arXiv subjects

Andras Czirok

Publications and source records attributed to Andras Czirok.

10 recordsLinked to original sources

arXiv2020

A biomimetic kidney tubule model

A critical barrier in the nephrology field is the lack of appropriate in vitro renal tubule models that allow manipulation of various mechanical factors, facilitating studies of disease pathophysiology and drug discovery. Here we report development of a novel in vitro assay system comprised of a renal tubule within an elasto-plastic extracellular matrix microenvironment. This in vitro tubule mimetic device consists of a container with two, pipette-accessible ports, filament-deposition (3D-) printed into 35 mm cell culture dishes. The container is filled with a hydrogel, such as a collagen I or fibrin gel, while a narrow masking tube is threaded through the ports. Following gelation, the masking material is pulled out leaving a tunnel within the gel. Seeding of the tunnels with M1 or MDCK renal epithelial cells through the side ports results in a monolayer with apical-basal polarity, such that laminin and fibronectin are present on the basal surface, while primary cilia project from the apical side of cells into the tubular lumen. The device is optically accessible, and can be live-imaged by phase contrast or epifluorescence microscopy. The lumen of the epithelial-lined tube can be connected through the side ports to a circulatory flow. We demonstrate that kidney epithelial cells are able to adjust the diameter of the model tubule by myosin-II dependent contractility. Furthermore, cells of the tubule are also able to remodel the surrounding hydrogel leading to budding from the main tubule. We propose that this versatile in vitro model system can be developed into a future pre-clinical tool to study pathophysiology of kidney diseases and identify therapeutic compounds.

q-bio.TO↗

arXiv2015

Myosin-II dependent cell contractility contributes to spontaneous nodule formation of mesothelioma cells

We demonstrate that characteristic nodules emerge in cultures of several malignant pleural mesothelioma (MPM) cell lines. Instead of excessive local cell proliferation, the nodules arise by Myosin II-driven cell contractility. The aggregation process can be prevented or reversed by suitable pharmacological inhibitors of acto-myosin contractility. A cell-resolved elasto-plastic model of the multicellular patterning process indicates that the morphology and size of the nodules as well as the speed of their formation is determined by the mechanical tension cells exert on their neighbors, and the stability of cell-substrate adhesion complexes. A linear stability analysis of a homogenous, self-tensioned Maxwell fluid indicates the unconditional presence of a patterning instability.

physics.bio-ph↗

arXiv2014

Cell resolved, multiparticle model of plastic tissue deformations and morphogenesis

We propose a three dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue plasticity is modeled by a stochastic process consisting of a connectivity change (addition or removal of a single link) followed by a complete relaxation to mechanical equilibrium. In particular, we assume that (i) two non-connected, but adjacent particles can form a new link; and (ii) the lifetime of links is reduced by tensile forces. We demonstrate that the proposed model yields a realistic macroscopic elasto-plastic behavior and we establish how microscopic model parameters affect the material properties at the macroscopic scale. Based on these results, microscopic parameter values can be inferred from tissue thickness, macroscopic elastic modulus and the magnitude and dynamics of intercellular adhesion forces. In addition to their mechanical role, model particles can also act as active simulation agents and modulate their connectivity according to specific rules. As an example, anisotropic link insertion and removal probabilities can give rise to local cell intercalation and large scale convergent extension movements. The proposed stochastic simulation of cell activities yields fluctuating tissue movements which exhibit the same autocorrelation properties as empirical data from avian embryos.

physics.bio-ph↗

arXiv2006

Network formation of tissue cells via preferential attraction to elongated structures

Vascular and non-vascular cells often form an interconnected network in vitro, similar to the early vascular bed of warm blooded embryos. Our time-lapse recordings show that the network forms by extending sprouts, i.e., multicellular linear segments. To explain the emergence of such structures, we propose a simple model of preferential attraction to stretched cells. Numerical simulations reveal that the model evolves into a quasi-stationary pattern containing linear segments, which interconnect above the critical volume fraction of 0.2. In the quasi-stationary state the generation of new branches offset the coarsening driven by surface tension. In agreement with empirical data, the characteristic size of the resulting polygonal pattern is density-independent within a wide range of volume fractions.

q-bio.CB↗

arXiv2006

Collective behavior of interacting self-propelled particles

We discuss biologically inspired, inherently non-equilibrium self-propelled particle models, in which the particles interact with their neighbours by choosing at each time step the local average direction of motion. We summarize some of the results of large scale simulations and theoretical approaches to the problem.

cond-mat.stat-mech↗

arXiv2006

Spontaneously ordered motion of self-propelled particles

We study a biologically inspired, inherently non-equilibrium model consisting of self-propelled particles. In the model, particles move on a plane with a velocity of constant magnitude; they locally interact with their neighbors by choosing at each time step a velocity direction equal to the average direction of their neighbors. Thus, in the limit of vanishing velocities the model becomes analogous to a Monte-Carlo realization of the classical XY ferromagnet. We show by large-scale numerical simulations that, unlike in the equilibrium XY model, a long-range ordered phase characterized by non-vanishing net flow $ϕ$ emerges in this system in a phase space domain bordered by a critical line along which the fluctuations of the order parameter diverge. The corresponding phase diagram as a function of two parameters, the amplitude of noise $η$ and the average density of the particles $\varrho$ is calculated and is found to have the form $η_c(\varrho)\sim \varrho^{1/2}$. We also find that $ϕ$ scales as a function of the external bias $h$ (field or ``wind'') according to a power law $ϕ\sim h^{0.9}$. In the ordered phase the system shows long-range correlated fluctuations and $1/f$ noise.

cond-mat.stat-mech↗

arXiv2006

Novel type of phase transition in a system of self-driven particles

A simple model with a novel type of dynamics is introduced in order to investigate the emergence of self-ordered motion in systems of particles with biologically motivated interaction. In our model particles are driven with a constant absolute velocity and at each time step assume the average direction of motion of the particles in their neighborhood with some random perturbation ($η$) added. We present numerical evidence that this model results in a kinetic phase transition from no transport (zero average velocity, $| {\bf v}_a | =0$) to finite net transport through spontaneous symmetry breaking of the rotational symmetry. The transition is continuous since $| {\bf v}_a |$ is found to scale as $(η_c-η)^β$ with $β\simeq 0.45$.

cond-mat.stat-mech↗

arXiv2000

Theory of periodic swarming of bacteria: application to Proteus mirabilis

The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common species exhibiting this type of growth) a series of concentric rings are developed as the bacteria multiply and swarm following a scenario periodically repeating itself. We have developed a theoretical description for this process in order to get a deeper insight into some of the typical processes governing the phenomena in systems of many interacting living units. All of our theoretical results are in excellent quantitative agreement with the complete set of available observations.

physics.bio-ph↗

arXiv1998

Hydrodynamics of bacterial motion

In this paper we present a hydrodynamic approach to describe the motion of migrating bacteria as a special class of self-propelled systems. Analytical and numerical calculations has been performed to study the behavior of our model in the turbulent-like regime and to show that a phase transition occurs as a function of noise strength. Our results can explain previous experimental observations as well as results of numerical simulations.

cond-mat.soft↗

arXiv1997

Collective motion of self-propelled particles: kinetic phase transition in one dimension

We demonstrate that a system of self-propelled particles (SPP) exhibits spontaneous symmetry breaking and self-organization in one dimension, in contrast with previous analytical predictions. To explain this surprising result we derive a new continuum theory that can account for the development of the symmetry broken state and belongs to the same universality class as the discrete SPP model.

cond-mat.stat-mech↗