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At least 109 records · Page 6

Advanced Polymer Characterization: Modular Operations for Spectral Alignment by Iterative Compression (MOSAIC)

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry encodes structural information across diverse homo- and copolymer ensembles, yet decrypting these spectra requires a systematic analytical approach. We introduce Modular Operations for Spectral Alignment by Iterative Compression (MOSAIC)─a general cipher algorithm that applies modular arithmetic to filter monomer-derived mass contributions and cluster MALDI peaks by nonconstitutional repeating units (non-CRUs). MOSAIC performs sequential modular operations using monomer mass differences as base units to compress complex spectral data, revealing end-group distributions and comonomer incorporation. As a demonstration, we applied MOSAIC to five copolymers formed by two different polymerization mechanisms. Furthermore, the resulting remainder–mass plots clearly resolve polymer homologs with distinct non-CRUs into visually apparent clusters, enabling intuitive assignment of mass spectral features.

Wang, Hanlin M. [University of Illinois at Urbana−↗

A strong blend in the morning: studying the circumgalactic medium before cosmic noon with strong, blended Ly α forest systems

ABSTRACT We study of the properties of a new class of circumgalactic medium absorbers identified in the Ly α forest: ‘Strong, Blended Lyman-α’ (or SBLA) absorption systems. We study SBLAs at 2.4 < z < 3.1 in SDSS-IV/eBOSS spectra by their strong extended Ly α absorption complexes covering 138 $\, \, {\rm km}\, {\rm s}^{-1}$ with an integrated $\log (N_{\rm H\, {\small I}}/\mathrm{cm}^{-2}) =16.04$$\substack{+0.05 \\ -0.06}$ and Doppler parameter b = 18.1$\substack{+0.7 \\ -0.4}$$\, \, {\rm km}\, {\rm s}^{-1}$. Clustering with the Ly α forest provides a large-scale structure bias of b = 2.34 ± 0.06 and halo mass estimate of $M_h \approx 10^{12}\, h^{-1}\, {\rm M_{\odot }}$ for our SBLA sample. We measure the ensemble mean column densities of 22 metal features in the SBLA composite spectrum and find that no single-population multiphase model for them is viable. We therefore explore the underlying SBLA population by forward modelling the SBLA absorption distribution. Based on covariance measurements and favoured populations we find that ≈25 per cent of our SBLAs have stronger metals. Using silicon only we find that our strong metal SBLAs trace gas with a log (nH/cm−3) > −2.40 for T = 103.5 K and show gas clumping on <210 parsec scales. We fit multiphase models to this strong subpopulation and find a low ionization phase with nH = 1 cm−3, T = 103.5 K, and [X/H] = 0.8, an intermediate ionization phase with log (nH/cm−3) = −3.05, T = 103.5 K and [X/H] = −0.8, and a poorly constrained higher ionization phase. We find that the low ionization phase favours cold, dense super-solar metallicity gas with a clumping scale of just 0.009 parsecs.

Morrison, Sean (ORCID:0000000267702627)↗

Timing of pulsars in the globular cluster omega centauri

We present the timing of the first five millisecond pulsars discovered in the globular cluster Omega Centauri and the discovery of a pulsar with a spin period of 3.68 ms. With a timing baseline of ~3.5 yr we are able to measure the derivative of the spin frequency ($\dot{\nu }$) for the first five pulsars. Upper limits on the pulsar line-of-sight acceleration are estimated and compared with predictions based on analytical models of the cluster. We find that PSRs J1326-4728B and D show large negative accelerations, which are in tension with the minimum acceleration predicted by analytical models. We searched for pulsed γ-ray signals using 14.3 yr of data from the Fermi Large Area Telescope. Although we found no evidence for γ-ray pulsations, PSRs J1326-4728A, B, C, and E are associated with X-ray sources. This suggests that the observed γ-ray emission from Omega Centauri is likely caused by the emission of the ensemble of MSPs. Finally, the linearly polarized emission from PSR J1326-4728A yields a rotation measure of -18 ± 8 rad m -2 .

