Related papers: Understanding Dynamics in Coarse-Grained Models: I…
Coarse-grained (CG) conformational surface hopping (SH) adapts the concept of multisurface dynamics, initially developed to describe electronic transitions in chemical reactions, to accurately describe classical molecular dynamics at a…
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…
A hydrodynamic description for an $s$-component mixture of inelastic, smooth hard disks (two dimensions) or spheres (three dimensions) is derived based on the revised Enskog theory for the single-particle velocity distribution functions. In…
Kinetically-constrained models are lattice-gas models that are used for describing glassy systems. By construction, their equilibrium state is trivial and there are no equal-time correlations between the occupancy of different sites. We…
We present multiscale graph-based reduction algorithms for upscaling heterogeneous and anisotropic diffusion problems. The proposed coarsening approaches begin by constructing a partitioning of the computational domain into a set of…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
We present a multiscale simulation algorithm for amorphous materials, which we illustrate and validate in a canonical case of dense granular flow. Our algorithm is based on the recently proposed Spot Model, where particles in a dense random…
Capturing the correct dynamics at the Coarse-Grained (CG) scale remains a central challenge in the advancement of systematic CG models for soft matter simulations. The Generalized Langevin Equation (GLE), rooted in the Mori-Zwanzig…
Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or…
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…
The aim of this work is the description of the chain formation phenomena observed in colloidal suspensions of superparamagnetic nanoparticles under high magnetic fields. We propose a new methodology based on an on-the-fly Coarse-Grain (CG)…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
We present results obtained from a set of cosmological hydrodynamic simulations of galaxy clusters, aimed at comparing predictions with observational data on the diversity between cool-core (CC) and non-cool-core (NCC) clusters. Our…
We investigate the direct enstrophy cascade of two-dimensional decaying turbulence in a flowing soap film channel. We use a coarse-graining approach that allows us to resolve the nonlinear dynamics and scale-coupling simultaneously in space…
Granular fluids consist of collections of activated mesoscopic or macroscopic particles (e.g., powders or grains) whose flows often appear similar to those of normal fluids. To explore the qualitative and quantitative description of these…
Coarse-grained (CG) models provide an effective route to reducing the complexity of molecular simulations (MD), but conventional approaches depend heavily on long all-atom MD trajectories to adequately sample configurational space. This…
The nature of coarse graining is intuitively "obvious", but it is rather difficult to find explicit and calculable models of the coarse graining process (and the resulting entropy flow) discussed in the literature. What we would like to…
The shear viscosity for a moderately dense granular binary mixture of smooth hard spheres undergoing uniform shear flow is determined. The basis for the analysis is the Enskog kinetic equation, solved first analytically by the…
In this paper, we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular dynamics. The latter are ubiquitous in physicochemical and biological…
Hard spheres are a central and important model reference system for both homogeneous and inhomogeneous fluid systems. In this paper we present new high-precision molecular-dynamics computer simulations for a hard sphere fluid at a planar…