Assoc. Prof. Bogdan Kaźmierczak, Ph.D., Dr. Habil. 

Doctoral thesis
1990  Warstwa przejściowa i asymptotyka rozwiązań nieliniowych cząstkowych równań różniczkowych typu reakcjidyfuzji. Zastosowanie w fizyce plazmy.
 456 
Habilitation thesis
20050428  Fale biegnące w ośrodkach nieliniowych 
Supervision of doctoral theses
1.  20160308  Dyzma Michał (IBIB PAN)  Modelowanie oscylacji stężeń jonów wapniowych w komórkach eukariotycznych z uwzględnieniem obszarów bezpośredniego kontaktu pomiędzy mitochondriami a retikulum endoplazmatycznym  1246 
Recent publications
1.  Adimy M.^{♦}, Chekroun A.^{♦}, Kaźmierczak B., Traveling waves in a coupled reaction–diffusion and difference model of hematopoiesis, Journal of Differential Equations, ISSN: 00220396, DOI: 10.1016/j.jde.2016.12.009, Vol.262, No.7, pp.40854128, 2017 Abstract: The formation and development of blood cells is a very complex process, called hematopoiesis. This process involves a small population of cells called hematopoietic stem cells (HSCs). The HSCs are undifferentiated cells, located in the bone marrow before they become mature blood cells and enter the blood stream. They have a unique ability to produce either similar cells (selfrenewal), or cells engaged in one of different lineages of blood cells: red blood cells, white cells and platelets (differentiation). The HSCs can be either in a proliferating or in a quiescent phase. In this paper, we distinguish between dividing cells that enter directly to the quiescent phase and dividing cells that return to the proliferating phase to divide again. We propose a mathematical model describing the dynamics of HSC population, taking into account their spatial distribution. The resulting model is a coupled reaction–diffusion equation and difference equation with delay. We study the existence of monotone traveling wave fronts and the asymptotic speed of spread. Keywords:Hematopoiesis, Agestructured population, Reaction–diffusion system with delay, Difference equation, Traveling wave front, Asymptotic speed of spread Affiliations:
 
2.  Bobrowski A.^{♦}, Kaźmierczak B., Kunze M.^{♦}, An averaging principle for fast diffusions in domains separated by semipermeable membranes, MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES, ISSN: 02182025, DOI: 10.1142/S0218202517500130, Vol.27, No.4, pp.663706, 2017 Abstract: We prove an averaging principle which asserts convergence of diffusion processes on domains separated by semipermeable membranes, when diffusion coefficients tend to infinity while the flux through the membranes remains constant. In the limit, points in each domain are lumped into a single state of a limit Markov chain. The limit chain’s intensities are proportional to the membranes’ permeability and inversely proportional to the domains’ sizes. Analytically, the limit is an example of a singular perturbation in which boundary and transmission conditions play a crucial role. This averaging principle is strongly motivated by recent signaling pathways models of mathematical biology, which are discussed toward the end of the paper. Keywords:Convergence of sectorial forms and of semigroups of operators, diffusion processes, boundary and transmission conditions, Freidlin–Wentzell averaging principle, singular perturbations, signaling pathways, kinase activity, intracellular calcium dynamics, neurotransmitters Affiliations:
 
3.  Białecki S., Kaźmierczak B., Nowicka D., Tsai J.C.^{♦}, Regularity of solutions to a reaction–diffusion equation on the sphere: the Legendre series approach, MATHEMATICAL METHODS IN THE APPLIED SCIENCES, ISSN: 01704214, DOI: 10.1002/mma.4390, pp.121, 2017 Abstract: In the paper, we study some ‘a priori’ properties of mild solutions to a single reaction–diffusion equation with discontinuous nonlinear reaction term on the twodimensional sphere close to its poles. This equation is the counterpart of the wellstudied bistable reaction–diffusion equation on the Euclidean plane. The investigation of this equation on the sphere is mainly motivated by the phenomenon of the fertilization of oocytes or recent studies of wave propagation in a model of immune cells activation, in which the cell is modeled by a ball. Because of the discontinuous nature of reaction kinetics, the standard theory cannot guarantee the solution existence and its smoothness properties. Moreover, the singular nature of the diffusion operator near the north/south poles makes the analysis more involved. Unlike the case in the Euclidean plane, the (axially symmetric) Green's function for the heat operator on the sphere can only be represented by an infinite series of the Legendre polynomials. Our approach is to consider a formal series in Legendre polynomials obtained by assuming that the mild solution exists. We show that the solution to the equation subject to the Neumann boundary condition is C1 smooth in the spatial variable up to the north/south poles and Hölder continuous with respect to the time variable. Our results provide also a sort of ‘a priori’ estimates, which can be used in the existence proofs of mild solutions, for example, by means of the iterative methods. Keywords:discontinuous reaction term, stationary fronts, sphere Affiliations:
 
