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At least 973 records · Page 54

Genome-scale phylogeny and comparative genomics of the fungal order Sordariales

The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chaetomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.

59 BASIC BIOLOGICAL SCIENCES↗

Estimating Higher-Order Moments Using Symmetric Tensor Decomposition

In this paper, we consider the problem of decomposing higher-order moment tensors, i.e., the sum of symmetric outer products of data vectors. Such a decomposition can be used to estimate the means in a Gaussian mixture model and for other applications in machine learning. The dth-order empirical moment tensor of a set of p observations of n variables is a symmetric d-way tensor. Our goal is to nd a low-rank tensor approximation comprising r $\ll$ p symmetric outer products. The challenge is that forming the empirical moment tensor costs O(pn d ) operations and O(n d ) storage, which may be prohibitively expensive; additionally, the algorithm to compute the low-rank approximation costs O(n d ) per iteration. Our contribution is avoiding formation of the moment tensor, computing the low-rank tensor approximation of the moment tensor implicitly using O(pnr) operations per iteration and no extra memory. This advance opens the door to more applications of higher-order moments since they can now be efficiently computed. We present numerical evidence of the computational savings and show an example of estimating the means for higher-order moments.

97 MATHEMATICS AND COMPUTING↗

Platform for 100 s Mbar equation of state measurements on the National Ignition Facility

Equation of state (EOS) measurements in the 100 s Mbar range are needed to underwrite models employed in the simulation of high energy density plasmas. To this end, a platform has been developed for fielding on the National Ignition Facility, capable of producing high-quality impedance match EOS data, wherein a planar, high-pressure, steady shock is driven into a sample package, and sample and reference standard shock velocities are measured. This platform, dubbed planar high pressure, or PHP, was fielded with an initial proof-of-concept shot in January 2023. The first PHP shot, aiming to study gold, demonstrated a pressure close to 400 Mbar, two orders of magnitude higher than previously reported gold EOS data.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

CTA and SWGO can discover Higgsino dark matter annihilation

Thermal Higgsino dark matter (DM), with a mass near 1.1 TeV, is one of the most well-motivated and untested DM candidates. Leveraging recent hydrodynamic cosmological simulations that give DM density profiles in Milky Way analog galaxies we show that the linelike gamma-ray signal predicted from Higgsino annihilation in the Galactic Center could be detected at high significance with the upcoming Cherenkov Telescope Array (CTA) and Southern Wide-field Gamma-ray Observatory (SWGO) for all but the most pessimistic DM profiles. We perform the most sensitive search to-date for the linelike signal using 15 years of data from the Fermi Large Area Telescope, coming within an order one factor of the necessary sensitivity to detect the Higgsino for some Milky Way analog DM density profiles. We show that H.E.S.S. has subleading sensitivity relative to Fermi for the Higgsino at present. In contrast, we analyze H.E.S.S. inner Galaxy data for the thermal wino model with a mass near 2.8 TeV; we find no evidence for a DM signal and exclude the wino by over a factor of two in cross section for all DM profiles considered. In the process, we identify and attempt to correct what appears to be an inconsistency in previous H.E.S.S. inner Galaxy analyses for DM annihilation related to the analysis effective area, which may weaken the DM cross-section sensitivity claimed in those works by around an order of magnitude.

