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At least 127 records · Page 7

A fast two-stage algorithm for non-negative matrix factorization in smoothly varying data

This article reports the study of algorithms for non-negative matrix factorization (NMF) in various applications involving smoothly varying data such as time or temperature series diffraction data on a dense grid of points. Utilizing the continual nature of the data, a fast two-stage algorithm is developed for highly efficient and accurate NMF. In the first stage, an alternating non-negative least-squares framework is used in combination with the active set method with a warm-start strategy for the solution of subproblems. In the second stage, an interior point method is adopted to accelerate the local convergence. The convergence of the proposed algorithm is proved. The new algorithm is compared with some existing algorithms in benchmark tests using both real-world data and synthetic data. Furthermore, the results demonstrate the advantage of the algorithm in finding high-precision solutions.

interior point method↗

Controlled electrochemical nutrient delivery to enhance marine primary productivity

Oceanic photosynthesis contributes to approximately half of the Earth’s net annual primary productivity. Marine photosynthetic productivity has a high degree of heterogeneity due to spatial and temporal co-limitations of light, temperature, and/or nutrients. Across coastal, near-shore, and open ocean regions, insufficient concentrations of key nutrients (e.g., N, P, Fe) can limit primary productivity. Although studies have shown a significant increase in primary productivity with the addition of low doses of trace nutrients, a sustainable approach to reliably deliver and maintain low doses of nutrients and ensure their bioavailability, remains a challenge. Chemical nutrient addition has relied on the use of chelating agents to ensure nutrient bioavailability, but synthetic chelators are persistent environmental pollutants. In this study, we demonstrate for the first time the use of a controlled electrochemical nutrient delivery (CEND) approach to accelerate the growth of phytoplankton without the need for such chelators. Our study uses commercial stainless-steel electrodes to deliver low concentrations of iron to enhance growth rates in the microalga Picochlorum celeri TG2. To demonstrate the process control offered by the CEND method, we evaluate iron delivery as a function of pulse time, pulse frequency, and rest time between pulses. Our data show that at the same total Fe dose of 163 ppb, electrochemical iron delivery can achieve 9.54 ± 0.58 mg biomass/µg Fe, which is comparable to 9.14 ± 0.17 mg biomass/µg Fe achieved with chemical iron additions that include the synthetic chelating agent ethylenediaminetetraacetic acid (EDTA). Further, when different total iron doses (163 ppb, 325 ppb, and 650 ppb) were delivered over 72 h using CEND, biomass yield per iron dose was higher at lower doses: 9.54 ± 0.58 mg biomass/µg Fe at 163 ppb vs. 4.32 ± 0.32 mg biomass/µg Fe at 650 ppb. This highlights the benefits of CEND in delivering frequent and low doses of nutrients for improved process efficiency. Preliminary assessments show both lower cost and reduced greenhouse gas emissions from electrochemical over chemical iron additions with EDTA. The CEND approach opens new pathways to enhance marine primary productivity, without the unintended environmental impacts of synthetic chelators.

analytical chemistry↗

Correlated solvent coordinates accelerate multi-donor proton-coupled electron transfer

The rate of charge transfer within a discrete donor–acceptor (D/A) pair is well-described by semi-classical electron transfer theory, but the effects of multiple equivalent redox sites remain less understood. We report a series of ground-state intramolecular proton-coupled electron transfer (PCET) complexes designed to isolate the effects of donor number, N, while holding geometry, coupling, and driving forces constant. The [Ru(L) 3−N (OH) N ] 2+ complexes incorporate one, two, or three identical phenolic electron donors linked to Ru through rigid phenanthroline bridges (OH = 2,4-di-tert-butyl-6-(1-methyl-1H-imidazo[4,5-f][1,10]phenanthrolin-2-yl)phenol). Upon flash photolysis and oxidative quenching with methyl viologen (MV 2+ ), the transient Ru(III) oxidizes an appended phenol by PCET with the hydrogen-bonded imidazole nitrogen atom functioning as the base. The rate increased by 3.4-fold and 5.7-fold (1.7-fold and 1.9-fold after statistical correction) for two- and three-donor complexes compared to the single-donor system. The supra-statistical acceleration is attributed to a reduced effective outer sphere reorganization energy (λ m ) modeled by a partially shared solvent reaction coordinate, in which a subset of solvent dipoles is already oriented to stabilize charge from any donor. The final phenoxyl radical state is localized due to the transfer of a proton, and the recombination reaction with the viologen radical is not accelerated. These results demonstrate the effects of solvent dynamics on intramolecular PCET rates, offering a new strategy for the design of synthetic charge transfer systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Community-Driven Metadata Standards for Agricultural Microbiome Research

Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of “required” and “desirable” metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for describing agricultural microbiome studies. We begin by briefly reviewing existing metadata standards relevant to agricultural microbiome research, and describe ongoing efforts to enhance the potential for integration of data across research studies. Our goal is not to delineate a fixed list of metadata requirements. Instead, we hope to advance the field by providing a starting point for discussion, and inspire researchers to adopt standardized procedures for collecting and reporting consistent and well-annotated metadata for agricultural microbiome research.

