Common methods of determining atomic polarizabilities suffer from the inclusion of nonlocal effects such as charge polarization. A new method is described for determining fully ab initio atomic polarizabilities based on calculating the response of atomic multipoles to the local electrostatic potential. The localized atomic polarizabilities are then used to calculate induction energies that are ...

First principles calculations of L3 XANES/ELNES of GaN and InN with both wurtzite and zinc-blende structures have been made using OLCAO (orthogonalized linear combinations of atomic orbitals) method. Supercells with more than 100 atoms were employed. A core-hole was rigorously included in the calculation, and the photo absorption cross section (PACS) between the initial and final states was com...

The apex atom of a W scanning probe tip reveals a nonspherical charge distribution as probed by a CO molecule bonded to a Cu(111) surface [Welker et al., Science 336, 444 (2012). Three high-symmetry images were observed and related to three low-index crystallographic directions of the W bcc crystal. Open questions remained, such as the detectability of a contamination of W tips by sample materi...

The toxicity of thirty para-substituted phenols on Tetrahymena pyriformis was modelled using an original methodology that uses the complex structural information of the compounds. Two models were built. The methodology allows atomic properties to be assigned to toxicity based on the selection of pairs of descriptors from the entire family, which is called Molecular Descriptors Family (MDF). One...

Current researches have showed that N3, N5-diaryl-2, 6-dimethyl -1, 4-dihydropyrine-3, 5- dicarboxamide analogues demonstrate notable anti-tubercular activity. In this study, Hantzsch condensation was used to design and synthesize new analogues of dihydropyridine (DHP). Different diary carboxamides were inserted at positions 3 and 5 of the DHP ring. 4(5)-chloro-2-ethyl-5(4)-imidazolyl moiety wa...

Initialization. The crystal structure from Ref. 1 is used as the starting point for simulations of the SecA-SecYEG complex. To meet the size-constraints of the Anton hardware,2,3 only SecA residues within 15 Å of the translocon in the crystal structure are included in the simulations. Specifically, if any atom within a residue of SecA is less than 15 Å from any atom within a residue of the tran...

The antituberculotic activity of some polyhydroxyxanthones was estimated using the Molecular Descriptors Family on Structure Activity Relationships methodology. From a total number of 298110 real and distinct calculated descriptors, 94843 were significantly different and entered into multiple linear regression analysis. The best performing bi-varied model was obtained by use of all polyhydroxyx...

Background The accuracy of ligand-protein docking may be affected by the presence of water molecules on the surface of proteins. Water can form complex bridging networks and can play a critical role in dictating the binding mode of ligands. A recent analysis of high-resolution crystal structures of ligand-protein complexes revealed that 85% of the complexes had one or more water molecules bridg...

An atomic snapshot object is an object that can be concurrently accessed by asynchronous processes prone to crash. It is made of m components (base atomic registers) and is defined by two operations: an update operation that allows a process to atomically assign a new value to a component and a snapshot operation that atomically reads and returns the values of all the components. To cope with t...

Molecular dynamics is of fundamental interest in natural science research. The capability of investigating molecular dynamics is one of the various motivations for ultrafast optics. We present our investigation of photoionization and nuclear dynamics in methyl iodine (CH3I) molecule with an X-ray pump X-ray probe scheme. The pump–probe experiment was realized with a two-mirror X-ray split and d...