79 ASTRONOMY AND ASTROPHYSICS↗

Scalable molecular dynamics on CPU and GPU architectures with NAMD

NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

high-performance computing↗

An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function

The evolutionary rates of functionally related genes often covary. We present a gene coevolution network inferred from examining nearly 3 million orthologous gene pairs from 332 budding yeast species spanning ~400 million years of evolution. Network modules provide insight into cellular and genomic structure and function. Examination of the phenotypic impact of network perturbation using deletion mutant data from the baker’s yeast Saccharomyces cerevisiae, which were obtained from previously published studies, suggests that fitness in diverse environments is affected by orthologous gene neighborhood and connectivity. Mapping the network onto the chromosomes of S. cerevisiae and Candida albicans revealed that coevolving orthologous genes are not physically clustered in either species; rather, they are often located on different chromosomes or far apart on the same chromosome. The coevolution network captures the hierarchy of cellular structure and function, provides a roadmap for genotype-to-phenotype discovery, and portrays the genome as a linked ensemble of genes.

59 BASIC BIOLOGICAL SCIENCES↗

Dark Energy Survey Year 3 results: redshift calibration of the weak lensing source galaxies

ABSTRACT Determining the distribution of redshifts of galaxies observed by wide-field photometric experiments like the Dark Energy Survey (DES) is an essential component to mapping the matter density field with gravitational lensing. In this work we describe the methods used to assign individual weak lensing source galaxies from the DES Year 3 Weak Lensing Source Catalogue to four tomographic bins and to estimate the redshift distributions in these bins. As the first application of these methods to data, we validate that the assumptions made apply to the DES Y3 weak lensing source galaxies and develop a full treatment of systematic uncertainties. Our method consists of combining information from three independent likelihood functions: self-organizing map p(z) (sompz), a method for constraining redshifts from galaxy photometry; clustering redshifts (WZ), constraints on redshifts from cross-correlations of galaxy density functions; and shear ratios (SRs), which provide constraints on redshifts from the ratios of the galaxy-shear correlation functions at small scales. Finally, we describe how these independent probes are combined to yield an ensemble of redshift distributions encapsulating our full uncertainty. We calibrate redshifts with combined effective uncertainties of σ〈z〉 ∼ 0.01 on the mean redshift in each tomographic bin.

79 ASTRONOMY AND ASTROPHYSICS↗

Electronic Spin Relaxation and Clustering in High-Pressure High-Temperature Synthesized Microcrystalline Diamond Particles with Reduced Nitrogen Content

The negatively charged nitrogen-vacancy (NV – ) color center in diamonds is widely studied because of numerous applications of this unique quantum system in sensing and quantum information sciences. While substitutional nitrogen is required to form the NV – centers in diamond, it also yields other paramagnetic defects─primarily the neutrally charged substitutional nitrogen centers (P1)─that decrease NV – spin coherence, which in turn degrades performance in applications. Herein, we investigate high-pressure high-temperature synthesized diamond microparticles (ca. 140–185 μm) having lower─ranging from 3 to 38 ppm─than the typical nitrogen content of type 1b diamond ( ca. 100 ppm and higher) typically used for the production of fluorescent diamond particles with NV – centers. A suite of electron paramagnetic resonance, optically detected magnetic resonance, and nuclear magnetic resonance methods are used to characterize spin properties of P1 and NV – centers in the particles. Upon decreasing the nitrogen content from 29 to 3 ppm, the ensemble NV – T 2 relaxation time increased by about 3-fold as measured directly in the Hahn Echo experiment at magnetic field of 1.2 T. Analysis of electronic relaxation of P1 centers revealed the existence of at least two distinct populations of P1 centers, consisting of fast and slower relaxing spins and allowed for an estimation of local concentrations. Even with <10 ppm nitrogen contents, the analysis indicated a highly heterogeneous distribution of P1 centers, suggesting the possibility of P1 spin clustering even at low nitrogen concentrations. The combined data demonstrate that the particles prepared from HPHT diamond with a low nitrogen content offer improved spin properties that are beneficial for NV – sensing applications.

