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DOE OSTI2022

Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria

Abstract Transcription rates are regulated by the interactions between RNA polymerase, sigma factor, and promoter DNA sequences in bacteria. However, it remains unclear how non-canonical sequence motifs collectively control transcription rates. Here, we combine massively parallel assays, biophysics, and machine learning to develop a 346-parameter model that predicts site-specific transcription initiation rates for any σ 70 promoter sequence, validated across 22132 bacterial promoters with diverse sequences. We apply the model to predict genetic context effects, design σ 70 promoters with desired transcription rates, and identify undesired promoters inside engineered genetic systems. The model provides a biophysical basis for understanding gene regulation in natural genetic systems and precise transcriptional control for engineering synthetic genetic systems.

42 ENGINEERING↗

DOE OSTI2022

NOvA 2020 official data release (13.6E20 neutrino + 12.5E20 antineutrino)

NOvA results of the 2020 joint analysis of nue appearance and numu disappearance data presented in Phys. Rev. D 106, 032004:https://doi.org/10.1103/PhysRevD.106.032004Note: these contained plots are slightly different from the ones shown at NEUTRINO 2020.Exposure: 13.6E20 protons on target, neutrino-enhanced beam12.5E20 protons on target, antineutrino-enhanced beamParameters not constrained by NOvA:- th13 is assumed to be Gaussian, ss2th13 = 0.085 +/- 0.003 (PDG 2019, Phys. Rev. D98, 030001 (2018) and 2019 update, https://pdg.lbl.gov/2019/listings/rpp2019-list-neutrino-mixing.pdf)- ss2th12 = 0.851, dm21=7.53e-5 are fixed at 2019 PDG valuesSignificances are obtained with the Feldman-Cousins procedure.Files contain TGraphs for the following:- ssth23 vs deltaCP 1,2,3 sigma and 90% CL contours, for NO or IO- dmsq32 vs ssth23 1,2,3 sigma and 90% CL contours, for NO or IO- deltaCP profile for NO UO, NO LO, IO LO, IO UO- ssth23 profile for NO, IO- dmsq32 profile for NO UO, NO LO, IO LO, IO UOContour files also include a TMarker with the best-fit parameters (in the NO)An additional file containing the predictions for all channels’ signal and background components computed at the NOvA best-fit oscillation parameters and systematic pull terms. Numu samples include the no-oscillation case as well.Please note that any fits performed with these histograms are not expected to exactly reproduce the official NOvA results as parameterizations of the numerous systematic uncertainties considered in the official fits are not included in this release.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

The dark energy survey: detection of weak lensing magnification of supernovae and constraints on dark matter haloes

The residuals of the distance moduli of Type Ia supernovae (SNe Ia) relative to a Hubble diagram fit contain information about the inhomogeneity of the Universe, due to weak lensing magnification by foreground matter. By correlating the residuals of the Dark Energy Survey Year 5 SN Ia sample (DES-SN5YR) with extragalactic foregrounds from the DES Y3 Gold catalogue, we detect the presence of lensing at |$6.0 \sigma$| significance. This is the first detection with a significance level above |$5\sigma$|⁠. Constraints on the effective mass-to-light ratios and radial profiles of dark matter haloes surrounding individual galaxies are also obtained. We show that the scatter of SNe Ia around the Hubble diagram is reduced by modifying the standardization of the distance moduli to include an easily calculable de-lensing (i.e. environmental) term. We use the de-lensed distance moduli to recompute cosmological parameters derived from SN Ia, finding in Flat wcold dark matter a difference of |$\Delta \Omega _{\rm M} = +0.036$| and |$\Delta w = -0.056$| compared to the unmodified distance moduli, a change of |$\sim 0.3\sigma$|⁠. We argue that our modelling of SN Ia lensing will lower systematics on future surveys with higher statistical power. We use the observed dispersion of lensing in DES-SN5YR to constrain |$\sigma _8$|⁠, but caution that the fit is sensitive to uncertainties at small scales. Nevertheless, our detection of SN Ia lensing opens a new pathway to study matter inhomogeneity that complements galaxy–galaxy lensing surveys and has unrelated systematics.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

