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At least 703 records · Page 39

A family of tubular pili from harmful algal bloom forming cyanobacterium Microcystis aeruginosa

Cyanobacteria are vital photosynthetic prokaryotes, but some form harmful algal blooms (cyanoHABs) that disrupt ecosystems and produce toxins. The mechanisms by which these blooms form have yet to be fully understood, particularly the role of extracellular components. Here, we present a 2.4 Å cryo-EM structure of a pilus, termed the cyanobacterial tubular (CT) pilus, found in the cyanoHAB-forming Microcystis aeruginosa. The pilin exhibits a unique protein fold, forming a tubular pilus structure with tight, double-layer anti-parallel β-sheet interactions. We show that CT pili are essential for buoyancy by facilitating the formation of micro-colonies, which increases drag force and prevents sinking. The CT pilus surface is heavily glycosylated with ten monosaccharide modifications per pilin. Furthermore, CT pili can enrich microcystin, potentially enhancing cellular resilience, and co-localize with iron-enriched extracellular matrix components. Thus, we propose that this pilus plays an important role in the proliferation of cyanoHABs. This just discovered pilus family appears to be widely distributed across several cyanobacterial orders. Our structural and functional characterization of CT pili provide insights into cyanobacterial cell morphology, physiology, and toxin interactions, and identify potential targets for disrupting bloom formation.

Cryoelectron microscopy↗

Perpendicular magnetofluid theory for magnetically confined plasmas in the collisionless limit

Note that the magnetically confined plasmas in thermonuclear fusion turn to be collisionless. Some particles are trapped by the inhomogeneous equilibrium field or by the waves, while some others keep circulating. One cannot expect the charged particles to be collectively localized in space by collisions along the magnetic field lines. Consequently, the fluid parameters relating to the parallel motion, such as parallel fluid velocity, become inadequate. In this paper, the perpendic- ular magnetofluid theory for magnetically confined plasmas in the collisionless limit is developed. It revises Braginskii’s transport theory by releasing the collisional dominance assumption. In the perpendicular direction, the particle spatial localization is solo resulted from the strong magnetic field, while the finite Larmor radius (FLR) effects are taken into account in the next order. In the parallel direction, the particle mobility feature is fully retained by constructing only the per- pendicular moments. Therefore, besides the FLR effects till order O($k$ $^{2}_{⊥}$ $ρ$ $^{2}_{i}$ ), the Landau damping, the trapped particle effects, and other parallel kinetic effects are all kept in the current formalism. Here, k ⊥ is the perpendicular wave number and ρ i is the ion Larmor radius. Here, the theory can be used both for the analytical and numerical studies of magnetically confined plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Throughput Measurements and Profile Analysis of Cloud Networks

Cloud networks utilize virtual connections to connect virtual machines distributed across cloud sites. They are increasingly deployed due to flexible provisioning using software and cost-effectiveness in not requiring to build physical network infrastructure. However, their extensive virtualization makes it unclear how well the established practices of conventional networks translate to them. Here, we study throughput measurements over a Google Cloud network using a matching hardware emulated conventional network, which provide production and exploratory conditions, respectively. The measurements span connections representing local, cross-continental and around the Earth distances. We study the effects of parallel flows, congestion control algorithms and retransmissions on the network throughput profile expressed as a function of RTT. We compare the throughput profile of Google Cloud network with those of emulated network under various loss conditions, including those too disruptive or expensive in the former. Our analysis based on the concave-convex shape and utilization-concavity coefficients of throughput profiles indicates an overall agreement of performance between the two networks, thereby justifying the use of conventional network emulations to analyze cloud networks. In terms of practical use, our study establishes that BBR and BBRv2 alpha TCP achieve higher throughput compared to loss-based congestion control algorithms under most network configurations, especially, under losses at large RTT.

Phanekham, Derek [Southern Methodist Univ., Dallas↗

Integrating PGAS and MPI-based Graph Analysis

This project demonstrates that Chapel programs can interface with MPI-based libraries written in C++ without storing multiple copies of shared data. Chapel is a language for productive parallel computing using global address spaces (PGAS). We identified two approaches to interface Chapel code with the MPI-based Grafiki and Trilinos libraries. The first uses a single Chapel executable to call a C function that interacts with the C++ libraries. The second uses the mmap function to allow separate executables to read and write to the same block of memory on a node. We also encapsulated the second approach in Docker/Singularity containers to maximize ease of use. Comparisons of the two approaches using shared and distributed memory installations of Chapel show that both approaches provide similar scalability and performance.

