Related papers: Autocatalytic systems and recombination: a reactio…
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…
The question of the onset of the homochirality on prebiotic Earth still remains a fundamental question in the quest for the origin of life. Recent works in this field introduce the concept of recycling, rather than the traditional open-flow…
A model of $s$ interacting species is considered with two types of dynamical variables. The fast variables are the populations of the species and slow variables the links of a directed graph that defines the catalytic interactions among…
Boolean networks have been widely used in many areas of science and engineering to represent various dynamical behaviour. In systems biology, they became useful tools to study the dynamical characteristics of large-scale biomolecular…
There has been a long debate on how new levels of organization have evolved. It might seem unlikely, as cooperation must prevail over competition. One well-studied example is the emergence of autocatalytic sets, which seem to be a…
Zero-one biochemical reaction networks are widely recognized for their importance in analyzing signal transduction and cellular decision-making processes. Degenerate networks reveal non-standard behaviors and mark the boundary where…
This paper presents a speculative model of the cognitive mechanisms underlying the transition from episodic to mimetic (or memetic) culture with the arrival of Homo erectus, which Donald [1991] claims paved the way for the unique features…
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…
Both natural ecosystems and biochemical reaction networks involve populations of heterogeneous agents whose cooperative and competitive interactions lead to a rich dynamics of species' abundances, albeit at vastly different scales. The…
Autocatalytic chemical networks play a predominant role in a large number of natural systems such as in metabolic pathways and in ecological networks. Despite recent efforts, the precise impact of thermodynamic constraints on these networks…
Explanation of exponential growth in self-reproduction is an important step toward elucidation of the origins of life because optimization of the growth potential across rounds of selection is necessary for Darwinian evolution. To produce…
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…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
Template directed replication of nucleic acids is at the essence of all living beings and a major milestone for any origin of life scenario. We here present an idealized model of prebiotic sequence replication, where binary polymers act as…
I analyse a model of an evolving network represented as a directed graph; each node corresponds to one molecular species and the links to catalytic interactions between species. Over short timescales the graph remains fixed while relative…
This paper develops some basic principles to study autocatalytic networks and exploit their structural properties in order to characterize their inherent fundamental limits and tradeoffs. In a dynamical system with autocatalytic structure,…
A model of an evolving network of interacting molecular species is shown to exhibit repeated rounds of crashes in which several species get rapidly depopulated, followed by recoveries. The network inevitably self-organizes into an…
We consider a natural class of reaction networks which consist of reactions where either two species can inactivate each other (i.e., sequestration), or some species can be transformed into another (i.e., transmutation), in a way that gives…
All biological processes are controlled by complex systems of enzymatic chemical reactions. Although the majority of enzymatic networks have very elaborate structures, there are many experimental observations indicating that some turnover…
Self-replicating systems based on information-coding polymers are of crucial importance in biology. They also recently emerged as a paradigm in material design on nano- and micro-scales. We present a general theoretical and numerical…