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 >

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 >

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 >

V.K. Tewary², D.T. Read²

CMES-Computer Modeling in Engineering & Sciences, Vol.6, No.4, pp. 359-372, 2004, DOI:10.3970/cmes.2004.006.359

Abstract An integrated Green's function and molecular dynamics technique is developed for multiscale modeling of a nanostructure in a semi-infinite crystal lattice. The equilibrium configuration of the atoms inside and around the nanostructure is calculated by using molecular dynamics that accounts for nonlinear interatomic forces. The molecular dynamics is coupled with the lattice statics Green's function for a large crystallite containing a million or more atoms. This gives a fully atomistic description of a nanostructure in a large crystallite that includes the effect of nonlinear forces. The lattice statics Green's function is then related to the… More >

L. G. Zhou¹, L. M. Hsiung², Hanchen Huang¹

CMES-Computer Modeling in Engineering & Sciences, Vol.6, No.3, pp. 245-252, 2004, DOI:10.3970/cmes.2004.006.245

Abstract Using molecular dynamics simulations, we study the deformation of polysynthetically twinned (PST) TiAl at room temperature. The simulation cell is pre-strained and thermodynamically relaxed to zero stress, so that no dislocations pre-exist in γ−α₂ interfaces. A uniaxial compression is then applied along one 1/6<112] direction. Our results show that interfacial dislocation pairs nucleate at the γ−α₂ interface under the compression. The glide and agglomeration of these dislocations lead to the nucleation of deformation twins from the interface. Based on our studies, twins may nucleate without pre-existing interfacial dislocations. Further we have monitored the propagation of the More >

T. Iwasaki¹ and H. Miura¹

CMES-Computer Modeling in Engineering & Sciences, Vol.4, No.5, pp. 551-558, 2003, DOI:10.3970/cmes.2003.004.551

Abstract We have developed a molecular-dynamics technique for investigating migration-induced failures in interconnect films for ULSIs. This technique was used to simulate grain-boundary grooving in Al and Cu films. The simulations showed that the grain-boundary grooves are formed by atomic diffusion at the grain boundary. To clarify what kind of underlay material is effective in suppressing this diffusion, we calculated the dependence of groove depth on the kind of underlay material. The calculation showed that the groove depth of the Al film decreases in the order: Al/Ta, Al/W, and Al/TiN while that of the Cu film More >

D.W. Brenner, O.A. Shenderova, D.A. Areshkin, J.D. Schall¹, S.-J. V. Frankland²

CMES-Computer Modeling in Engineering & Sciences, Vol.3, No.5, pp. 643-674, 2002, DOI:10.3970/cmes.2002.003.643

Abstract The derivation of a bond-order potential energy function and a self-consistent tight-binding scheme is presented, followed by a survey of the application of these methods to calculating properties of carbon nanostructures. The modeling studies discussed include properties of functionalized and kinked carbon nanotubes, Raman shifts for hydrogen stored in nanotubes, nanotubes in a composite, properties of nanotubes in applied potential (electrical) fields, and structures and properties of nanocones, nanodiamond clusters and rods, and hybrid diamond-nanotube structures. More >

Chengyu Wei^{1, 2}, Deepak Srivastava ², Kyeongjae Cho¹

CMES-Computer Modeling in Engineering & Sciences, Vol.3, No.2, pp. 255-262, 2002, DOI:10.3970/cmes.2002.003.255

Abstract The temperature dependence of the plastic collapse of single-wall carbon nanotubes under axial compression has been studied with classical molecular dynamics simulations using Tersoff-Brenner potential for C-C interactions. At zero temperature, an (8,0) single-wall carbon nanotube under axial compression collapses by forming fins-like structure which remains within the elastic limit of the system, in agreement of previous molecular dynamics study. At finite temperatures, however, we find that temperature dependent fluctuations can activate the formation of sp3 bonds, in agreement with a recently proposed plastic collapse mechanism of the same nanotube with a generalized tight-binding molecular More >

W. C. Liu, S. Q. Shi, C. H. Woo, Hanchen Huang¹

CMES-Computer Modeling in Engineering & Sciences, Vol.3, No.2, pp. 213-218, 2002, DOI:10.3970/cmes.2002.003.213

Abstract Using molecular dynamics method, we study the nucleation of dislocations and their subsequent propagation during the deposition of tungsten thin films under tension. Aiming to reveal the generic mechanisms of dislocation nucleation during the deposition of polycrystalline thin films, the case of tungsten on a substrate of the same material is considered. The substrate is under uniaxial tension along the [111] direction, with the thermodynamically favored (01^ˉˉ1) surface being horizontal. The simulation results indicate that the nucleation starts with a surface step, where a surface atom is pressed into the film along the [111^ˉˉ] More >

K. Nishimura¹, N. Miyazaki²

CMES-Computer Modeling in Engineering & Sciences, Vol.2, No.2, pp. 143-154, 2001, DOI:10.3970/cmes.2001.002.143

Abstract In this paper, we present a classical molecular dynamics algorithm and its implementation on Cray C90 and Fujitsu VPP700. The characters of this algorithm consist in a grid based on the block division of the atomic system and a neighbor list based on the use of a short range potential. The computer program is used for large scale simulations on a Cray C90 and a 32-node VPP700, and measurements of computational performance are reported. Then, we examine the interaction between a crack propagating and a tilt grain boundary under uniaxial tension using this computer program.… More >