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DOE OSTI2021

Experimental modal analysis of SSR1 cryomodule for numerical model tuning and validation

The present activity aims to test the Cryomodule SSR1 to validate the corresponding mixed multibody-finite element numerical model and to determine the range of frequencies in which the first natural modes of the structure lie. The experimental activity consisted of a hammer test of the cryomodule at an early assembly stage at which the internal parts, constituting the cold mass, are accessible and, thus, many accelerometers can be attached to the beam string. The comparison between the experimental results obtained for the sub-assembly and the numerical results obtained for the corresponding sub-model, derived from the previously developed complete model, allowed to assess the validity of the numerical model and to get feedback on the effectiveness of the placement of the sensors in capturing the dynamic response of the system during transportation.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

Interaction-induced velocity renormalization in magic-angle twisted multilayer graphene

Abstract Twistronics heterostructures provide a novel route to control the electronic single particle velocity and thereby to engineer strong effective interactions. Here we show that the reverse may also hold, i.e. that these interactions strongly renormalize the band structure. We demonstrate this mechanism for alternating-twist magic-angle three- and four-layer graphene at charge neutrality and in the vicinity of a phase transition which can be described by an Ising Gross-Neveu critical point corresponding, e.g. to the onset of valley Hall or Hall order. While the non-interacting model displays massless Dirac excitations with strongly different velocities, we show that interaction corrections make them equal in the infrared. However, the renormalization group flow of the velocities and of the coupling to the critical bosonic mode is strongly non-monotonic and dominated by the vicinity of a repulsive fixed point. We predict experimental consequences of this theory for tunneling and transport experiments and discuss the expected behavior at other quantum critical points, including those corresponding to intervalley coherent ordering.

Classen, Laura↗

DOE OSTI2021

Magnetic probe diagnostics of nonlinear standing waves and bulk ohmic electron power absorption in capacitive discharges

It is recognized that standing wave effects appearing in large-area, very-high-frequency capacitively coupled plasma (CCP) reactors cause center-high plasma non-uniformity. Using a high-frequency magnetic probe, we present a direct experimental diagnostic of the nonlinear standing waves and bulk ohmic electron power absorption dynamics in low pressure CCP discharges for different driving frequencies of 13.56, 30, and 60 MHz. The design, principle, calibration, and validation of the probe are described in detail. Spatial structures of the harmonics of the magnetic field, determined by the magnetic probe, were used to calculate the distributions of the harmonic current and the corresponding ohmic electron power deposition, providing insights into the behavior of nonlinear harmonics. At a low driving frequency, i.e. 13.56 MHz, no remarkable nonlinear standing waves were identified and the bulk ohmic electron power absorption was observed to be negligible. Here, the harmonic magnetic field/current was found to increase dramatically with the driving frequency, due to decreased sheath reactance and more remarkable nonlinear standing waves at a higher driving frequency, leading to the enhancements of the ohmic heating and the plasma density in the bulk, specifically at the electrode center. At a high driving frequency, i.e. 60 MHz, the high-order harmonic current density and the corresponding ohmic electron power absorption exhibited a similar node structure, with the main peak on axis, and one or more minor peaks between the electrode center and the edge, contributing to the center-high profile of the plasma density.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Deep learning symmetries and their Lie groups, algebras, and subalgebras from first principles

Abstract We design a deep-learning algorithm for the discovery and identification of the continuous group of symmetries present in a labeled dataset. We use fully connected neural networks to model the symmetry transformations and the corresponding generators. The constructed loss functions ensure that the applied transformations are symmetries and the corresponding set of generators forms a closed (sub)algebra. Our procedure is validated with several examples illustrating different types of conserved quantities preserved by symmetry. In the process of deriving the full set of symmetries, we analyze the complete subgroup structure of the rotation groups SO (2), SO (3), and SO (4), and of the Lorentz group S O ( 1 , 3 ) . Other examples include squeeze mapping, piecewise discontinuous labels, and SO (10), demonstrating that our method is completely general, with many possible applications in physics and data science. Our study also opens the door for using a machine learning approach in the mathematical study of Lie groups and their properties.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Exploring the nexus of many-body theories through neural network techniques: the tangent model

