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At least 361 records · Page 20

Web-accessible sorption database (Interim Progress Report)

This progress report (Level 4 Milestone Number M4SF-26LL010204053) summarizes research conducted at Lawrence Livermore National Laboratory (LLNL) within the Crystalline Host Rock Properties & Processes - LLNL Number SF-26LL01020405. This research is focused on the development of a web-accessible database of sorption data for minerals and rocks (bentonite backfill and crystalline host rock) that are likely to be present in a US hosted repository, including elevated temperature data that are expected in a DPC DGR scenario.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CyanoCyc cyanobacterial web portal

CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address the needs of the cyanobacterial research and biotechnology communities. The 277 annotated cyanobacterial genomes currently in CyanoCyc are supplemented with computational inferences including predicted metabolic pathways, operons, protein complexes, and orthologs; and with data imported from external databases, such as protein features and Gene Ontology (GO) terms imported from UniProt. Five of the genome databases have undergone manual curation with input from more than a dozen cyanobacteria experts to correct errors and integrate information from more than 1,765 published articles. CyanoCyc has bioinformatics tools that encompass genome, metabolic pathway and regulatory informatics; omics data analysis; and comparative analyses, including visualizations of multiple genomes aligned at orthologous genes, and comparisons of metabolic networks for multiple organisms. CyanoCyc is a high-quality, reliable knowledgebase that accelerates scientists’ work by enabling users to quickly find accurate information using its powerful set of search tools, to understand gene function through expert mini-reviews with citations, to acquire information quickly using its interactive visualization tools, and to inform better decision-making for fundamental and applied research.

59 BASIC BIOLOGICAL SCIENCES↗

Mercury Accumulation in a Stream Ecosystem: Linking Labile Mercury in Sediment Porewaters to Bioaccumulative Mercury in Trophic Webs

Mercury (Hg) deposition and accumulation in the abiotic and biotic environments of a stream ecosystem were studied. This study aimed to link labile Hg in porewater to bioaccumulative Hg in biota. Sediment cores, porewaters, and biota were sampled from four sites along the Fourmile Branch (SC, USA) and measured for total Hg (THg) and methyl-Hg (MHg) concentrations. Water quality parameters were also measured at the sediment–water interface (SWI) to model the Hg speciation. In general, Hg concentrations in porewaters and bulk sediment were relatively high, and most of the sediment Hg was in the solid phase as non-labile species. Surface sediment presented higher Hg concentrations than the medium and bottom layers. Mercury methylation and MHg production in the sediment was primarily influenced by sulfate levels, since positive correlations were observed between sulfate and Hg in the porewaters. The majority of Hg species at the SWI were in non-labile form, and the dominant labile Hg species was complexed with dissolved organic carbon. MHg concentrations in the aquatic food web biomagnified with trophic levels (biofilm, invertebrates, and fish), increasing by 3.31 times per trophic level. Based on the derived data, a modified MHg magnification model was established to estimate the Hg bioaccumulation at any trophic level using Hg concentrations in the abiotic environment (i.e., porewater).

54 ENVIRONMENTAL SCIENCES↗

TARDIS. II. Synergistic Density Reconstruction from Lyα Forest and Spectroscopic Galaxy Surveys with Applications to Protoclusters and the Cosmic Web

Looking at this work, we expand upon the Tomographic Absorption Reconstruction and Density Inference Scheme (TARDIS) in order to include multiple tracers while reconstructing matter density fields at Cosmic Noon (z ~ 2–3). In particular, we jointly reconstruct the underlying density field from simulated Lyα forest observations at z ~ 2.5 and an overlapping galaxy survey. We find that these data are synergistic, with the Lyα forest providing reconstruction of low-density regions and galaxy surveys tracing the density peaks. We find a more accurate power spectra reconstruction going to higher scales when fitting these two data sets simultaneously than when using either one individually. When applied to cosmic web analysis, we find that performing the joint analysis is equivalent to an Lγα survey with significantly increased sight-line spacing. Because we reconstruct the velocity field and matter field jointly, we demonstrate the ability to evolve the mock observed volume further to z = 0, allowing us to create a rigorous definition of a “protocluster” as regions that will evolve into clusters. We apply our reconstructions to study protocluster structure and evolution, finding for realistic survey parameters that we can provide accurate mass estimates of the z ≈ 2 structures and their z = 0 fate.

