Related papers: Small Open Chemical Systems Theory and Its Implica…

Inspired by one--dimensional light--particle systems, the dynamics of a non-Hamiltonian system with long--range forces is investigated. While the molecular dynamics does not reach an equilibrium state, it may be approximated in the…

The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as for instance the fluctuations in ribsome copy numbers for a gene regulatory network. While several…

The relevance of chaos to evolution is discussed in the context of the origin and maintenance of diversity and complexity. Evolution to the edge of chaos is demonstrated in an imitation game. As an origin of diversity, dynamic clustering of…

Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…

Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…

Biological living systems in general exhibit complex and diverse dynamics. The latter, in particular, is essential, since diversification increases the odds of survival of an organism while reducing the risk of extinction of the population.…

Self-regulation of living tissue as an example of self-organization phenomena in hierarchical systems of biological, ecological, and social nature is under consideration. The characteristic feature of these systems is the absence of any…

Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as…

We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate…

In this paper I am presenting an overview on several topics related to nonequilibrium fluctuations in small systems. I start with a general discussion about fluctuation theorems and applications to physical examples extracted from physics…

This paper studies a chemotaxis system where cells move in response to a chemical signal within a confined habitat. The model includes external source terms that combine local and nonlocal growth with dampening effects. The main focus is on…

We describe a mechanism for pronounced biochemical oscillations, relevant to microscopic systems, such as the intracellular environment. This mechanism operates for reaction schemes which, when modeled using deterministic rate equations,…

Chaos is an active research subject in the fields of science in recent years. it is a complex and an erratic behavior that is possible in very simple systems. in the present day, the chaotic behavior can be observed in experiments. Many…

Chemical processes in closed systems are poorly controllable since they always relax to equilibrium. Living systems avoid this fate and give rise to a much richer diversity of phenomena by operating under nonequilibrium conditions. Recent…

Isologous diversification theory for cell differentiation is proposed, based on simulations of interacting cells with biochemical networks and cell division process following consumption of some chemicals. According to the simulations of…

Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…

Simple active models of matter recapitulate complex biological phenomena. The out-of-equilibrium nature of these models, however, often makes them beyond the reach of first-principle descriptions. This limitation is particularly perplexing…

In nature self-organized systems as flock of birds, school of fishes or herd of sheeps have to deal with the presence of external agents such as predators or leaders which modify their internal dynamic. Such situations take into account a…

We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…

Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model…