97 MATHEMATICS AND COMPUTING↗

Evaluation of Graph Analytics Frameworks Using the GAP Benchmark Suite

The analysis of connected data is an increasingly important application in high-performance computing. Such analyses can reveal fraudulent patterns in financial transactions, optimize telecommunications networks, predict information flow in social networks, etc. However, the landscape of graph analytics is highly diverse. Graph algorithms stress processor architectures differently, and no one graph can represent all topologies. Consequently, no single approach or framework is expected to be optimal for all graph analytics problems. To help make sense of this diverse landscape, we evaluated four approaches to graph analytics: GraphBLAS, Galois, BGL17, GraphIt; and compare them against hand-tuned implementations that take advantage of hardware features on our test platform. Graph- BLAS formulates graph analytics as sparse linear algebra. Galois provides syntactic constructs for data parallelism over irregular data structures. BGL17 is a generic C++ template library for implementing graph algorithms. GraphIt provides a domain- specific language to describe and optimize graph algorithms. We use the GAP Benchmark Suite to establish baseline performance and guide the side-by-side evaluation of each framework. GAP consists of 30 tests: six graph analytics algorithms (breadth- first search, single-source shortest path, PageRank, betweenness centrality, connected components, and triangle counting) run on five graphs, each with different topological characteristics (e.g., high diameter, skewed degree distribution, high average degree). High-performance reference implementations are included for each benchmark algorithm. Because a graph can be loaded into memory a number of ways (e.g., flat file on disk, compressed sparse format, data frames, retrieved from SQL or NoSQL databases), our evaluation focused on computational performance rather than I/O. Our results show the relative strengths of each framework.

Graph algorithms, Benchmarking, shared-memory prog↗

Elucidating Drought-Tolerance Mechanisms in Plant Roots through 1H NMR Metabolomics in Parallel with MALDI-MS, and NanoSIMS Imaging Techniques

As direct mediators between plants and soil, roots play an important role in metabolic responses to environmental stresses such as drought, yet these responses are vastly uncharacterized on a plant-specific level, especially for co-occurring species. Here, we aim to examine the effects of drought on root metabolic profiles and carbon allocation pathways of three tropical rainforest species by combining cutting-edge metabolomic and imaging technologies in an in situ position-specific 13C-pyruvate root-labeling experiment. Further, washed (rhizosphere-depleted) and unwashed roots were examined to test the impact of microbial presence on root metabolic pathways. Drought had a species-specific impact on the metabolic profiles and spatial distribution in Piper sp. and Hibiscus rosa sinensis roots, signifying different defense mechanisms; Piper sp. enhanced root structural defense via recalcitrant compounds including lignin, while H. rosa sinensis enhanced biochemical defense via secretion of antioxidants and fatty acids. In contrast, Clitoria fairchildiana, a legume tree, was not influenced as much by drought but rather by rhizosphere presence where carbohydrate storage was enhanced, indicating a close association with symbiotic microbes. This study demonstrates how multiple techniques can be combined to identify how plants cope with drought through different drought-tolerance strategies and the consequences of such changes on below-ground organic matter composition.

Drought, Carbon cycle, MALDI-MSI, Metabolomics, Na↗

Pufferscale: Rescaling HPC Data Services for High Energy Physics Applications

User-space HPC data services are emerging as an appealing alternative to traditional parallel file systems, because of their ability to be tailored to application needs while eliminating unnecessary overheads incurred by POSIX compliance. The High Energy Physics (HEP) community is progressively turning towards such services to enable high-throughput accesses under heavy concurrency to billions of event data produced by instruments and consumed by subsequent analysis workflows. Such services would benefit from the possibility to be rescaled up and down to adapt to changing workloads, as experimental campaigns progress, in order to optimize resource usage. This paper formalizes rescaling a distributed storage system as a multi objective optimization problem considering three criteria: load balance, data balance, and duration of the rescaling operation. We propose a heuristic for rapidly finding a good approximate solution, while allowing users to weight the criteria as needed. The heuristic is evaluated with Pufferscale, a new rescaling manager for microservice-based distributed storage systems. To validate our approach in a real-world ecosystem, we showcase the use of Pufferscale as a means to enable storage malleability in the HEPnOS storage system for HEP applications.

