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At least 271 records · Page 15

The parallelism motifs of genomic data analysis

Genomic datasets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share these data with the research community, but some of these genomic data analysis problems require large-scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high-end parallel systems today and place different requirements on programming support, software libraries and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high-performance genomics analysis, including alignment, profiling, clustering and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or ‘motifs’ that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.

59 BASIC BIOLOGICAL SCIENCES↗

Primordial black holes and their mass spectra: The effects of mergers and accretion within stasis cosmologies

A variety of processes in the very early Universe can give rise to a population of primordial black holes (PBHs) with an extended mass spectrum. For certain mass spectra of this sort, it has been shown that the evaporation of these PBHs into radiation can drive the universe toward an epoch of cosmological stasis which can persist for a significant number of 𝑒-folds of cosmological expansion. However, in general, the initial mass spectrum which characterizes a population of PBHs at the time of production can subsequently be distorted by processes such as mergers and accretion. Here, in this paper, we examine the effects that these processes have on the spectra that lead to a PBH-induced stasis. Within such stasis models, we find that mergers have only a negligible effect on these spectra within the regime of interest for stasis. We likewise find that the effect of accretion is negligible in many cases of interest. However, we find that the effect of accretion on the PBH mass spectrum is non-negligible in situations in which this spectrum is particularly broad. In such situations, the stasis epoch is abridged or, in extreme cases, does not occur at all. Thus accretion plays a nontrivial role in constraining the emergence of stasis within scenarios which lead to extended PBH mass spectra.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Multigap electron-phonon superconductivity in the quasi-one-dimensional pnictide K 2 Mo 3 As 3

In this work, we show, using density functional calculations, that quasi-one-dimensional K 2 Mo 3 As 3 , which is closely related to K 2 Cr 3 As 3 and has very similar superconducting properties, is not close to magnetism and has conventional s wave electron-phonon superconductivity. This superconductivity is of multigap character due to different coupling on different Fermi surface sheets. This is discussed in relation to the properties of this family of quasi-one-dimensional pnictide superconductors. The results show that this family of superconductors provides a unique opportunity for studying the interplay of spin fluctuations and electron-phonon superconductivity in transition metal pnictides, and offer a path for sorting out the different proposed superconducting scenarios in this fascinating family of pnictide superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Natural anomaly mediation from the landscape with implications for LHC SUSY searches

Supersymmetric models with the anomaly-mediated supersymmetry (SUSY) breaking (AMSB) form for soft SUSY breaking terms arise in two different settings: (1) extra-dimensional models where SUSY breaking occurs in a sequestered sector, and (2) 4 − d models with dynamical SUSY breaking in a hidden sector where scalars gain masses of order the gravitino mass m 3 / 2 , but gaugino masses and trilinear soft terms are assumed to be of the AMSB form. Both models run into serious conflicts with (1) LHC sparticle and Higgs mass constraints, (2) constraints from winolike weakly interacting massive particle dark matter searches, and (3) bounds from naturalness. These conflicts may be avoided by introducing minor changes to the underlying phenomenological models consisting of nonuniversal bulk scalar Higgs masses and A terms, providing a setting for natural anomaly mediation (nAMSB). In nAMSB, the wino is still expected to be the lightest of the gauginos, but the Higgsinos are expected to be the lightest electroweakinos (EWinos) in accord with naturalness. We examine what sorts of spectra are expected to emerge when nAMSB arises from a string landscape setting: While model 2 can only be natural for a Higgs mass m h ≲ 123 GeV , model 1 can accommodate naturalness along with m h ∼ 125 GeV while still respecting LHC bounds on sparticle masses. We explore the LHC phenomenology of nAMSB models where we find that for Higgsino pair production, typically larger dilepton mass gaps arise from the soft dilepton-plus-jets signature than in models with gaugino mass unification. For wino-pair production, the higher m 3 / 2 portion of nAMSB parameter space is excluded by recent LHC bounds from gaugino pair production searches. We characterize the dominant LHC signatures arising from the remaining lower m 3 / 2 ∼ 90 – 200 TeV range of parameter space, which should be fully testable at high-luminosity LHC via EWino pair production searches. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Fuzzy gauge theory for quantum computers

