Related papers: Homeostasis and injectivity: a reaction network pe…
Understanding the insulin signaling cascade provides insights on the underlying mechanisms of biological phenomena such as insulin resistance, diabetes, Alzheimer's disease, and cancer. For this reason, previous studies utilized chemical…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
Concepts used in the scientific study of complex systems have become so widespread that their use and abuse has led to ambiguity and confusion in their meaning. In this paper we use information theory to provide abstract and concise…
We define a characteristic energy density based on the measurement of the two first moments of the extrinsic injected power smoothed over time. Using the stationarity, we show that this definition characterizes an energy per degrees freedom…
Resilience is a system's ability to maintain its function when perturbations and errors occur. Whilst we understand low-dimensional networked systems' behavior well, our understanding of systems consisting of a large number of components is…
An input-output approach to stability analysis is explored for networked systems with uncertain link dynamics. The main result consists of a collection of integral quadratic constraints, which together imply robust stability of the…
A multistationarity region is the part of a reaction network's parameter space that gives rise to multiple steady states. Mathematically, this region consists of the positive parameters for which a parametrized family of polynomial…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
This paper develops the concept of decomposition for chemical reaction networks, based on which a network decomposition technique is proposed to capture the stability of large-scale networks characterized by a high number of species, high…
Mechanisms of pattern formation---of which the Turing instability is an archetype---constitute an important class of dynamical processes occurring in biological, ecological and chemical systems. Recently, it has been shown that the Turing…
Bistability and multistationarity are properties of reaction networks linked to switch-like responses and connected to cell memory and cell decision making. Determining whether and when a network exhibits bistability is a hard and open…
In this paper we develop a theory to describe innovation processes in a network of interacting units. We introduce a stochastic picture that allows for the clarification of the role of fluctuations for the survival of innovations in such a…
Many illnesses are associated with an alteration of the immune system homeostasis due to any combination of factors, including exogenous bacterial insult, endogenous breakdown (e.g., development of a disease that results in immuno…
This article presents a biological neural network model driven by inhomogeneous Poisson processes accounting for the intrinsic randomness of synapses. The main novelty is the introduction of local interactions: each firing neuron triggers…
A class of systems is considered, where immobile species associated to distinct patches, the nodes of a network, interact both locally and at a long-range, as specified by an (interaction) adjacency matrix. Non local interactions are…
In real-world networks the interactions between network elements are inherently time-delayed. These time-delays can not only slow the network but can have a destabilizing effect on the network's dynamics leading to poor performance. The…
Irreversibility, in which a transient perturbation leaves a system in a new state, is an emergent property in systems of interacting entities. This property has well-established implications in statistical physics but remains underexplored…
Delays are an important phenomenon arising in a wide variety of real world systems. They occur in biological models because of diffusion effects or as simplifying modeling elements. We propose here to consider delayed stochastic reaction…
Maintaining stability in an uncertain environment is essential for proper functioning of living systems. Robust perfect adaptation (RPA) is a property of a system that generates an output at a fixed level even after fluctuations in input…
Can the topology of a network that consists of many particles interacting with each other change in complexity when a phase transition occurs? The answer to this question is particularly interesting to understand the nature of phase…