Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

All-atom force fields are important for predicting thermodynamic, structural, and dynamic properties of RNA. In this paper, results are reported for thermodynamic integration calculations of free energy differences of duplex formation when CG pairs in the RNA duplexes r(CCGG)(2), r(GGCC)(2), r(GCGC)(2), and r(CGCG)(2) are replaced by isocytidine-isoguanosine (iCiG) pairs. Agreement with experiment was improved when ε/ζ, α/γ, β, and χ torsional parameters in the AMBER99 force field were revised on the basis of quantum mechanical calculations. The revised force field, AMBER99TOR, brings free energy difference predictions to within 1.3, 1.4, 2.3, and 2.6 kcal/mol at 300 K, respectively, compared to experimental results for the thermodynamic cycles of CCGG → iCiCiGiG, GGCC → iGiGiCiC, GCGC → iGiCiGiC, and CGCG → iCiGiCiG. In contrast, unmodified AMBER99 predictions for GGCC → iGiGiCiC and GCGC → iGiCiGiC differ from experiment by 11.7 and 12.6 kcal/mol, respectively. In order to test the dynamic stability of the above duplexes with AMBER99TOR, four individual 50 ns molecular dynamics (MD) simulations in explicit solvent were run. All except r(CCGG)(2) retained A-form conformation for ≥82% of the time. This is consistent with NMR spectra of r(iGiGiCiC)(2), which reveal an A-form conformation. In MD simulations, r(CCGG)(2) retained A-form conformation 52% of the time, suggesting that its terminal base pairs may fray. The results indicate that revised backbone parameters improve predictions of RNA properties and that comparisons to measured sequence dependent thermodynamics provide useful benchmarks for testing force fields and computational methods.     

Olive oil or lard?: Distinguishing plant oils from animal fats in the archeological record of the eastern Mediterranean using gas chromatography/combustion/isotope ratio mass spectrometry

Distinguishing animal fats from plant oils in archaeological residues is not straightforward. Characteristic plant sterols, such as β-sitosterol, are often missing in archaeological samples and specific biomarkers do not exist for most plant fats. Identification is usually based on a range of characteristics such as fatty acid ratios, all of which indicate that a plant oil may be present, none of which uniquely distinguish plant oils from other fats. Degradation and dissolution during burial alter fatty acid ratios and remove short-chain fatty acids, resulting in degraded plant oils with similar fatty acid profiles to other degraded fats. Compound-specific stable isotope analysis of δ(13)C(18:0) and δ(13)C(16:0), carried out by gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS), has provided a means of distinguishing fish oils, dairy fats, ruminant and non-ruminant adipose fats, but plant oils are rarely included in these analyses. For modern plant oils where C(18:1) is abundant, δ(13)C(18:1) and δ(13)C(16:0) are usually measured. These results cannot be compared with archaeological data or data from other modern reference fats where δ(13)C(18:0) and δ(13)C(16:0) are measured, as C(18:0) and C(18:1) are formed by different processes resulting in different isotopic values. Eight samples of six modern plant oils were saponified, releasing sufficient C(18:0) to measure the isotopic values, which were plotted against δ(13)C(16:0). The isotopic values for these oils, with one exception, formed a tight cluster between ruminant and non-ruminant animal fats. This result complicates the interpretation of mixed fatty residues in geographical areas where both animal fats and plant oils were in use.     

Double node neighborhoods and families of simply connected -manifolds with

We introduce a new technique that is used to show that the complex projective plane blown up at 6, 7, or 8 points has infinitely many distinct smooth structures. None of these smooth structures admits smoothly embedded spheres with self-intersection , i.e., they are minimal. In addition, none of these smooth structures admits an underlying symplectic structure. Shortly after the appearance of a preliminary version of this article, Park, Stipsicz, and Szabo used the techniques described herein to show that the complex projective plane blown up at 5 points has infinitely many distinct smooth structures. In the final section of this paper we give a construction of such a family of examples.

     

Strain-induced bond buckling and its role in insulating properties of Cr-doped V2O3

Structural transformations around both V and Cr atoms in (V1-xCrx)2O3 across its metal-insulator transition (MIT) at x approximately 0.01 are studied by extended x-ray absorption fine-structure technique. Our new results for Cr made possible by the use of a novel x-ray analyzer that we developed reveal the substitutional mechanism of Cr doping. We find that this system has a buckled structure with short Cr-V and long V-V bonds. This system of bonds is disordered around the average trigonal lattice ascertained by x-ray diffraction. Such local distortions can result in a long range strain field that sets in around dilute Cr atoms in microscopic regions. We suggest that such locally strained regions should be insulating even at small x. The possibility of local insulating regions within a metallic phase, first suggested by Rice and Brinkman in 1972, remains unaccounted for in modern MIT theories.     

Cryogenic NMR spectroscopy of endohedral hydrogen-fullerene complexes

We have observed 1H NMR spectra of hydrogen molecules trapped inside modified fullerene cages under cryogenic conditions. Experiments on static samples were performed at sample temperatures down to 4.3 K, while magic-angle-spinning (MAS) experiments were performed at temperatures down to 20 K at spinning frequencies of 15 kHz. Both types of NMR spectra show a large increase in the intramolecular 1H-1H dipolar coupling at temperatures below 50 K, revealing thermal selection of a small number of spatial rotational states. The static and MAS spectra were compared to estimate the degree of sample heating in high-speed cryogenic MAS-NMR experiments. The cryogenic MAS-NMR data show that the site resolution of magic-angle-spinning NMR may be combined with the high signal strength of cryogenic operation and that cryogenic phenomena may be studied with chemical site selectivity.     

NMR probing of the spin polarization of the ν=5/2 quantum Hall state

Resistively detected nuclear magnetic resonance is used to measure the Knight shift of the 75As nuclei and determine the electron spin polarization of the fractional quantum Hall states of the second Landau level. We show that the 5/2 state is fully polarized within experimental error, thus confirming a fundamental assumption of the Moore-Read theory. We measure the electron heating under radio frequency excitation and show that we are able to detect NMR at electron temperatures down to 30 mK.     

Study on Flow Induced Nano Structures in iPP with Different Molecular Weight and Resulting Strength Behavior

Polypropylene samples in a wide molecular weight range between approx. 100 kg/mol to 1 600 kg/mol were processed by injection molding to thin walled micro specimens with respect to study shear induced crystallization phenomena under high shear rate and subsequently possible self reinforcement effects. The specimens nano structures were investigated and related deformation behavior under tensile studied. Novel morphologies have been detect and their micromechanical mechanism interpret and summarized.     

Superconducting transition temperatures of the system V1−xTixHy

T_c measurements for V_1?xTi_xH_y show that a decrease in T_c always occurs upon hydrogenation, but with slopes ($\text{?T}{}_{\mathrm{c}}\text{?y}\text{)}{}_{\mathrm{x}}$ that change with x. A phenomenological model is suggested, associating the T_c decrease in most of the range of x to changes in nominal number of conducting electrons and in the volume induced by the hydrogenation. The model roughly accounts for the variations in T_c in the V-rich alloys. It fails to explain the T_c variation at the Ti end.     

The solution and transport of water vapor in poly(acrylonitrile): a re-examination

Solubility (sorption) and transport measurements of water vapor in poly(acrylonitrile) reported by Stannett, Haider, Koros, and Hopfenberg have been re-interpreted in terms of an extension of the “dual-sorption” model for glassy polymers. The extension of the model assumes solubility and diffusion coefficients that are dependent on concentration, and partial immobilization of some of the penetrant species dissolved in the polymer. Satisfactory agreement has been obtained between theory and the experimental data.