On the extrapolation of magneto-hydro-static equilibria on the sun

Modeling the interface region between solar photosphere and corona is challenging, because the relative importance of magnetic and plasma forces change by several orders of magnitude. While the solar corona can be modeled by the force-free assumption, we need to take care about plasma forces (pressure gradient and gravity) in photosphere and chromosphere, here within the magneto-hydro-static (MHS) model. We solve the MHS equations with the help of an optimization principle and use vector magnetogram as boundary condition. Positive pressure and density are ensured by replacing them with two new basic variables. The Lorentz force during optimization is used to update the plasma pressure on the bottom boundary, which makes the new extrapolation works even without pressure measurement on the photosphere. Our code is tested by using a linear MHS model as reference. From the detailed analyses, we find that the newly developed MHS extrapolation recovers the reference model at high accuracy. The MHS extrapolation is, however, numerically more expensive than the nonlinear force-free field (NLFFF) extrapolation and consequently one should limit their application to regions where plasma forces become important, e.g. in a layer of about 2 Mm above the photosphere.Comment: accepted for publication in Ap

Magnetic reconnection at the earliest stage of solar flux emergence

On 2016 September 20, the Interface Region Imaging Spectrograph observed an active region during its earliest emerging phase for almost 7 hours. The Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory observed continuous emergence of small-scale magnetic bipoles with a rate of $\sim$10$^{16}$ Mx~s$^{-1}$. The emergence of magnetic fluxes and interactions between different polarities lead to frequent occurrence of ultraviolet (UV) bursts, which exhibit as intense transient brightenings in the 1400 \AA{} images. In the meantime, discrete small patches with the same magnetic polarity tend to move together and merge, leading to enhancement of the magnetic fields and thus formation of pores (small sunspots) at some locations. The spectra of these UV bursts are characterized by the superposition of several chromospheric absorption lines on the greatly broadened profiles of some emission lines formed at typical transition region temperatures, suggesting heating of the local materials to a few tens of thousands of kelvin in the lower atmosphere by magnetic reconnection. Some bursts reveal blue and red shifts of $\sim$100~km~s$^{-1}$ at neighboring pixels, indicating the spatially resolved bidirectional reconnection outflows. Many such bursts appear to be associated with the cancellation of magnetic fluxes with a rate of the order of $\sim$10$^{15}$ Mx~s$^{-1}$. We also investigate the three-dimensional magnetic field topology through a magneto-hydrostatic model and find that a small fraction of the bursts are associated with bald patches (magnetic dips). Finally, we find that almost all bursts are located in regions of large squashing factor at the height of $\sim$1 Mm, reinforcing our conclusion that these bursts are produced through reconnection in the lower atmosphere.Comment: ApJ, 10 figure

Does the non-force-freeness matter for the extrapolation of solar magnetic field?

Magnetic field extrapolation is a fundamental tool to reconstruct the three-dimensional solar coronal magnetic field. However, the prevalently used force-free field model might not be applicable in the lower atmosphere, where plasma \b{eta} is greater than 1. In this work, we perform extrapolation in active region 12158, based on an updated magnetohydrostatic (MHS) method. By comparing the results with those from the force-free field method of Current-Field Iteration in Spherical Coordinates (CFITS), we find that the overall properties, which are characterized by the magnetic free energy and helicity, are roughly the same after volume integral. The major differences lie in the magnetic configuration and the twist number of magnetic flux rope (MFR). A coherent MFR with twist around 1 is reproduced from CFITS. In another manner, two sets of MFR, which are highly twisted and slightly coupled, are derived by the MHS method. The latter one is better constrained by the high-resolution observations, such as the filament fibrils, pre-eruptive braiding characteristics and the eruptive double-J shaped hot channel. Overall, our work shows the MHS method is more promising to reproduce the magnetic fine structures that can well match the observations not only in the chromosphere but also in the corona. This initiates the necessity of reconsidering the simplification of low atmosphere for currently widely used nonlinear force-free extrapolation method, since such assumption will not only omit the magnetic structures at low atmosphere but also affect those obtained in the corona, and therefore bringing in ambiguity in interpreting the solar eruption.Comment: 19 pages, 6 figures, accepted by Ap