The 3D Kinematics of the Orion Nebula Cluster: NIRSPEC-AO Radial Velocities of the Core Population

The kinematics and dynamics of stellar and substellar populations within young, still-forming clusters provide valuable information for constraining theories of formation mechanisms. Using Keck II NIRSPEC+AO data, we have measured radial velocities for 56 low-mass sources within 4' of the core of the Orion Nebula Cluster (ONC). We also remeasure radial velocities for 172 sources observed with SDSS/APOGEE. These data are combined with proper motions measured using HST ACS/WFPC2/WFC3IR and Keck II NIRC2, creating a sample of 135 sources with all three velocity components. The velocities measured are consistent with a normal distribution in all three components. We measure intrinsic velocity dispersions of (${\sigma }_{{v}_{\alpha }}$, ${\sigma }_{{v}_{\delta }}$, ${\sigma }_{{v}_{r}}$) = (1.64 ± 0.12, 2.03 ± 0.13, ${2.56}_{-0.17}^{+0.16}$) km s –1 . Our computed intrinsic velocity dispersion profiles are consistent with the dynamical equilibrium models from Da Rio et al. (2014) in the tangential direction but not in the line-of-sight direction, possibly indicating that the core of the ONC is not yet virialized, and may require a nonspherical potential to explain the observed velocity dispersion profiles. We also observe a slight elongation along the north–south direction following the filament, which has been well studied in previous literature, and an elongation in the line-of-sight to tangential velocity direction. These 3D kinematics will help in the development of realistic models of the formation and early evolution of massive clusters.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Combined search for neutrinos from dark matter self-annihilation in the Galactic Center with ANTARES and IceCube

In this work, we present the results of the first combined dark matter search targeting the Galactic Centre using the ANTARES and IceCube neutrino telescopes. For dark matter particles with masses from 50 to 1000 GeV, the sensitivities on the self-annihilation cross section set by ANTARES and IceCube are comparable, making this mass range particularly interesting for a joint analysis. Dark matter self-annihilation through the $\tau^+\tau^-$, $\mu^+\mu^-$, $b\bar{b}$ and $W^+W^-$ channels is considered for both the Navarro-Frenk-White and Burkert halo profiles. In the combination of 2,101.6 days of ANTARES data and 1,007 days of IceCube data, no excess over the expected background is observed. Limits on the thermally-averaged dark matter annihilation cross section $\langle\sigma_A\upsilon\rangle$ are set. These limits present an improvement of up to a factor of two in the studied dark matter mass range with respect to the individual limits published by both collaborations. When considering dark matter particles with a mass of 200 GeV annihilating through the $\tau^+\tau^-$ channel, the value obtained for the limit is $7.44 \times 10^{-24} \text{cm}^{3}\text{s}^{-1}$ for the Navarro-Frenk-White halo profile. For the purpose of this joint analysis, the model parameters and the likelihood are unified, providing a benchmark for forthcoming dark matter searches performed by neutrino telescopes.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Tearing-mediated Alfvénic Turbulence in a Relativistic Plasma

In astrophysical relativistic plasmas, Alfvénic turbulence exists across a wide range of scales. Similar to a nonrelativistic case, this turbulence can be influenced by the tearing instability. We argue that in an ultrarelativistic pair plasma the tearing effects become significant at the critical scale given by ${a}_{t}\sim {d}_{\mathrm{rel}}{\left({L}_{\perp }/{d}_{\mathrm{rel}}\right)}^{n/(4+5n)}$, where L ⊥ represents the outer scale of the turbulence and d rel the relativistic electron inertial scale. Here n = 1 corresponds to the Harris magnetic configurations, while n = 2 applies to localized (non-Harris) magnetic profiles of turbulence-generated current sheets. Below the critical scale, the energy spectrum of magnetic fluctuations steepens to W(k)dk ∝ k -(7n+2)/3n dk. However, this happens only when $\tilde{\sigma }\ll {\left({L}_{\perp }/{d}_{\mathrm{rel}}\right)}^{(2+4n)/(4+5n)}$, where $\tilde{\sigma }$ is the magnetization parameter based on the magnetic fluctuations. If the opposite inequality holds, the Alfvénic cascade is instead affected by charge starvation at scales below ${a}_{\mathrm{ch}}\sim {d}_{\mathrm{rel}}{\left({d}_{\mathrm{rel}}/{L}_{\perp }\right)}^{1/3}{\tilde{\sigma }}^{2/3}$, and the energy spectrum becomes steeper than W(k)dk ∝ k -3 dk. When d rel is replaced by its nonrelativistic equivalent, our results agree with the nonrelativistic analysis of N. F. Loureiro & S. Boldyrev (2018). In the Harris case n = 1, they agree with the recent relativistic studies by I. Demidov & Y. Lyubarsky.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

