Related papers: Understanding Dynamics in Coarse-Grained Models: I…
Many coarse-grained models have been developed for equilibrium studies of lipid bilayer membranes. To achieve in simulations access to length-scales and time-scales difficult to attain in fully atomistic molecular dynamics, these…
Granular materials are involved in most industrial and environmental processes, as well as many civil engineering applications. Although significant advances have been made in understanding the statics and dynamics of cohesionless grains…
Fine-Grained Visual Classification (FGVC) is an important computer vision problem that involves small diversity within the different classes, and often requires expert annotators to collect data. Utilizing this notion of small visual…
The ubiquitous deployment of monitoring devices in urban flow monitoring systems induces a significant cost for maintenance and operation. A technique is required to reduce the number of deployed devices, while preventing the degeneration…
Granular materials such as sand, powders, and grains are omnipresent in daily life, industrial applications, and earth-science [1]. When unperturbed, they form stable structures that resemble the ones of other amorphous solids like metallic…
Mechanical stress plays an intricate role in gene expression in individual cells and sculpting of developing tissues. However, systematic methods of studying how mechanical stress and feedback help to harmonize cellular activities within a…
It is often stated that if one is presented with a snapshot of the positions of the molecules of a glass and one of a liquid, one is unable to tell the difference. Here we argue instead that given several such snapshots taken over a…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
We consider two basic types of coarse-graining: the Ehrenfests' coarse-graining and its extension to a general principle of non-equilibrium thermodynamics, and the coarse-graining based on uncertainty of dynamical models and Epsilon-motions…
Compared to top-down coarse-grained (CG) models, bottom-up approaches are capable of offering higher structural fidelity. This fidelity results from the tight link to a higher-resolution reference, making the CG model chemically specific.…
A versatile and transferable coarse-grained (CG) model was developed to investigate the self-assembly of two ubiquitous methacrylate-based copolymers: poly(ethylene oxide-b-methylmethacrylate) (PEO-b-PMMA) and poly(ethylene…
The objective of graph coarsening is to generate smaller, more manageable graphs while preserving key information of the original graph. Previous work were mainly based on the perspective of spectrum-preserving, using some predefined…
We present a detailed derivation and testing of our approach to rescale the dynamics of mesoscale simulations of coarse-grained polymer melts (I. Y. Lyubimov et al. J. Chem. Phys. \textbf{132}, 11876, 2010). Starting from the…
We investigate how various coarse-graining methods affect the scaling properties of long-range power-law correlated and anti-correlated signals, quantified by the detrended fluctuation analysis. Specifically, for coarse-graining in the…
Existing Data Parallel (DP) trainings for deep neural networks (DNNs) often experience limited scalability in speedup due to substantial communication overheads. While Overlapping technique can mitigate such problem by paralleling…
Condense phase molecular systems organize in wide range of distinct molecular configurations, including amorphous melt and glass as well as crystals often exhibiting polymorphism, that originate from their intricate intra- and…
To evaluate shear viscosity of ethylene glycol oligomers (EGO)/water binary mixture by means of coarse-grained molecular dynamics (CG-MD) simulations, we proposed the self-diffusion-coefficient-based parameterization of non-bonded…
Granular systems confined in a shallow box and driven by vertical vibration provide a simple geometry to study fluidized granular media. Grains gain kinetic energy vertically through collisions with the walls and redistribute it…
Using cyclic shear to drive a two dimensional granular system, we determine the structural characteristics for different inter-particle friction coefficients. These characteristics are the result of a competition between mechanical…
In this work, we review previously developed coarse-grained (CG) particle models for biological membrane and red blood cells (RBCs) and discuss the advantages of the CG particle method over the continuum and atomic simulations on modeling…