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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR

The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The interaction between transport-segment DNA and topoisomerase IA—crystal structure of MtbTOP1 in complex with both G- and T-segments

Abstract Each catalytic cycle of type IA topoisomerases has been proposed to comprise multistep reactions. The capture of the transport-segment DNA (T-segment) into the central cavity of the N-terminal toroidal structure is an important action, which is preceded by transient gate-segment (G-segment) cleavage and succeeded by G-segment religation for the relaxation of negatively supercoiled DNA and decatenation of DNA. The T-segment passage in and out of the central cavity requires significant domain–domain rearrangements, including the movement of D3 relative to D1 and D4 for the opening and closing of the gate towards the central cavity. Here we report a direct observation of the interaction of a duplex DNA in the central cavity of a type IA topoisomerase and its associated domain–domain conformational changes in a crystal structure of a Mycobacterium tuberculosis topoisomerase I complex that also has a bound G-segment. The duplex DNA within the central cavity illustrates the non-sequence-specific interplay between the T-segment DNA and the enzyme. The rich structural information revealed from the novel topoisomerase–DNA complex, in combination with targeted mutagenesis studies, provides new insights into the mechanism of the topoisomerase IA catalytic cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Kaposi's sarcoma herpesvirus exploits the DNA damage response to circularize its genome

Abstract To establish lifelong, latent infection, herpesviruses circularize their linear, double-stranded, DNA genomes through an unknown mechanism. Kaposi's sarcoma (KS) herpesvirus (KSHV), a gamma herpesvirus, is tightly linked with KS, primary effusion lymphoma, and multicentric Castleman's disease. KSHV persists in latently infected cells as a multi-copy, extrachromosomal episome. Here, we show the KSHV genome rapidly circularizes following infection, and viral protein expression is unnecessary for this process. The DNA damage response (DDR) kinases, ATM and DNA-PKcs, each exert roles, and absence of both severely compromises circularization and latency. These deficiencies were rescued by expression of ATM and DNA-PKcs, but not catalytically inactive mutants. In contrast, γH2AX did not function in KSHV circularization. The linear viral genomic ends resemble a DNA double strand break, and non-homologous DNA end joining (NHEJ) and homologous recombination (HR) reporters indicate both NHEJ and HR contribute to KSHV circularization. Last, we show, similar to KSHV, ATM and DNA-PKcs have roles in circularization of the alpha herpesvirus, herpes simplex virus-1 (HSV-1), while γH2AX does not. Therefore, the DDR mediates KSHV and HSV-1 circularization. This strategy may serve as a general herpesvirus mechanism to initiate latency, and its disruption may provide new opportunities for prevention of herpesvirus disease.

Li, Shijun↗
DOE OSTI2024

CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration

Abstract The CRISPR/Cas system has emerged as a powerful tool for genome editing in metabolic engineering and human gene therapy. However, locating the optimal site on the chromosome to integrate heterologous genes using the CRISPR/Cas system remains an open question. Selecting a suitable site for gene integration involves considering multiple complex criteria, including factors related to CRISPR/Cas-mediated integration, genetic stability, and gene expression. Consequently, identifying such sites on specific or different chromosomal locations typically requires extensive characterization efforts. To address these challenges, we have developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool leverages 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. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in three diverse species: Saccharomyces cerevisiae, Cupriavidus necator, and HEK293T cells. In addition, we developed a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate that CRISPR-COPIES will serve as a valuable tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, enable rapid strain construction to produce valuable biochemicals, and support human gene and cell therapy applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

Abstract The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA’s versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

An unexpected hydratase synthesizes the green light-absorbing pigment fucoxanthin

