Load balancing of parallel cell-based blood flow simulations

Alowayyed, Saad; Závodszky, Gábor; Azizi, Victor; Hoekstra, Alfons G.

doi:10.1016/j.jocs.2017.11.008

Cited by 12 publications

(13 citation statements)

References 12 publications

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“…40,49 It is based on a combination of the lattice Boltzmann method (LBM) which has been shown to reproduce accurate flow fields in vascular settings [50][51][52][53] and a high-performance implementation of the immersed boundary method (IBM). 54,55 The blood plasma is represented as an incompressible Newtonian fluid, and the cells are modelled as triangulated membrane meshes immersed in the plasma flow. Out of the more wide spread phenomenological models, 40,44,56,57 the one introduced by Závodszky et al 40 is employed in the current work due to its improved mechanical behaviour in the case of sustained shear rates over 1500 s −1 .…”

Section: A Numerical Methodsmentioning

confidence: 99%

Red blood cell and platelet diffusivity and margination in the presence of cross-stream gradients in blood flows

et al. 2019

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The radial distribution of cells in blood flow inside vessels is highly non-homogeneous. This leads to numerous important properties of blood, yet the mechanisms shaping these distributions are not fully understood. The motion of cells is governed by a variety of hydrodynamic interactions and cell-deformation mechanics. Properties, such as the effective cell diffusivity, are therefore difficult to investigate in flows other than pure shear flows. In this work, several single-cell, cell-pair, and large-scale many-cell simulations are performed using a validated numerical model. Apart from the single-cell mechanical validations, the arising flow profile, cell free layer widths, and cell drift velocities are compared to previous experimental findings. The motion of the cells at various radial positions and under different flow conditions is extracted, and evaluated through a statistical approach. An extended diffusive flux-type model is introduced which describes the cell diffusivities under a wide range of flow conditions and incorporates the effects of cell deformability through a shear dependent description of the cell collision cross sections. This model is applicable for both red blood cells and platelets. Further evaluation of particle trajectories shows that the margination of platelets cannot be the net result of gradients in diffusivity. However, the margination mechanism is strongly linked to the gradient of the hematocrit level. Finally, it shows that platelets marginate only until the edge of the red blood cell distribution and they do not fill the cell free layer.

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Section: A Numerical Methodsmentioning

confidence: 99%

Red blood cell and platelet diffusivity and margination in the presence of cross-stream gradients in blood flows

et al. 2019

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“…The computational efficiency of HemoCell has been demonstrated recently [2] where comprehensive studies has been done to investigate the fractional load imbalance overhead in a high-performance biofluid simulation. The authors found that in the…”

Section: Methodsmentioning

confidence: 99%

Understanding Malaria Induced Red Blood Cell Deformation Using Data-Driven Lattice Boltzmann Simulations

Tan

Závodszky

Sloot

2018

Lecture Notes in Computer Science

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Malaria remains a deadly disease that affected millions of people in 2016. Among the five Plasmodium (P.) parasites which contribute to malaria diseases in humans. P. falciparum is a lethal one which is responsible for the majority of the worldwide malaria related deaths. Since the banana-shaped stage V gametocytes play a crucial role in disease transmission, understanding the deformation of single stage V gametocytes may offer deeper insights into the development of the disease and provide possible targets for new treatment methods. In this study we used lattice Boltzmann-based simulations to investigate the effects of the stretching forces acting on infected red blood cells inside a slit-flow cytometer. The parameters that represent the cellular deformability of healthy and malaria infected red blood cells are chosen such that they mimic the deformability of these cells in a slit-flow cytometer. The simulation results show good agreement with experimental data and allow for studying the transportation of malaria infected red blood cell in blood circulation.

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“…This would cost many more CPU hours. In Azizi et al [18] and Alowayyed et al [19] more details can be found about the computational performance of HemoCell. Additionally, a continuum blood flow simulation of blood (with ρ = 1060 kg m −3 and ν = 3.3 × 10 −6 m 2 s −1 ) and PRP (with ρ = 1025 kg m −3 and ν = 1.1 × 10 −6 m 2 s −1 ) was performed.…”

Section: Cell-based Simulationsmentioning

confidence: 99%

Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined in vitro and cellular in silico study

et al. 2020

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The influence of the flow environment on platelet aggregation is not fully understood in high-shear thrombosis. The objective of this study is to investigate the role of a high shear rate in initial platelet aggregation. The haemodynamic conditions in a microfluidic device are studied using cell-based blood flow simulations. The results are compared with in vitro platelet aggregation experiments performed with porcine whole blood (WB) and platelet-rich-plasma (PRP). We studied whether the cell-depleted layer in combination with high shear and high platelet flux can account for the distribution of platelet aggregates. High platelet fluxes at the wall were found in silico . In WB, the platelet flux was about twice as high as in PRP. Additionally, initial platelet aggregation and occlusion were observed in vitro in the stenotic region. In PRP, the position of the occlusive thrombus was located more downstream than in WB. Furthermore, the shear rates and stresses in cell-based and continuum simulations were studied. We found that a continuum simulation is a good approximation for PRP. For WB, it cannot predict the correct values near the wall.

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Load balancing of parallel cell-based blood flow simulations

Cited by 12 publications

References 12 publications

Red blood cell and platelet diffusivity and margination in the presence of cross-stream gradients in blood flows

Red blood cell and platelet diffusivity and margination in the presence of cross-stream gradients in blood flows

Understanding Malaria Induced Red Blood Cell Deformation Using Data-Driven Lattice Boltzmann Simulations

Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined in vitro and cellular in silico study

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