ArticleBiomechanics and modeling in mechanobiology2018
Fibrin polymerization simulation using a reactive dissipative particle dynamics method.
Article in Biomechanics and modeling in mechanobiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Mesoscale Simulations of Blood Coagulation in Flow and Quiescent Domains Using SDPD.International journal for numerical methods in biomedical engineering · 2026Article
- Clots reveal anomalous elastic behavior of fiber networks.Science advances · 2024Article
- A simplified mesoscale 3D model for characterizing fibrinolysis under flow conditions.Scientific reports · 2023Article
- Mathematical modeling to understand the role of bivalent thrombin-fibrin binding during polymerization.PLoS computational biology · 2022Article
- Development of a mesoscopic framework spanning nanoscale protofibril dynamics to macro-scale fibrin clot formation.Journal of the Royal Society, Interface · 2021Article
- Investigating the two regimes of fibrin clot lysis: an experimental and computational approach.Biophysical journal · 2021Article
- Fracture mechanics analysis of fibrin fibers using mesoscale and continuum level methods.Informatics in medicine unlocked · 2021Article
- Multiscale Network Modeling of Fibrin Fibers and Fibrin Clots with Protofibril Binding Mechanics.Polymers · 2020Article
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Authors and funding
3 authors.
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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.
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