2021 International Conference on Information and Digital Technologies (IDT)
While a red blood cell moves in the vessel, it often changes its shape, adapting it to many obsta... more While a red blood cell moves in the vessel, it often changes its shape, adapting it to many obstacles or other objects. This behaviour is influenced by elastic properties of the cell. One need to take into account these elastic properties when modelling of red blood cells. The elastic properties are implemented in the models by means of elastic moduli. One of these moduli is the bending modulus. This modulus is important for maintaining the shape of the cell but especially it is ensuring a gradual return to its original state in case of deformation. The bending modulus is based on keeping the angles between each pair of adjacent triangles in the red blood cell’s mesh. In this article we focus on rotation of the cell in shear flow. By appropriately selected simulations, we want to investigate the rotation frequency of the cell and the influence of bending modulus on the rotation frequency.
2017 International Conference on Information and Digital Technologies (IDT), 2017
Cells in a shear flow exhibit tumbling and tank-treading. This rotational movement is characteriz... more Cells in a shear flow exhibit tumbling and tank-treading. This rotational movement is characterized by rotational frequency. In this work, we analyze and test a computational model of red blood cell by comparing simulated movement of a cell in a shear flow to the experimental data. We set up a computational experiment that recasts dynamical behavior of cells in a shear flow. We analyze the dependence of the rotational frequency of cells on the shear rate. Results show that the model including the stretching, bending, area and volume preservation moduli does not recover frequencies from the biological data. After adding the visco-elastic modulus, the simulations show compliance with the data.
2019 International Conference on Information and Digital Technologies (IDT), 2019
Extraction of data from video sequences of biological experiments is invaluable tool for evaluati... more Extraction of data from video sequences of biological experiments is invaluable tool for evaluation of computer simulations. For the extraction of data, such as cell velocities, their trajectories, even their deformation, sufficient quality of red blood cell detection is required. In case of incomplete detection, the subsequent tracking algorithm is only able to compensate for some errors. In this work, we will evaluate existing implementations for object detection with Convolutional Neural Networks, in order to provide a baseline and comparison for our task with existing methods.
Red blood cells are flexible during their movement in microchannels, they adapt easily to their i... more Red blood cells are flexible during their movement in microchannels, they adapt easily to their immediate environment and eventually return to their relaxed shape as soon as the environment exerts no forces on the cell. This behaviour is determined by elastic properties of red cell’s membrane which must be carefully taken in consideration when creating the computational model of red blood cell.
This paper is concerned with regularity of the solutions to the Maxwell-Landau-Lifshitz system de... more This paper is concerned with regularity of the solutions to the Maxwell-Landau-Lifshitz system describing ferromagnetic medium. We derive estimates for the solution, which can be used to control the Taylor remainder when estimating the error of a numerical scheme. Applications are widely used in the recording industry. We solve full Maxwell-Landau-Lifshitz (MLL) system in a bounded domain Ω ⊂ R ∂tm = −m× (∆m+H)− αm× (m× (∆m+H)), ∂tE+ σE−∇×H = 0, ∇ ·H+ β∇ ·m = 0, ∂tH+∇×E = −β∂tm, ∇ ·E = 0, where α, β and σ are physical constants, α > 0, σ ≥ 0. We consider Neumann boundary conditions ∂m ∂ν ∣
We propose a three dimensional model for the adhesion and rolling of biological cells on surfaces... more We propose a three dimensional model for the adhesion and rolling of biological cells on surfaces. We study cells moving in shear flow above a wall to which they can adhere via specific receptor-ligand bonds based on receptors from selectin as well as integrin family. The computational fluid dynamics are governed by the lattice-Boltzmann method. The movement and the deformation of the cells is described by the immersed boundary method. Both methods are fully coupled by implementing a two-way fluid-structure interaction. The adhesion mechanism is modelled by adhesive bonds including stochastic rules for their creation and rupture. We explore a simplified model with dissociation rate independent of the length of the bonds. We demonstrate that this model is able to resemble the mesoscopic properties, such as velocity of rolling cells.
We described a new technology for a fabrication of microfluidic components for lab on a chip appl... more We described a new technology for a fabrication of microfluidic components for lab on a chip application based on polydimethylsiloxane (PDMS). The combination of direct laser writing (DLW) lithography for patterning a microstructures and PDMS replica molding process were used. The microfluidic path was formatted after putting final chip on the top of glass slide. The prepared PDMS based microfluidic structure can be used in lab on a chip applications in sensing and biological measurements. Surface of the final chip structure was study by confocal microscope.
