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In recent years, diffusion models trained on equilibrium molecular distributions have proven effective for sampling biomolecules. Beyond direct sampling, the score of such a model can also be used to derive the forces that act on molecular…
Most natural systems operate far from equilibrium, displaying time-asymmetric, irreversible dynamics characterized by a positive entropy production while exchanging energy and matter with the environment. Although stochastic thermodynamics…
We study a stochastic model of collective motion in which individuals update their orientation through pairwise aligning or anti-aligning copying interactions. We analyze both annealed dynamics, where interaction types are chosen…
Pattern-forming nonequilibrium systems are ubiquitous in nature, from driven quantum matter and biological life forms to atmospheric and interstellar gases. Identifying universal aspects of their far-from-equilibrium dynamics and statistics…
We report an ultrafast and efficient way to create the maximum coherence between the two lower states in a -like atomic systems, driven by two nonlinearly chirped few-cycle pulses. The phenomenon of coherent population trapping and…
We argue that the stochastic dynamics of interacting agents which replicate, mutate and die constitutes a non-equilibrium physical process akin to aging in complex materials. Specifically, our study uses extensive computer simulations of…
In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact uniform sampling of the steady state fluxes in a genome…
This work presents a population genetic model of evolution, which includes haploid selection, mutation, recombination, and drift. The mutation-selection equilibrium can be expressed exactly in closed form for arbitrary fitness functions…
The equilibria formed by the self-gravitating, collisionless collapse of simple initial conditions have been investigated for decades. We present the results of our attempts to describe the equilibria formed in $N$-body simulations using…
Equilibrium thermodynamics is grounded in the law of energy conservation, with a specific focus on how systems exchange energy with their environment during transitions between equilibrium states. These transitions are typically…
Biological systems are typically highly open, non-equilibrium systems that are very challenging to understand from a statistical mechanics perspective. While statistical treatments of evolutionary biological systems have a long and rich…
To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if…
A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…
Results of numerical simulation constructed before strict mathematical model of an establishment of thermodynamic equilibrium in originally nonequilibrium cosmological ultrarelativistic plasma for the Universe with any acceleration in the…
Infinite population models are important tools for studying population dynamics of evolutionary algorithms. They describe how the distributions of populations change between consecutive generations. In general, infinite population models…
We present a construction of non-equilibrium steady states within conformal field theory. These states sustain energy flows between two quantum systems, initially prepared at different temperatures, whose dynamical properties are…
With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…
The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide…
We study the convergence to equilibrium of a class of nonlinear recombination models. In analogy with Boltzmann's H theorem from kinetic theory, and in contrast with previous analysis of these models, convergence is measured in terms of…
From the perspective of non-equilibrium statistical mechanics, modeling the velocity distribution of particles in non-equilibrium, steady-state plasmas presents a significant challenge. Under this context, a family of kappa distributions…