Donald F. Ward Jr.^*, William A. Williams^*, Nicole E. Schapiro^*, Samuel R. Christy^*, Genevieve L. Weber^*, Megan Salt, Robert F. Klees^*, Adele Boskey^†, George E. Plopper ^∗,‡

Molecular & Cellular Biomechanics, Vol.4, No.4, pp. 177-188, 2007, DOI:10.3970/mcb.2007.004.177

Abstract Focal adhesion kinase (FAK) is a key integrator of integrin-mediated signals from the extracellular matrix to the cytoskeleton and downstream signaling molecules. FAK is activated by phosphorylation at specific tyrosine residues, which then stimulate downstream signaling including the ERK1/2 pathway, leading to a variety of cellular responses. In this study, we examined the effects of FAK point mutations at tyrosine residues (Y397, Y925, Y861, and Y576/7) on osteogenic differentiation of human mesenchymal stem cells exposed to collagen I and cyclic tensile strain. Our results demonstrate that FAK signaling emanating from Y397, Y925, and to a More >

Xianwu Ling¹, S.N. Atluri¹

CMES-Computer Modeling in Engineering & Sciences, Vol.21, No.1, pp. 81-92, 2007, DOI:10.3970/cmes.2007.021.081

Abstract In this work, single wall carbon nanotubes (SWNTs) are shown to obey a hyperelastic constitutive model at moderate strains and temperatures. We consider the finite temperature effect via the local harmonic approach. The equilibrium configurations were obtained by minimizing the Helmholtz free energy of a representative atom in an atom-based cell model. We show that the strain energy can be fitted by two cubic polynomials, which consequently produces for the linear elasticity a linearly increasing tangent modulus below a critical strain and an almost linearly decreasing tangent modulus beyond the critical strain. To avoid the More >

Z. D. Han, S. N. Atluri¹

CMES-Computer Modeling in Engineering & Sciences, Vol.21, No.1, pp. 41-52, 2007, DOI:10.3970/cmes.2007.021.041

Abstract Straight-forward systematic derivations of the weakly singular boundary integral equations (BIEs) are presented, following the simple and directly-derived approach by Okada, Rajiyah, and Atluri (1989b) and Han and Atluri (2002). A set of weak-forms and their algebraic combinations have been used to avoid the hyper-singularities, by directly applying the "intrinsic properties'' of the fundamental solutions. The systematic decomposition of the kernel functions of BIEs is presented for regularizing the BIEs. The present approach is general, and is applied to developing weakly-singular BIEs for solids and acoustics successfully. More >

S. Sabchevski¹, I. Zhelyazkov², M. Thumm³, S. Illy⁴, B. Piosczyk⁵, T.-M. Tran^6,7, J. Gr. Pagonakis⁸

CMES-Computer Modeling in Engineering & Sciences, Vol.20, No.3, pp. 203-220, 2007, DOI:10.3970/cmes.2007.020.203

Abstract Computer aided design of powerful gyrotrons for electron cyclotron resonance heating and current drive of fusion plasmas requires adequate physical models and efficient software packages for analysis, comparison and optimization of their electron-optical systems through numerical experiments. In this paper, we present and discuss the current status of the simulation tools available to the researchers involved in the development of multi-megawatt gyrotrons for the ITER project, review some of their recent upgrades and formulate directions for further modifications and improvements. Illustrative examples used represent results from recent numerical investigations of real constructions. Some physical problems More >

Chein-Shan Liu¹

CMES-Computer Modeling in Engineering & Sciences, Vol.20, No.3, pp. 157-176, 2007, DOI:10.3970/cmes.2007.020.157

Abstract In many engineering applications the Lie group calculation is very important. With this in mind, the subject of this paper is for an in-depth investigation of time-varying linear systems, and its accompanied Lie group calculations. In terms of system matrix A in Eq. (11) and a one-order lower fundamental solution matrix associated with the sub-state matrix function A_s^s, we propose two methods to nilpotentlize the time-varying linear systems. As a consequence, we obtain two different calculations of the general linear group. Then, the nilpotent systems are further transformed to a unique new system Ż(t) = B(t)Z(t), which More >