Continuous gauge theories, because of their bosonic degrees of freedom, have an infinite-dimensional local Hilbert space. Encoding these degrees of freedom on qubit-based hardware demands some sort of “qubitization” scheme, where one approximates the behavior of a theory while using only finitely many degrees of freedom. We propose a novel qubitization strategy for gauge theories, called “fuzzy gauge theory,” building on the success of the fuzzy σ -model in earlier work. We provide arguments that the fuzzy gauge theory lies in the same universality class as regular gauge theory, in which case its use would obviate the need of any further limit besides the usual spatial continuum limit. Furthermore, we demonstrate that these models are relatively resource-efficient for quantum simulations. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Redundantly Amplified Information Suppresses Quantum Correlations in Many-Body Systems

We establish bounds on quantum correlations in many-body systems. They reveal what sort of information about a quantum system can be simultaneously recorded in different parts of its environment. Specifically, independent agents who monitor environment fragments can eavesdrop only on amplified and redundantly disseminated—hence, effectively classical—information about the decoherence-resistant pointer observable. We also show that the emergence of classical objectivity is signaled by a distinctive scaling of the conditional mutual information, bypassing hard numerical optimizations. Our results validate the core idea of quantum Darwinism: objective classical reality does not need to be postulated and is not accidental, but rather a compelling emergent feature of quantum theory that otherwise—in the absence of decoherence and amplification—leads to “quantum weirdness.” In particular, a lack of consensus between agents that access environment fragments is bounded by the information deficit, a measure of the incompleteness of the information about the system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Overcoming photobleaching in imaging of single barium atoms in a solid xenon matrix

Neutrinoless double beta decay is one of the most sensitive probes for new physics beyond the Standard Model of particle physics. One of the isotopes under investigation is 136 Xe, which would double beta decay into 136 Ba. Detecting the single 136 Ba daughter provides a sort of ultimate tool in the discrimination against backgrounds. Previous work demonstrated the ability to perform single atom imaging of Ba atoms in a single-vacancy site of a solid xenon matrix. In this paper, the effort to identify signal from individual barium atoms is extended to Ba atoms in a hexa-vacancy site in the matrix and is achieved despite increased photobleaching in this site. Abrupt fluorescence turn-off of a single Ba atom is also observed. Significant recovery of fluorescence signal lost through photobleaching is demonstrated upon annealing of Ba deposits in the Xe ice. Following annealing, it is observed that Ba atoms in the hexa-vacancy site exhibit antibleaching while Ba atoms in the tetra-vacancy site exhibit bleaching. This may be evidence for a matrix site transfer upon laser excitation. Our findings offer a path of continued research toward tagging of Ba daughters in all significant sites in solid xenon.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Stripe and bubble ratchets on asymmetric substrates

We show that various nonmonotonic ratchet effects can arise when mesophase pattern-forming systems, which exhibit anisotropic crystal, stripe, and bubble regimes, are coupled to one-dimensional asymmetric substrates under ac driving. The patterns emerge in the absence of a substrate when the ratio of attraction to repulsion is varied for particles with competing short-range attraction and long-range repulsion potentials. In the presence of the substrate, we find that the ratchet efficiency varies nonmonotonically with increasing attraction, depending upon how well the mesophase morphology matches the substrate spacing and periodicity. For strong repulsion, there is a weak but finite ratchet effect, while at intermediate attraction, there is a robust ratchet effect in which the system forms stripes aligned with the substrate symmetry direction. For strong attraction, large bubbles appear that have weak or no ratchet effects when the bubble width exceeds the substrate lattice spacing, causing the bubble to be only weakly coupled to the substrate. For very strong attraction, small bubbles form and undergo a strong ratchet effect with an efficiency that oscillates as a function of ac drive amplitude. Although the small bubble regime is a strongly correlated regime in which each bubble contains many particles, the system behaves as if it is in a single-particle regime since the bubble width is much smaller than the substrate lattice spacing. We map out the different rectification phases as a function of the pattern morphology, substrate strength, and ac drive amplitude. The pronounced ratchet effects that we observe in some regimes can be exploited for pattern sorting in hard and soft matter systems. Published by the American Physical Society 2024

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Wave-packet manipulation of He Rydberg states by a seeded free-electron laser

