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- ItemComputational modelling and simulation of cancer growth and migration within a 3D heterogeneous tissue: The effects of fibre and vascular structure(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2019) Macnamara, Cicely K.; Caiazzo, Alfonso; Ramis-Conde, Ignacio; Chaplain, Mark A.J.The term cancer covers a multitude of bodily diseases, broadly categorised by having cells which do not behave normally. Since cancer cells can arise from any type of cell in the body, cancers can grow in or around any tissue or organ making the disease highly complex. Our research is focused on understanding the specific mechanisms that occur in the tumour microenvironment via mathematical and computational modeling. We present a 3D individual-based model which allows one to simulate the behaviour of, and spatio-temporal interactions between, cells, extracellular matrix fibres and blood vessels. Each agent (a single cell, for example) is fully realised within the model and interactions are primarily governed by mechanical forces between elements. However, as well as the mechanical interactions we also consider chemical interactions, for example, by coupling the code to a finite element solver to model the diffusion of oxygen from blood vessels to cells. The current state of the art of the model allows us to simulate tumour growth around an arbitrary blood-vessel network or along the striations of fibrous tissue.
- ItemA gradient-robust well-balanced scheme for the compressible isothermal Stokes problem(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2019) Akbas, Mine; Gallouët, Thierry; Gaßmann, Almut; Linke, Alexander; Merdon, ChristianA novel notion for constructing a well-balanced scheme --- a gradient-robust scheme --- is introduced and a showcase application for a steady compressible, isothermal Stokes equations is presented. Gradient-robustness means that arbitrary gradient fields in the momentum balance are well-balanced by the discrete pressure gradient --- if there is enough mass in the system to compensate the force. The scheme is asymptotic-preserving in the sense that it degenerates for low Mach numbers to a recent inf-sup stable and pressure-robust discretization for the incompressible Stokes equations. The convergence of the coupled FEM-FVM scheme for the nonlinear, isothermal Stokes equations is proved by compactness arguments. Numerical examples illustrate the numerical analysis, and show that the novel approach can lead to a dramatically increased accuracy in nearly-hydrostatic low Mach number flows. Numerical examples also suggest that a straight-forward extension to barotropic situations with nonlinear equations of state is feasible.
- ItemChallenges for drift-diffusion simulations of semiconductors: A comparative study of different discretization philosophies(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2018) Farrell, Patricio; Peschka, DirkWe analyze and benchmark the error and the convergence order of finite difference, finite-element as well as Voronoi finite-volume discretization schemes for the drift-diffusion equations describing charge transport in bulk semiconductor devices. Three common challenges, that can corrupt the precision of numerical solutions, will be discussed: boundary layers at Ohmic contacts, discontinuties in the doping profile, and corner singularities in L-shaped domains. The influence on the order of convergence is assessed for each computational challenge and the different discretization schemes. Additionally, we provide an analysis of the inner boundary layer asymptotics near Ohmic contacts to support our observations.
- ItemModelling and simulation of flame cutting for steel plates with solid phases and melting(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2019) Arenas Jaén, Manuel J.; Hömberg, Dietmar; Lasarzik, Robert; Mikkonen, Pertti; Petzold, ThomasFlame cutting, finite element method, heat equation, phase transitions, transport equationThe goal of this work is to describe in detail a quasi-stationary state model which can be used to deeply understand the distribution of the heat in a steel plate and the changes in the solid phases of the steel and into liquid phase during the flame cutting process. We use a 3D-model similar to previous works from Thiebaud [1] and expand it to consider phases changes, in particular, austenite formation and melting of material. Experimental data is used to validate the model and study its capabilities. Parameters defining the shape of the volumetric heat source and the power density are calibrated to achieve good agreement with temperature measurements. Similarities and differences with other models from literature are discussed.
- ItemFunctional a posteriori error estimation for stationary reaction-convection-diffusion problems(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2014) Eigel, Martin; Samrowski, TatianaA functional type a posteriori error estimator for the finite element discretisation of the stationary reaction-convection-diffusion equation is derived. In case of dominant convection, the solution for this class of problems typically exhibits boundary layers and shock-front like areas with steep gradients. This renders the accurate numerical solution very demanding and appropriate techniques for the adaptive resolution of regions with large approximation errors are crucial. Functional error estimators as derived here contain no mesh-dependent constants and provide guaranteed error bounds for any conforming approximation. To evaluate the error estimator, a minimisation problem is solved which does not require any Galerkin orthogonality or any specific properties of the employed approximation space. Based on a set of numerical examples, we assess the performance of the new estimator. It is observed that it exhibits a good efficiency also with convection-dominated problem settings.