4.  Chatterjee P., Kaźmierczak B., Eigenfunction Approach to Transient Patterns in a Model of Chemotaxis, MATHEMATICAL MODELLING OF NATURAL PHENOMENA, ISSN: 09735348, DOI: 10.1051/mmnp/201611204, Vol.11, No.2, pp.4462, 2016 Abstract: In the paper we examine solutions to a model of cell movement governed by the chemotaxis phenomenon derived in [14] and established via macroscopic limits of corresponding microscopic cellbased models with extended cell representations. The model is given by two PDEs for the density of cells and the concentration of a chemical. To avoid singularities in cell density, the aggregating force of chemotaxis phenomenon is attenuated by a density dependent diffusion of cells, which grows to infinity with density tending to a certain critical value. In this paper we recover the quasiperiodic structures provided by this model by means of (local in time) expansion of the solution into a basis of eigenfunctions of the linearized system. Both planar and spherical geometries are considered. Keywords:pattern formation, chemotaxis, Turing bifurcation, eigenfunction expansion Affiliations:
 
5.  Białecki S., Kaźmierczak B., Tsai JC.^{♦}, Stationary waves on the sphere, SIAM JOURNAL ON APPLIED MATHEMATICS, ISSN: 00361399, DOI: 10.1137/140999384, Vol.75, No.4, pp.17611788, 2015 Abstract: In this paper, we investigate stationary waves on the sphere using the bistable reactiondiffusion system. The motivation of this study arises from the study of activation waves of B cells in immune systems. We analytically establish (i) the existence and uniqueness of stationary waves; (ii) the limiting wave profile for small diffusivity of diffusing species; and (iii) the stability of the constructed stationary waves. The stability result may suggest the critical role of stationary waves in the determination of initial data for initiating propagating waves on the sphere, which is consistent with the numerical results for the Bcell activation model. Keywords:stationary wave, sphere, bistable kinetics Affiliations:
 
6.  Crooks E.^{♦}, Kaźmierczak B., Lipniacki T., A spatially extended model of kinasereceptor interaction, SIAM JOURNAL ON APPLIED MATHEMATICS, ISSN: 00361399, DOI: 10.1137/110860926, Vol.73, No.1, pp.374400, 2013 Abstract: We perform a mathematical analysis of a spatially extended model describing mutual phosphorylation of cytosolic kinases and membrane receptors. The analyzed regulatory system is a part of signal transduction mechanisms, which enables communication of the cell with its extracellular environment or other cells. The mutual receptorkinase interaction is characteristic for immune receptors and Src family kinases. From the mathematical viewpoint, the considered system is interesting because it couples differential equations defined in a domain $\Omega$ and on its boundary $\partial\Omega$ via nonlinear Robin boundary conditions. Assuming a spherically symmetric framework, our approach is to consider an auxiliary problem in which the Robin boundary condition on the external boundary of the spherical shell $\Omega$ is replaced by a uniform Dirichlet boundary condition. This method allows us to find the stationary spherically symmetric solutions, both stable and unstable. Interestingly, numerical computations suggest also the existence of nonspherically symmetric unstable stationary solutions to the spherically symmetric problem. These conjectured solutions appear to lie between super and subsolutions that converge in time to two different stable spherically symmetric steady states. The study is completed by the proof of an existence theorem for a general version of the original system encompassing the earlier models. The theorem holds in domains of arbitrary shape, with a number of holes that may represent various organelles impenetrable to the considered kinases. The last result ensures that the problem in which the flux of active kinases (which replaces the source term) is determined by the Robintype boundary condition at the cell membrane is well posed. The considered generalized model may thus serve as a template for intracellular signal transduction analysis. Keywords:reactiondiffusion systems, Robintype boundary conditions, bistability, molecular signal transduction Affiliations:
 
