Dynamics of filaments of scroll waves

This has been written as a chapter for "Engineering Chemical Complexity II", and as such does not have an abstract.Comment: 18 pages, 10 figure

Role of a habitat's air humidity in Covid-19 mortality

Transient local over-dry environment might be a contributor and an explanation for the observed asynchronous local rises in Covid-19 mortality. We propose that a habitat's air humidity negatively correlate with Covid-19 morbidity and mortality, and support this hypothesis on the example of publicly available data from German federal states.Comment: 3 pages; 1 figure; as accepted to Science of the Total Environment on 15/04/202

Evolution of spiral and scroll waves of excitation in a mathematical model of ischaemic border zone

Abnormal electrical activity from the boundaries of ischemic cardiac tissue is recognized as one of the major causes in generation of ischemia-reperfusion arrhythmias. Here we present theoretical analysis of the waves of electrical activity that can rise on the boundary of cardiac cell network upon its recovery from ischaemia-like conditions. The main factors included in our analysis are macroscopic gradients of the cell-to-cell coupling and cell excitability and microscopic heterogeneity of individual cells. The interplay between these factors allows one to explain how spirals form, drift together with the moving boundary, get transiently pinned to local inhomogeneities, and finally penetrate into the bulk of the well-coupled tissue where they reach macroscopic scale. The asymptotic theory of the drift of spiral and scroll waves based on response functions provides explanation of the drifts involved in this mechanism, with the exception of effects due to the discreteness of cardiac tissue. In particular, this asymptotic theory allows an extrapolation of 2D events into 3D, which has shown that cells within the border zone can give rise to 3D analogues of spirals, the scroll waves. When and if such scroll waves escape into a better coupled tissue, they are likely to collapse due to the positive filament tension. However, our simulations have shown that such collapse of newly generated scrolls is not inevitable and that under certain conditions filament tension becomes negative, leading to scroll filaments to expand and multiply leading to a fibrillation-like state within small areas of cardiac tissue.Comment: 26 pages, 13 figures, appendix and 2 movies, as accepted to PLoS ONE 2011/08/0

BeatBox - HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology

The BeatBox simulation environment combines flexible script language user interface with the robust computational tools, in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level, so that cell excitation, tissue/anatomy models, stimulation protocols may be included into a BeatBox script, and simulation run either sequentially or in parallel (MPI) without re-compilation. BeatBox is a free software written in C language to be run on a Unix-based platform. It provides the whole spectrum of multi scale tissue modelling from 0-dimensional individual cell simulation, 1-dimensional fibre, 2-dimensional sheet and 3-dimensional slab of tissue, up to anatomically realistic whole heart simulations, with run time measurements including cardiac re-entry tip/filament tracing, ECG, local/global samples of any variables, etc. BeatBox solvers, cell, and tissue/anatomy models repositories are extended via robust and flexible interfaces, thus providing an open framework for new developments in the field. In this paper we give an overview of the BeatBox current state, together with a description of the main computational methods and MPI parallelisation approaches.Comment: 37 pages, 10 figures, last version submitted to PLOS ON

Non-standard Abilities of PostgreSQL

Import 22/07/2015Cílem bakalářské práce je prozkoumat nadstandardní vlastnosti databázového systému PostgreSQL nad rámec standardu SQL, respektive konkurečních databázových systémů a následně pro ně najít situace, ve kterých se dají vhodně uplatnit. V práci jsou nejprve postupně vyčteny možnosti uživatelské rozšířitelnosti PostgreSQL databáze a následně vybrány, zdokumentovány a zdůvodněny právě ty, které jsou jen obtížně nahraditelné vlastnostmi standardu SQL. Další část práce se soustředí na postup vytvoření jednoho praktického uživatelského rozšíření datábaze. Tato část podrobně popisuje, co všechno bylo při implementaci tohoto rozšíření nutno provést. Závěrečná část práce se pak stručně zabývá srovnáním dvou konkurečních SŘBD z hlediska rozšířitelnosti.The goal of this bachelor thesis is to explore non-standard abilities of PostgreSQL database system beyond the SQL standard respectively beyond other competitive database systems and to find situations of practical applications for these non-standard abilities subsenquently. As first there are listed user-defined extensibility options of the PostgreSQL database and then there are picked those that are difficult to replace with abilities of SQL standard. Next part of the thesis is focused on process of creating one practical user-defined extension of the database system. This part in detail describes what was needed for the implementation of that user-defined extension. Final part then briefly compares PostgreSQL database with two other database managements systems from the point of extensibility.460 - Katedra informatikyvelmi dobř

Dynamics of cardiac re-entry in micro-CT and serial histological sections based models of mammalian hearts

Cardiac re-entry regime of self-organised abnormal synchronisation underlie dangerous arrhythmias and fatal fibrillation. Recent advances in the theory of dissipative vortices, experimental studies, and anatomically realistic computer simulations, elucidated the role of cardiac re-entry interaction with fine anatomical features in the heart, and anatomy induced drift. The fact that anatomy and structural anisotropy of the heart is consistent within a species suggested its possible functional effect on spontaneous drift of cardiac re-entry. A comparative study of the anatomy induced drift could be used in order to predict evolution of atrial arrhythmia, and improve low-voltage defibrillation protocols and ablation strategies. Here, in micro-CT based model of rat pulmonary vein wall, and in sheep atria models based on high resolution serial histological sections, we demonstrate effects of heart geometry and anisotropy on cardiac re-entry anatomy induced drift, its pinning to fluctuations of thickness in the layer. The data sets of sheep atria and rat pulmonary vein wall are incorporated into the BeatBox High Performance Computing simulation environment. Re-entry is initiated at prescribed locations in the spatially homogeneous mono-domain models of cardiac tissue. Excitation is described by FitzHugh-Nagumo kinetics. In the in-silico models, isotropic and anisotropic conduction show specific anatomy effects and the interplay between anatomy and anisotropy of the heart. The main objectives are to demonstrate the functional role of the species hearts geometry and anisotropy on cardiac re-entry anatomy induced drift. In case of the rat pulmonary vein wall with ~90 degree transmural fibre rotation, it is shown that the joint effect of the PV wall geometry and anisotropy turns a plane excitation wave into a re-entry pinned to a small fluctuation of thickness in the wall