An ESPResSo  implementation of elastic objects immersed in a fluid

Cimrák, Ivan; Gusenbauer, Markus; Jančigová, Iveta

doi:10.1016/j.cpc.2013.12.013

Cited by 62 publications

(39 citation statements)

References 23 publications

(33 reference statements)

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“…Many features of the model have been implemented in the Object-in-fluid (OIF) framework [13], which is a part of a scientific open-source software package ESPResSo [14]. For further enhancements of our model, we work in various research directions.…”

Section: Prospective Developmentsmentioning

confidence: 99%

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Recent advances in mesh-based modeling of individual cells in biological fluids

Cimrák

Jančigová

Tóthová

2014

The 10th International Conference on Digital Technologies 2014

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The problem of modeling blood flow can be approached on different levels of accuracy. We investigate a model consisting of two major components: the fluid representing blood plasma and the elastic objects representing all types of cells in blood, e.g. red blood cells. The elastic objects are immersed in the fluid and they interact with each other.Our research is focused on spring-network models of elastic objects. We present the results concerning the scalability of meshes. We investigate the relation between mechanical properties of physical cells and the stiffness parameters of underlying meshes. Further, we present new metric that supplements energy-based approaches in cases when the energy is difficult to calculate.To demonstrate the abilities of our software implementation, we provide tests concerning the computational complexity. We show the significant speed-up caused by using templates when generating many cells with the same elastic properties. We also demonstrate the quadratic dependence of the computational time on increasing number of simulated cells.We suggest several directions for further model enhancements, such as better implementation of cell-cell collisions, inclusion of adhesion processes, monitoring the rupture of cells, and development of physically more relevant implementation of forces for some cell's elastic moduli.

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Section: Prospective Developmentsmentioning

confidence: 99%

“…Currently, using our Object-in-fluid framework [13], we are able to simulate few hundreds of cells in one thread. The code is parallelized and on our hardware (Nvidia Tesla M2090 with 64GB RAM and 2 Intel Xeon E5-2609 @ 2.40GHz CPUs) we can run up to 8 threads.…”

Section: Computational Complexitymentioning

confidence: 99%

Recent advances in mesh-based modeling of individual cells in biological fluids

Cimrák

Jančigová

Tóthová

2014

The 10th International Conference on Digital Technologies 2014

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“…Recently, we have developed a computational model of individual red blood cells, represented by boundary meshes of elastically interacting nodes . The cell model is implemented in a lattice Boltzmann fluid dynamics code using an immersed boundary method with full two‐way coupling . Due to this accurate cell model [validations have been performed with stretching experiments from literature ] and fast computations using the parallelized fluid dynamics code, the model of the red blood cell can be used to support the strain‐based bottom–up approach.…”

mentioning

confidence: 99%

Cell Damage Index as Computational Indicator for Blood Cell Activation and Damage

et al. 2018

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Shear‐induced hemolysis is a major concern in the design and optimization of blood‐contacting devices. Even with a small amount of mechanical stress, inflammatory reactions can be triggered in the cells. Blood damage is typically estimated using continuum fluid dynamics simulations. In this study, we report a novel cell damage index (CDI) obtained by simulations on the single‐cell level in a lattice Boltzmann fluid flow. The change of the cell surface area gives important information on mechanical stress of individual cells as well as for whole blood. We are using predefined basic channel designs to analyze and compare the newly developed CDI to the conventional blood damage calculations in very weak shear stress scenarios. The CDI can incorporate both volume fraction and channel geometry information into a single quantitative value for the characterization of flow in artificial chambers.

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“…One of the tools, which allows such approach is Object-in-fluid framework implemented in open source software ESPResSo [5], [6], [7]. In [6] author studies a rare cell capture rate according to the cell-fluid ratio in a channel with shifted obstacles.…”

Section: Introductionmentioning

confidence: 99%

Processing of Cells’ Trajectories Data for Blood Flow Simulation Model*

et al. 2018

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Abstract. Simulations of the red blood cells (RBCs) flow as a movement of elastic objects in a fluid, are developed to optimize microfluidic devices used for a blood sample analysis for diagnostic purposes in the medicine. Tracking cell behaviour during simulation helps to improve the model and adjust its parameters. For the optimization of the microfluidic devices, it is also necessary to analyse cell trajectories as well as likelihood and frequency of their occurrence in a particular device area, especially in the parts, where they can affect circulating tumour cells capture. In this article, we propose and verify several ways of processing and analysing the typology and trajectory stability in simulations with single or with a large number of red blood cells (RBCs) in devices with different topologies containing cylindrical obstacles.

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An ESPResSo implementation of elastic objects immersed in a fluid

Cited by 62 publications

References 23 publications

Recent advances in mesh-based modeling of individual cells in biological fluids

Recent advances in mesh-based modeling of individual cells in biological fluids

Cell Damage Index as Computational Indicator for Blood Cell Activation and Damage

Processing of Cells’ Trajectories Data for Blood Flow Simulation Model*

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