7.  Szopa P.^{♦}, Dyzma M., Kaźmierczak B., Membrane associated complexes in calcium dynamics modelling, PHYSICAL BIOLOGY, ISSN: 14783967, DOI: 10.1088/14783975/10/3/035004, Vol.10, pp.035004113, 2013 Abstract: Mitochondria not only govern energy production, but are also involved in crucial cellular signalling processes. They are one of the most important organelles determining the Ca2+ regulatory pathway in the cell. Several mathematical models explaining these mechanisms were constructed, but only few of them describe interplay between calcium concentrations in endoplasmic reticulum (ER), cytoplasm and mitochondria. Experiments measuring calcium concentrations in mitochondria and ER suggested the existence of cytosolic microdomains with locally elevated calcium concentration in the nearest vicinity of the outer mitochondrial membrane. These intermediate physical connections between ER and mitochondria are called MAM (mitochondriaassociated ER membrane) complexes. We propose a model with a direct calcium flow from ER to mitochondria, which may be justified by the existence of MAMs, and perform detailed numerical analysis of the effect of this flow on the type and shape of calcium oscillations. The model is partially based on the Marhl et al model. We have numerically found that the stable oscillations exist for a considerable set of parameter values. However, for some parameter sets the oscillations disappear and the trajectories of the model tend to a steady state with very high calcium level in mitochondria. This can be interpreted as an early step in an apoptotic pathway. Affiliations:
 
8.  Kaźmierczak B., Peradzyński Z., Calcium waves with mechanochemical couplings, MATHEMATICAL BIOSCIENCES AND ENGINEERING, ISSN: 15471063, DOI: 10.3934/mbe.2013.10.743, Vol.10, pp.743759, 2013 Abstract: As follows from experiments, waves of calcium concentration in biological tissues can be easily excited by a local mechanical stimulation. Therefore the complete theory of calcium waves should also take into account coupling between mechanical and chemical processes. In this paper we consider the existence of travelling waves for buffered systems, as in [22], completed, however, by an equation for mechanical equilibrium and respective mechanochemical coupling terms. Thus the considered, coupled system consists of reactiondiffusion equations (for the calcium and buffers concentrations) and equations for the balance of mechanical forces. Keywords:Calcium waves, reactiondiffusion systems, mechanochemical coupling Affiliations:
 
9.  El Khatib N.^{♦}, Genieys S.^{♦}, Kaźmierczak B., Volpert V.^{♦}, Reactiondiffusion model of artherosclerosis development, JOURNAL OF MATHEMATICAL BIOLOGY, ISSN: 03036812, DOI: 10.1007/s0028501104611, Vol.65, pp.349374, 2012 Abstract: Atherosclerosis begins as an inflammation in blood vessel walls (intima). The inflammatory response of the organism leads to the recruitment of monocytes. Trapped in the intima, they differentiate into macrophages and foam cells leading to the production of inflammatory cytokines and further recruitment of white blood cells. This selfaccelerating process, strongly influenced by lowdensity lipoproteins (cholesterol), results in a dramatic increase of the width of blood vessel walls, formation of an atherosclerotic plaque and, possibly, of its rupture. We suggest a 2D mathematical model of the initiation and development of atherosclerosis which takes into account the concentration of blood cells inside the intima and of pro and antiinflammatory cytokines. The model represents a reaction–diffusion system in a strip with nonlinear boundary conditions which describe the recruitment of monocytes as a function of the concentration of inflammatory cytokines. We prove the existence of travelling waves described by this system and confirm our previous results which suggest that atherosclerosis develops as a reaction–diffusion wave. The theoretical results are confirmed by the results of numerical simulations. Keywords:Atherosclerosis, Reaction–diffusion equations, Nonlinear boundary conditions, Existence of travellingwaves, Numerical simulations Affiliations:
 
10.  Gejji R.^{♦}, Kaźmierczak B., Alber M.^{♦}, Classification and stability of global inhomogeneous solutions of a macroscopic model of cell motion, MATHEMATICAL BIOSCIENCES, ISSN: 00255564, DOI: 10.1016/j.mbs.2012.03.009, Vol.238, pp.2131, 2012 Abstract: Many microorganisms use chemotaxis for aggregation, resulting in stable patterns. In this paper, the amoeba Dictyostelium discoideum serves as a model organism for understanding the conditions for aggregation and classification of resulting patterns. To accomplish this, a 1D nonlinear diffusion equation with chemotaxis that models amoeba behavior is analyzed. A classification of the steady state solutions is presented, and a Lyapunov functional is used to determine conditions for stability of inhomogenous solutions. Changing the chemical sensitivity, production rate of the chemical attractant, or domain length can cause the system to transition from having an asymptotic steady state, to having asymptotically stable singlestep solution and multistepped stable plateau solutions. Keywords:Aggregation, Chemotaxis, Inhomogenous stability, Lyapunov functional, Plateau solutions, Dictyostelium discoideum Affiliations:
 