59 BASIC BIOLOGICAL SCIENCES↗

MONTE CARLO CROSS SECTION LOOKUP KERNEL FOR THE CEREBRAS WSE-2 IN CSL

This is a small kernel that was used to collect data for an upcoming paper. We would like to have the code be open source so that the reviewers (and then readers) of the paper can see the whole code, and can reproduce/verify our results. This is not a fully featured application, it cannot produce any useful simulation results, it just executes a small abstracted kernel using synthetic data. The purpose of the kernel is to understand the basic performance characteristics of an HPC kernel on novel AI accelerator architectures. The main kernel is written in the CSL coding language for use with the Cerebras WSE-2 AI accelerator. The kernel represented is the Monte Carlo cross section lookup kernel, which is a small kernel used by the Monte Carlo neutral particle transport algorithm. There is also a baseline kernel written in CUDA that we will include in the repository to form a basis for comparing the WSE-2 to GPU.

Tramm, John↗

Thrust measurements of a hollow-cathode discharge

Thrust measurements of a hollow cathode mercury discharge were made with a synthetic mica target on a torsion pendulum. Thrust measurements were made for various target angles, tip temperatures, flow rates, keeper discharge powers, and accelerator electrode voltages. The experimental thrust data are compared with theoretical values for the case where no discharge power was employed.

Snyder, A.↗

Bat554: Machine Learning for Accelerated Life Prediction and Cell Design

This presentation describes work associated with the early prediction of life and failure modes using machine learning. Key areas which will be highlighted are the generation of synthetic data, the use of deep learning and other machine learning models and the use of machine learning to train life prediction models.

25 ENERGY STORAGE↗

Ground Motion Models (GMMs) Improvements Using Earthquake Simulations on High Performance Computers

A computationally efficient simulation platform was developed that can provide representative synthetic ground motions from crustal earthquakes in the Stable Continental Regions of Central and Eastern US (CEUS), using 3D modeling and high-performance computing. The main objective was to use synthetic ground motion to provide constrains to refinements of exiting ergodic Ground Motion Models (GMMs), for large magnitude earthquakes and near-fault distances, for which these models are less reliable. Physics-based broadband (0-5Hz) ground motion simulations were used to estimate the near-fault ground motion amplitudes and within event and between-event variabilities associated with fault rupture characteristics. As part of a strategy for selecting a reginal velocity model and validation of developed rupture modeling technique, ground motions from the moment magnitude Mw5.0 November 7, 2016, Cushing Oklahoma, and Mw5.8 September 3, 2016, Pawnee Oklahoma earthquakes were simulated. In our simulations we used a 3D regional velocity model that was based on Saikia’s 1D velocity model. Saikia’s model demonstrated better performance in modelling high frequency regional wave propagation for CEUS region. The proposed 3D model includes lateral variations added to the 1D background model using the stochastic scheme of Pitarka and Mellors. Comparisons of the simulations with recordings of both earthquakes demonstrated the reliability of our deterministic simulation approach while emphasizing the importance of including small-scale variability in the regional velocity model needed to reproduce the observed high-frequency wave scattering effects. As part of validation analysis, comparisons with different GMMs for a Mw6.5 earthquake in the CESUS region resulted in a very good match between the simulated and empirical ground motion models. Initial investigations of within-event and between-event ground motion variabilities for Mw6.5 scenario earthquakes on a strike-slip fault, suggest that they are strongly related to spatial slip and slip rate variations, average rupture velocity, rupture area and rupture initiation location. For certain scenarios we found that the ground motion variability observed at near-fault distances (< 5 km) also persists at longer distances. Regardless of the rupture scenario, the simulated ground motion tends to fully saturate at short distances and for all periods. The near-fault saturation has to do with the attenuation of waves propagating along the fault and local rupture radiation pattern that also contribute to stronger ground motion variation at such distances. Analysis of effects of rupture initiation location suggest that the peak ground motion (PGV) and spectral acceleration (SA) can be quite variable due to rupture directivity effects. Such effects are stronger at periods longer than 1s. The effect of the 1D velocity models and surface topography on simulated ground motion were investigated by comparing three component synthetic seismograms computed at selected sites. Effect of surface topography was considered using the ratio between spectral accelerations simulated for two 1D models with flat surface topography and realistic model with surface topography. Overall, the topography slightly amplifies (by ~30%) the ground motion amplitude in the frequency range 1-3Hz. The effect of topography is more visible in the surface and coda waves portion of the seismograms.