Carbon↗

Variations in the Width, Density, and Direction of the Palomar 5 Tidal Tails

Stars that escape globular clusters form tidal tails that are predominantly shaped by the global distribution of mass in the Galaxy, but also preserve a historical record of small-scale perturbations. Using deep grz photometry from DECaLS, we present highly probable members of the tidal tails associated with the evaporating globular cluster Palomar 5. These data yield the cleanest view of a stellar stream beyond ≈20 kpc and reveal: (1) a wide, low surface-brightness extension of the leading tail; (2) significant density variations along the stream; and (3) sharp changes in the direction of both the leading and the trailing tail. In the fiducial Milky Way model, a rotating bar perturbs the Palomar 5 tails and can produce streams with similar width and density profiles to those observed. However, the deviations of the stream track in this simple model do not match those observed in the Palomar 5 trailing tail, indicating the need for an additional source of perturbation. These discoveries open up the possibility of measuring the population of perturbers in the Milky Way, including dark-matter subhalos, with an ensemble of stellar streams and deep photometry alone.

79 ASTRONOMY AND ASTROPHYSICS↗

Spin-free formulation of the multireference driven similarity renormalization group: A benchmark study of first-row diatomic molecules and spin-crossover energetics

We report a spin-free formulation of the multireference (MR) driven similarity renormalization group (DSRG) based on the ensemble normal ordering of Mukherjee and Kutzelnigg (1997). This ensemble averages over all microstates of a given total spin quantum number, and therefore, it is invariant with respect to SU(2) transformations. As such, all equations may be reformulated in terms of spin-free quantities and they closely resemble those of spin-adapted closed-shell coupled cluster (CC) theory. The current implementation is used to assess the accuracy of various truncated MR-DSRG methods (perturbation theory up to third order and iterative methods with single and double excitations) in computing the constants of 33 first-row diatomic molecules. The accuracy trends for these first-row diatomics are consistent with our previous benchmark on a small subset of closed-shell diatomic molecules. We then present the first MR-DSRG application on transition-metal complexes by computing the spin splittings of the [Fe(H 2 O) 6 ] 2+ and [Fe(NH 3 ) 6 ] 2+ molecules. A focal point analysis (FPA) shows that third-order perturbative corrections are essential to achieve reasonably converged energetics. The FPA based on the linearized MR-DSRG theory with one- and two-body operators and up to a quintuple- ζ basis set predicts the spin splittings of [Fe(H 2 O) 6 ] 2+ and [Fe(NH 3 ) 6 ] 2+ to be –35.7 and –17.1 kcal mol –1 , respectively, showing good agreement with the results of local CC theory with singles, doubles, and perturbative triples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Confocal Raman Microscopy as a Probe of Material Deconstruction in Processed Low-Density Polyethylene Particles

Confocal Raman microscopy was applied to detect structural change within individual particles of low-density polyethylene (LDPE) following chemical and electrochemical processing steps that aimed to facilitate material decomposition. A high numerical aperture (NA) oil-immersion objective enabled depth-profiling through the near surface region (20 μm–40 μm) of irregularly shaped particles with an axial spatial resolution < 2 μm estimated from measurements of instrument detection efficiency profiles. Changes in vibrational bands sensitive to polyethylene crystallinity were evident following treatments and linked to the release of low molecular weight compounds present as additives and products of processing. Effects of processing were probed by monitoring the rise of Raman scattering intensity in vibrational modes associated with polyethylene chains in a zig-zag (trans) conformation near 1128 cm –1 , 1294 cm –1 , and 1418 cm –1 , signaling chain clustering and development of organized, crystalline-like assemblies. Pristine LDPE particles displayed a uniform structure across the near surface region, while particles treated initially with chemical extractant and then further processed displayed increasingly enhanced crystallinity up to the maximum depth probed (40 μm). As a step toward measurements on ensembles of particles, least squares modeling was adapted to derive pure component spectra reflecting crystallinity change within spectral datasets. The work demonstrates high spatial resolution Raman depth-profiling for the characterization of processed polymers using a high NA immersion objective to overcome the limitations of air-objectives often used for confocal Raman microscopy.