The Atacama Cosmology Telescope: Weighing Distant Clusters with the Most Ancient Light

We use gravitational lensing of the cosmic microwave background (CMB) to measure the mass of the most distant blindly selected sample of galaxy clusters on which a lensing measurement has been performed to date. In CMB data from the the Atacama Cosmology Telescope and the Planck satellite, we detect the stacked lensing effect from 677 near-infrared-selected galaxy clusters from the Massive and Distant Clusters of WISE Survey (MaDCoWS), which have a mean redshift of $\langle z\rangle =1.08$. There are currently no representative optical weak lensing measurements of clusters that match the distance and average mass of this sample. We detect the lensing signal with a significance of $4.2\sigma $. We model the signal with a halo model framework to find the mean mass of the population from which these clusters are drawn. Assuming that the clusters follow Navarro–Frenk–White (NFW) density profiles, we infer a mean mass of $\langle {M}_{500c}\rangle =\left(1.7\pm 0.4\right)\times {10}^{14}\,{M}_{\odot }$. We consider systematic uncertainties from cluster redshift errors, centering errors, and the shape of the NFW profile. These are all smaller than 30% of our reported uncertainty. This work highlights the potential of CMB lensing to enable cosmological constraints from the abundance of distant clusters populating ever larger volumes of the observable universe, beyond the capabilities of optical weak lensing measurements.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Transport across interfaces in symmetric orbifolds

We examine how conformal boundaries encode energy transport coefficients — namely transmission and reflection probabilities — of corresponding conformal interfaces in symmetric orbifold theories. These constitute a large class of irrational theories and are closely related to holographic setups. Our central goal is to compare such coefficients at the orbifold point (a field theory calculation) against their values when the orbifold is highly deformed (a gravity calculation) — an approach akin to past AdS/CFT-guided comparisons of physical quantities at strong versus weak coupling. At the orbifold point, we find that the (weighted-average) transport coefficients are simply averages of coefficients in the underlying seed theory. We then focus on the symmetric orbifold of the T 4 sigma model interface CFT dual to type IIB supergravity on the 3d Janus solution. We compare the holographic transmission coefficient, which was found by [1], to that of the orbifold point. We find that the profile of the transmission coefficient substantially increases with the coupling, in contrast to boundary entropy. We also present some related ideas about twisted-sector data encoded by boundary states.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

The Atacama Cosmology Telescope: Probing the baryon content of SDSS DR15 galaxies with the thermal and kinematic Sunyaev-Zel’dovich effects

