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Bede Publications

Publications resulting from researchers using the Bede supercomputer

2024

  • 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).

  • Dey, U., McCabe, E. E., & Bristowe, N. C. (2024). Prediction of Room-Temperature Electric Field Reversal of Magnetization in the Family of $A_4B_3$O$_9$ Layered Oxides. ArXiv. https://arxiv.org/abs/2405.01307

  • 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. In2024 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. 2024 Oct 16;64(20):8063-73.

  • 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

    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

  • 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

  • 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

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