Abstract In this paper, we present a physically informed neural network (NN) representation of the effective interactions associated with coupled-cluster downfolding models to describe chemical systems and processes. The NN representation not only allows us to evaluate the effective interactions efficiently for various geometrical configurations of chemical systems corresponding to various levels of complexity of the underlying wave functions, but also reveals that the bare and effective interactions are related by a tangent function of some latent variables. We refer to this characterization of the effective interaction as a tangent model. We discuss the connection between this tangent model for the effective interaction with the previously developed theoretical analysis that examines the difference between the bare and effective Hamiltonians in the corresponding active spaces.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Are permafrost microorganisms as old as permafrost?

ABSTRACT Permafrost describes the condition of earth material (sand, ground, organic matter, etc.) cemented by ice when its temperature remains at or below 0°C continuously for longer than 2 years. Evidently, permafrost is as old as the time passed from freezing of the earth material. Permafrost is a unique phenomenon and may preserve life forms it encloses. Therefore, in order to talk confidently about the preservation of paleo-objects in permafrost, knowledge about the geological age of sediments, i.e. when the sediments were formed, and permafrost age, when those sediments became permanently frozen, is essential. There are two types of permafrost—syngenetic and epigenetic. The age of syngenetic permafrost corresponds to the geological age of its sediments, whereas the age of epigenetic permafrost is less than the geological age of its sediments. Both of these formations preserve microorganisms and their metabolic products; however, the interpretations of the microbiological and molecular-biological data are inconsistent. This paper reviews the current knowledge of time–temperature history and age of permafrost in relation to available microbiological and metagenomic data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Kinetic and substrate complex characterization of RamA, a corrinoid protein reductive activase from Methanosarcina barkeri

ABSTRACT In microbial corrinoid-dependent methyltransferase systems, adventitious Co(I)-corrinoid oxidation halts catalysis and necessitates repair by ATP-dependent reductive activases. RamA, an activase with a C-terminal ferredoxin domain with two [4Fe-4S] clusters from methanogenic archaea, has been far less studied than the bacterial activases bearing an N-terminal ferredoxin domain with one [2Fe-2S] cluster. These differences suggest RamA might prove to have other distinctive characteristics. Here, we examine RamA kinetics and the stoichiometry of the corrinoid protein:RamA complex. Like bacterial activases, K+ stimulates RamA. Potassium stimulation had been questioned due to differences in the primary structure of bacterial and methanogen activases. Unlike one bacterial activase, ATP is not inhibitory allowing the first determination of apparent kinetic parameters for any corrinoid activase. Unlike bacterial activases, a single RamA monomer complexes a single corrinoid protein monomer. Alanine replacement of a RamA serine residue corresponding to the serine of one bacterial activase which ligates the corrinoid cobalt during complex formation led to only moderate changes in the kinetics of RamA. These results reveal new differences in the two types of corrinoid activases, and provide direct evidence for the proposal that corrinoid activases act as catalytic monomers, unlike other enzymes that couple ATP hydrolysis to difficult reductions.

Microbiology↗

DOE OSTI2023

Spectral induced polarization monitoring of induced calcite precipitation in subsurface sediments

Co-precipitation of contaminants within the crystalline structure of calcite is a promising natural attenuation or remedial technology being considered at contaminated sites. We explore the sensitivity of the spectral induced polarization (SIP) method to induced calcite precipitation in natural sediments as a path forward to non-invasively monitor these sites. We performed time-lapse column experiments using phased (I-IV) injections over 40 days on natural sediments from the Hanford Site (Washington State, USA). In the phased injections, abiotic calcite precipitation was induced and confirmed to have occurred. Previous work in glass beads and homogeneous sand was limited to high frequency detection of calcite, however in this work we observed the development of two polarization mechanisms, one at high frequency (>100 Hz) and one at low frequency (< 100 Hz). Based on the characteristic frequencies from the SIP high and low frequency regimes, characteristic length scales (L) were computed where the adsorption mode of Na+ versus Ca2+ was compared by using diffusion coefficients corresponding to Na+ versus an arithmetically averaged value for Na+ and Ca2+. Using the diffusion coefficient of Na+, the high frequency L was found to correlate well with the size of the calcite crystals. The low frequency L correlated well with the individual natural sediment grain sizes within the columns. During late experimental times (day 36 and 40), the characteristic low frequency in two of the experimental columns shifted to lower frequencies (<0.001 Hz) which may signify SIP sensitivity of the formed calcite with the sediment grains. In field applications, the development of a low frequency polarization length scale to monitor calcite precipitation is promising for field monitoring applications, however further laboratory work needs to be performed to examine the SIP sensitivity of calcite formation in the presence of to natural sediments

