Coarse-grained molecular dynamics simulations of fibrin polymerization: effects of thrombin concentration on fibrin clot structure

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


Studies suggest that patients with deep vein thrombosis and diabetes often have hypercoagulable blood plasma, leading to a higher risk of thromboembolism formation through the rupture of blood clots, which may lead to stroke and death. Despite many advances in the field of blood clot formation and thrombosis, the influence of mechanical properties of fibrin in the formation of thromboembolisms in platelet-poor plasma is poorly understood. In this paper, we combine the concepts of reactive molecular dynamics and coarse-grained molecular modeling to predict the complex network formation of fibrin clots and the branching of fibrin monomers. The 340-kDa fibrinogen molecule was converted into a coarse-grained molecule with nine beads, and using our customized reactive potentials, we simulated the formation and polymerization process of a fibrin clot. The results show that higher concentrations of thrombin result in higher branch-point formation in the fibrin clot structure. Our results also highlight many interesting properties, such as the formation of thicker or thinner fibers depending on the thrombin concentration. To the best of our knowledge, this is the first successful molecular polymerization study of fibrin clots to focus on thrombin concentration.


Coarse-grained MD Fibrinogen Molecular dynamics Blood clot Force field 



The 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, a partnership between the University of Georgia’s Office of the Vice President for Research and Office of the Vice President for Information Technology.


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Copyright information

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

Authors and Affiliations

  • Sumith Yesudasan
    • 1
  • Xianqiao Wang
    • 2
  • Rodney D. Averett
    • 1
  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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