
Programs and Algorithms of Numerical Mathematics 18 : Janov nad Nisou, June 1924, 2016 : proceedings of seminar
Chleboun, J. ; Kůs, Pavel ; Přikryl, Petr ; Segeth, Karel ; Šístek, Jakub ; Vejchodský, Tomáš
This book comprises papers that originated from the invited lectures, survey lectures, short communications, and posters presented at the 18th seminar Programs and Algorithms of Numerical Mathematics (PANM) held in Janov nad Nisou, Czech Republic, June 1924, 2016. All the papers have been peerreviewed. The seminar was organized by the Institute of Mathematics of the Czech Academy of Sciences under the auspices of EUMATHSIN.cz, Czech Network for Mathematics in Industry. It continued the previous seminars on mathematical software and numerical methods held (biennially, with only one exception) in Al šovice, Bratří kov, Janov nad Nisou, Ko řenov, L ázně Libverda, Dolní Maxov, and Prague in the period 19832014. The objective of this series of seminars is to provide a forum for presenting and discussing advanced theoretical as well as practical topics in numerical analysis, computer implementation of algorithms, new approaches to mathematical modeling, and single or multiprocessor applications of computational methods.


Programs and Algorithms of Numerical Mathematics 19 : Hejnice, June 2429, 2018 : proceedings of seminar
Chleboun, J. ; Kůs, Pavel ; Přikryl, Petr ; Rozložník, Miroslav ; Segeth, Karel ; Šístek, Jakub ; Vejchodský, Tomáš
These proceedings contain peerreviewed papers that are based on the invited lectures, survey lectures, short communications, and posters presented at the 19th seminar Programs and Algorithms of Numerical Mathematics (PANM) held in the International Center for Spiritual Rehabilitation, Hejnice, Czech Republic, June 2429, 2018. The seminar was organized by the Institute of Mathematics of the Czech Academy of Sciences under the auspices of EUMATHSIN.cz, Czech Network for Mathematics in Industry, and with the financial support provided by the RSJ Foundation. It continued the previous seminars on mathematical software and numerical methods held (biennially, with only one exception) in Alšovice, Bratříkov, Janov nad Nisou, Kořenov, Lázně Libverda, Dolní Maxov, and Prague in the period 19832016. The objective of this series of seminars is to provide a forum for presenting and discussing advanced topics in numerical analysis, computer implementation of numerical algorithms, new approaches to mathematical modeling, and single or multiprocessor applications of computational methods.


Numerical solution of convectiondiffusion problems by discontinuous Galerkin method
Vlasák, Miloslav ; Dolejší, Vít (advisor) ; Janovský, Vladimír (referee) ; Vejchodský, Tomáš (referee)
This work is concerned with the theoretical analysis of the discontinuous Galerkin finite element method. We use a discontinuous Galerkin formulation for a scalar convectiondiffusion equation with nonlinear convective term. The resulting semidiscretized equations with symmetric (SIPG) or nonsymmetric (NIPG) diffusive term are then discretized in time by Backward Differential formulae (BDF), implicit RungeKutta methods and Time discontinuous Galerkin. All of these schemes are linearized by a suitable explicit extrapolations to avoid nonlinearity in the convective term. These final schemes are theoretically analyzed and error estimates are derived. We also present some superconvergence result for Time discontinuous Galerkin for nonsymmetric operator. Numerical experiments verify the theoretical results.


Adaptive methods for singularly perturbed partial differential equations
Lamač, Jan ; Knobloch, Petr (advisor) ; Franz, Sebastian (referee) ; Vejchodský, Tomáš (referee)
This thesis deals with solving singularly perturbed convection diffusion equations. Firstly, we construct a matched asymptotic expansion of the solution of the singularly perturbed convectiondiffusion equation in 1D and derive a formula for the zerothorder asymptotic expansion in several two dimensional polygonal domains. Further, we present a set of stabilization meth ods for solving singularly perturbed problems and prove the uniform convergence of the Il'inAllenSouthwell scheme in 1D. Finally, we introduce a modification of the streamline upwind Petrov/Galerkin (SUPG) method on convectionoriented meshes. This new method enjoys several profitable properties such as the ful filment of the discrete maximum principle. Besides the analysis of the method and derivation of a priori error estimates in respective energy norms we also carry out several numerical experiments verifying the theoretical results.


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, CrankNicolson, 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 CrankNicolsonova 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


Stochastické modelování reakčnědifuzních 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, reactiondiusion 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, compartmentbased stochastic simulation algorithm and molecularbased stochastic simulation algorithm.


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 email address: janovsky@karlin.mff.cuni.cz Abstract: In this paper we study a microscopic followtheleader 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 NeimarkSacker bifurcations. We introduce so called POM and quasiPOM 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


Use of the hp discontinuous Galerkin method for a simulation of compressible flows
Tarčák, Karol ; Dolejší, Vít (advisor) ; Vejchodský, Tomáš (referee)
Title: Application of hpadaptive 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 NavierStokes equations. Firstly we summarize the construction of the viscous compressible flow model via NavierStokes partial differential equation and discontinuous Galerkin met hod. Then we propose an extension of an already known residuum estimate for stationary problems to nonstationary problems. We observe the beha vior of the proposed estimate and modify an existing hpadaptive 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


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 FokkerPlanck 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...


Automatic hpadaptivity on Meshes with ArbitraryLevel 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 hpadaptivity 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 hpadaptivity is enhanced even more by the ability of the algorithm to work with meshes with arbitrarylevel 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 hpadaptivity on meshes with arbitrarylevel hanging nodes. 1
