SDO/HMI survey of emerging active regions for helioseismology

Observations from the Solar Dynamics Observatory (SDO) have the potential for allowing the helioseismic study of the formation of hundreds of active regions, which would enable us to perform statistical analyses. Our goal is to collate a uniform data set of emerging active regions observed by the SDO/HMI instrument suitable for helioseismic analysis up to seven days before emergence. We restricted the sample to active regions that were visible in the continuum and emerged into quiet Sun largely avoiding pre-existing magnetic regions. As a reference data set we paired a control region (CR), with the same latitude and distance from central meridian, with each emerging active region (EAR). We call this data set, which is currently comprised of 105 emerging active regions observed between May 2010 and November 2012, the SDO Helioseismic Emerging Active Region (SDO/HEAR) survey. To demonstrate the utility of a data set of a large number of emerging active regions, we measure the relative east-west velocity of the leading and trailing polarities from the line-of-sight magnetogram maps during the first day after emergence. The latitudinally averaged line-of-sight magnetic field of all the EARs shows that, on average, the leading (trailing) polarity moves in a prograde (retrograde) direction with a speed of 121 +/- 22 m/s (-70 +/- 13 m/s) relative to the Carrington rotation rate in the first day. However, relative to the differential rotation of the surface plasma, the east-west velocity is symmetric, with a mean of 95 +/- 13 m/s. The SDO/HEAR data set will not only be useful for helioseismic studies, but will also be useful to study other features such as the surface magnetic field evolution of a large sample of EARs.Comment: Accepted by Astronomy and Astrophysics, 11 figures, one longtable; update corrects units in Figure

Reconstruction of Solar Subsurfaces by Local Helioseismology

Local helioseismology has opened new frontiers in our quest for understanding of the internal dynamics and dynamo on the Sun. Local helioseismology reconstructs subsurface structures and flows by extracting coherent signals of acoustic waves traveling through the interior and carrying information about subsurface perturbations and flows, from stochastic oscillations observed on the surface. The initial analysis of the subsurface flow maps reconstructed from the 5 years of SDO/HMI data by time-distance helioseismology reveals the great potential for studying and understanding of the dynamics of the quiet Sun and active regions, and the evolution with the solar cycle. In particular, our results show that the emergence and evolution of active regions are accompanied by multi-scale flow patterns, and that the meridional flows display the North-South asymmetry closely correlating with the magnetic activity. The latitudinal variations of the meridional circulation speed, which are probably related to the large-scale converging flows, are mostly confined in shallow subsurface layers. Therefore, these variations do not necessarily affect the magnetic flux transport. The North-South asymmetry is also pronounced in the variations of the differential rotation ("torsional oscillations"). The calculations of a proxy of the subsurface kinetic helicity density show that the helicity does not vary during the solar cycle, and that supergranulation is a likely source of the near-surface helicity.Comment: 17 pages, 10 figures, in "Cartography of the Sun and the Stars", Editors: Rozelot, Jean-Pierre, Neiner, Corali

Measuring rainfall from above and below the sea surface

Satellites play a major role in the determination of the rainfall at sea. Researchers at Southampton Oceanography Centre (SOC) have been involved in two projects addressing this task. First they have been instrumental in developing techniques to retrieve rain rate information from the 10+ years of dual-frequency altimeter data. The TOPEX radar measures rainfall via the attenuation it causes, producing a climatology that is independent of those derived from passive microwave (PM) and infrared (IR) sensors. Because TOPEX is an active microwave sensor, it can have a much smaller footprint than PM sensors. Therefore it can be used to estimate the size of rain cells, showing that the ITCZ and mid-latitude storm tracks are characterized by larger rain systems than elsewhere. TOPEX’s simultaneous recording of wind and wave data reveal that, for mid-latitude systems, rain is most likely in association with developing seas.All satellite-based datasets require validation, and SOC's work on the development and testing of acoustic rain gauges is the second aspect of this paper. By listening at a range of frequencies, an underwater hydrophone may distinguish the spectra of wind, rain, shipping etc., and estimate the wind speed or rain rate according to the magnitude of the signals. All our campaigns have shown a good acoustic response to changes in wind speed. However the quantitative inversion for recent trials has given values that are too high, possibly because of significant acoustic reflection from the sea bottom. The changes in spectral slope often agree with other observations of rain, although validation experiments in coastal regions are hampered by the extraneous sources present. Acoustic rain gauges would eventually see service not only for routine satellite validation, but also for real-time monitoring of locations of interest

Preferential sites for intramolecular glucosepane cross-link formation in type I collagen: A thermodynamic study