Distributed Storage System↗

Correlating dislocation structures to basal and prismatic slip bands near grain boundaries in tensile-tested Mg–4Al using a multiscale electron microscopy approach

Dislocation structures where basal and prismatic slip bands meet grain boundaries in tensile-tested Mg with 4 wt% Al (Mg–4Al) were studied using a multiscale electron microscopy approach to explore the assumptions made for the dislocation pileup theory: a) slip bands consist of dislocation arrays piling up near grain boundaries, and b) stress concentration in the adjacent grain is solely caused by dislocation pileup. After post-testing electron backscatter diffraction (EBSD) scans, focused-ion-beam (FIB) lift-out specimens were prepared from regions of interest so that the specimen plane is parallel to the bulk sample surface to allow for direct correlation between mesoscale and microscale characterization. High dislocation density and the dislocation arrays in the slip bands corroborated with the first assumption. Evidence of plastic deformation in all grains, however, showed that the second assumption was false. Additionally, dislocation structures including crystal rotation boundaries and dislocations dissociating to the basal plane provide additional stress relief mechanisms near grain boundaries that are not accounted for in many crystal plasticity models, which requires auxiliary models to more accurately predict the stress and strain distribution in a microstructure.

36 MATERIALS SCIENCE↗

Projective Hedging Algorithms for Multistage Stochastic Programming, Supporting Distributed and Asynchronous Implementation

Here we propose a decomposition algorithm for multistage stochastic programming that resembles the progressive hedging method of Rockafellar and Wets but is provably capable of several forms of asynchronous operation. We derive the method from a class of projective operator splitting methods fairly recently proposed by Combettes and Eckstein, significantly expanding the known applications of those methods. Our derivation assures convergence for convex problems whose feasible set is compact, subject to some standard regularity conditions and a mild “fairness” condition on subproblem selection. The method’s convergence guarantees are deterministic and do not require randomization, in contrast to other proposed asynchronous variations of progressive hedging. Computational experiments described in an online appendix show the method to outperform progressive hedging on large-scale problems in a highly parallel computing environment.

97 MATHEMATICS AND COMPUTING↗

P SI4 1.4: Open-source software for high-throughput quantum chemistry

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree–Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4 's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. We announce a rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Symmetry-resolved CO desorption and oxidation dynamics on O/Ru(0001) probed at the C K-edge by ultrafast X-ray spectroscopy

In this work, we report on carbon monoxide desorption and oxidation induced by 400 nm femtosecond laser excitation on the O/Ru(0001) surface probed by time-resolved X-ray absorption spectroscopy (TR-XAS) at the carbon K-edge. The experiments were performed under constant background pressures of CO (6x10 -8 Torr) and O 2 (3x10 -8 Torr). Under these conditions, we detect two transient CO species with narrow 2π* peaks, suggesting little 2π* interaction with the surface. Based on polarization measurements, we find that these two species have opposing orientations: (1) CO favoring a more perpendicular orientation and (2) CO favoring a more parallel orientation with respect to the surface. We also directly detect gas-phase CO 2 using a mass spectrometer and observe weak signatures of bent adsorbed CO 2 at slightly higher X-ray energies than the 2π* region. These results are compared to previously reported TR-XAS results at the O K-edge where the CO background pressure was three times lower (2x10 -8 Torr) while maintaining the same O 2 pressure. At the lower CO pressure, in the CO 2π* region, we observed adsorbed CO and a distribution of OC-O bond lengths close to the CO oxidation transition state, with little indication of gas-like CO. The shift towards 'gas-like' CO species may be explained by the higher CO exposure, which blocks O adsorption, decreasing O coverage and increasing CO coverage. These effects decrease the CO desorption barrier through dipole-dipole interaction, while simultaneously increasing the CO oxidation barrier.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Investigation of turbulent inflow specification in Euler–Lagrange simulations of mid-field spray

The process of atomization of a liquid jet by a parallel high-speed gas stream results in a spray, whose downstream development is of considerable interest to several applications. The round jet spray can be spatially divided into (i) a near-field (near-nozzle) region of liquid atomization and (ii) a downstream mid-field region of fully-dispersed droplets. In order to accurately model mid-field droplet dispersion, this work aims at developing a rigorous and robust injection model for Euler–Lagrange spray simulations. Results from experiments are used to obtain the relevant droplet number density, size distribution, and mean and standard deviation velocity distributions of the injection model, systematically in a step-by-step process. Two-phase large eddy simulations are performed by stochastically generating the Lagrangian droplets at the inlet of the mid-field region. Number flux, diameter distribution, mean velocity, and other time-averaged statistics at several downstream locations are shown to agree well with the corresponding experimental data.

