Related papers: Hydrogen peroxide thermochemical oscillator as dri…
Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the non-linear case of systems under non-equilibrium external…
Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behavior in…
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…
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 precursory dynamics, motivated by the analysis of recent experiments on solid-on-solid friction, is introduced in a continuous cellular automaton that mimics the essential physical contents of earthquake source processes. The resulting…
In a pioneering study experimental evidence was sought of thermosynthesis, a theoretical biological mechanism for free energy gain from thermal cycling that has been invoked as energy source for the origin of life. A PCR machine applied…
Context: In the laboratory, hydrogen peroxide (HOOH) was proven to be an intermediate product in the solid-state reaction scheme that leads to the formation of water on icy dust grains. When HOOH desorbs from the icy grains, it can be…
A general model for the early recognition and colocalization of homologous DNA sequences is proposed. We show, on a thermodynamic ground, how the distance between two homologous DNA sequences is spontaneously regulated by the concentration…
Self-replicability is the unique attribute observed in all the living organisms and the question how the life was physically initiated could be equivalent to the question how self-replicating informative polymers were formed in the abiotic…
Critical experimental design issues connecting energy transduction and inheritable information within a protocell are explored and elucidated. The protocell design utilizes a photo-driven energy transducer (a ruthenium complex) to turn…
The emergence of longer information-carrying and functional nucleotide polymers from random short strands was a major stepping stone at the dawn of life. But the formation of those polymers under temperature oscillation required some form…
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,…
Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even…
In previous papers, we have shown that, as the rotation of a neutron star slows down, it will be internally heated as a consequence of the progressively changing mix of particles (rotochemical heating). In previously studied cases…
Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…
Previous studies modelled the origin of life and the emergence of photosynthesis on the early Earth-i.e. the origin of plants-in terms of biological heat engines that worked on thermal cycling caused by suspension in convecting water. In…
By extending the crude Goldman-Hodgkin-Katz electrodiffusion model for resting-state membrane potentials in perfused giant axons of squid, we reformulate the Hodgkin-Huxley (HH) phenomenological quantitative model to create a new model…
Changes in the medium of biological cell nucleus under ion beam action is considered as a possible cause of cell functioning disruption in the living body. As the most long-lived molecular product appeared in the cell after the passage of…