11.  Dyzma M., Szopa P., Kaźmierczak B., Membrane associated complexes: new approach to calcium dynamics modeling, MATHEMATICAL MODELLING OF NATURAL PHENOMENA, ISSN: 09735348, DOI: 10.1051/mmnp/20127608, Vol.7, pp.3250, 2012 Abstract: Mitochondria are one of the most important organelles determining Ca2+ regulatory pathway in the cell. Recent experiments suggested the existence of cytosolic microdomains with locally elevated calcium concentration (CMDs) in the nearest vicinity of the outer mitochondrial membrane (OMM). These intermediate physical connections between endoplasmic reticulum (ER) and mitochodria are called MAM (mitochondriaassociated ER membrane) complexes. Ca2+ signaling, mitochodrial Ca2+ transport, MAMs, three pool model, bistability, apoptosis, Affiliations:
 
12.  Hat B., Kaźmierczak B., Lipniacki T., B cell activation triggered by the formation of the small receptor cluster: a computational study, PLOS COMPUTATIONAL BIOLOGY, ISSN: 1553734X, DOI: 10.1371/journal.pcbi.1002197, Vol.7, No.10, pp.113, 2011 Abstract: We proposed a spatially extended model of early events of B cell receptors (BCR) activation, which is based on mutual kinasereceptor interactions that are characteristic for the immune receptors and the Src family kinases. These interactions lead to the positive feedback which, together with two nonlinearities resulting from the double phosphorylation of receptors and MichaelisMenten dephosphorylation kinetics, are responsible for the system bistability. We demonstrated that B cell can be activated by a formation of a tiny cluster of receptors or displacement of the nucleus. The receptors and Src kinases are activated, first locally, in the locus of the receptor cluster or the region where the cytoplasm is the thinnest. Then the traveling wave of activation propagates until activity spreads over the whole cell membrane. In the models in which we assume that the kinases are free to diffuse in the cytoplasm, we found that the fraction of aggregated receptors, capable to initiate B cell activation decreases with the decreasing thickness of cytoplasm and decreasing kinase diffusion. When kinases are restricted to the cell membrane  which is the case for most of the Src family kinases  even a cluster consisting of a tiny fraction of total receptors becomes activatory. Interestingly, the system remains insensitive to the modest changes of total receptor level. The model provides a plausible mechanism of B cells activation due to the formation of small receptors clusters collocalized by binding of polyvalent antigens or arising during the immune synapse formation. Affiliations:
 
13.  Kaźmierczak B., Peradzyński Z., Calcium waves with fast buffers and mechanical effects, JOURNAL OF MATHEMATICAL BIOLOGY, ISSN: 03036812, DOI: 10.1007/s0028500903232, Vol.62, No.1, pp.138, 2011 Abstract: In the paper we consider the existence of calcium travelling waves for systems with fast buffers. We prove the convergence of the travelling waves to an asymptotic limit as the kinetic coefficients characterizing the interaction between calcium and buffers tend to infinity. To be more precise, we prove the convergence of the speeds as well as the calcium component concentration profile to the profile of the travelling wave of the reduced equation. Additionally, we take into account the effect of coupling between the mechanical and chemical processes and show the existence as well the monotonicity of the profiles of concentrations. This property guarantees their positivity. Keywords:Calcium waves, Reaction–diffusion systems, Mechanochemical coupling Affiliations:
 
14.  Szopa P., Lipniacki T., Kaźmierczak B., Exact solutions to a spatially extended model of kinasereceptor interaction, PHYSICAL BIOLOGY, ISSN: 14783967, DOI: 10.1088/14783975/8/5/055005, Vol.8, No.5, pp.055005117, 2011 Abstract: B and Mast cells are activated by the aggregation of the immune receptors. Motivated by this phenomena we consider a simple spatially extended model of mutual interaction of kinases and membrane receptors. It is assumed that kinase activates membrane receptors and in turn the kinase molecules bound to the active receptors are activated by transphosphorylation. Such a type of interaction implies positive feedback and may lead to bistability. In this study we apply the Steklov eigenproblem theory to analyze the linearized model and find exact solutions in the case of nonuniformly distributed membrane receptors. This approach allows us to determine the critical value of receptor dephosphorylation rate at which cell activation (by arbitrary small perturbation of the inactive state) is possible. We found that cell sensitivity grows with decreasing kinase diffusion and increasing anisotropy of the receptor distribution. Moreover, these two effects are cooperating. We showed that the cell activity can be abruptly triggered by the formation of the receptor aggregate. Since the considered activation mechanism is not based on receptor crosslinking by polyvalent antigens, the proposed model can also explain B cell activation due to receptor aggregation following binding of monovalent antigens presented on the antigen presenting cell. Affiliations:
 