We report a two-dimensional pump-control-probe spectroscopic study of the dynamics of singly excited He Rydberg-state wave packets with a seeded extreme ultraviolet (XUV) free-electron laser (FEL) source. A pair of coherent XUV pulses, defined by their coarse time separation and relative phase, created and manipulated the wave packets. The He atoms were postionized by infrared (IR) pulses, and the ion yield was measured as a function of XUV phase and IR arrival time. We tagged and sorted the relative phase of the XUV pulse pair on a single-shot basis by fitting each FEL spectrum with a suitable function that accounts for nonidealities of the XUV pulse pairs, associated with the seeding process; more generally, the fit returns the time-dependent electric field of the FEL spectra. The experimental two-dimensional maps of ion yields, measured as a function of IR (probe) delay and of XUV (pump-control) phase, were compared with the solution of the first-order time-dependent Schrödinger equation for this field. Despite the fact that the experimental conditions imply strong excitation, beyond the approximations of first-order perturbation theory, the simulated map satisfactorily reproduces the experimental one for temporally well-separated pulses. We show that by selecting data at appropriate values of pump-control phase, we enhance or suppress the amplitude of chosen wave-packet components consisting of two or more Rydberg states. When the temporal overlap of the pulse pair cannot be neglected, the phase reconstruction is underdetermined, and we provide a simplified comparison between data and simulations. Published by the American Physical Society 2024

Dumergue, Mathieu (ORCID:0000000236984406)↗

Tuning of altermagnetism by strain

For all collinear altermagnets, we sort out piezomagnetic free-energy invariants allowed in the nonrelativistic limit and relativistic piezomagnetic invariants bilinear in the Néel vector $\mathbf{L}$ and magnetization $\mathbf{M}$, which include strain-induced Dzyaloshinskii-Moriya interaction. The symmetry-allowed responses are fully determined by the nonrelativistic spin Laue group. In the nonrelativistic limit, two distinct mechanisms are discussed: the band-filling mechanism, which exists in metals and is illustrated using the simple two-dimensional Lieb lattice model, and the temperature-dependent exchange-driven mechanism, which is illustrated using first-principles calculations for transition-metal fluorides. The leading second-order nonrelativistic term in the strain-induced magnetization is also obtained for CrSb. Piezomagnetism due to the strain-induced Dzyaloshinskii-Moriya interaction is calculated from first principles for transition-metal fluorides, MnTe, and CrSb. Finally, we discuss triplet superconducting correlations supported by altermagnets and protected by inversion rather than time-reversal symmetry. We apply the nonrelativistic classification of Cooper pairs to describe the interplay between strain and superconductivity in the two-dimensional Lieb lattice and in bulk rutile structures. Here, we show that triplet superconductivity is, on average, unitary in an unstrained altermagnet, but becomes non-unitary under piezomagnetically active strain.

FOS: Physical sciences↗

Bent Laue crystal anatomy: new insights into focusing and energy-dispersion properties

X-ray Laue-type monochromators are common and essential optical components at many high-power X-ray facilities, e.g. synchrotron facilities. The X-ray optics of bent Laue crystals is a well developed area. An incident X-ray beam penetrating a bent Laue crystal will result in a diffracted beam with different angles and energies. There is a need for a way of organizing the rays that allows one to sort out the energy and spatial properties of the diffracted beam. The present work introduces a new approach for describing the general behaviour of bent Laue crystals from a ray-tracing point of view. This quasi-monochromatic beam approach provides an intuitive view of bent-crystal diffraction and leads to deeper understanding. It explains the energy and spatial properties of common and special cases of bent Laue optics, predicts phenomena that can improve energy-dispersion-related X-ray imaging techniques and provides a theoretical framework that makes ray-tracing simulation easier to realize.

36 MATERIALS SCIENCE↗

Direct recovery of interfacial topography from coherent X-ray reflectivity: model calculations for a 1D interface

The use of coherent X-ray reflectivity to recover interfacial topography is described using model calculations for a one-dimensional interface. The results reveal that the illuminated topography can be recovered directly from the measured reflected intensities. This is achieved through an analysis of the Patterson function, the Fourier transform of the scattering intensity (as a function of lateral momentum transfer, Q // , at fixed vertical momentum transfer, Q z ). Specifically, a second-order Patterson function is defined that reveals the discrete set of separations and contrast factors (i.e., the product of changes in the effective scattering factor) associated with discontinuities in the effective interfacial topography. Finally, it is shown that the topography is significantly over-determined by the measurements, and an algorithm is described that recovers the actual topography through a deterministic sorting of this information.

