Small Structures via Thermal Instability of Partially Ionized Plasma. I. Condensation Mode

(Shortened) Thermal instability of partially ionized plasma is investigated by linear perturbation analysis. According to the previous studies under the one fluid approach, the thermal instability is suppressed due to the magnetic pressure. However, the previous studies did not precisely consider the effect of the ion-neutral friction, since they did not treat the flow as two fluid which is composed of ions and neutrals. Then, we revisit the effect of the ion-neutral friction of the two fluid to the growth of the thermal instability. According to our study, (1) The instability which is characterized by the mean molecular weight of neutrals is suppressed via the ion-neutral friction only when the magnetic field and the friction are sufficiently strong. The suppression owing to the friction occurs even along the field line. If the magnetic field and the friction are not so strong, the instability is not stabilized. (2) The effect of the friction and the magnetic field is mainly reduction of the growth rate of the thermal instability of weakly ionized plasma. (3) The effect of friction does not affect the critical wavelength lambdaF for the thermal instability. This yields that lambdaF of the weakly ionized plasma is not enlarged even when the magnetic field exists. We insist that the thermal instability of the weakly ionized plasma in the magnetic field can grow up even at the small length scale where the instability under the assumption of the one fluid plasma can not grow owing to the stabilization by the magnetic field. (4) The wavelength of the maximum growth rate of the instability shifts shortward according to the decrement of the growth rate, because the friction is effective at rather larger scale. Therefore, smaller structures are expected to appear than those without the ion-neutral friction.Comment: To appear in Ap

Transmembrane helix dynamics of bacterial chemoreceptors supports a piston model of signalling.

Transmembrane α-helices play a key role in many receptors, transmitting a signal from one side to the other of the lipid bilayer membrane. Bacterial chemoreceptors are one of the best studied such systems, with a wealth of biophysical and mutational data indicating a key role for the TM2 helix in signalling. In particular, aromatic (Trp and Tyr) and basic (Arg) residues help to lock α-helices into a membrane. Mutants in TM2 of E. coli Tar and related chemoreceptors involving these residues implicate changes in helix location and/or orientation in signalling. We have investigated the detailed structural basis of this via high throughput coarse-grained molecular dynamics (CG-MD) of Tar TM2 and its mutants in lipid bilayers. We focus on the position (shift) and orientation (tilt, rotation) of TM2 relative to the bilayer and how these are perturbed in mutants relative to the wildtype. The simulations reveal a clear correlation between small (ca. 1.5 Å) shift in position of TM2 along the bilayer normal and downstream changes in signalling activity. Weaker correlations are seen with helix tilt, and little/none between signalling and helix twist. This analysis of relatively subtle changes was only possible because the high throughput simulation method allowed us to run large (n = 100) ensembles for substantial numbers of different helix sequences, amounting to ca. 2000 simulations in total. Overall, this analysis supports a swinging-piston model of transmembrane signalling by Tar and related chemoreceptors

Conformational Preferences of a 14-Residue Fibrillogenic Peptide from Acetylcholinesterase†

A 14-residue fragment from near the C-terminus of the enzyme acetylcholinesterase (AChE) is believed to have a neurotoxic/neurotrophic effect acting via an unknown pathway. While the peptide is α-helical in the full-length enzyme, the structure and association mechanism of the fragment are unknown. Using multiple molecular dynamics simulations, starting from a tetrameric complex of the association domain of AChE and systematicall disassembled subsets that include the peptide fragment, we show that the fragment is incapable of retaining its helicity in solution. Extensive replica exchange Monte Carlo folding and unfolding simulations in implicit solvent with capped and uncappted termini failed to converge to any consistent cluster of structures, suggesting that the fragment remains largely unstructured in solution under the conditions considered. Furthermore, extended molecular dynamics simulations of two steric zipper models show that the peptide is likely to form a zipper with antiparallel sheets and that peptides with mutations known to prevent fibril formation likely do so by interfering with this packing. The results demonstrate how the local environment of a peptide can stabilize a particular conformation

