This article was published in the journal Theoretical Chemistry Accounts [© Springer-Verlag] and the definitive version is available at: http://dx.doi.org/10.1007/s00214-015-1653-3Bone tissue is characterized by nanopores inside the collagen-apatite matrix where fluid can exist and flow. The description of the fluid flow within the bone has however mostly relied on a macroscopic continuum mechanical treatment of the system, and, for this reason, the role of these nanopores has been largely overlooked. However, neglecting the nanoscopic behaviour of fluid within the bone volume could result in large errors in the overall description of the dynamics of fluid. In this work, we have investigated the nanoscopic origin of fluid motion by conducting atomistic molecular dynamics simulations of water confined between two parallel surfaces of hydroxyapatite (HAP), which is the main mineral phase of mammalian bone. The polarizable core–shell interatomic potential model used in this work to simulate the HAP–water system has been extensively assessed with respect to ab initio calculations and experimental data. The structural (pair distribution functions), dynamical (self-diffusion coefficients) and transport (shear viscosity coefficients) properties of confined water have been computed as a function of the size of the nanopore and the temperature of the system. Analysis of the results shows that the dynamical and transport properties of water are significantly affected by the confinement, which is explained in terms of the layering of water on the surface of HAP as a consequence of the molecular interactions between the water molecules and the calcium and phosphate ions at the surface. Using molecular dynamics simulations, we have also computed the slip length of water on the surface of HAP, the value of which has never been reported before
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