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At least 667 records · Page 37

Metalloproteins in an Era of Modern Crystallography and Why the Beamline Matters

The Structural Molecular Biology (SMB) macromolecular crystallography (MC) group at the Stanford Synchrotron Radiation Lightsource (SSRL) have developed state-of-the-art capabilities tailored for metalloenzyme structural analysis. Metalloproteins sit at the center of biology’s most audacious chemistry. From multi-electron redox catalysis to radical rearrangements and light-driven transformations, metal sites give proteins access to reaction landscapes that would otherwise be inaccessible under ambient conditions. Yet their study presents a fundamental paradox for MC studies: the very X-rays we use to reveal atomic structure can alter the electronic states we seek to understand. As the field moves beyond static snapshots toward mechanistic insight, success increasingly depends on our ability to maintain metal centers in their native state throughout the experiment. The SSRL SMB-MC beamlines integrate a suite of capabilities specifically designed to address these challenges. By combining in situ spectroscopic verification, intelligent dose management, controlled reaction initiation, optimized anomalous diffraction, and real-time crystallographic diffraction analysis, these tools enable researchers to interrogate metalloproteins with unprecedented rigor. This article explores how these complementary approaches are reshaping our ability to capture metalloprotein chemistry, and what this means for mechanistic studies at synchrotron beamlines.

Maggiolo, Ailiena O. [SLAC National Accelerator La↗

A MODERN SEARCH FOR WOLF–RAYET STARS IN THE MAGELLANIC CLOUDS. II. A SECOND YEAR OF DISCOVERIES

The numbers and types of evolved massive stars found in nearby galaxies provide an exacting test of stellar evolution models. Because of their proximity and rich massive star populations, the Magellanic Clouds have long served as the linchpins for such studies. Yet the continued accidental discoveries of Wolf–Rayet (WR) stars in these systems demonstrate that our knowledge is not as complete as usually assumed. Therefore, we undertook a multi-year survey for WRs in the Magellanic Clouds. Our results from our first year (reported previously) confirmed nine new LMC WRs. Of these, six were of a type never before recognized, with WN3-type emission combined with O3-type absorption features. Yet these stars are 2–3 mag too faint to be WN3+O3 V binaries. Here we report on the second year of our survey, including the discovery of four more WRs, two of which are also WN3/O3s, plus two “slash” WRs. This brings the total of known LMC WRs to 152, 13 (8.2%) of which were found by our survey, which is now ∼60% complete. We find that the spatial distribution of the WN3/O3s is similar to that of other WRs in the LMC, suggesting that they are descended from the same progenitors. We call attention to the fact that 5 of the 12 known SMC WRs may in fact be similar WN3/O3s rather than the binaries they have often assumed to be. We also discuss our other discoveries: a newly discovered Onfp-type star, and a peculiar emission-line object. Finally, we consider the completeness limits of our survey.

79 ASTRONOMY AND ASTROPHYSICS↗

Modern hadron spectroscopy: a bridge between nuclear and particle physics

Here, in this talk I discuss aspects of hadron physics, which soon are expected to shed new light on the fundamental QCD phenomena. In the analysis of hadron reactions and their propertieds I emphasize similarities to the nuclear many body problem.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Property Variations in Modern REBCO Coated Conductors from Multiple Manufacturers

The complex, multilayer structure of REBCO Coated Conductor (CC) poses significant challenges in the fabrication of high magnetic field devices where large stresses may initiate various forms of damage. Our goal is to peer below the cartoon representations of CC so that, amongst other things, we might better understand whether a CC from one manufacturer is interchangeable with that from another. This involves knowledge of a broad range of electromagnetic, geometric, microstructural, and J c (θ,B,T) properties, and their variations that collectively pose challenges for the fault tolerance of REBCO CC devices. Accordingly, comparative measurements of J c , visualization of flux penetration with Magneto-Optical Imaging (MOI), tape geometry from Scanning Electron Microscopy (SEM) of polished cross-sections, and extensive optical microscopy was performed on recently purchased samples from multiple manufacturers. Our analyses reveal many deviations from or characteristics absent from manufacturers’ specifications, while a comparison of different manufacturers’ mechanically and laser slit tapes shows a diverse array of slitting characteristics amongst the manufacturers and variation in properties those made to the same specification. Laser slit tapes from several manufacturers reveal ablated edges with damaged regions extending up to 50 μm, comparable to the damaged region found in the mechanically slit CC of this study. Overall, the aim of this study is to flesh out appropriate ways to understand the real conductor below the manufacturers’ cartoons to avoid surprises in our REBCO CC coil development program. The goal of this work was to perform a broad array of characterizations of the type needed for validation of purpose for making high field magnets: to our surprise we found a wide range of properties which greatly impact the mechanical strength and electromagnetic performance of solenoids composed of these conductors and reinforced the need for a broad characterization program for each conductor prior to its implementation.