Tracking magnetic bright point motions through the solar atmosphere

High-cadence, multiwavelength observations and simulations are employed for the analysis of solar photospheric magnetic bright points (MBPs) in the quiet Sun. The observations were obtained with the Rapid Oscillations in the Solar Atmosphere (ROSA) imager and the Interferometric Bidimensional Spectrometer at the Dunn Solar Telescope. Our analysis reveals that photospheric MBPs have an average transverse velocity of approximately 1 km s−1, whereas their chromospheric counterparts have a slightly higher average velocity of 1.4 km s−1. Additionally, chromospheric MBPs were found to be around 63 per cent larger than the equivalent photospheric MBPs. These velocity values were compared with the output of numerical simulations generated using the MURAM code. The simulated results were similar, but slightly elevated, when compared to the observed data. An average velocity of 1.3 km s−1 was found in the simulated G-band images and an average of 1.8 km s−1 seen in the velocity domain at a height of 500 km above the continuum formation layer. Delays in the change of velocities were also analysed. Average delays of ∼4 s between layers of the simulated data set were established and values of ∼29 s observed between G-band and Ca II K ROSA observations. The delays in the simulations are likely to be the result of oblique granular shock waves, whereas those found in the observations are possibly the result of a semi-rigid flux tube

Detection of H Alpha Emission in a Methane (T-Type) Brown Dwarf

We report the detection of H{$\alpha$} emission in the T dwarf (methane brown dwarf) 2MASSW J1237392+652615 over three days using the Keck Low Resolution Imaging Spectrograph. The measured line flux, log(L$_{H{\alpha}}$/L$_{bol}$) = $-$4.3, is roughly consistent with early M dwarf activity levels and inconsistent with decreasing activity trends in late M and L dwarfs. Similar emission is not seen in two other T dwarfs. We speculate on several mechanisms that may be responsible for emission, including a strong magnetic field, continuous flaring, acoustic heat generation, and a close ($a$ $\sim$ 4 - 20 R$_{Jup}$) interacting binary, with the cooler component overflowing its Roche lobe. We suggest that the M9.5Ve PC 0025+0447 could be a warm analogue to 2MASS J1237+65, and may be powered by the latter mechanism.Comment: 14 pages, 3 figures, accepted by A

Free energy barrier for melittin reorientation from a membrane-bound state to a transmembrane state

An important step in a phospholipid membrane pore formation by melittin antimicrobial peptide is a reorientation of the peptide from a surface into a transmembrane conformation. In this work we perform umbrella sampling simulations to calculate the potential of mean force (PMF) for the reorientation of melittin from a surface-bound state to a transmembrane state and provide a molecular level insight into understanding peptide and lipid properties that influence the existence of the free energy barrier. The PMFs were calculated for a peptide to lipid (P/L) ratio of 1/128 and 4/128. We observe that the free energy barrier is reduced when the P/L ratio increased. In addition, we study the cooperative effect; specifically we investigate if the barrier is smaller for a second melittin reorientation, given that another neighboring melittin was already in the transmembrane state. We observe that indeed the barrier of the PMF curve is reduced in this case, thus confirming the presence of a cooperative effect

O VI Observations of the Onset of Convection Zones in Main-Sequence A Stars

If magnetic activity in outer stellar atmospheres is due to an interplay between rotation and subsurface convection, as is generally presumed, then one would not expect to observe indicators of activity in stars with T_eff > 8300 K. Any X-ray or ultraviolet line emission from hotter stars must be due either to a different mechanism or to an unresolved, active, binary companion. Due to their poor spatial resolution, X-ray instruments have been especially susceptible to source confusion. At wavelengths longward of 1216 Angstroms, the near ultraviolet spectra of stars hotter than this putative dividing line are dominated by photospheric continuum. We have used FUSE to obtain spectra of the subcoronal O VI emission lines, which lie at a wavelength where the photospheric continuum of the mid- and early-A stars is relatively weak. We observed 14 stars spanning a range in T_eff from 7720 to 10,000 K. Eleven of the 14 stars showed O VI emission lines, including 6 of the 8 targets with T_eff > 8300 K. At face value, this suggests that activity does not fall off with increasing temperature. However, the emission lines are narrower than expected from the projected rotational velocities of these rapidly-rotating stars, suggesting that the emission could come from unresolved late-type companions. Furthermore, the strength of the O VI emission is consistent with that expected from an unseen active K or M dwarf binary companinon, and the high x-ray to far uv luminosity ratios observed indicate that this must be the case. Our results are therefore consistent with earlier studies that have shown a rapid drop-off in activity at the radiative/convective boundary expected at T_eff about 8300 K, in agreement with conventional stellar structure models