calcium carbonate, calcite, precipitation, spectra↗

DOE OSTI2021

Patient-Reported Outcomes in Pediatric Cancer Registration Trials: A US Food and Drug Administration Perspective

Pediatric patient-reported outcome (PRO) data can help inform the US Food and Drug Administration’s (FDA’s) benefit-risk assessment of cancer therapeutics by quantifying symptom and functional outcomes from the patient’s perspective. This study assessed use of PROs in commercial pediatric oncology trials submitted to the FDA for regulatory review. FDA databases were searched to identify pediatric oncology product applications approved between 1997 and 2020. Sponsor-submitted documents were reviewed to determine whether PRO data were collected, which instruments were used, and the quality of collected data (ie, sample size, completion rates, and use of fit-for-purpose instruments). The role of PROs in each trial (endpoint hierarchy) was also recorded in addition to whether any PRO endpoints were included in product labeling. We reviewed 17 pediatric oncology applications, 4 of which included PRO data: denosumab, tisagenlecleucel, larotrectinib, and selumetinib. In these 4 instances, PROs served as exploratory endpoints and were not incorporated in product labeling. Trials that collected PRO data were phase II or phase I/II single-arm studies with sample sizes of 28 to 88 patients. Symptomatic adverse events (AEs) were characterized using clinician-reported Common Terminology Criteria for Adverse Events (CTCAE) without additional patient self-report. PROs were infrequently used in pediatric cancer registration trials. When PROs were used, PRO data were limited by lack of a clear research objective and corresponding prospective statistical analysis plan. Contemporary PRO symptom libraries, such as the National Cancer Institute’s Pediatric PRO-CTCAE, may provide an opportunity to better evaluate the occurrence and impact of symptomatic AEs, from the patient’s perspective, in pediatric oncology trials.

Oncology↗

DOE OSTI2020

Constraining the scatter in the galaxy–halo connection at Milky Way masses

In this work, we develop and implement two new methods for constraining the scatter in the relationship between galaxies and dark matter haloes. These new techniques are sensitive to the scatter at low halo masses, making them complementary to previous constraints that are dependent on clustering amplitudes or rich galaxy groups, both of which are only sensitive to more massive haloes. In both of our methods, we use a galaxy group finder to locate central galaxies in the Sloan Digital Sky Survey main galaxy sample. Our first technique uses the small-scale cross-correlation of central galaxies with all lower mass galaxies. This quantity is sensitive to the satellite fraction of low-mass galaxies, which is in turn driven by the scatter between haloes and galaxies. The second technique uses the kurtosis of the distribution of line-of-sight velocities between central galaxies and neighbouring galaxies. This quantity is sensitive to the distribution of halo masses that contain the central galaxies at fixed stellar mass. Theoretical models are constructed using peak halo circular velocity, Vpeak, as our property to connect galaxies to haloes, and all comparisons between theory and observation are made after first passing the model through the group-finding algorithm. We parametrize scatter as a lognormal distribution in M* at fixed Vpeak, σ[M*|Vpeak]. The cross-correlation technique yields a constraint of σ[M*|Vpeak] = 0.27 ± 0.05 dex at a mean Vpeak of 168 km s-1, corresponding to a scatter in log M* at fixed Mh of σ[M*|Mh] = 0.38 ± 0.06 dex at $M_\text{h}=10^{11.8}\, \text{M}_\odot$. The kurtosis technique yields σ[M*|Vpeak] = 0.30 ± 0.03 at Vpeak = 209 km s-1, corresponding to σ[M*|Mh] = 0.34 ± 0.04 at $M_\text{h}=10^{12.2}\, \text{M}_\odot$. The values of σ[M*|Mh] are significantly larger than the constraints at higher masses, in agreement with the results of hydrodynamic simulations. This increase is only partly due to the scatter between Vpeak and Mh, and it represents an increase of nearly a factor of 2 relative to the values inferred from clustering and group studies at high masses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Quantitative comparison of opacities calculated using the R -matrix and distorted-wave methods: Fe xvii

