Simulating Supersonic Turbulence in Magnetized Molecular Clouds

We present results of large-scale three-dimensional simulations of weakly magnetized supersonic turbulence at grid resolutions up to 1024^3 cells. Our numerical experiments are carried out with the Piecewise Parabolic Method on a Local Stencil and assume an isothermal equation of state. The turbulence is driven by a large-scale isotropic solenoidal force in a periodic computational domain and fully develops in a few flow crossing times. We then evolve the flow for a number of flow crossing times and analyze various statistical properties of the saturated turbulent state. We show that the energy transfer rate in the inertial range of scales is surprisingly close to a constant, indicating that Kolmogorov's phenomenology for incompressible turbulence can be extended to magnetized supersonic flows. We also discuss numerical dissipation effects and convergence of different turbulence diagnostics as grid resolution refines from 256^3 to 1024^3 cells.Comment: 10 pages, 3 figures, to appear in the proceedings of the DOE/SciDAC 2009 conferenc

Balanced carving turns in alpine skiing

In this paper, we analyse the model of pure carving turns in alpine skiing and snowboarding based on the usual assumption of approximate balance between forces and torques acting on the skier during the turn. The approximation of torque balance yields both lower and upper limits on the skier speed, which depend only on the sidecut radius of skis and the slope gradient. We use the model to simulate carving runs on slopes of constant gradient and find that pure carving is possible only on slopes of relatively small gradient, with the critical slope angle in the range of 8∘−20∘. The exact value depends mostly on the coefficient of snow friction and to a lesser degree on the sidecut radius of skis. Comparison with the practice of ski racing shows that the upper speed limit and the related upper limit on the slope gradient set by the model are too restrictive and so must be the assumption of torque balance used in the model. A more advanced theory is needed

Non-thermal radio emission from O-type stars. IV. Cyg OB2 No. 8A

We study the non-thermal radio emission of the binary Cyg OB2 No. 8A, to see if it is variable and if that variability is locked to the orbital phase. We investigate if the synchrotron emission generated in the colliding-wind region of this binary can explain the observations and we verify that our proposed model is compatible with the X-ray data. We use both new and archive radio data from the Very Large Array (VLA) to construct a light curve as a function of orbital phase. We also present new X-ray data that allow us to improve the X-ray light curve. We develop a numerical model for the colliding-wind region and the synchrotron emission it generates. The model also includes free-free absorption and emission due to the stellar winds of both stars. In this way we construct artificial radio light curves and compare them with the observed one. The observed radio fluxes show phase-locked variability. Our model can explain this variability because the synchrotron emitting region is not completely hidden by the free-free absorption. In order to obtain a better agreement for the phases of minimum and maximum flux we need to use stellar wind parameters for the binary components which are somewhat different from typical values for single stars. We verify that the change in stellar parameters does not influence the interpretation of the X-ray light curve. Our model has trouble explaining the observed radio spectral index. This could indicate the presence of clumping or porosity in the stellar wind, which - through its influence on both the Razin effect and the free-free absorption - can considerably influence the spectral index. Non-thermal radio emitters could therefore open a valuable pathway to investigate the difficult issue of clumping in stellar winds.Comment: 19 pages, 10 figures, accepted by A&

Exercise Training Prevents the Perivascular Adipose Tissue-induced Aortic Dysfunction with Metabolic Syndrome

The aim of the study was to determine the effects of exercise training on improving the thoracic perivascularadipose tissue (tPVAT) phenotype (inflammation, oxidative stress, and proteasome function) in metabolic syn-drome and its subsequent actions on aortic function.Methods:Lean and obese (model of metabolic syndrome) Zucker rats (n=8/group) underwent 8-weeks ofcontrol conditions or treadmill exercise (70% of max speed, 1 h/day, 5 days/week). At the end of the inter-vention, the tPVAT was removed and conditioned media was made. The cleaned aorta was attached to a forcetransducer to assess endothelium-dependent and independent dilation in the presence or absence of tPVAT-conditioned media. tPVAT gene expression, inflammatory /oxidative phenotype, and proteasome function wereassessed.Results:The mainfindings were that Ex induced: (1) a beige-like, anti-inflammatory tPVAT phenotype; (2) agreater abundance of•NO in tPVAT; (3) a reduction in tPVAT oxidant production; and (4) an improved tPVATproteasome function. Regarding aortic function, endothelium-dependent dilation was greater in exercised leanand obese groups vs. controls (p \u3c 0.05). Lean control tPVAT improved aortic relaxation, whereas obese controltPVAT decreased aortic relaxation. In contrast, the obese Ex-tPVAT increased aortic dilation, whereas the leanEx-tPVAT did not affect aortic dilation.Conclusion:Overall, exercise had the most dramatic impact on the obese tPVAT reflecting a change towards anenvironment with less oxidant load, less inflammation and improved proteasome function. Such beneficialchanges to the tPVAT micro-environment with exercise likely played a significant role in mediating the im-provement in aortic function in metabolic syndrome following 8 weeks of exercise