79 ASTRONOMY AND ASTROPHYSICS↗

Photometric Objects around Cosmic Webs (PAC) Delineated in a Spectroscopic Survey. I. Methods

We provide a method for estimating the projected density distribution ${\bar{n}}_{2}{w}_{p}({r}_{p})$ of photometric objects around spectroscopic objects in a spectroscopic survey. This quantity describes the distribution of photometric sources with certain physical properties (e.g., luminosity, mass, and color) around cosmic webs (PAC) traced by the spectroscopic objects. The method can make full use of current and future deep and wide photometric surveys to explore the formation of galaxies up to medium redshift (z s < 2) 3 with the aid of cosmological spectroscopic surveys that sample only a fairly limited species of objects (e.g., emission line galaxies). As an example, we apply the PAC method to the CMASS spectroscopic and HSC-SSP PDR2 photometric samples to explore the distribution of galaxies for a wide range of stellar masses from 10 9.0 to 10 12.0 M ⊙ around massive galaxies at z s ≈ 0.6. Using the abundance-matching method, we model ${\bar{n}}_{2}{w}_{p}({r}_{p})$ in N-body simulation using Markov chain Monte Carlo sampling, and we accurately measure the stellar–halo mass relation and stellar mass function for the whole mass range. We can also measure the conditional stellar mass function of satellites for central galaxies of different mass. The PAC method has many potential applications for studying the evolution of galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

Photometric Objects Around Cosmic Webs (PAC) Delineated in a Spectroscopic Survey. III. Accurate Measurement of Galaxy Stellar Mass Function with the Aid of Cosmological Redshift Surveys

We present a novel method to accurately measure the galaxy stellar mass function (GSMF) based upon the Photometric objects Around Cosmic webs (PAC) method developed in our first paper (Paper I) of the series. The method allows us to measure the GSMF to a lower-mass end that is not accessible to the spectroscopic sample used in the PAC. Compared with Paper I, the current measurement of GSMF is direct and model independent. We measure the GSMFs in the redshift ranges of z$^{3}_{s}$ < 0.2, 0.2 < z s < 0.4, and 0.5 < z s < 0.7 down to stellar masses of M* = 10 8.2 , 10 10.6 , and 10 10.6 M ⊙ , using the data from the Dark Energy Spectroscopic Instrument (DESI) Legacy Imaging Surveys and the spectroscopic samples of Slogan Digital Sky Survey (i.e., Main, LOWZ, and CMASS samples). Our results show that there is no evolution of GSMF from z s = 0.6 to z s = 0.1 for M* > 10 10.6 M ⊙ , and that there is a clear upturn at M* ≈ 10 9.5 M ⊙ toward smaller galaxies in the local GMSF at z s = 0.1. We provide an accurate double Schechter fit to the local GSMF for the entire range of M* and a table of our measurements at the three redshifts, which can be used to test theories of galaxy formation. Our method can achieve an accurate measurement of GSMF to the stellar mass limit where the spectroscopic sample is already highly incomplete (e.g., ~ 10 -3 ) for its target selection.

79 ASTRONOMY AND ASTROPHYSICS↗

Photometric Objects Around Cosmic Webs (PAC) Delineated in a Spectroscopic Survey. IV. High-precision Constraints on the Evolution of the Stellar–Halo Mass Relation at Redshift z < 0.7

Taking advantage of the Photometric objects Around Cosmic webs method developed in Paper I, we measure the excess surface density $\overline{n}$ 2 w p of the photometric objects around spectroscopic objects down to stellar masses 10 8.0 M ⊙ , 10 9.2 M ⊙ , and 10 9.8 M ⊙ in the redshift ranges of z s < 0.2, 0.2 < z s < 0.4, and 0.5 < z s < 0.7, respectively, using data from the DESI Legacy Imaging Surveys and spectroscopic samples from the Sloan Digital Sky Survey (i.e., the Main, LOWZ, and CMASS samples). We model the measured in an N-body simulation, using the abundance matching method, and we constrain the stellar–halo mass relations (SHMRs) in the three redshift ranges to percent levels. With the accurate modeling, we demonstrate that the stellar mass scatter for a given halo mass is nearly a constant, and that the empirical form of Behroozi et al. describes the SHMR better than the double-power-law form at low mass. Our SHMR accurately captures the downsizing of massive galaxies from z s = 0.7, while it also indicates that small galaxies are still growing faster than their host halos. The galaxy stellar mass functions (GSMFs) from our modeling are in perfect agreement with the model-independent measurements in Paper III, although the current work extends the GSMFs to a much smaller stellar mass. Based on the GSMFs and the SHMRs, we derive the stellar mass completeness and halo occupation distributions for the LOWZ and CMASS samples, which are useful for correctly interpreting their cosmological measurements, such as galaxy–galaxy lensing and redshift space distortion.

