arXiv subjects

Mariya Ptashnyk

Publications and source records attributed to Mariya Ptashnyk.

At least 37 records · Page 2Linked to original sources

arXiv2020

Multiscale analysis and simulation of a signalling process with surface diffusion

We present and analyse a model for cell signalling processes in biological tissues. The model includes diffusion and nonlinear reactions on the cell surfaces, and both inter- and intracellular signalling. Using techniques from the theory of two-scale convergence as well the unfolding method, we show convergence of the solutions to the model to solutions of a two-scale macroscopic problem. We also present a two-scale bulk-surface finite element method for the approximation of the macroscopic model. We report on some benchmarking results as well as numerical simulations in a biologically relevant regime that illustrate the influence of cell-scale heterogeneities on macroscopic concentrations.

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arXiv2020

From individual-based mechanical models of multicellular systems to free-boundary problems

In this paper we present an individual-based mechanical model that describes the dynamics of two contiguous cell populations with different proliferative and mechanical characteristics. An off-lattice modelling approach is considered whereby: (i) every cell is identified by the position of its centre; (ii) mechanical interactions between cells are described via generic nonlinear force laws; and (iii) cell proliferation is contact inhibited. We formally show that the continuum counterpart of this discrete model is given by a free-boundary problem for the cell densities. The results of the derivation demonstrate how the parameters of continuum mechanical models of multicellular systems can be related to biophysical cell properties. We prove an existence result for the free-boundary problem and construct travelling-wave solutions. Numerical simulations are performed in the case where the cellular interaction forces are described by the celebrated Johnson-Kendall-Roberts model of elastic contact, which has been previously used to model cell-cell interactions. The results obtained indicate excellent agreement between the simulation results for the individual-based model, the numerical solutions of the corresponding free-boundary problem and the travelling-wave analysis.

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arXiv2019

Mathematical Modelling of Auxin Transport in Plant Tissues: Flux meets Signalling and Growth

Plant hormone auxin has critical roles in plant growth, dependent on its heterogeneous distribution in plant tissues. Exactly how auxin transport and developmental processes such as growth coordinate to achieve the precise patterns of auxin observed experimentally is not well understood. Here we use mathematical modelling to examine the interplay between auxin dynamics and growth and their contribution to formation of patterns in auxin distribution in plant tissues. Mathematical models describing the auxin-related signalling pathway, PIN and AUX1 dynamics, auxin transport, and cell growth in plant tissues are derived. A key assumption of our models is the regulation of PIN proteins by the auxin-responsive ARF-Aux/IAA signalling pathway, with upregulation of PIN biosynthesis by ARFs. Models are analysed and solved numerically to examine the long-time behaviour and auxin distribution. Changes in auxin-related signalling processes are shown to be able to trigger transition between passage and spot type patterns in auxin distribution. The model was also shown to be able to generate isolated cells with oscillatory dynamics in levels of components of the auxin signalling pathway which could explain oscillations in levels of ARF targets that have been observed experimentally. Cell growth was shown to have influence on PIN polarisation and determination of auxin distribution patterns. Numerical simulation results indicate that auxin-related signalling processes can explain the different patterns in auxin distributions observed in plant tissues, whereas the interplay between auxin transport and growth can explain the `reverse-fountain' pattern in auxin distribution observed at plant root tips.

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arXiv2018

Homogenization of degenerate cross-diffusion systems

Two-scale homogenization limits of parabolic cross-diffusion systems in a heterogeneous medium with no-flux boundary conditions are proved. The heterogeneity of the medium is reflected in the diffusion coefficients or by the perforated domain. The diffusion matrix is of degenerate type and may be neither symmetric nor positive semi-definite, but the diffusion system is assumed to satisfy an entropy structure. Uniform estimates are derived from the entropy production inequality. New estimates on the equicontinuity with respect to the time variable ensure the strong convergence of a sequence of solutions to the microscopic problems defined in perforated domains.

