Glycocalyx is a highly charged layer of membrane-bound biological macromolecules attached to a cell membrane. This layer functions as a barrier between a cell and its surrounding. Glycocalyx also serves as a mediator for cell-cell interactions and protects a cell membrane from the direct action of physical forces and stresses allowing the membrane to maintain its integrity. Glycocalyx is also involved in development and progression of many diseases.Glycocalyx is composed of glycosaminoglycans, proteoglycans and other glycoproteins bearing acidic oligosaccharides and terminal sialic acids. Most glycocalyx associated proteins are transmembrane that can be linked to the cytoskeleton. This linkage not only restricts their position and constitutes the foundation of the glycocalyx structure, but it also allows signal transduction from the external to the internal parts of a cell. Here we focus on the endothelial cells' glycocalyx.The aim of this project is to employ Molecular Dynamics simulations to gain insight into the molecular structure and functions of the glycocalyx. This choice is justified by the fact that experimental studies of the glycocalyx are to a large extent restricted by its dynamic and soft nature driven by thermal fluctuations, implying that the glycocalyx has no unique state or structure but it instead is expected to fluctuate significantly in time. Only recent progress in the development of molecular simulation techniques and the availability of larger computer resources have fostered studies of complex biological systems such the glycolalyx itself.