Abstract The ketocarotenoid fucoxanthin and its derivatives can absorb blue–green light enriched in marine environments. Fucoxanthin is widely adopted by phytoplankton species as a main light-harvesting pigment, in contrast to land plants that primarily employ chlorophylls. Despite its supreme abundance in the oceans, the last steps of fucoxanthin biosynthesis have remained elusive. Here, we identified the carotenoid isomerase-like protein CRTISO5 as the diatom fucoxanthin synthase that is related to the carotenoid cis–trans isomerase CRTISO from land plants but harbors unexpected enzymatic activity. A crtiso5 knockout mutant in the model diatom Phaeodactylum tricornutum completely lacked fucoxanthin and accumulated the acetylenic carotenoid phaneroxanthin. Recombinant CRTISO5 converted phaneroxanthin into fucoxanthin in vitro by hydrating its carbon–carbon triple bond, instead of functioning as an isomerase. Molecular docking and mutational analyses revealed residues essential for this activity. Furthermore, a photophysiological characterization of the crtiso5 mutant revealed a major structural and functional role of fucoxanthin in photosynthetic pigment–protein complexes of diatoms. As CRTISO5 hydrates an internal alkyne physiologically, the enzyme has unique potential for biocatalytic applications. The discovery of CRTISO5 illustrates how neofunctionalization leads to major diversification events in evolution of photosynthetic mechanisms and the prominent brown coloration of most marine photosynthetic eukaryotes.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Exploration of Neutron-Rich Isotopes around N = 50 via the In-Flight Fission of a 345 MeV/Nucleon 238 U Beam

A search for new neutron-rich isotopes beyond $Z=28$ and $N=50$ was performed using a 345 MeV/nucleon $^{238}$U beam at RI Beam Factory in RIKEN Nishina Center. The BigRIPS separator and state-of-the-art radiation detectors were used to efficiently separate and identify the produced nuclei. For the first time, we have observed and determined the production cross sections for eight neutron-rich isotopes $^{72}$Cr, $^{74,75}$Mn, $^{77}$Fe, $^{79,80}$Co, $^{85}$Cu, and $^{90}$Ga. This study broadens our understanding of nuclear existence and paves the way for investigating the properties of neutron-rich medium-mass nuclei.

Shimizu, Yohei [RIKEN, Saitama (Japan); et al.]↗
DOE OSTI2022

Optimizing the Internal Cell Structure of the Radon Monitor Based on Electrostatic Collection Method

Abstract As Rn-222 decays, an alpha particle is emitted and the residual polonium nucleus recoils in the opposite direction. At the end of the recoil path, 88% of the polonium atoms have a positive charge and 12% are neutral. The electric potential distribution in the 60 ml hemispherical internal cell of the radon monitor based on electrostatic collection is studied for reducing the combined probability of the positively charged Po-218 and the OH− produced by the ionization of water vapour in the air. The COMSOL software is used to simulate the electric potential distribution in the internal cell of the radon monitor based on the electrostatic collection method at 27°C, a pressure of 0.1 Mpa. For improving the collection efficiency of Po-218 ions, the average collection time along vertical and oblique lines is calculated when the upper surface of the internal cell is plastic, uncharged metal and charged metal, respectively. Assuming that the gas in the internal cell is uniformly distributed, the results show that if the upper surface of the hemispherical internal cell is plastic or uncharged metal, the electric potential formed in the internal cell is more uniform, and it is beneficial to reduce the total collection time of the positively charged Po-218 ions, thereby improving collection efficiency. The simulation results can be used as an effective reference for optimizing the design of the internal cell structure of the radon monitor based on electrostatic collection method.

