Related papers: Emergence of information transmission in a prebiot…
Natural supports of information are given by random copolymers such as DNA or RNA where information is coded in the sequence of covalent bonds. At the molecular scale, the stochastic growth of a single copolymer with or without a template…
Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA)…
A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers…
In this paper, we present an analytical model for a diffusive molecular communication (MC) system with a reversible adsorption receiver in a fluid environment. The time-varying spatial distribution of the information molecules under the…
We present a spatially-extended system of chemical reactions exhibiting adaptation to time-dependent influxes of reactants. Here adaptation is defined as improved reproductive success, namely the ability of one of the many locally stable…
The random sequential adsorption (RSA) model has served as a paradigm for diverse phenomena in physical chemistry, as well as in other areas such as biology, ecology, and sociology. In the present work, we survey aspects of the RSA model…
We consider a sequential cascade of molecular first-reaction events towards a terminal reaction centre in which each reaction step is controlled by diffusive motion of the particles. The model studied here represents a typical reaction…
Biomolecular communication demands that interactions between parts of a molecular system act as scaffolds for message transmission. It also requires an evolving and organized system of signs - a communicative agency - for creating and…
How could primordial life, before the evolution of genetic systems, adapt to fluctuating environments and achieve homeostasis? This study proposes a minimal, chemically plausible model where homeostasis emerges from a simple chemical…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Cellular decision-making based on information received from the external environment is frequently initiated by transmembrane receptors. These receptors are known to propagate such information by triggering a series of irreversible,…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
The building of minimal self-reproducing systems with a physical embodiment (generically called protocells) is a great challenge, with implications for both theory and applied sciences. Although the classical view of a living protocell…
Origins of life research investigates how life could emerge from prebiotic chemistry only. One possible explanation provides the RNA world hypothesis. It states that life could emerge from RNA strands only, storing and transferring…
Reservoir computing (RC) is a state-of-the-art machine learning method that makes use of the power of dynamical systems (the reservoir) for real-time inference. When using biological complex systems as reservoir substrates, it serves as a…
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…
The RNA world hypothesis suggests a pathway of how life emerged on early earth. It assumes that life started with RNA based systems, capable of storing, transmitting and replicating information, envisioning that monomers and short RNA…
Understanding how biological homochirality emerged remains a challenge for the researchers interested in the origin of life. During the last decades, stable non-racemic steady states of nonequilibrium chemical systems have been discussed as…
Our world is ambiguous and this is reflected in the data we use to train our algorithms. This is particularly true when we try to model natural processes where collected data is affected by noisy measurements and differences in measurement…
We consider an unsupervised classifying agent that evolves by enforcing self-consistency of its labels under continual exposure to a data-generating environment. Because the agent's predictions feed back into its own regularized updates,…