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Mirheo: High-performance mesoscale simulations for microfluidics.

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Title:	Mirheo: High-performance mesoscale simulations for microfluidics.
Authors:	Alexeev, Dmitry¹ (AUTHOR), Amoudruz, Lucas¹ (AUTHOR), Litvinov, Sergey¹ (AUTHOR), Koumoutsakos, Petros¹ (AUTHOR) petros@ethz.ch
Source:	Computer Physics Communications. Sep2020, Vol. 254, pN.PAG-N.PAG. 1p.
Subjects:	Center of mass, Erythrocytes, Particle dynamics, Microfluidic devices, Programming languages, Python programming language
Abstract:	The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The design and operation of such devices can benefit from simulations that resolve flow-structure interactions at sub-micron resolution. We present a computational tool for large scale, efficient and high throughput mesoscale simulations of fluids and deformable objects at complex microscale geometries. The code employs dissipative particle dynamics for the description of the flow coupled with visco-elastic membrane model for red blood cells and can also handle rigid bodies and complex geometries. The software (Mirheo) is deployed on hybrid GPU/CPU architectures exhibiting unprecedented time-to-solution performance and excellent weak and strong scaling for a number of benchmark problems. Mirheo exploits the capabilities of GPU clusters, leading to speedup of up to 10X in terms of time to solution as compared to state-of-the-art software packages and reaches 90%–99% weak scaling efficiency on 512 nodes of the Piz Daint supercomputer. The software Mirheo relies on a Python interface to facilitate the solution and analysis of complex problems. Mirheo is an open source, potent computational tool that can greatly assist studies of microfluidics. Program Title: Mirheo Program Files doi: http://dx.doi.org/10.17632/n2dvz7htvn.1 Licensing provisions: MIT Programming language: C++, CUDA, Python Nature of problem: 3D simulations of microfluidic flows in complex geometries with suspended rigid bodies and deformable membranes such as cells, bacteria and microparticles. Solution method: Dissipative particle dynamics are used to represent the fluid. Cell membrane dynamics are described through potentials for shear and bending energies that are discretized on a triangular mesh and by additional constraints on cell volume and membrane area. The model incorporates membrane viscosity and interactions between membranes and the surrounding fluid. Rigid objects and boundaries are represented by groups of particles with prescribed center of mass and rotation quaternion. Time integration is performed using the Velocity-Verlet algorithm. Additional comments including restrictions and unusual features: The code runs on Nvidia GPU accelerators starting with the Kepler generation. [ABSTRACT FROM AUTHOR]
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Database:	Engineering Source

Description
Abstract:	The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The design and operation of such devices can benefit from simulations that resolve flow-structure interactions at sub-micron resolution. We present a computational tool for large scale, efficient and high throughput mesoscale simulations of fluids and deformable objects at complex microscale geometries. The code employs dissipative particle dynamics for the description of the flow coupled with visco-elastic membrane model for red blood cells and can also handle rigid bodies and complex geometries. The software (Mirheo) is deployed on hybrid GPU/CPU architectures exhibiting unprecedented time-to-solution performance and excellent weak and strong scaling for a number of benchmark problems. Mirheo exploits the capabilities of GPU clusters, leading to speedup of up to 10X in terms of time to solution as compared to state-of-the-art software packages and reaches 90%–99% weak scaling efficiency on 512 nodes of the Piz Daint supercomputer. The software Mirheo relies on a Python interface to facilitate the solution and analysis of complex problems. Mirheo is an open source, potent computational tool that can greatly assist studies of microfluidics. Program Title: Mirheo Program Files doi: http://dx.doi.org/10.17632/n2dvz7htvn.1 Licensing provisions: MIT Programming language: C++, CUDA, Python Nature of problem: 3D simulations of microfluidic flows in complex geometries with suspended rigid bodies and deformable membranes such as cells, bacteria and microparticles. Solution method: Dissipative particle dynamics are used to represent the fluid. Cell membrane dynamics are described through potentials for shear and bending energies that are discretized on a triangular mesh and by additional constraints on cell volume and membrane area. The model incorporates membrane viscosity and interactions between membranes and the surrounding fluid. Rigid objects and boundaries are represented by groups of particles with prescribed center of mass and rotation quaternion. Time integration is performed using the Velocity-Verlet algorithm. Additional comments including restrictions and unusual features: The code runs on Nvidia GPU accelerators starting with the Kepler generation. [ABSTRACT FROM AUTHOR]
ISSN:	00104655
DOI:	10.1016/j.cpc.2020.107298