O., Burnley, T., Cole, D., Real, A., Harris, S. and Gebbie-Rayet, J., 2025. Engineering Supercomputing Platforms for Biomolecular Applications. arXiv preprint arXiv:2506.15585. https://doi.org/10.48550/arXiv.2506.15585
  • Wu, L., Chen, Z. and Lan, J., 2025. HOI-Dyn: Learning interaction dynamics for human-object motion diffusion. Advances in Neural Information Processing Systems, 38, pp.90795-90825. https://doi.org/10.48550/arXiv.2507.01737
  • Yin, H., You, S., Han, J. and Chen, Z., 2025, April. Sequential joint dependency aware human pose estimation with state space model. In Proceedings of the AAAI Conference on Artificial Intelligence (Vol. 39, No. 9, pp. 9499-9507). https://ojs.aaai.org/index.php/AAAI/article/view/33029

2021 2022 2023 2024 2025 2026

2024

  • Adie, J., Chin, C., Li, J. and See, S., 2024. GAIA-Chem: a Global AI-accelerated Atmospheric Chemistry framework. In: American Meteorological Society’s 26th Conference on Atmospheric Chemistry. Baltimore, Maryland, 28 Jan–1 Feb 2024.
  • Adie, J., Chin, C., Li, J. and See, S., 2024. GAIA-Chem: a Framework for Global AI-accelerated Atmospheric Chemistry Modelling. In: The Platform for Advanced Scientific Computing (PASC) Conference 2024. Zurich, Switzerland, 3-5 June 2024. PASC Conference Papers.
  • Adie, J., Chin, C., Li, J. and See, S., 2024. GAIANet: Accelerating Atmospheric Chemistry Modelling with Deep Learning and Fourier Neural Operators, SupercomputingAsia 2024, Sydney, Australia, 19-22 Feb 2024.
  • Aniculaesei, C., Ha, T., Yoffe, S., Labun, L., Milton, S., McCary, E., Spinks, M.M., Quevedo, H.J., Labun, O.Z., Sain, R. and Hannasch, A., 2024. The acceleration of a high-charge electron bunch to 10 GeV in a 10-cm nanoparticle-assisted wakefield accelerator. Matter and Radiation at Extremes, 9(1). https://doi.org/10.1063/5.0161687
  • Broad, A.J., 2024. Can Attention-Inspired Artificial Intelligence Provide a Diagnostic Understanding of Colorectal Cancer Imaging Data? (Doctoral dissertation, University of Leeds). https://etheses.whiterose.ac.uk/id/oai_id/oai:etheses.whiterose.ac.uk:35698
  • Bryce, R., Alibay, I., Biggin, P. and Musleh, S., 2024. Analysis of protein-glycan recognition using absolute binding free energies. Theoretical and Computational Chemistry https://doi.org/10.1021/acs.jcim.4c01088
  • Clarke, E.L., Treanor, D., Bishop, D.T., Newton-Bishop, J. and Magee, D., 2024. Multi-level graph representations of melanoma whole slide images for identifying immune subgroups. In Graphs in Biomedical Image Analysis, and Overlapped Cell on Tissue Dataset for Histopathology: 5th MICCAI Workshop, GRAIL 2023 and 1st MICCAI Challenge, OCELOT 2023, Held in Conjunction with MICCAI 2023, Vancouver, BC, Canada, September 23, and October 4, 2023, Proceedings (p. 85). Springer Nature.https://doi.org/10.1007/978-3-031-55088-1_8
  • Do, T., Nguyen, B.X., Tran, Q.D., Nguyen, H., Tjiputra, E., Chiu, T.C. and Nguyen, A., 2024, May. Reducing non-IID effects in federated autonomous driving with contrastive divergence loss. In 2024 IEEE International Conference on Robotics and Automation (ICRA) (pp. 2190-2196). IEEE. doi: 10.1109/ICRA57147.2024.10611202
  • El-Sayed, S., McMahon, E., Musleh, S., Freeman, S., Brough, D., Kasher, P.R., Bryce, R.A. 2024 Virtual screening-led design of inhibitor scaffolds for the NLRP3 inflammasome Bioorganic Chemistry, 153, 107909. https://doi.org/10.1016/j.bioorg.2024.107909
