Related papers: Thermodynamic Binding Networks
A thermodynamically motivated neural network model is described that self-organizes to transport charge associated with internal and external potentials while in contact with a thermal reservoir. The model integrates techniques for rapid,…
In living systems, collective molecular behavior is driven by thermodynamic forces in the form of chemical gradients. Leveraging recent advances in the field of nonequilibrium physics, I show that increasing the thermodynamic force alone…
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…
The physical foundations of a variety of emerging technologies --- ranging from the applications of quantum entanglement in quantum information to the applications of nonequilibrium bulk and interface phenomena in microfluidics, biology,…
In this work the topological order at finite temperature in two-dimensional color code is studied. The topological entropy is used to measure the behavior of the topological order. Topological order in color code arises from the colored…
We study a generic model of self-assembling chains which can branch and form networks with branching points (junctions) of arbitrary functionality. The physical realizations include physical gels, wormlike micells, dipolar fluids and…
The question of characterization of the degree of non-equilibrium activity in active matter systems is studied in the context of a stochastic microswimmer model driven by a chemical cycle. The resulting dynamical properties and entropy…
Cells produce RNA and proteins via molecular templating networks. We show that information transmission in such networks is bounded by functions of a simple thermodynamic property of the network, regardless of complexity. Surprisingly,…
Thermodynamic uncertainty relations yield a lower bound on entropy production in terms of the mean and fluctuations of a current. We derive their general form for systems under arbitrary time-dependent driving from arbitrary initial states…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
Here we investigate how local properties of particles in a thermal bath influence the thermodynamics of the bath. We utilize nanothermodynamics, based on two postulates: that small systems can be treated self-consistently by coupling to an…
Algorithmic entropy can be seen as a special case of entropy as studied in statistical mechanics. This viewpoint allows us to apply many techniques developed for use in thermodynamics to the subject of algorithmic information theory. In…
We use rigorous non-equilibrium thermodynamic arguments to prove (i) the residual entropy of any system is bounded below by the experimentally (calorimetrically) determined absolute temperature entropy, which itself is bounded below by the…
A microscopic definition of the thermodynamic entropy in an isolated quantum system must satisfy (i) additivity, (ii) extensivity and (iii) the second law of thermodynamics. We show that the diagonal entropy, which is the Shannon entropy in…
Previously derived "global" thermodynamic speed limit theorems state that increasing the maximum speed with which a system can evolve between two given probability distributions over its states requires the system to produce more entropy in…
We develop a thermodynamic framework for modeling innovation adoption and abandonment dynamics using statistical mechanics. Starting from a mathematical model for an adoption distribution that fits empirically obtained date, we construct a…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
Filtered budgets for anelastic turbulence and a general expression of the turbulent sensible heat flux are derived for a multicomponent fluid with an arbitrary equation of state. A family of subgrid-scale closures is then found under the…
It is widely believed that the underlying reality behind statistical mechanics is a deterministic and unitary time evolution of a many-particle wave function, even though this is in conflict with the irreversible, stochastic nature of…
The second law of thermodynamics states that entropy production in macroscopic systems is non-negative, reaching zero only at thermodynamic equilibrium. As a corollary, this implies that the state trajectory of macroscopic systems is…