Publications associated with Advanced Computing Projects

How to reference the RNCA in scientific articles or conferences?

Exemplo em inglês: “This work was produced with the support of <Operacional Center> and it was funded by FCT I.P. under the project Advanced Computing Project <reference>, platform <name>”

If your publications, arising from an RNCA advanced computing project, are not listed on this page, please send the details to rnca(at)


  • M. Graça, D. Marques, S. Santander-Jiménez, L. Sousa and A. Ilic, Interpreting High Order Epistasis Using Sparse Transformers. 2023. IEEE/ACM Conference on Connected Health: Applications, Systems and Engineering Technologies (CHASE), Orlando, FL, USA, 2023, pp. 114-125. (Project: CPCA-IAC/AV/478750/2022@GCP)
  • Marques da Silva, J. A., Vieira de Carvalho, M., Cardoso Coelho, R. P., Rodrigues Lopes, I. A., & Andrade Pires, F. M. On the representativeness of polycrystalline models with transformation induced plasticity. Finite Elements in Analysis and Design, 2023. 215, 103875. (Project: CPCA/A1/420917/2021@INCD)
  • Silva JPB, Istrate MC, Hellenbrand M, Jan A., Becker MT, Symonowicz J., Figueiras FG, Lenzi V., Hill MO, Ghica C, Romanyuk KN, Gomes MJM, Di Martino G., Marques L., MacManus-Driscoll JL. Ferroelectricity and negative piezoelectric coefficient in orthorhombic phase pure ZrO2 thin films. Applied Materials Today. Volume 30, 101708, 2023. (Projects: CPCA/A2/5649/2020@HPC-UÉ and CPCA/A2/4628/2020@MACC)
in Silva JPB et al. 2023


Publications whose results were obtained with resources HPC-UÉ

  • Lenzi V., Silva JBP, Šmíd B, Matolín V., Istrate CM, Ghica C, MacManus-Driscoll JL, Marques L. Ferroelectricity induced by oxygen vacancies in rhombohedral ZrO2 thin films. Energy & Environmental Materials. 2022. (Project: CPCA/A1/415075/2021@HPCUE)

Publications whose results were obtained with resources MACC

  • Moreno M, Vilaça R and Ferreira PG. Scalable Transcriptomics Analysis with Dask: Applications in Data Science and Machine Learning. BMC Bioinformatics. 23:514 . 2022. (Project: CPCA/A2/2640/2020)
  • Santos JM, Thomaz LA, Assuncao PAA, da Silva Cruz JA, Távora LMN, Faria SMM, Hierarchical lossless coding of light fields with improved random access, Signal Processing: Image Communication, Volume 105, 2022, 116687, ISSN 0923-5965, (Project: CPCA_A00_6782_2020)
  • Luís, J.P.; Mata, A.I.; Simões,C.J.V.; Brito, R.M.M. Conformational Dynamics of the Soluble and Membrane-Bound Forms of Interleukin-1 Receptor Type-1: Insights into Linker Flexibility and Domain Orientation. Int. J. Mol. Sci. 2022, 23, 2599. (Project: CPCA/A0/7316/2020@MACC)
  • Zhan, G., Cai, ZF., Strutyński, K. et al. Observing polymerization in 2D dynamic covalent polymers. Nature 603, 835-840 (2022).
figure 2
in Zhan et al. 2022
  • Martins, N.M.C.; Covas, D.I.C. Induced Circulation by Plunging and Submerged Jets in Circular Water Storage Tanks Using CFD. Water 2022, 14, 1277.
  • Rajeev K. Dubey, M. Melle-Franco, and A. Mateo-Alonso. Inducing Single-Handed Helicity in a Twisted Molecular Nanoribbon. Journal of the American Chemical Society. 2022.144 (6), 2765-2774. DOI: 10.1021/jacs.1c12385
  • Faroughi, S.A.; Roriz, A.I.;Fernandes, C. A Meta-Model toPredict the Drag Coefficient of a Particle Translating in Viscoelastic Fluids: A Machine Learning Approach. Polymers 2022, 14, 430.
  • Fernandes, C., Faroughi, S.A., Ribeiro, R. et al. Finite volume simulations of particle-laden viscoelastic fluid flows: application to hydraulic fracture processes. Engineering with Computers (2022).

