YALES2BIO

IMAG, CNRS and Université Montpellier, France

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Related publications

International publications on blood flows

Nicoud, F., An adjoint‐based method for the computation of gradients in coagulation schemes , International Journal for Numerical Methods in Biomedical Engineering, (March), pp. 1–16. doi: 10.1002/cnm.3698, 2023
Sun, Y. et al. , A pipeline for the generation of synthetic cardiac color Doppler , IEEE TUFFC Journal, 69(3), pp. 932–941. doi: 10.1109/TUFFC.2021.3136620, 2022
Garreau, M. et al. , Accelerated sequences of 4D flow MRI using GRAPPA and compressed sensing : A comparison against conventional MRI and computational fluid dynamics , Magnetic Resonance Imaging, (June), pp. 1–15. doi: 10.1002/mrm.29404, 2022
Vixege, F. et al., Full-volume three-component intraventricular vector flow mapping by triplane color Doppler , Physics in Medicine and Biology. IOP Publishing, 67(9). doi: https://doi.org/10.1088/1361-6560/ac62fe, 2022
Berod, A. et al., A Heterogeneous Model of Endovascular Devices for the Treatment of Intracranial Aneurysms , International Journal for Numerical Methods in Biomedical Engineering, 38(2), p. e3552. doi: doi.org/10.1002/cnm.3552, 2021
Puiseux, T. et al., Numerical simulation of time-resolved 3D phase-contrast magnetic resonance imaging , PLoS ONE, 16(3), p. e0248816. doi: 10.1371/journal.pone.0248816, 2021
Matteoli, P., Nicoud, F. and Mendez, S. , Impact of the membrane viscosity on the tank-treading behavior of red blood cells , Physical Review Fluids. American Physical Society, 043602, pp. 1–21. doi: 10.1103/PhysRevFluids.6.043602, 2021
Taraconat, P. et al. , Detecting cells rotations for increasing the robustness of cell sizing by impedance measurements , with or without machine learning , Cytometry, 99(10), pp. 977–986. doi: 10.1002/cyto.a.24356, 2021
Manning, K. B., Nicoud, F. and Shea, S. M., Mathematical and computational modeling of device-induced thrombosis , Current Opinion in Biomedical Engineering. Elsevier Ltd, 20, p. 100349. doi: 10.1016/j.cobme.2021.100349, 2021
Vixege, F. et al., Physics-constrained intraventricular vector flow mapping by color Doppler , Physics in Medicine & Biology. IOP Publishing, 66, p. 245019. doi: https://doi.org/10.1088/1361-6560/ac3ffe, 2021
Mantilla, D. et al., Clinical impact of Sim & Size® simulation software in the treatment of patients with cerebral aneurysms with flow-diverter Pipeline stents , Interventional Neuroradiology, pp. 1–9. doi: https://doi.org/10.1177/15910199211068668, 2021
Rapadamnaba, R., Nicoud, F. and Mohammadi, B., Augmented patient-specific functional medical imaging by implicit manifold learning , International Journal for Numerical Methods in Biomedical Engineering, 36(e3325), pp. 1–20. doi: 10.1002/cnm.3325, 2020
Vixege, F. et al.. Intraventricular vector flow mapping 3-D by triplane Doppler echocardiography , Computer Methods in Biomechanics and Biomedical Engineering. Taylor & Francis, 23(sup1), pp. S300–S302. doi: 10.1080/10255842.2020.1816300, 2020
Taraconat, P., Gineys, J.-P., Isèbe, D., Nicoud, F. & Mendez, S. Numerical simulation of deformable particles in a Coulter counter , International Journal for Numerical Methods in Biomedical Engineering, e3243, 2019
Iss, C., Midou, D., Moreau, A., Held, D., Charrier, A., Mendez, S., Viallat, A. & Helfer, E. Self-organization of red blood cell suspensions under confined 2D flows , Soft Matter, Vol. 15, pp. 2971-2980, 2019
Puiseux, T., Sewonu, A., Meyrignac, O., Rousseau, H., Nicoud, F., Mendez, S. & Moreno, R., Reconciling PC-MRI and CFD: an in-vitro study, NMR in Biomedicine, Vol. 32(5), e4063, 2019