79 ASTRONOMY AND ASTROPHYSICS↗

Digital Twin for Optimizing Real-time Economy of the Integrated Energy Systems

Economic and safe operation of integrated energy systems (IES) requires real-time optimization (RTO) of the control and actions conducted on each system component. In this regard, digital twins (DTs), which consist of a physical system, a virtual system, and the data communication that occurs between the two, are essential for effective RTO. Through the data warehouse, the virtual system is constantly updated with real-time data from the physical system, and functions as the model in the optimization framework. The reduced-order model of the dynamic process model in the virtual system is used in the optimization framework. The optimization results are then returned, via the data warehouse, as control actions to the physical system. This work demonstrates the software capabilities of DT assets for an IES in the context of preparing a DT for an experimental system comprised of Idaho National Laboratory (INL)’s Thermal Energy Delivery System and battery system. For the virtual demonstration, the DTs encompass (1) a physical system, including the Modelica models of the Thermal Energy Delivery System and the battery system; (2) virtual optimization via the Optimization of Real-Time Capacity Allocation (ORCA) platform; and (3) the open-source data warehouse software DeepLynx. This work assesses the performance of ORCA, which utilizes a reduced-order model built using the Risk Analysis Virtual Environment (RAVEN) and trained on the Modelica models and real-time data pipeline through the graph database hosted in DeepLynx. The proposed optimization workflow will be an RTO model based on DTs and the data they generate.

25 ENERGY STORAGE↗

Probing atomic-scale symmetry breaking by rotationally invariant machine learning of multidimensional electron scattering

Abstract The 4D scanning transmission electron microscopy (STEM) method maps the structure and functionality of solids on the atomic scale, yielding information-rich data sets describing the interatomic electric and magnetic fields, structural and electronic order parameters, and other symmetry breaking distortions. A critical bottleneck is the dearth of analytical tools that can reduce complex 4D-STEM data to physically relevant descriptors. We propose an approach for the systematic exploration of 4D-STEM data using rotationally invariant variational autoencoders (rrVAE), which disentangle the general rotation of the object from other latent representations. The implementation of purely rotational rrVAE is discussed as are applications to simulated data for graphene and zincblende structures. The rrVAE analysis of experimental 4D-STEM data of defects in graphene is illustrated and compared to the classical center-of-mass analysis. This approach is universal for probing symmetry-breaking phenomena in complex systems and can be implemented for a broad range of diffraction methods.

36 MATERIALS SCIENCE↗

Renormalized approach to neutrinoless double-$β$ decay

The process at the heart of neutrinoless double-$β$ decay, $nn →\ pp\ e⁻ e⁻$ induced by a light Majorana neutrino, is investigated in pionless and chiral effective field theory. We show in various regularization schemes the need to introduce a short-range lepton-number-violating operator at leading order, confirming earlier findings. We demonstrate that such a short-range operator is only needed in spin-singlet $S$-wave transitions, while leading-order transitions involving higher partial waves depend solely on long-range currents. Calculations are extended to include next-to-leading-order corrections in perturbation theory, where to this order no additional undetermined parameters appear. We establish a connection based on chiral symmetry between neutrinoless double-$β$ decay and nuclear charge-independence breaking induced by electromagnetism. Data on the latter confirm the need for a leading-order short-range operator but do not allow for a full determination of the corresponding lepton-number-violating coupling. Using a crude estimate of this coupling, we perform ab initio calculations of the matrix elements for neutrinoless double-$β$ decay for 6 He and 12 Be. We speculate on the phenomenological impact of the leading short-range operator on the basis of these results.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Long plasma duration operation analyses with an international multi-machine (tokamaks and stellarators) database

Combined high-fusion performance and long-pulse operation is one of the key integration challenges for fusion energy development in magnetic devices. Addressing these challenges requires an integrated vision of physics and engineering aspects with the purpose of simultaneously increasing time duration and fusion performance. Significant progress has been made in tokamaks and stellarators, including very recent achievement in duration and/or performance. This progress is reviewed by analyzing the experimental data (109 plasma pulses with a total of 3200 data points, i.e. on average 29 data per pulse) provided by ten tokamaks (in alphabetical order: Axially Symmetric Divertor Experiment Upgrade, DIII-D, Experimental Advanced Superconducting Tokamak, Joint European Torus, JT-60 Upgrade, Korea Superconducting Tokamak Advanced Research, tokamak à configuration variable, Tokamak Fusion Test Reactor, Tore Supra, W Environment in Steady-State Tokamak) and two stellarators (Large Helical Device and Wendelstein 7-X) expanding the pioneering work of Kikuchi (Kikuchi M. and Azumi M. 2015 Frontiers in Fusion Research II: Introduction to Modern Tokamak Physics (Springer)). Data have been gathered up to January 2022 and coordination has been provided by the recently created International Energy Agency-International Atomic Energy Agency international Coordination on International Challenges on Long duration OPeration group. By exploiting the multi-machine international database, recent progress in terms of injected energies (e.g. 1730 MJ in L-mode, 425 MJ in H-mode), durations (1056 s in L-mode, 101 s in H-mode), injected powers, and sustained performance will be reviewed. Progress has been made to sustain long-pulse operation in tokamaks and stellarators with superconducting coils, actively cooled components, and/or with metallic walls. The graph of the fusion triple products as a function of duration shows a dramatic reduction of, at least two orders of magnitude when increasing the plasma duration from less than 1 s to 100 s. Indeed, long-pulse operation is usually reached in dominant electron-heating modes at reduced density (current drive optimization) but with low ion temperatures ranging from 1 to 3 keV for discharges above 100 s. Difficulties in extending the duration may arise from coupling high heating powers over long durations and the evolving plasma-wall interaction towards an unstable operational domain. Possible causes limiting the duration and critical issues to be addressed prior to ITER operation and DEMO design are reported and analyzed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A data-driven approach to modeling cancer cell mechanics during microcirculatory transport

