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Enhancing Adaptive Physics Refinement Simulations Through the Addition of Realistic Red Blood Cell Counts

Authors:

Sayan Roychowdhury,

Samreen T. Mahmud,

Aristotle Martin,

Daniel F. Puleri,

Erik W. Draeger,

Amanda RandlesAuthors Info & Claims

SC '23: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

Article No.: 41, Pages 1 - 13

https://doi.org/10.1145/3581784.3607105

Published: 11 November 2023 Publication History

SC '23: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

Enhancing Adaptive Physics Refinement Simulations Through the Addition of Realistic Red Blood Cell Counts

Pages 1 - 13

Abstract
Supplemental Material
References

Abstract

Simulations of cancer cell transport require accurately modeling mm-scale and longer trajectories through a circulatory system containing trillions of deformable red blood cells, whose intercellular interactions require submicron fidelity. Using a hybrid CPU-GPU approach, we extend the advanced physics refinement (APR) method to couple a finely-resolved region of explicitly-modeled red blood cells to a coarsely-resolved bulk fluid domain. We further develop algorithms that: capture the dynamics at the interface of differing viscosities, maintain hematocrit within the cell-filled volume, and move the finely-resolved region and encapsulated cells while tracking an individual cancer cell. Comparison to a fully-resolved fluid-structure interaction model is presented for verification. Finally, we use the advanced APR method to simulate cancer cell transport over a mm-scale distance while maintaining a local region of RBCs, using a fraction of the computational power required to run a fully-resolved model.

Supplemental Material

MP4 File - SC23 paper presentation recording for "Enhancing Adaptive Physics Refinement Simulations Through the Addition of Realistic Red Blood Cell Counts"

SC23 paper presentation recording for "Enhancing Adaptive Physics Refinement Simulations Through the Addition of Realistic Red Blood Cell Counts", by Sayan Roychowdhury, Samreen T. Mahmud, Aristotle Martin, Peter Balogh, Daniel F. Puleri, John Gounley, Erik W. Draeger and Amanda Randles

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References

[1]

Denis Wirtz, Konstantinos Konstantopoulos, and Peter C Searson. The physics of cancer: the role of physical interactions and mechanical forces in metastasis. Nature Reviews Cancer, 11(7):512--522, 2011.

[2]

Michael J Mitchell, Elizabeth Wayne, Kuldeepsinh Rana, Chris B Schaffer, and Michael R King. Trail-coated leukocytes that kill cancer cells in the circulation. Proceedings of the National Academy of Sciences, 111(3):930--935, 2014.

[3]

Ragav Sharma and Sandeep Sharma. Physiology, blood volume. 2018.

[4]

Daniel F Puleri, Sayan Roychowdhury, Peter Balogh, John Gounley, Erik W Draeger, Jeff Ames, Adebayo Adebiyi, Simbarashe Chidyagwai, Benjamín Hernández, Seyong Lee, et al. High performance adaptive physics refinement to enable large-scale tracking of cancer cell trajectory. In 2022 IEEE International Conference on Cluster Computing (CLUSTER), pages 230--242. IEEE, 2022.

[5]

Gregory Herschlag, John Gounley, Sayan Roychowdhury, Erik W Draeger, and Amanda Randles. Multi-physics simulations of particle tracking in arterial geometries with a scalable moving window algorithm. In 2019 IEEE International Conference on Cluster Computing (CLUSTER), pages 1--11. IEEE, 2019.

[6]

Peng Wang, Tom Abel, and Ralf Kaehler. Adaptive mesh fluid simulations on gpu. New Astronomy, 15(7):581--589, 2010.

[7]

Alan C Calder, BC Curts, LJ Dursi, Bruce Fryxell, Greg Henry, P MacNece, Kevin Olson, P Ricker, Robert Rosner, Francis X Timmes, et al. High-performance reactive fluid flow simulations using adaptive mesh refinement on thousands of processors. In SC'00: Proceedings of the 2000 ACM/IEEE Conference on Supercomputing, pages 56--56. IEEE, 2000.

Digital Library

[8]

Amanda Peters Randles, Vivek Kale, Jeff Hammond, William Gropp, and Efthimios Kaxiras. Performance analysis of the lattice Boltzmann model beyond Navier-Stokes. In Parallel & Distributed Processing (IPDPS), 2013 IEEE 27th International Symposium on, pages 1063--1074. IEEE, 2013.

Digital Library

[9]

Amanda Randles, Erik W Draeger, and Peter E Bailey. Massively parallel simulations of hemodynamics in the primary large arteries of the human vasculature. J Comp Sci, 9:70--75, 2015.

[10]

John Gounley, Erik W Draeger, and Amanda Randles. Immersed Boundary Method Halo Exchange in a Hemodynamics Application. LNCS, pages 441--455, 2019.

Digital Library

[11]

Jeff Ames, Daniel F Puleri, Peter Balogh, John Gounley, Erik W Draeger, and Amanda Randles. Multi-gpu immersed boundary method hemodynamics simulations. Journal of Computational Science, page 101153, 2020.

[12]

Shiyi Chen and Gary D Doolen. Lattice Boltzmann method for fluid flows. Ann Rev Fluid Mech, 30(1):329--364, 1998.

[13]

John Gounley, Erik W Draeger, and Amanda Randles. Numerical simulation of a compound capsule in a constricted microchannel. Procedia Comput Sci, 108: 175--184, 2017.

[14]

J. Walter, A.-V. Salsac, D. Barthès-Biesel, and P. Le Tallec. Coupling of finite element and boundary integral methods for a capsule in a Stokes flow. International Journal for Numerical Methods in Engineering, pages n/a-n/a, 2010. ISSN 00295981.

