MALDI-TOF/TOF de novo sequence analysis of 2-D PAGE-separated proteins from Halorhodospira halophila, a bacterium with unsequenced genome

Because protein identifications rely on matches with sequence databases, high-throughput proteomics is currently largely restricted to those species for which comprehensive sequence databases are available. The identification of proteins derived from organisms with unsequenced genomes mainly depends on homology searching. Here, we report the use of a simplified, gel-based, chemical derivatization strategy for de novo sequence analysis using a MALDI-TOF/TOF mass spectrometer. This approach allows the determination of de novo peptide sequences of up to 20 amino acid residues in length. The protocol was applied on a proteomic study of 2-D PAGE-separated proteins from Halorhodospira halophila, an extremophilic eubacterium with yet unsequenced genome. Using three different homology-based search algorithms, we were able to identify more than 30 proteins from this organism using subpicomole quantities of protein.     

A general entry to guaianolides. An illustrative synthesis of (±)-compressanolide

A short and efficient synthesis of a key intermediate $\text{2}$ for the formation of guaianolides is described. The potentiality of $\text{2}$ is illustrated by its transformation into the natural occurring guaianolide, (±)-compressanolide $\text{1}$.     

Theory of plasmon excitations in (SN)x

The anomalous anisotropy and dispersion of plasmons in polymeric sulfur nitride (SN)_x are explained within a model of an electron gas with an anisotropic effective mass ratio. Calculations in the random phase approximation yield very good agreement with the electron loss data. Exchange corrections for the model are shown to be small for systems of the (SN)_x type which exhibit reduced dimensionality.     

Photoluminescence of tetrahedral quantum-dot quantum wells

Taking into account the tetrahedral shape of a quantum-dot quantum well (QDQW) when describing excitonic states, phonon modes, and the exciton-phonon interaction in the structure, we obtain within a nonadiabatic approach a quantitative interpretation of the photoluminescence spectrum of a single CdS/HgS/CdS QDQW. We find that the exciton ground state in a tetrahedral QDQW is bright, in contrast to the dark ground state for a spherical QDQW. The position of the phonon peaks in the photoluminescence spectrum is attributed to interface optical phonons. We also show that the experimental value of the Huang-Rhys parameter can be obtained only within the nonadiabatic theory of phonon-assisted transitions.     

Stable vortex-antivortex molecules in mesoscopic superconducting triangles

A thermodynamically stable vortex-antivortex pattern has been revealed in equilateral mesoscopic type I superconducting triangles, contrary to type II superconductors where similar patterns are unstable. The stable vortex-antivortex "molecule" appears due to the interplay between two factors: a repulsive vortex-antivortex interaction in type I superconductors and the vortex confinement in the mesoscopic triangle.     

Vortex core deformation and stepper-motor ratchet behavior in a superconducting aluminum film containing an array of holes

We investigated experimentally the frequency dependence of a superconducting vortex ratchet effect by means of electrical transport measurements and modeled it theoretically using the time-dependent Ginzburg-Landau formalism. We demonstrate that the high frequency vortex behavior can be described as a discrete motion of a particle in a periodic potential, i.e., the so-called stepper-motor behavior. Strikingly, in the more conventional low frequency response a transition takes place from an Abrikosov vortex rectifier to a phase slip line rectifier. This transition is characterized by a strong increase in the rectified voltage and the appearance of a pronounced hysteretic behavior.     

Stability of bipolarons in the presence of a magnetic field

The stability of large Fröhlich bipolarons in the presence of a static magnetic field is investigated with the path integral formalism. We find that the application of a magnetic field (characterized by the cyclotron frequence ω _c) favors bipolaron formation: (i) the critical electronphonon coupling parameter α _c (above which the bipolaron is stable) decreases with increasing ω _c and (ii) the critical Coulomb repulsion strength U _c (below which the bipolaron is stable) increases with increasing ω _c. The binding energy and the corresponding variational parameters are calculated as a function of α, U and ω _c. Analytical results are obtained in various limiting cases. In the limit of strong electron-phonon coupling (α ? 1) we obtain for ω _c ? 1 that E _estim ? E _estim(ω _c = 0) + c(u)ω _c/α ⁴ with c(u) an explicitly calculated constant, dependent on the ratio u = U/α where U is the strength of the Coulomb repulsion. This relation applies both in 2D and in 3D, but with a different expression for c(u). For ω _c ? α ²? 1 we find in 3D E _estim ? ω _c - α ² A(u) ln²(ω _c/α ²), (also with an explicit analytical expression for A(u)) whereas in 2D E _estim ^2D ? ω _c - α√ω _cπ(u-2-√2)/2. The validity region of the Feynman-Jensen inequality for the present problem, bipolarons in a magnetic field, remains to be examined.     

Polarons and bipolarons in oxides

The physical properties of Fröhlich polarons and bipolarons are reviewed in relation to the recent experimental study of the mid-infrared absorption spectra of high- Tc cuprate superconductors, in particular, of Nd₂CuO_4-y , YBa₂Cu₃O_6+x and La₂CuO_4+x . The spectral region studied is of particular relevance for the open question of the presence of polarons and bipolarons in these materials, since it coincides with the frequency region where polaron and bipolaron absorption is to be expected. In our view, the optical absorption spectra as observed in the doped cuprates are a manifestation of the polaron type relaxed excited final states.