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Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
According to contemporary views, equilibrium constant is relevant only to true thermodynamic equilibria in isolated systems with one chemical reaction. The paper presents a novel formula that ties-up equilibrium constant and chemical system…
We study the diffusion process through an ideal polymer network, using numerical methods. Polymers are modeled by random walks on the bonds of a two-dimensional square lattice. Molecules occupy the lattice cells and may jump to the…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
The quasi-steady state assumption (QSSA) forms the basis for rigorous mathematical justification of the Michaelis-Menten formalism commonly used in modeling a broad range of intracellular phenomena. A critical supposition of QSSA-based…
The appearance of emergent symmetries in complex systems with components that can form composite units provides us with opportunities for design and control of exotic phase behaviour, for example by exploiting the dynamical symmetry…
How large ecosystems can create and maintain the remarkable biodiversity we see in nature is probably one of the biggest open questions in science, attracting attention from different fields, from Theoretical Ecology to Mathematics and…
We introduce a model of chemically active particles of a multi-component fluid that can change their interactions with other particles depending on their state. Since such switching of interactions can only be maintained by the input of…
A lattice model is presented for the simulation of dynamics in polymeric systems. Each polymer is represented as a chain of monomers, residing on a sequence of nearest-neighbor sites of a face-centered-cubic lattice. The polymers are self-…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Epistasis describes the phenomenon that mutations at different loci do not have independent effects with regard to certain phenotypes. Understanding the global epistatic landscape is vital for many genetic and evolutionary theories. Current…
The dynamics of one species chemical kinetics is studied. Chemical reactions are modelled by means of continuous time Markov processes whose probability distribution obeys a suitable master equation. A large deviation theory is formally…
Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations…
Polysaccharides are semi-flexible polymers composed of sugar residues with a myriad of important functions including structural support, energy storage and immunogenicity. The local conformation of such chains is a crucial factor governing…
By means of the isoconfigurational method we calculate the change in the propensity for motion that the structure of a glass-forming system experiences during its relaxation dynamics. The relaxation of such a system has been demonstrated to…
We here discuss the results of 3d MonteCarlo simulations of a minimal lattice model for gelling systems. We focus on the dynamics, investigated by means of the time autocorrelation function of the density fluctuations and the particle mean…
All biological processes are controlled by complex systems of enzymatic chemical reactions. Although the majority of enzymatic networks have very elaborate structures, there are many experimental observations indicating that some turnover…
We provide a detailed multiscale analysis of a system of particles interacting through a dynamical network of links. Starting from a microscopic model, via the mean field limit, we formally derive coupled kinetic equations for the particle…
We study a statistical model consisting of $N$ basic units which interact with each other by exchanging a physical entity, according to a given microscopic random law, depending on a parameter $\lambda$. We focus on the equilibrium or…
The work discusses specifics of phase transitions for metastable states of substances. The objects of condensed media physics are primarily equilibrium states of substances with metastable phases viewed as an exception, while the…