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At least 109 records · Page 6

Enhancing Distribution System Resilience: A First-Order Meta-RL Algorithm for Critical Load Restoration

The increasing frequency of extreme events and the integration of distributed energy resources (DERs) into modern grids have elevated the need for resilient and efficient critical load restoration strategies in distribution systems. However, the stochastic nature of renewable DERs, limited energy resource availability and the intricate nonlinearities inherent in complex grid control problem make the problem challenging. Although reinforcement learning (RL) and warm-start RL methods have shown promising results, their performance often falls short in rapidly adapting to new, unseen situations and typically requires exhaustive problem-specific tuning. To address these gaps, we propose a First-Order Meta-based RL (FOM-RL) algorithm within an online framework for adaptive and robust critical load restoration. By harnessing local DERs as the enabling technology, FOM-RL allows the RL agent to swiftly adapt to new unseen scenarios by leveraging previously acquired knowledge of different tasks. Experimental results provide evidence that proposed algorithm learns more efficiently and showcases generalization capabilities across diverse set of operational scenarios. Moreover, a rigorous theoretical analysis yields a tight sublinear regret bound, sensitive to temporal variability, with a task-averaged optimality gap bounded by O(VM+D*/(Tsquare root(M))). These results suggest that optimality improves with task similarity and an increased number of tasks M, reaffirming the efficacy and scalability of the proposed approach in addressing the complexities of critical load restoration in distribution systems.

complexity theory↗

Approaches to the Inverse Problem

In this talk, I describe some recent ideas relating to the spectral reconstruction inverse problem, which arises frequently in lattice QCD calculations of inclusive hadronic quantities, and provide some physical context for this work. Particular emphasis is given to a new method for rigorously bounding uncertainties using techniques from complex analysis.

Jay, William [Massachusetts Institute of Technolog↗

An Integrated Framework for Memory-Centric Analysis: From Trace Collection to Co-Design

The memory wall phenomenon—where advances in processor performance significantly outpace those in memory subsystems—poses a fundamental challenge for contemporary computing systems. In memory-bound applications, memory subsystem behavior dominates performance, yet existing analysis approaches present significant limitations: detailed microarchitectural simulators require days to weeks to simulate modest workloads; hardware performance counters provide only aggregate statistics that obscure temporal and spatial access patterns; and scaled simulation approaches face challenges in capturing certain behaviors that emerge at larger scales. These limitations reflect a processor-centric design philosophy increasingly misaligned with memory-bound workloads where detailed understanding of memory access patterns, cache hierarchy interactions, and contention is critical for effective optimization. This paper presents an integrated framework for memory-centric analysis that enables effective hardware-software co-design. We describe practical trace collection techniques, including hardware-assisted processor tracing with minimal overhead and portable software-based instrumentation with statistical sampling. We present multi-perspective analysis methods that examine memory behavior from temporal, sequential, spatial, and relational viewpoints, revealing distinct optimization opportunities invisible in aggregate metrics. We detail an architectural modeling framework that uses sampled traces with temporal interpolation and confidence-based filtering to evaluate cache and memory configurations. Evaluation on representative benchmarks demonstrates that this framework achieves practical accuracy (L2 cache errors of 2.64\%, confidence-filtered L3 errors of 9.92\%, bandwidth errors of 7.33\%) while providing substantial speedup (26.8×) over cycle-accurate simulation, enabling rapid design space exploration. We demonstrate how this integrated framework enables systematic identification of both hardware optimizations (memory controller tuning, bank partitioning, NUMA configuration) and software optimizations (data layout restructuring, prefetching strategies, memory-aware scheduling). Through this comprehensive treatment of the memory-centric analysis pipeline—from trace collection through architectural modeling to co-design application—we provide researchers and practitioners with practical techniques for addressing memory bottlenecks in contemporary computing systems.

