Jason F. Hammond¹, Elizabeth J. Stewart², John G. Younger³, Michael J.Solomon², David M. Bortz^4,5

CMES-Computer Modeling in Engineering & Sciences, Vol.98, No.3, pp. 295-340, 2014, DOI:10.32604/cmes.2014.098.295

Abstract The overall goal of this work is to develop a numerical simulation which correctly describes a bacterial biofilm fluid-structure interaction and separation process. In this, the first of a two-part effort, we fully develop a convergent scheme and provide numerical evidence for the method order as well as a full 3D separation simulation. We use an immersed boundary-based method (IBM) to model and simulate a biofilm with density and viscosity values different from than that of the surrounding fluid. The simulation also includes breakable springs connecting the bacteria in the biofilm which allows the inclusion of erosion and detachment into… More >

V.B.Shim ¹, K. Mithraratne ¹

CMES-Computer Modeling in Engineering & Sciences, Vol.98, No.3, pp. 279-294, 2014, DOI:10.32604/cmes.2014.098.279

Abstract The activation of NF-kB is an important precursor in developing melanoma. However the role of mechanical stimulation in the NF-kB activation has not been studied. We used a multiscale computational modeling approach to investigate the role of mechanical stimulation and the skin tissue internal structures in the activation of NF-kB. Our model is made up of three levels – 1) the macro level where a FE model of the Zygomaticus major muscle was developed; 2) the meso level where a micro FE model of the skin block using a sample from human cadaver was developed; 3) the cell level where… More >

T.I. Zohdi¹

CMES-Computer Modeling in Engineering & Sciences, Vol.98, No.3, pp. 261-277, 2014, DOI:10.32604/cmes.2014.098.261

Abstract A widespread use of lasers is for the ablation of biological tissue, in particular for dermal applications involving the removal of cancerous tissue, skin spots, aged skin and wrinkles. For a laser to ablate tissue, the power intensity must be sufficiently high to induce vaporization/burning of the target material. However, if performed improperly, the process can cause excessive microscale thermal injuries to surrounding healthy tissue. This motivates the present work, which attempts to develop and assemble simple models for the primary heat transfer mechanisms that occur during the process. First, in order to qualitatively understand the system, the terms that… More >

Qing Song Tu¹, Michelle Lee², Samuel Zhang², Shaofan Li¹

CMES-Computer Modeling in Engineering & Sciences, Vol.98, No.3, pp. 247-259, 2014, DOI:10.32604/cmes.2014.098.247

Abstract In this paper, we present molecular dynamics simulations of diffusion of Na⁺, K⁺, and Cl^- ions through the single-walled carbon nanotubes(SWCNTs) that are embedded into the membrane of cells in aqueous solutions. A simplified atomic cell model that considers bilayer membranes is employed to study the transportation of ions inside CNTs. The simulated results indicate that the diffusion properties of ions and selectivity of CNT with respect to ions are affected by biological complexity of the cell membrane. We have found that the ion diffusion only occurs in the CNTs with chirality higher than (8, 8), which is bigger than… More >

Eduardo M. B. Campello^1,2, Tarek I. Zohdi³

CMES-Computer Modeling in Engineering & Sciences, Vol.98, No.2, pp. 221-245, 2014, DOI:10.3970/cmes.2014.098.221

Abstract This work deals with the bombardment of a stream of particles possessing varying mean particle size, velocity and aspect ratio into a cell that has fixed (known) compliance characteristics. The particles are intended to penetrate the cell membrane causing zero or minimum damage and deliver foreign substances (which are attached to their surfaces) to the interior of the cell. We adopt a particle-based (discrete element method) computational model that has been recently developed by the authors to describe both the incoming stream of particles and the cell membrane. By means of parametric numerical simulations, treating the stream’s mean particle size,… More >

