Related papers: Predicting the thermodynamics by using state-depen…
In both classical and quantum thermodynamics, physical quantities are typically assigned objective values defined independently of our observations. We then refer to the 'work performed by a gas', or the 'entropy of the gas', regardless of…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
We investigate the formation of polycrystalline structures in a class of particle systems. The atomistic energy is modeled as a sum of particle energies that favor atoms being locally isometric to a reference lattice. The discrete frame…
Coarse-grain Lagrangian methods, such as Dissipative Particle Dynamics ( Hoogerbrugge et al., EPL, 1992), are suitable for describing mesoscopic fluid systems that include thermal fluctuations. However, the realistic simulation of liquids…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
We study whether the stationary state of two bulk-driven systems slowly exchanging particles can be described by the equality of suitably defined nonequilibrium chemical potentials. Our main result is that in a weak contact limit, chemical…
Our recent study reveals that macroscopic structure in thermodynamically equilibrium state and its temperature dependence for classical discrete system can be well-characterized by a single specially-selected microscopic state (which we…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
Mechanical interactions between biological cells may be mediated by secreted products, making them dependent on the local particle density. Here, we explore the generic physics of density-dependent attractive interactions. We show using…
Numerically optimized reduced descriptions of macromolecular liquids often present thermodynamic inconsistency with atomistic level descriptions even if the total correlation function, i.e. the structure, appears to be in agreement. An…
We present a systematic coarse-graining (CG) strategy for many particle molecular systems based on cluster expansion techniques. We construct a hierarchy of coarse-grained Hamiltonians with interaction potentials consisting of two, three…
Recently a number of approaches has been developed to connect the microscopic dynamics of particle systems to the macroscopic properties of systems in nonequilibrium stationary states, via the theory of dynamical systems. This way a direct…
A major current challenge poses the systematic construction of coarse-grained models that are dynamically consistent, and, moreover, might be used for systems driven out of thermal equilibrium. Here we present a novel prescription that…
We introduce the idea of weakly coherent collisional models, where the elements of an environment interacting with a system of interest are prepared in states that are approximately thermal, but have an amount of coherence proportional to a…
Identifying the relevant coarse-grained degrees of freedom in a complex physical system is a key stage in developing powerful effective theories in and out of equilibrium. The celebrated renormalization group provides a framework for this…
Traditional stochastic modeling of reactive systems limits the domain of applicability of the associated path thermodynamics to systems involving a single elementary reaction at the origin of each observed change in composition. An…
Using the probabilistic language of conditional expectations we reformulate the force matching method for coarse-graining of molecular systems as a projection on spaces of coarse observables. A practical outcome of this probabilistic…
As an extension to strain-gradient models of size-dependent plastic behaviour, this work proposes a model for a stress-gradient theory. The model is distinguished from earlier works on the topic by its being embedded in a thermodynamically…
The standard assumption for the equilibrium microcanonical state in quantum mechanics, that the system must be in one of the energy eigenstates, is weakened so as to allow superpositions of states. The weakened form of the microcanonical…
Thermofield dynamics has proven to be a very useful theory in high-energy physics, particularly since it permits the treatment of both time- and temperature-dependence on an equal footing. We here show that it also has an excellent…