15.  Kaźmierczak B., Piechór K., Traveling wave solutions of a model of skin pattern formation in a singular case, MATHEMATICAL METHODS IN THE APPLIED SCIENCES, ISSN: 01704214, DOI: 10.1002/mma.1359, Vol.34, No.3, pp.325337, 2011 Abstract: We study traveling wave solutions to a system of four nonlinear partial differential equations, which arise in a tissue interaction model for skin morphogenesis. Under the assumption that the strength of attachment of the epidermis to the basal lamina is sufficiently large, we prove the existence and uniqueness (up to a translation) of traveling wave solutions connecting two stationary states of the system with the dermis and epidermis cell densities being positive. We discuss the problem of the minimal wave speed. Keywords:skin morphogenesis, heteroclinic solutions, implicit function theorem Affiliations:
 
16.  Kaźmierczak B., Lipniacki T., Spatial gradients in kinase cascade regulation, IET SYSTEMS BIOLOGY, ISSN: 17518849, DOI: 10.1049/ietsyb.2010.0002, Vol.4, No.6, pp.348355, 2010 Abstract: The spatiotemporal kinetics of proteins and other substrates regulate cell fate and signaling. In this study, we consider a reaction–diffusion model of interaction of membrane receptors with a twostep kinase cascade. The receptors activate the ‘upstream’ kinase, which may diffuse over cell volume and activate the ‘downstream’ kinase, which is also diffusing. Both kinase species and receptors are inactivated by uniformly distributed phosphatases. The positive feedback, key to the considered dynamics, arises since the upstream kinase activates the receptors. Such a mutual interaction is characteristic for immune cell receptors. Based on the proposed model, we demonstrated that cell sensitivity (measured as a critical value of phosphatase activity at which cell maybe activated) increases with decreasing motility of receptorinteracting kinases and with increasing polarity of receptors distribution. These two effects are cooperating, the effect of receptors localisation close to one pole of the cell grows with the decreasing kinase diffusion and vanishes in the infinite diffusion limit. As the cell sensitivity increases with decreasing diffusion of receptorinteracting kinase, the overall activity of the downstream kinase increases with its diffusion. In conclusion, the analysis of the proposed model shows that, for the fixed substrate interaction rates, spatial distribution of the surface receptors together with the motility of intracellular kinases control cell signalling and sensitivity to extracellular signals. The increase of the cell sensitivity can be achieved by (i) localisation of receptors in a small subdomain of the cell membrane, (ii) lowering the motility of receptorinteracting kinase, (iii) increasing the motility of downstream kinases which distribute the signal over the whole cell. Affiliations:
 
17.  Kaźmierczak B., Dyzma M., Mechanical effects coupled with calcium waves, ARCHIVES OF MECHANICS, ISSN: 03732029, Vol.62, No.2, pp.121133, 2010 Abstract: In the paper we find explicit formulae for heteroclinic travelling wave solutions in the system of equations describing the dynamics of cytosolic calcium concentration and the accompanying mechanical phenomena. Keywords:calcium waves, reactiondiffusion systems, mechanochemical coupling Affiliations:
 
18.  Kaźmierczak B., Lipniacki T., Regulation of kinase activity by diffusion and feedback, JOURNAL OF THEORETICAL BIOLOGY, ISSN: 00225193, DOI: 10.1016/j.jtbi.2009.03.016, Vol.259, pp.291296, 2009 Abstract: In living cells proteins motilities regulate the spatiotemporal dynamics of molecular pathways. We consider here a reaction–diffusion model of mutual kinase–receptor activation showing that the strength of positive feedback is controlled by the kinase diffusion coefficient. For high diffusion, the activated kinase molecules quickly leave the vicinity of the cell membrane and cannot efficiently activate the receptors. As a result, in a broad range of parameters, the cell can be activated only if the kinase diffusion coefficient is sufficiently small. Our simple model shows that change in the motility of substrates may dramatically influence the cell responses. Keywords:Reaction–diffusion system, Signal transduction, Positive feedback, Kinase activation, Membrane receptors, Protein motility Affiliations:
 
