Related papers: Coarse-graining dynamics by telescoping down time-…
Plastic rearrangements play a crucial role in the characterization of soft-glassy materials, such as emulsions and foams. Based on numerical simulations of soft-glassy systems, we study the dynamics of plastic rearrangements at the…
Tissue dynamics and collective cell motion are crucial biological processes. Their biological machinery is mostly known, and simulation models such as the "active vertex model" (AVM) exist and yield reasonable agreement with experimental…
We derive a mesoscopic modeling and simulation technique that is very close to the technique known as dissipative particle dynamics. The model is derived from molecular dynamics by means of a systematic coarse-graining procedure. Thus the…
Granular systems present surprisingly complicated dynamics. In particular, nonlinear interactions and energy dissipation play important roles in these dynamics. Usually, constant coefficients of restitution are introduced phenomenologically…
Constructing atom-resolved states from low-resolution data is of practical importance in many areas of science and engineering. This problem is addressed in this paper in the context of multiscale factorization methods for molecular…
Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active,…
One of the most pressing issues for loop quantum gravity and spin foams is the construction of the continuum limit. In this paper, we propose a systematic coarse-graining scheme for three-dimensional lattice gauge models including spin…
In established theories of grain coarsening, grains disappear either by shrinking or by rotating as a rigid object to coalesce with an adjacent grain. Here we report a third mechanism for grain coarsening, in which a grain splits apart into…
We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from…
In this paper we are interested in the studying coarse-graining in field theories using the language of quantum open systems. Motivated by the ideas of Calzetta and Hu on correlation histories we employ the Zwanzig projection technique to…
We present the state-of-the-art theoretical modeling, molecular simulation, and coarse-graining strategies for the transport of gases and liquids in nanoporous materials (pore size 1-100 nm). Special emphasis is placed on the transport of…
In recent papers, we have argued that kinetically constrained coarse grained models can be applied to understand dynamic properties of glass forming materials, and we have used this approach in various applications that appear to validate…
We introduce a mesoscopic partition function for classical many-body systems based on a combined spatial and phase-space coarse-graining, replacing the canonical phase-space integral with a discrete sum over occupation numbers. The…
Dust grains play a major role in many astrophysical contexts. They affect the chemical, magnetic, dynamical, and optical properties of their environment, from galaxies down to the interstellar medium, star-forming regions, and…
We address the physical meaning of hydrodynamic approach related with the coarse graining scale in the frame work of variational formulation. We point out that the local thermal equilibrium does not necessarily play a critical role in the…
The coarsening process in a class of driven systems is studied. These systems have previously been shown to exhibit phase separation and slow coarsening in one dimension. We consider generalizations of this class of models to higher…
Electrostatic interactions between macroions largely govern the equilibrium thermodynamic and dynamical properties of charge-stabilized colloidal suspensions and polyelectrolyte solutions. Predicting the properties of such complex,…
The constituents of soft matter systems such as colloidal suspensions, emulsions, polymers, and biological tissues undergo microscopic random motion, due to thermal energy. They may also experience drift motion correlated over mesoscopic or…
Biological systems exhibit processes on a wide range of time and length scales. This work demonstrates that models, wherein the interaction between system constituents is captured by algebraic operations, inherently allow for successive…
Stochastic dynamics, such as molecular dynamics, are important in many scientific applications. However, summarizing and analyzing the results of such simulations is often challenging, due to the high dimension in which simulations are…