DOMMINO: a database of macromolecular interactions

With the growing number of experimentally resolved structures of macromolecular complexes, it becomes clear that the interactions that involve protein structures are mediated not only by the protein domains, but also by various non-structured regions, such as interdomain linkers, or terminal sequences. Here, we present DOMMINO (http://dommino.org), a comprehensive database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. The database complements SCOP domain annotations with domain predictions by SUPERFAMILY and is automatically updated every week. The database interface is designed to provide the user with a three-stage pipeline to study macromolecular interactions: (i) a flexible search that can include a PDB ID, type of interaction, SCOP family of interacting proteins, organism name, interaction keyword and a minimal threshold on the number of contact pairs; (ii) visualization of subunit interaction network, where the user can investigate the types of interactions within a macromolecular assembly; and (iii) visualization of an interface structure between any pair of the interacting subunits, where the user can highlight several different types of residues within the interfaces as well as study the structure of the corresponding binary complex of subunits

Adsorption of benzene on Si(100) from first principles

Adsorption of benzene on the Si(100) surface is studied from first principles. We find that the most stable configuration is a tetra-$\sigma$-bonded structure characterized by one C-C double bond and four C-Si bonds. A similar structure, obtained by rotating the benzene molecule by 90 degrees, lies slightly higher in energy. However, rather narrow wells on the potential energy surface characterize these adsorption configurations. A benzene molecule impinging on the Si surface is most likely to be adsorbed in one of three different di-$\sigma$-bonded, metastable structures, characterized by two C-Si bonds, and eventually converts into the lowest-energy configurations. These results are consistent with recent experiments.Comment: 4 pages, RevTex, 2 PostScript gzipped figure

On the interpretation of spin-polarized electron energy loss spectra

We study the origin of the structure in the spin-polarized electron energy loss spectroscopy (SPEELS) spectra of ferromagnetic crystals. Our study is based on a 3d tight-binding Fe model, with constant onsite Coulomb repulsion U between electrons of opposite spin. We find it is not the total density of Stoner states as a function of energy loss which determines the response of the system in the Stoner region, as usually thought, but the densities of Stoner states for only a few interband transitions. Which transitions are important depends ultimately on how strongly umklapp processes couple the corresponding bands. This allows us to show, in particular, that the Stoner peak in SPEELS spectra does not necessarily indicate the value of the exchange splitting energy. Thus, the common assumption that this peak allows us to estimate the magnetic moment through its correlation with exchange splitting should be reconsidered, both in bulk and surface studies. Furthermore, we are able to show that the above mechanism is one of the main causes for the typical broadness of experimental spectra. Finally, our model predicts that optical spin waves should be excited in SPEELS experiments.Comment: 11 pages, 7 eps figures, REVTeX fil

Radio-Frequency Spectroscopy

Contains reports on four research projects

Ferromagnetism and Temperature-Driven Reorientation Transition in Thin Itinerant-Electron Films

The temperature-driven reorientation transition which, up to now, has been studied by use of Heisenberg-type models only, is investigated within an itinerant-electron model. We consider the Hubbard model for a thin fcc(100) film together with the dipole interaction and a layer-dependent anisotropy field. The isotropic part of the model is treated by use of a generalization of the spectral-density approach to the film geometry. The magnetic properties of the film are investigated as a function of temperature and film thickness and are analyzed in detail with help of the spin- and layer-dependent quasiparticle density of states. By calculating the temperature dependence of the second-order anisotropy constants we find that both types of reorientation transitions, from out-of-plane to in-plane (``Fe-type'') and from in-plane to out-of-plane (``Ni-type'') magnetization are possible within our model. In the latter case the inclusion of a positive volume anisotropy is vital. The reorientation transition is mediated by a strong reduction of the surface magnetization with respect to the inner layers as a function of temperature and is found to depend significantly on the total band occupation.Comment: 10 pages, 8 figures included (eps), Phys Rev B in pres

Radio-Frequency Spectroscopy

Contains reports on three research projects

Radio-Frequency Spectroscopy

Contains reports on four research projects

Radio-Frequency Spectroscopy

Contains reports on four research projects

Optimizing decomposition of software architecture for local recovery

Cataloged from PDF version of article.The increasing size and complexity of software systems has led to an amplified number of potential failures and as such makes it harder to ensure software reliability. Since it is usually hard to prevent all the failures, fault tolerance techniques have become more important. An essential element of fault tolerance is the recovery from failures. Local recovery is an effective approach whereby only the erroneous parts of the system are recovered while the other parts remain available. For achieving local recovery, the architecture needs to be decomposed into separate units that can be recovered in isolation. Usually, there are many different alternative ways to decompose the system into recoverable units. It appears that each of these decomposition alternatives performs differently with respect to availability and performance metrics. We propose a systematic approach dedicated to optimizing the decomposition of software architecture for local recovery. The approach provides systematic guidelines to depict the design space of the possible decomposition alternatives, to reduce the design space with respect to domain and stakeholder constraints and to balance the feasible alternatives with respect to availability and performance. The approach is supported by an integrated set of tools and illustrated for the open-source MPlayer software