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The Linac Extension Area has been developed into a beamline area for testing accelerator components and techniques. Beginning commissioning activities in February 2023, we have delivered the first electron beam to the Linac Extension Area at the Advanced Photon Source at 425 MeV. In the present work, we summarise the principal accelerator components and review safety controls of the Linac Extension Area.
Exascale workloads are expected to incorporate data-intensive processing in close coordination with traditional physics simulations. These emerging scientific, data-analytics and machine learning applications need to access a wide variety of datastores in flat files and structured databases. Programmer productivity is greatly enhanced by mapping datastores into the application process's virtual memory space to provide a unified “in-memory” interface. Currently, memory mapping is provided by system software primarily designed for generality and reliability. However, scalability at high concurrency is a formidable challenge on exascale systems. Also, there is a need for extensibility to support new datastores potentially requiring HPC data transfer services. In this article, we present UMap , a scalable and extensible userspace service for memory-mapping datastores. Furthermore, through decoupled queue management, concurrency aware adaptation, and dynamic load balancing, UMap enables application performance to scale even at high concurrency. We evaluate UMap in data-intensive applications, including sorting, graph traversal, database operations, and metagenomic analytics. Our results show that UMap as a userspace service outperforms an optimized kernel-based service across a wide range of intra-node concurrency by 1.22-1.9 × . We performed two case studies to demonstrate UMap 's extensibility. First, a new datastore residing in remote memory is incorporated into UMap as an application-specific plugin. Second, we present a persistent memory allocator Metall built atop UMap for unified storage/memory.
Type 304H and 316H stainless steels are codified in the ASME Boiler and Pressure Vessel Code for Section III, Division 5, Class A construction for up to 1500F (816C) and 300,000 hours. Extension of the design lifetimes to 500,000 hours has been undertaken by various research projects and by the ASME Section III, Division 5 Code Committees. Due to a long-standing issue related to non-classical creep behavior on the use of the time to the onset of tertiary creep as one of the time-dependent allowable stress criteria, little progress was made in the extension of the time-dependent allowable stresses for Type 304H and 316H stainless steels. A recent effort by Dabrow and Nestell (Impact of Tertiary Creep on Time Dependent Allowable Stresses for Type 304H and 316H Stainless Steels, Report 0300-0003-RPT-001, MPR Associates, Alexandria, VA, 2020) has provided a rational method for the treatment of the highly variable data for the time to onset of tertiary creep. In this paper, the background formulas for determining the time-dependent allowable stress values of Type 304H and 316H stainless steels, as assembled from relevant project work, are presented. These updates and extensions are being recommended to the ASME Code committees for approval, and are subject to change upon feedback from ASME Section III Code committees.
Quantum computing (QC) is an emerging computational paradigm that leverages the laws of quantum mechanics to perform elementary logic operations. Existing programming models for QC were designed with fault-tolerant hardware in mind, envisioning stand-alone applications. However, the susceptibility of near-term quantum computers to noise limits their stand-alone utility. To better leverage limited computational strengths of noisy quantum devices, hybrid algorithms have been suggested whereby quantum computers are used in tandem with their classical counterparts in a heterogeneous fashion. This modus operandi calls out for a programming model and a high-level programming language that natively and seamlessly supports heterogeneous quantum-classical hardware architectures in a single-source-code paradigm. Motivated by the lack of such a model, we introduce a language extension specification, called QCOR, which enables single-source quantum-classical programming. Programs written using the QCOR library–based language extensions can be compiled to produce functional hybrid binary executables. After defining QCOR’s programming model, memory model, and execution model, we discuss how QCOR enables variational, iterative, and feed-forward QC. Additionally, QCOR approaches quantum-classical computation in a hardware-agnostic heterogeneous fashion and strives to build on best practices of high-performance computing. The high level of abstraction in the language extension is intended to accelerate the adoption of QC by researchers familiar with classical high-performance computing.
The Web Extensible Display Manager (WEDM) was first deployed at Jefferson Lab (JLab) in 2016 with the goal of rendering Extensible Display Manager (EDM) control screens on the web for the benefit of accessibility, and with version 2 our aim is to provide a more general purpose display toolkit by freeing ourselves from the constraints of the EDM dependency. Over the last few years WEDM has been extensively used at JLab for 24/7 information kiosks, on-call monitoring, and by remote users and staff. The software has also been deployed to Oak Ridge National Laboratory, and has become more robust as many bug fixes and contributions have been added. However, adoption and utility of the software as a general purpose control system display manager is limited by EDM, which is no longer actively maintained. A new toolkit can be built on modern frameworks, fully embrace web conventions and standards, and support multiple control system data sources. This new version is a result of a technology review and selection, and introduces a web inspired display file format, a web based display builder, new widgets, and a data interface intended to support pluggable data.