N. Osawa¹, K. Hashimoto¹, J. Sawamura¹, J. Kikuchi², Y. Deguchi², T. Yamaura²

CMES-Computer Modeling in Engineering & Sciences, Vol.20, No.1, pp. 43-54, 2007, DOI:10.3970/cmes.2007.020.043

Abstract A new hypothesis regarding heat transmission during line heating is proposed. It states that the distribution of the temperature of the gas adjacent to the plate, T_G, and the overall local heat transfer coefficient, α, depend only on the distance from the torch. An identification technique for T_G and α is developed. The validity of the employed hypothesis and the proposed technique is demonstrated by comparing the measured and identified T_G during a spot heating test. The plate temperature calculated by direct heat conduction analysis closely approximates the one measured for the spot and line heating tests, More >

Weiran Yuan¹, Pu Chen^1,2, Kaishin Liu^1,3

CMES-Computer Modeling in Engineering & Sciences, Vol.17, No.2, pp. 115-134, 2007, DOI:10.3970/cmes.2007.017.115

Abstract In this paper we propose a direct solution method for the quasi-unsymmetric sparse matrix (QUSM) arising in the Meshless Local Petrov-Galerkin method (MLPG). QUSM, which is conventionally treated as a general unsymmetric matrix, is unsymmetric in its numerical values, but nearly symmetric in its nonzero distribution of upper and lower triangular portions. MLPG employs trial and test functions in different functional spaces in the local domain weak form of governing equations. Consequently the stiffness matrix of the resultant linear system is a QUSM. The new solver for QUSM conducts a two-level unrolling technique for LDU factorization More >

Chein-Shan Liu ^1,2

CMES-Computer Modeling in Engineering & Sciences, Vol.17, No.2, pp. 73-94, 2007, DOI:10.3970/cmes.2007.017.073

Abstract The primary objectives of the present exposition focus on five different types of representations of the plastic equations obtained from an elastic-perfectly plastic model by employing different corotational stress rates. They are (a) an affine nonlinear system with a finite-dimensional Lie algebra, (b) a canonical linear system in the Minkowski space, (c) a non-canonical linear system in the Minkowski space, (d) the Lie-Poisson bracket formulation, and (e) a two-generator and two-bracket formulation. For the affine nonlinear system we prove that the Lie algebra of the vector fields is so(5,1), which has dimensions fifteen, and by the… More >

D. Soares Jr.^1,2, W.J. Mansur¹, D.L. Lima³

CMES-Computer Modeling in Engineering & Sciences, Vol.17, No.1, pp. 19-34, 2007, DOI:10.3970/cmes.2007.017.019

Abstract The present paper discussion is concerned with the development of robust and efficient algorithms to model propagation of interacting acoustic and elastic waves. The paper considers acoustic-elastic, acoustic-acoustic and elastic-elastic partitioned analyses of coupled systems; however, the focus here is the acoustic-elastic coupling considering finite elements and the acoustic-acoustic coupling considering finite elements and finite differences (other coupling procedures can be implemented analogously). One important feature of the algorithms presented is that they allow considering different time-steps for different sub-domains; so it is possible to substantially improve efficiency, accuracy and stability of the central difference More >

B. Obradovic¹, M. Radisic², G. Vunjak-Novakovic³

FDMP-Fluid Dynamics & Materials Processing, Vol.3, No.3, pp. 189-202, 2007, DOI:10.3970/fdmp.2007.003.189

Abstract Efficient transport of oxygen is one of the main requirements in tissue engineering systems in order to avoid cell death in the inner tissue regions and support uniform tissue regeneration. In this paper, we review approaches to design of tissue engineering systems with adequate oxygen delivery for cultivation of cartilage and myocardium, two distinctly different tissue types with respect to the tissue structure and oxygen requirements. Mathematical modeling was used to support experimental results and predict oxygen transport within the cultivated tissues and correlate it to the cell response and tissue properties. More >