Liqiang Lin¹, Xianqiao Wang², Xiaowei Zeng^1,3

CMES-Computer Modeling in Engineering & Sciences, Vol.98, No.2, pp. 203-220, 2014, DOI:10.3970/cmes.2014.098.203

Abstract The Voronoi tessellation is employed to describe cellular patterns and to simulate cell division and cell remodeling in epithelial tissue. First, Halton sequence is utilized to generate the random generators of Voronoi cell points. The centroidal Voronoi cell center is obtained by probabilistic Lloyd's method and polygonal structure of cell distribution is modeled. Based on the polygonal shape of cells, the instantaneous mechanism of cell division is applied to simulate the cell proliferation and remodeling. Four kinds of single-cell division algorithms are designed with the consideration of cleavage angle. From these simulations, we find that cell topological structure varies case… More >

S.M. Pradhan¹, K.S.Katti¹, D.R. Katti¹

CMES-Computer Modeling in Engineering & Sciences, Vol.98, No.2, pp. 181-201, 2014, DOI:10.3970/cmes.2014.098.181

Abstract Multiscale modeling of collagen fibril is carried out by incorporating the material properties of collagen obtained from steered molecular dynamics into the finite element model of collagen fibril with inclusion of crosslinks. The results indicate that the nonbonded interactions between collagen and mineral contribute to the significant enhancement of the elastic modulus of collagen fibril at all the crosslink densities in both the low strain and high strain regimes. The crosslinks are found to play an important role in the mechanical response of collagen fibril, the enhancement in elastic modulus ranging from 5-11% for various crosslink densities compared to the… More >

E. P. Yalcintas¹, J. Hu¹, Y. Liu^1,2, A. Voloshin^1,2,3

CMES-Computer Modeling in Engineering & Sciences, Vol.98, No.2, pp. 151-180, 2014, DOI:10.3970/cmes.2014.098.151

Abstract Mechanical behavior of cells plays a crucial role in response to external stimuli and environment. It is very important to elucidate the mechanisms of cellular activities like spreading and alignment as it would shed light on further biological concepts. In this study, a multi-scale computational approach is adopted by modeling the cytoskeleton of cell as a tensegrity structure. The model is based on the complementary force balance between the tension and compression elements, resembling the internal structure of cell cytoskeleton composed of microtubules and actin filaments. The effect of surface topology on strain energy of a spread cell is investigated… More >

J.B. Alford¹, D.C. Simkins¹, R.A. Rembert¹, L. Hoyte, MD²

CMES-Computer Modeling in Engineering & Sciences, Vol.98, No.2, pp. 129-149, 2014, DOI:10.3970/cmes.2014.098.129

Abstract Mechanical deformation of tissues in the female pelvic floor is believed to be central to understanding a number of important aspects of women’s health, particularly pelvic floor dysfunction. A 2008 study of US women reported the prevalence of pelvic floor disorders in the 20 and 39 years range as 9.7% with the prevalence increasing with age until it reaches roughly 50% in the 80 and older age group [Nygaard, Barber, Burgio, and et al (2008)]. Clinical observation indicates a strong correlation between problems such as pelvic organ prolapse/urinary incontinence and vaginal childbirth. It is thought that childbirth parameters like fetal… More >

Louis C. Foucard¹, John Pellegrino¹, Franck J. Vernerey^1,2

CMES-Computer Modeling in Engineering & Sciences, Vol.98, No.1, pp. 101-127, 2014, DOI:10.3970/cmes.2014.098.101

Abstract Many colloidal-sized particles encountered in biological and membranebased separation applications can be characterized as soft vesicles such as cells, yeast, viruses and surfactant micelles. The deformation of these vesicles is expected to critically affect permeation by accommodating pore shapes and sizes or enhancing the adhesion with a pore surface. Numerical and theoretical modelings will be critical to fully understand these processes and thus design novel filtration membranes that target, not only size, but deformability as a selection criterion. The present paper therefore introduces a multiscale strategy that enables the determination of the permeability of a fibrous network with respect to… More >