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At least 361 records · Page 20

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DOE OSTI2023

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold

The crystal structure of the domain of unknown function family 507 protein from Aquifex aeolicus is reported (AaDUF507, UniProt O67633, 183 residues). The structure was determined in two space groups (C222 1 and P3 2 21) at 1.9 Å resolution. The phase problem was solved by molecular replacement using an AlphaFold model as the search model. AaDUF507 is a Y-shaped α-helical protein consisting of an anti-parallel 4-helix bundle base and two helical arms that extend 30-Å from the base. The two crystal structures differ by a 25° rigid body rotation of the C-terminal arm. The tertiary structure exhibits pseudo-twofold symmetry. The structural symmetry mirrors internal sequence similarity: residues 11–57 and 102–148 are 30% identical and 53% similar with an E-value of 0.002. In one of the structures, electron density for an unknown ligand, consistent with nicotinamide or similar molecule, may indicate a functional site. Docking calculations suggest potential ligand binding hot spots in the region between the helical arms. Structure-based query of the Protein Data Bank revealed no other protein with a similar tertiary structure, leading us to propose that AaDUF507 represents a new protein fold.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Time-series forecasting using manifold learning, radial basis function interpolation, and geometric harmonics

We address a three-tier numerical framework based on nonlinear manifold learning for the forecasting of high-dimensional time series, relaxing the “curse of dimensionality” related to the training phase of surrogate/machine learning models. At the first step, we embed the high-dimensional time series into a reduced low-dimensional space using nonlinear manifold learning (local linear embedding and parsimonious diffusion maps). Then, we construct reduced-order surrogate models on the manifold (here, for our illustrations, we used multivariate autoregressive and Gaussian process regression models) to forecast the embedded dynamics. Finally, we solve the pre-image problem, thus lifting the embedded time series back to the original high-dimensional space using radial basis function interpolation and geometric harmonics. The proposed numerical data-driven scheme can also be applied as a reduced-order model procedure for the numerical solution/propagation of the (transient) dynamics of partial differential equations (PDEs). In conclusion, we assess the performance of the proposed scheme via three different families of problems: (a) the forecasting of synthetic time series generated by three simplistic linear and weakly nonlinear stochastic models resembling electroencephalography signals, (b) the prediction/propagation of the solution profiles of a linear parabolic PDE and the Brusselator model (a set of two nonlinear parabolic PDEs), and (c) the forecasting of a real-world data set containing daily time series of ten key foreign exchange rates spanning the time period 3 September 2001–29 October 2020.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Energetic particle physics: Chapter 7 of the special issue: on the path to tokamak burning plasma operation

We review the physics of energetic particles (EPs) in magnetically confined burning fusion plasmas with focus on advances since the last update of the ITER Physics Basis (Fasoli et al 2007 Nucl. Fusion 47 S264). Topics include basic EP physics, EP generation, diagnostics of EPs and instabilities, the interaction of EPs and thermal plasma instabilities, EP-driven instabilities, energetic particle modes (EPMs), and turbulence, linear and nonlinear stability and simulation of EP-driven instabilities and EPMs, 3D effects, scenario optimization strategies based on EP phase-space control, EPs in reduced field scenarios in ITER before DT, and the physics of runaway electrons. We describe the simulation and modeling of EPs in fusion plasmas, including instability drive and damping as well as EP transport, with a range of approaches from first-principles to reduced models, including gyrokinetic simulations, kinetic-MHD models, gyrofluid models, reduced models, and semi-analytical approaches.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Solving nuclear structure problems with the adaptive variational quantum algorithm