42 ENGINEERING↗

Cold-hot coupled waves in a flowing magnetized plasma

Abstract Nonlinear coupling of cold and hot waves in a flowing magnetized plasma is analyzed with the Vlasov equation. An analytical solution is obtained for cold waves of a small amplitude (weak flow) and a long wavelength. The distribution function is obtained by integrating the kinetic equation along a perturbed phase-space trajectory for a time-varying plasma flow. The kinetic description presents a generalized dispersion relation that involves resonances depending on cold and hot wave dispersions. Coherent fluid motion leads to radiation peaks in addition to the cyclotron harmonics, where the wavenumber of the cold wave determines the peak frequencies. The peaks appear narrow when the wave propagates perpendicular to the time-averaged flow while they become broad due to the Doppler effect when the wave propagates parallel to the flow. Fully kinetic particle-in-cell simulations corroborate the theoretical predictions. The dispersion relation and resulting wave spectra provide information about plasma parameters and flow properties.

Physics↗

Performance-Aligned LLMs for Generating Fast HPC Code

Optimizing scientific software is a difficult task because codebases are often large and complex, and performance can depend upon several factors including the algorithm, its implementation, and hardware among others. Causes of poor performance can originate from disparate sources and be difficult to diagnose. Recent years have seen a multitude of work that use large language models (LLMs) to assist in software development tasks. However, these tools are trained to model the distribution of code as text, and are not specifically designed to understand performance aspects of code. In this work, we introduce a reinforcement learning based methodology to align the outputs of code LLMs with performance. This allows us to build upon the current code modeling capabilities of LLMs and extend them to generate better performing code. Here, we demonstrate that our fine-tuned model improves the expected speedup of generated code over base models for a set of benchmark tasks from 0.9 to 1.6 for serial code and 1.9 to 4.5 for OpenMP parallel code.

Computer science↗

Variation of the Passive Film on Compositionally Concentrated Dual-Phase Al 0.3 Cr 0.5 Fe 2 Mn 0.25 Mo 0.15 Ni 1.5 Ti 0.3 and Implications for Corrosion

The passive film on a dual-phase Al 0.3 Cr 0.5 Fe 2 Mn 0.25 Mo 0.15 Ni 1.5 Ti 0.3 FCC + Heusler (L2 1 ) compositionally concentrated alloy formed during extended exposure to an applied potential in the passive range in dilute chloride solution was characterized. Each phase, with its own distinct composition of passivating elements, formed unique passive films separated by a heterophase interface. High-resolution, surface sensitive characterization enabled chemical analysis of the passive film formed over individual phases. The film formed over the L2 1 phase had a higher concentration of Al, Ni, and Ti, while the film formed over FCC phase was of similar thickness but contained comparatively higher Cr, Fe, and Mo concentrations, consistent with the differences in bulk microstructure composition. The passive film was continuous across phase boundaries and the distribution of passivating elements (Al, Cr, and Ti) indicated both phases were independently passivated. Spatially resolved analysis of the surface chemistry of the dual-phase CCA revealed that the cation with the highest composition in passive film formed on the FCC phase was Cr (52.4 at. pct) and for the L2 1 phase was Ti (53.1 at. pct) despite the bulk concentration of each element being below 20 at. pct in their respective phases. Al, Cr, and Ti were enriched in both phases within the passive film relative to their respective bulk compositions. In parallel studies, single-phase alloys with compositions representative of the FCC and L2 1 phases were synthesized to evaluate the corrosion behavior of each phase in isolation. The corrosion behavior of the dual-phase alloy showed passivity evidenced by a pitting potential of 0.615 V SCE in 0.01 M NaCl. The pitting potential and other electrochemical parameters suggested a combination of behaviors of both single-phase samples, suggesting that the global corrosion behavior may be represented by a composite theory applied to phases, their area fractions, and interphase length. However, the interphase in the dual-phase CCA was a local corrosion initiation site and may limit localized corrosion protectiveness. The alloy design implications for optimization of second phase structure and morphology are discussed.

