The colorful Helly theorem and colorful resolutions of ideals

We demonstrate that the topological Helly theorem and the algebraic Auslander-Buchsbaum theorem may be viewed as different versions of the same phenomenon. Using this correspondence we show how the colorful Helly theorem of I. Barany and its generalizations by G. Kalai and R. Meshulam translate to the algebraic side. Our main results are algebraic generalizations of these translations, which in particular give a syzygetic version of Helly’s theorem.     

Model Simulations of the Hengill Area,Southwestern Iceland

The Hengill Area is an important energy source for Reykjavík and surrounding area, both for electricity and district space heating. Two production fields are located in the area: Nesjavellir and Hellisheiei. Two other potential production fields are believed to be in the area. We present a new conceptual model supported by numerical calculations for the entire Hengill Area. Calculations were performed using the TOUGH2{{\tt TOUGH2}} software suite. The model contains nine layers consisting of 966 elements each (total of 8,964). Geological survey data, down-hole measurements, and production histories from the fields have been used to calibrate the model. The model has been used to predict how production will affect the geothermal fields. Information gathered throughout the production history, such as drawdown and changes in enthalpy, have been used to re-evaluate the size and the production capacity of the production fields. Different production scenarios, such as different energy throughput, have been simulated. The model simulations have also been used to estimate the capacity of potential future production fields.     

MeCAT—new iodoacetamide reagents for metal labeling of proteins and peptides

Besides protein identification via mass spectrometric methods, protein and peptide quantification has become more and more important in order to tackle biological questions. Methods like differential gel electrophoresis or enzyme-linked immunosorbent assays have been used to assess protein concentrations, while stable isotope labeling methods are also well established in quantitative proteomics. Recently, we developed metal-coded affinity tagging (MeCAT) as an alternative for accurate and sensitive quantification of peptides and proteins. In addition to absolute quantification via inductively coupled plasma mass spectrometry, MeCAT also enables sequence analysis via electrospray ionization tandem mass spectrometry. In the current study, we developed a new labeling approach utilizing an iodoacetamide MeCAT reagent (MeCAT-IA). The MeCAT-IA approach shows distinct advantages over the previously used MeCAT with maleinimide reactivity such as higher labeling efficiency and the lack of diastereomer formation during labeling. Here, we present a careful characterization of this new method focusing on the labeling process, which yields complete tagging with an excess of reagent of 1.6 to 1, less complex chromatographic behavior, and fragmentation characteristics of the tagged peptides using the iodoacetamide MeCAT reagent.     

Rotamer libraries of spin labelled cysteines for protein studies

Studies of structure and dynamics of proteins using site-directed spin labelling rely on explicit modelling of spin label conformations. The large computational effort associated with such modelling with molecular dynamics (MD) simulations can be avoided by a rotamer library approach based on a coarse-grained representation of the conformational space of the spin label. We show here that libraries of about 200 rotamers, obtained by iterative projection of a long MD trajectory of the free spin label onto a set of canonical dihedral angles, provide a representation of the underlying trajectory adequate for EPR distance measurements. Rotamer analysis was performed on selected X-ray structures of spin labelled T4 lysozyme mutants to characterize the spin label rotamer ensemble on a single protein site. Furthermore, predictions based on the rotamer library approach are shown to be in nearly quantitative agreement with electron paramagnetic resonance (EPR) distance data on the Na(+)/H(+) antiporter NhaA and on the light-harvesting complex LHCII whose structures are known from independent cryo electron microscopy and X-ray studies, respectively. Suggestions for the selection of labelling sites in proteins are given, limitations of the approach discussed, and requirements for further development are outlined.     

The classical Wigner method with an effective quantum force: application to the collinear H + H2 reaction

To improve the classical Wigner (CW) model, we recently proposed the classical Wigner model with an effective quantum force (CWEQF). The results of the CWEQF model are more accurate than those of the CW model. Still the simplicity of the CW model is retained. The quantum force was obtained by defining a characteristic distance η(0) between two Feynman paths that enter the expression for the flux-flux correlation function. η(0) was considered independent of the position along the reaction path. The CWEQF leads to a lowering of the effective potential barrier. Here we develop the method to use position dependent η(0) values. The method is also generalized to two dimensions. Applications are carried out on one-dimensional model problems and the two-dimensional H + H(2) collinear reaction.     

