Muhammad H. Zaman¹, Mohammad R. Kaazempur-Mofrad²

Molecular & Cellular Biomechanics, Vol.1, No.4, pp. 291-302, 2004, DOI:10.3970/mcb.2004.001.291

Abstract α-actinin, an actin binding protein, plays a key role in cell migration, cross-links actin filaments in the Z-disk, and is a major component of contractile muscle apparatus. The flexibility of the molecule is critical to its function. The flexibility of various regions of the molecule, including the linker connecting central subunits is studied using constant force steered molecular dynamics simulations. The linker, whose structure has been a subject of debate, is predicted to be semi-flexible. The flexibility of the linker is compared to all possible segments of equal length throughout the molecule. The stretching profile More >

Alvaro Valencia¹

Molecular & Cellular Biomechanics, Vol.1, No.3, pp. 221-232, 2004, DOI:10.3970/mcb.2004.001.221

Abstract Flow dynamics play an important role in the pathogenesis and treatment of intracranial aneurysms. The evaluation of the velocity field in the aneurysm dome and neck is important for the correct placement of endovascular coils, and the temporal and spatial variations of wall shear stress in the aneurysm are correlated with its growth and rupture. This numerical investigation describes the hemodynamic in two models of terminal aneurysm of the basilar artery. Aneurysm models with a aspect ratio of 1.0 and 1.67 were studied. Each model was subject to physiological representative waveform of inflow for a More >

A. Tsourkas, R. Weissleder^1,1

Molecular & Cellular Biomechanics, Vol.1, No.2, pp. 133-146, 2004, DOI:10.3970/mcb.2004.001.133

Abstract Traditionally, fluorescent and luminescent reporter proteins have been used as indicators of gene expression and protein localization. However, insightful mutagenesis and protein engineering strategies have transformed these simple passive reporters into active biological sensors. Molecular reporters are now being designed to alter their intrinsic optical properties in response to specific biomolecular interactions. Applications for these novel biological sensors range from monitoring intracellular pH and ion fluxes to detecting protein-protein interactions and enzymatic activity. The ability to monitor the dynamics of intracellular activity in response to external stimuli can help elucidate the cascade of events involved More >

M.V. Bayas^1,1, K.Schulten^2,2, D. Leckb,^3,3

Molecular & Cellular Biomechanics, Vol.1, No.2, pp. 101-112, 2004, DOI:10.3970/mcb.2004.001.101

Abstract The force-induced dissociation of the strand dimer interface in C-cadherin has been studied using steered molecular dynamics simulations. The dissociation occurred, without domain unraveling, after the extraction of the conserved trypthophans (Trp2) from their respective hydrophobic pockets. The simulations revealed two stable positions for the Trp2 side chain inside the pocket. The most internal stable position involved a hydrogen bond between the ring Ne of Trp2 and the backbone carbonyl of Glu90. In the second stable position, the aromatic ring is located at the pocket entrance. After extracting the two tryptophans from their pockets, the More >

Xiangli Liu¹, S. I. Golubov¹, C. H. Woo^1,2, Hanchen Huang³

CMES-Computer Modeling in Engineering & Sciences, Vol.5, No.6, pp. 527-540, 2004, DOI:10.3970/cmes.2004.005.527

Abstract A Green’s function technique is developed for the relaxation of simulation cell boundaries in the modelling of dislocation interactions using molecular dynamics. This method allows the replacement of fixed or periodical boundary conditions with flexible boundary conditions, thus minimizing the artificial effects due to images forces introduced by the fixed boundary condition, or the periodic repetition of simulation cells. The effectiveness of the Green’s function in the removal of the fixed boundary image forces is first checked in the atomistic simulation involving the glide of the a/2<110> dislocation in bcc tungsten. This method is then applied More >

J. C. Páscoa¹, A. C. Mendes¹, L. M. C. Gato², R. Elder³

CMES-Computer Modeling in Engineering & Sciences, Vol.6, No.6, pp. 537-546, 2004, DOI:10.3970/cmes.2004.006.537

Abstract The paper presents an aerodynamic design method for turbomachinery cascades of blades. The prescribed conditions are the aerodynamic blade load and the blade thickness distributions. An iterative procedure was implemented, based on the solution of the Euler equations, to seek the blade geometry that provides the specified design conditions. A central finite-volume explicit time-marching scheme is used to solve the Euler equations in two-dimensional flow. The numerical scheme uses an adaptive nonlinear artificial dissipation term based on the limiter theory. Starting with the results from the flow analysis through an initially guessed cascade geometry, the More >

R.Kanapady¹, K.K.Tamma²

CMES-Computer Modeling in Engineering & Sciences, Vol.6, No.2, pp. 189-208, 2004, DOI:10.3970/cmes.2004.006.189

Abstract An integrated design of generalized single step LMS methods for applications to nonlinear structural dynamics is described. The design of the mathematical framework encompasses all the traditional and new and recent optimal algorithms encompassing LMS methods, and readily permits the different a-form, v-form and d-form representations in a unique mathematical setting. As such, the theoretical developments and implementation aspects are detailed for subsequent applications to nonlinear structural dynamics problems. The developments naturally inherit a consistent treatment of nonlinear internal forces under the present umbrella of predictor multi-corrector generalized single step representations with a wide variety of algorithmic More >

Y. Bei¹, B.J. Fregly¹, W.G. Sawyer¹, S.A. Banks^1,2, N.H. Kim¹

CMES-Computer Modeling in Engineering & Sciences, Vol.6, No.2, pp. 145-152, 2004, DOI:10.3970/cmes.2004.006.145

Abstract Mild wear of ultra-high molecular weight polyethylene tibial inserts continues to affect the longevity of total knee replacements (TKRs). Using static finite element and elasticity analyses, previous studies have hypothesized that polyethylene wear can be reduced by using a thicker tibial insert to decrease contact pressures. To date, no study has taken this hypothesis to the next step by performing dynamic analyses under in vivo functional conditions to quantify the relationship between contact pressures, insert thickness, and mild wear. This study utilizes multibody dynamic simulations incorporating elastic contact to perform such analyses. \textit {In vivo} fluoroscopic… More >

Haiyi Liang¹, C.H. Woo^1,2, Hanchen Huang³, A.H.W. Ngan⁴, T.X. Yu⁵

CMES-Computer Modeling in Engineering & Sciences, Vol.6, No.1, pp. 105-114, 2004, DOI:10.3970/cmes.2004.006.105

Abstract Molecular dynamics (MD) simulations are performed to study crystalline plasticity during nano-indentation by comparing the elastic-plastic response of three copper substrates with surfaces (001), (110), and (111) crystallographic planes. The effects of elastic anisotropy and crystallographic symmetry on the reduced modulus, dislocation nucleation, and subsequent microstructure evolution, are investigated. The reduced modulus of (111) surface is found to be the largest, while that of (001) surface is the smallest. Elastic stress distribution calculated from finite element method (FEM) is qualitatively consistent with the MD simulation results. Significant differences exist in the deformation behavior in the More >

Spandan Maiti¹, Philippe H. Geubelle¹

CMES-Computer Modeling in Engineering & Sciences, Vol.5, No.2, pp. 91-102, 2004, DOI:10.3970/cmes.2004.005.091

Abstract The dynamic propagation and branching of a mode I crack in polycrystalline brittle materials like ceramics are investigated numerically using a 2-D explicit grain-based cohesive/volumetric finite element scheme. The granular microstructure of the ceramics is taken into account and the crack is restricted to propagate along the grain boundaries. Special emphasis is placed on studying the effect of grain size and cohesive parameters on the crack branching instability. More >