We present high signal-to-noise measurements (up to 12$\sigma$) of the average thermal Sunyaev Zel'dovich (tSZ) effect from optically selected galaxy groups and clusters and estimate their baryon content within a 2.1$^\prime$ radius aperture. Sources from the Sloan Digital Sky Survey (SDSS) Baryon Oscillation Spectroscopic Survey (BOSS) DR15 catalog overlap with 3,700 sq. deg. of sky observed by the Atacama Cosmology Telescope (ACT) from 2008 to 2018 at 150 and 98 GHz (ACT DR5), and 2,089 sq. deg. of internal linear combination component-separated maps combining ACT and $\it{Planck}$ data (ACT DR4). The corresponding optical depths, $\bar{\tau}$, which depend on the baryon content of the halos, are estimated using results from cosmological hydrodynamic simulations assuming an AGN feedback radiative cooling model. We estimate the mean mass of the halos in multiple luminosity bins, and compare the tSZ-based $\bar{\tau}$ estimates to theoretical predictions of the baryon content for a Navarro-Frenk-White profile. We do the same for $\bar{\tau}$ estimates extracted from fits to pairwise baryon momentum measurements of the kinematic Sunyaev-Zel'dovich effect (kSZ) for the same data set obtained in a companion paper. We find that the $\bar{\tau}$ estimates from the tSZ measurements in this work and the kSZ measurements in the companion paper agree within $1\sigma$ for two out of the three disjoint luminosity bins studied, while they differ by 2-3$\sigma$ in the highest luminosity bin. The optical depth estimates account for one third to all of the theoretically predicted baryon content in the halos across luminosity bins. Potential systematic uncertainties are discussed. The tSZ and kSZ measurements provide a step towards empirical Compton-$\bar{y}$-$\bar{\tau}$ relationships to provide new tests of cluster formation and evolution models.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Exploiting non-linear scales in galaxy–galaxy lensing and galaxy clustering: A forecast for the dark energy survey

ABSTRACT The combination of galaxy–galaxy lensing (GGL) and galaxy clustering is a powerful probe of low-redshift matter clustering, especially if it is extended to the non-linear regime. To this end, we use an N-body and halo occupation distribution (HOD) emulator method to model the redMaGiC sample of colour-selected passive galaxies in the Dark Energy Survey (DES), adding parameters that describe central galaxy incompleteness, galaxy assembly bias, and a scale-independent multiplicative lensing bias Alens. We use this emulator to forecast cosmological constraints attainable from the GGL surface density profile ΔΣ(rp) and the projected galaxy correlation function wp, gg(rp) in the final (Year 6) DES data set over scales $r_p=0.3\!-\!30.0\, h^{-1} \, \mathrm{Mpc}$. For a $3{{\ \rm per\ cent}}$ prior on Alens we forecast precisions of $1.9{{\ \rm per\ cent}}$, $2.0{{\ \rm per\ cent}}$, and $1.9{{\ \rm per\ cent}}$ on Ωm, σ8, and $S_8 \equiv \sigma _8\Omega _m^{0.5}$, marginalized over all halo occupation distribution (HOD) parameters as well as Alens. Adding scales $r_p=0.3\!-\!3.0\, h^{-1} \, \mathrm{Mpc}$ improves the S8 precision by a factor of ∼1.6 relative to a large scale ($3.0\!-\!30.0\, h^{-1} \, \mathrm{Mpc}$) analysis, equivalent to increasing the survey area by a factor of ∼2.6. Sharpening the Alens prior to $1{{\ \rm per\ cent}}$ further improves the S8 precision to $1.1{{\ \rm per\ cent}}$, and it amplifies the gain from including non-linear scales. Our emulator achieves per cent-level accuracy similar to the projected DES statistical uncertainties, demonstrating the feasibility of a fully non-linear analysis. Obtaining precise parameter constraints from multiple galaxy types and from measurements that span linear and non-linear clustering offers many opportunities for internal cross-checks, which can diagnose systematics and demonstrate the robustness of cosmological results.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Shortened Booster Bunch Lengths

Booster typically produces beam bunches that have a phase space profile with a low momentum spread but high time spread, correlating to longer bunch lengths. The goal of this study is to produce beam bunches that have a phase space profile with a high momentum spread but low time spread or narrow bunch lengths. This can be achieved by slowly increasing the RF cavities amplitudes (Adiabatic Excitation) or by oscillating the amplitudes (Quadratic Bunch Rotation, QBR) until the desired bunch lengths are achieved. Results show that when shortening the bunches using QBR, it showed the bunches had a length of 0.6ns (within 1 sigma) but beam losses were being incurred in the 8 GeV line which were a result of beam dispersion.

