Number of found documents: 2086
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Bohl-Marek decomposition applied to a class of biochemical networks with conservation properties
Papáček, Štěpán; Matonoha, Ctirad; Duintjer Tebbens, Jurjen
2023 - English
This study presents an application of one special technique, further called as Bohl-Marek decomposition, related to the mathematical modeling of biochemical networks with mass conservation properties. We continue in direction of papers devoted to inverse problems of parameter estimation for mathematical models describing the drug-induced enzyme production networks [3]. However, being aware of the complexity of general physiologically based pharmacokinetic (PBPK) models, here we focus on the case of enzyme-catalyzed reactions with a substrate transport chain [5]. Although our ultimate goal is to develop a reliable method for fitting the model parameters to given experimental data, here we study certain numerical issues within the framework of optimal experimental design [6]. Before starting an experiment on a real biochemical network, we formulate an optimization problem aiming to maximize the information content of the corresponding experiment. For the above-sketched optimization problem, the computational costs related to the two formulations of the same biochemical network, being (i) the classical formulation x˙(t) = Ax(t) + b(t) and (ii) the 'quasi-linear' Bohl-Marek formulation x˙M(t) = M(x(t)) xM(t), can be determined and compared. Keywords: Mathematical modeling; Biochemical network; Pharmacokinetic (PBPK) models Fulltext is available at external website.
Bohl-Marek decomposition applied to a class of biochemical networks with conservation properties

This study presents an application of one special technique, further called as Bohl-Marek decomposition, related to the mathematical modeling of biochemical networks with mass conservation properties. ...

Papáček, Štěpán; Matonoha, Ctirad; Duintjer Tebbens, Jurjen
Ústav teorie informace a automatizace, 2023

Validation of numerical simulations of a simple immersed boundary solver for fluid flow in branching channels
Keslerová, R.; Lancmanová, Anna; Bodnár, Tomáš
2023 - English
This work deals with the flow of incompressible viscous fluids in a two-dimensional branching channel. Using the immersed boundary method, a new finite difference solver was developed to interpret the channel geometry. The numerical results obtained by this new solver are compared with the numerical simulations of the older finite volume method code and with the results obtained with OpenFOAM. The aim of this work is to verify whether the immersed boundary method is suitable for fluid flow in channels with more complex geometries with difficult grid generation. Keywords: immersed boundary method; finite volume method; OpenFOAM Available in digital repository of the ASCR
Validation of numerical simulations of a simple immersed boundary solver for fluid flow in branching channels

This work deals with the flow of incompressible viscous fluids in a two-dimensional branching channel. Using the immersed boundary method, a new finite difference solver was developed to interpret the ...

Keslerová, R.; Lancmanová, Anna; Bodnár, Tomáš
Matematický ústav, 2023

Rooting algebraic vertices of convergent sequences
Hartman, David; Hons, T.; Nešetřil, J.
2023 - English
Structural convergence is a framework for convergence of graphs by Nešetřil andOssona de Mendez that unifies the dense (left) graph convergence and Benjamini-Schramm convergence. They posed a problem asking whether for a given sequenceof graphs (Gn) converging to a limit L and a vertexrofLit is possible to find asequence of vertices (rn) such thatLrooted atris the limit of the graphsGnrootedatrn. A counterexample was found by Christofides and Král’, but they showed thatthe statement holds for almost all vertices r of L. We offer another perspective to theoriginal problem by considering the size of definable sets to which the rootrbelongs.We prove that if r is an algebraic vertex (i.e. belongs to a finite definable set), thesequence of roots (rn) always exists. Available in digital repository of the ASCR
Rooting algebraic vertices of convergent sequences

Structural convergence is a framework for convergence of graphs by Nešetřil andOssona de Mendez that unifies the dense (left) graph convergence and Benjamini-Schramm convergence. They posed a problem ...

