Related papers: Unassigned distance geometry and the Buckminsterfu…

The reactions of fullerene C60 with atomic fluorine have been studied by unrestricted broken spin-symmetry Hartree-Fock (UBS HF) approach implemented in semiempirical codes based on AM1 technique. The calculations were focused on a…

This is an experimental case study in real algebraic geometry, aimed at computing the image of a semialgebraic subset of 3-space under a polynomial map into the plane. For general instances, the boundary of the image is given by two highly…

This paper presents a new method of constructing physical models in a geophysical inverse problem, when there are only a few possible physical property values in the model and they are reasonably known but the geometry of the target is…

Random sequential adsorption algorithm is a popular tool for modelling structure of monolayers built in irreversible adsorption experiments. However, this algorithm becomes very inefficient when the density of molecules in a layer rises.…

Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…

We present a permutation-invariant distance between atomic configurations, defined through a functional representation of atomic positions. This distance enables to directly compare different atomic environments with an arbitrary number of…

The application of powder diffraction methods in two-dimensional crystallography is regarded as intractable because of the uncertainties associated with overlapping reflections. Here, we report an approach that resolves these ambiguities…

Any object on earth has two fundamental properties: it is finite, and it is made of atoms. Structural information about an object can be obtained from diffraction amplitude measurements that account for either one of these traits.…

The recently developed evolutionary algorithm USPEX proved to be a tool that enables accurate and reliable prediction of structures for a given chemical composition. Here we extend this method to predict the crystal structure of polymers by…

Atomic force microscopy (AFM) is one of the most promising methods for investigating the structure of materials at the micro and nanoscale levels, as well as their local physical-mechanical properties. The experimental data obtained with…

We report that polymer amide [1] with a protein backbone of mainly glycine units and iron is present in the CV3 meteorites Acfer 086, Allende and KABA. The evidence for this is from particles of these meteorites after Folch extraction being…

This paper deepens into the analysis of the protein secondary structure using Frenet frame to describe the curvature and torsion of the discrete curve formed by the protein $\alpha$-carbons. We show how a simple criterion based on the…

Domain motions involved in the function of proteins can often be well described as a combination of motions along a handfull of low-frequency modes, that is, with the values of a few normal coordinates. This means that, when the functional…

The tree reconstruction problem is to find an embedded straight-line tree that approximates a given cloud of unorganized points in $\mathbb{R}^m$ up to a certain error. A practical solution to this problem will accelerate a discovery of new…

In the field of molecular electronics, particularly in quantum transport studies, the orientation of molecules plays a crucial role. This orientation, with respect to the electrodes, can be defined through the cavity of ring-shaped…

The interactions between atoms and molecules may be described by a potential energy function of the nuclear coordinates. Non-bonded interactions are dominated by repulsive forces at short range and attractive dispersion forces at long…

Despite the constant evolution of similarity searching research, it continues to face the same challenges stemming from the complexity of the data, such as the curse of dimensionality and computationally expensive distance functions.…

In applications throughout science and engineering one is often faced with the challenge of solving an ill-posed inverse problem, where the number of available measurements is smaller than the dimension of the model to be estimated. However…

Engineering atomic-scale structures allows great manipulation of physical properties and chemical processes for advanced technology. We show that the B atoms deployed at the centers of honeycombs in boron sheets, borophene, behave as nearly…

Several dimerization products of fullerene C60 are presented and thoroughly characterized with a quantum chemical DFT model augmented by dispersion. We reanalyze and expand significantly the number of known dimers from 12 to 41. Many of the…