Solar Ultraviolet Bursts in a Coordinated Observation of IRIS, Hinode and SDO

Solar ultraviolet (UV) bursts are small-scale compact brightenings in transition region images. The spectral profiles of transition region lines in these bursts are significantly enhanced and broadened, often with chromospheric absorption lines such as Ni~{\sc{ii}} 1335.203 and 1393.330 {\AA} superimposed. We investigate the properties of several UV bursts using a coordinated observation of the Interface Region Imaging Spectrograph (IRIS), Solar Dynamics Observatory (SDO), and \textit{Hinode} on 2015 February 7. We have identified 12 UV bursts, and 11 of them reveal small blueshifts of the Ni~{\sc{ii}} absorption lines. However, the Ni~{\sc{ii}} lines in one UV burst exhibit obvious redshifts of $\sim$20 km s$^{-1}$, which appear to be related to the cold plasma downflows observed in the IRIS slit-jaw images. We also examine the three-dimensional magnetic field topology using a magnetohydrostatic model, and find that some UV bursts are associated with magnetic null points or bald patches. In addition, we find that these UV bursts reveal no obvious coronal signatures from the observations of the Atmospheric Imaging Assembly (AIA) on board SDO and the EUV Imaging Spectrometer (EIS) on board \textit{Hinode}.Comment: will appear in the journal of Science China Technological Science

The high helium abundance and charge states of the interplanetary CME and its material source on the Sun

Identifying the source of the material within coronal mass ejections (CMEs) and understanding CME onset mechanisms are fundamental issues in solar and space physics. Parameters relating to plasma composition, such as charge states and He abundance (\ahe), may be different for plasmas originating from differing processes or regions on the Sun. Thus, it is crucial to examine the relationship between in-situ measurements of CME composition and activity on the Sun. We study the CME that erupted on 2014 September 10, in association with an X1.6 flare, by analyzing AIA imaging and IRIS spectroscopic observations and its in-situ signatures detected by Wind and ACE. We find that during the slow expansion and intensity increase of the sigmoid, plasma temperatures of 9 MK, and higher, first appear at the footpoints of the sigmoid, associated with chromospheric brightening. Then the high-temperature region extends along the sigmoid. IRIS observations confirm that this extension is caused by transportation of hot plasma upflow. Our results show that chromospheric material can be heated to 9 MK, and above, by chromospheric evaporation at the sigmoid footpoints before flare onset. The heated chromospheric material can transport into the sigmoidal structure and supply mass to the CME. The aforementioned CME mass supply scenario provides a reasonable explanation for the detection of high charge states and elevated \ahe\ in the associated ICME. The observations also demonstrate that the quasi-steady evolution in the precursor phase is dominated by magnetic reconnection between the rising flux rope and the overlying magnetic field structure.Comment: 10 pages, 5 figures, accepted for publication in ApJ

An Integrative Framework for Bayesian Variable Selection with Informative Priors for Identifying Genes and Pathways

The discovery of genetic or genomic markers plays a central role in the development of personalized medicine. A notable challenge exists when dealing with the high dimensionality of the data sets, as thousands of genes or millions of genetic variants are collected on a relatively small number of subjects. Traditional gene-wise selection methods using univariate analyses face difficulty to incorporate correlational, structural, or functional structures amongst the molecular measures. For microarray gene expression data, we first summarize solutions in dealing with ‘large p, small n’ problems, and then propose an integrative Bayesian variable selection (iBVS) framework for simultaneously identifying causal or marker genes and regulatory pathways. A novel partial least squares (PLS) g-prior for iBVS is developed to allow the incorporation of prior knowledge on gene-gene interactions or functional relationships. From the point view of systems biology, iBVS enables user to directly target the joint effects of multiple genes and pathways in a hierarchical modeling diagram to predict disease status or phenotype. The estimated posterior selection probabilities offer probabilitic and biological interpretations. Both simulated data and a set of microarray data in predicting stroke status are used in validating the performance of iBVS in a Probit model with binary outcomes. iBVS offers a general framework for effective discovery of various molecular biomarkers by combining data-based statistics and knowledge-based priors. Guidelines on making posterior inferences, determining Bayesian significance levels, and improving computational efficiencies are also discussed

A PLSPM-Based Test Statistic for Detecting Gene-Gene Co-Association in Genome-Wide Association Study with Case-Control Design

For genome-wide association data analysis, two genes in any pathway, two SNPs in the two linked gene regions respectively or in the two linked exons respectively within one gene are often correlated with each other. We therefore proposed the concept of gene-gene co-association, which refers to the effects not only due to the traditional interaction under nearly independent condition but the correlation between two genes. Furthermore, we constructed a novel statistic for detecting gene-gene co-association based on Partial Least Squares Path Modeling (PLSPM). Through simulation, the relationship between traditional interaction and co-association was highlighted under three different types of co-association. Both simulation and real data analysis demonstrated that the proposed PLSPM-based statistic has better performance than single SNP-based logistic model, PCA-based logistic model, and other gene-based methods