58 GEOSCIENCES↗

A graph-based network for predicting chemical reaction pathways in solid-state materials synthesis

Abstract Accelerated inorganic synthesis remains a significant challenge in the search for novel, functional materials. Many of the principles which enable “synthesis by design” in synthetic organic chemistry do not exist in solid-state chemistry, despite the availability of extensive computed/experimental thermochemistry data. In this work, we present a chemical reaction network model for solid-state synthesis constructed from available thermochemistry data and devise a computationally tractable approach for suggesting likely reaction pathways via the application of pathfinding algorithms and linear combination of lowest-cost paths in the network. We demonstrate initial success of the network in predicting complex reaction pathways comparable to those reported in the literature for YMnO 3 , Y 2 Mn 2 O 7 , Fe 2 SiS 4 , and YBa 2 Cu 3 O 6.5 . The reaction network presents opportunities for enabling reaction pathway prediction, rapid iteration between experimental/theoretical results, and ultimately, control of the synthesis of solid-state materials.

36 MATERIALS SCIENCE↗

Probing growth of metal–organic frameworks with X-ray scattering and vibrational spectroscopy

Nucleation and crystallization arising from liquid to solid phase are involved in a multitude of processes in fields ranging from materials science to biology. Controlling the thermodynamics and kinetics of growth is advantageous to help tune the formation of complex morphologies. In this report, we harness wide-angle X-ray scattering and vibrational spectroscopy to elucidate the mechanism for crystallization and growth of the metal–organic framework Co-MOF-74 within microscopic volumes enclosed in a capillary and an attenuated total reflection microchip reactor. The experiments reveal molecular and structural details of the growth processes, while the results of plane wave density functional calculations allow identification of lattice and linker modes in the formed crystals. Synthesis of the metal–organic framework with microscopic volumes leads to monodisperse and micron-sized crystals, in contrast to those typically observed under bulk reaction conditions. Reduction in the volume of reagents within the microchip reactor was found to accelerate the reaction rate. The coupling of spectroscopy with scattering to probe reactions in microscopic volumes promises to be a useful tool in the synthetic chemist's kit to understand chemical bonding and has potential in designing complex materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Development of a deep learning based automated data analysis for step-filter x-ray spectrometers in support of high-repetition rate short-pulse laser-driven acceleration experiments

We present a deep learning based framework for real-time analysis of a differential filter based x-ray spectrometer that is common on short-pulse laser experiments. The analysis framework was trained with a large repository of synthetic data to retrieve key experimental metrics, such as slope temperature. With traditional analysis methods, these quantities would have to be extracted from data using a time-intensive and manual analysis. Furthermore, this framework was developed for a specific diagnostic, but may be applicable to a wide variety of diagnostics common to laser experiments and thus will be especially crucial to the development of high-repetition rate (HRR) diagnostics for HRR laser systems that are coming online.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A divergent synthetic route to functional copolymer libraries via modular polymers

High-throughput polymer synthesis enables rapid exploration of chemical space but remains limited by batch-to-batch inconsistencies that can obscure structure–property relationship trends. To address this challenge, we developed a synthetic approach to produce multifunctional copolymers using post-polymerization modification of activated ester modular polymers with commercially available amines. Easily derivitized parent polymers—poly(tetrafluorophenyl acrylate) and poly(tetrafluorophenyl styrene sulfonate)—were synthesized by RAFT polymerization to yield single polymer batches containing highly reactive tetrafluorophenyl esters or sulfonate esters on each repeat unit. Tuning post-polymerization modification reaction conditions enabled the addition of sub-stoichiometric amounts of amines (relative to the repeat unit) to yield partially functionalized intermediates that could then be further derivatized. Reaction monitoring by 19 F NMR spectroscopy confirmed good control over these sequential post-polymerization modifications. This synthetic route produced a variety of copolymers with defined comonomer ratios while preserving the underlying polymer structure (degree of polymerization, dispersity, tacticity) for both the acrylate and styrene sulfonate backbones. We further applied this approach in a divergent manner to create a small library of structurally distinct copolymers from a single parent batch in three synthetic steps. This modular, divergent synthesis demonstrates a general route to structurally consistent copolymer libraries that enable systematic studies of structure–property relationships and can accelerate functional materials discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Developing Multi-Gene CRISPRa/I Programs to Accelerate DBTL Cycles in ABF Hosts Engineered for Chemical Production (CRADA 468)