ABSTRACT We present here a detailed calculation of opacities for Fe xvii at the physical conditions corresponding to the base of the Solar convection zone. Many ingredients are involved in the calculation of opacities. We review the impact of each ingredient on the final monochromatic and mean opacities (Rosseland and Planck). The necessary atomic data were calculated with the R-matrix and the distorted-wave (DW) methods. We study the effect of broadening, of resolution, of the extent of configuration sets and of configuration interaction to understand the differences between several theoretical predictions as well as the existing large disagreement with measurements. New Dirac R-matrix calculations including all configurations up to the n = 4, 5, and 6 complexes have been performed as well as corresponding Breit–Pauli DW calculations. The DW calculations have been extended to include autoionizing initial levels. A quantitative contrast is made between comparable DW and R-matrix models. We have reached self-convergence with n = 6 R-matrix and DW calculations. Populations in autoionizing initial levels contribute significantly to the opacities and should not be neglected. The R-matrix and DW results are consistent under the similar treatment of resonance broadening. The comparison with the experiment shows a persistent difference in the continuum while the filling of the windows shows some improvement. This study defines our path to the next generation of opacities and opacity tables for stellar modelling.

Delahaye, F.↗

DOE OSTI2021

The first spectroscopically confirmed brown dwarfs in NGC 2264

ABSTRACT We present spectroscopic follow-up observations of 68 red, faint candidates from our multi-epoch, multiwavelength, previously published survey of NGC 2264. Using near-infrared spectra from VLT/KMOS, we measure spectral types and extinction for 32 young low-mass sources. We confirm 13 as brown dwarfs in NGC 2264, with spectral types between M6 and M8, corresponding to masses between 0.02 and 0.08 M⊙. These are the first spectroscopically confirmed brown dwarfs in this benchmark cluster. 19 more objects are found to be young M-type stars of NGC 2264 with masses of 0.08–0.3 M⊙. 7 of the confirmed brown dwarfs as well as 15 of the M-stars have IR excess caused by a disc. Comparing with isochrones, the typical age of the confirmed brown dwarfs is <0.5–5 Myr. More than half of the newly identified brown dwarfs and very low-mass stars have ages <0.5 Myr, significantly younger than the bulk of the known cluster population. Based on the success rate of our spectroscopic follow-up, we estimate that NGC 2264 hosts 200–600 brown dwarfs in total (in the given mass range). This would correspond to a star-to-brown dwarf ratio between 2.5:1 and 7.5:1. We determine the slope of the substellar mass function as $\alpha = 0.43^{+0.41}_{-0.56}$; these values are consistent with those measured for other young clusters. This points to a uniform substellar mass function across all star-forming environments.