In order to understand the effect of cellular level features on the transport of circulating cancer cells in the microcirculation, there has been an increasing reliance on high-resolution in silico models. Accurate simulation of cancer cells flowing with blood cells requires resolving cellular-scale interactions in 3D, which is a significant computational undertaking warranting a cancer cell model that is both computationally efficient yet sufficiently complex to capture relevant behavior. Given that the characteristics of metastatic spread are known to depend on cancer type, it is crucial to account for mechanistic behavior representative of a specific cancer’s cells. To address this gap, in the present work we develop and validate a means by which an efficient and popular membrane model-based approach can be used to simulate deformable cancer cells and reproduce experimental data from specific cell lines. Here, cells are modeled using the immersed boundary method (IBM) within a lattice Boltzmann method (LBM) fluid solver, and the finite element method (FEM) is used to model cell membrane resistance to deformation. Through detailed comparisons with experiments, we (i) validate this model to represent cancer cells undergoing large deformation, (ii) outline a systematic approach to parameterize different cell lines to optimally fit experimental data over a range of deformations, and (iii) provide new insight into nucleated vs. non-nucleated cell models and their ability to match experiments. While many works have used the membrane-model based method employed here to model generic cancer cells, no quantitative comparisons with experiments exist in the literature for specific cell lines undergoing large deformation. Here, we describe a phenomenological, data-driven approach that can not only yield good agreement for large deformations, but explicitly detail how it can be used to represent different cancer cell lines. This model is readily incorporated into cell-resolved hemodynamic transport simulations, and thus offers significant potential to complement experiments towards providing new insights into various aspects of cancer progression.

59 BASIC BIOLOGICAL SCIENCES↗

Pairing symmetry of twisted bilayer graphene: A phenomenological synthesis

One of the outstanding questions in the study of twisted bilayer graphene—from both experimental and theoretical points of view—is the nature of its superconducting phase. In this paper we perform a comprehensive synthesis of existing experiments, and argue that experimental constraints are strong enough to allow the structure of the superconducting order parameter to be nearly uniquely determined. In particular, we argue that the order parameter is nodal, and is formed from an admixture of spin-singlet and spin-triplet Cooper pairs. This argument is made on phenomenological grounds, without committing to any particular microscopic model of the superconductor. Existing data is insufficient to determine the orbital parity of the order parameter, which could be either p wave or d wave. We propose a way in which the measurement of Andreev edge states can be used to distinguish between the two.

