Photoionization Models for High-density Gas

Relativistically broadened and redshifted 6.4–6.9 keV iron K lines are observed from many accretion powered objects, including X-ray binaries and active galactic nuclei. The existence of gas close to the central engine implies large radiation intensities and correspondingly large gas densities if the gas is to remain partially ionized. Simple estimates indicate that high gas densities are needed to allow for the survival of iron against ionization. These are high enough that rates for many atomic processes are affected by mechanisms related to interactions with nearby ions and electrons. Radiation intensities are high enough that stimulated processes can be important. Most models currently in use for interpreting relativistic lines use atomic rate coefficients designed for use at low densities and neglect stimulated processes. In our work so far we have presented atomic structure calculations with the goal of providing physically appropriate models at densities consistent with line-emitting gas near compact objects. In this paper we apply these rates to photoionization calculations, and produce ionization balance curves and X-ray emissivities and opacities that are appropriate for high densities and high radiation intensities. The final step in our program will be presented in a subsequent paper in which model atmosphere calculations will incorporate these rates into synthetic spectra

Properties of the Line-of-Sight Velocity Field in the Hot and X-ray Emitting Circumgalactic Medium of Nearby Simulated Disk Galaxies

The hot, X-ray-emitting phase of the circumgalactic medium in galaxies is believed to be the reservoir of baryons from which gas flows onto the central galaxy and into which feedback from AGN and stars inject mass, momentum, energy, and metals. These effects shape the velocity fields of the hot gas, which can be observed by X-ray IFUs via the Doppler shifting and broadening of emission lines. In this work, we analyze the gas kinematics of the hot circumgalactic medium of Milky Way-mass disk galaxies from the TNG50 simulation with synthetic observations to determine how future instruments can probe this velocity structure. We find that the hot phase is often characterized by outflows outward from the disk driven by feedback processes, radial inflows near the galactic plane, and rotation, though in other cases the velocity field is more disorganized and turbulent. With a spectral resolution of $\sim$1 eV, fast and hot outflows ($\sim$200-500 km s$^{-1}$) can be measured, depending on the orientation of the galaxy on the sky. The rotation velocity of the hot phase ($\sim$100-200 km s$^{-1}$) can be measured using line shifts in edge-on galaxies, and is slower than that of colder gas phases but similar to stellar rotation velocities. By contrast, the slow inflows ($\sim$50-100 km s$^{-1}$) are difficult to measure in projection with these other components. We find that the velocity measured is sensitive to which emission lines are used. Measuring these flows will help constrain theories of how the gas in these galaxies forms and evolves.Comment: 41 pages, 29 figures, submitted to Ap

LEM All-Sky Survey: Soft X-ray Sky at Microcalorimeter Resolution

The Line Emission Mapper (LEM) is an X-ray Probe with with spectral resolution ~2 eV FWHM from 0.2 to 2.5 keV and effective area >2,500 cm$^2$ at 1 keV, covering a 33 arcmin diameter Field of View with 15 arcsec angular resolution, capable of performing efficient scanning observations of very large sky areas and enabling the first high spectral resolution survey of the full sky. The LEM-All-Sky Survey (LASS) is expected to follow the success of previous all sky surveys such as ROSAT and eROSITA, adding a third dimension provided by the high resolution microcalorimeter spectrometer, with each 15 arcsec pixel of the survey including a full 1-2 eV resolution energy spectrum that can be integrated over any area of the sky to provide statistical accuracy. Like its predecessors, LASS will provide both a long-lasting legacy and open the door to the unknown, enabling new discoveries and delivering the baseline for unique GO studies. No other current or planned mission has the combination of microcalorimeter energy resolution and large grasp to cover the whole sky while maintaining good angular resolution and imaging capabilities. LASS will be able to probe the physical conditions of the hot phases of the Milky Way at multiple scales, from emission in the Solar system due to Solar Wind Charge eXchange, to the interstellar and circumgalactic media, including the North Polar Spur and the Fermi/eROSITA bubbles. It will measure velocities of gas in the inner part of the Galaxy and extract the emissivity of the Local Hot Bubble. By maintaining the original angular resolution, LASS will also be able to study classes of point sources through stacking. For classes with ~$10^4$ objects, it will provide the equivalent of 1 Ms of high spectral resolution data. We describe the technical specifications of LASS and highlight the main scientific objectives that will be addressed. (Abridged)Comment: White Paper in support of a mission concept to be submitted for the 2023 NASA Astrophysics Probes opportunity. This White Paper will be updated when required. 30 pages, 25 figure

How many human proteoforms are there?

Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA- and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry-based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease. We frame central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today. We use this framework to assess existing data and to ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?" We also explore prospects for improving measurements to better regularize protein-level biology and efficiently associate PTMs to function and phenotype

PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry

Prefractionation of complex mixtures of proteins derived from biological samples is indispensable for proteome analysis via top-down mass spectrometry (MS). Polyacrylamide gel electrophoresis (PAGE), which enables high-resolution protein separation based on molecular size, is a widely used technique in biochemical experiments and has the potential to be useful in sample fractionation for top-down MS analysis. However, the lack of a means to efficiently recover the separated proteins in-gel has always been a barrier to its use in sample prefractionation. In this study, we present a novel experimental workflow, called Passively Eluting Proteins from Polyacrylamide gels as Intact species for MS ("PEPPI-MS"), which allows top-down MS of PAGE-separated proteins. The optimization of Coomassie brilliant blue staining followed by the passive extraction step in the PEPPI-MS workflow enabled the efficient recovery of proteins, separated on commercial precast gels, from a wide range of molecular weight regions in under 10 min. Two-dimensional separation combining offline PEPPI-MS with online reversed-phase liquid chromatographic separation resulted in identification of over 1000 proteoforms recovered from the target region of the gel (≤50 kDa). Given the widespread availability and relatively low cost of traditional sodium dodecyl sulfate (SDS)-PAGE equipment, the PEPPI-MS workflow will be a powerful prefractionation strategy for top-down proteomics