Related papers: Energy landscapes and their relation to thermodyna…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
Chiral active matter widely exists in nature and emerges rich dynamical behaviors. Among these, chiral active particles (CAPs) with alignment effects show novel collective motions such as orderly rotating droplets and distinct phase…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
The basic quantity for the description of the statistical properties of physical systems is the density of states or equivalently the microcanonical entropy. Macroscopic quantities of a system in equilibrium can be computed directly from…
In order to gain a deeper understanding of complex systems and infer key information using minimal data, I classify all configurations based on classical probability, starting from the dimensions of energy and different categories of…
How useful it is to think about the potential energy landscape of a complex many-body system depends in large measure on how direct the connection is to the system's dynamics. In this paper we show that, within what we call the potential…
A geometric analysis of the global properties of the energy landscape of a minimalistic model of a polypeptide is presented, which is based on the relation between dynamical trajectories and geodesics of a suitable manifold, whose metric is…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
The elsewhere surmised topological origin of phase transitions is given here new important evidence through the analytic study of an exactly solvable model for which both topology and thermodynamics are worked out. The model is a mean-field…
We study a mean field model of a complex network, focusing on edge and triangle densities. Our first result is the derivation of a variational characterization of the entropy density, compatible with the infinite node limit. We then…
Multiscale thermodynamics is a theory of relations among levels of description. Energy and entropy are its two main ingredients. Their roles in the time evolution describing approach of a level (starting level) to another level involving…
The selection of an equilibrium state by maximising the entropy of a system, subject to certain constraints, is often powerfully motivated as an exercise in logical inference, a procedure where conclusions are reached on the basis of…
We describe a finite inhomogeneous three dimensional system of classical particles which interact through short and (or) long range interactions by means of a simple analytic spin model. The thermodynamic properties of the system are worked…
The climate system is a forced, dissipative, nonlinear, complex and heterogeneous system that is out of thermodynamic equilibrium. The system exhibits natural variability on many scales of motion, in time as well as space, and it is subject…
Entropy might be a not well defined concept if the system can undergo transformations involving stationary nonequilibria. It might be analogous to the heat content (once called ``caloric'') in transformations that are not isochoric (i.e.…
In systems with detailed balance, the stationary distribution and the equilibrium distribution are identical, creating a clear connection between energetic and entropic quantities. Many driven systems violate detailed balance and still pose…
Stochastic thermodynamics has largely succeeded in characterizing both equilibrium and far-from-equilibrium phenomena. Yet many opportunities remain for application to mesoscopic complex systems -- especially biological ones -- whose…
The microcanonical ensemble has long been a starting point for the development of thermodynamics from statistical mechanics. However, this approach presents two problems. First, it predicts that the entropy is only defined on a discrete set…
We review recent results on the potential energy landscape (PES) of model liquids. The role of saddle-points in the PES in connecting dynamics to statics is investigated, confirming that a change between minima-dominated and…
Statistical physics provides a useful perspective for the analysis of many complex systems; it allows us to relate microscopic fluctuations to macroscopic observations. Developmental biology, but also cell biology more generally, are…