Are the cohesive laws of interfaces sufficient for modelling fracture in polycrystals using the cohesive zone model? We examine this question by comparing a fully atomistic simulation of a silicon polycrystal to a finite element simulation with a similar overall geometry. The cohesive laws used in the finite element simulation are measured atomistically. We describe in detail how to convert the...

We present an extension of the coarse-grained MARTINI model for proteins and apply this extension to amyloid- and elastin-like peptides. Atomistic simulations of tetrapeptides, octapeptides, and longer peptides in solution are used as a reference to parametrize a set of pseudodihedral potentials that describe the internal flexibility of MARTINI peptides. We assess the performance of the resulti...

Force-based atomistic-continuum hybrid methods are the only known pointwise consistent methods for coupling a general atomistic model to a finite element continuum model. For this reason, and due to their algorithmic simplicity, force-based coupling methods have become a popular class of atomistic-continuum hybrid models as well as other types of multiphysics models. However, the recently disco...

Searching conformational ensembles of proteins remains a challenge in atomistic simulation of biomolecules. One approach to accelerate the protein sampling is to take advantage of rough energy surface from the coarse-grained model and, at the same time, to persist atomistic details from the all-atom model. Multiscale enhanced sampling (MSES) of all atoms and topology-based coarse-grained replic...

We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and covalent bonds below the rupture force. We obtain a significant difference between the atomistic simulations and the existing results in the literature based...

We present a new dual-resolution approach for coupling atomistic and coarse-grained models in molecular dynamics simulations of hydrated systems. In particular, a coarse-grained point dipolar water model is used to solvate molecules represented with standard all-atom force fields. A unique characteristic of our methodology is that the mixing of resolutions is direct, meaning that no additional ...

We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and it...

We study memory effects in a kinetic roughening model. For d=1, a different dynamic scaling is uncovered in the memory dominated phases; the Kardar-Parisi-Zhang scaling is restored in the absence of noise. dc=2 represents the critical dimension where memory is shown to smoothen the roughening front (alpha<or=0). Studies on a discrete atomistic model in the same universality class reconfirm the ...