Pearson, Samuel↗

DOE OSTI2021

Fractal dimension of optical cirrus in Stripe82

ABSTRACT The geometric characteristics of dust clouds provide important information on the physical processes that structure such clouds. One of such characteristics is the 2D fractal dimension D of a cloud projected on to the sky plane. In previous studies, which were mostly based on infrared (IR) data, the fractal dimension of individual clouds was found to be in a range from 1.1 to 1.7 with a preferred value of 1.2–1.4. In this work, we use data from Stripe82 of the Sloan Digital Sky Survey to measure the fractal dimension of the cirrus clouds. This is done here for the first time for optical data with significantly better resolution as compared to IR data. To determine the fractal dimension, the perimeter-area method is employed. We also consider IR (IRAS and Herschel) counterparts of the corresponding optical fields to compare the results between the optical and IR. We find that the averaged fractal dimension across all clouds in the optical is $\langle D \rangle =1.69^{+0.05}_{-0.05}$ which is significantly larger than the fractal dimension of its IR counterparts $\langle D\rangle =1.38^{+0.07}_{-0.06}$. We examine several reasons for this discrepancy (choice of masking and minimal contour level, image and angular resolution, etc.) and find that for approximately half of our fields the different angular resolution (point spread function) of the optical and IR data can explain the difference between the corresponding fractal dimensions. For the other half of the fields, the fractal dimensions of the IR and visual data remain inconsistent, which can be associated with physical properties of the clouds, but further physical simulations are required to prove it.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Cosmological Constraints from Gas Mass Fractions of Massive, Relaxed Galaxy Clusters

We present updated cosmological constraints from measurements of the gas mass fractions (f(gas)) of massive, dynamically relaxed galaxy clusters. Our new data set has greater leverage on models of dark energy, thanks to the addition of the Perseus cluster at low redshifts, two new clusters at redshifts z greater than or similar to 1, and significantly longer observations of four clusters at 0.6 < z < 0.9. Our low-redshift (z < 0.16) f(gas) data, combined with the cosmic baryon fraction measured from the cosmic microwave background (CMB), imply a Hubble constant of h = 0.722 +/- 0.067. Combining the full f(gas) data set with priors on the cosmic baryon density and the Hubble constant, we constrain the dark energy density to be Omega(Lambda) = 0.865 +/- 0.119 in non-flat Lambda cold dark matter (cosmological constant) models, and its equation of state to be in flat, constant-w models, respectively 41percent and 29percent tighter than our previous work, and comparable to the best constraints available from other probes. Combining f(gas), CMB, supernova, and baryon acoustic oscillation data, we also constrain models with global curvature and evolving dark energy. For the massive, relaxed clusters employed here, we find the scaling of f(gas) with mass to be consistent with a constant, with an intrinsic scatter that corresponds to just similar to 3percent in distance.

clusters: general – X-rays:↗

DOE OSTI2022

Kicks and induced spins of neutron stars at birth

ABSTRACT Using simulations of non-rotating supernova progenitors, we explore the kicks imparted to and the spins induced in the compact objects birthed in core collapse. We find that the recoil due to neutrino emissions can be a factor affecting core recoil, comparable to and at times larger than the corresponding kick due to matter recoil. This result would necessitate a revision of the general model of the origin of pulsar proper motions. In addition, we find that the sign of the net neutrino momentum can be opposite to the sign of the corresponding matter recoil. As a result, at times the pulsar recoil and ejecta can be in the same direction. Moreover, our results suggest that the duration of the dipole in the neutrino emissions can be shorter than the duration of the radiation of the neutron-star binding energy. This allows a larger dipole asymmetry to arise, but for a shorter time, resulting in kicks in the observed pulsar range. Furthermore, we find that the spin induced by the aspherical accretion of matter can leave the residues of collapse with spin periods comparable to those inferred for radio pulsars and that there seems to be a slight anticorrelation between the direction of the induced spin and the net kick direction. This could explain such a correlation among observed radio pulsars. Finally, we find that the kicks imparted to black holes are due to the neutrino recoil alone, resulting in birth kicks ≤100 km s−1 most of the time.

Astronomy & Astrophysics↗

DOE OSTI2022

The completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: cosmological implications from multitracer BAO analysis with galaxies and voids