Publications whose results were obtained with INCD resources

  • Pina A. F., Sousa S. F., Cerqueira N. M. F. S. A., ChemBioChem 2022, 23, e202100555.
  • Fernandes, H.S., Sousa, S.F. & Cerqueira, N.M.F.S.A. New insights into the catalytic mechanism of the SARS-CoV-2 main protease: an ONIOM QM/MM approach. Mol Divers 26, 1373-1381 (2022).
  • Bonilla, C., Hernández, A.E.C., Gonçalves, J. et al. Collider signatures of vector-like fermions from a flavor symmetric model. J. High Energ. Phys. 2022, 154.
  • Gadelho, J., Guedes Soares, C., Barajas, G., & Lara, J. L. CFD analysis of the PTO damping on the performance of an onshore dual chamber OWC. 2022. n C. Guedes Soares & T. A. Santos, Trends in Maritime Technology and Engineering Volume 2 (1st ed., pp. 381-389). CRC Press. (Project: CPCA/A1/407670/2021@INCD)
  • Gadelho, J., & Guedes Soares, C.,. Pneumatic performance improvement of an onshore dual chamber OWC using a CFD model. 2022. In Trends in Renewable Energies Offshore (Guedes Soares C., (Ed.). (Project: CPCA/A1/407670/2021@INCD)
  • Rosa A, Cardoso C, Vieira R, Faria R, Oliveira AR, Navarro G and Caldeira RMA (2022) Impact of Flash Flood Events on the Coastal Waters Around Madeira Island: The "Land Mass Effect". Front. Mar. Sci. 8:749638. doi: 10.3389/fmars.2021.749638
in Rosa et. al 2022

Publications whose results were obtained with LCA-UC resources

  • Couto C, Tong Q, Gernay T, Predicting the capacity of thin-walled beams at elevated temperature with machine learning, Fire Safety Journal, Volume 130, 2022, 103596, ISSN 0379-7112, (Project: CPCA/A1/6717/2020@LCAUC)
  • Couto C, Neural network models for the critical bending moment of uniform and tapered beams,Structures, Volume 41, 2022, Pages 1746-1762, ISSN 2352-0124, (Project: CPCA/A1/6717/2020@LCAUC)
  • Riaño A., K. Strutyński, M. Liu, C. T. Stoppiello, B. Lerma-Berlanga, A. Saeki, C. Martí-Gastaldo, A. N. Khlobystov, G. Valenti, F. Paolucci, M. Melle-Franco, A. Mateo-Alonso, An Expanded 2D Fused Aromatic Network with 90-Ring Hexagons. 2022. Angew. Chem. Int. Ed. 61, e202113657. (Project: CPCA/A2/2524/2020@LCAUC)


Publications whose results were obtained with resources HPC-UÉ

  • Lenzi V, Cavaleiro A, Fernandes F, Marques L, Diffusion of silver in Titanium Nitride: Insights from density functional theory and molecular dynamics, Applied Surface Science, 556:149738, 2021, (Project: CPCA_A2_5649_2020@HPCUE)
  • Coutinho J, Gouveia JD, Makino T, Ohshima T, Pastuović Ž., Bakrač L., Brodar T., and Capan I.. M center in 4H-SiC is a carbon self-interstitia.l. Phys. Rev. B 103, L180102. 2021. 021.149738 (Project: CPCA_A0_7277_2020@HPCUE)
in J. Coutinho et. al, 2021

Publications whose results were obtained with MACC resources

  • Almeida B.C.,Kaczmarek J.A, Figueiredo P.R., Prather KLJ and Carvalho ATP. Transcription factor allosteric regulation through substrate coordination to zinc, NAR Genomics and Bioinformatics 2021, 3 (2), (Project: CPCA_A2_4568_2020@MACC)
  • Fakhari A., Tukovic Z., Carneiro O.S., and Fernandes C. An Effective Interface Tracking Method for Simulating the Extrudate Swell Phenomenon. Polymers. Apr; 13(8): 1305. 2021. (Project: CPCA_A00_6057_2020)
  • Cruz F. and Mota J.,Structure and thermodynamics of empty clathrate hydrates below the freezing point of water. Phys Chem Chem. 23(30):16033-16043 . 2021. (Project: CPCA_A2_2613_2020)
  • Fernandes C., Faroughi S. A., Ribeiro R., Isabel A., McKinley G., (2021). Finite Volume Simulations of Particle-laden Viscoelastic Fluid Flows: Application To Hydraulic Fracture Processes. 10.21203/ (Project: CPCA_A2_6052_2020)
  • Gernot Eichmann, J. M. Pawlowski, and J. M. Silva. Mass generation in Landau-gauge Yang-Mills theory. 2021. Phys. Rev. D 104, 114016. (Project: CPCA_A0_7291_2020)
  • Fernandes, I.S., de Brito, M.S.e.C.A., Manrique, Y.A., Dias, M.M., Lopes, J.C.B. and Santos, R.J. (2021), Computational Fluid Dynamics Model of Two-Phase Flow in NETmix Reactors. Chem. Eng. Technol., 44: 2002-2010. (Project: CPCA_A0_7324_2020)
  • Matos J, Santos RJ, Dias MM andLopes JCB (2021) Mixing in the NETmix Reactor. Front. Chem. Eng. 3:771476. doi: 10.3389/fceng.2021.771476 (Project: CPCA_A0_7324_2020)

