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Large-scale molecular dynamics simulation of flow under complex structure of endothelial glycocalyx

Jiang, XZ; Feng, M; Luo, KH; Ventikos, Y; (2018) Large-scale molecular dynamics simulation of flow under complex structure of endothelial glycocalyx. Computers and Fluids , 173 pp. 140-146. 10.1016/j.compfluid.2018.03.014. (In press). Green open access

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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.

Type: Article
Title: Large-scale molecular dynamics simulation of flow under complex structure of endothelial glycocalyx
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.compfluid.2018.03.014
Publisher version: https://doi.org/10.1016/j.compfluid.2018.03.014
Language: English
Additional information: Copyright © 2018 The Authors. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Keywords: Large-scale, Molecular dynamics, Flow, Endothelial glycocalyx, Complex structure
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Mechanical Engineering
URI: https://discovery.ucl.ac.uk/id/eprint/10045874
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