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At least 397 records · Page 22

Fast GPU-Based Generation of Large Graph Networks From Degree Distributions

Synthetically generated, large graph networks serve as useful proxies to real-world networks for many graph-based applications. The ability to generate such networks helps overcome several limitations of real-world networks regarding their number, availability, and access. Here, we present the design, implementation, and performance study of a novel network generator that can produce very large graph networks conforming to any desired degree distribution. The generator is designed and implemented for efficient execution on modern graphics processing units (GPUs). Given an array of desired vertex degrees and number of vertices for each desired degree, our algorithm generates the edges of a random graph that satisfies the input degree distribution. Multiple runtime variants are implemented and tested: 1) a uniform static work assignment using a fixed thread launch scheme, 2) a load-balanced static work assignment also with fixed thread launch but with cost-aware task-to-thread mapping, and 3) a dynamic scheme with multiple GPU kernels asynchronously launched from the CPU. The generation is tested on a range of popular networks such as Twitter and Facebook, representing different scales and skews in degree distributions. Results show that, using our algorithm on a single modern GPU (NVIDIA Volta V100), it is possible to generate large-scale graph networks at rates exceeding 50 billion edges per second for a 69 billion-edge network. GPU profiling confirms high utilization and low branching divergence of our implementation from small to large network sizes. For networks with scattered distributions, we provide a coarsening method that further increases the GPU-based generation speed by up to a factor of 4 on tested input networks with over 45 billion edges.

97 MATHEMATICS AND COMPUTING↗

Chiral assemblies of pinwheel superlattices on substrates

The unique topology and physics of chiral superlattices make their self-assembly from nanoparticles highly sought after yet challenging in regard to (meta)materials. In this report we show that tetrahedral gold nanoparticles can transform from a perovskite-like, low-density phase with corner-to-corner connections into pinwheel assemblies with corner-to-edge connections and denser packing. Whereas corner-sharing assemblies are achiral, pinwheel superlattices become strongly mirror asymmetric on solid substrates as demonstrated by chirality measures. Liquid-phase transmission electron microscopy and computational models show that van der Waals and electrostatic interactions between nanoparticles control thermodynamic equilibrium. Variable corner-to-edge connections among tetrahedra enable fine-tuning of chirality. The domains of the bilayer superlattices show strong chiroptical activity as identified by photon-induced near-field electron microscopy and finite-difference time-domain simulations. The simplicity and versatility of substrate-supported chiral superlattices facilitate the manufacture of metastructured coatings with unusual optical, mechanical and electronic characteristics.

42 ENGINEERING↗

Preparations for quantum simulations of quantum chromodynamics in 1+1 dimensions. I. Axial gauge

Here, tools necessary for quantum simulations of 1+1 dimensional quantum chromodynamics are developed. When formulated in axial gauge and with two flavors of quarks, this system requires 12 qubits per spatial site with the gauge fields included via nonlocal interactions. Classical computations and D-wave’s quantum annealer advantage are used to determine the hadronic spectrum, enabling a decomposition of the masses and a study of quark entanglement. Color “edge” states confined within a screening length of the end of the lattice are found. IBM’s seven-qubit quantum computers, ibmq_jakarta and ibm_perth, are used to compute dynamics from the trivial vacuum in one-flavor QCD with one spatial site. More generally, the Hamiltonian and quantum circuits for time evolution of 1+1 dimensional SU(N c ) gauge theory with Nf flavors of quarks are developed, and the resource requirements for large-scale quantum simulations are estimated.

1+1 dimensions↗

Facile ab initio approach for self-localized polarons from canonical transformations

Electronic states in a crystal can localize due to strong electron-phonon (e-ph) interactions, forming so-called small polarons. Methods to predict the formation and energetics of small polarons are either computationally costly or not geared toward quantitative predictions. Here we show a formalism based on canonical transformations to compute the polaron formation energy and wave function using ab initio e-ph interactions. Comparison of the calculated polaron and band-edge energies allows us to determine whether charge carriers in a material favor a localized small polaron over a delocalized Bloch state. Due to its low computational cost, our approach enables efficient studies of the formation and energetics of small polarons, as we demonstrate by investigating electron and hole polaron formation in alkali halides and metal oxides and peroxides. We outline refinements of our scheme and extensions to compute transport in the polaron hopping regime.

