Related papers: Thermodynamically Consistent Coarse-Graining of Po…

The present work concerns the transferability of coarse-grained (CG) modeling in reproducing the dynamic properties of the reference atomistic systems across a range of parameters. In particular, we focus on implicit-solvent CG modeling of…

Coarse-grained (CG) modeling has gained significant attention in recent years due to its wide applicability in enhancing the spatiotemporal scales of molecular simulations. While CG simulations, often performed with Hamiltonian mechanics,…

We investigate fundamental connections between thermodynamics and quantum information theory. First, we show that the operational framework of thermal operations is nonequivalent to the framework of Gibbs-preserving maps, and we comment on…

Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent…

The connection between fundamental interactions acting in molecules in a fluid and macroscopically measured properties, such as the viscosity between colloidal particles coated with polymers, is studied here. The role that hydrodynamic and…

We assess Coarse Graining by studying different partitions of the phase space of the Baker transformation and the periodic torus automorphisms. It turns out that the shape of autocorrelation functions for the Baker transformation is more or…

To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that…

Two very basic constructions involving experimental procedures are the formation of coarse-grained versions of experiments, and the formation of branching sequential experiments. The latter allow for the conditioning of states on the…

We propose a thermodynamically consistent general-purpose model describing diffusion of a solute or a fluid in a solid undergoing possible phase transformations and damage, beside possible visco-inelastic processes. Also heat…

We review a few representative examples of granular experiments or models where phase separation, accompanied by domain coarsening, is a relevant phenomenon. We first elucidate the intrinsic non-equilibrium, or athermal, nature of granular…

We study the crystallization of a colloidal model system in presence of secondary nanoparticles acting as impurities. Using confocal microscopy, we show that the nanoparticles segregate in the grain boundaries of the colloidal polycrystal.…

We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…

Multiscale phenomena which include several processes occuring simultaneously at different length scales and exchanging energy with each other, are widespread in magnetism. These phenomena often govern the magnetization reversal dynamics,…

This paper presents a thermodynamically consistent model for multicomponent electrolyte solutions. The first part of this paper derives the general governing equations for nonequilibrium systems within the theory of nonequilibrium…

We present a coarse-graining strategy for reducing the number of particle species in mixtures to achieve a simpler system with higher diffusion while preserving the total particle number and characteristic dynamic features. As a system of…

Packing problems have been a source of fascination for millenia and their study has produced a rich literature that spans numerous disciplines. Investigations of hard-particle packing models have provided basic insights into the structure…

Bottom-up coarse-grained molecular dynamics models are parameterized using complex effective Hamiltonians. These models are typically optimized to approximate high dimensional data from atomistic simulations. In contrast, human validation…

With the birth of quantum information science, many tools have been developed to deal with many-body quantum systems. Although a complete description of such systems is desirable, it will not always be possible to achieve this goal, as the…

We formulate an effective-description framework for the dynamics of open quantum systems by extending the time-coarse-graining formalism to open systems. Our coarse-graining procedure efficiently removes high-frequency processes which are…

We study by means of numerical simulations the model of dissipative particle dynamics with energy conservation for the simple case of thermal conduction. It is shown that the model displays correct equilibrium fluctuations and reproduces…