[15]

Fehmi Cirak, Michael Ortiz, and Peter Schroder. Subdivision surfaces: a new paradigm for thin-shell finite-element analysis. Int J Numer Methods Eng, 47(12): 2039--2072, 2000.

[16]

Ou-Yang Zhong-Can and Wolfgang Helfrich. Bending energy of vesicle membranes: General expressions for the first, second, and third variation of the shape energy and applications to spheres and cylinders. Physical Review A, 39(10):5280, 1989.

[17]

Peter Balogh and Prosenjit Bagchi. A computational approach to modeling cellular-scale blood flow in complex geometry. J Comp Phys, 334:280--307, 2017.

Digital Library

[18]

Marianna Pepona, John Gounley, and Amanda Randles. Effect of constitutive law on the erythrocyte membrane response to large strains. Computers & Mathematics with Applications, 132:145--160, 2023.

Digital Library

[19]

Charles S Peskin. The immersed boundary method. Acta Numerica, 11:479--517, 2002.

[20]

Wai-Hung Liu and Andrew H Sherman. Comparative analysis of the cuthill-mckee and the reverse cuthill-mckee ordering algorithms for sparse matrices. SIAM Journal on Numerical Analysis, 13(2):198--213, 1976.

Digital Library

[21]

Axel R Pries, D Neuhaus, and P Gaehtgens. Blood viscosity in tube flow: dependence on diameter and hematocrit. American Journal of Physiology-Heart and Circulatory Physiology, 263(6):H1770--H1778, 1992.

[22]

Yuan-cheng Fung. Biomechanics: circulation. Springer Science & Business Media, 2013.

[23]

Axel R Pries, Timothy W Secomb, P Gaehtgens, and JF Gross. Blood flow in microvascular networks. experiments and simulation. Circulation research, 67(4): 826--834, 1990.

[24]

R. Skalak, A. Tozeren, R. P. Zarda, and S. Chien. Strain Energy Function of Red Blood Cell Membranes. Biophysical Journal, 13(3):245--264, 1973. ISSN 00063495.

[25]

Abhishek Jain and Lance L Munn. Determinants of leukocyte margination in rectangular microchannels. PloS one, 4(9):e7104, 2009.

[26]

Josephine Shaw Bagnall, Sangwon Byun, Shahinoor Begum, David T Miyamoto, Vivian C Hecht, Shyamala Maheswaran, Shannon L Stott, Mehmet Toner, Richard O Hynes, and Scott R Manalis. Deformability of tumor cells versus blood cells. Scientific reports, 5(1):1--11, 2015.

[27]

Timm Krüger, David Holmes, and Peter V Coveney. Deformability-based red blood cell separation in deterministic lateral displacement devices---a simulation study. Biomicrofluidics, 8(5):054114, 2014.

[28]

Sayan Roychowdhury, John Gounley, and Amanda Randles. Evaluating the influence of hemorheological parameters on circulating tumor cell trajectory and simulation time. In Proceedings of the Platform for Advanced Scientific Computing Conference, pages 1--10, 2020.

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Cited By

Valero-Lara PGodoy WMankad HTeranishi KVetter JBlaschke JSchanen M(2024)JACC: Leveraging HPC Meta-Programming and Performance Portability with the Just-in-Time and LLVM-based Julia LanguageProceedings of the SC '24 Workshops of the International Conference on High Performance Computing, Network, Storage, and Analysis10.1109/SCW63240.2024.00245(1955-1966)Online publication date: 17-Nov-2024
https://dl.acm.org/doi/10.1109/SCW63240.2024.00245
Wu RKabir MTruskey GRandles A(2024)Investigating the impact of sickle cell disease on red blood cell transport in complex capillary networks2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)10.1109/EMBC53108.2024.10781578(1-4)Online publication date: 15-Jul-2024
https://doi.org/10.1109/EMBC53108.2024.10781578

Index Terms

Enhancing Adaptive Physics Refinement Simulations Through the Addition of Realistic Red Blood Cell Counts
1. Applied computing
  1. Life and medical sciences
    1. Computational biology
      1. Biological networks
2. Computing methodologies
  1. Modeling and simulation
    1. Simulation types and techniques
      1. Massively parallel and high-performance simulations
      2. Multiscale systems

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Published In

cover image ACM Conferences

SC '23: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

November 2023

1428 pages

ISBN:9798400701092

DOI:10.1145/3581784

Chair:
Dorian Arnold,
Program Chair:
Rosa M Badia,
Program Co-chair:
Kathryn Mohror

Copyright © 2023 ACM.

Publication rights licensed to ACM. ACM acknowledges that this contribution was authored or co-authored by an employee, contractor or affiliate of the United States government. As such, the Government retains a nonexclusive, royalty-free right to publish or reproduce this article, or to allow others to do so, for Government purposes only.

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Publication History

Published: 11 November 2023

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SC '23: International Conference for High Performance Computing, Networking, Storage and Analysis

November 12 - 17, 2023

CO, Denver, USA

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Cited By

Valero-Lara PGodoy WMankad HTeranishi KVetter JBlaschke JSchanen M(2024)JACC: Leveraging HPC Meta-Programming and Performance Portability with the Just-in-Time and LLVM-based Julia LanguageProceedings of the SC '24 Workshops of the International Conference on High Performance Computing, Network, Storage, and Analysis10.1109/SCW63240.2024.00245(1955-1966)Online publication date: 17-Nov-2024
https://dl.acm.org/doi/10.1109/SCW63240.2024.00245
Wu RKabir MTruskey GRandles A(2024)Investigating the impact of sickle cell disease on red blood cell transport in complex capillary networks2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)10.1109/EMBC53108.2024.10781578(1-4)Online publication date: 15-Jul-2024
https://doi.org/10.1109/EMBC53108.2024.10781578

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