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The Helioseismic and Magnetic Imager (HMI) instrument and investigation as a part of the NASA Solar Dynamics Observatory (SDO) is designed to study convection-zone dynamics and the solar dynamo, the origin and evolution of sunspots, active regions, and complexes of activity, the sources and drivers of solar magnetic activity and disturbances, links between the internal processes and dynamics of the corona and heliosphere, and precursors of solar disturbances for space-weather forecasts. A brief overview of the instrument, investigation objectives, and standard data products is presented.

NASA’s Solar Dynamics Observatory (SDO) spacecraft was launched 11 February 2010 with three instruments onboard, including the Helioseismic and Magnetic Imager (HMI). After commissioning, HMI began normal operations on 1 May 2010 and has subsequently observed the Sun’s entire visible disk almost continuously. HMI collects sequences of polarized filtergrams taken at a fixed cadence with two 4096 × 4096 cameras, from which are computed arcsecond-resolution maps of photospheric observables that include line-of-sight velocity and magnetic field, continuum intensity, line width, line depth, and the Stokes polarization parameters [ I , Q , U , V ]. Two processing pipelines have been implemented at the SDO Joint Science Operations Center (JSOC) at Stanford University to compute these observables from calibrated Level-1 filtergrams, one that computes line-of-sight quantities every 45 seconds and the other, primarily for the vector magnetic field, that computes averages on a 720-second cadence. Corrections are made for static and temporally changing CCD characteristics, bad pixels, image alignment and distortion, polarization irregularities, filter-element uncertainty and nonuniformity, as well as Sun–spacecraft velocity. We detail the functioning of these two pipelines, explain known issues affecting the measurements of the resulting physical quantities, and describe how regular updates to the instrument calibration impact them. We also describe how the scheme for computing the observables is optimized for actual HMI observations. Initial calibration of HMI was performed on the ground using a variety of light sources and calibration sequences. During the five years of the SDO prime mission, regular calibration sequences have been taken on orbit to improve and regularly update the instrument calibration, and to monitor changes in the HMI instrument. This has resulted in several changes in the observables processing that are detailed here. The instrument more than satisfies all of the original specifications for data quality and continuity. The procedures described here still have significant room for improvement. The most significant remaining systematic errors are associated with the spacecraft orbital velocity.

The Helioseismic and Magnetic Imager (HMI) investigation will study the solar interior using helioseismic techniques as well as the magnetic field near the solar surface. The HMI instrument is part of the Solar Dynamics Observatory (SDO) that was launched on 11 February 2010. The instrument is designed to measure the Doppler shift, intensity, and vector magnetic field at the solar photosphere using the 6173 Fe I absorption line. The instrument consists of a front-window filter, a telescope, a set of wave plates for polarimetry, an image-stabilization system, a blocking filter, a five-stage Lyot filter with one tunable element, two wide-field tunable Michelson interferometers, a pair of 4096(exo 2) pixel cameras with independent shutters, and associated electronics. Each camera takes a full-disk image roughly every 3.75 seconds giving an overall cadence of 45 seconds for the Doppler, intensity, and line-of-sight magnetic-field measurements and a slower cadence for the full vector magnetic field. This article describes the design of the HMI instrument and provides an overview of the pre-launch calibration efforts. Overviews of the investigation, details of the calibrations, data handling, and the science analysis are provided in accompanying articles.

