Related papers: Deriving molecular bonding from macromolecular sel…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
Recent advances in scanning transmission electron and scanning tunneling microscopies allow researchers to measure materials structural and electronic properties, such as atomic displacements and charge density modulations, at an Angstrom…
Tight-binding (TB) molecular dynamics (MD) has emerged as a powerful method for investigating the atomic-scale structure of materials --- in particular the interplay between structural and electronic properties --- bridging the gap between…
Off-lattice Grand Canonical Monte Carlo simulations of the clean diamond (111) surface, based on the effective many-body Brenner potential, yield the $(2\times1)$ Pandey reconstruction in agreement with \emph{ab-initio} calculations and…
In this paper a new theory is developed for the self - assembly of associating molecules confined to a single spatial dimension, but allowed to explore all orientation angles. The interplay of the anisotropy of the pair potential and the…
The entanglement of hard-core bosons in square and honeycomb lattices with nearest-neighbor interactions is estimated by means of quantum Monte Carlo simulations and spin-wave analysis. The particular U(1)-invariant form of the concurrence…
Inspired by active shape morphing in developing tissues and biomaterials, we investigate two generic mechanochemical models where the deformations of a thin elastic sheet are driven by, and in turn affect, the concentration gradients of a…
Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…
We consider mechanically generated molecular braids composed of two molecules where long range interactions between them can be considered to be very weak. We describe a model that takes account of the thermal fluctuations of the braid,…
The deposition of a metal on a foreign substrate is studied by means of grand canonical Monte Carlo simulations and a lattice-gas model with pair potential interactions between nearest neighbors. The influence of temperature and surface…
The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium…
Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output.…
The breaking of a chemical bond is fundamental in most chemical reactions. To understand chemical processes in heterogeneous catalysis or on-surface polymerization the study of bond dissociation in molecules adsorbed on crystalline surfaces…
In this work we develop the first theory to model self assembling mixtures of single patch colloids and colloids with spherically symmetric attractions. In the development of the theory we restrict the interactions such that there are short…
A monte carlo density functional theory is developed for chain molecules which both intra and intermolecularly associate. The approach can be applied over a range of chain lengths. The theory is validated for the case of an associating…
The collective response of a system is profoundly shaped by the interaction dynamics between its constituent elements. In physics, tailoring these interactions can enable the observation of unusual phenomena that are otherwise inaccessible…
In vitro investigation of neural architectures requires cell positioning. For that purpose, micro-magnets have been developed on silicon substrates and combined with chemical patterning to attract cells to adhesive sites and keep them there…
Complex organic molecules (COMs) have been widely observed in molecular clouds and protostellar environments. One of the formation mechanisms of COMs is radical reactions on the icy grain surface driven by UV irradiation. While many…
Tissues are subjected to large external forces and undergo global deformations during morphogenesis. We use synthetic analogues of tissues to study the impact of cell-cell adhesion on the response of cohesive cellular assemblies under such…
A multiscale scheme combining molecular dynamics (MD) and microscopic phase-field theory is proposed to study the structural phase transformations in solids with inhomogeneous strain field. The approach calculates strain response based on…