Coarse Grain Molecular Dynamics Simulation of Fibrin Polymerization

Abstract: Studies suggests that patients with deep vein thrombosis and diabetes often have hy-per coagulable blood plasma leading to higher chances of forming thromboembolisms by the rupture of blood clots, which may lead to stroke and death. Despite the advances in the field of blood clot formation and lysis research, the change in mechanical properties and its impli-cation into the formation of thromboembolisms in platelet poor plasma is poorly understood. In this paper, we present a new computational method to simulate fibrin clot formation using molecular simulations. With an effective combination of reactive molecular dynamics con-cept and coarse graining principle, we have utilized the reactive coarse grain molecular dy-namics to predict the complex network formation of fibrin clots and the branching of the fi-brins. The heavy 340 kDa fibrinogen is converted into a simple spring-bead coarse grain sys-tem with 9 beads, and using our customized reactive potentials, we simulated the formation of the fibrin clot. Thus, formed fibrin clot agrees with the experimental results qualitatively, and to our best knowledge this is the first kind of molecular polymerization study of fibrin clot which can lead to improve our understanding about blood clot formation and its relation-ship with mechanical properties.