We compare line-of-sight magnetograms from the Helioseismic and Magnetic Imager (HMI) onboard the Solar Dynamics Observatory (SDO) and the Michelson Doppler Imager (MDI) onboard the Solar and Heliospheric Observatory (SOHO). The line-of-sight magnetic signal inferred from the calibrated MDI data is greater than that derived from the HMI data by a factor of 1.40. This factor varies somewhat with center-to-limb distance. An upper bound to the random noise for the 1′′ resolution HMI 720-second magnetograms is 6.3 Mx cm −2 , and 10.2 Mx cm −2 for the 45-second magnetograms. Virtually no p -mode leakage is seen in the HMI magnetograms, but it is significant in the MDI magnetograms. 12-hour and 24-hour periodicities are detected in strong fields in the HMI magnetograms. The newly calibrated MDI full-disk magnetograms have been corrected for the zero-point offset and underestimation of the flux density. The noise is 26.4 Mx cm −2 for the MDI one-minute full-disk magnetograms and 16.2 Mx cm −2 for the five-minute full-disk magnetograms observed with four-arcsecond resolution. The variation of the noise over the Sun’s disk found in MDI magnetograms is likely due to the different optical distortions in the left- and right-circular analyzers, which allows the granulation and p -mode to leak in as noise. Saturation sometimes seen in sunspot umbrae in MDI magnetograms is caused by the low intensity and the limitation of the onboard computation. The noise in the HMI and MDI line-of-sight magnetic-field synoptic charts appears to be fairly uniform over the entire map. The noise is 2.3 Mx cm −2 for HMI charts and 5.0 Mx cm −2 for MDI charts. No evident periodicity is found in the HMI synoptic charts.

The Helioseismic and Magnetic Imager (HMI) instrument is a major component of NASA's Solar Dynamics Observatory (SDO) spacecraft. Since commencement of full regular science operations on 1 May 2010, HMI has operated with remarkable continuity, e.g. during the more than five years of the SDO prime mission that ended 30 September 2015, HMI collected 98.4% of all possible 45-second velocity maps; minimizing gaps in these full-disk Dopplergrams is crucial for helioseismology. HMI velocity, intensity, and magnetic-field measurements are used in numerous investigations, so understanding the quality of the data is important. This article describes the calibration measurements used to track the performance of the HMI instrument, and it details trends in important instrument parameters during the prime mission. Regular calibration sequences provide information used to improve and update the calibration of HMI data. The set-point temperature of the instrument front window and optical bench is adjusted regularly to maintain instrument focus, and changes in the temperature-control scheme have been made to improve stability in the observable quantities. The exposure time has been changed to compensate for a 20% decrease in instrument throughput. Measurements of the performance of the shutter and tuning mechanisms show that they are aging as expected and continue to perform according to specification. Parameters of the tunable optical-filter elements are regularly adjusted to account for drifts in the central wavelength. Frequent measurements of changing CCD-camera characteristics, such as gain and flat field, are used to calibrate the observations. Infrequent expected events such as eclipses, transits, and spacecraft off-points interrupt regular instrument operations and provide the opportunity to perform additional calibration. Onboard instrument anomalies are rare and seem to occur quite uniformly in time. The instrument continues to perform very well.

The Helioseismic and Magnetic Imager onboard the Solar Dynamics Observatory (SDO/HMI) provides continuous full-disk observations of solar oscillations. We develop a data-analysis pipeline based on the time–distance helioseismology method to measure acoustic travel times using HMI Doppler-shift observations, and infer solar interior properties by inverting these measurements. The pipeline is used for routine production of near-real-time full-disk maps of subsurface wave-speed perturbations and horizontal flow velocities for depths ranging from 0 to 20 Mm, every eight hours. In addition, Carrington synoptic maps for the subsurface properties are made from these full-disk maps. The pipeline can also be used for selected target areas and time periods. We explain details of the pipeline organization and procedures, including processing of the HMI Doppler observations, measurements of the travel times, inversions, and constructions of the full-disk and synoptic maps. Some initial results from the pipeline, including full-disk flow maps, sunspot subsurface flow fields, and the interior rotation and meridional flow speeds, are presented.

Background Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues) tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues). Results Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94) model in which all model parameters can be functions of the relative solvent accessibility (RSA) of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio ω that varies linearly with RSA provides a better model fit than an RSA-independent ω or an ω that is estimated separately in individual RSA bins. We further show that the branch length t and the transition-transverion ratio κ also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94) model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between ω and RSA, and gene expression level affects both the intercept and the slope. Conclusions Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between ω and RSA implies that genes are better characterized by their ω slope and intercept than by just their mean ω .

