Related papers: Autocatalytic Networks: An Intimate Relation betwe…
We investigate global stability and dynamics of large ecological networks by classical methods of the dynamical system theory, including Hamiltonian methods, and averaging. Our analysis exploits the network topological structure, namely,…
We consider the dynamics of a reaction-diffusion system on a multigraph. The species share the same set of nodes but can access different links to explore the embedding spatial support. By acting on the topology of the networks we can…
Autocatalytic processes underlie diverse systems in which replication is triggered at interfaces, including heterogeneous catalysis on solid substrates, enzyme activity at membranes, viral infections, biofilm growth, and spatially…
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…
Autocatalysis is a deceptively simple concept, referring to the situation that a chemical species $X$ catalyzes its own formation. From the perspective of chemical kinetics, autocatalysts show a regime of super-linear growth. Given a…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
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…
In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses…
We analyze a model of interacting agents (e.g. prebiotic chemical species) which are represended by nodes of a network, whereas their interactions are mapped onto directed links between these nodes. On a fast time scale, each agent follows…
We define catalytic networks as chemical reaction networks with an essentially catalytic reaction pathway: one which is on in the presence of certain catalysts and off in their absence. We show that examples of catalytic networks include…
The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel…
In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g. metabolic pathways. Here we developed a theory to predict the sensitivity, i.e. the responses of concentrations and…
Complex chemical reaction networks, which underlie many industrial and biological processes, often exhibit non-monotonic changes in chemical species concentrations, typically described using nonlinear models. Such non-monotonic dynamics are…
Substrate modification networks are ubiquitous in living, biochemical systems. A higher-level hypergraph "skeleton" captures key information about which substrates are transformed in the presence of modification-specific enzymes. Many…
The co-evolution of network topology and dynamics is studied in an evolutionary Boolean network model that is a simple model of gene regulatory network. We find that a critical state emerges spontaneously resulting from interplay between…
Background: Autocatalytic sets are often considered a necessary (but not sufficient) condition for the origin and early evolution of life. Although the idea of autocatalytic sets was already conceived of many years ago, only recently have…
We determine conditions under which a random biochemical system is likely to contain a subsystem that is both autocatalytic and able to survive on some ambient `food' source. Such systems have previously been investigated for their…
Many decision-making algorithms draw inspiration from the inner workings of individual biological systems. However, it remains unclear whether collective behavior among biological species can also lead to solutions for computational tasks.…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…