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DOE OSTI2023

gRNA-SeqRET: a universal tool for targeted and genome-scale gRNA design and sequence extraction for prokaryotes and eukaryotes

High-throughput genetic screening is frequently employed to rapidly associate gene with phenotype and establish sequence-function relationships. With the advent of CRISPR technology, and the ability to functionally interrogate previously genetically recalcitrant organisms, non-model organisms can be investigated using pooled guide RNA (gRNA) libraries and sequencing-based assays to quantitatively assess fitness of every targeted locus in parallel. To aid the construction of pooled gRNA assemblies, we have developed an in silico design workflow for gRNA selection using the gRNA Sequence Region Extraction Tool (gRNA-SeqRET). Built upon the previously developed CCTop, gRNA-SeqRET enables automated, scalable design of gRNA libraries that target user-specified regions or whole genomes of any prokaryote or eukaryote. Additionally, gRNA-SeqRET automates the bulk extraction of any regions of sequence relative to genes or other features, aiding in the design of homology arms for insertion or deletion constructs. We also assess in silico the application of a designed gRNA library to other closely related genomes and demonstrate that for very closely related organisms Average Nucleotide Identity (ANI) > 95% a large fraction of the library may be of relevance. The gRNA-SeqRET web application pipeline can be accessed at https://grna.jgi.doe.gov. The source code is comprised of freely available software tools and customized Python scripts, and is available at https://bitbucket.org/berkeleylab/grnadesigner/src/master/ under a modified BSD open-source license (https://bitbucket.org/berkeleylab/grnadesigner).

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1984

Research in extragalactic astrophysics

The spatial distribution of clusters of galaxies and the large scale structure of the universe is investigated. Correlations in the spatial cluster distribution are much stronger than those seen for galaxies, and over scales much larger than previously anticipated. The following main studies are completed and published; (1) The determination of the correlation functions of rich clusters of galaxies, and its dependence on richness and other parameters. Very large scale structure exists in the universe, and rich clusters participate in this structure more efficiently than galaxies. (2) A complete catalog of superclusters, is determined. The selection criteria is that of a volume density enhancement, and is done in 3 dimensions. (3) The giant galaxy void in Bootes is found to be surrouned by rich, large superclusters from the catalog described above. (4) A very large scale void of rich clusters of galaxies is found in the study of the spatial distribution of rich clusters.

Bahcall, N.↗

DOE OSTI2024

Asymptotic Freedom at the Berezinskii-Kosterlitz-Thouless Transition without Fine-Tuning Using a Qubit Regularization

We propose a two-dimensional hard-core loop-gas model as a way to regularize the asymptotically free massive continuum quantum field theory that emerges at the Berezinskii-Kosterlitz-Thouless transition. Without fine-tuning, our model can reproduce the universal step-scaling function of the classical lattice X Y model in the massive phase as we approach the phase transition. This is achieved by lowering the fugacity of Fock-vacuum sites in the loop-gas configuration space to zero in the thermodynamic limit. Some of the universal quantities at the Berezinskii-Kosterlitz-Thouless transition show smaller finite size effects in our model as compared to the traditional X Y model. Our model is a prime example of qubit regularization of an asymptotically free massive quantum field theory in Euclidean space-time and helps understand how asymptotic freedom can arise as a relevant perturbation at a decoupled fixed point without fine-tuning. Published by the American Physical Society 2024

Physics↗

DOE OSTI2024

A Strong Gravitational Lens Is Worth a Thousand Dark Matter Halos: Inference on Small-scale Structure Using Sequential Methods

