Simulation details, Statistical Information, and Detailed and Supplementary post-processing and discussion from Large-scale molecular dynamics simulation of coupled dynamics of flow and glycocalyx: towards understanding atomic events on endothelial cell surface

Glycocalyx has a prominent role in orchestrating multiple biological processes occurring at the plasma membrane. In this paper, an all-atom flow/glycocalyx system is constructed with the bulk flow velocity in the physiologically relevant ranges for the first time. The system is simulated by molecular dynamics using 5.8 million atoms. Flow dynamics and statistics in the presence of the glycocalyx are presented and discussed. Complex dynamic behaviours of the glycocalyx, particularly the sugar chains, are observed in response to blood flow. In turn, the motion of glycocalyx, including swing and swirling, disturbs the flow by altering the velocity profiles and modifying vorticity distributions. As a result, the initially one-dimensional forcing is spread to all directions in the region near the endothelial cell surface. Furthermore, the coupled dynamics exist not only between the flow and the glycocalyx but also within the glycocalyx molecular constituents. Finally, comparisons of shear stress distributions between one-dimer and three-dimer cases reveal that the glycocalyx controls the emergence of high shear stresses, which provides new insight into the mechanism of mechanotransduction of the glycocalyx. These findings have relevance in pathologies of glycocalyx-related diseases, for example, in renal or cardiovascular conditions.