Related papers: Topologically protected modes in non-equilibrium s…
Chemically driven fluids can demix to form condensed droplets that exhibit phase behaviors not observed at equilibrium. In particular, nonequilibrium interfacial properties can emerge when the chemical reactions are driven differentially…
Topological invariants have proved useful for analyzing emergent function as they characterize a property of the entire system, and are insensitive to local details, disorder, and noise. They support boundary states, which reduce the system…
Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
Autocatalysis, the ability of a chemical system to make more of itself, is a crucial feature in metabolism and is speculated to have played a decisive role in the origin of life. Nevertheless, how autocatalytic systems behave far from…
Across all scales of the physical world, dynamical systems can often be usefully represented as abstract networks that encode the system's units and inter-unit interactions. Understanding how physical rules shape the topological structure…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…
In this work, we analyze the nonequilibrium thermodynamics of a class of neural networks known as Restricted Boltzmann Machines (RBMs) in the context of unsupervised learning. We show how the network is described as a discrete Markov…
Chemically active droplets provide simple models for cell-like systems that can grow and divide. Such active droplet systems are driven away from thermodynamic equilibrium and turn over chemically, which corresponds to a simple metabolism.…
Unlike fluids at thermal equilibrium, biomolecular mixtures in living systems can sustain nonequilibrium steady states, in which active processes modify the conformational states of the constituent molecules. Despite qualitative…
We build a rigorous nonequilibrium thermodynamic description for open chemical reaction networks of elementary reactions. Their dynamics is described by deterministic rate equations satisfying mass action law. Our most general framework…
It is shown that the structure of non-equilibrium thermodynamic system far from equilibrium can be captured in terms of a generalized "Nambu dynamics", in the presence of fluctuation effects in non-equilibrium thermodynamics. Triangular…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
The methods of non-equilibrium thermodynamics of systems with an interface have been applied to the study of transport processes in semiconductor junctions. A complete phenomenological model for drift-diffusion processes in a junction has…
We investigate the nonequilibrium stationary states of systems consisting of chemical reactions among molecules of several chemical species. To this end we introduce and develop a stochastic formulation of nonequilibrium thermodynamics of…
We consider a stochastic heat conduction model for solids composed by N interacting atoms. The system is in contact with two heat baths at different temperature $T_\ell$ and $T_r$. The bulk dynamics conserve two quantities: the energy and…
A binary fluid mixture in contact with lateral particle reservoirs is considered. By imposing different particle concentrations in these reservoirs, the system can be maintained under controlled non-equilibrium conditions. Previous…
Large time dynamics of reaction-diffusion systems modeling some irreversible reaction networks are investigated. Depending on initial masses, these networks possibly possess boundary equilibria, where some of the chemical concentrations are…
We consider biochemical reaction chains and investigate how random external fluctuations, as characterized by variance and coefficient of variation, propagate down the chains. We perform such a study under the assumption that the number of…
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…
One of the hallmarks of bulk topology is the existence of robust boundary localized states. For instance, a conventional $d$ dimensional topological system hosts $d{-}1$ dimensional surface modes, which are protected by non-spatial…