36 MATERIALS SCIENCE↗

Validating the simulation of beam-ion charge exchange in MAST Upgrade

Abstract Simulation of the impact of charge-exchange (CX) reactions on beam ions in the Mega Amp Spherical Tokamak (MAST) Upgrade was compared to measurements carried out with a fission chamber (neutron fluxes) and a fast ion deuterium-alpha (FIDA) diagnostic. A simple model was developed to reconstruct the outer-midplane neutral density based on measurements of deuterium-alpha emission from edge neutrals, and on Thomson scattering measurements of electron density and temperature. The main computational tools used were the ASCOT orbit-following code and the FIDASIM code for producing synthetic FIDA signals. The neutral density reconstruction agrees qualitatively with SOLPS-ITER modelling and yields a synthetic passive FIDA signal that is consistent with measurement. When CX losses of beam ions are accounted for, predicted neutron emission rates are quantitatively more consistent with measurement. It was necessary to account for CX losses of beam ions in simulations to reproduce the measured passive FIDA signal quantitatively and qualitatively. The results suggest that the neutral density reconstruction is a good approximation, that CX with edge neutrals causes significant beam-ion losses in MAST Upgrade, typically 20% of beam power, and that the ASCOT fast-ion CX model can be used to accurately predict the redistribution and loss of beam ions due to CX.

Physics↗

Aerodynamic Characterization of 3D Scanned Wind Turbine Blades Using Experimental and Computational Methods

This study presents an aerodynamic characterization of 3D scanned wind turbine blades using both experimental and computational methods. The research was conducted by Gulf Wind Technology and Sandia National Laboratories. The primary objective was to investigate the aerodynamic impacts of leading-edge manufacturing defects on wind turbine blades. The study utilized the Stratasys NEO 800 3D Printer for high-precision manufacturing and the GWT Accelerator Wind Tunnel for experimental testing. Computational simulations were performed using COMSOL Multiphysics to model the wind tunnel and analyze flow characteristics and OpenFOAM to study the aerodynamic impacts of leading-edge defects. OpenFAST was used to estimate how these defects can lead to revenue losses for wind farm operators as high as 6%. The results demonstrated significant aerodynamic performance variations due to defects, with detailed analysis provided through wind tunnel and CFD data. The findings contribute to the understanding of defect impacts on wind turbine blade performance and offer insights for future design improvements.

17 WIND ENERGY↗

Extracting Higher Central Charge from a Single Wave Function

A (2+1)D topologically ordered phase may or may not have a gappable edge, even if its chiral central charge c_ is vanishing. Recently, it was discovered that a quantity regarded as a "higher" version of chiral central charge gives a further obstruction beyond c_ to gapping out the edge. Here, in this Letter, we show that the higher central charges can be characterized by the expectation value of the partial rotation operator acting on the wave function of the topologically ordered state. This allows us to extract the higher central charge from a single wave function, which can be evaluated on a quantum computer. Our characterization of the higher central charge is analytically derived from the modular properties of edge conformal field theory, as well as the numerical results with the ν = 1/2 bosonic Laughlin state and the non-Abelian gapped phase of the Kitaev honeycomb model, which corresponds to U(1) 2 and Ising topological order, respectively. The Letter establishes a numerical method to obtain a set of obstructions to the gappable edge of (2+1)D bosonic topological order beyond c_, which enables us to completely determine if a (2+1)D bosonic Abelian topological order has a gappable edge or not. We also point out that the expectation values of the partial rotation on a single wave function put a constraint on the low-energy spectrum of the bulk-boundary system of (2+1)D bosonic topological order, reminiscent of the Lieb-Schultz-Mattis-type theorems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The Case for Optimized Edge-Centric Tractography at Scale

The anatomic validity of structural connectomes remains a significant uncertainty in neuroimaging. Edge-centric tractography reconstructs streamlines in bundles between each pair of cortical or subcortical regions. Although edge bundles provides a stronger anatomic embedding than traditional connectomes, calculating them for each region-pair requires exponentially greater computation. We observe that major speedup can be achieved by reducing the number of streamlines used by probabilistic tractography algorithms. To ensure this does not degrade connectome quality, we calculate the identifiability of edge-centric connectomes between test and re-test sessions as a proxy for information content. We find that running PROBTRACKX2 with as few as 1 streamline per voxel per region-pair has no significant impact on identifiability. Variation in identifiability caused by streamline count is overshadowed by variation due to subject demographics. This finding even holds true in an entirely different tractography algorithm using MRTrix. Incidentally, we observe that Jaccard similarity is more effective than Pearson correlation in calculating identifiability for our subject population.