Fan, Zhongkai (ORCID:0000000181247459)↗
DOE OSTI2021

Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers

The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case, developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Carrier Localization and Spontaneous Formation of Two-Dimensional Polarization Domain in Halide Perovskites

Halide perovskites are known for their rich phase diagram and superior performance in diverse optoelectronics applications. The latter property is often attributed to the long electron-hole recombination time, whose underlying physical mechanism has been a long-standing controversy. In this Letter, we investigate the transport and localization properties of electron and hole carriers in a prototypical halide perovskite (CsPbBr 3 ), through ab initio tight-binding nonadiabatic dynamics approach for large-scale (tens of nm size) supercell calculations, to simulate electron and ion dynamics on the same footing. Here, we found distinct structural, lattice polarization, and electron-phonon coupling properties at low (below 100 K) and high temperatures, consistent with experimental observations. In particular, at low temperature we find spontaneous formation of polar grain boundaries in the nonpolar bulk systems, which result in two-dimensional polarization patterns that serve to localize and separate electrons and holes. We reveal phonon-assisted variable-range hopping mostly responsible for low-temperature transport, and their characteristic frequency correlates with temperature-dependent phonon power spectrum and energy oscillation frequency in nonadiabatic dynamics. We answer the critical questions of long electron-hole recombination lifetime at low temperature and offer the correlation among polarization domains, electron-phonon couplings, and photocarrier dynamics.

Carrier generation & recombination↗
DOE OSTI2025

Fermi-surface driven frustrations in charge ordered kagome metal LuNb 6 ⁢Sn 6

The charge density wave (CDW), a translational symmetry breaking electronic liquid, plays a pivotal role in correlated quantum materials, such as high-𝑇 𝑐 superconductors and topological semimetals. Recently, CDWs that possibly intertwine with superconductivity and magnetism are observed in various kagome metals. However, the nature of CDWs and the role of the Fermi-surface (FS) topology in these materials remain an unresolved challenge. In this paper, we reveal the formation of CDWs in the newly discovered kagome metal LuNb 6 ⁢Sn 6 . Here, we observe a ‘‘yield sign’’-like hollow triangular diffuse scattering pattern and nearly complete softening of a flat optical phonon band near 𝐐 𝐻 = (1/3,1/3,1/2). The scattering intensity of the diffuse scattering displays divergent behavior as decreasing temperature until 𝑇 CDW = 70 K, where a competing CDW at 𝑄 CDW = (1/3,1/3,1/3) emerges. Combined with scanning tunneling microscopy/spectroscopy and first-principles calculations, our observations support a Fermi-surface driven frustration that suppresses the leading CDW instability at 𝐐 𝐻 . This frustration is relieved by the emergence of a subleading CDW at 𝑄 CDW . These results provide insights into the interplay between the Fermi surface, strong electron-phonon coupling, and charge density wave formation in quantum materials.

Yang, F. Z. [Oak Ridge National Laboratory (ORNL),↗
DOE OSTI2026

Cryogenic growth of aluminum: Structural morphology, optical properties, superconductivity, and microwave dielectric loss

We explore the molecular beam epitaxy synthesis of superconducting aluminum thin films grown on c-plane sapphire substrates at cryogenic temperatures of 6 K and compare their behavior with films synthesized at room temperature. We demonstrate that cryogenic growth increases structural disorder, producing crystalline grains that modify the optical, electrical, and superconducting properties of aluminum. We observe that cryogenic deposition changes the color of aluminum from fully reflective to yellow and correlate the pseudodielectric function and reflectance with structural changes in the film. We find that smaller grain sizes enhance the superconductivity of aluminum, increasing its critical temperature and critical field. We then estimate the superconducting gap and coherence length of Cooper pairs in aluminum in the presence of disorder. In conclusion, we fabricate superconducting microwave resonators on these films and find that, independently of the growth temperature, the system is dominated by two-level system loss with similar quality factors in the high- and low-power regimes. We further measure a higher kinetic inductance in the cryogenically grown films.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Observation of Orbital-Selective Dual Modulations in an Anisotropic Antiferromagnetic Kagome Metal TbTi 3 ⁢Bi 4

