Related papers: Florigenic and antiflorigenic signalling in plants
This article presents formalistic tool for description of structural and biochemical relations between cells in the course of development of the body of plants. This is flexible formalistic space, based on the Category theory and the Petri…
Finite systems such as atomic nuclei present at phase transition specific features different from those observed at the thermodynamic limit. Several characteristic signals were found in samples of events resulting from heavy ion collisions…
Signal processing in biological systems is delicately executed by specialised networks, which are modular assemblies of network motifs. The motifs are independently functional circuits found in enormous numbers in any living cell. A very…
Biological systems encode function not primarily in steady states, but in the structure of transient responses elicited by time-varying stimuli. Overshoots, biphasic dynamics, adaptation kinetics, fold-change detection, entrainment, and…
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6-10^9 decoy sites? Our analysis of 319 known TF binding motifs clearly…
Living cells inherently reorganize their intracellular structures in response to mechanical cues from their environment. Among these responses, the formation of actin-based stress fibers exhibits a series of structural transitions depending…
Living organisms produce metabolites of many types via their metabolisms. Especially, flavonoids, a kind of secondary metabolites, of plant species are interesting examples. Since plant species are believed to have specific flavonoids with…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
In this paper, we bring together our efforts in identifying and understanding nonequilibrium phase segregation driven by active processes in the living cell, with special focus on the segregation of cell membrane components driven by active…
Motivation: Recent studies of genomic-scale regulatory networks suggested that a feed-forward loop (FFL) circuitry is a key component of many such networks. This led to a study of the functional properties of different FFL types, where the…
Multicellular tissues are the building blocks of many biological systems and organs. These tissues are not static, but dynamically change over time. Even if the overall structure remains the same there is a turnover of cells within the…
The cell wall serves as a mechanical protection for the fungi and controls the traffic of molecules entering the cell. However, the optical role of the cell wall has not been fully investigated. In this work, we use a computational…
Several recent studies show that companion cells in flowering plant gametophytes relax epigenetic control of transposable elements (TEs) to promote production of small RNA that presumably assist nearby reproductive cells in management of…
Within the tumor microenvironment (TME), cancer cells use mechanotransduction pathways to convert biophysical forces to biochemical signals. However, the underlying mechanisms and functional significance of these pathways remain largely…
The cambium is a meristematic tissue in plant stems. Here, cell divisions occur that are required for radial growth of plant stems. Daughters of cell divisions within the cambium differentiate into woody xylem cells towards the inside of…
Plant morphogenesis relies on dynamic growth deformations at the cell and tissue scales driven by osmotic fluxes. A mechanistic understanding of this phenomenon demands a physical framework that integrates cell imbibition, tissue mechanics,…
T1 transitions, which are localised cell rearrangements, play an important role in the fluidization of epithelial monolayers. Using a multi-phase field model and an active elastic solid model, we show that although each cell undergoes T1…
Plants solve complex problems without centralized control, relying instead on growth-driven dynamics to sense, navigate, and optimize resource acquisition. This review presents a unified physical framework for understanding plant behavior…
Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…
A model of the regular arrangement of leaves on a plant stem (phyllotactic patterns) is proposed, based on a new plant pattern algorithm. Tripartite patterning is proposed to occur by the interaction of two signaling pathways. Each pathway…