Strong gravitational lenses are a singular probe of the Universe’s small-scale structure—they are sensitive to the gravitational effects of low-mass (<10 10 M ⊙ ) halos even without a luminous counterpart. Recent strong-lensing analyses of dark matter structure rely on simulation-based inference (SBI). Modern SBI methods, which leverage neural networks as density estimators, have shown promise in extracting the halo-population signal. However, it is unclear whether the constraints from these models are limited by the methodology or the data. In this study, we introduce an accelerator-optimized simulation pipeline that can generate lens images with realistic subhalo populations in milliseconds. Leveraging this simulator, we identify the main limitation of our fiducial SBI analysis: training set size. We then adopt a sequential neural posterior estimation (SNPE) approach, allowing us to refine the training distribution to align with the observed data. Using only one-fifth as many mock Hubble Space Telescope images, SNPE matches the constraints on the low-mass halo population produced by our best nonsequential model. Our experiments suggest that an over 3 order-of-magnitude increase in training set size and GPU hours would be required to achieve an equivalent result without sequential methods. While the full potential of the existing lens sample remains to be explored, the notable improvement in constraining power enabled by our sequential approach highlights that current constraints are limited primarily by methodology and not the data itself. Moreover, our results emphasize the need to treat training set generation and model optimization as interconnected stages of any cosmological analysis using SBI.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Atacama Large Aperture Submillimeter Telescope (AtLAST) science: Resolving the hot and ionized Universe through the Sunyaev-Zeldovich effect

An omnipresent feature of the multi-phase “cosmic web” — the large-scale filamentary backbone of the Universe — is that warm/hot (≳ 10 5 K) ionized gas pervades it. This gas constitutes a relevant contribution to the overall universal matter budget across multiple scales, from the several tens of Mpc-scale intergalactic filaments, to the Mpc intracluster medium (ICM), all the way down to the circumgalactic medium (CGM) surrounding individual galaxies, on scales from ~ 1 kpc up to their respective virial radii (~ 100 kpc). The study of the hot baryonic component of cosmic matter density represents a powerful means for constraining the intertwined evolution of galactic populations and large-scale cosmological structures, for tracing the matter assembly in the Universe and its thermal history. To this end, the Sunyaev-Zeldovich (SZ) effect provides the ideal observational tool for measurements out to the beginnings of structure formation. The SZ effect is caused by the scattering of the photons from the cosmic microwave background off the hot electrons embedded within cosmic structures, and provides a redshift-independent perspective on the thermal and kinematic properties of the warm/hot gas. Still, current and next-generation (sub)millimeter facilities have been providing only a partial view of the SZ Universe due to any combination of: limited angular resolution, spectral coverage, field of view, spatial dynamic range, sensitivity, or all of the above. In this paper, we motivate the development of a wide-field, broad-band, multi-chroic continuum instrument for the Atacama Large Aperture Submillimeter Telescope (AtLAST) by identifying the scientific drivers that will deepen our understanding of the complex thermal evolution of cosmic structures. On a technical side, this will necessarily require efficient multi-wavelength mapping of the SZ signal with an unprecedented spatial dynamic range (from arcsecond to degree scales) and we employ detailed theoretical forecasts to determine the key instrumental constraints for achieving our goals.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2011

Testing Einstein's Gravity on Large Scales

A little over a decade has passed since two teams studying high redshift Type Ia supernovae announced the discovery that the expansion of the universe was accelerating. After all this time, we?re still not sure how cosmic acceleration fits into the theory that tells us about the large-scale universe: General Relativity (GR). As part of our search for answers, we have been forced to question GR itself. But how will we test our ideas? We are fortunate enough to be entering the era of precision cosmology, where the standard model of gravity can be subjected to more rigorous testing. Various techniques will be employed over the next decade or two in the effort to better understand cosmic acceleration and the theory behind it. In this talk, I will describe cosmic acceleration, current proposals to explain it, and weak gravitational lensing, an observational effect that allows us to do the necessary precision cosmology.