Here we use the Lipkin-Meshkov-Glick (LMG) model and the valence-space nuclear shell model to examine the likely performance of variational quantum eigensolvers in nuclear-structure theory. The LMG model exhibits both a phase transition and spontaneous symmetry breaking at the mean-field level in one of the phases, features that characterize collective dynamics in medium-mass and heavy nuclei. We show that with appropriate modifications, the ADAPT-VQE algorithm, a particularly flexible and accurate variational approach, is not troubled by these complications. We treat up to 12 particles and show that the number of quantum operations needed to approach the ground-state energy scales linearly with the number of qubits. We find similar scaling when the algorithm is applied to the nuclear shell model with realistic interactions in the sd and pf shells. Although most of these simulations contain no noise, we use a noise model from real IBM hardware to show that for the LMG model with four particles, weak noise has no effect on the efficiency of the algorithm.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Cosmology of Sub-MeV Dark Matter Freeze-In

Dark matter (DM) could be a relic of freeze-in through a light mediator, where the DM is produced by extremely feeble, IR-dominated processes in the thermal standard model plasma. In the simplest viable models with DM lighter than 1 MeV, the DM has a small effective electric charge and is born with a nonthermal phase-space distribution. This DM candidate would cause observable departures from standard cosmological evolution. In this work, we combine data from the cosmic microwave background (CMB), Lyman-α forest, quasar lensing, stellar streams, and Milky Way satellite abundances to set limits on freeze-in DM masses up to ~20 keV, with the exact constraint depending on whether the DM thermalizes in its own sector. Further, we perform forecasts for the CMB-S4 experiment, the Hydrogen Epoch of Reionization Array, and the Vera Rubin Observatory, finding that freeze-in DM masses up to ~80 keV can be explored.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Pulse-by-pulse transient thermal deformation in crystal optics under high-repetition-rate FEL

Time-domain modeling of the thermal deformation of crystal optics can help define acceptable operational ranges across the pulse-energy repetition-rate phase space. In this paper, we have studied the transient thermal deformation of a water-cooled diamond crystal for a cavity-based X-ray free-electron laser (CBXFEL), either an X-ray free-electron laser oscillator (XFELO) or a regenerative amplifier X-ray free-electron laser (RAFEL), by numerical simulations including finite-element analysis and advanced data processing. Pulse-by-pulse transient thermal deformation of a 50 µm-thick diamond crystal has been performed with X-ray pulse repetition rates between 50 kHz and 1 MHz. Results for temperature and thermal deformation have been compared with the results of transient analysis using a continuous wave (CW) power loading. Temperature and thermal deformation results from pulse-by-pulse transient analysis vary with time about the results for the CW case for the same average power. The variation amplitude increases with pulse energy and decreases with repetition rate. When the repetition rate increases to infinity, both temperature and thermal deformation converge to the results for the CW case. Two critical time scales for the operation of crystal optics in a CBXFEL are (1) first-turn time, i.e. the time for the XFEL pulse to complete the first turn around the cavity so that the crystal sees the recirculated XFEL pulse, and (2) period-end time, i.e. the time that the next electron bunch arrives for the amplification, so that the crystal outcouples the amplified FEL power. For the same average power, simulation results show that the crystal thermal deformation seen by the XFEL beam decreases with repetition rate at the first-turn time of a 300 m-long cavity and increases with repetition rate at the period-end time. For the wavefront preservation requirement of the crystal optics, a pulse-energy versus repetition-rate phase space has been established. The upper bounds of the pulse energy at both first-turn and period-end times decreases with repetition rate, especially at the period-end time. The upper bound of the thermal deformation of the crystal at the period-end time for any repetition frequency can be estimated from the CW case. For a water-cooled diamond crystal of dimension 5 mm × 5 mm × 0.05 mm, the time to reach a quasi steady-state is about 50 ms for temperature and 50 µs for thermal deformation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Enhancement of HLW glass property-composition models

Since the WTP compositional space of HLW glasses is extremely large, development of HLW property-composition models is a multi-year task consisting of multiple phases. The primary focus of this work was to enhance the WTP HLW models of interest including PCT releases, spinel crystallization (T1%), viscosity, electrical conductivity, and TCLP-Cd response. Model development to predict nepheline formation upon CCC is the subject of a separate task. In particular, the earlier work has produced property-composition models for glass melt viscosity and glass melt electrical conductivity that showed good performance, while models for PCT releases and spinel crystallization (T1%) required improvement. Therefore, more efforts were directed in the present work to collect data and improve model performance for HLW glass PCT releases and spinel crystallization than for other properties. The present work is a continuation of earlier development phases and is responsive to the applicable Test Plan.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2026