Asymmetry of 13C labeled 3-pyruvate affords improved site specific labeling of RNA for NMR spectroscopy

Selective isotopic labeling provides an unparalleled window within which to study the structure and dynamics of RNAs by high resolution NMR spectroscopy. Unlike commonly used carbon sources, the asymmetry of 13C-labeled pyruvate provides selective labeling in both the ribose and base moieties of nucleotides using E. coli variants, that until now were not feasible. Here we show that an E. coli mutant strain that lacks succinate and malate dehydrogenases (DL323) and grown on [3-13C]-pyruvate affords ribonucleotides with site specific labeling at C5′ (~95%) and C1′ (~42%) and minimal enrichment elsewhere in the ribose ring. Enrichment is also achieved at purine C2 and C8 (~95%) and pyrimidine C5 (~100%) positions with minimal labeling at pyrimidine C6 and purine C5 positions. These labeling patterns contrast with those obtained with DL323 E. coli grown on [1, 3-13C]-glycerol for which the ribose ring is labeled in all but the C4′ carbon position, leading to multiplet splitting of the C1′, C2′ and C3′ carbon atoms. The usefulness of these labeling patterns is demonstrated with a 27-nt RNA fragment derived from the 30S ribosomal subunit. Removal of the strong magnetic coupling within the ribose and base leads to increased sensitivity, substantial simplification of NMR spectra, and more precise and accurate dynamic parameters derived from NMR relaxation measurements. Thus these new labels offer valuable probes for characterizing the structure and dynamics of RNA that were previously limited by the constraint of uniformly labeled nucleotides

Algorithmic comparisons of decaying, isothermal, supersonic turbulence

Contradicting results have been reported in the literature with respect to the performance of the numerical techniques employed for the study of supersonic turbulence. We aim at characterising the performance of different particle-based and grid-based techniques on the modelling of decaying supersonic turbulence. Four different grid codes (ENZO, FLASH, TVD, ZEUS) and three different SPH codes (GADGET, PHANTOM, VINE) are compared. We additionally analysed two calculations denoted as PHANTOM A and PHANTOM B using two different implementations of artificial viscosity. Our analysis indicates that grid codes tend to be less dissipative than SPH codes, though details of the techniques used can make large differences in both cases. For example, the Morris & Monaghan viscosity implementation for SPH results in less dissipation (PHANTOM B and VINE versus GADGET and PHANTOM A). For grid codes, using a smaller diffusion parameter leads to less dissipation, but results in a larger bottleneck effect (our ENZO versus FLASH runs). As a general result, we find that by using a similar number of resolution elements N for each spatial direction means that all codes (both grid-based and particle-based) show encouraging similarity of all statistical quantities for isotropic supersonic turbulence on spatial scales k<N/32 (all scales resolved by more than 32 grid cells), while scales smaller than that are significantly affected by the specific implementation of the algorithm for solving the equations of hydrodynamics. At comparable numerical resolution, the SPH runs were on average about ten times more computationally intensive than the grid runs, although with variations of up to a factor of ten between the different SPH runs and between the different grid runs. (abridged)Comment: accepted by A&A, 22 pages, 14 figure

Selective 13C labeling of nucleotides for large RNA NMR spectroscopy using an E. coli strain disabled in the TCA cycle