36 MATERIALS SCIENCE↗

A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs

One often observes small but measurable differences in the diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and may reveal the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step that could extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets. Mixed-state data can be obtained deliberately (through intentional perturbation) or inadvertently (while attempting to measure highly redundant single-crystal data). To the extent that different states adopt different molecular structures, one expects to observe differences in the crystals; each of the polystates will create a polymorph of the crystals. After mixed-state diffraction data have been measured, deliberately or inadvertently, the challenge is to sort the data into clusters that may represent relevant biological polystates. Here, this problem is addressed using a simple multi-factor clustering approach that classifies each data set using independent observables, thereby assigning each data set to the correct location in conformational space. This procedure is illustrated using two independent observables, unit-cell parameters and intensities, to cluster mixed-state data from chymotrypsinogen (ChTg) crystals. It is observed that the data populate an arc of the reaction trajectory as ChTg is converted into chymotrypsin.

36 MATERIALS SCIENCE↗

High-Efficiency Model Predictive Control for Star-Connected Cascaded H-Bridge STATCOM Under Unbalanced Conditions

This paper presents a high-efficiency model predictive control (HMPC), which is enabled by a sorting approach based on dc capacitor voltages to significantly reduce the exponentially-increasing switching states in cascaded Hbridge (CHB) converters. In addition, a generic discrete-time prediction model for star-connected CHB static synchronous compensator is proposed to address the issues due to either grid and/or load unbalances. Both simulation and hardware-in-loop experimental results are presented to validate the feasibility and effectiveness of the proposed HMPC strategy.

Li, Yufei↗

Design and Optimization of High-frequency Transformer for Isolated Single-Stage Three-Phase AC/DC Converter using Bidirectional Switches

This paper presents the design and optimization of the high-frequency transformer for an isolated single-stage threephase AC/DC converter enabled by the 4H-SiC BiDirectional Field Effect Transistor (BiDFET). Non-dominated Sorting Genetic Algorithm II (NSGA-II) is used to perform a multiobjective optimization to minimize loss, weight, and volume. A 20 kW, 50 kHz hardware prototype based on the selected optimal point is characterized by a power amplifier. The finite element analysis simulation results are also presented to validate the core magnetic flux density and winding electric field strength. The experimental prototype was tested at 800 Vdc/480 Vrms at 10 kW rated power.

BiDFET, High-frequency transformer, Multiobjective↗

Path-Based Dictionary Augmentation: A Framework for Improving $k$ -Sparse Image Processing

In this study, we have previously shown that augmenting orthogonal matching pursuit (OMP) with an additional step in the identification stage of each pursuit iteration yields improved $k$ -sparse reconstruction and denoising performance relative to baseline OMP. At each iteration a “path” or geodesic, is generated between the two dictionary atoms that are most correlated with the residual and from this path a new atom that has a greater correlation to the residual than either of the two bracketing atoms is selected. Here, we provide new computational results illustrating improvements in sparse coding and denoising on canonical datasets using both learned and structured dictionaries. The two methods of constructing a path are investigated for each dictionary type: the Euclidean geodesic formed by a linear combination of the two atoms and the 2-Wasserstein geodesic corresponding to the optimal transport map between the atoms. We prove here the existence of a higher-correlation atom in the Euclidean case under assumptions on the two bracketing atoms and introduce algorithmic modifications to improve the likelihood that the bracketing atoms meet those conditions. Although, we demonstrate our augmentation on OMP alone, in general it may be applied to any reconstruction algorithm that relies on the selection and sorting of high-similarity atoms during an analysis or identification phase.

97 MATHEMATICS AND COMPUTING↗

Enabling Scalable and Extensible Memory-mapped Datastores in Userspace

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.

97 MATHEMATICS AND COMPUTING↗

Online Power System Event Detection via Bidirectional Generative Adversarial Networks

Accurate and speedy detection of power system events is critical to enhancing the reliability and resiliency of power systems. Although supervised deep learning algorithms show great promise in identifying power system events, they require a large volume of high-quality event labels for training. This paper develops a bidirectional anomaly generative adversarial network (GAN)-based algorithm to detect power system events using streaming PMU data, which does not rely on a huge amount of event labels. By introducing conditional entropy constraint in the objective function of GAN and graph signal processing-based PMU sorting technique, our proposed algorithm significantly outperforms state-of-the-art event detection algorithms in terms of accuracy. To facilitate the adoption of the proposed algorithm, a prototype online platform is also developed using Apache Hadoop, Kafka, and Spark to enable real-time event detection. Here, the accuracy and computational efficiency of the proposed algorithm are validated using a large-scale real-world PMU dataset from the Eastern Interconnection of the United States.

24 POWER TRANSMISSION AND DISTRIBUTION↗