Representing molecule-surface interactions with symmetry-adapted neural networks

The accurate description of molecule-surface interactions requires a detailed knowledge of the underlying potential-energy surface (PES). Recently, neural networks (NNs) have been shown to be an efficient technique to accurately interpolate the PES information provided for a set of molecular configurations, e.g. by first-principles calculations. Here, we further develop this approach by building the NN on a new type of symmetry functions, which allows to take the symmetry of the surface exactly into account. The accuracy and efficiency of such symmetry-adapted NNs is illustrated by the application to a six-dimensional PES describing the interaction of oxygen molecules with the Al(111) surface.Comment: 13 pages including 8 figures; related publications can be found at http://www.fhi-berlin.mpg.de/th/th.htm

Temperature dependence of the vibrational spectrum of porphycene: a qualitative failure of classical-nuclei molecular dynamics

The temperature dependence of vibrational spectra can provide information about structural changes of a system and also serve as a probe to identify different vibrational mode couplings. Fully anharmonic temperature-dependent calculations of these quantities are challenging due to the cost associated with statistically converging trajectory-based methods, especially when accounting for nuclear quantum effects. Here, we train a high-dimensional neural network potential energy surface for the porphycene molecule based on data generated with DFT-B3LYP, including pairwise van der Waals interactions. In addition, we fit a kernel ridge regression model for the molecular dipole moment surface. The combination of this machinery with thermostatted path integral molecular dynamics (TRPMD) allows us to obtain well-converged, full-dimensional, fully-anharmonic vibrational spectra including nuclear quantum effects, without sacrificing the first-principles quality of the potential-energy surface or the dipole surface. Within this framework, we investigate the temperature and isotopologue dependence of the high-frequency vibrational fingerprints of porphycene. While classical-nuclei dynamics predicts a red shift of the vibrations encompassing the NH and CH stretches, TRPMD predicts a strong blue shift in the NH-stretch region and a smaller one in the CH-stretch region. We explain this behavior by analyzing the modulation of the effective potential with temperature, which arises from vibrational coupling between quasi-classical thermally activated modes and high-frequency quantized modes

Non-adiabatic Effects in the Dissociation of Oxygen Molecules at the Al(111) Surface

The measured low initial sticking probability of oxygen molecules at the Al(111) surface that had puzzled the field for many years was recently explained in a non-adiabatic picture invoking spin-selection rules [J. Behler et al., Phys. Rev. Lett. 94, 036104 (2005)]. These selection rules tend to conserve the initial spin-triplet character of the free O2 molecule during the molecule's approach to the surface. A new locally-constrained density-functional theory approach gave access to the corresponding potential-energy surface (PES) seen by such an impinging spin-triplet molecule and indicated barriers to dissociation which reduce the sticking probability. Here, we further substantiate this non-adiabatic picture by providing a detailed account of the employed approach. Building on the previous work, we focus in particular on inaccuracies in present-day exchange-correlation functionals. Our analysis shows that small quantitative differences in the spin-triplet constrained PES obtained with different gradient-corrected functionals have a noticeable effect on the lowest kinetic energy part of the resulting sticking curve.Comment: 17 pages including 11 figures; related publications can be found at http://www.fhi-berlin.mpg.de/th/th.htm

A New Type of distributed Enamel based Clearing Electrode

Clearing electrodes can be used for electron cloud (EC) suppression in high intensity particle accelerators. In this paper the use of low and highly resistive layers on a dielectric substrate are examined. The beam coupling impedance of such a structure is evaluated. Furthermore the clearing efficiency as well as technological issues are discussed

Coulomb parameters and photoemission for the molecular metal TTF-TCNQ

We employ density-functional theory to calculate realistic parameters for an extended Hubbard model of the molecular metal TTF-TCNQ. Considering both intra- and intermolecular screening in the crystal, we find significant longer-range Coulomb interactions along the molecular stacks, as well as inter-stack coupling. We show that the long-range Coulomb term of the extended Hubbard model leads to a broadening of the spectral density, likely resolving the problems with the interpretation of photoemission experiments using a simple Hubbard model only.Comment: 4 pages, 2 figure

A Study of the Correlation between Endoscopic and Histological Diagnoses in Gastroduodenitis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72433/1/j.1572-0241.1987.tb01777.x.pd

Comparison of Aquatic-Insect Habitat and Diversity Above and Below Road Crossings in Low-Order Streams

The effects of road crossings on fish communities have been extensively studied; yet little attention has been given to macroinvertebrate communities. This study evaluated physical stream characteristics, water quality, and aquatic-insect richness from above and below road crossings of low-order streams in the Ouachita National Forest in Arkansas. Fifteen road crossings were sampled during October and November 2005. Erosion was significantly higher below road crossings than above. Sites downstream of road crossings had significantly lower pH and significantly higher turbidity than sites upstream of road crossings. Despite differences in water quality and habitat, there was no apparent difference in aquatic-insect richness from above and below road crossings based on the EPT index, suggesting that road crossings did not act as barriers to insect movement. The water-quality differences observed were well within acceptable limits and likely not biologically important

Nucleation mechanism for the direct graphite-to-diamond phase transition

Graphite and diamond have comparable free energies, yet forming diamond from graphite is far from easy. In the absence of a catalyst, pressures that are significantly higher than the equilibrium coexistence pressures are required to induce the graphite-to-diamond transition. Furthermore, the formation of the metastable hexagonal polymorph of diamond instead of the more stable cubic diamond is favored at lower temperatures. The concerted mechanism suggested in previous theoretical studies cannot explain these phenomena. Using an ab initio quality neural-network potential we performed a large-scale study of the graphite-to-diamond transition assuming that it occurs via nucleation. The nucleation mechanism accounts for the observed phenomenology and reveals its microscopic origins. We demonstrated that the large lattice distortions that accompany the formation of the diamond nuclei inhibit the phase transition at low pressure and direct it towards the hexagonal diamond phase at higher pressure. The nucleation mechanism proposed in this work is an important step towards a better understanding of structural transformations in a wide range of complex systems such as amorphous carbon and carbon nanomaterials