Mendez Rojano, R., Mendez, S., Lucor, D., Ranc, A., Giansily-blaizot, M., Schved, J.-F. and Nicoud, F., Biomechanics and Modeling in Mechanobiology Kinetics of the coagulation cascade including the contact activation system : Sensitivity analysis and model reduction, Biomechanics and Modeling in Mechanobiology, Vol. 18(4), pages 1139-1153, 2019
Mendez S. & Abkarian, M., In-plane elasticity controls the full dynamics of red blood cells in shear flow , Physical Review Fluids, Vol. 3(10), 101101, 2018
Mauer, J., Mendez, S., Lanotte, L., Nicoud, F., Abkarian, M., Gompper, G. & Fedosov, D. A., Flow-Induced Transitions of Red Blood Cell Shapes under Shear , Physical Review Letters, Vol 121, 118103, 2018
Rapadamnaba, R., Nicoud, F. and Mohammadi, B., Backward sensitivity analysis and reduced-order covariance estimation in noninvasive parameter identification for cerebral arteries, International Journal for Numerical Methods in Biomedical Engineering (e3170), pp. 1–24, 2018 <\li>
Mendez Rojano, R., Mendez & Nicoud, F., Introducing the pro-coagulant contact system in the numerical assessment of device-related thrombosis , Biomechanics and Modeling in Mechanobiology, Vol. 17(3), 2018
Siguenza, J., Pott, D., Mendez, S., Sonntag, S., Kaufmann, T., Steinseifer, U. & Nicoud, F., Fluid-structure interaction of a pulsatile flow with an aortic valve model: a combined experimental and numerical study , International Journal for Numerical Methods in Biomedical Engineering, Vol. 34(4), 2018
Lal, R., Nicoud, F., Le Bars, E., Deverdun, J., Molino, F., Costalat, V., & Mohammadi, B., Non Invasive Blood Flow Features Estimation in Cerebral Arteries from Uncertain Medical Data , Annals of Biomedical Engineering, in press, 2017
Assi, K., Gay, E., Chnafa, C., Mendez, S., Nicoud, F., Abascal, J., Lantelme, P.,Tournoux, F. & Garcia, D., Intraventricular vector flow mapping—a Doppler-based regularized problem with automatic model selection , Physics in Medicine & Biology, Vol. 62(17), pages 7131-7147, 2017
Nicoud, F., Chnafa, C., Siguenza, J., Zmijanovic, V. & Mendez, S. , Large-Eddy Simulation of Turbulence in Cardiovascular Flows , in Biomedical Technology Modeling, Experiments and Simulation, Lecture Notes in Applied and Computational Mechanics, Vol. 84, pages 147-167, 2017
Siguenza, J., Mendez & Nicoud, F., , How should the optical tweezers experiment be used to characterize the red blood cell membrane mechanics? , Biomechanics and Modeling in Mechanobiology, Vol. 16(5), pages 1645-1657, 2017
Zmijanovic, V., Mendez, S., Moureau, V. & Nicoud, F., About the Numerical Robustness of Biomedical Benchmark Cases: Interlaboratory FDA's Idealized Medical Device, International Journal for Numerical Methods in Biomedical Engineering, Vol. 33(1), pages 1-17 e02789, 2017.
Lanotte, L., Mauer, J., Mendez, S., Fedosov, D. A., Fromental, J.-M., Claveria, V., Nicoud, F., Gompper, G. & Abkarian, M., Red cells' dynamic morphologies govern blood shear thinning under microcirculatory flow conditions , Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, pages 13289-13294, 2016
Siguenza, J., Mendez, S., Ambard, D., Dubois, F., Jourdan, F., Mozul, R. & Nicoud, F., Validation of an immersed thick boundary method for simulating fluid-structure interactions of deformable membranes , Journal of Computational Physics, Vol. 322, pages 723-746, 2016.
Lal, R., Mohammadi, B. & Nicoud, F., Data assimilation for identification of cardiovascular network characteristics , International Journal for Numerical Methods in Biomedical Engineering, Vol. 02824, pages 1-17, 2016.
Chnafa, C., Mendez, S. & Nicoud, F., Image-based simulations show important flow fluctuations in a normal left ventricle: what could be the implications? , Annals of Biomedical Engineering, Vol. 44(11), pages 3346-3358, 2016.
Loiseau, E., Massiera, G., Mendez, S., Aguilar Martinez, P. & Abkarian, M., Microfluidic study of enhanced deposition of sickle cells at acute corners and its possible role in vaso-occlusion, Biophysical Journal, Vol. 108, pages 2623-2632, 2015.