The extension IAC at CWRU is funded for 3 years to conduct 10 assessments of small and medium-sized manufacturing facilities each year in Eastern Great Lakes region. Total 30 assessments was proposed in the SOPO but due to the Covid-19 pandemic, the IAC program was suspended for 1.5 years. A total of 20 assessments was contracted to the extension IAC at CWRU which have been successfully accomplished. In the proposal, we proposed to train 18 students in the extension IAC program, and actually we selected and trained 19 students even though the IAC project was suspended during half of its project period.
Abstract Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high‐resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor‐1, which is targeted by osteoporosis drugs. These results should motivate other structure‐based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.
Abstract Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high‐resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor‐1, which is targeted by osteoporosis drugs. These results should motivate other structure‐based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.
Property models are becoming more widely adopted by commercial Calphad databases, but they are not nearly as common in non-commercial or traditional academic Calphad databases. A primary driver is that user-friendly Calphad modeling tools that support property models are not widely available. Here we present new property modeling capabilities that have been implemented in ESPEI (the Extensible, Self-optimizing Phase Equilibrium Infrastructure). These capabilities include both generating property model parameters from data and improvements to the algorithmic selection of the most appropriate model from a series of candidates. Additionally, two illustrative examples are given that use ESPEI to fit different property models. First, we generate molar volume model parameters for Group IV, V, and VI refractory BCC alloys based on the model by Lu et al. (2005). Second, we demonstrate the extensibility of ESPEI’s property modeling capabilities by implementing a custom PyCalphad model for BCC elastic stiffness parameters to generate and compare parameters to the ones assessed by Marker et al. (2018) using the same data. Property models generated by ESPEI can be used in PyCalphad or further optimized with uncertainty quantification using ESPEI.
Neural operators can learn nonlinear mappings between function spaces and offer a new simulation paradigm for real-time prediction of complex dynamics for realistic diverse applications as well as for system identification in science and engineering. Herein, we investigate the performance of two neural operators, which have shown promising results so far, and we develop new practical extensions that will make them more accurate and robust and importantly more suitable for industrial-complexity applications. The first neural operator, DeepONet, was published in 2019 (Lu et al., 2019), and its original architecture was based on the universal approximation theorem of Chen & Chen (1995). The second one, named Fourier Neural Operator or FNO, was published in 2020, and it is based on parameterizing the integral kernel in the Fourier space. DeepONet is represented by a summation of products of neural networks (NNs), corresponding to the branch NN for the input function and the trunk NN for the output function; both NNs are general architectures, e.g., the branch NN can be replaced with a CNN or a ResNet. According to Kovachki et al. (2021), FNO in its continuous form can be viewed conceptually as a DeepONet with a specific architecture of the branch NN and a trunk NN represented by a trigonometric basis. In order to compare FNO with DeepONet computationally for realistic setups, we develop several extensions of FNO that can deal with complex geometric domains as well as mappings where the input and output function spaces are of different dimensions. We also develop an extended DeepONet with special features that provide inductive bias and accelerate training, and we present a faster implementation of DeepONet with cost comparable to the computational cost of FNO, which is based on the Fast Fourier Transform. Here we consider 16 different benchmarks to demonstrate the relative performance of the two neural operators, including instability wave analysis in hypersonic boundary layers, prediction of the vorticity field of a flapping airfoil, porous media simulations in complex-geometry domains, etc. We follow the guiding principles of FAIR (Findability, Accessibility, Interoperability, and Reusability) for scientific data management and stewardship. The performance of DeepONet and FNO is comparable for relatively simple settings, but for complex geometries the performance of FNO deteriorates greatly. We also compare theoretically the two neural operators and obtain similar error estimates for DeepONet and FNO under the same regularity assumptions.
Consolidative thoracic radiation therapy (TRT) has been shown to improve outcomes for patients with extensive stage small cell lung cancer. We hypothesized that the addition of ipilimumab (IPI) and nivolumab (NIVO) after TRT would improve outcomes for patients with extensive stage small cell lung cancer.
