Related papers: Coarse-graining the vertex model and its response …
Dense monolayers of living cells display intriguing relaxation dynamics, reminiscent of soft and glassy materials close to the jamming transition, and migrate collectively when space is available, as in wound healing or in cancer invasion.…
Biological cells can actively tune their intracellular architecture according to their overall shape. Here we explore the rheological implication of such coupling in a minimal model of a dense cellular material where each cell exerts an…
Auto-chemotaxis, the directed movement of cells along gradients in chemicals they secrete, is central to the formation of complex spatiotemporal patterns in biological systems. Since the introduction of the Keller--Segel model, numerous…
Simulations of condensed matter systems often focus on the dynamics of a few distinguished components but require integrating the dynamics of the full system. A prime example is a molecular dynamics simulation of a (macro)molecule in…
Coordinated cellular movements are key processes in tissue morphogenesis. Using a cell-based modeling approach we study the dynamics of epithelial layers lining surfaces with constant and varying curvature. We demonstrate that extrinsic…
In a companion paper, we put forth a thermodynamic model for complex formation via a chemical reaction involving multiple macromolecular species, which may subsequently undergo liquid-liquid phase separation and a further transition into a…
We study the two-dimensional (2D) shear flow of amorphous solids within variants of an elastoplastic model, paying particular attention to spatial correlations and time fluctuations of, e.g., local stresses. The model is based on the local…
We derive a course grained, continuum model of the 2D vertex model, applicable for different underlying geometries, and allowing for analytical analysis of an otherwise numerical model. Using a geometric approach and out--of--equilibrium…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
Molecular dynamics simulations are carried out to investigate mechanical properties and porous structure of binary glasses subjected to steady shear. The model vitreous systems were prepared via thermal quench at constant volume to a…
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…
An adequate control of cell response in tissue engineering applications is of utmost importance to obtain products suitable to clinical practice. This paper is the first part of a series of two connected publications in which we study via…
Vertex models are a popular approach to modeling the mechanical and dynamical properties of dense biological tissues, describing the tissue as a network of connected polygons representing the cells. Recently a class of two-dimensional…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
We explore a systematic approach to studying the dynamics of evolving networks at a coarse-grained, system level. We emphasize the importance of finding good observables (network properties) in terms of which coarse grained models can be…
The vertex model is a popular framework for modelling tightly packed biological cells, such as confluent epithelia. Cells are described by convex polygons tiling the plane and their equilibrium is found by minimizing a global mechanical…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
Cell migration is important in many biological processes, including embryonic development, cancer metastasis, and wound healing. In these tissues, a cell's motion is often strongly constrained by its neighbors, leading to glassy dynamics.…
Many types of motile cells perform durotaxis, namely, directed migration following gradients of substrate stiffness. Recent experiments have revealed that cell monolayers can migrate toward stiffer regions even when individual cells do not…
A plethora of natural and industrial shear-driven granular flows exhibit particle-size segregation. Its occurrence is commonly attributed to two primary mechanisms: kinetic sieving and squeeze expulsion. While kinetic sieving is relatively…