Gajaria, Dhruv Mayur↗

A Framework for Error-Bounded Approximate Computing, with an Application to Dot Products

Approximate computing techniques, which trade off the computation accuracy of an algorithm for better performance and energy efficiency, have been successful in reducing computation and power costs in several domains. However, error sensitive applications in high-performance computing are unable to benefit from existing approximate computing strategies that are not developed with guaranteed error bounds. While approximate computing techniques can be developed for individual high-performance computing applications by domain specialists, this often requires additional theoretical analysis and potentially extensive software modification. Hence, the development of low-level error-bounded approximate computing strategies that can be introduced into any high-performance computing application without requiring additional analysis or significant software alterations is desirable. In this paper, we provide a contribution in this direction by proposing a general framework for designing error-bounded approximate computing strategies and apply it to the dot product kernel to develop \bf qdot---an error-bounded approximate dot product kernel. Following the introduction of qdot, here we perform a theoretical analysis that yields a deterministic bound on the relative approximation error introduced by qdot. Empirical tests are performed to illustrate the tightness of the derived error bound and to demonstrate the effectiveness of qdot on a synthetic dataset, as well as two scientific benchmarks---the conjugate gradient (CG) and power methods. In some instances, using qdot for the dot products in CG can result in many components being quantized to half precision without increasing the iteration count required for convergence to the same solution as CG using a double precision dot product.

97 MATHEMATICS AND COMPUTING↗

New dark matter analysis of milky way dwarf satellite galaxies with madhatv2

We obtain bounds on dark matter annihilation using 14 years of publicly available Fermi-LAT data from a set of 54 dwarf spheroidal galaxies, using spectral information from 16 energy bins. We perform this analysis using our updated and publicly available code , which can be used to test a variety of models for dark matter particle physics and astrophysics in an accessible manner. In particular, we note that including Carina III in the analysis strengthens constraints on s -wave annihilation into two-body Standard Model final states by a factor of ∼ 3 but broadens the error on the constraint due to the large uncertainty of its J -factor. Our findings illustrate the importance of verifying if Carina III is in fact a dwarf spheroidal galaxy and measuring more precisely its J -factor. More generally, they highlight the significance of forthcoming discoveries of nearby ultrafaint dwarfs for dark matter indirect detection. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Crystal structure of Methanococcus jannaschii dihydroorotase with substrate bound

Here, we report the X-ray structural analysis of dihydroorotase from Methanococcus jannaschii co-crystallized with dihydroorotate at pH 6.5. The crystals are isomorphous with the crystals of the apoenzyme, with space group P3 2 21 and unit-cell dimensions a = b = 111.4, c = 101.2 Å. The structure was refined to R = 0.169 and R free = 0.186 at a resolution of 1.87 Å at room temperature. During crystallization the degradative reaction took place, and the electron density in the active site corresponds to the substrate carbamoyl aspartate. Carbamoyl aspartate interacts with the protein in the active site in a manner similar to that observed for Escherichia coli and human dihydroorotases. However, the flexible loop (residues 140–151) adopts both conformations in the crystal, loop-out and loop-in, with the loop-out conformation having higher occupancy. This contrasts with our expectations for the flexible loop to be exclusively in the loop-in conformation, which is the conformation that it adopts to stabilize the binding of the substrate in the known systems. Additional studies with substrate analogs that resemble carbamoyl aspartate and different crystallization conditions would provide further insight into the conformation of the flexible loop in this system.

Methanococcus jannaschii↗

Leveraging Extremal Dependence to Better Characterize the 2021 Pacific Northwest Heatwave

Abstract In late June, 2021, a devastating heatwave affected the US Pacific Northwest and western Canada, breaking numerous all-time temperature records by large margins and directly causing hundreds of fatalities. The observed 2021 daily maximum temperature across much of the U.S. Pacific Northwest exceeded upper bound estimates obtained from single-station temperature records even after accounting for anthropogenic climate change, meaning that the event could not have been predicted under standard univariate extreme value analysis assumptions. In this work, we utilize a flexible spatial extremes model that considers all stations across the Pacific Northwest domain and accounts for the fact that many stations simultaneously experience extreme temperatures. Our analysis incorporates the effects of anthropogenic forcing and natural climate variability in order to better characterize time-varying changes in the distribution of daily temperature extremes. We show that greenhouse gas forcing, drought conditions and large-scale atmospheric modes of variability all have significant impact on summertime maximum temperatures in this region. Our model represents a significant improvement over corresponding single-station analysis, and our posterior medians of the upper bounds are able to anticipate more than 96% of the observed 2021 high station temperatures after properly accounting for extremal dependence. Supplementary materials accompanying this paper appear online.

