More Like this

1. CMZoom III: Spectral line data release

   https://doi.org/10.1093/mnras/stad388  

   Callanan, Daniel ; Longmore, Steven N. ; Battersby, Cara ; Hatchfield, H. Perry ; Walker, Daniel L. ; Henshaw, Jonathan ; Keto, Eric ; Barnes, Ashley ; Ginsburg, Adam ; Kauffmann, Jens ; et al ( February 2023 , Monthly Notices of the Royal Astronomical Society)

   We present an overview and data release of the spectral line component of the SMA Large Program, CMZoom. CMZoom observed 12CO (2–1), 13CO (2–1), and C18O (2–1), three transitions of H2CO, several transitions of CH3OH, two transitions of OCS, and single transitions of SiO and SO within gas above a column density of N(H2) ≥ 1023 cm−2 in the Central Molecular Zone (CMZ; inner few hundred pc of the Galaxy). We extract spectra from all compact 1.3 mm CMZoom continuum sources and fit line profiles to the spectra. We use the fit results from the H2CO 3(0, 3)–2(0, 2) transition to determine the source kinematic properties. We find ∼90 per cent of the total mass of CMZoom sources have reliable kinematics. Only four compact continuum sources are formally self-gravitating. The remainder are consistent with being in hydrostatic equilibrium assuming that they are confined by the high external pressure in the CMZ. We find only two convincing proto-stellar outflows, ruling out a previously undetected population of very massive, actively accreting YSOs with strong outflows. Finally, despite having sufficient sensitivity and resolution to detect high-velocity compact clouds (HVCCs), which have been claimed as evidence for intermediate mass black holes interacting with molecular gas clouds, we find no suchmore »objects across the large survey area.

   « less
2. PHANGS–JWST First Results: Stellar-feedback-driven Excitation and Dissociation of Molecular Gas in the Starburst Ring of NGC 1365?

   https://doi.org/10.3847/2041-8213/aca973  

   Liu, Daizhong ; Schinnerer, Eva ; Cao, Yixian ; Leroy, Adam ; Usero, Antonio ; Rosolowsky, Erik ; Kruijssen, J. M. Diederik ; Chevance, Mélanie ; Glover, Simon C. O. ; Sormani, Mattia C. ; et al ( February 2023 , The Astrophysical Journal Letters)

   We compare embedded young massive star clusters (YMCs) to (sub-)millimeter line observations tracing the excitation and dissociation of molecular gas in the starburst ring of NGC 1365. This galaxy hosts one of the strongest nuclear starbursts and richest populations of YMCs within 20 Mpc. Here we combine near-/mid-IR PHANGS–JWST imaging with new Atacama Large Millimeter/submillimeter Array multi-JCO (1–0, 2–1 and 4–3) and [Ci] (1–0) mapping, which we use to trace CO excitation viaR₄₂=I_CO(4−3)/I_CO(2−1)andR₂₁=I_CO(2−1)/I_CO(1−0)and dissociation viaR_CICO=I_[CI](1−0)/I_CO(2−1)at 330 pc resolution. We find that the gas flowing into the starburst ring from northeast to southwest appears strongly affected by stellar feedback, showing decreased excitation (lowerR₄₂) and increased signatures of dissociation (higherR_CICO) in the downstream regions. There, radiative-transfer modeling suggests that the molecular gas density decreases and temperature and [CI/CO] abundance ratio increase. We compareR₄₂andR_CICOwith local conditions across the regions and find that both correlate with near-IR 2μm emission tracing the YMCs and with both polycyclic aromatic hydrocarbon (11.3μm) and dust continuum (21μm) emission. In general,R_CICOexhibits ∼0.1 dex tighter correlations thanR₄₂, suggestingCito be a more sensitive tracer of changing physical conditions in the NGC 1365 starburst than CO (4–3). Our results are consistent with a scenario where gas flows into the two armmore »regions along the bar, becomes condensed/shocked, forms YMCs, and then these YMCs heat and dissociate the gas.

