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] |
| Copyright of Computer Physics Communications is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 143740048 AccessLevel: 6 PubType: Periodical PubTypeId: serialPeriodical PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Mirheo: High-performance mesoscale simulations for microfluidics. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Alexeev%2C+Dmitry%22">Alexeev, Dmitry</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Amoudruz%2C+Lucas%22">Amoudruz, Lucas</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Litvinov%2C+Sergey%22">Litvinov, Sergey</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Koumoutsakos%2C+Petros%22">Koumoutsakos, Petros</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> petros@ethz.ch</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Computer+Physics+Communications%22">Computer Physics Communications</searchLink>. Sep2020, Vol. 254, pN.PAG-N.PAG. 1p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Center+of+mass%22">Center of mass</searchLink><br /><searchLink fieldCode="DE" term="%22Erythrocytes%22">Erythrocytes</searchLink><br /><searchLink fieldCode="DE" term="%22Particle+dynamics%22">Particle dynamics</searchLink><br /><searchLink fieldCode="DE" term="%22Microfluidic+devices%22">Microfluidic devices</searchLink><br /><searchLink fieldCode="DE" term="%22Programming+languages%22">Programming languages</searchLink><br /><searchLink fieldCode="DE" term="%22Python+programming+language%22">Python programming language</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: 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] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Computer Physics Communications is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1016/j.cpc.2020.107298 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 1 StartPage: N.PAG Subjects: – SubjectFull: Center of mass Type: general – SubjectFull: Erythrocytes Type: general – SubjectFull: Particle dynamics Type: general – SubjectFull: Microfluidic devices Type: general – SubjectFull: Programming languages Type: general – SubjectFull: Python programming language Type: general Titles: – TitleFull: Mirheo: High-performance mesoscale simulations for microfluidics. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Alexeev, Dmitry – PersonEntity: Name: NameFull: Amoudruz, Lucas – PersonEntity: Name: NameFull: Litvinov, Sergey – PersonEntity: Name: NameFull: Koumoutsakos, Petros IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 09 Text: Sep2020 Type: published Y: 2020 Identifiers: – Type: issn-print Value: 00104655 Numbering: – Type: volume Value: 254 Titles: – TitleFull: Computer Physics Communications Type: main |
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