- ItemError control for the approximation of Allen-Cahn and Cahn-Hilliard equations with a logarithmic potential(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2010) Bartels, Sören; Müller, RüdigerA fully computable upper bound for the finite element approximation error of Allen-Cahn and Cahn-Hilliard equations with logarithmic potentials is derived. Numerical experiments show that for the sharp interface limit this bound is robust past topological changes. Modifications of the abstract results to derive quasi-optimal error estimates in different norms for lowest order finite element methods are discussed and lead to weaker conditions on the residuals under which the conditional error estimates hold.
- ItemA reduced-order modeling for efficient design study of artificial valve in enlarged ventricular outflow tracts(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2015) Caiazzo, Alfonso; Guibert, Romain; Vignon-Clementel, Irene E.A computational approach is proposed for efficient design study of a reducer stent to be percutaneously implanted in enlarged right ventricular outflow tracts (RVOT). The need for such a device is driven by the absence of bovine or artificial valves which could be implanted in these RVOT to replace the absent or incompetent native valve, as is often the case over time after Tetralogy of Fallot repair. Hemodynamics are simulated in the stented RVOT via a reduce order model based on proper orthogonal decomposition (POD), while the artificial valve is modeled as a thin resistive surface. The reduced order model is obtained from the numerical solution on a reference device configuration, then varying the geometrical parameters (diameter) for design purposes. To validate the approach, forces exerted on the valve and on the reducer are monitored, varying with geometrical parameters, and compared with the results of full CFD simulations. Such an approach could also be useful for uncertainty quantification. Device design, percutaneous pulmonary valve replacement, proper orthogonal decomposition (POD), finite element method, blood flow CFD, repaired Tetralogy of Fallot.
- ItemA Stokes-consistent backflow stabilization for physiological flows(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2014) Bertoglio, Cristobal; Caiazzo, AlfonsoIn computational fluid dynamics incoming flow at open boundaries, or emphbackflow, often yields to unphysical instabilities for high Reynolds numbers. It is widely accepted that this is due to the incoming energy arising from the convection term, which cannot be empha priori controlled when the velocity field is unknown at the boundary. In order to improve the robustness of the numerical simulations, we propose a stabilized formulation based on a penalization of the residual of a weak Stokes problem on the open boundary, whose viscous part controls the incoming convective energy, while the inertial term contributes to the kinetic energy. We also present different strategies for the approximation of the boundary pressure gradient, which is needed for defining the stabilization term. The method has the advantage that it does not require neither artificial modifications or extensions of the computational domain. Moreover, it is consistent with the Womersley solution. We illustrate our approach on numerical examples
- ItemA tangential regularization method for backflow stabilization in hemodynamics(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2013) Bertoglio, Cristóbal; Caiazzo, AlfonsoIn computational simulations of fluid flows, instabilities at the Neumann boundaries may appear during backflow regime. It is widely accepted that this is due to the incoming energy at the boundary, coming from the convection term, which cannot be controlled when the velocity field is unknown. We propose a stabilized formulation based on a local regularization of the fluid velocity along the tangential directions on the Neumann boundaries. The stabilization term is proportional to the amount of backflow, and does not require any further assumption on the velocity profile. The perfomance of the method is assessed on a twoand three-dimensional Womersley flows, as well as considering a hemodynamic physiological regime in a patient-specific aortic geometry.
- ItemMulti-dimensional modeling and simulation of semiconductor nanophotonic devices(Berlin : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2019) Kantner, Markus; Höhne, Theresa; Koprucki, Thomas; Burger, Sven; Wünsche, Hans-Jürgen; Schmidt, Frank; Mielke, Alexander; Bandelow, UweSelf-consistent modeling and multi-dimensional simulation of semiconductor nanophotonic devices is an important tool in the development of future integrated light sources and quantum devices. Simulations can guide important technological decisions by revealing performance bottlenecks in new device concepts, contribute to their understanding and help to theoretically explore their optimization potential. The efficient implementation of multi-dimensional numerical simulations for computer-aided design tasks requires sophisticated numerical methods and modeling techniques. We review recent advances in device-scale modeling of quantum dot based single-photon sources and laser diodes by self-consistently coupling the optical Maxwell equations with semiclassical carrier transport models using semi-classical and fully quantum mechanical descriptions of the optically active region, respectively. For the simulation of realistic devices with complex, multi-dimensional geometries, we have developed a novel hp-adaptive finite element approach for the optical Maxwell equations, using mixed meshes adapted to the multi-scale properties of the photonic structures. For electrically driven devices, we introduced novel discretization and parameter-embedding techniques to solve the drift-diffusion system for strongly degenerate semiconductors at cryogenic temperature. Our methodical advances are demonstrated on various applications, including vertical-cavity surface-emitting lasers, grating couplers and single-photon sources.