59 BASIC BIOLOGICAL SCIENCES↗

Polarization-dependent resonant inelastic x-ray scattering of β-Ga2O3: An experimental and computational study

The bulk electronic structure of β-Ga2O3 single crystals was investigated using oxygen K-edge x-ray emission and absorption spectroscopy as well as resonant inelastic soft x-ray scattering. Spectra were obtained for different orientations of the crystal planes with respect to the polarization vector of the incident x-ray beam. The spectra are analyzed with calculations based on density functional theory and using the Bethe–Salpeter equation in the ocean code to take the core–hole interaction into account. These calculations correctly capture all the main features in the experimental spectra, demonstrating the potential of the approach to predict the electronic properties of similar compounds. We find a pronounced anisotropy as a function of the excitation polarization vector and significant differences in the spectral contributions from the inequivalent oxygen atoms of β-Ga2O3.

Pyatenko, Elizaveta↗

Unraveling the intrinsic atomic physics behind x-ray absorption line shifts in warm dense silicon plasmas

Here, we present a novel free-energy density functional theory (DFT)-based methodology for optical property calculations of warm dense matter to cover a wide range of thermodynamic conditions and photon energies including the entire x-ray range. It uses Mermin–Kohn–Sham density functional theory with exchange-correlation (XC) thermal effects taken into account via a fully temperature dependent generalized gradient approximation XC functional. The methodology incorporates a combination of the ab initio molecular dynamics (AIMD) snapshotted Kubo–Greenwood optic data with a single-atom in simulation cell calculations to close the photon energy gap between the L and K edges and extend the K-edge tail toward many-keV photon energies. This gap arises in the standard scheme due to a prohibitively large number of bands required for the Kubo–Greenwood calculations with AIMD snapshots. Kubo–Greenwood data on snapshots provide an accurate description of optic properties at low photon frequencies slightly beyond the L-edge and x-ray absorption near edges structure (XANES) spectra, while data from periodic calculations with single atoms cover the tail regions beyond the edges. To demonstrate its applicability to mid-Z materials where the standard DFT-based approach is not computationally feasible, we have applied it to opacity calculations of warm dense silicon plasmas. These first-principles calculations revealed a very interesting phenomon of red-to-blue shift in K–L (1s → 2p) and K-edge absorptions along both isotherm and isochore, which are absent in most continuum-lowering models of traditional plasma physics. This new physics phenomenon can be attributed to the underlying competition between the screening of deeply bound core electrons and the screening of outer-shell electrons caused by warm-dense-plasma conditions. We further demonstrate that the ratio of 1s → 2p to the K-edge x-ray absorptions can be used to characterize warm-dense-plasma conditions. Eventually, based on our absorption calculations, we have established a first-principles opacity table (FPOT) for silicon in a wide range of material densities and temperatures.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Sensor-Assisted Fault Mitigation in Quantum Computation

We propose a method for assisting fault mitigation in quantum computation through the use of sensors, co-located near physical qubits. Specifically, we consider using transition edge sensors co-located on silicon substrates hosting superconducting qubits to monitor for energy injection from ionizing radiation that has been demonstrated to increase decoherence in transmon qubits. We generalize from these two physical device concepts and explore the potential advantages of co-located sensors to assist fault mitigation in quantum computation. In the simplest scheme, co-located sensors beneficially assist rejection of calculations potentially affected by environmental disturbances. Investigating the potential computational advantage further required development of an extension to the standard formulation of quantum error correction. In a specific case the standard three-qubit, bit flip quantum correction code, we show that given a 20% overall error probability per qubit, approximately 90% of repeated calculation attempts are correctable. However, when sensor-detectable errors account for 45% of overall error probability, the use of colocated sensors uniquely associated with independent qubits, boosts the fraction of correct final-state calculations to 96% at the cost of rejecting 7% of repeated calculation attempts.

Orrell, John L.↗

Adrastea: An Efficient FPGA Design Environment for Heterogeneous Scientific Computing and Machine Learning