Dlhoročné skúsenosti s vyučovaním na technických vysokých školách nás presviedčajú o tom, že defi... more Dlhoročné skúsenosti s vyučovaním na technických vysokých školách nás presviedčajú o tom, že definície, vety a tvrdenia, tak ako sa učia v matematike, sú pre veľkú časť študentov inžinierskeho zamerania príliš abstraktné. Namiesto pomoci, ktorú matematika môže študentovi ponúknuť, sa tak stáva strašiakom, ktorý mu nedovolí urobiť potrebný krok medzi abstraktnou formuláciou a aplikáciami. Riešením úloh v učebnici čitateľ získa presvedčenie o pravdivosti tvrdení bez toho, aby musel pochopiť exaktný dôkaz.
A three dimensional computational model of fluid-object interaction has been employed in investig... more A three dimensional computational model of fluid-object interaction has been employed in investigation of local stresses during the motion of red blood cells in simple shear flow. The RBC membrane can withstand a finite strain, beyond which it ruptures. The generally accepted threshold value is 4% for the total areal strain. We have designed an in silico experiment where the total areal strain reached 4%. It has been noted previously that locally this value may be much larger with shorter exposure duration. During the simulation, we have analyzed local stresses of the membrane. Besides the areal strain we employed the time of exposure to a certain strain in order to include the possible cumulative damage of the membrane during the process. We have investigated the following two quantities: the maximal local strain and the cumulative load of local strain. We tracked down the locations on the membrane where these quantities reached their maximal values. We suggest that the cumulative load of local areal str...
One of the most important characteristics of red blood cells is their elasticity and ability to r... more One of the most important characteristics of red blood cells is their elasticity and ability to return to original biconcave shape after external forces stop acting on them. There are several conservation laws that together govern this return and one of them is the area conservation. In this paper, we focus on local area conservation and introduce a new way of modeling it using a spring network model. We take into account the current shape of the network triangles and find the proportional allocation of area conservation forces, which would for individual triangles preserve their shapes. Since the force contributions in each node are combined from all adjacent triangles, the final resulting shape might not be the same, but overall effect on the triangulations is positive in the sense that this approach tends to regularize them.
2021 International Conference on Information and Digital Technologies (IDT)
While a red blood cell moves in the vessel, it often changes its shape, adapting it to many obsta... more While a red blood cell moves in the vessel, it often changes its shape, adapting it to many obstacles or other objects. This behaviour is influenced by elastic properties of the cell. One need to take into account these elastic properties when modelling of red blood cells. The elastic properties are implemented in the models by means of elastic moduli. One of these moduli is the bending modulus. This modulus is important for maintaining the shape of the cell but especially it is ensuring a gradual return to its original state in case of deformation. The bending modulus is based on keeping the angles between each pair of adjacent triangles in the red blood cell’s mesh. In this article we focus on rotation of the cell in shear flow. By appropriately selected simulations, we want to investigate the rotation frequency of the cell and the influence of bending modulus on the rotation frequency.
2017 International Conference on Information and Digital Technologies (IDT), 2017
Cells in a shear flow exhibit tumbling and tank-treading. This rotational movement is characteriz... more Cells in a shear flow exhibit tumbling and tank-treading. This rotational movement is characterized by rotational frequency. In this work, we analyze and test a computational model of red blood cell by comparing simulated movement of a cell in a shear flow to the experimental data. We set up a computational experiment that recasts dynamical behavior of cells in a shear flow. We analyze the dependence of the rotational frequency of cells on the shear rate. Results show that the model including the stretching, bending, area and volume preservation moduli does not recover frequencies from the biological data. After adding the visco-elastic modulus, the simulations show compliance with the data.
2019 International Conference on Information and Digital Technologies (IDT), 2019
Extraction of data from video sequences of biological experiments is invaluable tool for evaluati... more Extraction of data from video sequences of biological experiments is invaluable tool for evaluation of computer simulations. For the extraction of data, such as cell velocities, their trajectories, even their deformation, sufficient quality of red blood cell detection is required. In case of incomplete detection, the subsequent tracking algorithm is only able to compensate for some errors. In this work, we will evaluate existing implementations for object detection with Convolutional Neural Networks, in order to provide a baseline and comparison for our task with existing methods.
