Dissociative recombination of H+(H2O)3 and D+(D2O)3 water cluster ions with electrons: cross sections and branching ratios

Dissociative recombination (DR) of the water cluster ions H(+)(H(2)O)(3) and D(+)(D(2)O)(3) with electrons has been studied at the heavy-ion storage ring CRYRING (Manne Siegbahn Laboratory, Stockholm University). For the first time, absolute DR cross sections have been measured for H(+)(H(2)O)(3) in the energy range of 0.001-0.8 eV, and relative cross sections have been measured for D(+)(D(2)O)(3) in the energy range of 0.001-1.0 eV. The DR cross sections for H(+)(H(2)O)(3) are larger than previously observed for H(+)(H(2)O)(n) (n=1,2), which is in agreement with the previously observed trend indicating that the DR rate coefficient increases with size of the water cluster ion. Branching ratios have been determined for the dominating product channels. Dissociative recombination of H(+)(H(2)O)(3) mainly results in the formation of 3H(2)O+H (probability of 0.95+/-0.05) and with a possible minor channel resulting in 2H(2)O+OH+H(2) (0.05+/-0.05). The dominating channels for DR of D(+)(D(2)O)(3) are 3D(2)O+D (0.88+/-0.03) and 2D(2)O+OD+D(2) (0.09+/-0.02). The branching ratios are comparable to earlier DR results for H(+)(H(2)O)(2) and D(+)(D(2)O)(2), which gave 2X(2)O+X (X=H,D) with a probability of over 0.9.     

Embedding nearly-spanning bounded degree trees

We derive a sufficient condition for a sparse graph G on n vertices to contain a copy of a tree T of maximum degree at most d on (1 − ε)n vertices, in terms of the expansion properties of G. As a result we show that for fixed d ≥ 2 and 0 < ε < 1, there exists a constant c = c(d, ε) such that a random graph G(n, c/n) contains almost surely a copy of every tree T on (1 − ε)n vertices with maximum degree at most d. We also prove that if an (n, D, λ)-graph G (i.e., a D-regular graph on n vertices all of whose eigenvalues, except the first one, are at most λ in their absolute values) has large enough spectral gap D/λ as a function of d and ε, then G has a copy of every tree T as above. Research supported in part by a USA-Israeli BSF grant, by NSF grant CCR-0324906, by a Wolfensohn fund and by the State of New Jersey. Research supported in part by USA-Israel BSF Grant 2002-133, and by grants 64/01 and 526/05 from the Israel Science Foundation. Research supported in part by NSF CAREER award DMS-0546523, NSF grant DMS-0355497, USA-Israeli BSF grant, and by an Alfred P. Sloan fellowship.     

Note making a <Emphasis Type="Italic">K</Emphasis><Subscript>4</Subscript>-free graph bipartite

We show that every K ₄-free graph G with n vertices can be made bipartite by deleting at most n ²/9 edges. Moreover, the only extremal graph which requires deletion of that many edges is a complete 3-partite graph with parts of size n/3. This proves an old conjecture of P. Erdős. Research supported in part by NSF CAREER award DMS-0546523, NSF grant DMS-0355497, USA-Israeli BSF grant, and by an Alfred P. Sloan fellowship.     

Binding of intercalating and groove-binding cyanine dyes to bacteriophage t5

The interaction between four related cyanine dyes and bacteriophage T5 is investigated with fluorescence and absorption spectroscopy. The dyes, which differ in size, charge, and mode of DNA-binding, penetrate the capsid and bind the DNA inside. The rate of association decreases progressively with increasing dye size, from a few minutes for YO to more than 50 h for YOYO (at 37 degrees C). The relative affinity for the phage DNA is a factor of about 0.2 lower than for the same T5-DNA when free in solution. Comparison of groove-bound BOXTO-PRO and intercalating YO-PRO shows that the reduced affinity is not due to DNA extension but perhaps influenced by competition with other cationic DNA-binding agents inside the capsid. Although, the extent of dye binding to the phages decreases with increasing external ionic strength, the affinity relative to free DNA increases, which indicates a comparatively weak screening of electrostatic interactions inside the phage. The rate of binding increases with increasing ionic strength, reflecting an increase in effective pore size of the capsid as electrostatic interactions are screened and/or a faster diffusion of the dye through the DNA matrix inside the capsid as the DNA affinity is reduced. A combination of electron microscopy, light scattering, and linear dichroism show that the phages are intact after YO-PRO binding, whereas a small degree of capsid rupture cannot be excluded with BOXTO-PRO.     

