Velocity Amplitudes in Global Convection Simulations: The Role of the Prandtl Number and Near-Surface Driving

Several lines of evidence suggest that the velocity amplitude in global simulations of solar convection, U, may be systematically over-estimated. Motivated by these recent results, we explore the factors that determine U and we consider how these might scale to solar parameter regimes. To this end, we decrease the thermal diffusivity $\kappa$ along two paths in parameter space. If the kinematic viscosity $\nu$ is decreased proportionally with $\kappa$ (fixing the Prandtl number $P_r = \nu/\kappa$), we find that U increases but asymptotes toward a constant value, as found by Featherstone & Hindman (2016). However, if $\nu$ is held fixed while decreasing $\kappa$ (increasing $P_r$), we find that U systematically decreases. We attribute this to an enhancement of the thermal content of downflow plumes, which allows them to carry the solar luminosity with slower flow speeds. We contrast this with the case of Rayleigh-Benard convection which is not subject to this luminosity constraint. This dramatic difference in behavior for the two paths in parameter space (fixed $P_r$ or fixed $\nu$) persists whether the heat transport by unresolved, near-surface convection is modeled as a thermal conduction or as a fixed flux. The results suggest that if solar convection can operate in a high-$P_r$ regime, then this might effectively limit the velocity amplitude. Small-scale magnetism is a possible source of enhanced viscosity that may serve to achieve this high-$P_r$ regime.Comment: 34 Pages, 8 Figures, submitted to a special issue of "Advances in Space Research" on "Solar Dynamo Frontiers

DNA Topology and the Initiation of Virus DNA Packaging

<div><p>During progeny assembly, viruses selectively package virion genomes from a nucleic acid pool that includes host nucleic acids. For large dsDNA viruses, including tailed bacteriophages and herpesviruses, immature viral DNA is recognized and translocated into a preformed icosahedral shell, the prohead. Recognition involves specific interactions between the viral packaging enzyme, terminase, and viral DNA recognition sites. Generally, viral DNA is recognized by terminase’s small subunit (TerS). The large terminase subunit (TerL) contains translocation ATPase and endonuclease domains. In phage lambda, TerS binds a sequence repeated three times in <i>cosB</i>, the recognition site. TerS binding to <i>cosB</i> positions TerL to cut the concatemeric DNA at the adjacent nicking site, <i>cosN</i>. TerL introduces staggered nicks in <i>cosN</i>, generating twelve bp cohesive ends. Terminase separates the cohesive ends and remains bound to the <i>cosB</i>-containing end, in a nucleoprotein structure called Complex I. Complex I docks on the prohead’s portal vertex and translocation ensues. DNA topology plays a role in the TerS^λ-<i>cosB</i>^<i>λ</i> interaction. Here we show that a site, <i>I2</i>, located between <i>cosN</i> and <i>cosB</i>, is critically important for an early DNA packaging step. <i>I2</i> contains a complex static bend. <i>I2</i> mutations block DNA packaging. <i>I2</i> mutant DNA is cut by terminase at <i>cosN in vitro</i>, but <i>in vivo</i>, no <i>cos</i> cleavage is detected, nor is there evidence for Complex I. Models for what packaging step might be blocked by <i>I2</i> mutations are presented.</p></div

Early DNA packaging steps at which <i>I2</i> might act.

<p>Four steps at which an <i>I2</i> defect might interrupt DNA packaging are numbered. The step blocked for <i>Aam42</i> terminase is also indicated. Model 1a: Failure to separate the newly created cohesive ends, followed by dissociation of terminase, and re-ligation that reseals the nicks. Model 1b: Reannealing of the cohesive ends followed by religation. Model 2: <i>I2</i> mutations block formation of, or destabilize, Complex I. Note that accompanying Complex I formation, the R_end DNA end is released and subject to exonuclease digestion; this is indicated by R_end. Model 3: <i>I2</i> mutations interfere with proper threading of the DNA through the motor assembly so that the DNA is translocated into the cytoplasm and is subject to exonuclease digestion. DNA represents the nuclease-susceptible virion DNA. The <i>Aam42</i> defect is the absence of an intact prohead binding domain at the C-terminus of TerL, which prevents Complex I from docking on the portal and assembling an active motor [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154785#pone.0154785.ref035" target="_blank">35</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154785#pone.0154785.ref049" target="_blank">49</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154785#pone.0154785.ref050" target="_blank">50</a>].</p

Bacteria, Phages, and Plasmids.

<p>Bacteria, Phages, and Plasmids.</p

Effect of <i>I2</i> mutations on <i>in vitro cos</i> cleavage.

<p><i>I2</i>-containing 2.9 kb pOER1-5 DNAs (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154785#pone.0154785.t002" target="_blank">Table 2</a>), linearized with AatII, were used as <i>cos</i>-cleavage substrates. After heating at 70°C for 10 min, to melt cohesive ends the 0.6 (L) and 2.3 (R) kb reaction products were run on agarose gels and stained with ethidium bromide. Band intensity was measured with a Typhoon phosphoimager. Reactions were done in the presence (left panel) and absence (right panel) of IHF (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154785#sec015" target="_blank">Materials and Methods</a>).</p