Experimental protocol for phase 1 of the APARC QUOCA (QUasibiennial oscillation and Ozone Chemistry interactions in the Atmosphere) working group

The quasi-biennial oscillation (QBO) is the main mode of variability in the tropical stratosphere, influencing the predictability of other regions in the atmosphere through its teleconnections to the stratospheric polar vortices and coupling to surface tropical and extratropical variability. However, climate and forecasting models consistently underestimate QBO amplitudes in the lower stratosphere, likely contributing to their failure to simulate these teleconnections. One underexplored contributor to model biases is missing representation of ozone-radiative feedbacks, which enhance temperature variability in the lower stratosphere, particularly at periods at and greater than the QBO (>28 months). While previous studies suggest that ozone-radiative feedbacks can impact QBO periods, amplitudes and the associated secondary circulation in the lower stratosphere, the reported impacts differ widely among models and are hard to interpret due to differences in methodology. To this end, here we propose a coordinated experimental protocol – held joint between the Atmospheric Processes and their Role in Climate (APARC) Quasi-Biennial Oscillation Initiative (QBOi) and Chemistry Climate Modeling Initiative (CCMI) activities – which is aimed at assessing the coupling between stratospheric ozone, temperature and the circulation. We use the proposed experiments to define the ozone feedback on the QBO in both present-day and idealized (abrupt quadrupling of carbon dioxide) climates. While primary focus is on the QBO, the proposed protocol also enables analysis of other aspects of ozone-radiative-dynamical coupling in the atmosphere, including impacts on the Brewer-Dobson Circulation and tropospheric eddy-driven jet responses to future climate change. Here we document the scientific rationale and design of the QUOCA Phase 1 experiments, summarize the data request, and give a brief overview of participating models. Preliminary results using the NASA Goddard Institute for Space Studies E2-2 climate model are used to illustrate sensitivities to certain methodological choices.

Environmental sciences↗

DOE OSTI2023

Revealing the Statistics of Extreme Events Hidden in Short Weather Forecast Data

Extreme weather events have significant consequences, dominating the impact of climate on society. While high-resolution weather models can forecast many types of extreme events on synoptic timescales, long-term climatological risk assessment is an altogether different problem. A once-in-a-century event takes, on average, 100 years of simulation time to appear just once, far beyond the typical integration length of a weather forecast model. Therefore, this task is left to cheaper, but less accurate, low-resolution or statistical models. But there is untapped potential in weather model output: despite being short in duration, weather forecast ensembles are produced multiple times a week. Integrations are launched with independent perturbations, causing them to spread apart over time and broadly sample phase space. Collectively, these integrations add up to thousands of years of data. We establish methods to extract climatological information from these short weather simulations. Using ensemble hindcasts by the European Center for Medium-range Weather Forecasting archived in the subseasonal-to-seasonal (S2S) database, we characterize sudden stratospheric warming (SSW) events with multi-centennial return times. Consistent results are found between alternative methods, including basic counting strategies and Markov state modeling. By carefully combining trajectories together, we obtain estimates of SSW frequencies and their seasonal distributions that are consistent with reanalysis-derived estimates for moderately rare events, but with much tighter uncertainty bounds, and which can be extended to events of unprecedented severity that have not yet been observed historically. These methods hold potential for assessing extreme events throughout the climate system, beyond this example of stratospheric extremes.