We present Adrastea, an efficient FPGA design environment for developing scientific machine learning applications. FPGA development is challenging, from deployment, proper toolchain setup, programming methods, interfacing FPGA kernels, and more importantly, the need to explore design space choices to get the best performance and area usage from the FPGA kernel design. Adrastea provides an automated and scalable design flow to parameterize, implement, and optimize complex FPGA kernels and associated interfaces. We show how virtualization of the development environment via virtual machines is leveraged to simplify the setup of the FPGA toolchain while deploying the FPGA boards and while scaling up the automated design space exploration to leverage multiple machines concurrently. Adrastea provides an automated build and test environment of FPGA kernels. By exposing design space hyper-parameters, Adrastea can automatically search the design space in parallel to optimize the FPGA design for a given metric, usually performance or area. Adrastea simplifies the task of interfacing with the FPGA kernels with a simplified interface API. To demonstrate the capabilities of Adrastea, we implement a complex random forest machine learning kernel with 10,000 input features while achieving extremely low computing latency without loss of prediction accuracy, which is required by a scientific edge application at SNS. We also demonstrate Adrastea using an FFT kernel and show that for both applications Adrastea is able to systematically and efficiently evaluate different design options, which reduced the time and effort required to develop the kernel from months of manual work to days of automatic builds.

Young, Aaron↗

An ontology-based knowledge graph for representing interactions involving RNA molecules

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to each patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are constantly produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph (KG) encompassing biological knowledge about RNAs gathered from more than 60 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.

59 BASIC BIOLOGICAL SCIENCES↗

Spatially separating redox centers on 2D carbon nitride with cobalt single atom for photocatalytic H 2 O 2 production

Redox cocatalysts play crucial roles in photosynthetic reactions, yet simultaneous loading of oxidative and reductive cocatalysts often leads to enhanced charge recombination that is detrimental to photosynthesis. This study introduces an approach to simultaneously load two redox cocatalysts, atomically dispersed cobalt for improving oxidation activity and anthraquinone for improving reduction selectivity, onto graphitic carbon nitride (C 3 N 4 ) nanosheets for photocatalytic H 2 O 2 production. Spatial separation of oxidative and reductive cocatalysts was achieved on a two-dimensional (2D) photocatalyst, by coordinating cobalt single atom above the void center of C 3 N 4 and anchoring anthraquinone at the edges of C 3 N 4 nanosheets. Such spatial separation, experimentally confirmed and computationally simulated, was found to be critical for enhancing surface charge separation and achieving efficient H 2 O 2 production. This center/edge strategy for spatial separation of cocatalysts may be applied on other 2D photocatalysts that are increasingly studied in photosynthetic reactions.

2D photocatalyst↗

Sphynx

Sphynx is a software library for parallel graph partitioning and load balancing. It partitions a set of vertices in a graph such that the vertex parts are balanced, and the edge cut is approximately minimized. The primary use case is to partition a computational graph into smaller tasks that can be assigned to processors (cores) for efficient parallel computing. Sphynx is based on the Trilinos scientific computing toolkit so can run on both multi-CPU and multi-GPU systems. SAND2020-12183 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Boman, Erik↗

DUNE Software and Computing Research and Development

The international collaboration designing and constructing the Deep Underground Neutrino Experiment (DUNE) at the Long-Baseline Neutrino Facility (LBNF) has developed a two-phase strategy toward the implementation of this leading-edge, large-scale science project. The ambitious physics program of Phase I and Phase II of DUNE is dependent upon deployment and utilization of significant computing resources, and successful research and development of software (both infrastructure and algorithmic) in order to achieve these scientific goals. This submission discusses the computing resources projections, infrastructure support, and software development needed for DUNE during the coming decades as an input to the European Strategy for Particle Physics Update for 2026. The DUNE collaboration is submitting four main contributions to the 2026 Update of the European Strategy for Particle Physics process. This submission to the 'Computing' stream focuses on DUNE software and computing. Additional inputs related to the DUNE science program, DUNE detector technologies and R&D, and European contributions to Fermilab accelerator upgrades and facilities for the DUNE experiment, are also being submitted to other streams.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Differentially Private Synthesis and Sharing of Network Data Via Bayesian Exponential Random Graph Models

Abstract Network data often contain sensitive relational information. One approach to protecting sensitive information while offering flexibility for network analysis is to share synthesized networks based on the information in originally observed networks. We employ differential privacy (DP) and exponential random graph models (ERGMs) and propose the DP-ERGM method to synthesize network data. We apply DP-ERGM to two real-world networks. We then compare the utility of synthesized networks generated by DP-ERGM, the DyadWise Randomized Response (DWRR) approach, and the Synthesis through Conditional distribution of Edge given nodal Attribute (SCEA) approach. In general, the results suggest that DP-ERGM preserves the original information significantly better than two other approaches in network structural statistics and inference for ERGMs and latent space models. Furthermore, DP-ERGM satisfies node DP through modeling the global network structure with ERGM, a stronger notion of privacy than the edge DP under which DWRR and SCEA operate.

graph synthesis↗