Orbital selectivity is pivotal in dictating the phase diagrams of multiorbital systems, with prominent examples including the orbital-selective Mott phase and superconductivity. The intercalation of anisotropic layers represents an effective method for enhancing orbital selectivity and thereby shaping the low-energy physics of multiorbital systems. Despite its potential, related experimental studies, especially those elucidating the correlation between orbital selectivity and magnetism, remain limited. In this work, we systematically examine the interplay between orbital selectivity and magnetism in the newly discovered anisotropic kagome TbTi 3 ⁢Bi 4 single crystal, and report the coexistence of orbital-selective dual-band modulations (𝑞 1 ∼ 1/3⁢𝑎*, 𝑞 2 ∼ 0.28⁢𝑏*) within the antiferromagnetic (AFM) state. By combining soft x-ray and vacuum ultraviolet angle-resolved photoemission spectroscopy measurements, neutron powder diffraction, scanning tunneling microscopy, and density-functional-theory calculations, we identify these dual-band reconstructions as manifestations of the AFM order driven by a (approximately 1/3, 0.28, 0) nesting instability of the intercalated Tb 5⁢𝑑 𝑥⁢𝑧 orbitals. These orbital-selective modulations induce unusual momentum-dependent band folding and lead to the emergence of Dirac cones only at the $\bar{M}$ 1 point, signaling a topological phase transition in the AFM state. Importantly, the discovery of orbital-selective (approximately 1/3, 0.28, 0) AFM order offers crucial insights into the mechanism underlying the fractional magnetization plateau in this kagome AFM metal. Our findings not only underscore the essential role of both conducting and localized electrons in determining the magnetic orders of Ln⁢Ti 3 ⁢Bi 4 (Ln = lanthanide) kagome metals but also offer a pathway for manipulating magnetism through selective control of anisotropic electronic structures.

Zhang, Renjie [Shanghai Jiao Tong University (Chin↗
DOE OSTI2025

Fracton models from product codes

We explore a deep connection between fracton order and product codes. In particular, we propose and analyze conditions on classical seed codes which lead to fracton order in the resulting quantum product codes. Depending on the properties of the input codes, product codes can realize either Type-I or Type-II fracton models, in both nonlocal and local constructions. For the nonlocal case, we show that a recently proposed model of lineons on nonlocal graphs can be obtained as a hypergraph product code. Interestingly, constrained mobility in this model arises only from energy barriers associated with the graph. For the local case, we introduce a novel type of classical LDPC code defined on a planar aperiodic tiling. By considering the specific example of the pinwheel tiling, we demonstrate the systematic construction of local Type-I and Type-II fracton models as product codes. Our work establishes product codes as a natural setting for exploring fracton order.

Fractons↗
DOE OSTI2026

Validation of the DESI DR2 Ly⁢ 𝛼 BAO analysis using synthetic datasets

The second data release (DR2) of the Dark Energy Spectroscopic Instrument (DESI), containing data from the first three years of observations, doubles the number of Lyman-α (Ly α) forest spectra in DR1 and it provides the largest dataset of its kind. To ensure a robust validation of the baryonic acoustic oscillation (BAO) analysis using Ly α forests, we have made significant updates compared to DR1 to both the mocks and the analysis framework used in the validation. In particular, we present CoLoRe-QL, a new set of Lyα mocks that use a quasilinear input power spectrum to incorporate the nonlinear broadening of the BAO peak. Here, we have also increased the number of realizations used in the validation to 400, compared to the 150 realizations used in DR1. Finally, we present a detailed study of the impact of quasar redshift errors on the BAO measurement, and we compare different strategies to mask damped Lyman-α absorbers in our spectra. The BAO measurement from the Ly α dataset of DESI DR2 is presented in a companion publication.