  • Gardasevic, T. and Noy, A. 2024. 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
  • Gravett, M.S., Klebl, D.P., Harlen, O.G., Read, D.J., Muench, S.P., Harris, S.A. and Peckham, M., 2024. Exploiting cryo-EM structures of actomyosin-5a to reveal the physical properties of its lever. Structure, 32(12), pp.2316-2324.
  • Jain, A., Yoffe, S.R., Ersfeld, B., Holt, G.K., Gupta, D.N. and Jaroszynski, D.A., 2024. The effect of laser pulse evolution on down-ramp injection in laser wakefield accelerators. Scientific Reports, 14(1), p.19127. https://www.nature.com/articles/s41598-024-69049-4
  • Lantra, Z., Wright, S.A. and Mudalige, G.R., 2024, August. OP-PIC-an Unstructured-Mesh Particle-in-Cell DSL for Developing Nuclear Fusion Simulations. In Proceedings of the 53rd International Conference on Parallel Processing (pp. 294-304). https://doi.org/10.1145/3673038.3673130
  • Li, J., Amador, C. and Wilson, M.R., 2024. Computational predictions of interfacial tension, surface tension, and surfactant adsorption isotherms. Physical Chemistry Chemical Physics, 26(15), pp.12107-12120. https://doi.org/10.1039/D3CP06170A
  • Motlagh GM, Fathi F, Brigham JC, & Jimack PK. 2025 Deep learning for inverse material characterization. Computer Methods in Applied Mechanics and Engineering, 436, 117650. https://doi.org/10.1016/j.cma.2024.117650
  • Musleh, S., Alibay, I., Biggin, P.C. and Bryce, R.A., 2024. Analysis of glycan recognition by concanavalin A using absolute binding free energy calculations. Journal of Chemical Information and Modeling, 64(20), p.8063. https://doi.org/10.1021/acs.jcim.4c01088
  • Nesabi, A., Kalayan, J., Al-Rawashdeh, S., Ghattas, M.A. and Bryce, R.A., 2024. Molecular dynamics simulations as a guide for modulating small molecule aggregation. Journal of computer-aided molecular design, 38(1), p.11. doi:10.1007/s10822-024-00557-1
  • Pollak, H., Degiacomi, M.T. and Erastova, V., 2024. Modeling realistic clay systems with ClayCode. Journal of Chemical Theory and Computation, 20(21), p.9606. https://pubs.acs.org/doi/10.1021/acs.jctc.4c00987
  • Rahimikia, E. and Drinkall, F. 2024. Re(Visiting) Large Language Models in Finance. SSRN. doi: 10.2139/ssrn.4963618
  • Shepherd, J.W., Guilbaud, S., Zhou, Z., Howard, J., Burman, M., Schaefer, C., Kerrigan, A., Steele-King, C., Noy, A., and Leake, M.C. 2024 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
  • Tidey, J.P., Dey, U., Sanchez, A.M., Chen, W.T., Chen, B.H., Chuang, Y.C., Fernandez-Diaz, M.T., Bristowe, N.C., Beanland, R. and Senn, M.S., 2024. Structural origins of dielectric anomalies in the filled tetragonal tungsten bronze Sr2NaNb5O15. Communications Materials, 5(1), p.71. https://www.nature.com/articles/s43246-024-00508-1
  • Turner, C., Pardo, LM., et al. 2024. Deep learning predicted perceived age is a reliable approach for analysis of facial ageing: A proof of principle study. Journal of the European Academy of Dermatology and Venereology, Volume 38, Issue 12 pp. 2295-2302 https://doi.org/10.1111/jdv.20365
  • Zhao, R., Xue H., Lu, S., Greenwell, H.C., Erastova, V. 2024. Revealing crucial effects of reservoir environment and hydrocarbon fractions on fluid behaviour in kaolinite pores, Chemical Engineering Journal, Volume 489,151362, https://doi.org/10.1016/j.cej.2024.151362.

