The blood flow and transportation of molecules in the cardiovascular system plays crucial role in the genesis and progression of atherosclerosis. Atherosclerosis shows predilection in regions of the arterial tree with hemodynamic particularities, as local disturbances of wall shear stress in space, and locally high concentrations of lipoprotein. A semi-permeable nature of the arterial wall computational model is incorporated with hydraulic conductivity and permeability treated as wall shear stress dependent. Six image-based human diseased right coronary arteries (RCA) are used to elucidate the low-density lipoprotein (LDL) transport. The 3D reconstruction technique is a combination of angiography and IVUS. The numerical simulation couples the flow equations with the transport equation applying realistic boundary conditions at the wall. The coupling of fluid dynamics and solute dynamics at the endothelium is achieved by the Kedem-Katchalsky equation (water infiltration). The luminal surface LDL concentration at the arterial wall is flow-dependent with local variations due to geometric features. The relationship between WSS and luminal surface concentration of LDL indicates that LDL is elevated at locations where WSS is low. There is medium correlation (Pearson) between low WSS and high LDL. The degree of elevation in luminal surface LDL concentration is mostly affected by the water infiltration velocity at the vessel wall. Under constant water infiltration the shear dependent endothelial permeability effects, in comparison to those using constant value, are marginal. Area-averaged normalized LDL concentration over the RCAs, using constant water infiltration and endothelial permeability is 3.6% higher than that at the entrance. Area-averaged normalized LDL concentration over the RCAs, using shear dependent water infiltration and endothelial permeability is 9.6%. Perspective computational fluid dynamics users, incorporating mass transfer (LDL) within the blood flow, are forced to treat the problem using shear dependent endothelial values.