Gas on the Sun's surface has been observed 1 , 2 , 3 , 4 to flow away from the equator towards both poles. If the same flow persists to great depths, it could play an important dynamical role in the eleven-year sunspot cycle, by carrying the magnetic remnants of the sunspots to high latitudes 5 . An even deeper counterflow, which would be required to maintain mass balance, could explain why new sunspots form at lower latitudes as the cycle progresses 6 . These deep flows would also redistribute angular momentum within the Sun, and therefore help to maintain the faster rotation of the equator relative to the poles 7 . Here we report the detection, using helioseismic tomography, of the longitude-averaged subsurface flow in the outer 4% of the Sun. We find that the subsurface flow is approximately constant in this depth range, and that the speed is similar to that seen on the surface. This demonstrates that the surface flow penetrates deeply, so that it is likely to be an important factor in solar dynamics.

We present a study of two spectral lines, Fe I 6173 Å and Ni I 6768 Å, that were candidates to be used in the Helioseismic and Magnetic Imager (HMI) for observing Doppler velocity and the vector magnetic field. The line profiles were studied using the Mt. Wilson Observatory, the Advanced Stokes Polarimeter and the Kitt Peak-McMath Pierce telescope and one-meter Fourier transform spectrometer atlas. Both Fe I and Ni I profiles have clean continua and no blends that threaten instrument performance. The Fe I line is 2% deeper, 15% narrower, and has a 6% smaller equivalent width than the Ni I line. The potential of each spectral line to recover pre-assigned solar conditions is tested using a least-squares minimization technique to fit Milne-Eddington models to tens of thousands of line profiles that have been sampled at five spectral positions across the line. Overall, the Fe I line has a better performance than the Ni I line for vector-magnetic-field retrieval. Specifically, the Fe I line is able to determine field strength, longitudinal and transverse flux four times more accurately than the Ni I line in active regions. Inclination and azimuthal angles can be recovered to [asymptotically =]2^sup °^ above 600 Mx cm^sup -2^ for Fe I and above 1000 Mx cm^sup -2^ for Ni I. Therefore, the Fe I line better determines the magnetic-field orientation in plage, whereas both lines provide good orientation determination in penumbrae and umbrae. We selected the Fe I spectral line for use in HMI due to its better performance for magnetic diagnostics while not sacrificing velocity information. The one exception to the better performance of the Fe I line arises when high field strengths combine with high velocities to move the spectral line beyond the effective sampling range. The higher g ^sub eff^ of Fe I means that its useful range of velocity values in regions of strong magnetic field is smaller than Ni I.[PUBLICATION ABSTRACT]

Fluorescent proteins (FP) homologous to the green fluorescent protein (GFP) from the jellyfish Aequorea victoria have revolutionized biomedical research due to their usefulness as genetically encoded fluorescent labels. Fluorescent proteins from copepods are particularly promising due to their high brightness and rapid fluorescence development. Here we report two novel FPs from Pontella mimocerami (Copepoda, Calanoida, Pontellidae), which were identified via fluorescence screening of a bacterial cDNA expression library prepared from the whole-body total RNA of the animal. The proteins are very similar in sequence and spectroscopic properties. They possess high molar extinction coefficients (79,000 M(-1) cm(-)) and quantum yields (0.92), which make them more than two-fold brighter than the most common FP marker, EGFP. Both proteins form oligomers, which we were able to counteract to some extent by mutagenesis of the N-terminal region; however, this particular modification resulted in substantial drop in brightness. The spectroscopic characteristics of the two P. mimocerami proteins place them among the brightest green FPs ever described. These proteins may therefore become valuable additions to the in vivo imaging toolkit.