Prescod-Weinstein, Chandra↗

DOE OSTI2026

The DESI DR1 peculiar velocity survey: Growth rate measurements from the galaxy power spectrum

The large-scale structure of the Universe and its evolution encapsulate a wealth of cosmological information. A powerful means of unlocking this knowledge lies in measuring the auto-power spectrum and/or the cross-power spectrum of the galaxy density and momentum fields, followed by the estimation of cosmological parameters based on these spectrum measurements. In this study, we generalize the cross-power spectrum model to accommodate scenarios in which the density and momentum fields are derived from distinct galaxy surveys. The growth rate of the large-scale structures of the Universe, commonly represented as fσ 8 , was extracted by jointly fitting the monopole and quadrupole moments of the auto-density power spectrum, the monopole of the auto-momentum power spectrum, and the dipole of the cross-power spectrum. Our estimators, theoretical models, and parameter-fitting framework were tested using mocks, confirming their robustness and accuracy in retrieving the fiducial growth rate from simulation. These techniques were then applied to analyse the power spectrum of the DESI Bright Galaxy Survey and Peculiar Velocity Survey. The fit result of the growth rate is fσ8 = 0.440$^{+0.080}_{−0.096}$ at effective redshift zeff = 0.07. By synthesizing the fitting outcomes from correlation functions, maximum likelihood estimation, and the power spectrum, a consensus value is yielded of fσ 8 (z eff = 0.07) = 0.450$^{+0.055}_{−0.055}$, and correspondingly we obtain γ = 0.580$^{+0.110}_{−0.110}$, Ω m = 0.301$^{+0.011}_{−0.011}$, and σ 8 = 0.834$^{+0.032}_{−0.032}$. The measured fσ8 and γ are consistent with the prediction of the Λ cold dark matter model and general relativity.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Studying dark matter with observations of small-scale structure

The standard Lambda Cold Dark Matter model provides an accurate description of our universe on large spatial scales; however, it remains poorly tested on scales smaller than our Milky Way galaxy. The smallest, faintest, and most dark-matter-dominated galaxies are exceptional laboratories for studying the fundamental properties of dark matter and galaxy formation. Our Milky Way galaxy is surrounded by dozens of ultra-faint “dwarf” galaxies, which have only recently been discovered thanks to the unprecedented sensitivity of large digital sky surveys. As telescopes grow larger and more powerful, we continue to find fainter, more distant, and more dark-matter-dominated galaxies. In addition, we are now able to study faint galaxies beyond the Local Volume. I will describe recent observational programs to study faint galaxies, and how observations of faint galaxies can help address some of the foremost open questions in physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

3D CFD Model Validation Using Benchmark Data of 1/16th Scaled VHTR Upper Plenum and Development of Wall Heat-Transfer Correlation For Laminar Flow

With support from the U.S. Department of Energy-Office of Nuclear Energy’s (DOE-NE’s) Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, an effort has been pursued to support high-temperature gas-cooled reactor (HTGR) technology development and its modeling and simulation needs. There is a particular need for advanced modeling and simulation tools to predict thermal-fluid behavior in the nuclear reactor primary system, especially in the core and the lower and upper plena, during safety-related transients. In this report, two main such activities are presented relevant to the HTGRs: (1) three-dimensional (3D) computational fluid dynamics (CFD) validation using benchmark data from the upper plenum of Texas A&M University’s 1/16th scaled very-high-temperature gas-cooled reactor (VHTR), and (2) development of wall heat-transfer correlation for laminar flow in a wall-heated pipe. The CFD tool validation exercises can be helpful to choose the models and CFD tools to simulate and design specific components of the HTRGs such as upper plenum where jet mixing is a complex phenomenon. In a loss of forced circulation event, the laminar flow can be observed during the development of natural circulation flow. This work includes the development and validation of heat transfer correlations for laminar flow using the Nek5000 CFD code due to limited available experimental data for laminar flow conditions to guide low-order models (1D). In this report, the flow characteristics of a single isothermal jet discharging into the upper plenum was investigated using the Nek5000 Large-Eddy Simulation (LES) CFD tool. Several numerical simulations were performed for various jet-discharged Reynolds numbers ranging from 3,413 to 12,819. A grid-independent study was performed. The numerical results of mean velocity, root-mean-square fluctuating velocity, and Reynolds stress were compared against the benchmark data. Good agreement was obtained between simulated and measured data for axial mean velocities, except near the upper plenum hemisphere. The maximum predicted errors for axial mean velocities at various normalized coolant channel diameter heights of 1, 5, and 10 are 1.56%, 1.88%, and 3.82%, respectively. In addition, the predicted root-mean-square fluctuating velocity and Reynolds stress are qualitatively in agreement with the experimental data. The Nek5000 code was used to develop wall-heat transfer correlation for laminar flow in a cylindrical tube. Several simulations were performed for various Reynolds flow and wall-heat fluxes. A new heat transfer correlation was developed using data from Nek5000 simulation results and regression functions in Matlab. The developed heat transfer correlation is valid for various Reynolds flows from 200 to 2000. The predicted R² value for model fit was 0.875, which ensures that 87.5% of the model data lies on the Nek5000 data. Moreover, a machine learning (ML) tool was used to train and test the Nek5000 data. A good fit of the ML-based model was observed with the test data.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2020

