Related papers: Random autocatalytic networks
Perfect adaptation in a dynamical system is the phenomenon that one or more variables have an initial transient response to a persistent change in an external stimulus but revert to their original value as the system converges to…
Chemical reaction networks are often used to model and understand biological processes such as cell signaling. Under the framework of chemical reaction network theory, a process is modeled with a directed graph and a choice of kinetics,…
A central challenge in the origin of life is understanding how catalytic peptide-like polymers and information-bearing nucleic acid-like polymers emerged as an interde-pendent system. This study constructs a primordial cognitive model…
Autocatalytic cores are minimal units in reaction networks (RNs) responsible for the emergence of autocatalysis. In the absence of explicit catalysis, i.e., when an entity appears both as reactant and product in the same reaction, they are…
In this paper we prove the well-posedness of non-autonomous deterministic and stochastic reaction-diffusion equations with a polynomial reaction term. Concerning the stochastic problem, we also prove a new result on the space-time…
Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…
It is a long-standing question in origin-of-life research whether the information content of replicating molecules can be maintained in the presence of replication errors. Extending standard quasispecies models of non-enzymatic replication,…
This paper describes a 2D particle system in which autopoietic vesicles that are able to grow, repair, and reproduce can emerge from an initial random distribution of individual components. The reproduction process also exhibits inheritance…
The evolution of autocatalytic sets (ACS) is a widespread process in biological, chemical and ecological systems which is of great significance in many applications, such as the evolution of new species or complex chemical organizations. In…
Efforts to catalogue the structure of metabolic networks have generated highly detailed, genome-scale atlases of biochemical reactions in the cell. Unfortunately, these atlases fall short of capturing the kinetic details of metabolic…
Stochastic chemical processes are described by the chemical master equation satisfying the law of mass-action. We first ask whether the dual master equation, which has the same steady state as the chemical master equation, but with inverted…
Standard Random Boolean Networks display an order-disorder phase transition. We add to the standard Random Boolean Networks a disconnection rule which couples the control and order parameters. By this way, the system is driven to the…
This paper is an invited layperson summary for The Academic of the paper referenced on the last page. We summarize how the formal framework of autocatalytic networks offers a means of modeling the origins of self-organizing, self-sustaining…
Chemically fueled supramolecular systems can exhibit complex, time-dependent behaviors reminiscent of living matter when maintained far from equilibrium by continuous energy or fuel consumption. Here, we introduce a minimal…
Motivated by investigating multistationarity in biochemical systems, we address saddle-node bifurcations for chemical reaction networks endowed with general kinetics. At positive equilibria, we identify structural network conditions that…
We study the scheduling problem of a self-replicating factory. We show that by maintaining a sufficiently large inventory of intermediate metabolites and catalysts required for self-replication, optimal replication times can be achieved by…
Motivation: Many biochemical pathways are known, but the numerous parameters required to correctly explore the dynamics of the pathways are not known. For this reason, algorithms that can make inferences by looking at the topology of a…
Information thermodynamics relates the rate of change of mutual information between two interacting subsystems to their thermodynamics when the joined system is described by a bipartite stochastic dynamics satisfying local detailed balance.…
Informally, a chemical reaction network is "atomic" if each reaction may be interpreted as the rearrangement of indivisible units of matter. There are several reasonable definitions formalizing this idea. We investigate the computational…
We consider the population dynamics of a set of species whose network of catalytic interactions is described by a directed graph. The relationship between the attractors of this dynamics and the underlying graph theoretic structures like…