Wahiduzzaman, Md. [Department of Chemistry and Bio↗

Real-time dynamics and structures of supported subnanometer catalysts via multiscale simulations

Understanding the performance of subnanometer catalysts and how catalyst treatment and exposure to spectroscopic probe molecules change the structure requires accurate structure determination under working conditions. Experiments lack simultaneous temporal and spatial resolution and could alter the structure, and similar challenges hinder first-principles calculations from answering these questions. Here, we introduce a multiscale modeling framework to follow the evolution of subnanometer clusters at experimentally relevant time scales. We demonstrate its feasibility on Pd adsorbed on CeO 2 (111) at various catalyst loadings, temperatures, and exposures to CO. We show that sintering occurs in seconds even at room temperature and is mainly driven by free energy reduction. It leads to a kinetically (far from equilibrium) frozen ensemble of quasi-two-dimensional structures that CO chemisorption and infrared experiments probe. CO adsorption makes structures flatter and smaller. High temperatures drive very rapid sintering toward larger, stable/metastable equilibrium structures, where CO induces secondary structure changes only.

36 MATERIALS SCIENCE↗

Precision redshift-space galaxy power spectra using Zel'dovich control variates

Numerical simulations in cosmology require trade-offs between volume, resolution and run-time that limit the volume of the Universe that can be simulated, leading to sample variance in predictions of ensemble-average quantities such as the power spectrum or correlation function(s). Sample variance is particularly acute at large scales, which is also where analytic techniques can be highly reliable. This provides an opportunity to combine analytic and numerical techniques in a principled way to improve the dynamic range and reliability of predictions for clustering statistics. In this paper we extend the technique of Zel'dovich control variates, previously demonstrated for 2-point functions in real space, to reduce the sample variance in measurements of 2-point statistics of biased tracers in redshift space. We demonstrate that with this technique, we can reduce the sample variance of these statistics down to their shot-noise limit out to k ~ 0.2 h Mpc -1 . This allows a better matching with perturbative models and improved predictions for the clustering of e.g. quasars, galaxies and neutral Hydrogen measured in spectroscopic redshift surveys at very modest computational expense. We discuss the implementation of ZCV, give some examples and provide forecasts for the efficacy of the method under various conditions.

79 ASTRONOMY AND ASTROPHYSICS↗

Influence of Local Water Vapor Analysis Uncertainty on Ensemble Forecasts of Tropical Cyclogenesis Using Hurricane Irma (2017) as a Testbed

Abstract Tropical cyclone formation is known to require abundant water vapor in the lower to middle troposphere within the incipient disturbance. In this study, we assess the impacts of local water vapor analysis uncertainty on the predictability of the formation of Hurricane Irma (2017). To this end, we reduce the magnitude of the incipient disturbance’s water vapor perturbations obtained from an ensemble-based data assimilation system that constrained moisture by assimilating all-sky infrared and microwave radiances. Five-day ensemble forecasts are initialized two days before genesis using each set of modified analysis perturbations. Growth of convective differences and intensity uncertainty are evaluated for each ensemble forecast. We observe that when initializing an ensemble forecast with only moisture uncertainty within the incipient disturbance, the resulting intensity uncertainty at every lead time exceeds half that of an ensemble containing initial perturbations to all variables throughout the domain. Although ensembles with different initial moisture uncertainty amplitudes reveal a similar pathway to genesis, uncertainty in genesis timing varies substantially across ensembles since moister members exhibit earlier spinup of the low-level vortex. These differences in genesis timing are traced back to the first 6–12 h of integration, when differences in the position and intensity of mesoscale convective systems across ensemble members develop more quickly with greater initial moisture uncertainty. In addition, the rapid growth of intensity uncertainty may be greatly modulated by the diurnal cycle. Ultimately, this study underscores the importance of targeting the incipient disturbance with high spatiotemporal water vapor observations for ingestion into data assimilation systems. Significance Statement Hurricanes form from clusters of thunderstorms that organize into a coherent system. One of the key ingredients for the formation process is an abundance of moisture. In this study, we test the sensitivity of hurricane formation to the initial moisture content in the vicinity of the cluster of thunderstorms that would become Hurricane Irma (2017). To do so, we initialize sets of forecasts each having a different variability of initial moisture content within the embryonic disturbance. Our results show that the predictability of hurricane formation is highly dependent on the uncertainty of the moisture content within the initial disturbance. Consequently, more high-quality observations of the moisture within the precursor disturbances to hurricanes are expected to improve forecasts of their formation.