19.  Khatib N.El.^{♦}, Génieys S.^{♦}, Kaźmierczak B., Volpert V.^{♦}, Mathematical modelling of atherosclerosis as an inflammatory disease, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY AMATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, ISSN: 1364503X, DOI: 10.1098/rsta.2009.0142, Vol.18, No.4, pp.345352, 2009 Abstract: Atherosclerosis is an inflammatory disease. The atherosclerosis process starts when lowdensity lipoproteins (LDLs) enter the intima of the blood vessel, where they are oxidized (oxLDLs). The antiinflammatory response triggers the recruitment of monocytes. Once in the intima, the monocytes are transformed into macrophages and foam cells, leading to the production of inflammatory cytokines and further recruitment of monocytes. This autoamplified process leads to the formation of an atherosclerotic plaque and, possibly, to its rupture. In this paper we develop two mathematical models based on reaction–diffusion equations in order to explain the inflammatory process. The first model is onedimensional: it does not consider the intima’s thickness and shows that low oxLDL concentrations in the intima do not lead to a chronic inflammatory reaction. Intermediate oxLDL concentrations correspond to a bistable system, which can lead to a travelling wave that can be initiated by certain conditions, such as infection or injury. High oxLDL concentrations correspond to a monostable system, and even a small perturbation of the noninflammatory case leads to travellingwave propagation, which corresponds to a chronic inflammatory response. The second model we suggest is twodimensional: it represents a reaction–diffusion system in a strip with nonlinear boundary conditions to describe the recruitment of monocytes as a function of the cytokines’ concentration. We prove the existence of travelling waves and confirm our previous results, which show that atherosclerosis develops as a reaction–diffusion wave. The results of the two models are confirmed by numerical simulations. The latter show that the twodimensional model converges to the onedimensional one if the thickness of the intima tends to zero. Keywords:mathematical modelling, biomathematics, partial differential equations, travelling waves, reaction–diffusion equations, atherosclerosis Affiliations:
 
20.  Alber M.^{♦}, Gejji R.^{♦}, Kaźmierczak B., Existence of global solutions of a macroscopic model of cellular motion in a chemotactic field, APPLIED MATHEMATICS LETTERS, ISSN: 08939659, DOI: 10.1016/j.aml.2009.05.013, Vol.22, No.11, pp.16451648, 2009 Abstract: Existence of global classical solutions of a class of reaction–diffusion systems with chemotactic terms is demonstrated. This class contains a system of equations derived recently as a continuous limit of the stochastic discrete cellular Potts model. This provides mathematical justification for using numerical solutions of this system for modeling cellular motion in a chemotactic field. Keywords:Reaction–diffusion systems, Nonlinear diffusion, Global existence, Continuous limit, Cellular motion, Chemotaxis Affiliations:
 
21.  Newman S.A.^{♦}, Christley S.^{♦}, Glimm T.^{♦}, Hentschel H.G.^{♦}, Kaźmierczak B., Zhang Y.T.^{♦}, Zhu J.^{♦}, Alber M.^{♦}, Multiscale models for vertebrate limb development, CURRENT TOPICS IN DEVELOPMENTAL BIOLOGY, ISSN: 00702153, Vol.81, pp.311340, 2008 Abstract: Dynamical systems in which geometrically extended model cells produce and interact with diffusible (morphogen) and nondiffusible (extracellular matrix) chemical fields have proved very useful as models for developmental processes. The embryonic vertebrate limb is an apt system for such mathematical and computational modeling since it has been the subject of hundreds of experimental studies, and its normal and variant morphologies and spatiotemporal organization of expressed genes are well known. Because of its stereotypical proximodistally generated increase in the number of parallel skeletal elements, the limb lends itself to being modeled by Turingtype systems which are capable of producing periodic, or quasiperiodic, arrangements of spot and stripelike elements. This chapter describes several such models, including, (i) a system of partial differential equations in which changing cell density enters into the dynamics explicitly, (ii) a model for morphogen dynamics alone, derived from the latter system in the “morphostatic limit” where cell movement relaxes on a much slower timescale than cell differentiation, (iii) a discrete stochastic model for the simplified pattern formation that occurs when limb cells are placed in planar culture, and (iv) several hybrid models in which continuum morphogen systems interact with cells represented as energyminimizing mesoscopic entities. Progress in devising computational methods for handling 3D, multiscale, multimodel simulations of organogenesis is discussed, as well as for simulating reaction–diffusion dynamics in domains of irregular shape. Affiliations:
 