A Model for Turbulence Spectra in the Equilibrium Range of the Stable Atmospheric Boundary Layer

Stratification can cause turbulence spectra to deviate from Kolmogorov's isotropic -5/3 power law scaling in the universal equilibrium range at high Reynolds numbers. However, a consensus has not been reached with regard to the exact shape of the spectra. Here we propose a shape of the turbulent kinetic energy and temperature spectra in horizontal wavenumber for the equilibrium range that consists of three regimes at small Froude number: the buoyancy subrange, a transition region, and the isotropic inertial subrange through dimensional analysis and substantial revision of previous theoretical approximation. These spectral regimes are confirmed by various observations in the atmospheric boundary layer. The representation of the transition region in direct numerical simulations will require large-scale separation between the Dougherty-Ozmidov scale and the Kolmogorov scale for strongly stratified turbulence at high Reynolds numbers, which is still challenging computationally. In addition, we suggest that the failure of Monin-Obukhov similarity theory in the very stable atmospheric boundary layer is due to the fact that it does not consider the buoyancy scale that characterizes the transition region.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Joint analysis of Dark Energy Survey Year 3 data and CMB lensing from SPT and P l a n c k . II. Cross-correlation measurements and cosmological constraints

Cross-correlations of galaxy positions and galaxy shears with maps of gravitational lensing of the cosmic microwave background (CMB) are sensitive to the distribution of large-scale structure in the Universe. Such cross-correlations are also expected to be immune to some of the systematic effects that complicate correlation measurements internal to galaxy surveys. We present measurements and modeling of the cross-correlations between galaxy positions and galaxy lensing measured in the first three years of data from the Dark Energy Survey with CMB lensing maps derived from a combination of data from the 2500 deg 2 SPT-SZ survey conducted with the South Pole Telescope and full-sky data from the Planck satellite. The CMB lensing maps used in this analysis have been constructed in a way that minimizes biases from the thermal Sunyaev Zel’dovich effect, making them well suited for cross-correlation studies. The total signal-to-noise of the cross-correlation measurements is 23.9 (25.7) when using a choice of angular scales optimized for a linear (nonlinear) galaxy bias model. Here we use the cross-correlation measurements to obtain constraints on cosmological parameters. For our fiducial galaxy sample, which consist of four bins of magnitude-selected galaxies, we find constraints of Ω m =0.272$^{+0.032}_{-0.052}$ and S 8 ≡σ8$\sqrt{Ω_m/0.3}$=0.736$^{+0.032}_{-0.028}$ (Ω m =0.245$^{+0.026}_{-0.044}$ and S 8 =0.734$^{+0.035}_{-0.028}$) when assuming linear (nonlinear) galaxy bias in our modeling. Considering only the cross-correlation of galaxy shear with CMB lensing, we find Ω m =0.270$^{+0.043}_{-0.061}$ and S 8 =0.740$^{+0.034}_{-0.029}$. Our constraints on S8 are consistent with recent cosmic shear measurements, but lower than the values preferred by primary CMB measurements from Planck.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

ForestFlow: predicting the Lyman-α forest clustering from linear to nonlinear scales

