Yes (2092)
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2092
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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. ...
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 ...
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 and Ossona de Mendez that unifies the dense (left) graph convergence and Benjamini-Schramm convergence. They posed a problem asking whether for a given sequence of graphs (Gn) converging to a limit L and a vertex r of L it is possible to find a sequence of vertices (rn) such that L rooted at r is the limit of the graphs Gn rooted at rn. A counterexample was found by Christofides and Král’, but they showed that the statement holds for almost all vertices r of L. We offer another perspective to the original problem by considering the size of definable sets to which the root r belongs. We prove that if r is an algebraic vertex (i.e. belongs to a finite definable set), the sequence of roots (rn) always exists.
Keywords:
rooting; algebraic vertices; convergent sequences
Available in digital repository of the ASCR
Rooting algebraic vertices of convergent sequences
Structural convergence is a framework for convergence of graphs by Nešetřil and Ossona de Mendez that unifies the dense (left) graph convergence and Benjamini-Schramm convergence. They posed a problem ...
Drivers of Private Equity Activity across Europe: An East-West Comparison
Kočenda, Evžen; Shivendra, R.
2023 - English
We investigate the key macroeconomic and institutional determinants of fundraising and investment activities and compare them across Europe, covering 13 Central and Eastern European (CEE) and 16 Western European (WE) countries. Five macroeconomic variables and nineteen institutional variables are selected. These variables are studied using panel data analysis with fixed effects and random effects models over an eleven-year observation period (2010–2020). Bayesian Model Averaging (BMA) is applied to select the key variables. Our results suggest that macroeconomic variables have no significant impact on fundraising and investment activity in either region. Investment activity is a significant driver of fundraising across Europe. Similarly, fundraising and divestment activity are significant drivers of investments across Europe. Institutional variables, however, affect fundraising and investment activity differently. While investment freedom has a significant effect on funds raised in the WE and CEE countries, government integrity and trade freedom are both significant determinants of investments in both European regions. In addition, the results demonstrate that, in contrast to the WE region, fundraising in the CEE region is not country specific. We investigate the key macroeconomic and institutional determinants of fundraising and investment activities and compare them across Europe, covering 13 Central and Eastern European (CEE) and 16 Western European (WE) countries. Five macroeconomic variables and nineteen institutional variables are selected. These variables are studied using panel data analysis with fixed effects and random effects models over an eleven-year observation period (2010–2020). Bayesian Model Averaging (BMA) is applied to select the key variables. Our results suggest that macroeconomic variables have no significant impact on fundraising and investment activity in either region. Investment activity is a significant driver of fundraising across Europe. Similarly, fundraising and divestment activity are significant drivers of investments across Europe. Institutional variables, however, affect fundraising and investment activity differently. While investment freedom has a significant effect on funds raised in the WE and CEE countries, government integrity and trade freedom are both significant determinants of investments in both European regions. In addition, the results demonstrate that, in contrast to the WE region, fundraising in the CEE region is not country specific.
Keywords:
Private equity; Fundraising; Investment
Fulltext is available at external website.
Drivers of Private Equity Activity across Europe: An East-West Comparison
We investigate the key macroeconomic and institutional determinants of fundraising and investment activities and compare them across Europe, covering 13 Central and Eastern European (CEE) and 16 ...
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 ...
Deep learning methods for the acoustic emission methods to evaluate an onset of plastic straining
Parma, Slavomír; Kovanda, Martin; Chlada, Milan; Štefan, Jan; Kober, Jan; Feigenbaum, H. P.; Plešek, Jiří
2023 - English
Development of phenomenological plasticity models, hardening rules, and plasticity theories relies on experimental data of plastic straining. The experimental data are usually measured as the stress–strain response of the material being loaded and do not provide any clues or information about the local response of\nmaterial. In this paper, we analyze the plastic deformation of the material using the acoustic emission method and current state-of-the-art neural network models such as the InceptionTime architecture.
Keywords:
metal plasticity; strain hardening; acoustic emission; neural networks
Fulltext is available at external website.
Deep learning methods for the acoustic emission methods to evaluate an onset of plastic straining
Development of phenomenological plasticity models, hardening rules, and plasticity theories relies on experimental data of plastic straining. The experimental data are usually measured as the ...
Model order reduction for particle-laden flows: systems with rotations and discrete transport operators
Kovárnová, A.; Isoz, Martin
2023 - English
In the present work, we concentrate on particle-laden flows as an example of industry-relevant transport-dominated systems. Our previously-developed framework for data-driven model order reduction (MOR) of such systems, the shifted proper orthogonal decomposition with interpolation via artificial neural networks, is further extended by improving the handling of general transport operators. First, even with intrusive MOR approaches, the underlying numerical solvers can provide only discrete realizations of transports linked to the movement of individual particles in the system. On the other hand, our MOR methodology requires continuous transport operators. Thus, the original framework was extended by the possibility to reconstruct continuous approximations of known discrete transports via another artificial neural network. Second, the treatment of rotation-comprising transports was significantly improved.
Keywords:
model order reduction; shifted POD; artificial neural networks; CFD-DEM; Open- FOAM
Fulltext is available at external website.
Model order reduction for particle-laden flows: systems with rotations and discrete transport operators
In the present work, we concentrate on particle-laden flows as an example of industry-relevant transport-dominated systems. Our previously-developed framework for data-driven model order reduction ...
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 ...
Underground Spaces In Bosonožský Hájek Nature Reserve And Their Geoeducation Importance
Kirchner, Karel; Kuda, František; Baldík, V.; Kubalíková, Lucie
2023 - English
Bosonožský hájek Natural Reserve (Brno, South Moravia) is a very important site from the Earth Science point of view, however, its geodiversity values have been rather overlooked and omitted in the past (the object of legal protection is the occurrence of well-preserved forest ecosystems and endangered species). In the last decades, a series of field work and geophysical measurements has been carried out and the Earth Science phenomena have been identified and described here. These are represented by a dense network of gullies that developed in Pleistocene loess and that are both of natural and anthropogenic origin (some gullies probably developed along the old paths) and specific underground spaces (so called dugouts). Until now, the dugouts in South Moravia have been investigated mainly by archaeologists and those in Bosonožský hájek NR have not been described in detail yet. This brief contribution brings new information about three underground landforms and their possible relationship to the age and development of the gullies. The possibility of different interpretations of the origin of these specific landforms can be considered an opportunity in the field of Earth Science (geosciences) education and as an interesting complement of tourist and recreational activities on site.
Keywords:
gully network; loess; dugouts; Earth Science education
Fulltext is available at external website.
Underground Spaces In Bosonožský Hájek Nature Reserve And Their Geoeducation Importance
Bosonožský hájek Natural Reserve (Brno, South Moravia) is a very important site from the Earth Science point of view, however, its geodiversity values have been rather overlooked and omitted in the ...
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 ...
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