K. Kakuda¹, Y. Maeda¹

The International Conference on Computational & Experimental Engineering and Sciences, Vol.14, No.1, pp. 37-42, 2010, DOI:10.3970/icces.2010.014.037

Abstract The applications of a finite element scheme to one-dimensional linear advection-diffusion equation, the incompressible Navier-Stokes equations, and compressible Euler system of equations are presented. The mesh-based scheme is the Petrov-Galerkin weak formulation with exponential weighting functions. Some numerical results demonstrate the workability and the validity of the present approach. More >

B.Cheng¹, R.K.L. Su¹

The International Conference on Computational & Experimental Engineering and Sciences, Vol.15, No.3, pp. 75-84, 2010, DOI:10.3970/icces.2010.015.075

Abstract Deep reinforced concrete (RC) coupling beams with low shear span ratios and conventionally reinforced shear stirrups tend to fail in a brittle way with limited ductility and deformability under reversed cyclic loading. Experimental studies have shown that bolting restrained steel plate (BRSP) to existing deep RC coupling beams can enhance the deformability and energy dissipation while maintaining the flexural stiffness, improving the beams' performance during an earthquake. In this study, a nonlinear finite element package ATENA was used to simulate the overall behavior of three previously tested BRSP retrofitted coupling beams. This paper presents the More >

R. M. Ardito Marretta^*, F. Ales^†

Molecular & Cellular Biomechanics, Vol.7, No.4, pp. 225-266, 2010, DOI:10.3970/mcb.2010.007.225

Abstract In this paper, cell cycle in higher eukaryotes and their molecular networks signals both inG1/SandG2/Mtransitions are replicatedin silico. Biochemical kinetics, converted into a set of differential equations, and system control theory are employed to design multi-nested digital layers to simulate protein-to-protein activation and inhibition for cell cycle dynamics in the presence of damaged genomes. Sequencing and controlling the digital process of four micro-scale species networks (p53/Mdm2/DNA damage, p21mRNA/cyclin-CDK complex, CDK/CDC25/wee1/ SKP2/APC/CKI and apoptosis target genes system) not only allows the comprehension of the mechanisms of these molecule interactions but paves the way for unraveling the… More >

R. M. Ardito Marretta^∗,†, G. Barbaraci^‡

Molecular & Cellular Biomechanics, Vol.7, No.3, pp. 135-164, 2010, DOI:10.3970/mcb.2010.007.135

Abstract Upon severe DNA damage, p21 acts in a dual mode; on the one hand, it inhibits the cyclin-CDK complex for arresting the G2/M transition and on the other hand, it indirectly becomes an apoptotic factor by activating - in sequence - the retinoblastoma protein, E2F1 and APAF1 expressions. But, in a cancer cells proliferation, the mechanisms of, and participants in, the apoptosis failure remain unclear. Since the p21/p53/Mdm2 proteins network normally involves a digital response in a cancer cell, through an original design of a cell signalling-protein simulator, we demonstrate,in silico, that apoptosis phase instability More >

Rami K Korhonen^∗,†, Sang-Kuy Han^‡, Walter Herzog^‡

Molecular & Cellular Biomechanics, Vol.7, No.3, pp. 125-134, 2010, DOI:10.3970/mcb.2010.007.125

Abstract Changes in the osmotic environment cause changes in volume of isolated cells and cells in tissue explants, and the osmotic environment becomes hypotonic in cartilage diseases such as osteoarthritis (OA). However, it is not known how cells respond to a hypotonic osmotic challenge when situated in the fully intact articular cartilage.
A confocal laser scanning microscope was used to image chondrocytes of intact rabbit patellae in an isotonic (300 mOsm) and hypotonic (172 mOsm) immersion medium. Cell volumes were calculated before and 5, 15, 60, 120 and 240 minutes after the change in saline concentration. Local… More >

Fan Song^*

Molecular & Cellular Biomechanics, Vol.7, No.1, pp. 13-24, 2010, DOI:10.3970/mcb.2010.007.013

Abstract The electrostatic interaction effects including the interaction potential, force and torque between the neighboring chondroitin sulfate glycosaminoglycan (CS-GAG) molecular chains in the bottle brush conformation of proteoglycan aggrecan are obtained as the functions of the minimum separation distance and the mutual angle between the molecular chains based on an asymptotic solution of the Poisson-Boltzmann equation that the CS-GAGs satisfy under the normal physiological conditions of articular cartilage. The present study indicates that the electrostatic interactions are not only associated intimately with the separation distance and the mutual angle, which are shown as purely exponential in… More >

K. Kakuda¹, A. Seki¹, Y. Yamauchi¹

CMES-Computer Modeling in Engineering & Sciences, Vol.69, No.3, pp. 281-306, 2010, DOI:10.3970/cmes.2010.069.281

Abstract A finite element scheme based on the concept of TVD (total variation diminishing) with a flux-limiter for the hyperbolic systems of conservation laws is presented. The numerical flux is formulated effectively by the weighted integral form using exponential weighting functions. The TVD finite element scheme is applied to a Riemann problem, namely the shock-tube problem, for the Euler system of equations. Numerical results demonstrate the workability and the validity of the present approach through comparison with the exact solutions. More >

Y.C. Shiah¹, C. L. Tan², R.F. Lee¹

CMES-Computer Modeling in Engineering & Sciences, Vol.69, No.2, pp. 167-198, 2010, DOI:10.3970/cmes.2010.069.167

Abstract In this paper, fully explicit, algebraic expressions are derived for the first and second derivatives of the Green's function for the displacements in a three dimensional anisotropic, linear elastic body. These quantities are required in the direct formulation of the boundary element method (BEM) for determining the stresses at internal points in the body. To the authors' knowledge, similar quantities have never previously been presented in the literature because of their mathematical complexity. Although the BEM is a boundary solution numerical technique, solutions for the displacements and stresses at internal points are sometimes required for More >

Ching Kong Chao^1,2, Chin Kun Chen³, Fu Mo Chen⁴

CMES-Computer Modeling in Engineering & Sciences, Vol.69, No.2, pp. 119-142, 2010, DOI:10.3970/cmes.2010.069.119

Abstract A general solution to a three-phase elliptic inclusion problem subjected to a remote uniform load is provided in this paper. Analysis of the present elasticity problem is rather tedious due to the presence of material inhomogeneities and complex geometric configurations. Based on the technique of conformal mapping and the method of analytical continuation in conjunction with the alternating technique, the general expressions of the displacement and stresses in each layer medium are derived explicitly in a series form. The effects of the material combinations and geometric configurations on the interfacial stresses are discussed in detail More >

Chun-Lang Yeh¹

CMES-Computer Modeling in Engineering & Sciences, Vol.67, No.3, pp. 175-210, 2010, DOI:10.3970/cmes.2010.067.175

Abstract Previous studies of nano-scale liquid threads have almost entirely been devoted to the investigation of a single liquid thread in a periodic fundamental cell. This paper is the first to study the vaporization process of two nano-scale liquid threads coexisting in a periodic fundamental cell by molecular dynamics (MD) simulation. Because of the interaction between the two liquid threads, the vaporization process is different from that of a single liquid thread in a periodic fundamental cell. This study discusses the influences of the liquid thread radius, fundamental cell length, and relative position of the two… More >