Related papers: Emergence of information transmission in a prebiot…
Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of…
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.…
It has been pointed out that if an autocatalytic cycle produces primitive membrane chemicals, it can compose a self-maintaining proto cell. Moreover, it is known that a proto cell can divide itself spontaneously as it grows. An unsolved…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in…
Many biological, physical, and social interactions have a particular dependence on where they take place. In living cells, protein movement between the nucleus and cytoplasm affects cellular response (i.e., proteins must be present in the…
Recent progress in machine learning has sparked increased interest in utilizing this technology to predict the outcomes of chemical reactions. The ultimate aim of such endeavors is to develop a universal model that can predict products for…
Life and physical sciences have always been quick to adopt the latest advances in machine learning to accelerate scientific discovery. Examples of this are cell segmentation or cancer detection. Nevertheless, these exceptional results are…
We propose a physically-realisable biochemical device that is coupled to a biochemical reservoir of mutual information, fuel molecules and a chemical bath. Mutual information allows work to be done on the bath even when the fuel molecules…
Artificial organisms are computer programs that self-replicate, mutate, compete and evolve. How do these lifelike information-processing behaviours could arise in diverse far-from-equilibrium physical systems remains an open question. Here,…
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,…
Nonreciprocity, a hallmark of nonequilibrium systems, can generate dynamics not possible near thermodynamic equilibrium, including oscillatory and rotating patterns. The onset of temporal oscillations is often evident in linearized…
In this paper, we present a probabilistic analysis of a dynamical particle model for the self-adaptive immune response to cancer, as proposed by the first author in a previous work. The model is motivated by the interplay between immune…
Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However,…
Cellular life requires the presence of a set of biochemical mechanisms in order to maintain a predictable process of growth and division. Several attempts have been made towards the building of minimal protocells from a top-down approach,…
Phase transitions are the macroscopic manifestation of microscopic processes that drive a system towards a new state. The detailed evolution of these processes, particularly in abrupt phase transitions, are currently not fully understood.…
We construct a simple model of a proto-cell that simulates a stochastic dynamics of abstract chemicals on a two-dimensional lattice. We assume that chemicals catalyze their reproduction through interaction with each other, and that between…
We consider a network, bonds of which are being sequentially removed; that is done at random, but conditioned on the system remaining connected (Self-Repairing Bond Percolation SRBP). This model is the simplest representative of a class of…
We consider the adsorption of a random heteropolymer onto an interface within the model by Garel et al. [1] by taking into account self-interactions between the monomers. Within the replica trick and by using a self-consistent preaveraging…
Life on earth is distinguished by long-lived correlations in time. The patterns of material organization that characterize living organisms today are contingent on events that occurred billions of years ago. This contingency is a necessary…