Dynamics and Heating of the Magnetic Network on the Sun: Efficiency of mode transformation

We aim to identify the physical processes which occur in the magnetic network of the chromosphere and which contribute to its dynamics and heating. Specifically, we study the propagation of transverse (kink) MHD waves which are impulsively excited in flux tubes through footpoint motions. When these waves travel upwards, they get partially converted to longitudinal waves through nonlinear effects (mode coupling). By solving the nonlinear, time-dependent MHD equations we find that significant longitudinal wave generation occurs in the photosphere typically for Mach numbers as low as 0.2 and that the onset of shock formation occurs at heights of about 600 km above the photospheric base. We also investigate the compressional heating due to longitudinal waves and the efficiency of mode coupling for various values of the plasma $\beta$, that parameterises the magnetic field strength in the network. We find that this efficiency is maximum for field strengths corresponding to $\beta\approx 0.2$, when the kink and tube wave speeds are almost identical. This can have interesting observational implications. Furthermore, we find that even when the two speeds are different, once shock formation occurs, the longitudinal and transverse shocks exhibit strong mode coupling.Comment: 8 pages, 3 figure

Determining Peptide Partitioning Properties via Computer Simulation

The transfer of polypeptide segments into lipid bilayers to form transmembrane helices represents the crucial first step in cellular membrane protein folding and assembly. This process is driven by complex and poorly understood atomic interactions of peptides with the lipid bilayer environment. The lack of suitable experimental techniques that can resolve these processes both at atomic resolution and nanosecond timescales has spurred the development of computational techniques. In this review, we summarize the significant progress achieved in the last few years in elucidating the partitioning of peptides into lipid bilayer membranes using atomic detail molecular dynamics simulations. Indeed, partitioning simulations can now provide a wealth of structural and dynamic information. Furthermore, we show that peptide-induced bilayer distortions, insertion pathways, transfer free energies, and kinetic insertion barriers are now accurate enough to complement experiments. Further advances in simulation methods and force field parameter accuracy promise to turn molecular dynamics simulations into a powerful tool for investigating a wide range of membrane active peptide phenomena

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

Time-dependent hydrogen ionisation in the solar chromosphere. I: Methods and first results

An approximate method for solving the rate equations for the hydrogen populations was extended and implemented in the three-dimensional radiation (magneto-)hydrodynamics code CO5BOLD. The method is based on a model atom with six energy levels and fixed radiative rates. It has been tested extensively in one-dimensional simulations. The extended method has been used to create a three-dimensional model that extends from the upper convection zone to the chromosphere. The ionisation degree of hydrogen in our time-dependent simulation is comparable to the corresponding equilibrium value up to 500 km above optical depth unity. Above this height, the non-equilibrium ionisation degree is fairly constant over time and space, and tends to be at a value set by hot propagating shock waves. The hydrogen level populations and electron density are much more constant than the corresponding values for statistical equilibrium, too. In contrast, the equilibrium ionisation degree varies by more than 20 orders of magnitude between hot, shocked regions and cool, non-shocked regions. The simulation shows for the first time in 3D that the chromospheric hydrogen ionisation degree and electron density cannot be calculated in equilibrium. Our simulation can provide realistic values of those quantities for detailed radiative transfer computations.Comment: 8 pages, 7 figure

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

Chromospheric seismology above sunspot umbrae

The acoustic resonator is an important model for explaining the three-minute oscillations in the chromosphere above sunspot umbrae. The steep temperature gradients at the photosphere and transition region provide the cavity for the acoustic resonator, which allows waves to be both partially transmitted and partially reflected. In this paper, a new method of estimating the size and temperature profile of the chromospheric cavity above a sunspot umbra is developed. The magnetic field above umbrae is modelled numerically in 1.5D with slow magnetoacoustic wave trains travelling along magnetic fieldlines. Resonances are driven by applying the random noise of three different colours---white, pink and brown---as small velocity perturbations to the upper convection zone. Energy escapes the resonating cavity and generates wave trains moving into the corona. Line of sight (LOS) integration is also performed to determine the observable spectra through SDO/AIA. The numerical results show that the gradient of the coronal spectra is directly correlated with the chromosperic temperature configuration. As the chromospheric cavity size increases, the spectral gradient becomes shallower. When LOS integrations is performed, the resulting spectra demonstrate a broadband of excited frequencies that is correlated with the chromospheric cavity size. The broadband of excited frequencies becomes narrower as the chromospheric cavity size increases. These two results provide a potentially useful diagnostic for the chromospheric temperature profile by considering coronal velocity oscillations

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

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

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