Bradford, G.↗

Modern Senicide in the Face of a Pandemic: An Examination of Public Discourse and Sentiment About Older Adults and COVID-19 Using Machine Learning

Objectives This study examined public discourse and sentiment regarding older adults and COVID-19 on social media and assessed the extent of ageism in public discourse. Methods Twitter data (N = 82,893) related to both older adults and COVID-19 and dated from January 23 to May 20, 2020, were analyzed. We used a combination of data science methods (including supervised machine learning, topic modeling, and sentiment analysis), qualitative thematic analysis, and conventional statistics. Results The most common category in the coded tweets was “personal opinions” (66.2%), followed by “informative” (24.7%), “jokes/ridicule” (4.8%), and “personal experiences” (4.3%). The daily average of ageist content was 18%, with the highest of 52.8% on March 11, 2020. Specifically, more than 1 in 10 (11.5%) tweets implied that the life of older adults is less valuable or downplayed the pandemic because it mostly harms older adults. A small proportion (4.6%) explicitly supported the idea of just isolating older adults. Almost three-quarters (72.9%) within “jokes/ridicule” targeted older adults, half of which were “death jokes.” Also, 14 themes were extracted, such as perceptions of lockdown and risk. A bivariate Granger causality test suggested that informative tweets regarding at-risk populations increased the prevalence of tweets that downplayed the pandemic. Discussion Ageist content in the context of COVID-19 was prevalent on Twitter. Information about COVID-19 on Twitter influenced public perceptions of risk and acceptable ways of controlling the pandemic. Finaly, public education on the risk of severe illness is needed to correct misperceptions.

60 APPLIED LIFE SCIENCES↗

Synthetic light-cone catalogues of modern redshift and weak lensing surveys with abacussummit

ABSTRACT The joint analysis of different cosmological probes, such as galaxy clustering and weak lensing, can potentially yield invaluable insights into the nature of the primordial Universe, dark energy, and dark matter. However, the development of high-fidelity theoretical models is a necessary stepping stone. Here, we present public high-resolution weak lensing maps on the light-cone, generated using the N-body simulation suite abacussummit, and accompanying weak lensing mock catalogues, tuned to the Early Data Release small-scale clustering measurements of the Dark Energy Spectroscopic Instrument. Available in this release are maps of the cosmic shear, deflection angle, and convergence fields at source redshifts ranging from z = 0.15 to 2.45 as well as cosmic microwave background convergence maps for each of the 25 base-resolution simulations ($L_{\rm box} = 2000\, h^{-1}\, {\rm Mpc}$ and Npart = 69123) as well as for the two huge simulations ($L_{\rm box} = 7500\, h^{-1}\, {\rm Mpc}$ and Npart = 86403) at the fiducial abacussummit cosmology. The pixel resolution of each map is 0.21 arcmin, corresponding to a healpix Nside of 16 384. The sky coverage of the base simulations is an octant until z ≈ 0.8 (decreasing to about 1800 deg2 at z ≈ 2.4), whereas the huge simulations offer full-sky coverage until z ≈ 2.2. Mock lensing source catalogues are sampled matching the ensemble properties of the Kilo-Degree Survey, Dark Energy Survey, and Hyper Suprime-Cam data sets. The mock catalogues are validated against theoretical predictions for various clustering and lensing statistics, such as correlation multipoles, galaxy–shear, and shear–shear, showing excellent agreement. All products can be downloaded via a Globus endpoint (see Data Availability section).

79 ASTRONOMY AND ASTROPHYSICS↗

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

Abstract Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.

Sehnal, David↗

Mathematics in modern immunology

Mathematical and statistical methods enable multidisciplinary approaches that catalyse discovery. Together with experimental methods, they identify key hypotheses, define measurable observables and reconcile disparate results. Here, we collect a representative sample of studies in T-cell biology that illustrate the benefits of modelling–experimental collaborations and that have proven valuable or even groundbreaking. Furthermore, we conclude that it is possible to find excellent examples of synergy between mathematical modelling and experiment in immunology, which have brought significant insight that would not be available without these collaborations, but that much remains to be discovered.

60 APPLIED LIFE SCIENCES↗

Assessing correlated truncation errors in modern nucleon-nucleon potentials

We test the BUQEYE model of correlated effective field theory (EFT) truncation errors on Reinert, Krebs, and Epelbaum's semilocal momentum-space implementation of the chiral EFT (𝜒⁢EFT ) expansion of the nucleon-nucleon (NN) potential. This Bayesian model hypothesizes that dimensionless coefficient functions extracted from the order-by-order corrections to NN observables can be treated as draws from a Gaussian process (GP). We combine a variety of graphical and statistical diagnostics to assess when predicted observables have a 𝜒⁢EFT convergence pattern consistent with the hypothesized GP statistical model. Our conclusions are that, first, the BUQEYE model is generally applicable to the potential investigated here, which enables statistically principled estimates of the impact of higher EFT orders on observables. Second, parameters defining the extracted coefficients such as the expansion parameter 𝑄 must be well chosen for the coefficients to exhibit a regular convergence pattern—a property we exploit to obtain posterior distributions for such quantities. Third, the assumption of GP stationarity across lab energy and scattering angle is not generally met; this necessitates adjustments in future work. We provide a workflow and interpretive guide for our analysis framework, and show what can be inferred about probability distributions for 𝑄, the EFT breakdown scale Λ 𝑏 , the scale associated with soft physics in the 𝜒⁢EFT potential 𝑚 eff , and the GP hyperparameters. All our results can be reproduced using a publicly available Jupyter notebook, which can be straightforwardly modified to analyze other 𝜒⁢EFT NN potentials.

Bayesian methods↗

Momentum distributions and short-range correlations in the deuteron and He 3 with modern chiral potentials

In this work we study momentum distributions and short-range correlation probabilities in A = 2 and A = 3 systems. First, we show results with phenomenological and meson-theoretic two- and three-nucleon forces to verify consistency with previous similar studies. We then apply most recent high-quality chiral nucleon-nucleon potentials up to fifth order in the chiral expansion together with the leading chiral three-nucleon force. The focal points of our investigations are the model dependence of one- and two-body momentum distributions and the impact of threebody forces on them.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