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Biomechanics and Modeling in Mechanobiology

, Volume 17, Issue 5, pp 1389–1403 | Cite as

Fibrin polymerization simulation using a reactive dissipative particle dynamics method

  • Sumith Yesudasan
  • Xianqiao Wang
  • Rodney D. Averett
Original Paper

Abstract

The study on the polymerization of fibrinogen molecules into fibrin monomers and eventually a stable, mechanically robust fibrin clot is a persistent and enduring topic in the field of thrombosis and hemostasis. Despite many research advances in fibrin polymerization, the change in the structure of fibrin clots and its influence on the formation of a fibrous protein network are still poorly understood. In this paper, we develop a new computational method to simulate fibrin clot polymerization using dissipative particle dynamics simulations. With an effective combination of reactive molecular dynamics formularies and many body dissipative particle dynamics principles, we constructed the reactive dissipative particle dynamics (RDPD) model to predict the complex network formation of fibrin clots and branching of the fibrin network. The 340 kDa fibrinogen molecule is converted into a spring-bead coarse-grain system with 11 beads using a topology representing network algorithm, and using RDPD, we simulated polymerization and formation of the fibrin clot. The final polymerized structure of the fibrin clot qualitatively agrees with experimental results from the literature, and to the best of our knowledge this is the first molecular-based study that simulates polymerization and structure of fibrin clots.

Graphical abstract

Keywords

Reactive dissipative particle dynamics Fibrinogen Molecular dynamics Fibrin clot Force field 

Notes

Acknowledgements

Research reported in this publication was supported by the National Heart, Lung, and Blood Institute of the National Institutes of Health under Award Number K01HL115486. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. This study was also supported in part by resources and technical expertise from the Georgia Advanced Computing Resource Center (GACRC), a partnership between the University of Georgia’s Office of the Vice President for Research and Office of the Vice President for Information Technology.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

Supplementary material 1 (mp4 22818 KB)

Supplementary material 2 (mp4 22808 KB)

Supplementary material 3 (mov 61376 KB)

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© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.School of Chemical, Materials, and Biomedical EngineeringUniversity of GeorgiaAthensUSA
  2. 2.School of Environmental, Civil, Agricultural and Mechanical EngineeringUniversity of GeorgiaAthensUSA

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