Atherosclerosis develops from oxidized low-density lipoprotein molecules (LDL). When oxidized LDL evolves in plaque formations within an artery wall, a series of reactions occur to repair the damage to the artery wall caused by oxidized LDL. Macrophages accumulate inside arterial intima, they started to collect oxidized LDL and form foam cells. Smooth muscle cells accumulate in the atherosclerotic arterial intima, where they proliferate and secrete extracellular matrix to form a fibrous cap. In this study, experimental model of LDL transport on the isolated blood vessel from rabbit on high fat diet after 8 weeks is simulated numerically by using a specific model and histological data. The 3D blood flow is governed by the Navier-Stokes equations, together with the continuity equation. Mass transfer within the blood lumen and through the arterial wall is coupled with the blood flow by the convection-diffusion equation. LDL transport in lumen of the vessel is described by Kedem-Katchalsky equations. The inflammatory process is solved using three additional reaction-diffusion partial differential equations. Matching of histological rabbit data is performed using 3D histological image reconstruction and 3D deformation of elastic body. Computed concentrations of labeled LDL of 5.2 % and macrophages distribution of 4.2% inside the media are found to be in good agreement with experimental results. This simulation study provides a useful tool for understanding and prediction of LDL transport through the arterial wall and evolution of atherosclerotic plaques.