Related papers: The Mechanism of Pattern Transitions between Forma…
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…
Blebs are balloon-shaped membrane protrusions that form during many physiological processes. Using computer simulation of a particle-based model for self-assembled lipid bilayers coupled to an elastic meshwork, we investigated the phase…
We study pattern formation in a chemotaxis model of bacteria and soil carbon dynamics as an example system where transient dynamics can give rise to pattern formation outside of Turing unstable regimes. We use a detailed analysis of the…
One possible mechanism to explain how animals got their coat patterns was proposed by Alan Turing. He assumed that two kinds of morphogens diffuse on a surface and interact with each other, generating a reaction-diffusion mechanism. We…
Superficial (two dimensional) crack patterns appear when a thin layer of material elastically attached to a substrate contracts. We study numerically the maturation process undergone by these crack patterns when they are allowed to adapt in…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
Via molecular dynamics simulations, we study the kinetics in a phase separating active matter model. Quantitative results for the isotropic bicontinuous pattern formation, its growth and aging, studied, respectively, via the two-point…
We study the surface diffusion of the model cyanobacterium Synechocystis sp. PCC $6803$ during the incipient stages of cell contact with a glass surface in the dilute regime. We observe a twitching motility with alternating immobile…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
Drying of biologically-relevant sessile droplets, including passive systems (like DNA and proteins), as well as active microbial systems comprising bacteria and algae, have garnered considerable attention over the last decades. Distinct…
Soft tissues - such as ligaments and tendons - primarily consist of solid (collagen, predominantly) and liquid phases. Understanding the interaction between such components and how they change under physiological loading sets the basis for…
We study the behaviour of interacting self-propelled particles, whose self-propulsion speed decreases with their local density. By combining direct simulations of the microscopic model with an analysis of the hydrodynamic equations obtained…
Sperm traverse their microenvironment through viscous fluid by propagating flagellar waves; the waveform emerges as a consequence of elastic structure, internal active moments, and low Reynolds number fluid dynamics. Engineered…
We give a description of cell diffusion in a soft tissue, paying special attention to the coupling of force, matter, and microforce balance laws through a suitable dissipation principle. To this end, we cast our framework into a multi-level…
Mesh-like structures, such as mucus gel or cytoskeleton networks, are ubiquitous in biological systems. These intricate structures are composed of cross-linked, semi-flexible bio-filaments, crucial to numerous biological processes. In many…
The time distribution of relaxation events in an aging system is investigated via molecular dynamics simulations. The focus is on the distribution functions of the first passage time, $p_1(\Delta t)$, and the persistence time, $p(\tau)$. In…
We present a field theory to describe the composition of a surface spontaneously exchanging matter with its bulk environment. By only assuming matter conservation in the system, we show with extensive numerical simulations that, depending…
Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…
Efficient pattern separation in dentate gyrus plays an important role in storing information in the hippocampus. Current knowledge of the structure and function of the hippocampus, entorhinal cortex and dentate gyrus, in pattern separation…
This paper develops a point-mutation model describing the evolutionary dynamics of a population of adult stem cells. Such a model may prove useful for quantitative studies of tissue aging and the emergence of cancer. We consider two modes…