Numeric reconstruction of cytoskeleton with finite element method and topology optimization method

The importance of mechanical aspects related to cell activity and its environment is becoming more evident due to their influence in stem cell differentiation and in the development of diseases such as atherosclerosis. The mechanical tension homeostasis is related to normal tissue behavior and its lack may be related to the formation of cancer, which shows a higher mechanical tension. Due to the complexity of cellular activity, the application of simplified models may elucidate which factors are really essential and which have a marginal effect. The development of a systematic method to reconstruct the elements involved in the perception of mechanical aspects by the cell may accelerate substantially the validation of these models. This work proposes the development of a routine capable of reconstructing the topology of focal adhesions and the actomyosin portion of the cytoskeleton from the displacement field generated by the cell on a flexible substrate. Another way to think of this problem is to develop an algorithm to reconstruct the forces applied by the cell from the measurements of the substrate displacement, which would be characterized as an inverse problem. For these kind of problems, the Topology Optimization Method (TOM) is suitable to find a solution. TOM is consisted of an iterative application of an optimization method and an analysis method to obtain an optimal distribution of material in a fixed domain. One way to experimentally obtain the substrate displacement is through Traction Force Microscopy (TFM), which also provides the forces applied by the cell. Along with systematically generating the distributions of focal adhesion and actin-myosin for the validation of simplified models, the algorithm also represents a complementary and more phenomenological approach to TFM. As a first approximation, actin fibers and flexible substrate are represented through two-dimensional linear Finite Element Method. Actin contraction is modeled as an initial stress of the FEM elements. Focal adhesions connecting actin and substrate are represented by springs. The algorithm was applied to data obtained from experiments regarding cytoskeletal prestress and micropatterning, comparing the numerical results to the experimental ones

Finite volume effects in chiral perturbation theory with twisted boundary conditions

We study the effects of a finite cubic volume with twisted boundary conditions on pseudoscalar mesons. We apply Chiral Perturbation Theory in the p-regime and introduce the twist by means of a constant vector field. The corrections of masses, decay constants, pseudoscalar coupling constants and form factors are calculated at next-to-leading order. We detail the derivations and compare with results available in the literature. In some case there is disagreement due to a different treatment of new extra terms generated from the breaking of the cubic invariance. We advocate to treat such terms as renormalization terms of the twisting angles and reabsorb them in the on-shell conditions. We confirm that the corrections of masses, decay constants, pseudoscalar coupling constants are related by means of chiral Ward identities. Furthermore, we show that the matrix elements of the scalar (resp. vector) form factor satisfies the Feynman–Hellman Theorem (resp. the Ward–Takahashi identity). To show the Ward–Takahashi identity we construct an effective field theory for charged pions which is invariant under electromagnetic gauge transformations and which reproduces the results obtained with Chiral Perturbation Theory at a vanishing momentum transfer. This generalizes considerations previously published for periodic boundary conditions to twisted boundary conditions. Another method to estimate the corrections in finite volume are asymptotic formulae. Asymptotic formulae were introduced by Lüscher and relate the corrections of a given physical quantity to an integral of a specific amplitude, evaluated in infinite volume. Here, we revise the original derivation of Lüscher and generalize it to finite volume with twisted boundary conditions. In some cases, the derivation involves complications due to extra terms generated from the breaking of the cubic invariance. We isolate such terms and treat them as renormalization terms just as done before. In that way, we derive asymptotic formulae for masses, decay constants, pseudoscalar coupling constants and scalar form factors. At the same time, we derive also asymptotic formulae for renormalization terms. We apply all these formulae in combination with Chiral Perturbation Theory and estimate the corrections beyond next-to-leading order. We show that asymptotic formulae for masses, decay constants, pseudoscalar coupling constants are related by means of chiral Ward identities. A similar relation connects in an independent way asymptotic formulae for renormalization terms. We check these relations for charged pions through a direct calculation. To conclude, a numerical analysis quantifies the importance of finite volume corrections at next-to-leading order and beyond. We perform a generic Analysis and illustrate two possible applications to real simulations.

Effective cell-centred time-domain Maxwell's equations numerical solvers

This research work analyses techniques for implementing a cell-centred finite-volume time-domain (ccFV-TD) computational methodology for the purpose of studying microwave heating. Various state-of-the-art spatial and temporal discretisation methods employed to solve Maxwell's equations on multidimensional structured grid networks are investigated, and the dispersive and dissipative errors inherent in those techniques examined. Both staggered and unstaggered grid approaches are considered. Upwind schemes using a Riemann solver and intensity vector splitting are studied and evaluated. Staggered and unstaggered Leapfrog and Runge-Kutta time integration methods are analysed in terms of phase and amplitude error to identify which method is the most accurate and efficient for simulating microwave heating processes. The implementation and migration of typical electromagnetic boundary conditions. from staggered in space to cell-centred approaches also is deliberated. In particular, an existing perfectly matched layer absorbing boundary methodology is adapted to formulate a new cell-centred boundary implementation for the ccFV-TD solvers. Finally for microwave heating purposes, a comparison of analytical and numerical results for standard case studies in rectangular waveguides allows the accuracy of the developed methods to be assessed. © 2004 Elsevier Inc. All rights reserved.