Hartman, Christopher M.↗

Nature of molybdenum carbide surfaces for catalytic hydrogen dissociation using machine-learned potentials: an ensemble-averaged perspective

Molybdenum carbides with an electronic structure similar to noble metals have gained attention as a promising low-cost catalyst for biomass valorization and the hydrogen evolution reaction. However, our fundamental understanding of the catalyst surface and how different phases of these catalysts behave at varying reaction conditions is limited to ground state density functional theory calculations as ab initio molecular dynamics (AIMD) is computationally prohibitive at relevant length and time scales. Here, in this work, we train a multi-atomic cluster expansion (MACE) machine-learned interatomic potentials (MLIP) to study hydrogen dissociation and dynamics over Mo, δ-MoC, α-Mo 2 C, and β-Mo 2 C surfaces at varying temperatures and hydrogen partial pressures. Our simulations identify unique and different molecular and atomic hydrogen adsorption sites on different surfaces that do not depend on the temperature. At low hydrogen pressures, the surface coverage is monolayer, which transitions to two-layer adsorption at higher pressures. We find that atomic hydrogen diffusion and recombinations are preferred over molybdenum atom hollow sites, while the diffusion over carbon-terminated facets was negligible, signifying particularly strong C–H interactions. In contrast, molecular hydrogen adsorption occurs mostly atop Mo or the bridging sites. At a comparable hydrogen loading, β-Mo 2 C (001) is the most active surface for hydrogen dissociation reaction. This work provides insights into the dynamic nature of the hydrogen dissociation chemistry and the diversity of hydrogen adsorption sites on molybdenum carbides.

08 HYDROGEN↗

From Points to Planes: A Workflow for Converting Three‐Dimensional Point Cloud Data Into Discrete Fracture Network Flow and Transport Models

We present the Point cLoud Algorithm for NEtwork Extraction of Discrete Fracture Networks (PLANE-DFN), a point cloud–based algorithm for automatic fracture network extraction designed to support discrete fracture network (DFN) modeling workflows. PLANE-DFN segments three-dimensional fracture planes from raw point cloud data using RANdom SAmple Consensus coupled with statistical outlier removal and density-based clustering to isolate individual fracture features. Each candidate plane is constrained against site-specific structural constraints based on strike and dip. After segmentation, each fracture is converted into a 2-D convex polygon suitable for meshing and simulation. The PLANE-DFN algorithm is validated by comparing geometric and flow and transport data against data from dfnWorks simulations with ensembles of plane-fit networks. We find that the flow and transport in plane-fit networks are comparable to dfnWorks-generated networks when realistic network geometry is maintained. The PLANE-DFN algorithm provides an automated and streamlined workflow to transform point clouds of data into DFN network geometry.