Zhang, Likun (ORCID:0000000154584556)↗

Vanilloid-dependent TRPV1 opening trajectory from cryo EM ensemble analysis

Single particle cryo-EM often yields multiple protein conformations within a single dataset, but experimentally deducing the temporal relationship of these conformers within a conformational trajectory is not trivial. Here, we use thermal titration methods and cryo-EM in an attempt to obtain temporal resolution of the conformational trajectory of the vanilloid receptor TRPV1 with resiniferatoxin (RTx) bound. Based on our cryo-EM ensemble analysis, RTx binding to TRPV1 appears to induce intracellular gate opening first, followed by selectivity filter dilation, then pore loop rearrangement to reach the final open state. This apparent conformational wave likely arises from the concerted, stepwise, additive structural changes of TRPV1 over many subdomains. Greater understanding of the RTx-mediated long-range allostery of TRPV1 could help further the therapeutic potential of RTx, which is a promising drug candidate for pain relief associated with advanced cancer or knee arthritis.

59 BASIC BIOLOGICAL SCIENCES↗

Weighted relaxation for multigrid reduction in time

Current trends in computer architectures now mean that faster computation speed must come primarily from increased concurrency, not faster clock speeds, which are stagnating. Thus, this situation creates bottlenecks for serial algorithms, including the well-known bottleneck for sequential time-integration, where each individual time-value (i.e., time-step) is computed sequentially. One approach to alleviate this and achieve parallelism in time is with multigrid. Here, in this work, we consider multigrid-reduction-in-time (MGRIT), a multilevel method applied to the time dimension that computes multiple time-steps in parallel. Like all multigrid methods, MGRIT relies on the complementary relationship between relaxation on a fine-grid and a correction from the coarse grid to solve the problem. All current MGRIT implementations are based on unweighted-Jacobi relaxation; here we introduce the concept of weighted relaxation to MGRIT. We derive new convergence bounds for weighted relaxation, and use this analysis to guide the selection of relaxation weights. Numerical results then demonstrate that by choosing appropriate non-unitary relaxation weights, one can achieve faster convergence rates and lower iteration counts for MGRIT when compared with unweighted relaxation. In most cases, weighted relaxation yields a 10%–20% saving in iterations, which is significant when using large high-performance computers. For A-stable integration schemes, results also illustrate that under-relaxation can restore convergence in some cases where unweighted relaxation is not convergent.

97 MATHEMATICS AND COMPUTING↗

Toward reducing uncertainty quantification costs in DEM models of particulate flow: Testing simple, sensitivity-based, forward uncertainty propagation techniques

The performance of two conceptually-simple uncertainty quantification techniques are tested against the rigorous nested-loop sampling technique of Roy and Oberkampf (Comput Methods Appl Mech Eng, 200: 2131–2144, 2011) (herein called full-sampling) using two very small-scale DEM-based models of particulate flow (one gas-solid flow and one granular flow). The first simplified forward uncertainty propagation technique, reduced-sampling, uses a sensitivity analysis to eliminate uncertain inputs that have little impact on the model output prior to nested-loop sampling. The second technique, boundary-sampling, uses a sensitivity analysis to inform the selection of two bounding cases for each key model output. In conclusion, the uncertainties in the model outputs obtained via the reduced- and boundary-sampling methods agree well with those from full-sampling for both the gas-solid and granular flow models while yielding computational savings of 65–75% (reduced sampling) and 94–97% (boundary sampling).

42 ENGINEERING↗

Fractionation of Oxygen Isotopes in Uranium Oxides during Peroxide Precipitation and Dry Air Calcination

The interaction between uranium and oxygen-containing substrates is nearly ubiquitous within the nuclear fuel cycle. Given the well-known and predictable oxygen stable isotope compositions of atmospheric oxygen and meteoric waters around the world, the use of these isotopes as a potential geolocation or processing signature of uranium compounds has been of interest within the nuclear safeguards community. This study focuses on measuring the oxygen-stable isotope composition of synthetically produced uranium oxides to determine the mechanism and extent of fractionation during materials processing relevant to the nuclear fuel cycle. Here, metastudtite [UO 2 O 2 (H 2 O) 2 ] samples were first produced using water and hydrogen peroxide of a known oxygen isotope composition. This starting material was calcined in dry air at temperatures ranging from 300 °C to 1000 °C for 20 h producing oxides ranging in composition from UO 3 +x (0 ≤ x ≤ 0.5) to U 3 O 8 . In addition, calcinations between 500 and 800 °C were performed at different time intervals to evaluate the rate of isotopic equilibration. The δ 18 O values of water bound to metastudtite were measured by thermogravimetric analysis coupled to isotope ratio infrared spectroscopy (TGA–IRIS). A redesigned fluorination manifold was constructed at the University of Utah and was used to extract the bulk oxygen from precipitated and calcined products using bromine pentafluoride (BrF 5 ). Mineralization water on metastudtite (measured by TGA–IRIS) was closely associated with the aqueous environment of precipitation with a fractionation of +3.5 ± 0.6‰. In contrast, bulk oxygen from metastudtite (measured by fluorination and gas chromatography combined with isotope ratio mass spectrometry) was found to have an inconsistent fractionation with precipitation water. Samples calcined in dry air exhibited a wide range of oxygen isotope compositions which increased from δ 18 O = +1.4 ± 0.9‰ at 300 °C to +17.3 ± 0.9‰ at 1000 °C. This variation in δ 18 O values was a result of oxygen exchange with atmospheric O 2 and was found to be rapid at calcination temperatures greater than 600°C—with equilibration occurring in less than 2 h. These results provide insights into the incorporation and exchange of oxygen isotopes during precipitation and calcination processes comparable to those employed within the nuclear fuel cycle and establish a foundation for future investigations to build upon.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens

