Related papers: Branching, Capping, and Severing in Dynamic Actin …
The structural reorganization of the actin cytoskeleton is facilitated through the action of motor proteins that crosslink the actin filaments and transport them relative to each other. Here, we present a combined experimental-computational…
The interface dynamics of a 3D cell immersed in a 3D extracellular matrix is investigated. We suggest a 3D generalization of a known 2D minimal phase field model suggested in [1] for the description of keratocyte motility. Our model…
Morphological trends in growing colonies of living cells are at the core of physiological and evolutionary processes. Using active gel equations, which include cell division, we show that shape changes during the growth can be regulated by…
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…
Cytoskeletons are self organized networks based on polymerized proteins, actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality…
Centering and decentering of cellular components is essential for internal organization of cells and their ability to perform basic cellular functions such as division and motility. How cells achieve proper localization of their components…
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…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…
Channel formation and branching is widely seen in physical systems where movement of fluid through a porous structure causes the spatiotemporal evolution of the medium in response to the flow, in turn causing flow pathways to evolve. We…
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…
A dynamic model for cell differentiation is studied, where cells with internal chemical reaction dynamics interact with each other and replicate. It leads to spontaneous differentiation of cells and determination, as is discussed in the…
Biomolecules, such as proteins and RNAs, can phase separate in the cytoplasm of cells to form biomolecular condensates. Such condensates are liquid-like droplets that can wet biological surfaces such as membranes. Many molecules that…
The conformational dynamics of a single protein molecule in a shear flow is investigated using Brownian dynamics simulations. A structure-based coarse grained model of a protein is used. We consider two proteins, ubiquitin and integrin, and…
Neuronal networks constitute a special class of dynamical systems, as they are formed by individual geometrical components, namely the neurons. In the existing literature, relatively little attention has been given to the influence of…
Many real-world complex networks arise as a result of a competition between growth and rewiring processes. Usually the initial part of the evolution is dominated by growth while the later one rather by rewiring. The initial growth allows…
In cell membranes, proteins and lipids diffuse in a highly crowded and heterogeneous landscape, where aggregates and dense domains of proteins or lipids obstruct the path of diffusing molecules. In general, hindered motion gives rise to…
Biological functions rely on ordered structures and intricately controlled collective dynamics. In contrast to systems in thermodynamic equilibrium, order is typically established and sustained in stationary states by continuous dissipation…
Recent research has shown that motile cells can adapt their mode of propulsion to the mechanical properties of the environment in which they find themselves--crawling in some environments while swimming in others. The latter can involve…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
The motility of a fish keratocyte on a flat substrate exhibits two distinct regimes: the non-migrating and the migrating one. In both configurations the shape is fixed in time and, when the cell is moving, the velocity is constant in…