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Structure formation and constant reorganization of the actin cytoskeleton are key requirements for the function of living cells. Here we show that a minimal reconstituted system consisting of actin filaments, crosslinking molecules and…
One of the most ancient forms of life dating to ~3.5 billion years ago, cyanobacteria are highly abundant organisms that convert light into energy and motion, often within conjoined filaments and larger colonies. We study how gradients of…
The Turing patterning mechanism is believed to underly the formation of repetitive structures in development, such as zebrafish stripes and mammalian digits, but it has proved difficult to isolate the specific biochemical species…
This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular…
How patterns and structures undergo symmetry breaking and self-organize within biological systems from initially homogeneous states is a key issue for biological development. The activator-inhibitor (AI) mechanism, derived from…
During batch growth on mixtures of two growth-limiting substrates, microbes consume the substrates either sequentially or simultaneously. These growth patterns are manifested in all types of bacteria and yeasts. The ubiquity of these growth…
Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA)…
Cyanobacteria sequester photosynthetic enzymes into microcompartments which facilitate the conversion of carbon dioxide into sugars. Geometric similarities between these structures and self-assembling viral capsids have inspired models that…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
Rhythmic and sequential segmentation of the embryonic body plan is a vital developmental patterning process in all vertebrate species. However, a theoretical framework capturing the emergence of dynamic patterns of gene expression from the…
Motility coupled to responsive behavior is essential for many microorganisms to seek and establish appropriate habitats. One of the simplest possible responses, reversing the direction of motion, is believed to enable filamentous…
Growth in bacterial populations generally depends on the environment (availability and quality of nutrients, presence of a toxic inhibitor, product inhibition..). Here, we build a model to describe the action of a bacteriostatic antibiotic,…
Filamentous cyanobacteria can show fascinating examples of nonequilibrium self-organization, which however are not well-understood from a physical perspective. We investigate the motility and collective organization of colonies of these…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
Mixing of two fluids can lead to the formation of a precipitate. If one of the fluids is injected into a confined space filled with the other, a created precipitate disrupts the flow locally and forms complex spatiotemporal patterns. The…
Despite simplicity, the synchronous cellular automaton [D.A. Young, Math. Biosci. 72, 51 (1984)] enables reconstructing basic features of patterns of skin. Our extended model allows studying the formatting of patterns and their temporal…
The regulatory mechanisms driving progression of the yeast cell cycle appears to be comprised of an interacting network of transcription factors (TFs), cyclin-dependent kinases (CDK) and ubiquitin ligases. From a systems perspective the…
One of the most important problems in contemporary science, and especially in biology, is to reveal mechanisms of pattern formation. On the level of biological tissues, patterns form due to interactions between cells. These interactions can…
Under hard-agar and nutrient-rich conditions, a cell of $Bacillus$ $subtilis$ grows as a single filament owing to the failure of cell separation after each growth and division cycle. The self-elongating filament of cells shows sequential…
Collective behavior of bacterial colonies plays critical roles in adaptability, survivability, biofilm expansion and infection. We employ an individual-based model of an interstitial biofilm to study emergent pattern formation based on the…