Abdelhamid, Maan↗

DOE OSTI2024

Shortened Booster Bunch Lengths

Abdelhamid, Maan↗

DOE OSTI2023

Beam Dynamics Challenges in the Muon g-2 Experiment

The muon&s;s anomalous magnetic moment $a_{\mu}$ has hinted at physics beyond the standard model for nearly 20 years. The Muon $g-2$ experiment at Fermilab aims to measure $a_{\mu}$ to 140 parts per billion (ppb) precision. The 460 ppb result from its first data run (Run-1), released in 2021, agreed with the previous 2006 Brookhaven Muon $g-2$ result. The experimental average stands in tension with the standard model theory $a_{\mu}$ prediction by $4.2 \sigma$. The result of Run-2/3 data analysis is set be released in summer 2023, and will improve on the Run-1 precision by a factor of two. With the data collected in all six runs, the experiment is on track to produce a 140 ppb measurement of $a_{\mu}$. If the experiment and theory central values are both unchanged, the tension would exceed $5 \sigma$. The measurement is accomplished by injecting muons into a magnetic storage ring and precisely measuring two observable frequencies: $\omega_a$, the muons&s; anomalous precession frequency, and $\tilde{\omega}&s;_p$, the precession frequency of protons which determines the magnetic field strength experienced by the muons. This thesis presents a selection of muon beam dynamics effects which are critical for reaching the experiment precision goal. A system of detectors assists with the challenging beam injection into the storage ring, and a measurement of the injected beam provides input for simulating the stored beam dynamics. A new method is introduced to reduce a critical systemic caused by time dependence in the stored beam momentum, enabled by a detector which directly profiles the stored beam. Finally the analysis of $\tilde{\omega}&s;_p$, the muon-weighted magnetic field, for the Run-2/3 result is presented. Systematics of $\tilde{\omega}&s;_p$ due to beam effects are evaluated in detail, and shown to be sub-dominant.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

CODEX weak lensing mass catalogue and implications on the mass–richness relation

The COnstrain Dark Energy with X-ray clusters (CODEX) sample contains the largest flux limited sample of X-ray clusters at 0.35 < z < 0.65. It was selected from ROSAT data in the 10 000 square degrees of overlap with BOSS, mapping a total number of 2770 high-z galaxy clusters. We present here the full results of the CFHT CODEX programme on cluster mass measurement, including a reanalysis of CFHTLS Wide data, with 25 individual lensing-constrained cluster masses. We employ lensfit shape measurement and perform a conservative colour–space selection and weighting of background galaxies. Using the combination of shape noise and an analytic covariance for intrinsic variations of cluster profiles at fixed mass due to large-scale structure, miscentring, and variations in concentration and ellipticity, we determine the likelihood of the observed shear signal as a function of true mass for each cluster. We combine 25 individual cluster mass likelihoods in a Bayesian hierarchical scheme with the inclusion of optical and X-ray selection functions to derive constraints on the slope α, normalization β, and scatter σln λ|μ of our richness–mass scaling relation model in log-space: ${\langle {\rm In}\,\, \lambda\!\!\mid\!\!\mu\rangle = \alpha\mu + \beta,} $ with μ = ln (M 200c /M piv ), and M piv = 10 14.81 M ⊙ . We find a slope $\alpha = 0.49^{+0.20}_{-0.15}$, normalization $\exp (\beta) = 84.0^{+9.2}_{-14.8}$, and $\sigma _{\ln \lambda | \mu } = 0.17^{+0.13}_{-0.09}$ using CFHT richness estimates. In comparison to other weak lensing richness–mass relations, we find the normalization of the richness statistically agreeing with the normalization of other scaling relations from a broad redshift range (0.0 < z < 0.65) and with different cluster selection (X-ray, Sunyaev–Zeldovich, and optical).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Measuring the thermal and ionization state of the low- z IGM using likelihood free inference