The extracellular matrix (ECM) undergoes progressive age-related stiffening and loss of proteolytic digestibility due to an increase in concentration of advanced glycation end products (AGEs). The most abundant AGE, glucosepane, accumulates in collagen with concentrations over 100 times greater than all other AGEs. Detrimental collagen stiffening properties are believed to play a significant role in several age-related diseases such as osteoporosis and cardiovascular disease. Currently little is known of the potential location of covalently cross-linked glucosepane formation within collagen molecules; neither are there reports on how the respective cross-link sites affect the physical and biochemical properties of collagen. Using fully atomistic molecular dynamics simulations (MD) we have identified six sites where the formation of a covalent intra-molecular glucosepane cross-link within a single collagen molecule in a fibrillar environment is energetically favourable. Identification of these favourable sites enables us to align collagen cross-linking with experimentally observed changes to the ECM. For example, formation of glucosepane was found to be energetically favourable within close proximity of the Matrix Metalloproteinase-1 (MMP1) binding site, which could potentially disrupt collagen degradation.fals

A first-principles comparison of the electronic properties of MgC_{y}Ni_{3} and ZnC_{y}Ni_{3} alloys

First-principles, density-functional-based electronic structure calculations are employed to study the changes in the electronic properties of ZnC_{y}Ni_{3} and MgC_{y}Ni_{3} using the Korringa-Kohn-Rostoker coherent-potential approximation method in the atomic sphere approximation (KKR-ASA CPA). As a function of decreasing C at%, we find a steady decrease in the lattice constant and bulk modulus in either alloys. However, the pressure derivative of the bulk modulus displays an opposite trend. Following the Debye model, which relates the pressure derivative of the bulk modulus with the average phonon frequency of the crystal, it can thus be argued that ZnCNi_{3} and its disordered alloys posses a different phonon spectra in comparison to its MgCNi_{3} counterparts. This is further justified by the marked similarity we find in the electronic structure properties such as the variation in the density of states and the Hopfield parameters calculated for these alloys. The effects on the equation of state parameters and the density of states at the Fermi energy, for partial replacement of Mg by Zn are also discussed.Comment: 19 pages, 15 figure

A generic expression system to produce proteins that co-assemble with alkane thiol SAM

Surface biology aims to observe and control biological processes by combining bio-, surface, and physical chemistry. Self-assembled monolayers (SAM) on gold surfaces have provided excellent methods for nanoscale surface preparation for such studies. However, extension of this work requires the specific immobilization of whole protein domains and the direct incorporation of recombinant proteins into SAM is still problematic. In this study a short random coil peptide has been designed to insert into thioalkane layers by formation of a hydrophobic helix. Surface plasmon resonance (SPR) studies show that specific immobilization via the internal cysteine is achieved. Addition of the peptide sequence to the terminus of a protein at the genetic level enables the production of a range of recombinant fusion-proteins with good yield. SPR shows that the proteins display the same gold-binding behavior as the peptide. It is shown that cell growth control can be achieved by printing the proteins using soft lithography with subsequent infilling with thioalkanes The expression plasmid is constructed so that any stable protein domain can be easily cloned, expressed, purified and immobilized

Engineered mosaic protein polymers; a simple route to multifunctional biomaterials

Abstract: Background: Engineered living materials (ELMs) are an exciting new frontier, where living organisms create highly functional materials. In particular, protein ELMs have the advantage that their properties can be manipulated via simple molecular biology. Caf1 is a protein ELM that is especially attractive as a biomaterial on account of its unique combination of properties: bacterial cells export it as a massive, modular, non-covalent polymer which is resistant to thermal and chemical degradation and free from animal material. Moreover, it is biologically inert, allowing the bioactivity of each 15 kDa monomeric Caf1 subunit to be specifically engineered by mutagenesis and co-expressed in the same Escherichia coli cell to produce a mixture of bioactive Caf1 subunits. Results: Here, we show by gel electrophoresis and transmission electron microscopy that the bacterial cells combine these subunits into true mosaic heteropolymers. By combining two separate bioactive motifs in a single mosaic polymer we demonstrate its utility by stimulating the early stages of bone formation by primary human bone marrow stromal cells. Finally, using a synthetic biology approach, we engineer a mosaic of three components, demonstrating that Caf1 complexity depends solely upon the variety of monomers available. Conclusions: These results demonstrate the utility of engineered Caf1 mosaic polymers as a simple route towards the production of multifunctional biomaterials that will be useful in biomedical applications such as 3D tissue culture and wound healing. Additionally, in situ Caf1 producing cells could create complex bacterial communities for biotechnology. Graphical abstract

Bounding biomass in the Fisher equation

The FKPP equation with a variable growth rate and advection by an incompressible velocity field is considered as a model for plankton dispersed by ocean currents. If the average growth rate is negative then the model has a survival-extinction transition; the location of this transition in the parameter space is constrained using variational arguments and delimited by simulations. The statistical steady state reached when the system is in the survival region of parameter space is characterized by integral constraints and upper and lower bounds on the biomass and productivity that follow from variational arguments and direct inequalities. In the limit of zero-decorrelation time the velocity field is shown to act as Fickian diffusion with an eddy diffusivity much larger than the molecular diffusivity and this allows a one-dimensional model to predict the biomass, productivity and extinction transitions. All results are illustrated with a simple growth and stirring model.Comment: 32 Pages, 13 Figure