22.  Kaźmierczak B., Volpert V.^{♦}, Travelling calcium waves in systems with nondiffusing buffers, MATHEMATICAL MODELS AND METHODS IN APPLIED SCIENCES, ISSN: 02182025, Vol.18, No.6, pp.883912, 2008 Abstract: The existence and structural stability of travelling waves of systems of the free cytosolic calcium concentration in the presence of immobile buffers are studied. The proof is carried out by passing to zero with the diffusion coefficients of buffers. Thus, its method is different from Ref. 13 where the existence is proved straightforwardly. Keywords:Calcium dynamics, travelling waves, implicit function theorem Affiliations:
 
23.  Kaźmierczak B., Volpert V.^{♦}, Calcium waves in systems with immobile buffers as a limit of waves for systems with nonzero diffusion, NONLINEARITY, ISSN: 09517715, DOI: 10.1088/09517715/21/1/004, Vol.21, pp.7196, 2008 Abstract: We study the existence and properties of calcium waves in the presence of buffers. The model represents a reaction–diffusion system of equations with some diffusion coefficients equal to zero. They correspond to immobile buffers. The proof of the existence of travelling waves is carried out by passing to zero in the diffusion coefficients. Affiliations:
 
24.  Kaźmierczak B., Volpert V.^{♦}, Mechanochemical calcium waves in systems with immobile buffers, ARCHIVES OF MECHANICS, ISSN: 03732029, Vol.60, No.1, pp.322, 2008 Abstract: We study the existence of travelling waves of the free cytosolic calcium concentration in the presence of immobile buers. We also take into account the mechanochemical interaction. In the proof we use the a priori estimates for solutions of systems with diusing buers and pass to zero with their diusion coefficients. Affiliations:
 
25.  Kaźmierczak B., Existence of global solutions to a model of chondrogenesis, MATHEMATICAL METHODS IN THE APPLIED SCIENCES, ISSN: 01704214, DOI: 10.1002/mma.1034, Vol.21, pp.264283, 2008 Abstract: The paper considers conditions sufficient for the existence of classical Cmath image solutions to a new model of chondrogenesis during the vertebrate limb formation. We assume that the diffusion coefficient of the fibronectin is positive and that the function describing the interaction between the fibronectin and cells satisfies some additional properties. Keywords:bone pattern formation, chemotaxis, invariant region method Affiliations:
 
26.  Alber M.^{♦}, Glimm T.^{♦}, Hentschel H.G.^{♦}, Kaźmierczak B., Zhang Y.T.^{♦}, Zhu J.^{♦}, Newman S.A.^{♦}, The morphostatic limit for a model of skeletal pattern formation in the vertebrate limb, BULLETIN OF MATHEMATICAL BIOLOGY, ISSN: 00928240, DOI: 10.1007/s1153800792643, Vol.70, pp.460483, 2007 Abstract: A recently proposed mathematical model of a “core” set of cellular and molecular interactions present in the developing vertebrate limb was shown to exhibit patternforming instabilities and limb skeletonlike patterns under certain restrictive conditions, suggesting that it may authentically represent the underlying embryonic process (Hentschel et al., Proc. R. Soc. B 271, 1713–1722, 2004). The model, an eightequation system of partial differential equations, incorporates the behavior of mesenchymal cells as “reactors,” both participating in the generation of morphogen patterns and changing their state and position in response to them. The full system, which has smooth solutions that exist globally in time, is nonetheless highly complex and difficult to handle analytically or numerically. According to a recent classification of developmental mechanisms (SalazarCiudad et al., Development 130, 2027–2037, 2003), the limb model of Hentschel et al. is “morphodynamic,” since differentiation of new cell types occurs simultaneously with cell rearrangement. This contrasts with “morphostatic” mechanisms, in which cell identity becomes established independently of cell rearrangement. Under the hypothesis that development of some vertebrate limbs employs the core mechanism in a morphostatic fashion, we derive in an analytically rigorous fashion a pair of equations representing the spatiotemporal evolution of the morphogen fields under the assumption that cell differentiation relaxes faster than the evolution of the overall cell density (i.e., the morphostatic limit of the full system). This simple reaction–diffusion system is unique in having been derived analytically from a substantially more complex system involving multiple morphogens, extracellular matrix deposition, haptotaxis, and cell translocation. We identify regions in the parameter space of the reduced system where Turingtype pattern formation is possible, which we refer to as its “Turing space.” Obtained values of the parameters are used in numerical simulations of the reduced system, using a new Galerkin finite element method, in tissue domains with nonstandard geometry. The reduced system exhibits patterns of spots and stripes like those seen in developing limbs, indicating its potential utility in hybrid continuumdiscrete stochastic modeling of limb development. Lastly, we discuss the possible role in limb evolution of selection for increasingly morphostatic developmental mechanisms. Keywords:Limb development, Chondrogenesis, Mesenchymal condensation, Reaction–diffusion model Affiliations:
 