36 MATERIALS SCIENCE↗

Investigating the effects of electron bounce-cyclotron resonance on plasma dynamics in capacitive discharges operated in the presence of a weak transverse magnetic field

Recently, Patil et al. [Phys. Rev. Res. 4, 013059 (2022)] have reported the existence of an enhanced operating regime when a low-pressure (5 mTorr) capacitively coupled discharge (CCP) is driven by a very high radio frequency (60 MHz) source in the presence of a weak external magnetic field applied parallel to its electrodes. Their particle-in-cell simulations show that a significantly higher bulk plasma density and ion flux can be achieved at the electrode when the electron cyclotron frequency equals half of the applied radio frequency for a given fixed voltage. In the present work, we take a detailed look at this phenomenon and further delineate the effect of this “electron bounce-cyclotron resonance (EBCR)” on the electron and ion dynamics of the system. We find that the ionization collision rate and stochastic heating are maximum under resonance condition. The electron energy distribution function also indicates that the population of tail-end electrons is highest for the case where EBCR is maximum. Formation of electric field transients in the bulk plasma region is also seen at lower values of applied magnetic field. Finally, we demonstrate that the EBCR-induced effect is a low-pressure phenomenon and weakens as the neutral gas pressure increases. The potential utility of this effect to advance the operational performance of CCP devices for industrial purposes is discussed in this report.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Multiphase Modeling in a Parallel Plate Fluidized Bed Receiver for Concentrating Solar Power

A novel high temperature particle solar receiver is developed by using a light trapping planar cavity configuration. As particles fall through the cavity, the concentrated solar radiation warms the boundaries of the receiver and in turn heats the particles. Particles flow through the system, forming a packed bed at the lower end, leaving the system from the bottom at a constant flow rate. Air is introduced to the system as the fluidizing medium to improve particle heat transfer and mixing. A laboratory scale cavity receiver is built and a near IR quartz lamp is used to provide flux to the vertical wall of the heat exchanger. The system is modeled using a continuum two-fluid method. The computational model matches the experimental system size and the particle size distribution is assumed monodisperse. A conduction model that accounts for the effects of solid concentration is implemented, and the heat flux boundary condition matches the experimental setup. Radiative heat transfer is estimated using a widely used correlation during the post-processing step to determine an overall heat transfer coefficient. The model is validated against testing data and achieves less than 30% discrepancy and a heat transfer coefficient greater than 1000 W/m2K.

CSP↗

Rise and fall of Mott insulating gaps in YNiO 3 paramagnets as a reflection of symmetry breaking and remaking

The YNiO 3 nickelate is a paradigm d-electron oxide that manifests the intriguing temperature-mediated sequence of three phases transitions from (i) magnetically ordered insulator to (ii) paramagnetic (PM) insulator and then to (iii) PM metal. Such phenomena raised the question of the nature of the association of magnetism and structural symmetry breaking with the appearance in (i) and (ii) and disappearance in (iii) of insulating band gaps. It is demonstrated here that first-principles mean-field–like density-functional theory (DFT), driven by molecular dynamics temperature evolution, can describe not only the origin of the magnetically long-range ordered insulating phase (i), but also the creation of an insulating paramagnet (ii) that lacks spin- long-range order, and of a metallic paramagnet (iii) as temperature rises. This approach provides the patterns of structural and magnetic symmetry breaking at different temperatures, in parallel with band gaps obtained when the evolving geometries are used as input to DFT electronic band-structure calculations. This disentangles the complex interplay among spin, charge, and orbital degrees of freedom. Analysis shows that the success in describing the rise and fall of the insulating band gaps along the phase transition sequence is enabled by allowing sufficient flexibility in describing diverse local structural and magnetic motifs as input to DFT. This entails the use of sufficiently large supercells that allow expressing structural disproportionation of octahedra, as well as a description of PM phases as a distribution of local magnetic moments (rather than using a single averaged moment). It appears that the historic dismissal of mean-field–like DFT as being unable to describe such Mott-like transitions was premature, as it was based on consideration of averaged crystallographic unit cells, a description that washes out local symmetry-breaking motifs. The magnetically ordered insulating YNiO 3 phase (i) and the PM insulating phase (ii) result in DFT from allowing symmetry breaking, evident already by considering the athermal internal energy. In contrast, the PM metallic phase (iii) is formed thermally by smearing out thus weakening symmetry breaking. Analysis of snapshots of the different forms of structural vs magnetic symmetry breaking shows that only the loss of the polymorphous distribution of magnetic moments existing in (ii) causes the fall of the band gap, resulting in the metallic state in (iii). Finally, the interesting conclusion is that such a description of the rise [in phases (i) and (ii)] and fall [in phase (iii)] of the insulating gap does not rely on the traditional Mott-like strong correlation understanding, but on breaking and remaking of magnetic and structural symmetries reflected in energy lowering.

36 MATERIALS SCIENCE↗