Shaper-assisted full-phase characterization of UV pulses without a spectrometer

A full-phase measurement of low-energy femtosecond UV pulses is presented. The method relies on phase retrieval of measured sonogram traces and is greatly simplified by a two-dimensional shaper-assisted cross correlation setup. As all required pulses are generated by the pulse shaper, the method is free of external references and additional tunable filter setups.     

An efficient and robust numerical algorithm for estimating parameters in Turing systems

We present a new algorithm for estimating parameters in reaction–diffusion systems that display pattern formation via the mechanism of diffusion-driven instability. A Modified Discrete Optimal Control Algorithm (MDOCA) is illustrated with the Schnakenberg and Gierer–Meinhardt reaction–diffusion systems using PDE constrained optimization techniques. The MDOCA algorithm is a modification of a standard variable step gradient algorithm that yields a huge saving in computational cost. The results of numerical experiments demonstrate that the algorithm accurately estimated key parameters associated with stationary target functions generated from the models themselves. Furthermore, the robustness of the algorithm was verified by performing experiments with target functions perturbed with various levels of additive noise. The MDOCA algorithm could have important applications in the mathematical modeling of realistic Turing systems when experimental data are available.     

Analysis of RNA sequence structure maps by exhaustive enumeration I. Neutral networks

Summary Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of allGC andAU sequences with chain lengths up to 30. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based on statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them that ofneutral networks (being sets of sequences folding into the same structure). Exhaustive enumeration allows to test several previously suggested relations: the number of (minimum free energy) secondary structures as a function of the chain length as well as the frequency distribution of structures at constant chain length (commonly resulting in generalized forms ofZipf's law).

---

Analyse der Beziehungen zwischen RNA-Sequenzen und Sekundärstrukturen durch vollständige Faltung, 1. Mitt. Faltung, Neutrale Netzwerke

Zusammenfassung Die globalen Benziehungen zwischen RNA-Sequenzen und Sekundärstrukturen werden als Abbildungen aus einem Raum aller Sequenzen in einen Raum aller Strukturen aufgefaßt. Diese Abbildungen werden durch Falten aller binären Sequenzen desGC-undAU-Alphabets mit Kettenlängen bis zun=30 untersucht. Die berechneten Strukturdaten werden durch vollständiges Abzählen ausgewertet und als eine exakte Referenz zum Überprüfen analytischer Resultate aus mathematischen Modellen sowie zum Testen statistisch erhobener Proben verwendet. Einige neuartige Konzepte zur Beschreibung der Beziehungen zwischen Sequenzen und Strukturen werden eingehend untersucht, unter ihnen der Begriff derneutralen Netzwerke. Ein neutrales Netzwerk besteht aus allen Sequenzen, die eine bestimmte Struktur ausbilden. Vollständiges Abzählen ermöglicht beispielsweise die Bestimmung aller Strukturen minimaler freier Energie in Abhängigkeit von der Kettenlänge ebenso wie die Bestimmung der Häufigkeitsverteilungen der Strukturen bei konstanten Kettenlängen. Die letzteren folgen einer verallgemeinerten FormZipfschen Gesetzes.

     

Reasons for the decomposition of the fungicide thiram during preparation of fruit and vegetable samples and consequences for residue analysis

The concentration of thiram in aqueous solution decreases by 50-75% within 20 min in the presence of cut pieces of apple, cucumber or celeriac with a section surface area of 160 cm2 each. The decomposition rate is predominantly influenced by the section surface area of the cut fruit and vegetable samples. Denaturing reaction conditions (exchange of the solvent water by methanol; boiling of sample material) will significantly slow down the decomposition rate. It was concluded that the thiram decomposition had been caused by enzymes on the section surface of the fruit and vegetable samples. For a specific determination of thiram, a simple rinsing of the intact fruit and vegetable material was appropriate as extraction method. For the screening of thiram residues, the often used Keppel method, which determines CS2 from thiram or dithiocarbamates seems to be applicable even if samples had been coarsely cut, since decomposition of the CS2-forming intermediates is slower than the breakdown of thiram itself. Therefore, specific determination of thiram is necessary only, if maximum residue limits for dithiocarbamates are not adhered to.     

The NiII,HgII and CuII complexes of 12‐membered‐ring mixed‐donor macrocycles

The structures of di­aqua(1,7‐dioxa‐4‐thia‐10‐aza­cyclo­do­decane)­nickel dinitrate, [Ni(C₈H₁₇NO₂S)(H₂O)₂](NO₃)₂, (I), bis­(nitrato‐O,O′)(1,4,7‐trioxa‐10‐aza­cyclo­do­decane)­mercury, [Hg(NO₃)₂(C₈H₁₇NO₃)], (II), and aqua­(nitrato‐O)(1‐oxa‐4,7,10‐tri­aza­cyclo­do­decane)copper nitrate, [Cu(NO₃)(C₈H₁₉N₃O)(H₂O)]NO₃, (III), reveal each macrocycle binding in a tetradentate manner. The conformations of the ligands in (I) and (III) are the same and distinct from that identified for (II). These differences are in agreement with molecular‐mechanics predictions of ligand conformation as a function of metal‐ion size.     