58 GEOSCIENCES↗

DOE OSTI2022

Modeling impacts of ice-nucleating particles from marine aerosols on mixed-phase orographic clouds during 2015 ACAPEX field campaign

Abstract. A large fraction of annual precipitation over the western United States comes from wintertime orographic clouds associated with atmospheric rivers (ARs). Transported African and Asian dust and marine aerosols from the Pacific Ocean may act as ice-nucleating particles (INPs) to affect cloud and precipitation properties over the region. Here we explored the effects of INPs from marine aerosols on orographic mixed-phase clouds and precipitation at different AR stages for an AR event observed during the 2015 ACAPEX field campaign under low dust (<0.02 cm−3) conditions. Simulations were conducted using the chemistry version of the Weather Research and Forecasting Model coupled with the spectral-bin microphysics at 1 km grid spacing, with ice nucleation connected with dust and marine aerosols. By comparing against airborne and ground-based observations, accounting for marine INP effects improves the simulation of AR-precipitation. The marine INPs enhance the formation of ice and snow, leading to less shallow warm clouds but more mixed-phase and deep clouds, as well as to a large spillover effect of precipitation after AR landfall. The responses of cloud and precipitation to marine INPs vary with the AR stages, with more significant effects before AR landfall and post-AR than after AR landfall, mainly because the moisture and temperature conditions change with the AR evolution. This work suggests weather and climate models need to consider the impacts of marine INPs since their contribution is notable under low dust conditions despite the much lower relative ice nucleation efficiency of marine INPs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

A Fine-grained Asynchronous Bulk Synchronous parallelism model for PGAS applications

The Partitioned Global Address Space (PGAS) model is well suited for executing irregular applications on cluster-based systems, due to its efficient support for short, one-sided messages. Separately, the actor model has been gaining popularity as a productive asynchronous message-passing approach for distributed objects in enterprise and cloud computing platforms, typically implemented in languages such as Erlang, Scala or Rust. To the best of our knowledge, there has been no past work on using the actor model to deliver both productivity and scalability to irregular PGAS applications with large number of small messages. In this paper, we introduce a new programming system for PGAS applications, in which point-to-point remote operations can be expressed as fine-grained asynchronous actor messages. In our approach, the programmer does not need to worry about programming complexities related to message aggregation and termination detection. Our approach can be viewed as extending the classical Bulk Synchronous Parallelism model with fine-grained asynchronous communications within a phase or superstep. Here, we believe that our approach offers a desirable point in the productivity-performance space for PGAS applications, with more scalable performance and higher productivity relative to past approaches. Specifically, for seven irregular mini-applications from the Bale Kernels and three graph kernels executed using 2048 cores in the NERSC Cori system, our approach shows geometric mean performance improvements of ≥ 20X relative to standard PGAS versions (UPC and OpenSHMEM) while maintaining comparable productivity to those versions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Deep learning on the 2-dimensional Ising model to extract the crossover region with a variational autoencoder

The 2-dimensional Ising model on a square lattice is investigated with a variational autoencoder in the non-vanishing field case for the purpose of extracting the crossover region between the ferromagnetic and paramagnetic phases. The encoded latent variable space is found to provide suitable metrics for tracking the order and disorder in the Ising configurations that extends to the extraction of a crossover region in a way that is consistent with expectations. The extracted results achieve an exceptional prediction for the critical point as well as agreement with previously published results on the configurational magnetizations of the model. The performance of this method provides encouragement for the use of machine learning to extract meaningful structural information from complex physical systems where little a priori data is available.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Prompt and non-prompt J/ψ production cross sections at midrapidity in proton-proton collisions at $ \sqrt{\mathrm{s}} $ = 5.02 and 13 TeV