79 ASTRONOMY AND ASTROPHYSICS↗

Filaments of the Slime Mold Cosmic Web and How They Affect Galaxy Evolution

Abstract We present a novel approach for identifying cosmic web filaments within theDisPerSEstructure identification framework, using cosmic density field estimates from the Monte Carlo Physarum Machine (MCPM), inspired by the slime mold organism. We apply our method to the IllustrisTNG (TNG100) cosmological simulations and investigate the impact of filaments on galaxies. The MCPM density field is superior to the Delaunay tessellation field estimator in tracing the true underlying matter distribution and allows filaments to be identified with higher fidelity, finding more low-prominence/diffuse filaments. Using our new filament catalogs, we find that ≳90% of galaxies are located within ∼1.5 Mpc of a filamentary spine, with little change in the median star formation activity with distance to the nearest filament. Instead, we uncover a differential effect of the local filament line density, Σ fil (MCPM)—the total MCPM overdensity per unit length along a filament segment—on galaxy formation: most galaxies are quenched and gas-poor near high-line density filaments atz≤ 1. At earlier times, the filamentary environment appears to have no effect on galactic gas supply and quenching. Atz= 0, quenching in log ( M * / M ⊙ ) ≳ 10.5 galaxies is mainly driven by mass, while lower-mass galaxies are significantly affected by the filament line density. Satellites are far more susceptible to filaments than centrals. The local environments of massive halos are not sufficient to account for the effect of filament line density on gas removal and quenching. Our new approach holds great promise for observationally identifying filaments from galaxy surveys such as SDSS and DESI.

Astronomy & Astrophysics↗

JHTDB-wind: a web-accessible large-eddy simulation database of a wind farm with virtual sensor querying

This paper introduces JHTDB-wind (https://turbulence.idies.jhu.edu/datasets/windfarms, last access: 11 November 2025), a publicly accessible database containing large-eddy simulation (LES) data from wind farms. Building on the framework of the Johns Hopkins Turbulence Database (JHTDB), which hosts direct numerical simulation (DNS) and some LES datasets of canonical turbulent flows, JHTDB-wind stores the 4D space–time history of the flow and provides users the ability to access and query the data via a web-based virtual sensor interface. The initial dataset comprises LES results from a large wind farm with 10×6 turbines, modeled using a filtered actuator line method, under conventionally neutral atmospheric conditions. These data comprise 1 h (hour) of flow field data (velocity, pressure, potential temperature deviation, subgrid-scale (SGS) eddy viscosity, and turbine forces, approximately 15 TB (terabytes) and wind turbine data – including both turbine-level operational quantities and blade-level aerodynamic quantities (approximately 1.3 TB) – stored in Zarr and Parquet formats, respectively. Data retrieval is facilitated by the giverny Python package, allowing remote users to query the database in Python or MATLAB (C and Fortran support are available for flow field data). This paper details the simulation setup and demonstrates data access through examples that analyze wind farm flow structures and turbine performance. The framework is extensible to future datasets, including the JHTDB-wind diurnal cycle simulation analyzed in Xiao et al. (2025).

17 WIND ENERGY↗

CRISPR-COPIES: Web Tool

CRISPR/Cas system has emerged as a powerful genome-editing tool for metabolic engineering and human gene therapy. However, the conundrum of where to integrate heterologous genes on the chromosome using the CRISPR/Cas system remains an open question. Selecting a site for gene integration requires incorporation of complex criteria such as factors involved in CRISPR/Cas-mediated integration, genetic stability, and gene expression and therefore, usually requires strenuous characterization of sites on particular or different chromosomal locations. To address these issues, we developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. The tool applies ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. This submission contains the code we developed to create a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate CRISPR-COPIES will serve as a useful tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, rapid strain construction to produce valuable biochemicals, and human gene and cell therapy.

Bioinformatics↗

Web belt load measuring instrument has excellent stability

Web belt system measures belt or strap load. It is partially disassembled and installed on an existing belt without cutting or re-threading the belt. A strain gage, installed on one of the support beams, eliminates errors due to uneven loading.

Walker, R. R.↗