In order to provide efficient methods to diagnosis cerebral disease (such as cancer, stroke and MS), understanding mass transfer process into tissues and identifying some changes which happen during brain disease is very important. Since it is a very sensitive issue, in this thesis, a comprehensive model of mass transfer in the brain capillary and extra-vascular space is presented for better understanding of mass transfer in the tissues and its differences when the tissues are cancerous. It should be mentioned that lattice Boltzmann method is used in this model to simulate fluid flow in the capillary. The amount of mass transfer in the normal and abnormal capillaries is identified and some parameters which have effects on this process are recognized by using this model. In fact, to determine the factors influencing the mass transfer in a damaged tissue not only is helpful in diagnosis the disease, but also can be used for its treatment. The main advantage of this simulation is the direct application of the real data and taking into account the different parameters as the functions of time and position simultaneously which is highly accurate and easy to use as well. In this thesis, the transfer of contrast agent in capillary lumen, blood brain barrier and the extra-vascular space is considered. The obtained results are compared with existing experimental data and numerical and analytical results and very good agreements are obtained. The results obtained for diffusion of the contrast agent in a damaged capillary by using gamma function as the input function, is in good agreement with the existing analytical and experimental data. It should be mentioned that there are different parameters which affect the mass diffusion into the tissue. The amount of capillary destruction due to illness, factors affecting the red blood cell behavior, capillaries structure and the rate of injection affect the variation of contrast agent concentration in blood and tissues. It is necessary to study the factors affected the contrast agent concentration because the amount of concentration determines the amount of mass diffusion in blood and tissues and consequently indicates the extent of damage or abnormalities of tissues. In this thesis, in addition to determining the diffusion coefficient for damaged tissue, the effect of dead cells in infarcted tissue, the stenosis severity, the capillary curvature and RBC deformation are investigated. Generally, the present results show that the variation of contrast agent concentration is a function of some parameters which can change the wall shear stress. In other words, all factors which affect the wall shear stress can change mass transfer in the capillary wall. The present results show that, even in the region with low shear stress and also in the region with high shear stress, the probability of accumulate and diffusion of particles is high. So, it can be concluded that in addition to shear stress, flow patterns such as vortex, secondary flow and etc. can be effective for accumulating and traort of particles. It should be mentioned that in this thesis, a hybrid 3D method is suggested to simulate red blood cell motion in the blood. This method in addition to enough accuracy, in terms of run time is also affordable. Keywords: Blood brain barrier, lattice Boltzmann method, effective diffusion coefficient, porosity, contrast agent.