Adsorption of trimethyl phosphate on maghemite, hematite, and goethite nanoparticles

Adsorption of trimethyl phosphate (TMP) on well-characterized hematite, maghemite and goethite nanoparticles was studied by in situ DRIFT spectroscopy as a model system for adsorption of organophosphorous (OP) compounds on iron minerals. The iron minerals were characterized by X-ray diffraction (XRD), Raman spectroscopy, transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), specific surface area, and pore size distribution. The minerals were found to consist of stoichimetrically and morphologically well-defined maghemite, hematite, and goethite nanoparticles. Analysis of in situ diffuse reflectance Fourier transform (DRIFT) spectroscopy shows that TMP bonds mainly to Lewis acid Fe sites through the O phosphoryl atom (-P═O-Fe) on hematite and maghemite. On goethite most TMP molecules bond to Br?nstedt acid surface OH groups and form hydrogen bonded surface complexes. The vibrational mode analysis and uptake kinetics suggest two main reasons for the observed trend of reactivity toward TMP (hematite > maghemite > goethite): (i) larger number of accessible Lewis acid adsorption sites on hematite; (ii) stronger interaction between the Lewis acid Fe sites and the phosphoryl O atom on TMP for hematite and maghemite compared to goethite with concomitant formation of surface coordinated TMP and dimethyl phosphate intermediates. As a result, on the oxides a surface oxidation pathway dominates during the initial adsorption, which results in the formation of surface methoxy and formate. In contrast, on goethite a slower hydrolysis pathway is identified, which eventually yields phosphoric acid. The observed trends of the reactivity and analysis of the corresponding surface structure and particle morphology suggest an intimate relation between the surface chemistry of exposed crystal facets on the iron minerals. These results are important to understand OP surface chemistry on iron minerals.     

Haloperoxidase activity of oxovanadium(V) thiobisphenolates

By employing the 2,2'-thiobis(2,4-di-tert-butylphenolate) ligand ((S)L(2-)) a novel oxovanadium(V) complex, (PPh(4))(2)[(S)LV(O)(μ(2)-O)(2)V(O)(S)L] (1), was synthesised that exhibits haloperoxidase activity: on addition of H(2)O(2) a sequence of successive peroxide formation and intramolecular thioether oxidation events (sulfoxide and sulfone) led to a mixture of five products, which were all identified unambiguously, partly through an independent synthesis and characterisation. It was shown that internal thioether oxidation proceeds through peroxide formation, but the sulfoxidation of external thioether functions requires further activation of the peroxide function by protons or alkyl cations. Consistently, the employment of tBuOOH instead of H(2)O(2) led to a very active system for the catalytic sulfoxidation of thioethers.     

K‐edge XANES analysis of sulfur compounds: an investigation of the relative intensities using internal calibration

Sulfur K‐edge XANES (X‐ray absorption near‐edge structure) spectroscopy is an excellent tool for determining the speciation of sulfur compounds in complex matrices. This paper presents a method to quantitatively determine the kinds of sulfur species in natural samples using internally calibrated reference spectra of model compounds. Owing to significant self‐absorption of formed fluorescence radiation in the sample itself the fluorescence signal displays a non‐linear correlation with the sulfur content over a wide concentration range. Self‐absorption is also a problem at low total absorption of the sample when the sulfur compounds are present as particles. The post‐edge intensity patterns of the sulfur K‐edge XANES spectra vary with the type of sulfur compound, with reducing sulfur compounds often having a higher post‐edge intensity than the oxidized forms. In dilute solutions (less than 0.3–0.5%) it is possible to use sulfur K‐edge XANES reference data for quantitative analysis of the contribution from different species. The results show that it is essential to use an internal calibration system when performing quantitative XANES analysis. Preparation of unknown samples must take both the total absorption and possible presence of self‐absorbing particles into consideration.     

Two-Dimensional Distance Correlation Maps from Pulsed Triple Electron Resonance (TRIER) on Proteins with Three Paramagnetic Centers

Recently, we introduced the pulsed triple electron resonance (TRIER) experiment, which correlates dipolar frequencies of molecules with three electron spins. These correlation patterns contain valuable information: in combination with double electron–electron resonance (DEER) they allow to interpret distance distributions of biological systems that exist in more than one conformation. Together with an improved sequence and new data processing, we were now for the first time able to obtain two-dimensional distance correlation maps of the previously investigated model compounds as well as of spin-labeled proteins. For this we applied two-dimensional approximate Pake transformation to TRIER data. This enabled us to get distance correlation plots from two triple-labeled protein samples that were in good agreement with DEER data and simulations. With such information it should then be possible to assign peaks in DEER distance distributions for macromolecules that can exist in more than one conformation.     

Survival of Dipolar Splittings between Equivalent Nuclei in High-Speed MAS-NMR—Interpretation of the 31P Coupling Patterns for Tetraphosphorus Decaoxide

Unexpected splittings in solid-state MAS-NMR spectra can indicate high rather than low local symmetry. A quantitative analysis of the resulting lineshapes provides information about geometry from a different range of space and time averaging than that of X-ray crystallography, as is demonstrated here for tetraphosphorus decaoxide (spectra on the right).