On large scales, the Lyman-α forest provides insights into the expansion history of the Universe, while on small scales, it imposes strict constraints on the growth history, the nature of dark matter, and the sum of neutrino masses. This work introduces ForestFlow, a novel framework that bridges the gap between large- and small-scale analyses, which have traditionally relied on distinct modeling approaches. Using conditional normalizing flows, ForestFlow predicts the two Lyman-α linear biases (b δ and b η ) and six parameters describing small-scale deviations of the three-dimensional flux power spectrum (P 3D ) from linear theory as a function of cosmology and intergalactic medium physics. These are then combined with a Boltzmann solver to make consistent predictions, from arbitrarily large scales down to the nonlinear regime, for P 3D and any other statistics derived from it. Trained on a suite of 30 fixed-and-paired cosmological hydrodynamical simulations spanning redshifts from z = 2 to 4.5, ForestFlow achieves 3 and 1.5% precision in describing P 3D and the one-dimensional flux power spectrum (P 1D ) from linear scales to k = 5 Mpc −1 and k ∥ = 4 Mpc −1 , respectively. Thanks to its conditional parameterization, ForestFlow shows similar performance for ionization histories and two ΛCDM model extensions – massive neutrinos and curvature – even though none of these are included in the training set. This framework will enable full-scale cosmological analyses of Lyman-α forest measurements from the DESI survey.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Non-supersymmetric $AdS_6$ and the swampland

We discuss infinite families of non-supersymmetric AdS 6 solutions in Type IIB string theory. They are siblings of supersymmetric solutions which are associated with (p,q) 5-brane webs and holographically dual to 5d SCFTs engineered by those brane webs. The non-supersymmetric backgrounds carry identical 5-brane charges and are connected to the supersymmetric ones by RG flows. We study the stability of the non-supersymmetric solutions, identifying perturbative and non-perturbative decay channels for all the backgrounds explicitly available. We also identify likely decay mechanisms for solutions that have not been constructed explicitly but may be expected to exist based on brane web considerations. Finally, we exclude scale separation by constructing universal spin 2 modes with masses comparable to the mass-scale of the cosmological constant.

supersymmetry breaking↗

DOE OSTI2022

Microphysics of early dark energy

Early dark energy (EDE) relies on scalar field dynamics to resolve the Hubble tension, by boosting the pre-recombination length scales and thereby raising the CMB-inferred value of the Hubble constant into agreement with late universe probes. However, the collateral effect of scalar field microphysics on the linear perturbation spectra appears to preclude a fully satisfactory solution. H 0 is not raised without the inclusion of a late universe prior, and the “S 8 -tension”, a discrepancy between early- and late-universe measurements of the structure growth parameter, is exacerbated. What if EDE is not a scalar field? Here, we investigate whether different microphysics, encoded in the constitutive relationships between pressure and energy density fluctuations, can relieve these tensions. We show that EDE with an anisotropic sound speed can soften both the H 0 and S 8 tensions while still providing a quality fit to CMB data. Future observations from the CMB-S4 experiment may be able to distinguish the underlying microphysics at the 4σ level, and thereby test whether a scalar field or some richer physics is at work.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2012

The Prompt-afterglow Connection in Gamma-ray Bursts: a Comprehensive Statistical Analysis of Swift X-ray Light-curves

We present a comprehensive statistical analysis of Swift X-ray light-curves of Gamma- Ray Bursts (GRBs) collecting data from more than 650 GRBs discovered by Swift and other facilities. The unprecedented sample size allows us to constrain the rest-frame X-ray properties of GRBs from a statistical perspective, with particular reference to intrinsic time scales and the energetics of the different light-curve phases in a common rest-frame 0.3-30 keV energy band. Temporal variability episodes are also studied and their properties constrained. Two fundamental questions drive this effort: i) Does the X-ray emission retain any kind of "memory" of the prompt γ-ray phase? ii) Where is the dividing line between long and short GRB X-ray properties? We show that short GRBs decay faster, are less luminous and less energetic than long GRBs in the X-rays, but are interestingly characterized by similar intrinsic absorption. We furthermore reveal the existence of a number of statistically significant relations that link the X-ray to prompt γ-ray parameters in long GRBs; short GRBs are outliers of the majority of these 2-parameter relations. However and more importantly, we report on the existence of a universal 3-parameter scaling that links the X-ray and the γ-ray energy to the prompt spectral peak energy of both long and short GRBs: E(sub X,iso)∝ E(sup 1.00+/-0.06)(sub γ,iso) /E(sup 0.60+/-0.10)(sub pk).