27.  Kaźmierczak B., Volpert V.^{♦}, Travelling waves in partially degenerated reaction diffusion systems, Mathematical Modelling of Natural Phenomena, Vol.2, pp.106125, 2007  
28.  Alber M.^{♦}, Hentschel H.G.E.^{♦}, Kaźmierczak B., Newman S.A.^{♦}, Existence of solutions to a new model of biological pattern formation, JOURNAL OF MATHEMATICAL ANALYSIS AND APPLICATIONS, ISSN: 0022247X, DOI: 10.1016/j.jmaa.2004.11.026, Vol.308, pp.175194, 2005 Abstract: In this paper we study the existence of classical solutions to a new model of skeletal development in the vertebrate limb. The model incorporates a general term describing adhesion interaction between cells and fibronectin, an extracellular matrix molecule secreted by the cells, as well as two secreted, diffusible regulators of fibronectin production, the positivelyacting differentiation factor (“activator”) TGFβ, and a negativelyacting factor (“inhibitor”). Together, these terms constitute a pattern forming system of equations. We analyze the conditions guaranteeing that smooth solutions exist globally in time. We prove that these conditions can be significantly relaxed if we add a diffusion term to the equation describing the evolution of fibronectin. Affiliations:
 
29.  Chaturvedi R.^{♦}, Huang C.^{♦}, Kaźmierczak B., Schneider T.^{♦}, Izaguirre J.^{♦}, Glimm T.^{♦}, Hentschel H.G.E.^{♦}, Glazier J.^{♦}, Newman S.^{♦}, Alber M.^{♦}, On multiscale approaches to threedimensional modelling of morphogenesis, JOURNAL OF THE ROYAL SOCIETY INTERFACE, ISSN: 17425689, DOI: 10.1098/rsif.2005.0033, Vol.2, pp.237253, 2005 Abstract: In this paper we present the foundation of a unified, objectoriented, threedimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction–diffusion model and a state automaton with welldefined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complexdevelopmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb. Affiliations:
 
30.  Alber M.^{♦}, Glimm T.^{♦}, Hentschel H.G.E.^{♦}, Kaźmierczak B., Newman S.^{♦}, Stability of an ndimensional patterns in a generalized turing system: implications for a biological patterns formation, NONLINEARITY, ISSN: 09517715, DOI: 10.1088/09517715/18/1/007, Vol.18, pp.125138, 2005 Abstract: The stability of Turing patterns in an ndimensional cube (0, π)n is studied, where n ≥ 2. It is shown by using a generalization of a classical result of Ermentrout concerning spots and stripes in two dimensions that under appropriate assumptions only sheetlike or nodulelike structures can be stable in an ndimensional cube. Other patterns can also be stable in regions comprising products of lowerdimensional cubes and intervals of appropriate length. Stability results are applied to a new model of skeletal pattern formation in the vertebrate limb. Affiliations:
 
31.  Peradzyński Z., Kaźmierczak B., On mechanochemical calcium waves, ARCHIVE OF APPLIED MECHANICS, ISSN: 09391533, DOI: 10.1007/s0041900503927, Vol.74, pp.827833, 2005 Abstract: The influence of mechanochemical coupling on calcium concentration waves is considered. The propagation of calcium waves is described by a reaction–diffusion equation with the reaction term dependent on the mechanical stress responsible for the release of calcium. Similarly the balance of mechanical forces is influenced by the calcium concentration through the socalled traction force. Keywords:Calcium waves, Reaction–diffusion systems, Mechanochemical coupling Affiliations:
 
32.  Belk M.^{♦}, Kaźmierczak B., Volpert V.^{♦}, Existence of reactiondiffusionconvection waves in unbounded cylinders, International Journal of Mathematics and Mathematical Sciences, Vol.2, pp.169193, 2005  
33.  Kaźmierczak B., Fale biegnące w ośrodkach z dyfuzją, Foundations of Science, ISSN: 12331821, Vol.6, No.47, pp.2947, 2005 
Conference papers
1.  Dyzma M.M., Szopa P., Kaźmierczak B., Membrane associated complexes: new approach to calcium dynamics modeling, 16th National Conference on Applications of Mathematics in Biology and Medicine, 20100914/0918, Krynica (PL), pp.3541, 2010 