36 MATERIALS SCIENCE↗

PLANC: Parallel Low-rank Approximation with Nonnegativity Constraints

In this work, we consider the problem of low-rank approximation of massive dense nonnegative tensor data, for example, to discover latent patterns in video and imaging applications. As the size of data sets grows, single workstations are hitting bottlenecks in both computation time and available memory. We propose a distributed-memory parallel computing solution to handle massive data sets, loading the input data across the memories of multiple nodes, and performing efficient and scalable parallel algorithms to compute the low-rank approximation. We present a software package called Parallel Low-rank Approximation with Nonnegativity Constraints, which implements our solution and allows for extension in terms of data (dense or sparse, matrices or tensors of any order), algorithm (e.g., from multiplicative updating techniques to alternating direction method of multipliers), and architecture (we exploit GPUs to accelerate the computation in this work). We describe our parallel distributions and algorithms, which are careful to avoid unnecessary communication and computation, show how to extend the software to include new algorithms and/or constraints, and report efficiency and scalability results for both synthetic and real-world data sets.

97 MATHEMATICS AND COMPUTING↗

Order-Disorder Transitions in ( Ca x Sr 1 - x ) 3 Rh 4 Sn 13

The classification of structural phase transitions as displacive or order-disorder in character is usually based on spectroscopic data above the transition. Here, we use single crystal x-ray diffraction to investigate structural correlations in the quasiskutterudites, (Ca x Sr 1-x ) 3 Rh 4 Sn 13 , which have a quantum phase transition at x ~ 0.9. Three-dimensional pair distribution functions show that the amplitudes of local atomic displacements are temperature independent below the transition and persist to well above the transition, a signature of order-disorder behavior. The implications for the associated electronic transitions are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Field-induced intermediate ordered phase and anisotropic interlayer interactions in α-RuCl 3

In α-RuCl 3 , an external magnetic field applied within the honeycomb plane can induce a transition from a magnetically ordered state to a disordered state that is potentially related to the Kitaev quantum spin liquid. In zero field, single crystals with minimal stacking faults display a low-temperature state with in-plane zigzag antiferromagnetic order and a three-layer periodicity in the direction perpendicular to the honeycomb planes. In this work, we present angle-dependent magnetization, ac susceptibility, and thermal transport data that demonstrate the presence of an additional intermediate-field ordered state at fields below the transition to the disordered phase. Neutron-diffraction results show that the magnetic structure in this phase is characterized by a six-layer periodicity in the direction perpendicular to the honeycomb planes. Theoretically, the intermediate ordered phase can be accounted for by including spin-anisotropic couplings between the layers in a three-dimensional spin model. Together, this demonstrates the importance of interlayer exchange interactions in α-RuCl 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Using Bayesian Methodology to Estimate Liquefied Natural Gas Leak Frequencies

This analysis provides estimates on the leak frequencies of nine components found in liquefied natural gas (LNG) facilities. Data was taken from a variety of sources, with 25 different data sets included in the analysis. A hierarchical Bayesian model was used that assumes that the log leak frequency follows a normal distribution and the logarithm of the mean of this normal distribution is a linear function of the logarithm of the fractional leak area. This type of model uses uninformed prior distributions that are updated with applicable data. Separate models are fit for each component listed. Five order-of-magnitude fractional leak areas are considered, based on the flow area of the component. Three types of supporting analyses were performed: sensitivity of the model to the data set used, sensitivity of the leak frequency estimates to differences in the model structure or prior distributions, and sufficiency of sample sized used for convergence. Recommended leak frequency distributions for all component types and leak sizes are given. These leak frequency predictions can be used for quantitative risk assessments in the future.

03 NATURAL GAS↗

Rock Valley Accelerated Weight Drop Seismic Data Processing and Picking of P-wave and S-wave Arrival Times

Rock Valley, in the southern end of the Nevada National Security Site, hosts a fault system that was responsible for a shallow (< 3 km below surface ) magnitude 3.7 earthquake in May 1993. In order to better understand this system, seismic properties of the shallow subsurface need to be better constrained. In April and May of 2021, accelerated weight drop (AWD) active-source seismic data were recorded in order to measure P- and S-wave travel-times for the area. This report describes the processing and phase picking of the recorded seismic waveforms. In total, we picked 7,982 P-wave arrivals at offsets up to ~2500 m, and 4,369 S-wave arrivals at offsets up to ~2200 m. These travel-time picks can be inverted for shallow P-wave and S-wave velocity structure in future studies.