The production of J /ψ is measured at midrapidity ( |y| < 0 . 9) in proton-proton collisions at $ \sqrt{s} $ = 5 . 02 and 13 TeV, through the dielectron decay channel, using the ALICE detector at the Large Hadron Collider. The data sets used for the analyses correspond to integrated luminosities of $ \mathcal{L} $ int = 19.4 ± 0.4 nb - 1 and $ \mathcal{L} $ int = 32.2 ± 0.5 nb - 1 at $ \sqrt{s} $ = 5 . 02 and 13 TeV, respectively. The fraction of non-prompt J /ψ mesons, i.e. those originating from the decay of beauty hadrons, is measured down to a transverse momentum p T = 2 GeV /c (1 GeV /c ) at $ \sqrt{s} $ = 5 . 02 TeV (13 TeV). The p T and rapidity ( y ) differential cross sections, as well as the corresponding values integrated over p T and y , are carried out separately for prompt and non-prompt J /ψ mesons. The results are compared with measurements from other experiments and theoretical calculations based on quantum chromodynamics (QCD). The shapes of the p T and y distributions of beauty quarks predicted by state-of-the-art perturbative QCD models are used to extrapolate an estimate of the $ \mathrm{b}\overline{\mathrm{b}} $ pair cross section at midrapidity and in the total phase space. The total $ \mathrm{b}\overline{\mathrm{b}} $ cross sections are found to be $ {\sigma}_{\mathrm{b}\overline{\mathrm{b}}} $ = 541 ± 45 (stat . ) ± 69 $ {\left(\mathrm{syst}.\right)}_{-12}^{+10} $ (extr . ) μ b and $ {\sigma}_{\mathrm{b}\overline{\mathrm{b}}} $ = 218 ± 37 (stat . ) ± 31 $ {\left(\mathrm{syst}.\right)}_{-9.1}^{+8.2} $ (extr . ) μ b at $ \sqrt{s} $ = 13 and 5.02 TeV, respectively. The value obtained from the combination of ALICE and LHCb measurements in pp collisions at $ \sqrt{s} $ = 13 TeV is also provided.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Modeling quasielastic interactions of monoenergetic kaon decay-at-rest neutrinos

Monoenergetic muon neutrinos at 236 MeV are readily produced in intense medium-energy proton facilities (≳2–3GeV) when a positive kaon decays at rest (KDAR; K + →μ + ν μ ). These neutrinos provide a unique opportunity to both study the neutrino interaction and probe the nucleus with a monoenergetic weak-interaction-only tool. We present cross-section calculations for quasielastic scattering of these 236-MeV neutrinos off 12 C and 40 Ar, paying special attention to low-energy aspects of the scattering process. Our model takes the description of the nucleus in a mean-field approach as the starting point, where we solve Hartree-Fock equations using a Skyrme type nucleon-nucleon interaction. Thereby, we introduce long-range nuclear correlations by means of a continuum random-phase approximation (CRPA) framework where we solve the CRPA equations using a Green's function method. The model successfully describes (e,e') data on 12 C and 40 Ca in the kinematic region that overlaps with the KDAR ν μ phase space. In addition to these results, we present future prospects for precision KDAR cross-section measurements and applications of our calculations in current and future experiments that will utilize these neutrinos.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Signatures of QCD conductivities in heavy-ion collisions

Dissipative processes are pivotal for understanding the hydrodynamic evolution of hot and dense quantum chromodynamics (QCD) matter created in relativistic nuclear collisions. The interplay of multiple conserved charges—net baryon, strangeness, and electric charge—is of particular interest. Here, we simulate the longitudinal hydrodynamic evolution with the three diffusion currents in a hydrodynamic model with a lattice-QCD-based equation of state, NEOS -4 D , and estimate rapidity distributions including diffusive corrections to the phase-space distribution in the presence of multiple charges, which ensure charge conservation at particlization. We determine the response of particle yields at midrapidity to changes in the diagonal and off-diagonal conductivities. Inversely, we find that most components of the conductivity matrix can be constrained experimentally using identified particle multiplicities at different collision energies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Measurements of ${\Xi }{^-}$ and $\overline{\Xi }{^+}$ production in proton–proton interactions at $\sqrt{s_{NN}}$ = 17.3 $\hbox {Ge}\hbox {V}$ in the NA61/SHINE experiment