Dynamic fluid-structure interactions using finite volume unstructured mesh procedures

A three-dimensional finite volume, unstructured mesh (FV-UM) method for dynamic fluid–structure interaction (DFSI) is described. Fluid structure interaction, as applied to flexible structures, has wide application in diverse areas such as flutter in aircraft, wind response of buildings, flows in elastic pipes and blood vessels. It involves the coupling of fluid flow and structural mechanics, two fields that are conventionally modelled using two dissimilar methods, thus a single comprehensive computational model of both phenomena is a considerable challenge. Until recently work in this area focused on one phenomenon and represented the behaviour of the other more simply. More recently, strategies for solving the full coupling between the fluid and solid mechanics behaviour have been developed. A key contribution has been made by Farhat et al. [Int. J. Numer. Meth. Fluids 21 (1995) 807] employing FV-UM methods for solving the Euler flow equations and a conventional finite element method for the elastic solid mechanics and the spring based mesh procedure of Batina [AIAA paper 0115, 1989] for mesh movement. In this paper, we describe an approach which broadly exploits the three field strategy described by Farhat for fluid flow, structural dynamics and mesh movement but, in the context of DFSI, contains a number of novel features: a single mesh covering the entire domain, a Navier–Stokes flow, a single FV-UM discretisation approach for both the flow and solid mechanics procedures, an implicit predictor–corrector version of the Newmark algorithm, a single code embedding the whole strategy.

A three dimensional finite volume approach to the thermo-mechanical modelling of the shape casting of metals

This paper presents a three dimensional, thermos-mechanical modelling approach to the cooling and solidification phases associated with the shape casting of metals ei. Die, sand and investment casting. Novel vortex-based Finite Volume (FV) methods are described and employed with regard to the small strain, non-linear Computational Solid Mechanics (CSM) capabilities required to model shape casting. The CSM capabilities include the non-linear material phenomena of creep and thermo-elasto-visco-plasticity at high temperatures and thermo-elasto-visco-plasticity at low temperatures and also multi body deformable contact with which can occur between the metal casting of the mould. The vortex-based FV methods, which can be readily applied to unstructured meshes, are included within a comprehensive FV modelling framework, PHYSICA. The additional heat transfer, by conduction and convection, filling, porosity and solidification algorithms existing within PHYSICA for the complete modelling of all shape casting process employ cell-centred FV methods. The termo-mechanical coupling is performed in a staggered incremental fashion, which addresses the possible gap formation between the component and the mould, and is ultimately validated against a variety of shape casting benchmarks.

GENERALIZED FINITE ELEMENT METHOD FOR NONLINEAR THREE-DIMENSIONAL ANALYSIS OF SOLIDS

The Generalized Finite Element Method (GFEM) is employed in this paper for the numerical analysis of three-dimensional solids tinder nonlinear behavior. A brief summary of the GFEM as well as a description of the formulation of the hexahedral element based oil the proposed enrichment strategy are initially presented. Next, in order to introduce the nonlinear analysis of solids, two constitutive models are briefly reviewed: Lemaitre`s model, in which damage and plasticity are coupled, and Mazars`s damage model suitable for concrete tinder increased loading. Both models are employed in the framework of a nonlocal approach to ensure solution objectivity. In the numerical analyses carried out, a selective enrichment of approximation at regions of concern in the domain (mainly those with high strain and damage gradients) is exploited. Such a possibility makes the three-dimensional analysis less expensive and practicable since re-meshing resources, characteristic of h-adaptivity, can be minimized. Moreover, a combination of three-dimensional analysis and the selective enrichment presents a valuable good tool for a better description of both damage and plastic strain scatterings.

Power Factor Calculation by the Finite Element Method

The use of finite element analysis (FEA) to design electrical motors has increased significantly in the past few years due the increasingly better performance of modern computers. Even though the analytical software remains the most used tool, the FEA is widely used to refine the analysis and gives the final design to be prototyped. The power factor, a standard data of motor manufactures data sheet is important because it shows how much reactive power is consumed by the motor. This data becomes important when the motor is connected to network. However, the calculation of power factor is not an easy task. Due to the saturation phenomena the input motor current has a high level of harmonics that cannot be neglected. In this work the FEA is used to evaluate a proposed (not limitative) methodology to estimate the power factor or displacement factor of a small single-phase induction motor. Results of simulations and test are compared.

The Equilibrium Flux Method for the calculation of flows with non-equilbrium chemical reactions

The Equilibrium Flux Method [1] is a kinetic theory based finite volume method for calculating the flow of a compressible ideal gas. It is shown here that, in effect, the method solves the Euler equations with added pseudo-dissipative terms and that it is a natural upwinding scheme. The method can be easily modified so that the flow of a chemically reacting gas mixture can be calculated. Results from the method for a one-dimensional non-equilibrium reacting flow are shown to agree well with a conventional continuum solution. Results are also presented for the calculation of a plane two-dimensional flow, at hypersonic speed, of a dissociating gas around a blunt-nosed body.