Fluorescent and electroactive cyclic assemblies from perylene tetracarboxylic acid bisimide ligands and metal phosphane triflates

Tetraaryloxy-substituted perylene tetracarboxylic acid bisimides with one or two 4-pyridyl receptor substituents at the imide functionality were synthesized and employed in transition metal directed self-assembly with Pd(II) and Pt(II) phosphane triflates. Upon mixing of the components, quantitative formation of functional molecular square-type complexes containing four dye molecules and model complexes of a 2:1 (perylene bisimide ligand:transition metal ion) stoichiometry was observed. The isolated metallosupramolecular squares were characterized by 1H and 31P [1H] NMR spectroscopy as well as conventional electrospray ionization (ESI) and ESI-FTICR mass spectrometry, which gave evidence for the structure and the high stability of these giant cyclic dye assemblies (molecular weight (3a) 8172, Pt-Pt corner diagonal ca. 3.4 nm). Studies of the optical absorption and fluorescence properties and the electrochemistry and spectroelectrochemistry of both the perylene bisimide ligands and the perylene bisimide metal complexes show that Pt(II) coordination does not interfere with the optical and electrochemical properties of the perylene bisimide ligands; this gives squares with high fluorescence quantum yields (phiF (3a)=0.88) and three fully reversible redox couples. The latter could be unambiguously related to quantitative formation of perylene bisimide radical cations (E1/2 = +0.93 V vs. Fc/Fc+), radical anions (E1/2= - 1.01 V vs. Fc/Fc+), and dianions (E1/2 = -1.14 V vs. Fc/Fc+); these redox reactions change the charge state of the cyclic assembly from +12 to zero. In contrast, Pd(II) coordination influenced the electrochemical properties of the assembly because of an irreversible palladium reduction at E1/2= -1.15 V versus Fc/Fc+. Finally, dynamic ligand exchange processes between different metallosupramolecular assemblies were investigated by multinuclear NMR and electrospray mass spectrometry. These studies confirmed the reversible nature of the pyridine-Pt(II)/Pd(II) coordination process.     

P588, A SECOND RETINAL-CONTAINING PIGMENT IN HALOBACTERIUM HALOBIUM

Abstract— Halobacterium mutant strains with defects in the biosynthesis of various pigments have been isolated. One of these strains, mutant ET-15, is incapable of producing the light-driven proton pump bacteriorhodopsin and the carotenoid bacterioruberin. However, ET-15 synthesizes another photochemically active, retinal-containing pigment, P₅₈₈, which mediates light-induced proton uptake enhanced by uncouplers. P₅₈₈ and bacteriorhodopsin are simultaneously present in wild-type cells grown under normal conditions; however, they can be distinguished by the following criteria.

• 1 They can be separated by independent mutational events.
• 2 Proton ionophores such as FCCP diminish bacteriorhodopsin-driven proton translocation but enhance P₅₈₈-mediated proton flows. We define here proton translocations which can be diminished by the addition of uncouplers (e.g. FCCP) as ‘active’, others which can be enhanced by FCCP as ‘passive’.
• 3 The kinetic and spectral properties of the photocycle intermediates of bacteriorhodopsin and P₅₈₈ are different.
• 4 The action spectrum for photocycling of P₅₈₈ is red-shifted with respect to that for bacteriorhodopsin.

A comparison of action spectra for proton translocations with that for photocycling links pigment P₅₈₈ and light-driven, passive proton uptake by ET-15 envelope vesicles. When chemically bleached P₅₈₈ was regenerated with all-trans-retinal, both photochemical activity and light-induced proton inflow were restored to equal extents. This identifies P₅₈₈ with the energizer for the passive proton flows.     

Crystal structure,dimensionality, and 4d electron distribution in K0.30MoO3 and Rb0.30MoO3

Single crystals of K_0.30MoO₃ and Rb_0.30MoO₃ were synthesized by electrolytic reduction of MoO₃/ A₂MoO₄ melts. The crystal structures were refined from X-ray diffraction data (3265 and 1280 independent reflections, respectively). The finalR andwR factors were 0.037 and 0.047 for the K bronze and 0.031 and 0.033 for the Rb bronze. The lattice parameters of the body-centered cells used in the present refinements were: K_0.30Mo0₃,a = 16.2311(7),b = 7.5502(4),c = 9.8614(4)A?,β = 94.895(4)^o; Rb_0.30MoO₃,a = 16.361(3),b = 7.555(1),c = 10.094(2)A?,β = 93.87(5)^o. The 4d electron distribution over the 20 Mo sites [4Mo(1), 8Mo(2), 8Mo(3)] of the unit cell are 10, 45, and 45% for K_0.30Mo0₃ and 14, 43, and 43% for Rb_0.30MoO₃, respectively. In both cases about 90% of the 4d electrons are situated on those sites which contribute to the electrical conductivity. The variations of the lattice parameters versus temperature are reported. The thermal linear-expansion coefficient is highly anisotropic. The structural dimensionality depends upon the sublattice under consideration. The K, Mo, and O sublattices are mono-, two-, and three-dimensional, respectively. The relationship between the structural dimensionality of K_0.30MoO₃ and the physical properties is discussed.