   « less
3. A wind-blown bubble in the Central Molecular Zone cloud G0.253+0.016

   https://doi.org/10.1093/mnras/stab3039  

   Henshaw, Jonathan D. ; Krumholz, Mark R. ; Butterfield, Natalie O. ; Mackey, Jonathan ; Ginsburg, Adam ; Haworth, Thomas J. ; Nogueras-Lara, Francisco ; Barnes, Ashley T. ; Longmore, Steven N. ; Bally, John ; et al ( December 2021 , Monthly Notices of the Royal Astronomical Society)

   G0.253+0.016, commonly referred to as ‘the Brick’ and located within the Central Molecular Zone, is one of the densest (≈103–4 cm−3) molecular clouds in the Galaxy to lack signatures of widespread star formation. We set out to constrain the origins of an arc-shaped molecular line emission feature located within the cloud. We determine that the arc, centred on $\lbrace l_{0},b_{0}\rbrace =\lbrace 0{_{.}^{\circ}} 248,\, 0{_{.}^{\circ}} 018\rbrace$, has a radius of 1.3 pc and kinematics indicative of the presence of a shell expanding at $5.2^{+2.7}_{-1.9}$ $\mathrm{\, km\, s}^{-1}$. Extended radio continuum emission fills the arc cavity and recombination line emission peaks at a similar velocity to the arc, implying that the molecular gas and ionized gas are physically related. The inferred Lyman continuum photon rate is NLyC = 1046.0–1047.9 photons s−1, consistent with a star of spectral type B1-O8.5, corresponding to a mass of ≈12–20 M⊙. We explore two scenarios for the origin of the arc: (i) a partial shell swept up by the wind of an interloper high-mass star and (ii) a partial shell swept up by stellar feedback resulting from in situ star formation. We favour the latter scenario, finding reasonable (factor of a few) agreement between its morphology, dynamics, and energetics and those predicted formore »an expanding bubble driven by the wind from a high-mass star. The immediate implication is that G0.253+0.016 may not be as quiescent as is commonly accepted. We speculate that the cloud may have produced a ≲103 M⊙ star cluster ≳0.4 Myr ago, and demonstrate that the high-extinction and stellar crowding observed towards G0.253+0.016 may help to obscure such a star cluster from detection.

   « less
4. First Detection of the Molecular Cloud Population in the Extended Ultraviolet Disk of M83

   https://doi.org/10.3847/1538-4357/ac9dfc  

   Koda, Jin ; Watson, Linda ; Combes, Françoise ; Rubio, Monica ; Boissier, Samuel ; Yagi, Masafumi ; Thilker, David ; Lee, Amanda M. ; Komiyama, Yutaka ; Morokuma-Matsui, Kana ; et al ( December 2022 , The Astrophysical Journal)

   We report a CO(J= 3−2) detection of 23 molecular clouds in the extended ultraviolet (XUV) disk of the spiral galaxy M83 with the Atacama Large Millimeter/submillimeter Array. The observed 1 kpc²region is at about 1.24 times the optical radius (R₂₅) of the disk, where CO(J= 2–1) was previously not detected. The detection and nondetection, as well as the level of star formation (SF) activity in the region, can be explained consistently if the clouds have the mass distribution common among Galactic clouds, such as Orion A—with star-forming dense clumps embedded in thick layers of bulk molecular gas, but in a low-metallicity regime where their outer layers are CO-deficient and CO-dark. The cloud and clump masses, estimated from CO(3−2), range from 8.2 × 10²to 2.3 × 10⁴M_⊙and from 2.7 × 10²to 7.5 × 10³M_⊙, respectively. The most massive clouds appear similar to Orion A in star formation activity as well as in mass, as expected if the cloud mass structure is common. The overall low SF activity in the XUV disk could be due to the relative shortage of gas in the molecular phase. The clouds are distributed like chains up to 600 pc (or longer) in length, suggesting thatmore »the trigger of cloud formation is on large scales. The common cloud mass structure also justifies the use of high-JCO transitions to trace the total gas mass of clouds, or galaxies, even in the high-zuniverse. This study is the first demonstration that CO(3−2) is an efficient tracer of molecular clouds even in low-metallicity environments.

