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 >

A. Colombo¹, U. Galvanetto²

CMES-Computer Modeling in Engineering & Sciences, Vol.53, No.3, pp. 235-254, 2009, DOI:10.3970/cmes.2009.053.235

Abstract The paper addresses the problem of computing the stable manifolds of equilibria and limit cycles of saddle type in piecewise smooth dynamical systems. All singular points that are generically present along one-dimensional or two-dimensional manifolds are classified and such a classification is then used to define a method for the numerical computation of the stable manifolds. Finally the proposed method is applied to the case of a stick-slip oscillator. More >

Yi W. Wan¹, Huan J. Keh²

CMES-Computer Modeling in Engineering & Sciences, Vol.53, No.1, pp. 73-94, 2009, DOI:10.3970/cmes.2009.053.073

Abstract The problem of the rotation of a rigid particle of revolution about its axis in a viscous fluid is studied theoretically in the steady limit of low Reynolds number. The fluid is allowed to slip at the surface of the particle. A singularity method based on the principle of distribution of a set of spherical singularities along the axis of revolution within a prolate particle or on the fundamental plane within an oblate particle is used to find the general solution for the fluid velocity field that satisfies the boundary condition at infinity. The slip… More >

Yu Miao¹, Qiao Wang¹, Bihai Liao^1,2, Junjie Zheng¹

CMES-Computer Modeling in Engineering & Sciences, Vol.53, No.1, pp. 1-22, 2009, DOI:10.3970/cmes.2009.053.001

Abstract As a truly meshless method, the Hybrid Boundary Node method (Hybrid BNM) does not require a `boundary element mesh', either for the purpose of interpolation of the solution variables or for the integration of `energy'. This paper presents a further development of the Hybrid BNM to the 2D elastodynamics. Based on the radial basis function (RBF) and the Hybrid BNM, it presents an inherently meshless, boundary-only technique, which named dual hybrid boundary node method (DHBNM), for solving 2D elastodynamics. In this study, the RBFs are employed to approximate the inhomogeneous terms via dual reciprocity method More >

A.R. da Silva¹, A. Silveira-Neto^2,3, D.A. Rade^2,4, R.Francis⁴, E.A. Santos⁴

CMES-Computer Modeling in Engineering & Sciences, Vol.50, No.3, pp. 285-304, 2009, DOI:10.3970/cmes.2009.050.285

Abstract In the context of computational fluid dynamics a numerical investigation of incompressible flow around fixed pairs of rigid circular cylinders was carried out. The two-dimensional filtered Navier-Stokes equations with the Smagorinsky sub-grid scale model were solved using a Cartesian non-uniform grid. The immersed Boundary Method with the Virtual Physical Model was used in order to model the presence of two circular cylinders embedded in the flow. The fractional time step method was used to couple pressure and velocity fields. The simulations were carried out for Reynolds number equal to 72,000 for pitch ratio equal to More >

Chun-Lang Yeh ¹

CMES-Computer Modeling in Engineering & Sciences, Vol.50, No.3, pp. 253-284, 2009, DOI:10.3970/cmes.2009.050.253

Abstract This paper investigates the instability of a liquid thread by molecular dynamics (MD) simulation. The influences of liquid thread radius, fundamental cell length, and temperature are discussed. Snapshots of molecules, number of liquid particles formed, and density field are analyzed. Two linear stability criteria, namely Rayleigh's stability criterion and Kim's stability criterion, are accessed for their validity in molecular scale. It is found that a liquid thread is more unstable and produces more liquid particles in the fundamental cell when it is thinner or at a higher temperature. In addition, a liquid thread with a More >