Analysis of functionally graded sandwich plate structures with piezoelectric skins, using B-spline finite strip method

Functionally graded materials are composite materials wherein the composition of the constituent phases can vary in a smooth continuous way with a gradation which is function of its spatial coordinates. This characteristic proves to be an important issue as it can minimize abrupt variations of the material properties which are usually responsible for localized high values of stresses, and simultaneously providing an effective thermal barrier in specific applications. In the present work, it is studied the static and free vibration behaviour of functionally graded sandwich plate type structures, using B-spline finite strip element models based on different shear deformation theories. The effective properties of functionally graded materials are estimated according to Mori-Tanaka homogenization scheme. These sandwich structures can also consider the existence of outer skins of piezoelectric materials, thus achieving them adaptive characteristics. The performance of the models, are illustrated through a set of test cases. (C) 2012 Elsevier Ltd. All rights reserved.

Tensile behaviour of a structural adhesive at high temperatures by the extended finite element method

Component joining is typically performed by welding, fastening, or adhesive-bonding. For bonded aerospace applications, adhesives must withstand high-temperatures (200°C or above, depending on the application), which implies their mechanical characterization under identical conditions. The extended finite element method (XFEM) is an enhancement of the finite element method (FEM) that can be used for the strength prediction of bonded structures. This work proposes and validates damage laws for a thin layer of an epoxy adhesive at room temperature (RT), 100, 150, and 200°C using the XFEM. The fracture toughness (G Ic ) and maximum load ( ); in pure tensile loading were defined by testing double-cantilever beam (DCB) and bulk tensile specimens, respectively, which permitted building the damage laws for each temperature. The bulk test results revealed that decreased gradually with the temperature. On the other hand, the value of G Ic of the adhesive, extracted from the DCB data, was shown to be relatively insensitive to temperature up to the glass transition temperature (T g ), while above T g (at 200°C) a great reduction took place. The output of the DCB numerical simulations for the various temperatures showed a good agreement with the experimental results, which validated the obtained data for strength prediction of bonded joints in tension. By the obtained results, the XFEM proved to be an alternative for the accurate strength prediction of bonded structures.

Feasibility of the extended finite element method for the simulation of composite bonded joints

Adhesive-bonding for the unions in multi-component structures is gaining momentum over welding, riveting and fastening. It is vital for the design of bonded structures the availability of accurate damage models, to minimize design costs and time to market. Cohesive Zone Models (CZM’s) have been used for fracture prediction in structures. The eXtended Finite Element Method (XFEM) is a recent improvement of the Finite Element Method (FEM) that relies on traction-separation laws similar to those of CZM’s but it allows the growth of discontinuities within bulk solids along an arbitrary path, by enriching degrees of freedom. This work proposes and validates a damage law to model crack propagation in a thin layer of a structural epoxy adhesive using the XFEM. The fracture toughness in pure mode I (GIc) and tensile cohesive strength (sn0) were defined by Double-Cantilever Beam (DCB) and bulk tensile tests, respectively, which permitted to build the damage law. The XFEM simulations of the DCB tests accurately matched the experimental load-displacement (P-d) curves, which validated the analysis procedure.

Toroid inductor development for a SIC DC-DC converter up to 150kW, based on finite element method

Dissertação para a obtenção do grau de Mestre em Engenharia Electrotécnica Ramo de Energia

Numerical simulations of Lamb waves in plates using a semi-analytical finite element method

Magdeburg, Univ., Fak. für Maschinenbau, Diss., 2011

Numerical analysis of finite volume schemes for population balance equations

Magdeburg, Univ., Fak. für Mathematik, Diss., 2011

Simulación de fluidos inmiscibles con el Particle Finite Element Method (PFEM)

Proyecto de investigación realizado a partir de una estancia en el Centro Internacional de Métodos Computacionales en Ingeniería (CIMEC), Argentina, entre febrero y abril del 2007. La simulación numérica de problemas de mezclas mediante el Particle Finite Element Method (PFEM) es el marco de estudio de una futura tesis doctoral. Éste es un método desarrollado conjuntamente por el CIMEC y el Centre Internacional de Mètodos Numèrics en l'Enginyeria (CIMNE-UPC), basado en la resolución de las ecuaciones de Navier-Stokes en formulación Lagrangiana. El mallador ha sido implementado y desarrollado por Dr. Nestor Calvo, investigador del CIMEC. El desarrollo del módulo de cálculo corresponde al trabajo de tesis de la beneficiaria. La correcta interacción entre ambas partes es fundamental para obtener resultados válidos. En esta memoria se explican los principales aspectos del mallador que fueron modificados (criterios de refinamiento geométrico) y los cambios introducidos en el módulo de cálculo (librería PETSc, algoritmo predictor-corrector) durante la estancia en el CIMEC. Por último, se muestran los resultados obtenidos en un problema de dos fluidos inmiscibles con transferencia de calor.