Tei-Chen Chen^1,2, Heng-Chieh Wang¹, Shu-Fan Wu¹, Yen-Hung Lin¹

The International Conference on Computational & Experimental Engineering and Sciences, Vol.9, No.4, pp. 247-262, 2009, DOI:10.3970/icces.2009.009.247

Abstract Mechanical properties of materials in the micro- and nano-meter scale have been successfully obtained by using the indentation technique. Up to now, large-scale atomistic models to simulate the experimental condition, however, still remain computationally demanding. In this article, a simple and accurate method is proposed to derive the intermolecular potential functions of coarse-grained molecular dynamics (CGMD) suitable for various single crystalline materials. This CGMD technique is then provided to simulate nano-indentation process to verify its accuracy and reliability. Simulation results evaluated by CGMD approach are obtained and compared to those predicted by MD. It is More >

Youngmin Lee, Jae Shin Park, Seyoung Im

The International Conference on Computational & Experimental Engineering and Sciences, Vol.10, No.2, pp. 51-52, 2009, DOI:10.3970/icces.2009.010.051

Abstract We study energetics and mobility of dislocations in silicon crystal in atomistic scale. The electronic structure of silicon affects its dynamics, so that it is analyzed with tight-binding method for high accuracy, emerged as a useful method for studying structural and dynamical properties of covalent systems. The tight biding potential used for silicon crystalline is the one of GSP known as a transferable potential. Due to the nature of rare events, the analysis is executed by action-derived molecular dynamics (ADMD) calculations. The changes of the system energy due to dislocation glide are explored with a More >

Sergei Bronnikov¹, Sergei Kostromin, Vyacheslav Zuev

The International Conference on Computational & Experimental Engineering and Sciences, Vol.9, No.4, pp. 207-214, 2009, DOI:10.3970/icces.2009.009.207

Abstract Kinetics of the ordered phase growth in a melted multi-component liquid crystalline mixture subjected to a deep cooling was studied using polarizing optical microscopy. The droplets of the ordered phase revealed in the optical images across the phase transition were segmented and treated statistically. In the resulting histograms, two overlapping statistical ensembles related to two main components of the mixture were recognized. These ensembles were successfully described using principles of irreversible thermodynamics and the mean droplet diameters within both ensembles were determined. Analysis of the mean droplet diameter as a function of time allowed recognition More >

Yohsuke Imai, Hitoshi Kondo, Young Ho KANG, Takuji Ishikawa Chwee Teck Lim, Takami Yamaguchi

The International Conference on Computational & Experimental Engineering and Sciences, Vol.9, No.3, pp. 205-206, 2009, DOI:10.3970/icces.2009.009.205

Abstract Malaria is one of the most serious infectious diseases on earth. We have about five hundred million patients with two million deaths. When a malaria parasite invades and matures inside a red blood cell (RBC), the infected RBC (IRBC) becomes stiffer and cytoadherent. We propose a numerical model of hemodynamics arising from malaria infection. Our model is based on a Lagrangian and free mesh method (particle) method. A spring network model is employed to compute elastic force generated by the deformation of IRBC membrane. Adhesive property of IRBCs to surrounding cells is also expressed by More >

Chun-Lang Yeh¹

The International Conference on Computational & Experimental Engineering and Sciences, Vol.9, No.2, pp. 81-94, 2009, DOI:10.3970/icces.2009.009.081

Abstract In this study, the vaporization process of a nanojet is investigated by molecular dynamics simulation. Liquid argon nanojet made of 44000 Lennard-Jones molecules is investigated under various simulation parameters to examine their influence on the nanojet vaporization process. Snapshots of the molecules, evolution of the density field, and evolution of the intermolecular force are analyzed. The present simulation results can provide insight into the fundamental mechanism of the atomization process and will be helpful for the design of nanojet devices such as nano-printer or nano-sprayer. More >

Siva A. Vanapalli^∗,†, Yixuan Li^†, Frieder Mugele^†, Michel H. G. Duits^†

Molecular & Cellular Biomechanics, Vol.6, No.4, pp. 191-202, 2009, DOI:10.3970/mcb.2009.006.191

Abstract Endogenous granules (EGs) that consist of lipid droplets and mitochondria have been commonly used to assess intracellular mechanical properties via multiple particle tracking microrheology (MPTM). Despite their widespread use, the nature of interaction of EGs with the cytoskeletal network and the type of forces driving their dynamics - both of which are crucial for the interpretation of the results from MPTM technique - are yet to be resolved. In this report, we study the dynamics of endogenous granules in mammalian cells using particle tracking methods. We find that the ensemble dynamics of EGs is diffusive… More >

Yoshitaka Shimada^∗,†, Taiji Adachi^∗,†,‡, Yasuhiro Inoue^∗,†, Masaki Hojo^∗

Molecular & Cellular Biomechanics, Vol.6, No.3, pp. 161-174, 2009, DOI:10.3970/mcb.2009.006.161

Abstract The actin filament, which is the most abundant component of the cytoskeleton, plays important roles in fundamental cellular activities such as shape determination, cell motility, and mechanosensing. In each activity, the actin filament dynamically changes its structure by polymerization, depolymerization, and severing. These phenomena occur on the scales ranging from the dynamics of actin molecules to filament structural changes with its deformation due to the various forces, for example, by the membrane and solvent. To better understand the actin filament dynamics, it is important to focus on these scales and develop its mathematical model. Thus,… More >

Jae-In Kim¹, Hyoseon Jang², Jeong-Hee Ahn³, Kilho Eom⁴, Sungsoo Na⁵

CMC-Computers, Materials & Continua, Vol.9, No.2, pp. 137-152, 2009, DOI:10.3970/cmc.2009.009.137

Abstract Protein dynamics is essential for gaining insight into biological functions of proteins. Although protein dynamics is well delineated by molecular model, the molecular model is computationally prohibited for simulating large protein structures. In this work, we provide the three-dimensional coarser-grained anisotropic model (CGAM), which is based on model reduction applicable to large protein structures. It is shown that CGAM achieves the fast computation on low-frequency modes, quantitatively comparable to original structural model such as elastic network model (ENM). This indicates that the CGAM by model reduction method enable us to understand the functional motion of More >

A.P.S.Selvadurai¹

CMES-Computer Modeling in Engineering & Sciences, Vol.52, No.3, pp. 259-278, 2009, DOI:10.3970/cmes.2009.052.259

Abstract The paper deals with a computational approach for modelling the fragmentation of ice sheets during their impact with stationary structures. The modelling takes into consideration the intact continuum behaviour of the ice as a rate-sensitive elastoplastic material. During impact, the ice sheet can undergo fragmentation, which is controlled by a brittle strength criterion based on the current stress state. The fragmentation allows the generation of discrete elements of the ice sheet, the movements of which are governed by the equations of motion. The contact between individual fragments is governed by a Coulomb criterion. The individual More >

Delfim Soares Jr.¹

CMES-Computer Modeling in Engineering & Sciences, Vol.54, No.2, pp. 201-222, 2009, DOI:10.3970/cmes.2009.054.201

Abstract In this work, meshless methods based on the local Petrov-Galerkin approach are employed for the time-domain analysis of interacting fluid and solid systems. For the spatial discretization of the acoustic fluid and elastodynamic solid sub-domains involved in the coupled analyses, MLPG formulations adopting Gaussian weight functions as test functions are considered, as well as the moving least square method is used to approximate the incognita fields. For time discretization, the Houbolt's method is adopted. The fluid-solid coupled analysis is accomplished by an iterative algorithm. In this iterative approach, each sub-domain of the global model is More >