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Modelling is an essential procedure in analyzing and controlling a given logical dynamic system (LDS). It has been proved that deterministic LDS can be modeled as a linear-like system using algebraic state space representation. However, due…
This paper introduces a linear state-space model with time-varying dynamics. The time dependency is obtained by forming the state dynamics matrix as a time-varying linear combination of a set of matrices. The time dependency of the weights…
As the quantification of metabolism, nonequilibrium steady states play a central role in living matter, but are beyond the purview of equilibrium statistical mechanics. Here we develop a fermionic theory of nonequilibrium steady states in…
A classical particle system coupled with a thermostat driven by an external constant force reaches its steady state when the ensemble-averaged drift velocity does not vary with time. The statistical mechanics of such a system is derived…
We study three different experiments that involve dry friction and periodic driving, and which employ both single and many-particle systems. These experimental set-ups, besides providing a playground for investigation of frictional effects,…
The conditions of thermodynamic equilibrium, local thermodynamic equilibrium, and statistical equilibrium are discussed in detail. The equations of statistical equilibrium and the supplementary equations are shown together with the…
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…
Aspects of the modern dynamical systems approach to thermodynamics of stationary states out of equilibrium with attention to the original conceptions which arose at the beginnings of Statistical Mechanics
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
In this paper, we introduce a data-driven modeling approach for dynamics problems with latent variables. The state-space of the proposed model includes artificial latent variables, in addition to observed variables that can be fitted to a…
The statistical mechanics of a one-dimensional Ising model in thermal equilibrium is well-established, textbook material. Yet, when driven far from equilibrium by coupling two sectors to two baths at different temperatures, it exhibits…
We report the first experimental realization of pattern formation in a spatially extended nonlinear system when the system is alternated between two states, neither of which exhibits patterning. Dynamical equations modeling the system are…
When modelling driven steady states of matter, it is common practice either to choose transition rates arbitrarily, or to assume that the principle of detailed balance remains valid away from equilibrium. Neither of those practices is…
We study the emergence of typicality in classical systems with a large number of binary state variables. We show analytically that for sufficiently large subsets of the complete state space, state functions which can be associated with…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
The gap in statistics between multi-variate and time-series analysis can be bridged by using entropy statistics and recent developments in multi-dimensional scaling. For explaining the evolution of the sciences as non-linear dynamics, the…
A model is proposed that describes the evolution of a mixed state of a quantum system for which gain and loss of energy or amplitude are present. Properties of the model are worked out in detail. In particular, invariant subspaces of the…
We simulate by lattice Boltzmann the steady shearing of a binary fluid mixture undergoing phase separation with full hydrodynamics in two dimensions. Contrary to some theoretical scenarios, a dynamical steady state is attained with finite…
We consider dynamical systems evolving near an equilibrium statistical state where the interest is in modelling long term behavior that is consistent with thermodynamic constraints. We adjust the distribution using an entropy-optimizing…
Laboratory experiments with bacterial colonies, under well-controlled conditions often lead to evolutionary diversification, where at least two ecotypes emerge from an initially monomorphic population. Empirical evidence suggests that such…