ABSTRACT We present a new approach to measure the power-law temperature density relationship $T=T_0 (\rho/ \bar{\rho })^{\gamma -1}$ and the UV background photoionization rate $\Gamma _{{{{\rm H\, {\small I}}}}{}}$ of the intergalactic medium (IGM) based on the Voigt profile decomposition of the Ly α forest into a set of discrete absorption lines with Doppler parameter b and the neutral hydrogen column density $N_{\rm H\, {\small I}}$. Previous work demonstrated that the shape of the $b-N_{{{{\rm H\, {\small I}}}}{}}$ distribution is sensitive to the IGM thermal parameters T0 and γ, whereas our new inference algorithm also takes into account the normalization of the distribution, i.e. the line-density dN/dz, and we demonstrate that precise constraints can also be obtained on $\Gamma _{{{{\rm H\, {\small I}}}}{}}$. We use density-estimation likelihood-free inference (DELFI) to emulate the dependence of the $b-N_{{{{\rm H\, {\small I}}}}{}}$ distribution on IGM parameters trained on an ensemble of 624 nyx hydrodynamical simulations at z = 0.1, which we combine with a Gaussian process emulator of the normalization. To demonstrate the efficacy of this approach, we generate hundreds of realizations of realistic mock HST/COS data sets, each comprising 34 quasar sightlines, and forward model the noise and resolution to match the real data. We use this large ensemble of mocks to extensively test our inference and empirically demonstrate that our posterior distributions are robust. Our analysis shows that by applying our new approach to existing Ly α forest spectra at z ≃ 0.1, one can measure the thermal and ionization state of the IGM with very high precision ($\sigma _{\log T_0} \sim 0.08$ dex, σγ ∼ 0.06, and $\sigma _{\log \Gamma _{{{{\rm H\, {\small I}}}}{}}} \sim 0.07$ dex).

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

DASSH-F: Subchannel Based Thermal Analysis

The DASSH thermal analysis code is designed to rapidly allow a reactor design engineer to obtain flow rates requirements that satisfy peak temperature constraints in the domain. The advantage of using DASSH over a hand calculation is that it has a more rigorous treatment of the pin power distribution and coolant heat transfer within an assembly and between assemblies. The advantage of using DASSH over a conventional 3D subchannel code or a computational fluid dynamics code (CFD) is that it can obtain the desired solution in a matter of minutes in serial with minor computer memory needs. The DASSH methodology for pin lattice models is virtually identical to SUPERENERGY-2 with additional functionalities taken from follow on work to SUPERENERGY-2 done at ANL in the 1980s. DASSH today is an integral component of the Argonne Fast Reactor analysis suite for reactor design work. DASSH obtains the power distribution from a coupled neutron-gamma heating calculation in GAMSOR (including DIF3D) at each time point of a companion fuel cycle analysis calculation with REBUS. The domain in DASSH assumes a hexagonal grid typical for fast reactors with much of the geometry information taken from the DIF3D model. DASSH assumes the assemblies that are loaded into each grid position are ducted to control the coolant flow. The user can alternatively provide their own geometry and power profile instead of inheriting it from DIF3D. Considerable detail is given on the subchannel formulation of DASSH in this document. Much of the formulation and design of the code builds upon research done by previous authors with little new investigation. Thus the decisions made in developing the subchannel model used in DASSH have their origins over 50 years ago. Much of the heat transfer methodology in DASSH is built upon correlations for both the coolant mixing and heat transfer coefficients for pins and ducts. DASSH is thus not a rigorous treatment of a given problem, but a rapid assessment of the temperature field that has known limitations with respect to an experimental measurement or CFD calculation. The DASSH input and output are detailed along with usage of the software. The DASSH output provides tables of evaluated material properties and key coolant and pin temperature results. DASSH can create Python scripts that generate domain summary pictures. DASSH can also generate assembly temperature maps and VTK output files which allow the DASSH solution to be visualized. As the primary purpose of the DASSH software is to compute the coolant and fuel pin temperature distribution for a given model of a reactor, much of the output focus is giving the user quick summary tables needed to assess the performance of a given orifice flow specification. The present version of DASSH has a crude orifice search capability and a sufficient orifice flow search capability. The flow search tries to meet user specified constraints for 1) peak 2-sigma clad temperature, 2) peak coolant temperature, and 3) desired bulk outlet temperature. This document serves as the manual for the Fortran based DASSH software that was developed to replace the Python version of DASSH developed as part of the VTR program.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