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Motivation: With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to…
The cytoskeleton is an important subsystem of cells that is involved for example in cell division and locomotion. It consists of filaments that are cross-linked by molecular motors that can induce relative sliding between filaments and…
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular…
The Filament Based Lamellipodium Model (FBLM) is a two-phase two-dimensional continuum model, describing the dynamcis of two interacting families of locally parallel actin filaments (C.Schmeiser and D.Oelz, How do cells move? Mathematical…
Most conspicuous organisms are multicellular and most multicellular organisms develop somatic cells to perform specific, non-reproductive tasks. The ubiquity of this division of labor suggests that it is highly advantageous. In this paper,…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
We compare the informational architecture of biological and random networks to identify informational features that may distinguish biological networks from random. The study presented here focuses on the Boolean network model for…
The plasma membrane of human red blood cells consists of a lipid bilayer attached to a regular network of underlying cytoskeletal polymers. We model this system at a dynamic coarse-grained level, treating the bilayer as an elastic sheet and…
Collective cell migration is a key driver of embryonic development, wound healing, and some types of cancer invasion. Here we provide a physical perspective of the mechanisms underlying collective cell migration. We begin with a catalogue…
Flocks of birds, schools of fish, mixtures of motors and cytoskeletal filaments, swimming bacteria and driven granular media are systems of interacting motile units that exhibit collective behaviour. These can all be described as active…
Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for understanding tissue homeostasis and stable developmental processes. However, numerical simulations…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
The dispersal of cells from an initially constrained location is a crucial aspect of many physiological phenomena ranging from morphogenesis to tumour spreading. In such processes, the way cell-cell interactions impact the motion of single…
The shape of a cell influences and it is influenced by interactions with its neighbouring partners. Here, we introduce a coarse-grained model of non-reciprocal interactions between single-cell organisms to study emergent morphologies during…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…
Although continuous advances in theoretical modelling of Molecular Communications (MC) are observed, there is still an insuperable gap between theory and experimental testbeds, especially at the microscale. In this paper, the development of…
A Boolean network model of the cell-cycle regulatory network of fission yeast (Schizosaccharomyces Pombe) is constructed solely on the basis of the known biochemical interaction topology. Simulating the model in the computer, faithfully…
This contribution belongs to a combinatorial approach to hyperbolic geometry and it is aimed at possible applications to computer simulations. It is based on the splitting method which was introduced by the author and which is reminded in…
Myxococcus xanthus cells self-organize into aligned groups, clusters, at various stages of their lifecycle. Formation of these clusters is crucial for the complex dynamic multi-cellular behavior of these bacteria. However, the mechanism…