   « less
5. Simulation Data for Design of Peptides that Fold and Self-Assemble on Graphite

   https://doi.org/10.5281/zenodo.6426152  

   Comer, Jeffrey ; Thakkar, Ravindra ; Velásquez-Silva, Astrid ; Miranda-Carvajal, Ingrid ( January 2022 )

   Abstract

   <p>This data set for the manuscript entitled &#34;Design of Peptides that Fold and Self-Assemble on Graphite&#34; includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or Amber prmtop format), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.</p> <p>Version: 2.0</p> <p>Changes versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.</p> <p><br /> Conventions Used in These Files<br /> &#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;</p> <p>Structure Files<br /> ----------------<br /> - graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.)</p> <p>- graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)<br /> - repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)<br /> - freeTop_*.pdb (same as the above pdb files, but the carbons of the lower graphene layer have been placed at a single z value and marked for restraints in NAMD)<br /> - amber_*.prmtop (combined topology and parameter files for Amber force field simulations)<br /> - repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)</p> <p>Force Field Parameters<br /> ----------------------<br /> CHARMM format parameter files:<br /> - par_all36m_prot.prm (CHARMM36m FF for proteins)<br /> - par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.<br /> - toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)</p> <p>Template NAMD Configuration Files<br /> ---------------------------------<br /> These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):<br /> - template_min.namd (minimization)<br /> - template_eq.namd (NPT equilibration with lower graphene fixed)<br /> - template_abf.namd (for adaptive biasing force)</p> <p>Minimization<br /> -------------<br /> - namd/min_*.0.namd</p> <p>Equilibration<br /> -------------<br /> - namd/eq_*.0.namd</p> <p>Adaptive biasing force calculations<br /> -----------------------------------<br /> - namd/eabfZRest7_graph_chp1404.0.namd<br /> - namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)</p> <p>Log Files<br /> ---------<br /> For each NAMD configuration file given in the last two sections, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log.</p> <p>Simulation Output<br /> -----------------<br /> The simulation output files (which match the names of the NAMD configuration files) are in the output/ directory. Files with the extensions .coor, .vel, and .xsc are coordinates in NAMD binary format, velocities in NAMD binary format, and extended system information (including cell size) in text format. Files with the extension .dcd give the trajectory of the atomic coorinates over time (and also include system cell information). Due to storage limitations, large DCD files have been omitted or replaced with new DCD files having the prefix stride50_ including only every 50 frames. The time between frames in these files is 50 * 50000 steps/frame * 4 fs/step &#61; 10 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst.</p> <p>Scripts<br /> -------<br /> Files with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first.</p> <p><br /> CONTENTS<br /> &#61;&#61;&#61;&#61;&#61;&#61;&#61;&#61;</p> <p>The directory contents are as follows. The directories Sim_Figure-1 and Sim_Figure-8 include README.txt files that describe the files and naming conventions used throughout this data set.</p> <p>Sim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite–water interface.</p> <p>Sim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite–water interface.</p> <p>Sim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.</p> <p>Sim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.</p> <p>Sim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 295 K.</p> <p>Sim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.</p> <p>Sim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).</p> <p>Sim_Figure-7: Free energy calculations for folding, adsorption, and pairing for the peptide CHP1404 (sequence: cyc(GTGSGTG-GPGG-GCGTGTG-SGPG)). For folding, we calculate the PMF as function of RMSD by replica-exchange umbrella sampling (in the subdirectory Folding_CHP1404_Graphene/). We make the same calculation in solution, which required 3 seperate replica-exchange umbrella sampling calculations (in the subdirectory Folding_CHP1404_Solution/). Both PMF of RMSD calculations for the scrambled peptide are in Folding_scram1404/. For adsorption, calculation of the PMF for the orientational restraints and the calculation of the PMF along z (the distance between the graphene sheet and the center of mass of the peptide) are in Adsorption_CHP1404/ and Adsorption_scram1404/. The actual calculation of the free energy is done by a shell script (&#34;doRestraintEnergyError.sh&#34;) in the 1_free_energy/ subsubdirectory. Processing of the PMFs must be done first in the 0_pmf/ subsubdirectory. Finally, files for free energy calculations of pair formation for CHP1404 are found in the Pair/ subdirectory.</p> <p>Sim_Figure-8: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) where the peptides are far above the graphene–water interface in the initial configuration.</p> <p>Sim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.</p> <p>Sim_Figure-9_scrambled: Two replicates of a simulation of nine peptide molecules with the control sequence cyc(GGTPTTGGGGGGSGGPSGTGGC) at the graphite–water interface at 370 K.</p> <p>Sim_Figure-10: Adaptive biasing for calculation of the free energy of the folded peptide as a function of the angle between its long axis and the zigzag directions of the underlying graphene sheet.</p> <p> </p>
   

   Other

   This material is based upon work supported by the US National Science Foundation under grant no. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562, through allocation BIO200030.
   More>>