Related papers: Siphons in chemical reaction networks
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…
Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical…
Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction…
We investigate six operations on chemical reaction networks, all of which have been proven to preserve important dynamical properties, namely, the capacity for nondegenerate multistationarity (multiple steady states) and periodic orbits.…
The essence of a chemical reaction lies in the redistribution and reorganization of electrons, which is often manifested through electron transfer or the migration of electron pairs. These changes are inherently discrete and abrupt in the…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…
Low-temperature plasmas are partially ionized gases, where ions and neutrals coexist in a highly reactive environment. This creates a rich chemistry, which is often difficult to understand in its full complexity. In this work, we develop a…
Topological protection has emerged as an organizing principle for understanding and engineering robust collective behavior in electronic and material systems. Recent work suggests that topology may also play a role in organizing stochastic…
This Thesis presents research at the boundary between Statistical Physics and Biology. First, we have devised a class of Boolean constraint satisfaction problems (CSP) whose solutions describe the feasible operational states of a chemical…
We study the homogenization of a diffusion process which takes place in a binary structure formed by an ambiental connected phase surrounding a suspension of very small spheres distributed in an $\veps$-periodic network. The asymptotic…
This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…
Persistency is the property, for differential equations in $\R^n$, that solutions starting in the positive orthant do not approach the boundary. For chemical reactions and population models, this translates into the non-extinction property:…
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…
Chimera states in networks of coupled oscillators occur when some fraction of the oscillators synchronise with one another, while the remaining oscillators are incoherent. Several groups have studied chimerae in networks of identical…
The article presents results of preliminary study of solutions to recently offered basic thermodynamic equation for equilibrium in chemical systems with focus on chaotic behavior. Classical part of that equation was investigated earlier in…
Living systems operate out of equilibrium, continuously consuming energy to sustain organised, functional states. Their emergent behaviour usually relies on a set of interconnected chemical reaction networks (CRNs) driven by external fluxes…
Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we…
We introduce a new topological descriptor of a network called the density decomposition which is a partition of the nodes of a network into regions of uniform density. The decomposition we define is unique in the sense that a given network…
We study the problem of computing a minimal subset of nodes of a given asynchronous Boolean network that need to be controlled to drive its dynamics from an initial steady state (or attractor) to a target steady state. Due to the phenomenon…