Casas, L. [Institut de Física d’Altes Energies (IF↗
DOE OSTI2025

Coherent phonon pairs and rotational symmetry breaking of charge density wave order in the kagome superconductor CsV 3 Sb 5

Here, in this work we perform ultrafast time-resolved reflectivity measurements to study the symmetry breaking in the charge-density wave (CDW) phase of CsV 3 ⁢Sb 5 . By extracting the coherent phonon spectrum in the CDW phase of CsV 3 ⁢Sb 5 , we discover close phonon pairs near 1.3 THz and 3.1 THz, as well as a new mode at 1.84 THz. The 1.3 THz phonon pair and the 1.84 THz mode are observed up to the CDW transition temperature. Combining density-functional theory calculations, we show that these phonon pairs arise from the coexistence of Star of David and inverse Star of David distortions combined with sixfold rotational symmetry breaking. An anisotropy in the magnitude of transient reflectivity change is also revealed at the onset of CDW order. Our results thus indicate broken sixfold rotational symmetry in the charge-density wave state of CsV 3⁢ Sb 5 , along with the absence of nematic fluctuation above 𝑇 CDW . Meanwhile, the measured coherent phonon spectrum in the CDW phase of CsV 3 ⁢Sb 5−𝑥 ⁢Sn 𝑥 with 𝑥 = 0.03–0.04 matches the staggered inverse Star of David with interlayer 𝜋 phase shift. This CDW structure contrasts with undoped CsV3⁢Sb5 and explains the evolution from a phonon pair to a single mode at 1.3 THz by 𝑥 = 0.03–0.04 Sn doping.

Deng, Qinwen [Univ. of Pennsylvania, Philadelphia,↗
DOE OSTI2025

The Dark Energy Camera All Data Everywhere cosmic shear project V: Constraints on cosmology and astrophysics from 270 million galaxies across 13,000 deg$^2$ of the sky

We present constraints on models of cosmology and astrophysics using cosmic shear data vectors from three datasets: the northern and southern Galactic cap of the Dark Energy Camera All Data Everywhere (DECADE) project, and the Dark Energy Survey (DES) Year 3. These data vectors combined consist of 270 million galaxies spread across 13,000 ${\rm deg}^2$ of the sky. We first extract constraints for $Λ$CDM cosmology and find $S_8= 0.805^{+0.019}_{-0.019}$ and $Ω_{\rm m} = 0.262^{+0.023}_{-0.036}$, which is consistent within $1.9 σ$ of constraints from the Planck satellite. Extending our analysis to dynamical dark energy models shows that lensing provides some (but still minor) improvements to existing constraints from supernovae and baryon acoustic oscillations. Finally, we study six different models for the impact of baryons on the matter power spectrum. We show the different models provide consistent constraints on baryon suppression, and associated cosmology, once the astrophysical priors are sufficiently wide. Current scale-cut approaches for mitigating baryon contamination result in a residual bias of $\approx 0.3σ$ in the $S_8, Ω_{\rm m}$ posterior. Using all scales with dedicated baryon modeling leads to negligible improvement as the new information is used solely to self-calibrate the baryon model on small scales. Additional non-lensing datasets, and/or calibrations of the baryon model, will be required to access the full statistical power of the lensing measurements. The combined dataset in this work represents the largest lensing dataset to date (most galaxies, largest area) and provides an apt testing ground for analyses of upcoming datasets from Stage IV surveys. The DECADE shear catalogs, data vectors, and likelihoods are made publicly available.

Anbajagane, D. [Chicago U., Astron. Astrophys. Ctr↗
DOE OSTI2025

Reconstructing the Wave Function of Magnetic Topological Insulators MnBi 2 ⁢Te 4 and MnBi 4 ⁢Te 7 Using Spin-Resolved Photoemission

Despite their importance for exotic quantum effects, the surface electronic structure of magnetic topological insulators MnBi 2 ⁢Te 4 and MnBi 4 ⁢Te 7 remains poorly understood. Using high-efficiency spin- and angle-resolved photoemission spectroscopy, we directly image the spin-polarization and orbital character of the surface states in both compounds and map our observations onto a model wave function to describe the complex spin-orbital texture, which solidifies our understanding of the surface band structure by establishing the single-band nature of the most prominent states. Most importantly, our analysis reveals a new mechanism for reducing the magnetic gap of the topological surface states based on the orbital composition of the wave function.

Han, Xue [SLAC National Accelerator Laboratory (SL↗