2021 2022 2023 2024 2025 2026

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
  • El-Sayed, S.E., 2023. Treatment of inflammation: Novel Inhibitors of the Inflammasome (Doctoral dissertation, The University of Manchester (United Kingdom)).
  • Godson, L., Alemi, N., Nsengimana, J., Cook, G.P., Clarke, E.L., Treanor, D., Bishop, D.T., Newton-Bishop, J. and Magee, D., 2023, October. Multi-level graph representations of melanoma whole slide images for identifying immune subgroups. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 85-96). Cham: Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-55088-1_8
  • Horton, J.T., Boothroyd, S., Behara, P.K., Mobley, D.L. and Cole, D.J., 2023. A transferable double exponential potential for condensed phase simulations of small molecules. 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. https://arxiv.org/abs/2312.14815
  • Lin, Y., Whitehouse, P.L., Valentine, A.P. and Woodroffe, S.A., 2023. GEORGIA: A graph neural network based EmulatOR for glacial isostatic adjustment. Geophysical Research Letters, 50(18), p.e2023GL103672. doi: 1029/2023GL103672
  • Tang, H., Li, H., Prakaash, D., Pedebos, C., Qiu, X., Sauer, D.B., Khalid, S., Duerr, K. and Robinson, C.V., 2023. The solute carrier SPNS2 recruits PI (4, 5) P2 to synergistically regulate transport of sphingosine-1-phosphate. Molecular Cell, 83(15), pp.2739-2752. doi: 1016/j.molcel.2023.06.033
  • Vu, Q.V. 2023. Machine learning approach towards predicting turbulent fluid flow using convolutional neural networks. PhD thesis, University of Sheffield. https://etheses.whiterose.ac.uk/id/eprint/33008/
  • Walls, N. Essays on Academic Innovation & Labour Markets. 2023. Doctoral Thesis, University of Durham. https://etheses.dur.ac.uk/15139/
  • Wilson, M.R. and Yu, G., 2023. Computer simulations of a twist bend nematic (NTB): A coarse-grained simulation of the phase behaviour of the liquid crystal dimer CB7CB. Crystals, 13(3), p.502. doi: 3390/cryst13030502
  • Zuzic, L., Marzinek, J.K., Anand, G.S., Warwicker, J. and Bond, P.J., 2023. A pH-dependent cluster of charges in a conserved cryptic pocket on flaviviral envelopes. Elife, 12, p.e82447. doi: 10.7554/eLife.82447

