Related papers: Enzyme-Substrate Complex Formation Modulates Diffu…
A mesoscopic continuum model is employed to analyse the transport mechanisms and structure formation during the redistribution stage of deposition experiments where organic molecules are deposited on a solid substrate with periodic…
Realistic examples of reaction-diffusion phenomena governing spatial and spatiotemporal pattern formation are rarely isolated systems, either chemically or thermodynamically. However, even formulations of `open' reaction-diffusion systems…
We study analytically and numerically a model metabolic cycle composed of an arbitrary number of species of catalytically active particles. Each species converts a substrate into a product, the latter being used as the substrate by the next…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
We discuss the shear viscosity of a Newtonian solution of catalytic enzymes and substrate molecules. The enzyme is modeled as a two-state dimer consisting of two spherical domains connected with an elastic spring. The enzymatic…
Pattern formation in reaction-diffusion systems is of great importance in surface micro-patterning [Grzybowski et al. Soft Matter. 1, 114 (2005)], self-organization of cellular micro-organisms [Schulz et al. Annu. Rev. Microbiol. 55, 105…
In vivo and in vitro cells rely on the support of an underlying biocompatible substrate, such as the extracellular matrix or a culture substrate, to spread and proliferate. The mechanical and chemical properties of such structures play a…
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…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
We show that the force generated by active enzyme molecules are strong enough to influence the dynamics of their surroundings under artificial crowded environments. We measured the behavior of polymer microparticles in a…
We numerically examine a binary system of particles with repulsive interactions, where one species is driven by a rotating drive and the other is subjected either to a constant drive in a fixed direction or to a rotating drive that is out…
Recent experiments have revealed that the diffusivity of exothermic and fast enzymes is enhanced when they are catalytically active, and different physical mechanisms have been explored and quantified to account for this observation. We…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…
Multisite covalent modification of proteins is omnipresent in eukaryotic cells. A well-known example is the mitogen-activated protein kinase (MAPK) cascade, where in each layer of the cascade a protein is phosphorylated at two sites. It has…
Cells and organisms follow aligned structures in their environment, a process that can generate persistent migration paths. Kinetic transport equations are a popular modelling tool for describing biological movements at the mesoscopic…
Chemotaxis of enzymes in response to gradients in the concentration of their substrate has been widely reported in recent experiments, but a basic understanding of the process is still lacking. Here, we develop a microscopic theory for…
Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
Robustness of spatial pattern against perturbations is an indispensable property of developmental processes for organisms, which need to adapt to changing environments. Although specific mechanisms for this robustness have been extensively…
[Background] Several studies have mentioned network modularity -- that a network can easily be decomposed into subgraphs that are densely connected within and weakly connected between each other -- as a factor affecting metabolic…