Related papers: Coarse-graining strategy for modeling effective, h…
A recently introduced systematic approach to derivations of the macroscopic dynamics from the underlying microscopic equations of motions in the short-memory approximation [Gorban et al, Phys. Rev. E, 63, 066124 (2001)] is presented in…
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to…
We systematically studied the validity and transferability of effective, coarse-grained, pair potentials in ultrasoft colloidal systems. We focused on amphiphilic dendrimers, macromolecules which can aggregate into clusters of overlapping…
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…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
Coarse-Graining (CG) models are low resolution approximation of high resolution models, such as all-atomic (AA) models. An effective CG model is expected to reproduce equilibrium values of sufficient physical quantities of its AA model,…
Increasing the efficiency of materials design and discovery remains a significant challenge, especially given the prohibitively large size of chemical compound space. The use of a chemically transferable coarse-grained model enables…
We investigate experimentally the diffusion properties of a bidimensional bidisperse dry granular material under quasistatic cyclic shear.The comparison of these properties with results obtained both in computer simulations of hard spheres…
We analyze one thousand independent equilibrium trajectories of a system of 155 Lennard Jones particles to separate in a model-free approach the role of temperature and the role of the explored potential energy landscape basin depth in the…
The theory to reconstruct the atomistic-level chain diffusion from the accelerated dynamics that is measured in mesoscale simulations of the coarse-grained system, is applied here to the dynamics of cis-1,4-Polybutadiene melts where each…
Discrete element method simulations of confined bidisperse granular shear flows elucidate the balance between diffusion and segregation that can lead to either mixed or segregated states, depending on confining pressure. Results indicate…
Functional connectivity estimates are highly sensitive to analysis choices and can be dominated by noise when the number of sampled time points is small relative to network dimensionality. This issue is particularly acute in fMRI, where…
Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…
We propose a mesoscopic model of binary fluid mixtures with tunable viscosity ratio based on a two-range pseudo-potential lattice Boltzmann method, for the simulation of soft flowing systems. In addition to the short range repulsive…
We discuss a Bayesian formulation to coarse-graining (CG) of PDEs where the coefficients (e.g. material parameters) exhibit random, fine scale variability. The direct solution to such problems requires grids that are small enough to resolve…
A computational tool for coarse-graining nonlinear systems of ordinary differential equations in time is discussed. Three illustrative model examples are worked out that demonstrate the range of capability of the method. This includes the…
Athermal plastic flows were simulated for the Kob-Andersen binary Lennard-Jones system and its repulsive version in which the sign of the attractive terms is changed to a plus. Properties evaluated from simulations at different densities…
The well-known results concerning a dilute Bose gas with the short-range repulsive interaction should be reconsidered due to a thermodynamic inconsistency of the method being basic to much of the present understanding of this subject and…
We use an "equation-free", coarse-grained computational approach to accelerate molecular dynamics-based computations of demixing (segregation) of dissimilar particles subject to an upward gas flow (gas-fluidized beds). We explore the…
We use a recently-derived reformulation of the diffusion constant [Stillinger F H and Debenedetti P G 2005 J. Phys. Chem. B 109 6604] to investigate heterogeneous dynamics and non-Gaussian diffusion in a binary Lennard-Jones mixture. Our…