相关论文: Joining and decomposing reaction networks

Recent research shows that a faulty or sub-optimally operating metabolic network can often be rescued by the targeted removal of enzyme-coding genes--the exact opposite of what traditional gene therapy would suggest. Predictions go as far…

"Every object that biology studies is a system of systems." (Fran\c{c}ois Jacob, 1974). Most networks feature intricate architectures originating from tinkering, a repetitive use of existing components where structures are not invented but…

Many real-world complex systems such as social, biological, information as well as technological systems results of a decentralized and unplanned evolution which leads to a common structuration. Irrespective of their origin, these so-called…

Novel experimental techniques reveal the simultaneous activity of larger and larger numbers of neurons. As a result there is increasing interest in the structure of cooperative -- or correlated -- activity in neural populations, and in the…

We consider two (2D) and three (3D) dimensional granular systems exposed to compression, and ask what is the influence of the number of physical dimensions on the properties of the interaction networks that spontaneously form as these…

Networks effectively capture interactions among components of complex systems, and have thus become a mainstay in many scientific disciplines. Growing evidence, especially from biology, suggest that networks undergo changes over time, and…

We study the multistationarity for the reaction networks with one-dimensional stoichiometric subspaces, and we focus on the networks admitting finitely many positive steady states. We prove that if a network admits multistationarity, then…

Despite their topological complexity almost all functional properties of metabolic networks can be derived from steady-state dynamics. Indeed, many theoretical investigations (like flux-balance analysis) rely on extracting function from…

Given a metabolic network in terms of its metabolites and reactions, our goal is to efficiently compute the minimal knock out sets of reactions required to block a given behaviour. We describe an algorithm which improves the computation of…

Tipping elements in the Earth System receive increased scientific attention over the recent years due to their nonlinear behavior and the risks of abrupt state changes. While being stable over a large range of parameters, a tipping element…

A stochastic reaction-diffusion model is studied on a networked support. In each patch of the network two species are assumed to interact following a non-normal reaction scheme. When the interaction unit is replicated on a directed linear…

We introduce the notion of corresponding a chemical reaction network to a split network translation, and use this novel process to extend the scope of existing network-based theory for characterizing the steady state set of mass-action…

The spatially distributed reaction networks are indispensable for the understanding of many important phenomena concerning the development of organisms, coordinated cell behavior, and pattern formation. The purpose of this brief discussion…

A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…

Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…

Small-world networks are the focus of recent interest because they appear to circumvent many of the limitations of either random networks or regular lattices as frameworks for the study of interaction networks of complex systems. Here, we…

The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and…

The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…

In the study of reaction networks and the polynomial dynamical systems that they generate, special classes of networks with important properties have been identified. These include reversible, weakly reversible}, and, more recently,…

We introduce and solve a model which considers two coupled networks growing simultaneously. The dynamics of the networks is governed by the new arrival of network elements (nodes) making preferential attachments to pre-existing nodes in…