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Register a new userNumerical Methods to Compute Stresses and Displacements from Cellular Forces: Application to the Contraction of Tissue
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Added by
Qiyao Peng
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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We consider a mathematical model for wound contraction, which is based on solving a momentum balance under the assumptions of isotropy, homogeneity, Hookes Law, infinitesimal strain theory and point forces exerted by cells. However, point forces, described by Dirac Delta distributions lead to a singular solution, which in many cases may cause trouble to finite element methods due to a low degree of regularity. Hence, we consider several alternatives to address point forces, that is, whether to treat the region covered by the cells that exert forces as part of the computational domain or as holes in the computational domain. The formalisms develop into the immersed boundary approach and the hole approach, respectively. Consistency between these approaches is verified in a theoretical setting, but also confirmed computationally. However, the hole approach is much more expensive and complicated for its need of mesh adaptation in the case of migrating cells while it increases the numerical accuracy, which makes it hard to adapt to the multi-cell model. Therefore, for multiple cells, we consider the polygon that is used to approximate the boundary of cells that exert contractile forces. It is found that a low degree of polygons, in particular triangular or square shaped cell boundaries, already give acceptable results in engineering precision, so that it is suitable for the situation with a large amount of cells in the computational domain.
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We propose a new algorithm to compute the X-ray transform of an image represented by unit (pixel/voxel) basis functions. The fundamental issue is equivalently calculating the intersection lengths of the ray with associated units. For any given ray, we first derive the sufficient and necessary condition for non-vanishing intersectability. By this condition, we then distinguish the units that produce valid intersections with the ray. Only for those units rather than all the individuals, we calculate the intersection lengths by the obtained analytic formula. The proposed algorithm is adapted to 2D/3D parallel beam and 2D fan beam. Particularly, we derive the transformation formulas and generalize the algorithm to 3D circular and helical cone beams. Moreover, we discuss the intrinsic ambiguities of the problem itself, and present a solution. The algorithm not only possesses the adaptability with regard to the center position, scale and size of the image, but also is suited to parallelize with optimality. The comparison study demonstrates the proposed algorithm is fast, more complete, and is more flexible with respect to different scanning geometries and different basis functions. Finally, we validate the correctness of the algorithm by the aforementioned scanning geometries.
The Poisson-Nernst-Planck equations with generalized Frumkin-Butler-Volmer boundary conditions (PNP-FBV) describe ion transport with Faradaic reactions and have applications in a wide variety of fields. Using an adaptive time-stepper based on a second-order variable step-size, semi-implicit, backward differentiation formula (VSSBDF2), we observe that when the underlying dynamics is one that would have the solutions converge to a steady state solution, the adaptive time-stepper produces solutions that nearly converge to the steady state and that, simultaneously, the time-step sizes stabilize at a limiting size $dt_infty$. Linearizing the SBDF2 scheme about the steady state solution, we demonstrate that the linearized scheme is conditionally stable and that this is the cause of the adaptive time-steppers behaviour. Mesh-refinement, as well as a study of the eigenvectors corresponding to the critical eigenvalues, demonstrate that the conditional stability is not due to a time-step constraint caused by high-frequency contributions. We study the stability domain of the linearized scheme and find that it can have corners as well as jump discontinuities.
Partial differential equations (PDEs) are used, with huge success, to model phenomena arising across all scientific and engineering disciplines. However, across an equally wide swath, there exist situations in which PDE models fail to adequately model observed phenomena or are not the best available model for that purpose. On the other hand, in many situations, nonlocal models that account for interaction occurring at a distance have been shown to more faithfully and effectively model observed phenomena that involve possible singularities and other anomalies. In this article, we consider a generic nonlocal model, beginning with a short review of its definition, the properties of its solution, its mathematical analysis, and specific concrete examples. We then provide extensive discussions about numerical methods, including finite element, finite difference, and spectral methods, for determining approximate solutions of the nonlocal models considered. In that discussion, we pay particular attention to a special class of nonlocal models that are the most widely studied in the literature, namely those involving fractional derivatives. The article ends with brief considerations of several modeling and algorithmic extensions which serve to show the wide applicability of nonlocal modeling.
In this work, we introduce a novel abstract framework for the stability and convergence analysis of fully coupled discretisations of the poroelasticity problem and apply it to the analysis of Hybrid High-Order (HHO) schemes. A relevant feature of the proposed framework is that it rests on mild time regularity assumptions that can be derived from an appropriate weak formulation of the continuous problem. To the best of our knowledge, these regularity results for the Biot problem are new. A novel family of HHO discretisation schemes is proposed and analysed, and their performance numerically evaluated.
We provide a comparative analysis of qualitative features of different numerical methods for the inhomogeneous geometric Brownian motion (IGBM). The conditional and asymptotic mean and variance of the IGBM are known and the process can be characterised according to Fellers boundary classification. We compare the frequently used Euler-Maruyama and Milstein methods, two Lie-Trotter and two Strang splitting schemes and two methods based on the ordinary differential equation (ODE) approach, namely the classical Wong-Zakai approximation and the recently proposed log-ODE scheme. First, we prove that, in contrast to the Euler-Maruyama and Milstein schemes, the splitting and ODE schemes preserve the boundary properties of the process, independently of the choice of the time discretisation step. Second, we derive closed-form expressions for the conditional and asymptotic means and variances of all considered schemes and analyse the resulting biases. While the Euler-Maruyama and Milstein schemes are the only methods which may have an asymptotically unbiased mean, the splitting and ODE schemes perform better in terms of variance preservation. The Strang schemes outperform the Lie-Trotter splittings, and the log-ODE scheme the classical ODE method. The mean and variance biases of the log-ODE scheme are very small for many relevant parameter settings. However, in some situations the two derived Strang splittings may be a better alternative, one of them requiring considerably less computational effort than the log-ODE method. The proposed analysis may be carried out in a similar fashion on other numerical methods and stochastic differential equations with comparable features.
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