2021 2022 2023 2024 2025 2026

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. and Li, F.W., 2022, August. STIT: Spatio-Temporal Interaction Transformers for Human-Object Interaction Recognition in Videos. In 2022 26th International Conference on Pattern Recognition (ICPR) (pp. 3287-3294). IEEE. doi: 1109/ICPR56361.2022.9956030
  • Almushyti, M. and Li, F.W., 2022. Distillation of human–object interaction contexts for action recognition. Computer Animation and Virtual Worlds, 33(5), p.e2107. doi: 10.1002/cav.2107
  • Bieniek, M.K., Cree, B., Pirie, R., Horton, J.T., Tatum, N.J. and Cole, D.J., 2022. An open-source molecular builder and free energy preparation workflow. Communications chemistry, 5(1), p.136. doi: 10.1038/s42004-022-00754-9
  • El-Sayed, S., Freeman, S. and Bryce, R.A., 2022. A selective review and virtual screening analysis of natural product inhibitors of the NLRP3 inflammasome. Molecules, 27(19), p.6213. doi: 3390/molecules27196213
  • El‐Sayed, S., Freeman, S. and Bryce, R.A., 2022. Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation. Protein science, 31(10), p.e4420. doi: 1002/pro.4420
  • Godson, L., Alemi, N., Nsengimana, J., Cook, G.P., Clarke, E.L., Treanor, D., Bishop, T., Newton-Bishop, J., Gooya, A. 2022. Weakly-supervised learning for image-based classification of primary melanomas into genomic immune subgroups. PMLR 172:423-440. https://proceedings.mlr.press/v172/godson22a.html
  • Gupta, D.N., Yoffe, S.R., Jain, A., Ersfeld, B. and Jaroszynski, D.A., 2022. Propagation of intense laser pulses in plasma with a prepared phase-space distribution. Scientific Reports, 12(1), p.20368. DOI: 10.1038/s41598-022-24664-x
  • Hancox, Z. and Relton, S.D., 2022, September. Temporal graph-based CNNs (TG-CNNs) for online course dropout prediction. In International Symposium on Methodologies for Intelligent Systems (pp. 357-367). Cham: Springer International Publishing. 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. and Anwar, J., 2022. Open force field BespokeFit: automating bespoke torsion parametrization at scale. Journal of Chemical Information and modeling, 62(22), p.5622. doi: 1021/acs.jcim.2c01153
  • Huang, G. and Bors, A.G., 2022, January. Busy-quiet video disentangling for video classification. In 2022 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV) (pp. 756-765). IEEE. doi: 1109/WACV51458.2022.00083
  • Kristoffersen, E.L., Burman, M., Noy, A. and Holliger, P., 2022. Rolling Circle RNA Synthesis Catalysed by RNA. eLife, 11, p. e75186. https://doi.org/10.7554/eLife.75186
  • McKinney, A.F. and Willcocks, C.G., 2022. Megapixel Image Generation with Step-Unrolled Denoising Autoencoders. arXiv preprint arXiv:2206.12351.
    https://doi.org/10.48550/arXiv.2206.12351
  • O'Connor J., Domínguez J.M., Rogers B.D., Lind S.J., Stansby P.K. 2022. Eulerian incompressible smoothed particle hydrodynamics on multiple GPUs. Computer Physics Communications, 273 doi: 1016/j.cpc.2021.108263
  • Ringrose, C., Horton, J.T., Wang, L.P. and Cole, D.J., 2022. Exploration and validation of force field design protocols through QM-to-MM mapping. Physical Chemistry Chemical Physics, 24(28), pp.17014-17027. doi: 1039/d2cp02864f
  • Smith, M., Tamerus, A. and Hasnip, P., 2022. Portable acceleration of materials modeling software: CASTEP, GPUs, and OpenACC. Computing in Science & Engineering, 24(1), pp.46-55. https://doi.org/10.1109/MCSE.2022.3141714
  • Watson, G.D., Chan, E.W., Leake, M.C. and Noy, A., 2022. Structural interplay between DNA-shape protein recognition and supercoiling: the case of IHF. Computational and Structural Biotechnology Journal, 20, pp. 5264-5274. https://doi.org/10.1016/j.csbj.2022.09.020
  • Wilson, M.R., Yu, G., Potter, T.D., Walker, M., Gray, S.J., Li, J. and Boyd, N.J., 2022. Molecular simulation approaches to the study of thermotropic and lyotropic liquid crystals. Crystals, 12(5), p.685. doi: 3390/cryst12050685
  • Yu, G. and Wilson, M.R., 2022. All-atom simulations of bent liquid crystal dimers: the twist-bend nematic phase and insights into conformational chirality. Soft Matter, 18(15), pp.3087-3096. doi: 1039/d2sm00291d
  • Zuzic, L. A. 2022. Simulation Approach to Cryptic Pocket Discovery in Viral Envelopes. PhD thesis, University of Manchester

2021 2022 2023 2024 2025 2026

2021

  • Gupta, D.N., Yoffe, S.R., Jain, A., Ersfeld, B. and Jaroszynski, D.A., 2021. Plasma guiding using a chaperone pre-pulse for stable wakefield generation. https://doi.org/10.21203/rs.3.rs-679840/v1
  • Hudson G.T., Moubayed N.A.2021. Ask me in your own words: paraphrasing for multitask question answering. PeerJ Computer Science, 7, pp. 1 - 16 doi: 10.7717/PEERJ-CS.759
  • Li, L., Ismail, K.N., Shum, H.P. and Breckon, T.P., 2021, December. 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. ArXiv. doi: 10.1109/3DV53792.2021.00130
  • Liang, L., Xia, G. and Bonatto, A., 2021, May. Study of The Electron Seeded Proton Self-modulation Using FBPIC. In Proceedings of the 12th International Particle Accelerator Conference.https://doi.org/10.18429/JACoW-IPAC2021-WEPAB174
  • Yang L., Horton J.T., Payne M.C., Penfold T.J., Cole D.J. 2021. Modeling Molecular Emitters in Organic Light-Emitting Diodes with the Quantum Mechanical Bespoke Force Field. Journal of Chemical Theory and Computation, 17 (8), pp. 5021 - 5033 https://doi.org/10.1021/acs.jctc.1c00135
  • Yoffe S.R., Ersfeld B., Gupta D.N., Jain A., Tooley M.P., Holt G.K., Jaroszynski D.A. 2021. Controlling the group velocity of an intense laser pulse using a pre-pulse. Proceedings of SPIE - The International Society for Optical Engineering, 11778 doi: 1117/12.2595294
  • Zhu J., Kelly T. 2021 Seamless Satellite-image Synthesis. Computer Graphics Forum, 40 (7), pp. 193 - 204 doi: 1111/cgf.14413

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