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Computer modeling of the inner ear
Perlácová, Tereza ; Jungwirth, Pavel (advisor) ; Vejchodský, Tomáš (referee)
Do mechanického modelu kochley zavádzame implicitné numerické metódy. Tes- tujeme konkrétne štyri metódy: implicitný Euler, Crank-Nicolson, BDF druhého a tretieho rádu na lineárnej a nelineárnej verzii modelu. Nelineárny model obsahuje funkciu so saturujúcou vlastnosťou. Aplikácia implicitných metód na nelineárny model vedie na sústavu nelineárnych rovníc. Predstavujeme dva spôsoby, ako túto sústavu numericky riešiť. Prvý z nich zahrňuje nelinearitu do pravej strany novovzniknutej lineárnej sústavy. Druhý robí linearizáciu nelineárnej funkcie. V práci porovnávame oba spôsoby z hľadiska efektivity a sledujeme ich konvergenciu k referenčnému riešeniu. Pre hodnotu tolerancie, ktorú používame na určenie numerickej konvergencie, je prvý spôsob efektívnejší. V úplne nelineárnom režime druhý spôsob zlyháva, pretože nekon- verguje k referenčnému riešeniu. Výsledkom porovnania implicitných metód je, že Crank-Nicolsonova metóda s prvým spôsobom riešenia nelineárnej sústavy je pre účely nášho modelu najlepšia. Použitie tejto metódy v mechanickom modeli nám umožňuje vytvoriť ľubovoľne presné prepojenie medzi mechanickým a elektrickým modelom kochley, rešpektujúc fyziológiu človeka. 1
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Stochastické modelování reakčně-difuzních procesů v biologii
Lipková, Jana ; Maslowski, Bohdan (advisor) ; Vejchodský, Tomáš (referee)
Many biological processes can be described in terms of chemical reactions and diffusion. In this thesis, reaction-diusion mechanisms related to the formation of Turing patterns are studied. Necessary and sufficient conditions under which Turing instability occur is presented. Behaviour of Turing patterns is investigated with a use of deterministic approach, compartment-based stochastic simulation algorithm and molecular-based stochastic simulation algorithm.
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A traffic flow with a bottelneck
Kovařík, Adam ; Janovský, Vladimír (advisor) ; Vejchodský, Tomáš (referee)
Title: A traffic flow with a bottelneck Author: Adam Kovařík Department: Department of Numerical Mathematics Supervisor: prof. RNDr. Vladimír Janovský, DrSc. Supervisor's e-mail address: janovsky@karlin.mff.cuni.cz Abstract: In this paper we study a microscopic follow-the-leader traffic model on a circu- lar road with a bottleneck. We assume that all drivers are identical and overtaking is not permitted. We sketch a small part of the rich dynamics of the model including Hopf and Neimark-Sacker bifurcations. We introduce so called POM and quasi-POM solutions and an algorithm how to search them. The main goal of this work is to investigate how the optimal velocity model with a bottleneck deals with so called aggressive behavior of dri- vers. The effect of variable reaction time and a combination of both named factors is also tested. Using numerical simulations we'll find out that aggressiveness and faster reactions have positive effect on traffic flow. In the end we discuss models with two bottlenecks and with one extraordinary driver. Keywords: dynamical systems, ODEs, traffic flow, bottleneck, aggressiveness. 1
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Use of the hp discontinuous Galerkin method for a simulation of compressible flows
Tarčák, Karol ; Dolejší, Vít (advisor) ; Vejchodský, Tomáš (referee)
Title: Application of hp-adaptive discontinuous Galerkin method to com- pressible flow simulation Author: Karol Tarčák Department: Department of Numerical Mathematics Supervisor: prof. RNDr. Vít Dolejší, Ph.D., DSc. Abstract: In the present work we study an residuum estimate of disconti- nuous Galerkin method for the solution of Navier-Stokes equations. Firstly we summarize the construction of the viscous compressible flow model via Navier-Stokes partial differential equation and discontinuous Galerkin met- hod. Then we propose an extension of an already known residuum estimate for stationary problems to non-stationary problems. We observe the beha- vior of the proposed estimate and modify an existing hp-adaptive algorithm to use our estimate. Finally we apply the modified algorithm on test cases and present adapted meshes from the numerical experiments. Keywords: discontinuous Galerkin method, adaptivity, error estimate 4
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Deterministické a stochastické modely v molekulární a buněčné biologii
Krasnovský, Pavol ; Vejchodský, Tomáš (advisor) ; Klebanov, Lev (referee)
This thesis presents the main methods that are used to model the time evolution of the number of molecules in a cell. Two of the main aims in cell biology are to compute first the transi- tion probability function and second the density of the invariant measure. These two problems imply a number of conditions and hence we also include the ergodic theory and theory of the invariant measure. We use two illustrative examples of the application of the previously mentioned theories. We verify the necessary and sufficient conditions for the computation of the transition probability function and the density of the invariant measure in case of two types of a chemical system. The probability function and the density are then given by a numerical solution to the Fokker-Planck equation in both the dynamic and the stationary case. Furthermore, we compare the obtained solu- tions to the results from the Monte Carlo simulation. We find that the solutions give almost identical results as the Monte Carlo simulation. At the end of this thesis, we formulate and analyze a chemical system represented by a human cell infected by an influenza virus. Given the complexity of the sys- tem, we compute the results using the Monte Carlo method. In addition we define this problem by a stochastic differential equation with random...