Gamma-Ray Bursts↗

DOE OSTI2020

Characterization of Uranium Foil Irradiations at the WSU TRIGA Reactor Using a New Reactor Model in Scale

A new reactor model of the Washington State University TRIGA was developed in the SCALE neutron transport code, and its fidelity was verified by comparison to MCNP and available data for several reactor parameters. The model was used to characterize irradiations designed to produce the short-lived actinides 237 U and 239 U, two key isotopes for nuclear forensics. These short-lived actinides, their decay daughters 237Np and 239Pu, and total fissions (via 99 Mo) were measured in irradiated foils at Los Alamos National Laboratory and other labs with good agreement among parent/daughter pairs and among labs. The laboratory-measured isotope ratios were used as a benchmark for the model determination of reaction rates. The flux distribution in the foils was also determined. Finally, using the continuous energy TSUNAMI-3D module of SCALE, a sensitivity/uncertainty analysis was performed to determine the effects on foil reactions caused by other system-wide reactions and by uncertainties in the known cross-sections.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

NASA NTRS1981

Universal binding energy relations in metallic adhesion

Scaling relations which map metallic adhesive binding energy onto a single universal binding energy curve are discussed in relation to adhesion, friction, and wear in metals. The scaling involved normalizing the energy to the maximum binding energy and normalizing distances by a suitable combination of Thomas-Fermi screening lengths. The universal curve was found to be accurately represented by E*(A*)= -(1+beta A) exp (-Beta A*) where E* is the normalized binding energy, A* is the normalized separation, and beta is the normalized decay constant. The calculated cohesive energies of potassium, barium, copper, molybdenum, and samarium were also found to scale by similar relations, suggesting that the universal relation may be more general than for the simple free electron metals.

Ferrante, J.↗

DOE OSTI2025

Atacama Cosmology Telescope DR6 and DESI: Structure growth measurements from the cross-correlation of DESI legacy imaging galaxies and CMB lensing from ACT DR6 and 𝑃⁢𝑙⁢𝑎⁢𝑛⁢𝑐⁢𝑘 PR4

We measure the growth of cosmic density fluctuations on large scales and across the redshift range 0.3 < 𝑧 < 0.8 through galaxy clustering and the cross-correlation of the ACT data release 6 cosmic microwave background (CMB) lensing map and galaxies from the Dark Energy Spectroscopic Instrument Legacy Survey, using three galaxy samples spanning the redshifts of 0.3 ≲ 𝑧 ≲ 0.45, 0.45 ≲ 𝑧 ≲ 0.6, 0.6 ≲ 𝑧 ≲ 0.8. We adopt a scale cut where nonlinear effects are negligible, so that the cosmological constraints are derived from the linear regime. We determine the amplitude of matter fluctuations over all three redshift bins using Atacama Cosmology Telescope (ACT) data alone to be 𝑆 8 ≡ 𝜎 8 ⁢(Ω 𝑚 /0.3) 0.5 =0.772 ± 0.040 in a joint analysis combining the three redshift bins and ACT lensing alone. Using a combination of ACT and Planck data we obtain 𝑆 8 = 0.765 ± 0.032. The lowest redshift bin used is the least constraining and exhibits a ∼2⁢𝜎 tension with the other redshift bins; thus we also report constraints excluding the first redshift bin, giving 𝑆 8 = 0.785 ± 0.033 for the combination of ACT and Planck. This result is in excellent agreement at the 0.3⁢𝜎 level with measurements from galaxy lensing, but is 1.8⁢𝜎 lower than predictions based on Planck primary CMB data. Understanding whether this hint of discrepancy in the growth of structure at low redshifts arises from a fluctuation, from systematics in data, or from new physics is a high priority for forthcoming CMB lensing and galaxy cross-correlation analyses.

cosmic microwave background↗