We use objective boundary conditions and self-consistent charge density-functional-based tight-binding to simulate at the atomistic scale the formation of helices in narrow graphene nanoribbons with armchair edges terminated with fluorine and hydrogen. We interpret the microscopic data using an inextensible, unshearable elastic rod model, which considers both bending and torsional strains. When...

In this paper we develop and test a hybrid multiscale method for coupling atomistic and continuum simulations. Our goal is to bridge the gap on both the time and space scales between the microscopic (atomistic) and macroscopic (continuum) models. A macroscale solver for diffusion equation, here the finite difference scheme, is used on a coarse grid, while Monte Carlo simulation for random walks...

There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best ac...

Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the ato...

The spreading of polymer droplets is studied using molecular dynamics simulations. To study the dynamics of both the precursor foot and the bulk droplet, large hemispherical drops of 200 000 monomers are simulated using a bead-spring model for polymers of chain length 10, 20, and 40 monomers per chain. We compare spreading on flat and atomistic surfaces, chain length effects, and different appl...

Molecular dynamics simulations are carried out in a systematic manner to develop a coarse grain model for multiple-of-three carbon n-alkanes. The procedure involves optimizing harmonic bond and bend parameters, and Lennard-Jones nonbonded parameters, to match observables taken from fully atomistic simulations and from experiment. The experimental values used consist of surface tension and bulk ...

The δ phase of plutonium with the fcc structure exhibits an unusual negative thermal expansion (NTE) over its narrow temperature range of stability, 593-736 K. An accurate description of the anomalous high-temperature volume effect of plutonium goes beyond the current capability of electronic-structure calculations. We propose an atomistic scheme to model the thermodynamic properties of δ-Pu ba...

We propose an upscaling scheme for the passage from atomistic to continuum mechanical models of crystalline solids. It is based on a Taylor expansion of the deformation function up to a given order and describes the material properties to a higher extent than commonly used continuum mechanical models. In particular, the discreteness effects of the underlying atomistic model are captured. The qu...

An atomistic model of the growth kinetics of stressed solid-solid phase transformations is presented. Solid phase epitaxial growth of (001) Si was used for comparison of new and prior models with experiments. The results indicate that the migration of crystal island ledges in the growth interface may involve coordinated atomic motion. The model accounts for morphological instabilities during st...