Escherichia coli (E. coli) is an ideal organism to tailor-make labeled nucleotides for biophysical studies of RNA. Recently, we showed that adding labeled formate enhanced the isotopic enrichment at protonated carbon sites in nucleotides. In this paper, we show that growth of a mutant E. coli strain DL323 (lacking succinate and malate dehydrogenases) on 13C-2-glycerol and 13C-1,3-glycerol enables selective labeling at many useful sites for RNA NMR spectroscopy. For DL323 E. coli grown in 13C-2-glycerol without labeled formate, all the ribose carbon atoms are labeled except the C3′ and C5′ carbon positions. Consequently the C1′, C2′ and C4′ positions remain singlet. In addition, only the pyrimidine base C6 atoms are substantially labeled to ~96% whereas the C2 and C8 atoms of purine are labeled to ~5%. Supplementing the growth media with 13C-formate increases the labeling at C8 to ~88%, but not C2. Not unexpectedly, addition of exogenous formate is unnecessary for attaining the high enrichment levels of ~88% for the C2 and C8 purine positions in a 13C-1,3-glycerol based growth. Furthermore, the ribose ring is labeled in all but the C4′ carbon position, such that the C2′ and C3′ positions suffer from multiplet splitting but the C5′ position remains singlet and the C1′ position shows a small amount of residual C1′–C2′ coupling. As expected, all the protonated base atoms, except C6, are labeled to ~90%. In addition, labeling with 13C-1,3-glycerol affords an isolated methylene ribose with high enrichment at the C5′ position (~90%) that makes it particularly attractive for NMR applications involving CH2-TROSY modules without the need for decoupling the C4′ carbon. To simulate the tumbling of large RNA molecules, perdeuterated glycerol was added to a mixture of the four nucleotides, and the methylene TROSY experiment recorded at various temperatures. Even under conditions of slow tumbling, all the expected carbon correlations were observed, which indicates this approach of using nucleotides obtained from DL323 E. coli will be applicable to high molecular weight RNA systems

Peptide Conformer Acidity Analysis of Protein Flexibility Monitored by Hydrogen Exchange†

ABSTRACT: The amide hydrogens that are exposed to solvent in the high-resolution X-ray structures of ubiquitin, FK506-binding protein, chymotrypsin inhibitor 2, and rubredoxin span a billion-fold range in hydroxide-catalyzed exchange rates which are predictable by continuum dielectric methods. To facilitate analysis of transiently accessible amides, the hydroxide-catalyzed rate constants for every backbone amide of ubiquitin were determined under near physiological conditions. With the previously reported NMR-restrained molecular dynamics ensembles of ubiquitin (PDB codes 2NR2 and 2K39) used as representations of the Boltzmann-weighted conformational distribution, nearly all of the exchange rates for the highly exposed amides were more accurately predicted than by use of the high-resolution X-ray structure. More strikingly, predictions for the amide hydrogens of the NMR relaxation-restrained ensemble that become exposed to solvent in more than one but less than half of the 144 protein conformations in this ensemble were almost as accurate. In marked contrast, the exchange rates for many of the analogous amides in the residual dipolar coupling-restrained ubiquitin ensemble are substantially overestimated, as was particularly evident for the Ile 44 to Lys 48 segment which constitutes the primary interaction site for the proteasome targeting enzymes involved in polyubiquitylation. For both ensembles, “excited state ” conformers in this active site region having markedly elevated peptide acidities are represented at a population level that is 102 to 103 abov

Fractional deuteration applied to biomolecular solid-state NMR spectroscopy

Solid-state Nuclear Magnetic Resonance can provide detailed insight into structural and dynamical aspects of complex biomolecules. With increasing molecular size, advanced approaches for spectral simplification and the detection of medium to long-range contacts become of critical relevance. We have analyzed the protonation pattern of a membrane-embedded ion channel that was obtained from bacterial expression using protonated precursors and D2O medium. We find an overall reduction of 50% in protein protonation. High levels of deuteration at Hα and Hβ positions reduce spectral congestion in (1H,13C,15N) correlation experiments and generate a transfer profile in longitudinal mixing schemes that can be tuned to specific resonance frequencies. At the same time, residual protons are predominantly found at amino-acid side-chain positions enhancing the prospects for obtaining side-chain resonance assignments and for detecting medium to long-range contacts. Fractional deuteration thus provides a powerful means to aid the structural analysis of complex biomolecules by solid-state NMR

Accessing ns–μs side chain dynamics in ubiquitin with methyl RDCs

This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098–6107, 2001; Lakomek in J Biomol NMR 34:101–115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-τc dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time τc. In fact, the average amplitude of motion expressed in terms of order parameters S2 associated with the supra-τc window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959–8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471–1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains