Voronoia4RNA (http://proteinformatics.charite.de/voronoia4rna/) is a structural database storing precalculated atomic volumes, atomic packing densities (PDs) and coordinates of internal cavities for currently 1869 RNAs and RNA-protein complexes. Atomic PDs are a measure for van der Waals interactions. Regions of low PD, containing water-sized internal cavities, refer to local structure flexibil...

The increasing need for precise determination of the atomic arrangement of non-periodic structures in materials design and the control of nanostructures explains the growing interest in quantitative transmission electron microscopy. The aim is to extract precise and accurate numbers for unknown structure parameters including atomic positions, chemical concentrations and atomic numbers. For this...

In an earlier paper (Ghose A. K.; Crippen, G. M. J. Comput. Chem. 1986, 7, 565) the need of atomic physicochemical properties for three-dimensional-structure-directed quantitative structure-activity relationships was demonstrated, and it was shown how atomic parameters can be developed to successfully evaluate the molecular water-1-octanol partition coefficient, which is a measure of hydrophobi...

Coarse-grained models represent attractive approaches to analyze and simulate ribonucleic acid (RNA) molecules, for example, for structure prediction and design, as they simplify the RNA structure to reduce the conformational search space. Our structure prediction protocol RAGTOP (RNA-As-Graphs Topology Prediction) represents RNA structures as tree graphs and samples graph topologies to produce...

Some micromagnetic phenomena can be modelled by a minimization problem of a nonconvex energy. A numerical method to compute the micromagnetic field, which gives rise to a finite dimensional unconstrained minimization problem, is given and analyzed. In our method, the Maxwell’s equation defined on the whole space is solved by a finite element method using artificial boundary, and the highly osci...

The purpose of this work is to present a new method to extract the electron density ([Formula: see text]) and the effective atomic number (Z eff) from dual-energy CT images, based on a Karhunen-Loeve expansion (KLE) of the atomic cross section per electron. This method was used to calibrate a Siemens Definition CT using the CIRS phantom. The predicted electron density and effective atomic numbe...

Magnetic force microscopy (MFM) allows one to image the domain structure of ferromagnetic samples by probing the dipole forces between a magnetic probe tip and a magnetic sample. The magnetic domain structure of the sample depends on the alignment of the individual atomic magnetic moments. It is desirable to be able to image both individual atoms and domain structures with a single probe. Howev...

This paper offers an account of the semantics of count nous. I show that neither the atomic/nonatomic distinction nor the homogeneous/non-homogeneous distinction is sufficient to explain the semantic contrast between mass and count nouns, since there are mass nouns which are atomic, and there are count nouns which are homogeneous. Starting from a version of Chierchia's 1998a account of the sema...

A model-based method is proposed to relatively quantify the chemical composition of atomic columns using high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images. The method is based on a quantification of the total intensity of the scattered electrons for the individual atomic columns using statistical parameter estimation theory. In order to apply this the...

The analysis of nanomechanical properties is becoming an increasingly useful tool in a large variety of fields, ranging from biology to polymer science. The Atomic Force Microscope, AFM, can bridge the information about morphology, obtained with outstanding resolution, to local mechanical properties. When performing an AFM nanoindentation, the rough force curve, i.e. the plot of voltage output ...