CO adsorption on Pt induced Ge nanowires

Using density functional theory, we investigate the possible adsorption sites of CO molecules on the recently discovered Pt induced Ge nanowires on Ge(001). Calculated STM images are compared to experimental STM images to identify the experimentally observed adsorption sites. The CO molecules are found to adsorb preferably onto the Pt atoms between the Ge nanowire dimer segments. This adsorption site places the CO in between two nanowire dimers, pushing them outward, blocking the nearest equivalent adsorption sites. This explains the observed long-range repulsive interaction between CO molecules on these Pt induced nanowires.Comment: 12 pages, 10 figure

Models and Simulations in Material Science: Two Cases Without Error Bars

We discuss two research projects in material science in which the results cannot be stated with an estimation of the error: a spectro- scopic ellipsometry study aimed at determining the orientation of DNA molecules on diamond and a scanning tunneling microscopy study of platinum-induced nanowires on germanium. To investigate the reliability of the results, we apply ideas from the philosophy of models in science. Even if the studies had reported an error value, the trustworthiness of the result would not depend on that value alone.Comment: 20 pages, 2 figure

Formation of Pt induced Ge atomic nanowires on Pt/Ge(001): a DFT study

Pt deposited onto a Ge(001) surface gives rise to the spontaneous formation of atomic nanowires on a mixed Pt-Ge surface after high temperature annealing. We study possible structures of the mixed surface and the nanowires by total energy (density functional theory) calculations. Experimental scanning tunneling microscopy images are compared to the calculated local densities of states. On the basis of this comparison and the stability of the structures, we conclude that the formation of nanowires is driven by an increased concentration of Pt atoms in the Ge surface layers. Surprisingly, the atomic nanowires consist of Ge instead of Pt atoms.Comment: 4 pages, 3 figure

Reply to 'Comment on "Extending Hirshfeld-I to bulk and periodic materials" '

The issues raised in the comment by T.A. Manz are addressed through the presentation of calculated atomic charges for NaF, NaCl, MgO, SrTiO$_3$ and La$_2$Ce$_2$O$_7$, using our previously presented method for calculating Hirshfeld-I charges in Solids [J. Comput. Chem.. doi: 10.1002/jcc.23088]. It is shown that the use of pseudo-valence charges is sufficient to retrieve the full all-electron Hirshfeld-I charges to good accuracy. Furthermore, we present timing results of different systems, containing up to over $200$ atoms, underlining the relatively low cost for large systems. A number of theoretical issues is formulated, pointing out mainly that care must be taken when deriving new atoms in molecules methods based on "expectations" for atomic charges.Comment: 7 pages, 2 Tables, 2 figure

Extending Hirshfeld-I to bulk and periodic materials

In this work, a method is described to extend the iterative Hirshfeld-I method, generally used for molecules, to periodic systems. The implementation makes use of precalculated pseudo-potential based charge density distributions, and it is shown that high quality results are obtained for both molecules and solids, such as ceria, diamond, and graphite. The use of such grids makes the implementation independent of the solid state or quantum chemical code used for studying the system. The extension described here allows for easy calculation of atomic charges and charge transfer in periodic and bulk systems.Comment: 11 pages, 4 Tables, 5 Figures, pre-referee draft only, much extended post referee version only available at publishe

The Formation of Self-Assembled Nanowire Arrays on Ge(001): a DFT Study of Pt Induced Nanowire Arrays

Nanowire (NW) arrays form spontaneously after high temperature annealing of a submonolayer deposition of Pt on a Ge(001) surface. These NWs are a single atom wide, with a length limited only by the underlying beta-terrace to which they are uniquely connected. Using ab-initio density functional theory (DFT) calculations we study possible geometries of the NWs and substrate. Direct comparison to experiment is made via calculated scanning tunneling microscope (STM) images. Based on these images, geometries for the beta-terrace and the NWs are identified, and a formation path for the nanowires as function of increasing local Pt density is presented. We show the beta-terrace to be a dimer row surface reconstruction with a checkerboard pattern of Ge-Ge and Pt-Ge dimers. Most remarkably, comparison of calculated to experimental STM images shows the NWs to consist of germanium atoms embedded in the Pt-lined troughs of the underlying surface, contrary to what was assumed previously in experiments.Comment: 6 pages, 4 figures, E-proceedings of 2009 MRS spring Meetin

Assigning probabilities to non-Lipschitz mechanical systems

We present a method for assigning probabilities to the solutions of initial value problems that have a Lipschitz singularity. To illustrate the method, we focus on the following toy-example: $\ddot{r} = r^\alpha$, $r(t=0) =0$, and $\dot{r}\mid_{r(t=0)} =0$, where the dots indicate derivatives to time and $\alpha \in ]0,1[$. This example has a physical interpretation as a mass in a uniform gravitational field on a dome of particular shape; the case with $\alpha=1/2$ is known as Norton's dome. Our approach is based on (1) finite difference equations, which are deterministic, (2) a uniform prior on the phase space, and (3) non-standard analysis, which involves infinitesimals and which is conceptually close to numerical methods from physical praxis. This allows us to assign probabilities to the solutions of the initial value problem in the original, indeterministic model.Comment: 13 figure

Can Europium Atoms form Luminescent Centres in Diamond: A combined Theoretical-Experimental Study

The incorporation of Eu into the diamond lattice is investigated in a combined theoretical-experimental study. The large size of the Eu ion induces a strain on the host lattice, which is minimal for the Eu-vacancy complex. The oxidation state of Eu is calculated to be 3+ for all defect models considered. In contrast, the total charge of the defect-complexes is shown to be negative -1.5 to -2.3 electron. Hybrid-functional electronic-band-structures show the luminescence of the Eu defect to be strongly dependent on the local defect geometry. The 4-coordinated Eu substitutional dopant is the most promising candidate to present the typical Eu3+ luminescence, while the 6-coordinated Eu-vacancy complex is expected not to present any luminescent behaviour. Preliminary experimental results on the treatment of diamond films with Eu-containing precursor indicate the possible incorporation of Eu into diamond films treated by drop-casting. Changes in the PL spectrum, with the main luminescent peak shifting from approximately 614 nm to 611 nm after the growth plasma exposure, and the appearance of a shoulder peak at 625 nm indicate the potential incorporation. Drop-casting treatment with an electronegative polymer material was shown not to be necessary to observe the Eu signature following the plasma exposure, and increased the background luminescence.Comment: 12 pages, 7 figures, 5 table

DFT study of Pt-induced Ge(001) reconstructions

Pt deposited on a Ge(001) surface spontaneously forms nanowire arrays. These nanowires are thermodynamically stable and can be hundreds of atoms long. The nanowires only occur on a reconstructed Pt-Ge-surface where they fill the troughs between the dimer rows on the surface. This unique connection between the nanowires and the underlying substrate make a thorough understanding of the latter necessary for understanding the growth of the nanowires. In this paper we study possible surface reconstructions containing 0.25 and 0.5 of a monolayer of Pt. Comparison of calculated STM images to experimental STM images of the surface reconstruction reveal that the Pt atoms are located in the top layer, creating a structure with rows of alternating Pt-Ge and Ge-Ge dimers in a c(4x2) arrangement. Our results also show that Pt atoms in the second or third layer can not be responsible for the experimentally observed STM images.Comment: 16 pages, 13 figure