We construct cosmic void catalogues with the dive void finder upon SDSS BOSS DR12 and eBOSS DR16 galaxy samples with BAO reconstruction, and perform a joint BAO analysis using different types of galaxies and the corresponding voids. The BAO peak is evident for the galaxy–galaxy, galaxy–void, and void–void correlation functions of all data sets, including the ones cross-correlating LRG and ELG samples. Two multitracer BAO fitting schemes are tested, one combining the galaxy and void correlation functions with a weight applied to voids, and the other using a single BAO dilation parameter for all clustering measurements. Both methods produce consistent results with mock catalogues, and on average ~10 per cent improvements of the BAO statistical uncertainties are observed for all samples, compared to the results from galaxies alone. By combining the clustering of galaxies and voids, the uncertainties of BAO measurements from the SDSS data are reduced by 5–15 per cent, yielding 0.9 per cent, 0.8 per cent, 1.1 per cent, 2.3 per cent, and 2.9 per cent constraints on the distance $D_{_{\rm V}}(z)$, at effective redshifts 0.38, 0.51, 0.70, 0.77, and 0.85, respectively. When combined with BAO measurements from SDSS MGS, QSO, and Lyα samples, as well as the BBN results, we obtain $H_0 = 67.58 \pm 0.91\, {\rm km}\, {\rm s}^{-1}\, {\rm Mpc}^{-1}$, Ω m = 0.290 ± 0.015, and $\Omega _\Lambda h^2 = 0.3241 \pm 0.0079$ in the flat-ΛCDM framework, where the 1σ uncertainties are around 6 per cent, 6 per cent, and 17 per cent smaller respectively, compared to constraints from the corresponding anisotropic BAO measurements without voids and LRG–ELG cross-correlations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

Identifying Anomalous DESI Galaxy Spectra with a Variational Autoencoder

The tens of millions of spectra being captured by the Dark Energy Spectroscopic Instrument (DESI) provide tremendous discovery potential. In this work we show how Machine Learning, in particular Variational Autoencoders (VAE), can detect anomalies in a sample of approximately 200,000 DESI spectra comprising galaxies, quasars and stars. We demonstrate that the VAE can compress the dimensionality of a spectrum by a factor of 100, while still retaining enough information to accurately reconstruct spectral features. We then detect anomalous spectra as those with high reconstruction error and those which are isolated in the VAE latent representation. The anomalies identified fall into two categories: spectra with artefacts and spectra with unique physical features. Awareness of the former can help to improve the DESI spectroscopic pipeline; whilst the latter can lead to the identification of new and unusual objects. To further curate the list of outliers, we use the Astronomaly package which employs Active Learning to provide personalised outlier recommendations for visual inspection. In this work we also explore the VAE latent space, finding that different object classes and subclasses are separated despite being unlabelled. We demonstrate the interpretability of this latent space by identifying tracks within it that correspond to various spectral characteristics. For example, we find tracks that correspond to increasing star formation and increase in broad emission lines along the Balmer series. In upcoming work we hope to apply the methods presented here to search for both systematics and astrophysically interesting objects in much larger datasets of DESI spectra.

Nicolaou, C. [University Coll. London] (ORCID:0000↗

DOE OSTI2025

Cryo-EM structures of DNA-free and DNA-bound BsaXI: architecture of a Type IIB restriction–modification enzyme

Abstract We have determined multiple cryogenic electron microscopy (cryo-EM) structures of the Type IIB restriction–modification enzyme BsaXI. Such enzymes cleave DNA on both sides of their recognition sequence and share features of Types I, II, and III restriction systems. BsaXI forms a heterotrimeric (RM)2S assemblage in the presence and absence of bound DNA. Two unique structural motifs—a multi-helical “knob” and a long antiparallel double-helical “paddle”—are involved in DNA binding and cleavage. Binding of the DNA target triggers a large conformational change from an ‘open’ to ‘closed’ configuration, resulting in a mixture of two different conformations with respect to the positioning of the S subunit and its target recognition domains on the enzyme’s bipartite DNA target site. Structure-guided mutagenesis studies implicated two clusters of residues in the RM subunit as being critical for DNA cleavage, both are located proximal to a DNA cleavage site. One corresponds to a canonical PD-(D/E)xK endonuclease site in the N-terminal endonuclease domain, while the other corresponds to residues clustered within the paddle motif (near to the C-terminal end of the RM subunit). This analysis facilitates a comparison of three potential mechanisms by which such enzymes cleave DNA on each side of the bound target.

Shen, Betty W.↗