Using a tight-binding atomistic simulation, we simulate the recent atomic-force microscopy experiments probing the slipperiness of graphene flakes made slide against a graphite surface. Compared to previous theoretical models, where the flake was assumed to be geometrically perfect and rigid, while the substrate is represented by a static periodic potential, our fully-atomistic model includes q...

New techniques and applications of atomistic molecular simulation methods are reported. Their aim is to provide a better understanding of the molecular basis of experimental results. To this end, calculations are performed of experimentally measurable observables. These are then compared to experimental results, thus validating the computational models and procedures. Finally, the simulations a...

We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of large molecules into the atomistic domain through a mesoscopic region. We show that the triple-scale scheme is robust against the details of the mesoscopic mod...

A technique that melds an atomistic description of the interfacial region with a coarse-grained description of the far regions of the solid substrates is presented and applied to a two-dimensional model contact consisting of planar solid substrates separated by a monolayer fluid film. The hybrid method yields results in excellent agreement with the "exact" (i.e., fully atomistic) results. The i...

The rebinding effect is a phenomenon which occurs when observing a ligand-receptor binding process. On the macro scale this process comprises the Markov property. This Makovian view is spoiled when switching to the atomistic scale of a binding process. We therefore suggest a model which accurately describes the rebinding effect on the atomistic scale by allowing “intermediate” bound states. Thi...

This article considers the blending of atomistic and continuum problems on a bridging subdomain building upon the ideas introduced in [1, 2, 7]. The continuity of the atomistic and continuum solutions is imposed by a constraint operator using Lagrange multipliers. These methods are stated in an abstract form. The consistency of these methods is analyzed. A new blending model is designed using m...

The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propa...

An atomistic calculation of the interaction between peptide motifs and enantiomeric odorant molecules (carvone and camphor) is performed. The peptide motifs are mimics of segments of the helical receptor structure. The model shows that the enantiomers of carvone have distinctly different interaction profile with all peptides considered, but the enantiomers of camphor do not exhibit any signific...

The subband structure of nanowires is commonly obtained through an atomistic tight binding approach. In this work an alternative, continuum based method is investigated, namely a two-band k ·p approximation of the conduction band structure. A derivation of the subband Schrödinger equations from the bulk model and their numerical solution are presented for [100] nanowires. Self-consistent simula...

Monoand poly-disperse melts of oligomers (average length 10 monomers) of trans-1,4-polyisoprene are simulated in full atomistic detail. The force-field is developed by means of a mixture of ab initio quantum-chemistry and an automatic generation of empirical parameters. Comparisons to NMR and scattering experiments validate the model. The local reorientation dynamics shows that for C−H vectors ...