The dynamic thermo-mechanical behavior of pure aluminum has attracted renewed interest lately due to experimental observations of an anomalous increase in Hugoniot Elastic Limit (HEL) at incipient plasticity and elevated temperatures in polycrystalline pure metals. In context of current dislocation-mediated plasticity models for metals, this increase in dynamic strength is indicative of a transition in the rate controlling mechanism for dislocation glide from being thermally assisted to phonon-drag restricted due to increase in phonon viscosity at elevated temperatures. Though these studies have helped to shed light on these important mechanisms operative in FCC metals at incipient plasticity, the extent to which they contribute to flow stress, particularly at larger strains, remains unclear. Here, we address these questions through a combined experimental and modeling effort focused on investigating the evolution of dynamic flow stress in polycrystalline aluminum using experimental data gathered from a series of combined pressure-and-shear plate impact (PSPI) experiments designed to reveal the flow stress of pure aluminum at strain rates ~ 10 5 /s, plastic strains of up to 40% and temperatures ranging from room to 866 K. In all cases, the flow stress of aluminum, as inferred from the measured transverse particle velocity histories at the free surface of an elastic tungsten carbide target plate, reveals saturation with increasing plastic strains at stress levels that decrease with increasing test temperatures. Numerical simulations are performed to correlate the experimentally observed temperature and strain rate dependence of flow stress at small and large plastic strains using the Austin-McDowell dislocation-mediated plasticity model parametrized to normal plate impact experiments conducted in an earlier study by Zaretsky and Kanel (2012). Extensions to the model are made to better represent dynamic behavior of pure aluminum at larger plastic strains as observed in elevated temperature split Hopkinson Pressure bar (SPHB) experiments of Samanta (1971) and Lindholm and Yeakly (1965), and the combined pressure-and-shear plate-impact experiments conducted in the present study. The main theoretical extension to the Austin-McDowell model made in this paper is the introduction of a new rate- and temperature- dependent dynamic recovery function, which can potentially allow for an effective reduction in the rate of accumulation of dislocations at large plastic strains. The numerical predictions of the revised and re-calibrated plasticity model are brought into agreement with the experimental observations, correlating sufficiently well with dynamic yield stress at incipient plasticity and the flow stress levels at larger plastic strains, plastic strain rates in the range 10 3 – 10 6 /s, and elevated temperatures up to near melt. The model, in concert with the experimental measurements, suggests that at incipient plasticity the rate governing mechanism for plastic flow is phonon-drag restricted dislocation glide, whereas, at higher magnitudes of plastic strain, it transitions to stress-assisted thermally activated glide. The transition between these two rate governing mechanisms is controlled by the evolution of dislocations throughout the deformation process.
A new extension for MCNP has been developed that incorporates the NCrystal thermal scattering package in the form of a Fortran to C++ wrapper, which adds the capability to describe thermal neutron scattering in the NCrystal formalism instead of the ACE tabular format. This can be used to described poly- or single-crystalline materials as well as liquids. In conclusion, the functionality of this extension to MCNP is illustrated using a layered crystal monochromator, leakage of neutrons from a moderating sphere of material, and by simulating criticality benchmarks.
Herein we describe the moist dynamics formulation implemented within the graphics processing unit-resident large-eddy simulation FastEddy® model, which includes a simple saturation adjustment scheme for condensation and evaporation processes. Two LES model intercomparison exercises for non-precipitating shallow cumulus clouds are simulated in order to validate this model extension, including a static forcing and a time-dependent forcing case. Overall, we find our dynamical, thermodynamical and microphysical quantities, along with turbulence variability and fluxes, to be commensurate with the corresponding model intercomparison results. In addition, sensitivities to specific model settings are investigated. Among these settings, it is shown that boundary layer and cloud layer structure and characteristics are sensitive to use of higher-order advection schemes impacting the vertical distribution of cloud content and associated turbulence statistics. Increasing the timescale of the saturation scheme leads to enhanced liquid water presence and decreases vertical velocity variance within the cloud deck. In some cases, these sensitivities agree with the model-to-model variability reported in the intercomparison exercises, highlighting the important role of specific model implementation choices in the context of shallow cumulus convection simulations. These analyses and findings also provide the basis for future extensions and applications of FastEddy® for modeling moist convection and precipitation scenarios.
Abstract A key open question in the study of layered superconducting nickelate films is the role that hydrogen incorporation into the lattice plays in the appearance of the superconducting state. Due to the challenges of stabilizing highly crystalline square planar nickelate films, films are prepared by the deposition of a more stable parent compound which is then transformed into the target phaseviaa topotactic reaction with a strongly reducing agent such as CaH 2 . Recent studies, both experimental and theoretical, have introduced the possibility that the incorporation of hydrogen from the reducing agent into the nickelate lattice may be critical for the superconductivity. In this work, we use secondary ion mass spectrometry to examine superconducting La 1−x X x NiO 2 / SrTiO 3 (X= Ca and Sr) and Nd 6 Ni 5 O 12 / NdGaO 3 films, along with non-superconducting NdNiO 2 / SrTiO 3 and (Nd,Sr)NiO 2 / SrTiO 3 . We find no evidence for extensive hydrogen incorporation across a broad range of samples, including both superconducting and non-superconducting films. Theoretical calculations indicate that hydrogen incorporation is broadly energetically unfavorable in these systems, supporting our conclusion that extensive hydrogen incorporation is not generally required to achieve a superconducting state in layered square-planar nickelates.