Hartman, David; Hons, T.; Nešetřil, J.
Ústav informatiky, 2023

On the problem of singular limit
Caggio, Matteo; Ducomet, B.; Nečasová, Šárka; Tang, T.
2023 - English
We consider the problem of singular limit of the compressible Euler system confined to a straight layer Ωδ = (0, δ)×R², δ > 0. In the regime of low Mach number limit and reduction of dimension the convergence to the strong solution of the 2D incompressible Euler system is shown. Keywords: compressible Euler equations; dissipative measure-valued solutions; low Mach number; thin domain Available in digital repository of the ASCR
On the problem of singular limit

We consider the problem of singular limit of the compressible Euler system confined to a straight layer Ωδ = (0, δ)×R², δ > 0. In the regime of low Mach number limit and reduction of dimension the ...

Caggio, Matteo; Ducomet, B.; Nečasová, Šárka; Tang, T.
Matematický ústav, 2023

Some Robust Approaches to Reducing the Complexity of Economic Data
Kalina, Jan
2023 - English
The recent advent of complex (and potentially big) data in economics requires modern and effective tools for their analysis including tools for reducing the dimensionality (complexity) of the given data. This paper starts with recalling the importance of Big Data in economics and with characterizing the main categories of dimension reduction techniques. While there have already been numerous techniques for dimensionality reduction available, this work is interested in methods that are robust to the presence of outlying measurements (outliers) in the economic data. Particularly, methods based on implicit weighting assigned to individual observations are developed in this paper. As the main contribution, this paper proposes three novel robust methods of dimension reduction. One method is a dimension reduction within a robust regularized linear regression, namely a sparse version of the least weighted squares estimator. The other two methods are robust versions of feature extraction methods popular in econometrics: robust principal component analysis and robust factor analysis. Keywords: dimensionality reduction; Big Data; variable selection; robustness; sparsity Fulltext is available at external website.
Some Robust Approaches to Reducing the Complexity of Economic Data

The recent advent of complex (and potentially big) data in economics requires modern and effective tools for their analysis including tools for reducing the dimensionality (complexity) of the given ...

Kalina, Jan
Ústav teorie informace a automatizace, 2023

Statistical Method Selection Matters: Vanilla Methods in Regression May Yield Misleading Results
Kalina, Jan
2023 - English
The primary aim of this work is to illustrate the importance of the choice of the appropriate methods for the statistical analysis of economic data. Typically, there exist several alternative versions of common statistical methods for every statistical modeling task and the most habitually used (“vanilla”) versions may yield rather misleading results in nonstandard situations. Linear regression is considered here as the most fundamental econometric model. First, the analysis of a world tourism dataset is presented, where the number of international arrivals is modeled for 140 countries of the world as a response of 14 pillars (indicators) of the Travel and Tourism Competitiveness Index. Heteroscedasticity is clearly recognized in the dataset. However, the Aitken estimator, which would be the standard remedy in such a situation, is revealed here to be very inappropriate, regression quantiles represent a much more suitable solution here. The second illustration with artificial data reveals standard regression quantiles to be unsuitable for data contaminated by outlying values, their recently proposed robust version turns out to be much more appropriate. Both illustrations reveal that choosing suitable methods represent an important (and often difficult) part of the analysis of economic data. Keywords: linear regression; assumptions; non-standard situations; robustness; diagnostics Fulltext is available at external website.
Statistical Method Selection Matters: Vanilla Methods in Regression May Yield Misleading Results

The primary aim of this work is to illustrate the importance of the choice of the appropriate methods for the statistical analysis of economic data. Typically, there exist several alternative versions ...

Kalina, Jan
Ústav informatiky, 2023

Fractionally Isomorphic Graphs and Graphons
Hladký, Jan; Hng, Eng Keat
2023 - English
Available in digital repository of the ASCR
Fractionally Isomorphic Graphs and Graphons

Hladký, Jan; Hng, Eng Keat
Ústav informatiky, 2023

Can extended bodies follow geodesic trajectories?
Lukes-Gerakopoulos, Georgios; Mukherjee, Sajal
2023 - English
We provide an extension of the analysis on whether an extended test body can follow a geodesic trajectory given by Mukherjee et al. (2022). In particular, we consider a test body in a pole-dipole-quadrupole approximation under the Ohashi-Kyrian-Semer´ak spin supplementary condition moving in the Schwarzschild and Kerr background. Using orbital setups under which a pole-dipole body can follow geodesic motion, we explore under which conditions this can also take place in the pole-dipole-quadrupole approximation when only the mass quadrupole is taken into account. For our analysis, we employ the assumption that the dipole contribution and the quadrupole contribution vanish independentlly. Keywords: Mathisson–Papapetrou–Dixon equations; particle dynamics; black holes; chaos Fulltext is available at external website.
Can extended bodies follow geodesic trajectories?

