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Papers

This page contains a list of selected papers that have extensively used FabSim3, or its predecessor FabSim.

Note

This list is maintained manually, and may not contain certain (recent) relevant publications.

Core FabSim3 papers

  • Groen, D., Arabnejad, H., Suleimenova, D., Edeling, W., Raffin, E., Xue, Y., Bronik, K., Monnier, N. and Coveney, P.V., 2023. FabSim3: An automation toolkit for verified simulations using high performance computing. Computer Physics Communications, 283, p.108596.
  • Groen, D., Arabnejad, H., Jancauskas, V., Edeling, W.N., Jansson, F., Richardson, R.A., Lakhlili, J., Veen, L., Bosak, B., Kopta, P. and Wright, D.W., 2021. VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations. Philosophical Transactions of the Royal Society A, 379(2197), p.20200221.
  • Suleimenova, D., Arabnejad, H., Edeling, W.N., Coster, D., Luk, O.O., Lakhlili, J., Jancauskas, V., Kulczewski, M., Veen, L., Ye, D. and Zun, P., 2021. Tutorial applications for Verification, Validation and Uncertainty Quantification using VECMA toolkit. Journal of Computational Science, 53, p.101402.
  • Groen, D., Bhati, A.P., Suter, J., Hetherington, J., Zasada, S.J. and Coveney, P.V., 2016. FabSim: facilitating computational research through automation on large-scale and distributed e-infrastructures. Computer Physics Communications, 207, pp.375-385.

FabSim3 application papers

Materials

  • Suter, J.L., Groen, D. and Coveney, P.V., 2015. Chemically Specific Multiscale Modeling of Clay–Polymer Nanocomposites Reveals Intercalation Dynamics, Tactoid Self‐Assembly and Emergent Materials Properties. Advanced Materials, 27(6), pp.966-984.
  • Suter, J.L., Groen, D. and Coveney, P.V., 2015. Mechanism of exfoliation and prediction of materials properties of clay–polymer nanocomposites from multiscale modeling. Nano letters, 15(12), pp.8108-8113.

Migration

  • Suleimenova, D. and Groen, D., 2020. How Policy Decisions Affect Refugee Journeys in South Sudan: A Study Using Automated Ensemble Simulations. Journal of Artificial Societies and Social Simulation, 23(1).
  • Suleimenova, D., Arabnejad, H., Edeling, W.N. and Groen, D., 2021. Sensitivity-driven simulation development: a case study in forced migration. Philosophical Transactions of the Royal Society A, 379(2197), p.20200077.
  • Xue, Y., Li, M., Arabnejad, H., Suleimenova, D., Jahani, A., Geiger, B.C., Wang, Z., Liu, X. and Groen, D., 2022. Camp Location Selection in Humanitarian Logistics: A Multiobjective Simulation Optimization Approach. In International Conference on Computational Science (pp. 497-504). Springer, Cham.
  • Suleimenova, D., Low, W. and Groen, D., 2022. An Agent-Based Forced Displacement Simulation: A Case Study of the Tigray Crisis. In International Conference on Computational Science (pp. 83-89). Springer, Cham.
  • Groen, D., Bell, D., Arabnejad, H., Suleimenova, D., Taylor, S.J. and Anagnostou, A., 2019, December. Towards modelling the effect of evolving violence on forced migration. In 2019 Winter Simulation Conference (WSC) (pp. 297-307). IEEE.

COVID-19

  • Edeling, W., Arabnejad, H., Sinclair, R., Suleimenova, D., Gopalakrishnan, K., Bosak, B., Groen, D., Mahmood, I., Crommelin, D. and Coveney, P.V., 2021. The impact of uncertainty on predictions of the CovidSim epidemiological code. Nature Computational Science, 1(2), pp.128-135.
  • Mahmood, I., Arabnejad, H., Suleimenova, D., Sassoon, I., Marshan, A., Serrano-Rico, A., Louvieris, P., Anagnostou, A., Taylor, S.J., Bell, D. and Groen, D., 2020. FACS: a geospatial agent-based simulator for analysing COVID-19 spread and public health measures on local regions. Journal of Simulation, pp.1-19.

BioMD

  • Bhati, A.P., Wan, S., Wright, D.W. and Coveney, P.V., 2017. Rapid, accurate, precise, and reliable relative free energy prediction using ensemble based thermodynamic integration. Journal of chemical theory and computation, 13(1), pp.210-222.

Bloodflow

  • Itani, M.A., Schiller, U.D., Schmieschek, S., Hetherington, J., Bernabeu, M.O., Chandrashekar, H., Robertson, F., Coveney, P.V. and Groen, D., 2015. An automated multiscale ensemble simulation approach for vascular blood flow. Journal of computational science, 9, pp.150-155.

Earthquake modelling

  • Daub, E.G., Arabnejad, H., Mahmood, I. and Groen, D., 2021. Uncertainty quantification of dynamic earthquake rupture simulations. Philosophical Transactions of the Royal Society A, 379(2197), p.20200076.