Two plasmid-encoded dihydrofolate reductase (DHFR) isoforms, DfrA1 and DfrA5, that give rise to high levels of resistance in Gram-negative bacteria were structurally and biochemically characterized to reveal the mechanism of TMP resistance and to support phylogenic groupings for drug development against antibiotic resistant pathogens. Preliminary screening of novel antifolates revealed related chemotypes that showed high levels of inhibitory potency against Escherichia coli chromosomal DHFR (EcDHFR), DfrA1, and DfrA5. Kinetics and biophysical analysis, coupled with crystal structures of trimethoprim bound to EcDHFR, DfrA1 and DfrA5, and two propargyl-linked antifolates (PLA) complexed with EcDHFR, DfrA1 and DfrA5, were determined to define structural features of the substrate binding pocket and guide synthesis of pan-DHFR inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

Erratum: Planck 2018 results: VI. Cosmological parameters

In the original version, the bounds given in Eqs. (87a) and (87b) on the contribution to the early-time optical depth, (15,30), contained a numerical error in deriving the 95th percentile from the Monte Carlo samples. The corrected 95% upper bounds are: τ(15,30) < 0:018 (lowE, flat τ(15, 30), FlexKnot), (1) τ(15, 30) < 0:023 (lowE, flat knot, FlexKnot): (2) These bounds are a factor of 3 larger than the originally reported results. Consequently, the new bounds do not significantly improve upon previous results from Planck data presented in Millea & Bouchet (2018) as was stated, but are instead comparable. Equations (1) and (2) give results that are now similar to those of Heinrich & Hu (2021), who used the same Planck 2018 data to derive a 95% upper bound of 0.020 using the principal component analysis (PCA) model and uniform priors on the PCA mode amplitudes.

79 ASTRONOMY AND ASTROPHYSICS↗

Toward exascale whole-device modeling of fusion devices: Porting the GENE gyrokinetic microturbulence code to GPU

GENE solves the five-dimensional gyrokinetic equations to simulate the development and evolution of plasma microturbulence in magnetic fusion devices. The plasma model used is close to first principles and computationally very expensive to solve in the relevant physical regimes. In order to use the emerging computational capabilities to gain new physics insights, several new numerical and computational developments are required. Here, we focus on the fact that it is crucial to efficiently utilize GPUs (graphics processing units) that provide the vast majority of the computational power on such systems. In this paper, we describe the various porting approaches considered and given the constraints of the GENE code and its development model, justify the decisions made, and describe the path taken in porting GENE to GPUs. We introduce a novel library called gtensor that was developed along the way to support the process. Performance results are presented for the ported code, which in a single node of the Summit supercomputer achieves a speed-up of almost 15× compared to running on central processing unit (CPU) only. Typical GPU kernels are memory-bound, achieving about 90% of peak. Our analysis shows that there is still room for improvement if we can refactor/fuse kernels to achieve higher arithmetic intensity. We also performed a weak parallel scalability study, which shows that the code runs well on a massively parallel system, but communication costs start becoming a significant bottleneck.