Publications whose results were obtained with INCD resources

  • Castellanos P., Brito A. C., Chainho P., Quintella B.R., da Costa L., França S., Cabral H., Costa J. L., CoastNet Dataset From Mondego, Tejo and Mira Estuaries: Multiparametric Measurements During 2020. 2021. Frontiers in Marine Science. Volume 8. DOI=10.3389/fmars.2021.707089 (Project: CPCA_A2_7255_2020@INCD)
  • Cereja, R., V. Brotas, J.P.C. Cruz, M. Rodrigues & A.C. Brito. Tidal and physicochemical effects on phytoplankton community variability at Tagus estuary (Portugal). Frontiers in Marine Science, 8: 675699. 2021. (Project: CPCA_A2_7255_2020)
  • França, S., V.F. Fonseca, S.E. Tanner, R.P. Vasconcelos, P. Reis-Santos, A. Maia, M. Ruano, I. Cardoso, S. Henriques, M.P. Pais, P. Brandão, A.C. Brito, P. Castellanos, P. Chainho, B. Quintella, L. Costa, M.J. Costa, J.L. Costa & H.N. Cabral. Historical data in the CoastNet Geoportal: documenting fish assemblages in Portuguese estuaries. Frontiers in Marine Science, 8: 685294 . 2021. (Project: CPCA_A2_7255_2020)
  • Bonilla C.,Carcamo Hernandez AE, Goncalves J, Freitas FF, Morais AP and Pasechnik R. Collider signatures of vector-like fermions from a flavor symmetric 2HDM. 2021. URL
  • D. Quelhas, J. Carneiro, M. Lopes-Marques, J. Jaeken, E. Martins, J.F. Rocha, S.S. Teixeira Carla, C.R. Ferreira, S.F. Sousa, L. Azevedo, Assessing the effects of PMM2 variants on protein stability, Molecular Genetics and Metabolism, Volume 134, Issue 4, 2021, Pages 344-352, ISSN 1096-7192,
  • Serrano, C., Teixeira, C.S.S., Cooper, D.N. et al. Compensatory epistasis explored by molecular dynamics simulations. Hum Genet 140, 1329-1342 (2021).
  • Vieira, T.F.; Martins, F.G.; Moreira, J.P.; Barbosa, T.; Sousa, S.F. In Silico Identification of Possible Inhibitors for Protein Kinase B (PknB) of Mycobacterium tuberculosis. Molecules 2021, 26, 6162.
  • Santos-Pereira C,Rocha J. F., Fernandes H. S., Rodrigues L. R., Côrte-Real M., Sousa S. F., The milk-derived lactoferrin inhibits V-ATPase activity by targeting its V1 domain, International Journal of Biological Macromolecules, Volume 186, 2021, Pages 54-70, ISSN 0141-8130,
  • Martins, F.G.; Melo, A.; Sousa, S.F. Identification of New Potential Inhibitors of Quorum Sensing through a Specialized Multi-Level Computational Approach. Molecules 2021, 26, 2600. (Project: CPCA/A00/7140/2020@INCD)
  • Teixeira MAL, Nygren A, Ravara A, Vieira PE, Hernández JC, Costa FO (2021) The small polychaete Platynereis dumerilii revealed as a large species complex with fourteen MOTUs in European marine habitats. ARPHA Conference Abstracts 4: e64937. (Project: CPCA_A1_7359_2020)
  • Parracho J. O., Thomaz L. A., Távora L. M. N., . Assunção P. A. A and S Faria . M. M., "Cross-modality Lossless Compression of PET-CT Images," 2021 Telecoms Conference (ConfTELE), 2021, pp. 1-6, doi: 10.1109/ConfTELE50222.2021.9435467 (Project: CPCA_A2_6986_2020).

Other publications


  • Pedro J., Ramôa B., Nóbrega J. M., and Fernandes C., Verification and validation of openinjmoldsim, an open-source solver to model the filling stage of thermoplastic injection molding, Fluids, vol. 5, iss. 2, p. 84. 2020. Project@MACC
In Pedro J. et al, 2020

Last updated on Feb-28