ProteinDF is a density functional program, which is designed to perform molecular orbital calculations on large bio-molecules such as proteins. In ProteinDF, the standard Gaussian basis sets and the resolution of identity method are employed and it is implemented using the object oriented program language, C++. In this study, we report that we have succeeded in the implementation of the B3LYP in ProteinDF. The B3LYP is one of the most reliable density functionals and more accurate electronic structure calculations on proteins become available. In this paper, we report details of our program implementation stressing the program tuning and parallelization, followed by some pilot calculations.

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In this paper, the effect of the imposed shear flow on the diffusion of swimming model micro-organisms in a semi-dilute suspension is investigated. A swimming micro-organism is modelled as a squirming sphere with prescribed tangential surface velocity. Effects of inertia and Brownian motion are neglected. The three-dimensional movement of 27 identical squirmers in a simple shear flow, contained in a cube with periodic boundary conditions, is computed, for random initial positions and orientations, by the Stokesian-dynamics method. When a shear flow is induced in the suspension, the diffusion tensor is no longer isotropic. We investigated the effect of the shear rate, squirming velocity, squirming mode and volume fraction on the unisotropic property of the diffusion tensor. The results show that the diffusivity, when it exists, is strongly dependent on the direction relative to the shear flow, the squirming velocity and the volume fraction.

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Human skin consists of epidermis, dermis and hypodermis, and their constitutions and mechanical properties are quite different. From the biomechanical standpoint, we have proposed a five-layered skin model and an aging model, where the elastic constants and thicknesses alter linearly with aging, and found that the specific buckling mode switches from the stratum corneum buckling to the epidermis buckling in the aging process. The buckling mode switch (BMS) causes a sudden enlargement of wrinkles and an increase of mechanical damages, and consequently leads to a rapid formation of permanent aged wrinkles. In this study, we used a three-layered skin model for further investigation on the validity of BMS, since the upper three layers were enough to investigate the BMS. We first clarified the buckling characteristics of multilayered structure and the mechanism of BMS, and next showed the occurrence point of BMS and its possibility through a parametric study on the specific buckling mode within the feasible range of the elastic constants and thicknesses. Moreover, we confirmed that our aging scenario with the BMS was consistent with the actual age-related changes in the material parameters, and found that the aging process of skin may cause the BMS.

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Medical imaging methods are generally used to diagnostics of respiratory diseases. The information of detailed lung morphology has been available by high-resolution CT images. Although, the CT images can show the structure of lung, there is no system to estimate the function of lung from image quantitatively. In this study, we simulated the pulmonary airflow based on the numerical calculation of 3-D fluid dynamics using CT image based voxel data. To derive the pressure and velocity profiles in the bronchi, we used the SMAC method with QUICK scheme. The area of fluid was defined as bronchi having the diameter larger than 1.5 mm (three times of the voxel size). Calculated results showed that the pressure gradient became large at the bronchial generation larger than 3rd. This behavior was consistent with 1-D analytical estimation. We could also reproduce the difference of pressure along each airway and the time-dependent behavior of airflow. The method of this study can provide the important therapeutic information of respiratory diseases.

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Because the rupture risk for cerebral aneurysms is very low and comparable risk of surgical complications has been reported, it is very important to predict the rupture risk individually. Patient-specific simulations based on medical images such as CT and MRI enable us calculate hemodynamic and solid tensile stress acting on individual aneurysms, which play important roles in growth and rupture of aneurysms. In this paper, fluid-structure interaction (FSI) analyses of a cerebral aneurysm at the middle cerebral artery (MCA) bifurcation are presented. The peripheral vasculature model with a 0D structural recursive tree model is incorporated and coupled with the 3D FSI simulation to simulate outflow through two branches accurately. The results are compared with FSI simulation with prescribed pressure variation at the outlets. The comparison shows that the pressure at the two outlets are nearly identical and the flow division to the two branches is nearly the same as what we see in the simulation without the peripheral vasculature model. The results suggest that the role of the peripheral vasculature in the MCA aneurysm FSI is not significant.

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