Mendez S., Chnafa C., Gibaud E., Siguenza, J., Moureau V. & Nicoud F., YALES2BIO: A Computational Fluid Dynamics Software Dedicated to the Prediction of Blood Flows in Biomedical Devices, IFMBE Proceedings Series, Vol. 46, pages 7-10, 2015.
Siguenza J., Mendez S. & Nicoud, F., Characterisation of a dedicated mechanical model for red blood cells: numerical simulations of optical tweezers experiment, Computer Methods in Biomechanics and Biomedical Engineering, Vol. 17(supp 1), pages 28-29, 2014.
Martins Afonso M., Mendez S. & Nicoud, F., On the damped oscillations of an elastic quasi-circular membrane in a two-dimensional incompressible fluid , J. Fluid Mech., Vol. 746, pages 300-331, 2014.
Chnafa C., Mendez S. & Nicoud, F., Image-based large-eddy simulation in a realistic left heart , Comp. Fluids, Vol. 94, pages 173-187, 2014.
Chnafa C., Mendez S., Moreno R. & Nicoud, F., Using image-based CFD to investigate the intracardiac turbulence , In "Modeling the Heart and the Circulatory System" Ed. A. Quarteroni. Springer MS&A, Vol. 14, 2015.
Mendez S., Gibaud E. & Nicoud F., An unstructured solver for simulations of deformable particles in flows at arbitrary Reynolds numbers , Journal of Computational Physics, Vol. 256(1), pages 465-483, 2014.
Baya Toda H., Cabrit O., Truffin K., Bruneaux G. and Nicoud F. Assessment of subgrid-scale models with an LES-dedicated experimental database: the pulsatile impinging jet in turbulent cross- flow. Physics of Fluids, 26, pp. 075108, 2014
Gibaud E., Siguenza J., Mendez S. and Nicoud F., Towards numerical prediction of red blood cells dynamics within a cytometer. , Computer Methods in Biomechanics and Biomedical Engineering, 16(supp 1), pp. 9-10, 2013
Chnafa C., Mendez S., Nicoud F., Moreno R., Nottin S. and Schuster I. Image-based patient-specific simulation: a computational modelling of the human left heart haemodynamics. Computer Methods in Biomechanics and Biomedical Engineering, 15(supp 1), pp. 74-75, 2012
Midulla M., Moreno R., Baali A., Chau M., Negre-Salvayre A., Nicoud F., Pruvo J-P, Haulon S. Rousseau H. Haemodynamic imaging of thoracic stent-grafts by computational fluid dynamics (CFD): presentation of a patient-specific method combining magnetic resonance imaging and numerical simulations. European Radiology, 22(10), 2094-2102, 2012
Nicoud F., Baya Toda H., Cabrit O., Bose S. and Lee J. Using singular values to build a subgrid-scale model for large eddy simulations. Physics of Fluids, 23 (8), pp. 085106, 2011

YALES2BIO Thesis

Gibaud, E., Numerical simulation of red blood cells flowing in a blood analyzer. PhD Thesis report, Université de Montpellier, 2015.
Chnafa, C., Using image-based large-eddy simulations to investigate the intracardiac flow and its turbulent nature. PhD Thesis report, Université Montpellier 2, 2014.

Publications/Reports on the numerics (YALES2/YALES2BIO)

Malandain, M., Maheu, N. and Moureau V, Optimization of the deflated Conjugate Gradient algorithm for the solving of elliptic equations on massively parallel machines, Journal of Computational Physics, 238, 32-47, 2013.
Malandain, M., Simulation massivement parallele des ecoulements turbulents a faible nombre de Mach. These, INSA Rouen, 2012.
Vantieghem, S., Numerical simulations of quasi-static magnetohydrodynamics using an unstructured finite volume solver: development and applications PhD Thesis, Université Libre de Bruxelles, 2011.
Enjalbert, N., Modelisation avancée de la combustion turbulente diphasique en régime de forte dilution par les gaz brulés. These, INSA Rouen, 2011.
Moureau V., Domingo P. and Vervisch, L., Design of a massively parallel CFD code for complex geometries, Compte-rendus Mécanique, 339(2-3), 141-148, 2011.