The relative importance of introgression for diversification has long been a highly disputed topic in speciation research and remains an open question despite the great attention it has received over the past decade. Gene flow leaves traces in the genome similar to those created by incomplete lineage sorting (ILS), and identification and quantification of gene flow in the presence of ILS is challenging and requires knowledge about the true phylogenetic relationship among the species. We use whole nuclear, plastid, and organellar genomes from 12 species in the rapidly radiated, ecologically diverse, actively hybridizing genus of peatmoss (Sphagnum) to reconstruct the species phylogeny and quantify introgression using a suite of phylogenomic methods. We found extensive phylogenetic discordance among nuclear and organellar phylogenies, as well as across the nuclear genome and the nodes in the species tree, best explained by extensive ILS following the rapid radiation of the genus rather than by postspeciation introgression. Our analyses support the idea of ancient introgression among the ancestral lineages followed by ILS, whereas recent gene flow among the species is highly restricted despite widespread interspecific hybridization known in the group. Our results contribute to phylogenomic understanding of how speciation proceeds in rapidly radiated, actively hybridizing species groups, and demonstrate that employing a combination of diverse phylogenomic methods can facilitate untangling complex phylogenetic patterns created by ILS and introgression.
Satellite galaxies of the Milky Way with high mass-to-light ratios and little baryon content, i.e., dwarf spheroidal galaxies (dSphs), are among the most promising targets to detect or constrain the nature of dark matter (DM) through its final annihilation products into high-energy photons. Previously, the assumption that DM emission from dSphs is pointlike has been used to set strong constraints on DM candidates using data from the Fermi Large Area Telescope (LAT). However, due to their high DM densities and proximity, dSphs actually have sufficient angular extension to be detected by the Fermi-LAT. Here, we perform a comprehensive analysis about the impact of accounting for angular extension in the search for gamma-ray DM signals toward known dSphs with Fermi-LAT. Further, we show that, depending on the dSph under consideration, limits on the DM cross section can be weakened by up to a factor of 2–2.5, while the impact on the stacked, i.e., combined, limits is at most 1.5–1.8 depending on the annihilation channel. This result is of relevance when comparing dSph limits to other multimessenger DM constraints and for testing the DM interpretation of anomalous “excesses.”
We constrain six possible extensions to the Λ cold dark matter (CDM) model using measurements from the Dark Energy Survey’s first three years of observations, alone and in combination with external cosmological probes. The DES data are the two-point correlation functions of weak gravitational lensing, galaxy clustering, and their cross-correlation. We use simulated data vectors and blind analyses of real data to validate the robustness of our results to astrophysical and modeling systematic errors. In many cases, constraining power is limited by the absence of theoretical predictions beyond the linear regime that are reliable at our required precision. The Λ CDM extensions are dark energy with a time-dependent equation of state, nonzero spatial curvature, additional relativistic degrees of freedom, sterile neutrinos with eV-scale mass, modifications of gravitational physics, and a binned σ 8 ( z ) model which serves as a phenomenological probe of structure growth. For the time-varying dark energy equation of state evaluated at the pivot redshift we find ( w p , w a ) = ( - 0.9 9 - 0.17 + 0.28 , - 0.9 ± 1.2 ) at 68% confidence with z p = 0.24 from the DES measurements alone, and ( w p , w a ) = ( - 1.0 3 - 0.03 + 0.04 , - 0. 4 - 0.3 + 0.4 ) with z p = 0.21 for the combination of all data considered. Curvature constraints of Ω k = 0.0009 ± 0.0017 and effective relativistic species N eff = 3.1 0 - 0.16 + 0.15 are dominated by external data, though adding DES information to external low-redshift probes tightens the Ω k constraints that can be made without cosmic microwave background observables by 20%. For massive sterile neutrinos, DES combined with external data improves the upper bound on the mass m eff by a factor of 3 compared to previous analyses, giving 95% limits of ( Δ N eff , m eff ) ≤ ( 0.28 , 0.20 eV ) when using priors matching a comparable Planck analysis. For modified gravity, we constrain changes to the lensing and Poisson equations controlled by functions Σ ( k , z ) = Σ 0 Ω Λ ( z ) / Ω Λ , 0 and μ ( k , z ) = μ 0 Ω Λ ( z ) / Ω Λ , 0 , respectively, to Σ 0 = 0. 6 - 0.5 + 0.4 from DES alone and ( Σ 0 , μ 0 ) = ( 0.04 ± 0.05 , 0.0 8 - 0.19 + 0.21 ) for the combination of all data, both at 68% confidence. Overall, we find no significant evidence for physics beyond Λ CDM .