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arXiv2018

Homogenization of some degenerate pseudoparabolic variational inequalities

Multiscale analysis of a degenerate pseudoparabolic variational inequality, modelling the two-phase flow with dynamical capillary pressure in a perforated domain, is the main topic of this work. Regularisation and penalty operator methods are applied to show the existence of a solution of the nonlinear degenerate pseudoparabolic variational inequality defined in a domain with microscopic perforations, as well as to derive a priori estimates for solutions of the microscopic problem. The main challenge is the derivation of a priori estimates for solutions of the variational inequality, uniformly with respect to the regularisation parameter and to the small parameter defining the scale of the microstructure. The method of two-scale convergence is used to derive the corresponding macroscopic obstacle problem.

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arXiv2017

Homogenization of biomechanical models for plant tissues

In this paper homogenization of a mathematical model for plant tissue biomechanics is presented. The microscopic model constitutes a strongly coupled system of reaction-diffusion-convection equations for chemical processes in plant cells, the equations of poroelasticity for elastic deformations of plant cell walls and middle lamella, and Stokes equations for fluid flow inside the cells. The chemical process in cells and the elastic properties of cell walls and middle lamella are coupled because elastic moduli depend on densities involved in chemical reactions, whereas chemical reactions depend on mechanical stresses. Using homogenization techniques we derive rigorously a macroscopic model for plant biomechanics. To pass to the limit in the nonlinear reaction terms, which depend on elastic strain, we prove the strong two-scale convergence of the displacement gradient and velocity field.

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arXiv2017

Mathematical Modelling and Analysis of the Brassinosteroid and Gibberellin Signalling Pathways and their Interactions

The plant hormones brassinosteroid (BR) and gibberellin (GA) have important roles in a wide range of processes involved in plant growth and development. In this paper we derive and analyse new mathematical models for the BR signalling pathway and for the crosstalk between the BR and GA signalling pathways. To analyse the effects of spatial heterogeneity of the signalling processes, along with spatially-homogeneous ODE models we derive coupled PDE-ODE systems modelling the temporal and spatial dynamics of molecules involved in the signalling pathways. The values of the parameters in the model for the BR signalling pathway are determined using experimental data on the gene expression of BR biosynthetic enzymes. The stability of steady state solutions of our mathematical model, shown for a wide range of parameters, can be related to the BR homeostasis. Our results for the crosstalk model suggest that the interaction between transcription factors BZR and DELLA exerts more influence on the dynamics of the signalling pathways than BZR-mediated biosynthesis of GA, suggesting that the interaction between transcription factors may constitute the principal mechanism of the crosstalk between the BR and GA signalling pathways. In general, perturbations in the GA signalling pathway have larger effects on the dynamics of components of the BR signalling pathway than perturbations in the BR signalling pathway on the dynamics of the GA pathway. The perturbation in the crosstalk mechanism also has a larger effect on the dynamics of the BR pathway than of the GA pathway. Large changes in the dynamics of the GA signalling processes can be observed only in the case where there are disturbances in both the BR signalling pathway and the crosstalk mechanism.

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arXiv2016

Stochastic homogenization of the Keller-Segel chemotaxis system

In this paper, we focus on the Keller-Segel chemotaxis system in a random heterogeneous domain. We assume that the corresponding diffusion and chemotaxis coefficients are given by stationary ergodic random fields and apply stochastic two-scale convergence methods to derive the homogenized macroscopic equations. In establishing our results, we also derive a priori estimates for the Keller-Segel system that rely only on the boundedness of the coefficients; in particular, no differentiability assumption on the diffusion and chemotaxis coefficients for the chemotactic species is required. Finally, we prove the convergence of a periodization procedure for approximating the homogenized macroscopic coefficients.

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arXiv2016

Stability of nonconstant stationary solutions in a reaction-diffusion equation coupled to the system of ordinary differential equations

In this paper we study pattern formation arising in a system of a single reaction-diffusion equation coupled with subsystem of ordinary differential equations, describing spatially-distributed growth of clonal populations of precancerous cells, whose proliferation is controled by growth factors diffusing in the extracellular medium and binding to the cell surface. We extend the results on the existence of nonhomogenous stationary solutions obtained in the previous work of one of the authors to a general Hill-type production function and full parameter set. Using spectral analysis and perturbation theory we derive conditions for the linearized stability of such spatial patterns.

