Most Ligand-Based Classification Benchmarks Reward Memorization Rather than Generalization

Undetected overfitting can occur when there are significant redundancies between training and validation data. We describe AVE, a new measure of training-validation redundancy for ligand-based classification problems that accounts for the similarity amongst inactive molecules as well as active. We investigated seven widely-used benchmarks for virtual screening and classification, and show that the amount of AVE bias strongly correlates with the performance of ligand-based predictive methods irrespective of the predicted property, chemical fingerprint, similarity measure, or previously-applied unbiasing techniques. Therefore, it may be that the previously-reported performance of most ligand-based methods can be explained by overfitting to benchmarks rather than good prospective accuracy

Density functional simulation of the BaZrO3 (011) surface structure

The atomic structure and charge redistribution of different terminations of BaZrO3 (011) surfaces have been studied using density functional simulations. We found that the O-terminated (011) flat surface had the smallest cleavage energy among (011) surfaces, but this value was still twice as large as for the formation of a pair of complimentary (001) surfaces. The density functional calculations allowed us to estimate the excess surface Gibb's free energy and to compare stability of different (011) surfaces as a function of chemical environment. In addition, we compared stability of BaZrO3 (011) surfaces with respect to BaZrO3 (001) surfaces. Within boundaries, where BaZrO3 does not decompose, only the Ba- and O-terminated (011) surfaces appeared to be stable. However, if (001) surfaces are also taken into consideration, the BaO-terminated (001) surface is the only stable surface among all considered (001) and (011) surfaces

Calculations for antiferrodistortive phase of SrTiO3 perovskite: hybrid density functional study

The electronic and atomic structure of SrTiO3 crystals below the antiferrodistortive phase transition observed at 105 K is calculated using the hybrid B3PW functional as implemented in the ab initio CRYSTAL-2003 computer code. Such a combination of non-local exchange and correlation permits the calculation for the first time of the TiO6 octahedron rotational angle and the ratio c/a of tetragonal lattice constants in excellent agreement with experimental data. The level splitting of the bottom of the conduction band is found to be very small, <1 meV. The predicted phase-transition induced change of the optical gap from indirect to direct is confirmed by experimental photoconductivity data

Electron Cloud at High Beam Currents

The density and the wake elds of the e-cloud are quite dierent at low and high beam currents. The wake elds are derived and applied to the upgraded PEP-II B-factory.

Ab initio Calculations for SrTiO_3 (100) Surface Structure

Results of detailed calculations for SrTiO_3 (100) surface relaxation and the electronic structure for the two different terminations (SrO and TiO_2) are discussed. These are based on ab initio Hartree-Fock (HF) method with electron correlation corrections and Density Functional Theory (DFT) with different exchange-correlation functionals, including hybrid (B3PW, B3LYP) exchange techniques. Results are compared with previous ab initio plane wave LDA calculations. All methods agree well on both surface energies and on atomic displacements. Considerable increase of Ti[Single Bond]O chemical bond covalency nearby the surface is predicted, along with a gap reduction, especially for the TiO_2 termination

Atomistic simulation of SrTiO3(001) surface relaxation

The (001) surface relaxation of the cubic perovskite SrTiO3 crystal has been studied using the shell model. The positions of atoms in several surface layers embedded in the electrostatic field of the remainder of the crystal are calculated. We show that Ti4+, Sr2+ and O2- ions in six near-surface layers are displaced differently from their crystalline sites which leads to the creation of so-called surface rumpling, a dipole moment, and an electric field in the near-surface region. Calculated atomic displacements are compared with LEED experimental data