String kernels and high-quality data set for improved prediction of kinked helices in α-helical membrane proteins

The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. For the particular case of kink prediction, we generated a data set of 132 membrane proteins containing 1014 manually labeled helices and examined the environment of kinks. Our sequence analysis confirms the great relevance of proline and reveals disproportionately high occurrences of glycine and serine at kink positions. The structural analysis shows significantly different solvent accessible surface area mean values for kinked and nonkinked helices. More important, we used this data set to validate string kernels for support vector machines as a new kink prediction method. Applying the new predictor, about 80% of all helices could be correctly predicted as kinked or nonkinked even when focusing on small helical fragments. The results exceed recently reported accuracies of alternative approaches and are a consequence of both the method and the data set.     

Raman spectra of long chain hydrocarbons: anharmonic calculations, experiment and implications for imaging of biomembranes

First-principles anharmonic vibrational calculations are carried out for the Raman spectrum of the C-H stretching bands in dodecane, and for the C-D bands in the deuterated molecule. The calculations use the Vibrational Self-Consistent Field (VSCF) algorithm. The results are compared with liquid-state experiments, after smoothing the isolated-molecule sharp-line computed spectra. Very good agreement between the computed and experimental results is found for the two systems. The combined theoretical and experimental results provide insights into the spectrum, elucidating the roles of symmetric and asymmetric CH(3) and CH(2) hydrogenic stretches. This is expected to be very useful for the interpretation of spectra of long-chain hydrocarbons. The results show that anharmonic effects on the spectrum are large. On the other hand, vibrational degeneracy effects seem to be rather modest at the resolution of the experiments. The degeneracy effects may have more pronounced manifestations in higher-resolution experiments. The results show that first-principles anharmonic vibrational calculations for hydrocarbons are feasible, in good agreement with experiment, opening the way for applications to many similar systems. The results may be useful for the analysis of CARS imaging of lipids, for which dodecane is a representative molecule. It is suggested that first-principles vibrational calculations may be useful also for CARS imaging of other systems.     

Diamine-catalyzed conjugate addition to acrylate derivatives

Diamines were found to promote catalytic conjugate addition of α-cyano active methine nucleophiles to various acrylate derivatives.     

Derivatization-independent cholesterol analysis in crude lipid extracts by liquid chromatography/mass spectrometry: applications to a rabbit model for atherosclerosis

Direct measurement of various sterols in crude lipid extracts in a single experiment from limited biological samples is challenging. Current mass spectrometry (MS) based approaches usually require chemical derivatization before subjecting to MS analysis. Here, we present a derivatization-independent method for analyzing various sterols, including cholesterol and its congeners, using liquid chromatography and atmospheric pressure chemical ionization mass spectrometry. Based on the specific tandem mass spectrometry pattern of cholesterol, multiple reaction monitoring (MRM) transitions were used to quantify free cholesterol and its fatty acyl esters. Several cholesterol oxidation products could also be measured using the upfront liquid chromatography separation and specific MRM transitions. The method was validated alongside established enzymatic assays in measuring total cholesterol. As a proof of concept, we analyzed plasma sterols in rabbits administrated with a high cholesterol diet (HCD) which is a classical atherosclerotic model. Free cholesterol, cholesterol esters, 7-hydroxycholesterol, and 7-ketocholesterol were elevated in plasma of rabbits on HCD. This method could also serve as an excellent tool for quantitative analysis of other sterols such as ergosterol and sitosterol in other organisms beside mammalian. In Saccharomyces cerevisiae, our results indicated dramatic increases of the ratio of ergosterol esters to free ergosterol in both yeh2Δ and tgl1Δ cells, which are consistent with the function of the respective enzymes.     

Spin polarization of the neutral exciton in a single quantum dot

While efficient nuclear polarization has earlier been reported for the charged exciton in InAs/GaAs quantum dots at zero external magnetic field, we report here on a surprisingly high degree of circular polarization, up to ≈60%$\approx 60\%$, for the neutral exciton emission in individual InAs/GaAs dots. This high degree of polarization is explained in terms of the appearance of an effective nuclear magnetic field which stabilizes the electron spin. The nuclear polarization is manifested in experiments as a detectable Overhauser shift. In turn, the nuclei located inside the dot are exposed to an effective electron magnetic field, the Knight field. This nuclear polarization is understood as being due to the dynamical nuclear polarization by an electron localized in the QD. The high degree of polarization for the neutral exciton is also suggested to be due to separate in-time capture of electrons and holes into the QD.     

Elastic building blocks for confined sheets

We study the behavior of thin elastic sheets that are bent and strained under a weak, smooth confinement. We show that the emerging shapes exhibit the coexistence of two types of domains. A focused-stress patch is subject to a geometric, piecewise-inextensibility constraint, whereas a diffuse-stress region is characterized by a mechanical constraint-the dominance of a single component of the stress tensor. We discuss the implications of our findings for the analysis of elastic sheets under various types of forcing.