Related papers: Random autocatalytic networks
We describe a large class of chemical reaction networks, those endowed with a subtle structural property called concordance. We show that the class of concordant networks coincides precisely with the class of networks which, when taken with…
Chemical reactions often proceed through the formation and the consumption of intermediate species. An example is the creation and subsequent degradation of the substrate-enzyme complexes in an enzymatic reaction. In this paper we provide a…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the…
We present a geometric framework to study the growth-division dynamics of cells and protocells, and demonstrate that self-reproduction emerges only when a system's growth dynamics and division strategy are mutually compatible. Using several…
What determines biodiversity in nature is a prominent issue in ecology, especially in biotic resource systems that are typically devoid of cross-feeding. Here, we show that by incorporating pairwise encounters among consumer individuals…
Recently it has been demonstrated that causal entropic forces can lead to the emergence of complex phenomena associated with human cognitive niche such as tool use and social cooperation. Here I show that even more fundamental traits…
A stochastic model for a chemical reaction network is embedded in a one-parameter family of models with species numbers and rate constants scaled by powers of the parameter. A systematic approach is developed for determining appropriate…
We study the problem of how a ``living'' system complex in structure can respond perfectly to local changes in the environment. Such a system is assumed to consist of a distributed ``living'' medium and a hierarchical ``supplying'' network…
The Turing patterning mechanism is believed to underly the formation of repetitive structures in development, such as zebrafish stripes and mammalian digits, but it has proved difficult to isolate the specific biochemical species…
An explanatory model for the emergence of evolvable units must display emerging structures that (1) preserve themselves in time (2) self-reproduce and (3) tolerate a certain amount of variation when reproducing. To tackle this challenge,…
High-throughput data acquisition in synthetic biology leads to an abundance of data that need to be processed and aggregated into useful biological models. Building dynamical models based on this wealth of data is of paramount importance to…
All intelligence is collective intelligence, in the sense that it is made of parts which must align with respect to system-level goals. Understanding the dynamics which facilitate or limit navigation of problem spaces by aligned parts thus…
In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development…
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 consider discrete-space continuous-time Markov models of reaction networks and provide sufficient conditions for the following stability condition to hold: each state in a closed, irreducible component of the state space is positive…
Community ecologists are principally occupied with the proposition that natural assemblages of species exhibit orderliness and with identifying its causes. Plant-pollinator networks exhibit a variety of orderly properties, one of which is…
Subharmonic response is a well known phenomena in, e.g., deterministic nonlinear dynamical systems. We investigate the conditions under which such subharmonic oscillations can persist for a long time in open systems with stochastic dynamics…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…
Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While programming such energy barriers…