58 GEOSCIENCES↗

Data-driven learning of Mori–Zwanzig operators for isotropic turbulence

Developing reduced-order models for turbulent flows, which contain dynamics over a wide range of scales, is an extremely challenging problem. In statistical mechanics, the Mori–Zwanzig (MZ) formalism provides a mathematically exact procedure for constructing reduced-order representations of high-dimensional dynamical systems, where the effects due to the unresolved dynamics are captured in the memory kernel and orthogonal dynamics. Turbulence models based on MZ formalism have been scarce due to the limited knowledge of the MZ operators, which originates from the difficulty in deriving MZ kernels for complex nonlinear dynamical systems. In this work, we apply a recently developed data-driven learning algorithm, which is based on Koopman's description of dynamical systems and Mori's linear projection operator, on a set of fully resolved isotropic turbulence datasets to extract the Mori–Zwanzig operators. With data augmentation using known turbulence symmetries, the extracted Markov term, memory kernel, and orthogonal dynamics are statistically converged and the generalized fluctuation–dissipation relation can be verified. The properties of the memory kernel and orthogonal dynamics, and their dependence on the choices of observables are investigated to address the modeling assumptions that are commonly used in MZ-based models. A series of numerical experiments are then constructed using the extracted kernels to evaluate the memory effects on prediction. The results show that the prediction errors are strongly affected by the choice of observables and can be further reduced by including the past history of the observables in the memory kernel.

97 MATHEMATICS AND COMPUTING↗

Filament-Free Bulk Resistive Memory Enables Deterministic Analogue Switching

Digital computing is nearing its physical limits as computing needs and energy consumption rapidly increase. Analogue-memory-based neuromorphic computing can be orders of magnitude more energy efficient at data-intensive tasks like deep neural networks, but has been limited by the inaccurate and unpredictable switching of analogue resistive memory. Filamentary resistive random access memory (RRAM) suffers from stochastic switching due to the random kinetic motion of discrete defects in the nanometer-sized filament. Here, this stochasticity is overcome by incorporating a solid electrolyte interlayer, in this case, yttria-stabilized zirconia (YSZ), toward eliminating filaments. Filament-free, bulk-RRAM cells instead store analogue states using the bulk point defect concentration, yielding predictable switching because the statistical ensemble behavior of oxygen vacancy defects is deterministic even when individual defects are stochastic. Both experiments and modeling show bulk-RRAM devices using TiO2-X switching layers and YSZ electrolytes yield deterministic and linear analogue switching for efficient inference and training. Bulk-RRAM solves many outstanding issues with memristor unpredictability that have inhibited commercialization, and can, therefore, enable unprecedented new applications for energy-efficient neuromorphic computing. Beyond RRAM, this work shows how harnessing bulk point defects in ionic materials can be used to engineer deterministic nanoelectronic materials and devices.

36 MATERIALS SCIENCE↗

Graph identification of proteins in tomograms ( GRIP‐Tomo )

Abstract In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases for refinement. We hypothesized that the topological connectivity of protein structures is invariant, and they are distinctive for the purpose of protein identification from distorted data presented in volume densities. Three‐dimensional densities of a protein or a complex from simulated tomographic volumes were transformed into mathematical graphs as observables. We systematically introduced data distortion or defects such as missing fullness of data, the tumbling effect, and the missing wedge effect into the simulated volumes, and varied the distance cutoffs in pixels to capture the varying connectivity between the density cluster centroids in the presence of defects. A similarity score between the graphs from the simulated volumes and the graphs transformed from the physical protein structures in point data was calculated by comparing their network theory order parameters including node degrees, betweenness centrality, and graph densities. By capturing the essential topological features defining the heterogeneous morphologies of a network, we were able to accurately identify proteins and homo‐multimeric complexes from 10 topologically distinctive samples without realistic noise added. Our approach empowers future developments of tomogram processing by providing pattern mining with interpretability, to enable the classification of single‐domain protein native topologies as well as distinct single‐domain proteins from multimeric complexes within noisy volumes.

59 BASIC BIOLOGICAL SCIENCES↗