Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel

The crystal structure of the open conformation of a bacterial voltage-gated sodium channel pore from Magnetococcus sp. (NaVMs) has provided the basis for a molecular dynamics study defining the channel’s full ion translocation pathway and conductance process, selectivity, electrophysiological characteristics, and ion-binding sites. Microsecond molecular dynamics simulations permitted a complete time-course characterization of the protein in a membrane system, capturing the plethora of conductance events and revealing a complex mixture of single and multi-ion phenomena with decoupled rapid bidirectional water transport. The simulations suggest specific localization sites for the sodium ions, which correspond with experimentally determined electron density found in the selectivity filter of the crystal structure. These studies have also allowed us to identify the ion conductance mechanism and its relation to water movement for the NavMs channel pore and to make realistic predictions of its conductance properties. The calculated single-channel conductance and selectivity ratio correspond closely with the electrophysiology measurements of the NavMs channel expressed in HEK 293 cells. The ion translocation process seen in this voltage-gated sodium channel is clearly different from that exhibited by members of the closely related family of voltage-gated potassium channels and also differs considerably from existing proposals for the conductance process in sodium channels. These studies simulate sodium channel conductance based on an experimentally determined structure of a sodium channel pore that has a completely open transmembrane pathway and activation gate

Excitation of Oscillations in the Magnetic Network on the Sun

We examine the excitation of oscillations in the magnetic network of the Sun through the footpoint motion of photospheric magnetic flux tubes located in intergranular lanes. The motion is derived from a time series of high-resolution G band and continuum filtergrams using an object-tracking technique. We model the response of the flux tube to the footpoint motion in terms of the Klein-Gordon equation, which is solved analytically as an initial value problem for transverse (kink) waves. We compute the wave energy flux in upward propagating transverse waves. In general we find that the injection of energy into the chromosphere occurs in short-duration pulses, which would lead to a time variability in chromospheric emission that is incompatible with observations. Therefore, we consider the effects of turbulent convective flows on flux tubes in intergranular lanes. The turbulent flows are simulated by adding high-frequency motions (periods 5-50 s) with an amplitude of 1 km s^{-1}. The latter are simulated by adding random velocity fluctuations to the observationally determined velocities. In this case we find that the energy flux is much less intermittent and can in principle carry adequate energy for chromospheric heating.Comment: 11 pages, 5 figures, figure 1 is in color, all files gzippe

The energy of waves in the photosphere and lower chromosphere: 1. Velocity statistics

Acoustic waves are one of the primary suspects besides magnetic fields for the chromospheric heating process to temperatures above radiative equilibrium (RE). We derived the mechanical wave energy as seen in line-core velocities to obtain a measure of mechanical energy flux with height for a comparison with the energy requirements in a semi-empirical atmosphere model. We analyzed a 1-hour time series and a large-area map of Ca II H spectra on the traces of propagating waves. We analyzed the velocity statistics of several spectral lines in the wing of Ca II H, and the line-core velocity of Ca II H. We converted the velocity amplitudes into volume and mass energy densities. For comparison, we used the increase of internal energy necessary to lift a RE atmosphere to the HSRA temperature stratification. We find that the velocity amplitude grows in agreement with linear wave theory and thus slower with height than predicted from energy conservation. The mechanical energy of the waves above around z~500 km is insufficient to maintain the chromospheric temperature rise in the semi-empirical HSRA model. The intensity variations of the Ca line core (z~1000 km) can be traced back to the velocity variations of the lowermost forming spectral line considered (z~ 250 km). The chromospheric intensity, and hence, (radiation) temperature variations are seen to be induced by passing waves originating in the photosphere.Comment: 13 pages, 15 figures + 2 pages Appendix, 5 figures, submitted to A &

A New Version of Reimers' law of Mass Loss Based on a Physical Approach

We present a new semi-empirical relation for the mass loss of cool stellar winds, which so far has frequently been described by "Reimers' law". Originally, this relation was based solely on dimensional scaling arguments without any physical interpretation. In our approach, the wind is assumed to result from the spill-over of the extended chromosphere, possibly associated with the action of waves, especially Alfven waves, which are used as guidance in the derivation of the new formula. We obtain a relation akin to the original Reimers law, but which includes two new factors. They reflect how the chromospheric height depends on gravity and how the mechanical energy flux depends, mainly, on effective temperature. The new relation is tested and sensitively calibrated by modelling the blue end of the Horizontal Branch of globular clusters. The most significant difference from mass loss rates predicted by the Reimers relation is an increase by up to a factor of 3 for luminous late-type (super-)giants, in good agreement with observations.Comment: 12 pages, 4 figures, accepted by ApJ Letter

The C. elegans Lifespan Machine

The measurement of lifespan pervades aging research. Because lifespan results from complex interactions between genetic, environmental and stochastic factors, it varies widely even among isogenic individuals. The action of molecular mechanisms on lifespan is therefore visible only through their statistical effects on populations. Survival assays in C. elegans provided critical insights into evolutionarily conserved determinants of aging. To enable the rapid acquisition of survival curves at arbitrary statistical resolution, we developed a scalable imaging and analysis platform to observe nematodes over multiple weeks across square meters of agar surface at 8 μm resolution. The method generates a permanent visual record of individual deaths from which survival curves are constructed and validated, producing data consistent with the manual method for several mutants in both standard and stressful environments. Our approach allows rapid, detailed reverse-genetic and chemical screens for effects on survival and enables quantitative investigations into the statistical structure of aging

Fundamental parameters, integrated RGB mass loss and dust production in the Galactic globular cluster 47 Tucanae

Fundamental parameters and time-evolution of mass loss are investigated for post-main-sequence stars in the Galactic globular cluster 47 Tucanae (NGC 104). This is accomplished by fitting spectral energy distributions (SEDs) to existing optical and infrared photometry and spectroscopy, to produce a true Hertzsprung--Russell diagram. We confirm the cluster's distance as 4611 (+213, -200) pc and age as 12 +/- 1 Gyr. Horizontal branch models appear to confirm that no more RGB mass loss occurs in 47 Tuc than in the more-metal-poor omega Centauri, though difficulties arise due to inconsistencies between the models. Using our SEDs, we identify those stars which exhibit infrared excess, finding excess only among the brightest giants: dusty mass loss begins at a luminosity of ~ 1000 Lsun, becoming ubiquitous above 2000 Lsun. Recent claims of dust production around lower-luminosity giants cannot be reproduced, despite using the same archival Spitzer imagery.Comment: 22 pages, 17 figures, accepted ApJ

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

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

Lipid membranes for membrane proteins

Andreas Kukol, ‘Lipid membranes for membrane proteins in Molecular Modeling of Proteins (Clifton: Humana Press/Sringer, 2015), ISBN: 978-1-4939-1464-7, e-BOOK ISBN: 978-1-4939-1465-4Peer reviewe