Related papers: Structure identification methods for atomistic sim…
A methodology is developed to identify clusters in a bulk phase which are topologically equivalent to certain reference clusters. The selected reference clusters are the Morse clusters with 13 or less atoms and the 13 atom clusters found in…
An algorithm for determining crystal structures from diffraction data is described which does not rely on the usual Fourier-space formulations of atomicity. The new algorithm implements atomicity constraints in real-space, as well as…
Structure is the most basic and important property of crystalline solids; it determines directly or indirectly most materials characteristics. However, predicting crystal structure of solids remains a formidable and not fully solved…
The prediction of energetically stable crystal structures formed by a given chemical composition is a central problem in solid-state physics. In principle, the crystalline state of assembled atoms can be determined by optimizing the energy…
Most current methods for identifying coherent structures in spatially-extended systems rely on prior information about the form which those structures take. Here we present two new approaches to automatically filter the changing…
The latest research of the proportionality of atomic weights of chemical elements made it possible to obtain 3 x 3 matrices for the calculation of information coefficients of proportionality Ip that can be used for 3D modeling of the…
A quantitative descriptor of local atomic environments is often required for the analysis of atomistic data. Descriptors of the local atomic environment ideally provide physically and chemically intuitive insight. This requires descriptors…
The analysis of defects and defect dynamics in crystalline materials is important for fundamental science and for a wide range of applied engineering. With increasing system size the analysis of molecular-dynamics simulation data becomes…
Here we address the challenge of profiling causal properties and tracking the transformation of chemical compounds from an algorithmic perspective. We explore the potential of applying a computational interventional calculus based on the…
Accessing structures of molecules, crystals, and complex interfaces with atomic level details is vital to the understanding and engineering of materials, chemical reactions, and biochemical processes. Currently, determination of accurate…
The bond orientational order parameters originally introduced by Steinhardt \emph{et. al.} [Phys. Rev. B \textbf{28}, 784 (1983)] are a common tool for local structure characterization in soft matter studies. Recently, Mickel \emph{et. al.}…
We consider several patchy particle models that have been proposed in literature and we investigate their candidate crystal structures in a systematic way. We compare two different algorithms for predicting crystal structures: (i) an…
One endeavour of modern physical chemistry is to use bottom-up approaches to design materials and drugs with desired properties. Here we introduce an atomistic structure learning algorithm (ASLA) that utilizes a convolutional neural network…
Atom probe tomography is frequently employed to characterize the elemental distribution in solids with atomic resolution. Here we review and discuss the potential of this technique to locally probe chemical bonds. Two processes characterize…
Detecting structures at the particle scale within plastically deformed crystalline materials allows a better understanding of the occurring phenomena. While previous approaches mostly relied on applying hand-chosen criteria on different…
Most of the current understanding of structure-property relations at the molecular and the supramolecular scales can be formulated in terms of the stability of and the interactions between a limited number of recurring structural motifs…
Evolutionary crystal structure prediction proved to be a powerful approach for studying a wide range of materials. Here, we present a specifically designed algorithm for the prediction of the structure of complex crystals consisting of…
An improved neighbor list algorithm is proposed to reduce unnecessary interatomic distance calculations in molecular simulations. It combines the advantages of Verlet table and cell linked list algorithms by using cell decomposition…
Complex systems are usually represented as an intricate set of relations between their components forming a complex graph or network. The understanding of their functioning and emergent properties are strongly related to their structural…
Relevant to broad applied fields and natural processes, interfacial ionic hydrates has been widely studied by ultrahigh-resolution atomic force microscopy (AFM). However, the complex relationship between AFM signal and the investigated…