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arXiv2015

Homogenization of a system of elastic and reaction-diffusion equations modelling plant cell wall biomechanics

In this paper we present a derivation and multiscale analysis of a mathematical model for plant cell wall biomechanics that takes into account both the microscopic structure of a cell wall coming from the cellulose microfibrils and the chemical reactions between the cell wall's constituents. Particular attention is paid to the role of pectin and the impact of calcium-pectin cross-linking chemistry on the mechanical properties of the cell wall. We prove the existence and uniqueness of the strongly coupled microscopic problem consisting of the equations of linear elasticity and a system of reaction-diffusion and ordinary differential equations. Using homogenization techniques (two-scale convergence and periodic unfolding methods) we derive a macroscopic model for plant cell wall biomechanics.

math.AP↗

arXiv2015

Multiscale analysis of signalling processes in tissues with non-periodic distribution of cells

In this paper a microscopic model for a signalling process in the cardiac muscle tissue of the left ventricular wall, comprising non-periodic fibrous microstructure is considered. To derive the macroscopic equations we approximate the non-periodic microstructure by the corresponding locally-periodic microstructure. Then applying the methods of the locally-periodic (l-p) unfolding operator, locally-periodic two-scale (l-t-s) convergence on oscillating surfaces and l-p boundary unfolding operator we obtain the macroscopic problem for a signalling process in the heart muscle tissue.

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arXiv2015

Homogenization of a viscoelastic model for plant cell wall biomechanics

The microscopic structure of a plant cell wall is given by cellulose microfibrils embedded in a cell wall matrix. In this paper we consider a microscopic model for interactions between viscoelastic deformations of a plant cell wall and chemical processes in the cell wall matrix. We consider elastic deformations of the cell wall microfibrils and viscoelastic Kelvin--Voigt type deformations of the cell wall matrix. Using homogenization techniques (two-scale convergence and periodic unfolding methods) we derive macroscopic equations from the microscopic model for cell wall biomechanics consisting of strongly coupled equations of linear viscoelasticity and a system of reaction-diffusion and ordinary differential equations. As is typical for microscopic viscoelastic problems, the macroscopic equations for viscoelastic deformations of plant cell walls contain memory terms. The derivation of the macroscopic problem for degenerate viscoelastic equations is conducted using a perturbation argument.

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arXiv2015

Periodic homogenization and material symmetry in linear elasticity

Here homogenization theory is used to establish a connection between the symmetries of a periodic elastic structure associated with the microscopic properties of an elastic material and the material symmetries of the effective, macroscopic elasticity tensor. Previous results of this type exist but here more general symmetries on the microscale are considered. Using an explicit example, we show that it is possible for a material to be fully anisotropic on the microscale and yet the symmetry group on the macroscale can contain elements other than plus or minus the identity. Another example demon- strates that not all material symmetries of the macroscopic elastic tensor are generated by symmetries of the periodic elastic structure.

math-ph↗

arXiv2015

Locally periodic unfolding method and two-scale convergence on surfaces of locally periodic microstructures

In this paper we generalize the periodic unfolding method and the notion of two-scale convergence on surfaces of periodic microstructures to locally periodic situations. The methods that we introduce allow us to consider a wide range of non-periodic microstructures, especially to derive macroscopic equations for problems posed in domains with perforations distributed non-periodically. Using the methods of locally periodic two-scale convergence (l-t-s) on oscillating surfaces and the locally periodic (l-p) boundary unfolding operator, we are able to analyze differential equations defined on boundaries of non-periodic microstructures and consider non-homogeneous Neumann conditions on the boundaries of perforations, distributed non-periodically.

