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A Molecular Dynamics Based Multi-scale Platelet Aggregation Model and Its High-Throughput Simulation

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Parallel and Distributed Computing, Applications and Technologies (PDCAT 2021)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 13148))

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Abstract

In this paper, we develop a multi-scale model to simulate the aggregation of platelets in a low shear-coefficient flow. In this multi-scale model, the Morse potential is used to describe the interaction between the \(\alpha \mathrm {II}b\beta 3\) receptor and fibrinogen, the dissipative particle dynamics (DPD) is used to simulate fluids on the macro-scale, and the coarse-grained molecular dynamics (CGMD) is used to simulate the fine-scale receptors’ biochemical reactions. Moreover, with the assistance of the high-throughput simulations on the heterogeneous cluster, we calibrate the parameters for the Morse potential which are critical in the proper simulation of the aggregation of platelets. With this model, we simulate the long-term behaviour of thrombus formation constructed by many platelets. Our simulating results are consistent with in-vitro experiments on contact areas and detaching forces. Moreover, it reduces the computational cost significantly.

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Acknowledgment

The research was supported in part by NSFC Grant 12071496, Guangdong Provincial NSF Grant 2017B030311001, Guangdong Province Key Laboratory of Computational Science at the Sun Yat-sen University (2020B1212060032), and Nantong Science & Technology Research Plan (No. JC2021133). This work also benefited from resources made available at the National Supercomputer Center in Kunshan.

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Authors and Affiliations

  1. School of Science, Nantong University, Nantong, 226019, Jiangsu, China

    Zhipeng Xu

  2. School of Computer Science and Engineering and Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou, 510006, Guangdong, China

    Qingsong Zou

Authors
  1. Zhipeng Xu
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  2. Qingsong Zou
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Corresponding author

Correspondence to Qingsong Zou .

Editor information

Editors and Affiliations

  1. Sun Yat-sen University, Guangzhou, Guangdong, China

    Hong Shen

  2. Sun Yat-sen University, Guangzhou, China

    Yingpeng Sang

  3. Shenzhen Institute of Advanced Technology, Shenzhen, China

    Yong Zhang

  4. Sun Yat-sen University, Guangzhou, China

    Nong Xiao

  5. University of Georgia, Athens, GA, USA

    Hamid R. Arabnia

  6. University of Utah, Salt Lake City, USA

    Geoffrey Fox

  7. Western Michigan University, Kalamazoo, MI, USA

    Ajay Gupta

  8. Stevens Institute of Technology, Hoboken, NJ, USA

    Manu Malek

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Xu, Z., Zou, Q. (2022). A Molecular Dynamics Based Multi-scale Platelet Aggregation Model and Its High-Throughput Simulation. In: Shen, H., et al. Parallel and Distributed Computing, Applications and Technologies. PDCAT 2021. Lecture Notes in Computer Science(), vol 13148. Springer, Cham. https://doi.org/10.1007/978-3-030-96772-7_8

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  • DOI: https://doi.org/10.1007/978-3-030-96772-7_8

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-96771-0

  • Online ISBN: 978-3-030-96772-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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