Related papers: Enzyme-Substrate Complex Formation Modulates Diffu…
We study general linear transport-reaction systems on an arbitrary dimensional hypercube with periodic boundary conditions. Transport-reaction systems are often used to model the finite speed movement and interaction of particles, bacteria…
We performed an extensive numerical study of a two-dimensional reaction-diffusion system of the activator-inhibitor type in which domain patterns can form. We showed that both multidomain and labyrinthine patterns may form spontaneously as…
A large number of studies have shown the existence of metabolic covalent modifications in different molecular structures, able to store biochemical information that is not encoded by the DNA. Some of these covalent mark patterns can be…
We consider a reaction-diffusion system with discontinuous reaction terms modeled by non-ideal relays. The system is motivated by an epigenetic population model of evolution of two-phenotype bacteria which switch phenotype in response to…
Many transport processes in nature take place on substrates, often considered as unidimensional lanes. These unidimensional substrates are typically non-static: affected by a fluctuating environment, they can undergo conformational changes.…
This paper investigates the conditions for the stability and emergence of patterns in a new three-component reaction-diffusion system. The system describes the coexistence and interaction of water reservoirs, vegetation, and bushfire…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…
Naively, one expects the information communicated by an enzyme downstream within a signaling network, in which the enzyme is embedded, to grow monotonically with the enzyme's rate of product formation. However, here we observe that this…
Stick-slip motion, a common phenomenon observed during crawling of cells, is found to be strongly sensitive to the substrate stiffness. Stick-slip behaviours have previously been investigated typically using purely elastic substrates. For a…
Single enzyme chemotaxis is a phenomenon by which a non-equilibrium spatial distribution of an enzyme is created and maintained by concentration gradients of the substrate and product of the catalyzed reaction. These gradients can arise…
We develop a theory of reversible diffusion-controlled reactions with generalized binding/unbinding kinetics. In this framework, a diffusing particle can bind to the reactive substrate after a random number of arrivals onto it, with a given…
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
The mechanical environment of a substrate plays a key role in influencing the behavior of adherent biological cells. Traditional tunable substrates have limitations as their mechanical properties cannot be dynamically altered in-situ during…
The study of pattern-forming instabilities in reaction-diffusion systems on growing or otherwise time-dependent domains arises in a variety of settings, including applications in developmental biology, spatial ecology, and experimental…
Epithelial-Mesenchymal Transition (EMT), and the corresponding reverse process, Mesenchymal-Epithelial Transition (MET), are dynamic and reversible cellular programs orchestrated by many changes at biochemical and morphological levels. A…
We study the enzymatic degradation of an elastic fiber under tension using an an isotropic random-walk model, coupled with binding-unbinding reactions that weaken the fiber. The fiber is represented by a chain of elastic springs in series,…
Phase separation in passive systems leads to uncontrolled droplet growth, limiting structural control in soft materials and cells. We identify a generic mechanism to arrest coarsening based on chemical interconversion between molecular…
Substrate modification networks are ubiquitous in living, biochemical systems. A higher-level hypergraph "skeleton" captures key information about which substrates are transformed in the presence of modification-specific enzymes. Many…
Coupling diffusion process of signaling molecules with nonlinear interactions of intracellular processes and cellular growth/transformation leads to a system of reaction-diffusion equations coupled with ordinary differential equations…
We study chemical pattern formation in a fluid between two flat plates and the effect of such patterns on the formation of convective cells. This patterning is made possible by assuming the plates are chemically reactive or release reagents…