Germaschewski, K. (ORCID:0000000284956354)↗

Accelerating and stabilizing the convergence of vibrational self-consistent field calculations via the direct inversion of the iterative subspace (vDIIS) algorithm

The vibrational self-consistent field (VSCF) method yields anharmonic states and spectra for molecular vibrations, and it serves as the starting point for more sophisticated correlated-vibration methods. Convergence of the iterative, non-linear optimization in VSCF calculations can be erratic or altogether unsuccessful, particularly for chemical systems involving low-frequency motions. In this work, a vibrational formulation of the Direct Inversion of the Iterative Subspace method of Pulay is presented and investigated. This formulation accounts for distinct attributes of the vibrational and electronic cases, including the expansion of each single-mode vibrational wavefunction in its own basis set. The resulting Direct Inversion of the Iterative Subspace method is shown to substantially accelerate VSCF convergence in all convergent cases as well as rectify many cases where Roothaan-based methods fail. Performance across systems ranging from small, rigid molecules to weakly bound molecular clusters is investigated in this analysis.

Chemistry↗

7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system

Abstract The modified nucleosides 2′-deoxy-7-cyano- and 2′-deoxy-7-amido-7-deazaguanosine (dPreQ0 and dADG, respectively) recently discovered in DNA are the products of the bacterial queuosine tRNA modification pathway and the dpd gene cluster, the latter of which encodes proteins that comprise the elaborate Dpd restriction–modification system present in diverse bacteria. Recent genetic studies implicated the dpdA, dpdB and dpdC genes as encoding proteins necessary for DNA modification, with dpdD–dpdK contributing to the restriction phenotype. Here we report the in vitro reconstitution of the Dpd modification machinery from Salmonella enterica serovar Montevideo, the elucidation of the roles of each protein and the X-ray crystal structure of DpdA supported by small-angle X-ray scattering analysis of DpdA and DpdB, the former bound to DNA. While the homology of DpdA with the tRNA-dependent tRNA-guanine transglycosylase enzymes (TGT) in the queuosine pathway suggested a similar transglycosylase activity responsible for the exchange of a guanine base in the DNA for 7-cyano-7-deazaguanine (preQ0), we demonstrate an unexpected ATPase activity in DpdB necessary for insertion of preQ0 into DNA, and identify several catalytically essential active site residues in DpdA involved in the transglycosylation reaction. Further, we identify a modification site for DpdA activity and demonstrate that DpdC functions independently of DpdA/B in converting preQ0-modified DNA to ADG-modified DNA.

59 BASIC BIOLOGICAL SCIENCES↗

Constraints on the polarization angle oscillations of the Crab Nebula with the Simons Array and its applications to the search for axionlike particles

Here, we present a search for polarization oscillation of the Crab Nebula, also known as Tau A, at millimeter wavelengths using observations with the Simons Array, the successor experiment to POLARBEAR. We follow up on previous work by POLARBEAR using 90 GHz band data of the 2023 observing season of the Simons Array to evaluate the variability of Tau A’s polarization angle. Tau A is widely used as a polarization angle calibration source in millimeter-wave astronomy, and thus it is necessary to validate the stability. Additionally, an interesting application of the time-resolved polarimetry of Tau A is to search for axionlike particles (ALPs). We do not detect a global signal across the frequencies considered in this analysis and place a median 95% upper bound of polarization oscillation amplitude A < 0.12° over oscillation frequencies from 3.39 yr -1 to 1.50 day -1 . This constrains the ALP-photon coupling at a median 95% upper bound of g aγγ < 3.84 × 10 -12 × (m a /10 -21 eV) in the mass range from 4.4 × 10 -22 to 7.2 × 10 -20 eV, assuming the ALP constitutes all of dark matter, its field is a stochastic Gaussian field, and it is the sole source of Tau A’s polarization angle oscillation. Additionally, we do not detect signal at the frequencies where 2.5σ hints were previously reported by POLARBEAR, but we do not exclude these signals at the 95% confidence level.

Adkins, Tylor [University of California, Berkeley]↗

Dielectronic satellite emission from a solid-density Mg plasma: Relationship to models of ionization potential depression

Here, we report on experiments where solid-density Mg plasmas are created by heating with the focused output of the Linac Coherent Light Source x-ray free-electron laser. We study the K-shell emission from the helium- and lithium-like ions using Bragg crystal spectroscopy. Observation of the dielectronic satellites in lithium-like ions confirms that the M-shell electrons appear bound for these high charge states. An analysis of the intensity of these satellites indicates that when modeled with an atomic-kinetics code, the ionization potential depression model employed needs to produce depressions for these ions which lie between those predicted by the well known Stewart-Pyatt and Ecker-Kroll models. These results are largely consistent with recent density functional theory calculations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