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Large-scale molecular dynamics simulation of flow under complex structure of endothelial glycocalyx. (English) Zbl 1410.76481

Summary: In this research, large-scale molecular dynamics (MD) simulations are 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 is proposed. Following the flowchart, physiological and accelerating flow cases are simulated to reveal velocity and shear stress distributions over the dendritic (tree-like) structure of the glycocalyx, thereby contributing to the understanding of the influence of biomolecular complex structures on flow profiles. Besides, the selection of a thermostat algorithm is discussed. Results show 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 is 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.

MSC:

76Z05 Physiological flows
92C35 Physiological flow

Software:

SETTLE; VMD; NAMD
PDFBibTeX XMLCite
Full Text: DOI

References:

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