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Automatic hp-adaptivity on Meshes with Arbitrary-Level Hanging Nodes in 3D
Kůs, Pavel ; Vejchodský, Tomáš (advisor) ; Segeth, Karel (referee) ; Dolejší, Vít (referee)
The thesis is concerned with theoretical and practical aspects of the hp- adaptive finite element method for solving elliptic and electromagnetic prob- lems described by partial differential equations in three spatial dimensions. Besides the standard element refinements, the hp-adaptivity allows indepen- dent adaptation of degrees of the polynomial approximation as well. This leads to exponentially fast convergence even for problems with singularities. The efficiency of the hp-adaptivity is enhanced even more by the ability of the algorithm to work with meshes with arbitrary-level hanging nodes. This generality, however, leads to great complexity of the implementation. There- fore, the thesis concentrates on the mathematical analysis of algorithms that have led to successful implementation of the method. In addition, the the- sis discusses the numerical integration in 3D and the implementation of the method itself. Finally, numerical results obtained by this new implemen- tation are presented. They confirm advantages of hp-adaptivity on meshes with arbitrary-level hanging nodes. 1
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Diskrétní princip maxima v metodě konečných prvků prvního řádu
Klejchová, Martina ; Vejchodský, Tomáš (advisor) ; Knobloch, Petr (referee)
In this thesis we study the discrete maximum principle for a diffusion-reaction problem solved by means of various types of nite elements. The work includes the brief characterization of the problem and of the nite element method, de nition of the discrete maximum principle and general conditions for its validity. The main focus of this work is in the analysis of such geometric conditions for the shape and possibly also for the size of the speci c nite elements that guarantee the validity of the discrete maximum principle. Namely, we analyze conditions for intervals, triangles, rectangles, tetrahedra, blocks and triangular prisms.
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Konečné prvky v elektromagnetismu kompatibilní s De Rhamovým diagramem
Rybář, Vojtěch ; Doležel, Ivo (advisor) ; Vejchodský, Tomáš (referee)
Title: Finite elements for electromagnetics compatible with de Rham di- agram Author: Vojtěch Rybář Department: Department of Numerical Mathematics Supervisor: prof. Ing. Ivo Doležel, CSc. Abstract: The present work is devoted to the lowest-order finite elements for solving time-harmonic Maxwell's equations in two dimensions. Suc- cessful approximation of these equations requires the finite element spaces to be compatible with the de Rham diagram. However, the most often used basis functions (the Whitney functions) do not comply with this diagram. Therefore, we construct compatible bases and study their prop- erties. Since the construction is not unique, we investigate the influence of the particular choice on the conditioning of the corresponding finite element matrices. Finally, we utilize the special structure of the stiffness matrices, propose a few iterative schemes, and compare their convergence. Keywords: Maxwell's equations, edge finite element, de Rham diagram, finite element basis 1
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Computation of an anisotropic and nonlinear magnetic field by the finite element method
Kunický, Zdeněk ; Křížek, Michal (referee) ; Vejchodský, Tomáš (advisor)
In the present work we study the modelling of stationary magnetic fields in nonlinear anisotropic media by FEM. The magnetic characteristics of such materials are thoroughly examined and eventually applied to the construction of a full 2D model of an anisotropic steel sheet. Some improvements in the construction in comparison with the ones previously published are achieved. We also present an extension of a 3D model of steel and dielectric laminations for anisotropic sheets. We point out that the standard formulations and the subsequent theorems for the boundary value problems in fact do not correspond with the physical situation. Instead, we propose new formulations that reflect the real physical properties of matter. General existence and uniqueness theorems for the obtained boundary value problems are proved as well as the convergence theorems for the discrete solutions. Finally, the conventional and full 2D model of an anisotropic steel sheet are compared in two transformer core models using the adaptive Newton-Raphson iterative scheme and the obtained results are presented and analysed.
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Computational comparison of hp-adaptive approaches
Kubásek, Petr ; Feistauer, Miloslav (referee) ; Vejchodský, Tomáš (advisor)
Cílem této práce je porovnat řízení hp-adaptivního procesu pomocí referenčního řešení a různých aposteriorních odhadů chyby. Tyto přístupy jsou porovnávány z hlediska globální diskretizační chyby a potřebného počtu stupňů volnosti. Konkrétně se zabýváme explicitními residuálními odhady, implicitními residuálními odhady Dirichletova a Neumannova typu a hierarchickými odhady. Všechny odhady jsou v práci podrobně odvozeny včetně jejich nejvýznamnějších vlastností. Jednotlivé přístupy jsou srovnávány pomocí numerických experimentů. Na jejich základě lze ríci, že nejlepších výsledků dosahuje adaptivita řízená pomocí referenčního řešení společně s implicitním Dirichletovým odhadem. Referenční řešení se zdá být nejspolehlivější metodou zatímco implicitní Dirichletův odhad je, s výjimkou některých případů, nejrychlejší.
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