Related papers: Peridynamic Model for Single-Layer Graphene Obtain…
Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…
Twisted graphene layers (TGLs) provide a powerful platform for investigating multiple quantum phenomena, yet their scalable deployment is hindered by the lack of reliable synthesis with precise angle. Here, benefited from a deeper…
We address a simple but fundamental issue arising in the study of graphene, as well as of other systems that have a crystalline structure with more than one atom per unit cell. For these systems, the choice of the tight-binding basis is not…
In this work, a coarse-graining method previously proposed by the authors in a companion paper based on solving diffusion equations is applied to CFD-DEM simulations, where coarse graining is used to obtain solid volume fraction, particle…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
Phosphorene, a monolayer of black phosphorus (BP), is an elemental two-dimensional material with interesting physical properties, such as high charge carrier mobility and exotic anisotropic in-plane properties. To fundamentally understand…
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…
With the guidance offered by nonequilibrium statistical thermodynamics, simulation techniques are elevated from brute-force computer experiments to systematic tools for extracting complete, redundancy-free and consistent coarse grained…
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…
In this publication we introduce SAMPLE, a structure search approach for commensurate organic monolayers on inorganic substrates. Such monolayers often show rich polymorphism with diverse molecular arrangements in differently shaped unit…
This paper introduces a new structural phase field crystal (PFC) type model that expands the PFC methodology to a wider class of structurally complex crystal structures than previously possible. Specifically, our new approach allows for…
Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
The exceptional mechanical properties of graphene have made it attractive for nano-mechanical devices and functional composite materials. Two key aspects of graphene's mechanical behavior are its elastic and adhesive properties. These are…
A state-based peridynamic formulation for linear elastic shells is presented. The emphasis is on introducing, possibly for the first time, a general surface based peridynamic model to represent the deformation characteristics of structures…
We develop a polycrystal graph neural network (PGNN) model for predicting the effective properties of polycrystalline materials, using the Li7La3Zr2O12 ceramic as an example. A large-scale dataset with >5000 different three-dimensional…
Predicting the ground-state 3D molecular conformations from 2D molecular graphs is critical in computational chemistry due to its profound impact on molecular properties. Deep learning (DL) approaches have recently emerged as promising…
Moir\'e systems have emerged in recent years as a rich platform to study strong correlations. Here, we will discuss a simple, experimentally feasible setup based on periodically strained graphene that reproduces several key aspects of…
Grain boundary (GB) energy is a fundamental property that affects the form of grain boundary and plays an important role to unveil the behavior of polycrystalline materials. With a better understanding of grain boundary energy distribution…
The Single Chain Mean Field theory is used to simulate the equilibrium structure of phospholipid membranes at the molecular level. Three levels of coarse-graining of DMPC phospholipid surfactants are present: the detailed 44-beads double…