Related papers: Autocatalytic Sets and RNA Secondary Structure
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…
In this paper, we use the biological domain knowledge incorporated into stochastic models for ab initio RNA secondary-structure prediction to improve the state of the art in joint compression of RNA sequence and structure data (Liu et al.,…
Even the simplest organisms are too complex to have spontaneously arisen fully-formed, yet precursors to first life must have emerged ab initio from their environment. A watershed event was the appearance of the first entity capable of…
For understanding the origin of life, it is essential to explain the development of a compartmentalized structure, which undergoes growth and division, from a set of chemical reactions. In this study, a hypercycle with two chemicals that…
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…
We propose a novel definition of life in terms of which its emergence in the universe is expected, and its ever-creative open-ended evolution is entailed by no law. Living organisms are Kantian Wholes that achieve Catalytic Closure,…
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…
Autocatalysis is thought to have played an important role in the earliest stages of the origin of life. An autocatalytic cycle (AC) is a set of reactions that results in stoichiometric increase in its constituent chemicals. When the…
By using the point model of reaction kinetics we have studied the stochastic properties of the lifetime of small systems controlled by autocatalytic reaction A+X -> X+X -> A+X, X -> B. Assuming that a system is living only when the number…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
There is an abundance of complex dynamic systems that are critical to our daily lives and our society but that are hardly understood, and even with today's possibilities to sense and collect large amounts of experimental data, they are so…
We claim that networks are created according to the priority attachment mechanism and we show a simple model which uses the priority attachment to generate both synthetic and close to empirical networks. Priority attachment is a mechanism…
We study a model for the evolution of chemical species under a combination of population dynamics on a short time scale and a selection mechanism on a longer time scale. Least fit nodes are replaced by new nodes whose links are attached to…
In small systems, quantitative discrepancies between stochastic and deterministic descriptions of chemical kinetics can be significant, with their magnitude depending on the specific reaction network. Here, we study the Finke-Watzky…
The origin of life is one of the greatest mysteries. The mechanism for the synthesis of DNA is synonymous with the chemical origin of life, and theories have been developed along many lines of reasoning, but resolving all requirements…
We explore the emergence of complex structures within reaction networks, focusing on nuclear reaction networks relevant to stellar nucleosynthesis. The work presents a theoretical framework rooted in Chemical Organization Theory (COT) to…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
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…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…