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arXiv2015

The impact of microfibril orientations on the biomechanics of plant cell walls and tissues: modelling and simulations

It is known that the orientation of cellulose microfibrils within plant cell walls has an important impact on the morphogenesis of plant cells and tissues. Viewing the shape of a plant cell as a square prism or cylinder with the axis aligning with the primary direction of expansion and growth, the orientation of the microfibrils within the cell wall on the sides of the cell is known. However, not much is known about their orientation at the ends of the cell. Here we investigate the impact of the orientation of cellulose microfibrils within a plant cell wall at the ends of the cell by solving the equations of linear elasticity numerically. Three different scenarios for the orientation of the microfibrils are considered. The macroscopic elastic properties of the cell wall are obtained using homogenization theory from the microscopic description of the elastic properties of the cell wall microfibrils and wall matrix. It is found that the orientation of the microfibrils in the upper and lower parts of cell walls do not affect the expansion of the cell in the direction of its axis but do affect its expansion in the lateral directions. The arrangement of the microfibrils in the upper and lower parts of cell walls is especially important in the case of directed forces acting on plant cell walls and tissues.

q-bio.CB↗

arXiv2015

Homogenization of oxygen transport in biological tissues

In this paper, we extend previous work on the mathematical modeling of oxygen transport in biological tissues (Matzavinos et al., 2009). Specifically, we include in the modeling process the arterial and venous microstructure within the tissue by means of homogenization techniques. We focus on the two-layer tissue architecture investigated in (Matzavinos et al., 2009) in the context of abdominal tissue flaps that are commonly used for reconstructive surgery. We apply two-scale convergence methods and unfolding operator techniques to homogenize the developed microscopic model, which involves different unit-cell geometries in the two distinct tissue layers (skin layer and fat tissue) to account for different arterial branching patterns.

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arXiv2014

Global Hopf Bifurcation in the ZIP regulatory system

Regulation of zinc uptake in roots of Arabidopsis thaliana has recently been modeled by a system of ordinary differential equations based on the uptake of zinc, expression of a transporter protein and the interaction between an activator and inhibitor. For certain parameter choices the steady state of this model becomes unstable upon variation in the external zinc concentration. Numerical results show periodic orbits emerging between two critical values of the external zinc concentration. Here we show the existence of a global Hopf bifurcation with a continuous family of stable periodic orbits between two Hopf bifurcation points. The stability of the orbits in a neighborhood of the bifurcation points is analyzed by deriving the normal form, while the stability of the orbits in the global continuation is shown by calculation of the Floquet multipliers. From a biological point of view, stable periodic orbits lead to potentially toxic zinc peaks in plant cells. Buffering is believed to be an efficient way to deal with strong transient variations in zinc supply. We extend the model by a buffer reaction and analyze the stability of the steady state in dependence of the properties of this reaction. We find that a large enough equilibrium constant of the buffering reaction stabilizes the steady state and prevents the development of oscillations. Hence, our results suggest that buffering has a key role in the dynamics of zinc homeostasis in plant cells.

math.DS↗

arXiv2014

Hopf Bifurcation in a Gene Regulatory Network Model: Molecular Movement Causes Oscillations

Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse a mathematical model of a canonical gene regulatory network consisting of a single negative feedback loop between a protein and its mRNA (e.g. the Hes1 transcription factor system). The model consists of two partial differential equations describing the spatio-temporal interactions between the protein and its mRNA in a 1-dimensional domain. Such intracellular negative feedback systems are known to exhibit oscillatory behaviour and this is the case for our model, shown initially via computational simulations. In order to investigate this behaviour more deeply, we next solve our system using Green's functions and then undertake a linearized stability analysis of the steady states of the model. Our results show that the diffusion coefficient of the protein/mRNA acts as a bifurcation parameter and gives rise to a Hopf bifurcation. This shows that the spatial movement of the mRNA and protein molecules alone is sufficient to cause the oscillations. This has implications for transcription factors such as p53, NF-$κ$B and heat shock proteins which are involved in regulating important cellular processes such as inflammation, meiosis, apoptosis and the heat shock response, and are linked to diseases such as arthritis and cancer.

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