54 ENVIRONMENTAL SCIENCES↗

Structure based virtual screening identifies small molecule effectors for the sialoglycan binding protein Hsa

Infective endocarditis (IE) is a cardiovascular disease often caused by bacteria of the viridans group of streptococci, which includes Streptococcus gordonii and Streptococcus sanguinis. Previous research has found that serine-rich repeat (SRR) proteins on the S. gordonii bacterial surface play a critical role in pathogenesis by facilitating bacterial attachment to sialylated glycans displayed on human platelets. Despite their important role in disease progression, there are currently no anti-adhesive drugs available on the market. Here, we performed structure-based virtual screening using an ensemble docking approach followed by consensus scoring to identify novel small molecule effectors against the sialoglycan binding domain of the SRR adhesin protein Hsa from the S. gordonii strain DL1. The screening successfully predicted nine compounds which were able to displace the native ligand (sialyl-T antigen) in an in vitro assay and bind competitively to Hsa. Furthermore, hierarchical clustering based on the MACCS fingerprints showed that eight of these small molecules do not share a common scaffold with the native ligand. This study indicates that SRR family of adhesin proteins can be inhibited by diverse small molecules and thus prevent the interaction of the protein with the sialoglycans. This opens new avenues for discovering potential drugs against IE.

60 APPLIED LIFE SCIENCES↗

Coupled cluster and dislocation dynamics modeling of microstructure evolution in irradiated materials

We develop here a coupled cluster and dislocation dynamics framework to study the microstructure evolution of irradiated materials. The framework not only accounts for the three dimensional diffusion of radiation-generated clusters, but also their interaction with dislocation networks and the resultant climb motion of discrete dislocations within finite crystals. The framework is solved with a superposition solution scheme, and is applied to investigate the evolution of the irradiation-induced dislocation loops in zirconium (Zr), considering the effects of various bias factors including the diffusion anisotropy difference (DAD) of interstitials and interstitial clusters, the dislocation bias of defects to discrete dislocation segments, and the production bias of defects from the radiation cascade. We find that the DAD is the most critical factor influencing the kinetics of the loop evolution in Zr, while the recombination/interaction of mobile defects can induce a strong spatial dependence of the loop evolution together with the DAD. Here, the method is also adopted to study the evolution of interstitial $\langle$a$\rangle$ and vacancy $\langle$c$\rangle$ dislocation loop ensembles consistent with the microstructure observed during irradiation-induced growth of Zr. Our findings not only reveal the spatial dependence of the size and ellipticity of the dislocation loops, but also suggest a limit on the anisotropy factor of interstitials to reproduce the co-growth of $\langle$a$\rangle$ and $\langle$c$\rangle$ loops in zirconium, in good agreement with experimental observations and other simulation results.

Bias factors↗

Clustering of LRGs in the DECaLS DR8 Footprint: Distance Constraints from Baryon Acoustic Oscillations Using Photometric Redshifts

A photometric redshift sample of luminous red galaxies (LRGs) obtained from the DECam Legacy Survey (DECaLS) is analyzed to probe cosmic distances by exploiting the wedge approach of the two-point correlation function. Although the cosmological information is highly contaminated by the uncertainties existing in the photometric redshifts from the galaxy map, an angular diameter distance can be probed at the perpendicular configuration in which the measured correlation function is minimally contaminated. An ensemble of wedged correlation functions selected up to a given threshold based on having the least contamination was studied in previous work (Sridhar & Song 2019) using simulations, and the extracted cosmological information was unbiased within this threshold. Furthermore, we apply the same methodology for analyzing the LRG sample from DECaLS, which will provide the optical imaging for targeting two-thirds of the Dark Energy Spectroscopic Instrument footprint and measure the angular diameter distances at z = 0.69 and z = 0.87 to be D A (0.697) = (1529 ± 73 Mpe)(r d /r d.fid ) and D A (0.874) = (1674 ± 102 Mpe)(r d /r d.fid ) with a fractional error of 4.77% and 6.09%, respectively. We obtain a value of H 0 = 66.58 ± 5.31 km s -1 Mpc -1 , which supports the H 0 measured by all other baryon acoustic oscillation results and is consistent with the ΛCDM model.

79 ASTRONOMY AND ASTROPHYSICS↗