We provide an extension of the analysis on whether an extended test body can follow a geodesic trajectory given by Mukherjee et al. (2022). In particular, we consider a test body in a ...

Lukes-Gerakopoulos, Georgios; Mukherjee, Sajal
Astronomický ústav, 2023

Interpolation with restrictions -- role of the boundary conditions and individual restrictions
Valášek, Jan; Sváček, P.
2023 - English
The contribution deals with the remeshing procedure between two computational finite element meshes. The remeshing represented by the interpolation of an approximate solution onto a new mesh is needed in many applications like e.g. in aeroacoustics, here we are particularly interested in the numerical flow simulation of a gradual channel collapse connected with a~severe deterioration of the computational mesh quality. Since the classical Lagrangian projection from one mesh to another is a dissipative method not respecting conservation laws, a conservative interpolation method introducing constraints is described. The constraints have form of Lagrange multipliers enforcing conservation of desired flow quantities, like e.g. total fluid mass, flow kinetic energy or flow potential energy. Then the interpolation problem turns into an error minimization problem, such that the resulting quantities of proposed interpolation satisfy these physical properties while staying as close as possible to the results of Lagrangian interpolation in the L2 norm. The proposed interpolation scheme does not impose any restrictions on mesh generation process and it has a relatively low computational cost. The implementation details are discussed and test cases are shown. Keywords: interpolation; Lagrange multiplier; Lagrange projection Available in digital repository of the ASCR
Interpolation with restrictions -- role of the boundary conditions and individual restrictions

The contribution deals with the remeshing procedure between two computational finite element meshes. The remeshing represented by the interpolation of an approximate solution onto a new mesh is needed ...

Valášek, Jan; Sváček, P.
Matematický ústav, 2023

Dynamics of dissolved organic carbon in surface water during extreme rainfall-runoff events
Matoušková, M.; Fraindová, K.; Bejčková, M.; Kliment, Z.; Vlach, V.; Vlček, Lukáš
2023 - English
The release of a greater amount of natural organic matter (NOM) within climate change is registered in many catchments with peatbog areas. The aim of our research is to study the dynamics of releasing dissolved organic carbon (DOC) into surface water in headwater areas with peatbogs. DOC concentrations are analysed in relation to extreme rainfall-runoff (R-R) events and according to the hydrological preconditions of the basin. These preconditions are described using selected hydroclimatic variables (14 days before the R-R event). The source data comes from stations of the Faculty of Science, Charles University, and the Czech Hydrometeorological Institute. For the evaluation of relations and processes, the Principal component analysis (PCA), hysteresis loops or Pearson correlation coefficient was used. The lag time of DOCmax for Qmax, the dependence of DOCmax and groundwater levels were studied. The influence of flow rate on the decline and ascent phases of DOC\nconcentrations by hysteresis loops and the influence of the number of partial flow maximums on the amount of transported DOC during the R-R event was analysed. Our first results show that great influence on the dynamic of DOC concentration in surface water has the change in groundwater-levels in the peatbog and the outflow amount during the R-R event. The hydroclimatic preconditions of the basin have also a significant influence on the DOC release. Changes in concentrations during R-R events also occurred for other compounds that were studied additionally. Particularly significant was the increase in metals (mainly Fe, Al, Mn) and base cation (K) and decrease in nitrate nitrogen. Keywords: natural organic matter; dissolved organic carbon; peatbog; surface water Fulltext is available at external website.
Dynamics of dissolved organic carbon in surface water during extreme rainfall-runoff events

The release of a greater amount of natural organic matter (NOM) within climate change is registered in many catchments with peatbog areas. The aim of our research is to study the dynamics of releasing ...

Matoušková, M.; Fraindová, K.; Bejčková, M.; Kliment, Z.; Vlach, V.; Vlček, Lukáš
Ústav pro hydrodynamiku, 2023

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