The production of $\Xi (1321)^{-}$ and $\overline{\Xi }(1321)^{+}$ hyperons in inelastic $p+p$ interactions is studied in a fixed target experiment at a beam momentum of 158 $\hbox {Ge}\hbox {V}\!/\!c$. Double differential distributions in rapidity ${y}$ and transverse momentum $p_{T}$ are obtained from a sample of 33M inelastic events. They allow to extrapolate the spectra to full phase space and to determine the mean multiplicity of both ${\Xi }{^-}$ and $\overline{\Xi }{^+} $. The rapidity and transverse momentum spectra are compared to transport model predictions. The ${\Xi }{^-} $ mean multiplicity in inelastic $p+p$ interactions at 158 $\hbox {Ge}\hbox {V}\!/\!c$ is used to quantify the strangeness enhancement in A+A collisions at the same centre-of-mass energy per nucleon pair.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Quantifying CanESM5 and EAMv1 sensitivities to Mt. Pinatubo volcanic forcing for the CMIP6 historical experiment

Large volcanic eruptions reaching the stratosphere have caused marked perturbations to the global climate including cooling at the Earth's surface, changes in large-scale circulation and precipitation patterns and marked temporary reductions in global ocean heat content. Many studies have investigated these effects using climate models; however, uncertainties remain in the modelled response to these eruptions. This is due in part to the diversity of forcing datasets that are used to prescribe the distribution of stratospheric aerosols resulting from these volcanic eruptions, as well as uncertainties in optical property derivations from these datasets. To improve this situation for the sixth phase of the Coupled Model Intercomparison Project (CMIP6), a two-step process was undertaken. First, a combined stratospheric aerosol dataset, the Global Space-based Stratospheric Aerosol Climatology (GloSSAC; 1979–2016), was constructed. Next, GloSSAC, along with information from ice cores and Sun photometers, was used to generate aerosol distributions, characteristics and optical properties to construct a more consistent stratospheric aerosol forcing dataset for models participating in CMIP6. This “version 3” of the stratospheric aerosol forcing has been endorsed for use in all contributing CMIP6 simulations. Recent updates to the underlying GloSSAC from version 1 to version 1.1 affected the 1991–1994 period and necessitated an update to the stratospheric aerosol forcing from version 3 to version 4. As version 3 remains the official CMIP6 input, quantification of the impact on radiative forcing and climate is both relevant and timely for interpreting results from experiments such as the CMIP6 historical simulations. This study uses two models, the Canadian Earth System Model version 5 (CanESM5) and the Energy Exascale Earth System Model (E3SM) Atmosphere Model version 1 (EAMv1), to estimate the difference in instantaneous radiative forcing in simulated post-Pinatubo climate response when using version 4 instead of version 3. Differences in temperature, precipitation and radiative forcings are generally found to be small compared to internal variability. An exception to this is differences in monthly temperature anomalies near 24 km altitude in the tropics, which can be as large as 3 °C following the eruption of Mt. Pinatubo.

58 GEOSCIENCES↗

DOE OSTI2025

Dynamics-based halo model for large scale structure

Accurate modeling of the one-to-two halo transition has long been difficult to achieve. Here, we demonstrate that physically motivated halo definitions that respect the bimodal phase-space distribution of dark matter particles near halos resolves this difficulty. Specifically, the two phase-space components are overlapping and correspond to (1) particles orbiting the halo and (2) particles infalling into the halo for the first time. Motivated by this decomposition, García et al. [Mon. Not. R. Astron. Soc. 521, 2464 (2023)] advocated for defining halos as the collection of particles orbiting their self-generated potential. This definition identifies the traditional one-halo term of the halo-mass correlation function with the distribution of orbiting particles around a halo, while the two-halo term governs the distribution of infalling particles. We use dark matter simulations to demonstrate that the distribution of orbiting particles is finite and can be characterized by a single physical scale 𝑟 h , which we refer to as the halo radius. The two-halo term is described using a simple yet accurate empirical model based on the Zel’dovich correlation function. We further demonstrate that the halo radius imprints itself on the distribution of infalling particles at small scales. Our final model for the halo-mass correlation function is accurate at the ≈ 2% level for 𝑟∈ [0.1, 50] ℎ −1 Mpc. The Fourier transform of our best-fit model describes the halo-mass power spectrum with comparable accuracy for 𝑘 ∈ [0.06, 6.0] ℎ Mpc −1 .

79 ASTRONOMY AND ASTROPHYSICS↗