Abstract
In this research, large-scale molecular dynamics (MD) simulations were conducted to study the fluid dynamics inside the endothelial glycocalyx layer. A work flowchart regarding constructing the flow/glycocalyx system, undertaking production simulation using the MD method and post-processing was proposed. Following the flowchart, physiological and accelerating flow cases were simulated to reveal velocity and shear stress distributions over the dendritic (tree-like) structure of the glycocalyx, thereby contributing to understanding of the influence of biomolecular complex structures on flow profiles. Besides, the selection of thermostat algorithm was discussed. Results have shown that when the forcing is below a critical value, the velocity fluctuates around a zero mean along the height in the presence of the dendritic glycocalyx. When the forcing is larger than a critical value, the bulk flow was accelerated excessively, departing from the typical physiological flow. Furthermore, distributions of shear stress magnitude among three sub-regions in the ectodomain indicate that shear stress is enhanced near the membrane surface but is impaired in the sugar-chain-rich region due to the flow regulation by sugar chains. Finally, comparisons of velocity evolutions under two widely used thermostats (Lowe-Andersen and Berendsen thermostats) imply that the Lowe-Andersen algorithm is a suitable thermostat for flow problems.
Highlights
Human metabolism requires exchange of materials between circulating blood and tissues
To generate a physiological flow, we first hierarchically decreased the external force on every oxygen atom of water molecules in the ectodomain
The accelerating case was conducted for a physical time of 15 ns, for vx in the last 5 ns is approaching 1 m/s which is typical for most abnormal situations [19]
Summary
Human metabolism requires exchange of materials between circulating blood and tissues. The material exchange occurs across a thin layer of endothelial cells located in the luminal surface of the blood vessels, known as the endothelium. The glycocalyx, a network of membrane-bound proteoglycans and glycoproteins, is located on the apical surface of vascular endothelial cells and is the first barrier in direct contact with blood [2]. The endothelial glycocalyx layer is related to many cardiovascular and renal diseases or illness, such as diabetes [3], ischemia/reperfusion [4], and atherosclerosis [5]. Electron micrograph of endothelium shows that the endothelial glycocalyx features its dendritic (tree-like) structure [6,7] and is exposed to the blood flow. To better understand the pathologies of glycocalyx-related cardiovascular diseases, the flow profile under the dendritic structure of the glycocalyx should be resolved
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