Related papers: Non Equilibrium Transitions in a Polymer Replicati…
Living systems produce "persistent" copies of information-carrying polymers, in which template and copy sequences remain correlated after physically decoupling. We identify a general measure of the thermodynamic efficiency with which these…
Living systems produce copies of information-carrying molecules such as DNA by assembling monomer units into finite-length oligomer (short polymer) copies. We explore the role of initiation and termination of the copy process in the…
A simple analytical framework to study the molecular quasispecies evolution of finite populations is proposed, in which the population is assumed to be a random combination of the constiyuent molecules in each generation,i.e., linkage…
We investigate a reversible polymerization process in which individual polymers aggregate and fragment at a rate proportional to their molecular weight. We find a nonequilibrium phase transition despite the fact that the dynamics are…
We provide a non-equilibrium thermodynamic description of the life-cycle of a droplet based, chemically feasible, system of protocells. By coupling the protocells metabolic kinetics with its thermodynamics, we demonstrate how the system can…
The nonequilibrium phase transition in a system of diffusing, coagulating particles in the presence of a steady input and evaporation of particles is studied. The system undergoes a transition from a phase in which the average number of…
Templated copying is the central operation by which biology produces complex molecules. Cells copy sequence information from DNA to RNA and on into proteins, which are the molecules responsible for the function and regulation of cellular…
Entropy serves as a central observable in equilibrium thermodynamics. However, many biological and ecological systems operate far from thermal equilibrium. Here we show that entropy production can characterize the behavior of such…
In biochemistry, heteropolymers encoding biological information are assembled out of equilibrium by sequentially incorporating available monomers found in the environment. Current models of polymerization treat monomer incorporation as a…
We study a nonlinear recombination model from population genetics as a combinatorial version of the Kac-Boltzmann equation from kinetic theory. Following Kac's approach, the nonlinear model is approximated by a mean field linear evolution…
The population dynamics and stability of ecosystems of interacting species is studied from the perspective of non-equilibrium thermodynamics by assuming that species, through their biotic and abiotic interactions, are units of entropy…
This position paper argues that next-generation non-equilibrium-inspired generative models will provide the essential foundation for better modeling real-world complex dynamical systems. While many classical generative algorithms draw…
Templated copolymerization, in which information stored in the sequence of a heteropolymer template is copied into another polymer product, is the mechanism behind all known methods of genetic information transfer. A key aspect of templated…
Measures of wealth and production have been found to scale superlinearly with the population of a city. Therefore, it makes economic sense for humans to congregate together in dense settlements. A recent model of population dynamics showed…
Cyclic (rock-paper-scissors-type) population models serve to mimic complex species interactions. Focusing on a paradigmatic three-species model with mutations in one dimension, we observe an interplay between equilibrium and non-equilibrium…
This work presents a general unifying theoretical framework for quantum non-equilibrium systems. It is based on a re-statement of the dynamical problem as one of inferring the distribution of collision events that move a system toward…
Computing equilibrium concentrations of molecular complexes is generally analytically intractable and requires numerical approaches. In this work we focus on the polymer-monomer level, where indivisible molecules (monomers) combine to form…
We present a new and general Monte Carlo iteration method for generalized ensembles. It consists of two elements: (1) a simple algorithm to distinguish between distributions arising from respectively equilibrium- and non-equilibrium…
Non-reciprocal interactions are prevalent in various complex systems leading to phenomena that cannot be described by traditional equilibrium statistical physics. Although non-reciprocally interacting systems composed of two populations…
Active systems evade the rules of equilibrium thermodynamics by constantly dissipating energy at the level of their microscopic components. This energy flux stems from the conversion of a fuel, present in the environment, into sustained…