Red blood cells are flexible during their movement in microchannels, they adapt easily to their i... more Red blood cells are flexible during their movement in microchannels, they adapt easily to their immediate environment and eventually return to their relaxed shape as soon as the environment exerts no forces on the cell. This behaviour is determined by elastic properties of red cell’s membrane which must be carefully taken in consideration when creating the computational model of red blood cell.
This paper is concerned with regularity of the solutions to the Maxwell-Landau-Lifshitz system de... more This paper is concerned with regularity of the solutions to the Maxwell-Landau-Lifshitz system describing ferromagnetic medium. We derive estimates for the solution, which can be used to control the Taylor remainder when estimating the error of a numerical scheme. Applications are widely used in the recording industry. We solve full Maxwell-Landau-Lifshitz (MLL) system in a bounded domain Ω ⊂ R ∂tm = −m× (∆m+H)− αm× (m× (∆m+H)), ∂tE+ σE−∇×H = 0, ∇ ·H+ β∇ ·m = 0, ∂tH+∇×E = −β∂tm, ∇ ·E = 0, where α, β and σ are physical constants, α > 0, σ ≥ 0. We consider Neumann boundary conditions ∂m ∂ν ∣
We propose a three dimensional model for the adhesion and rolling of biological cells on surfaces... more We propose a three dimensional model for the adhesion and rolling of biological cells on surfaces. We study cells moving in shear flow above a wall to which they can adhere via specific receptor-ligand bonds based on receptors from selectin as well as integrin family. The computational fluid dynamics are governed by the lattice-Boltzmann method. The movement and the deformation of the cells is described by the immersed boundary method. Both methods are fully coupled by implementing a two-way fluid-structure interaction. The adhesion mechanism is modelled by adhesive bonds including stochastic rules for their creation and rupture. We explore a simplified model with dissociation rate independent of the length of the bonds. We demonstrate that this model is able to resemble the mesoscopic properties, such as velocity of rolling cells.
We described a new technology for a fabrication of microfluidic components for lab on a chip appl... more We described a new technology for a fabrication of microfluidic components for lab on a chip application based on polydimethylsiloxane (PDMS). The combination of direct laser writing (DLW) lithography for patterning a microstructures and PDMS replica molding process were used. The microfluidic path was formatted after putting final chip on the top of glass slide. The prepared PDMS based microfluidic structure can be used in lab on a chip applications in sensing and biological measurements. Surface of the final chip structure was study by confocal microscope.
Dlhoročné skúsenosti s vyučovaním na technických vysokých školách nás presviedčajú o tom, že defi... more Dlhoročné skúsenosti s vyučovaním na technických vysokých školách nás presviedčajú o tom, že definície, vety a tvrdenia, tak ako sa učia v matematike, sú pre veľkú časť študentov inžinierskeho zamerania príliš abstraktné. Namiesto pomoci, ktorú matematika môže študentovi ponúknuť, sa tak stáva strašiakom, ktorý mu nedovolí urobiť potrebný krok medzi abstraktnou formuláciou a aplikáciami. Riešením úloh v učebnici čitateľ získa presvedčenie o pravdivosti tvrdení bez toho, aby musel pochopiť exaktný dôkaz.
A three dimensional computational model of fluid-object interaction has been employed in investig... more A three dimensional computational model of fluid-object interaction has been employed in investigation of local stresses during the motion of red blood cells in simple shear flow. The RBC membrane can withstand a finite strain, beyond which it ruptures. The generally accepted threshold value is 4% for the total areal strain. We have designed an in silico experiment where the total areal strain reached 4%. It has been noted previously that locally this value may be much larger with shorter exposure duration. During the simulation, we have analyzed local stresses of the membrane. Besides the areal strain we employed the time of exposure to a certain strain in order to include the possible cumulative damage of the membrane during the process. We have investigated the following two quantities: the maximal local strain and the cumulative load of local strain. We tracked down the locations on the membrane where these quantities reached their maximal values. We suggest that the cumulative load of local areal str...
One of the most important characteristics of red blood cells is their elasticity and ability to r... more One of the most important characteristics of red blood cells is their elasticity and ability to return to original biconcave shape after external forces stop acting on them. There are several conservation laws that together govern this return and one of them is the area conservation. In this paper, we focus on local area conservation and introduce a new way of modeling it using a spring network model. We take into account the current shape of the network triangles and find the proportional allocation of area conservation forces, which would for individual triangles preserve their shapes. Since the force contributions in each node are combined from all adjacent triangles, the final resulting shape might not be the same, but overall effect on the triangulations is positive in the sense that this approach tends to regularize them.
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Papers by Ivan Cimrak