Bacterial metabolism is comprised of large and complex gene networks that can produce valuable chemical products. Sophisticated organism engineering efforts are required to optimize production of high-value compounds from these networks. In principle, synthetic multi-gene transcriptional programs could be constructed to reengineer these networks for efficient industrial chemical production. In practice, however, our incomplete ability to understand and model the underlying networks, combined with our limited ability to predictably control the expression of multiple genes makes achieving this goal difficult. To overcome these challenges, we will combine new CRISPR-Cas multi-gene expression programs with computational modeling, machine learning, and multi-omics data to enhance the efficacy of design-build-test-learn (DBTL) cycles. For industrially promising microorganisms in early stages of development, creating technologies for rapidly engineering complex multi-gene programs could be transformative for accelerating data- and model-driven strain design. New CRISPR-Cas tools allow programmable gene activation (CRISPRa) or repression (CRISPRi) at multiple genes simultaneously, using the catalytically inactive Cas9 protein (dCas9) with guide RNAs that recognize DNA targets through predictable Watson-Crick base pairing. To enable accelerated DBTL cycles, we will combine these technologies with advanced Agile BioFoundry (ABF) capabilities for multi-omics data collection and machine learning. We will demonstrate the immediate applicability of these tools by rapidly improving the production of an industrial aromatic in multiple ABF organisms. We recently identified and optimized new transcriptional activators that can be linked to programmable CRISPR-Cas DNA binding domains to activate gene expression in E. coli. We can now use these CRISPRa tools as generalizable trans-acting regulators for combinatorial multi-gene expression tuning that can be easily transferred to new pathways and networks without additional genome engineering. We anticipate these tools will also transfer to new hosts. We have recently found that CRISPRa systems developed in E. coli can be readily ported to Pseudomonas putida, suggesting that multi-gene CRISPRa/i programs for diverse ABF organisms may be within reach.

59 BASIC BIOLOGICAL SCIENCES↗

A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens

At its current rate, the rise of antimicrobial-resistant (AMR) infections is predicted to paralyze our industries and healthcare facilities while becoming the leading global cause of loss of human life. With limited new antibiotics on the horizon, we need to invest in alternative solutions. Bacteriophages (phages)–viruses targeting bacteria–offer a powerful alternative approach to tackle bacterial infections. Despite recent advances in using phages to treat recalcitrant AMR infections, the field lacks systematic development of phage therapies scalable to different applications. We propose a Phage Foundry framework to establish metrics for phage characterization and to fill the knowledge and technological gaps in phage therapeutics. Coordinated investment in AMR surveillance, sampling, characterization, and data sharing procedures will enable rational exploitation of phages for treatments. A fully realized Phage Foundry will enhance the sharing of knowledge, technology, and viral reagents in an equitable manner and will accelerate the biobased economy.

59 BASIC BIOLOGICAL SCIENCES↗

Design of Ternary Correlation Filters to Reduce Probability of Error

The problem of designing ternary phase and amplitude filters (TPAF's) that reduce the probability of image misclassification for a two-class image set is studied. The Fisher ratio is used as a measure of the correct classification rate, and an attempt is made to maximize this quantity in the filter designs. Given the nonanalytical nature of the design problem, a simulated annealing optimization technique is employed. Computer simulation results are presented for several cases including single in-class and out-of-class image sets and multiple image sets corresponding to the design of synthetic discriminant function filters. Significant improvements are found in expected rates of correct classification in comparison to binary phase-only filters and other TPAF designs. Approaches to accelerate the filter design process are also discussed.

Downie, John D.↗

Synthetic aperture radar imaging of moving ocean waves

A theory for the radar imaging of ocean waves is presented under the assumptions that a swell propagates through an ensemble of Bragg scatterers and that the integration time of the synthetic aperture radar (SAR) is small compared to the angular velocity of the swell. Results are presented which show image development and distortions caused by the radial velocities and accelerations of the swell. Neglecting small wave bunching and tilts due to the longer underlying waves, and considering only one-dimensional geometries, the mechanism of wave motions are considered and their efforts on the production of the usual intensity pattern representing the wave image are studied. The analysis shows that in certain situations a processed image can appear which has twice the spatial period of the actual long wave on the ocean, which can confuse the interpretation of ocean wave analysis.

Swift, C. T.↗

Electrochemically induced crystallization of amorphous materials in molten MgCl2: boron nitride and hard carbon

A novel and versatile strategy for the amorphous-to-crystalline transformation of boron nitride (BN) with the capability to control the degree of crystallization was developed through an electrochemical pathway using MgCl 2 at low temperature (750 °C). This procedure can be extended to the transformation of amorphous carbon to graphite, which significantly reduces the energy and cost, accelerates the synthesis process and could potentially replace industrial graphite synthesis globally. Therefore, the synthesized graphite exhibits much enhanced electrochemical performance at high charge–discharge rates (5C) compared to commercial synthetic graphite.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Energetic Electrons Accelerated and Trapped in a Magnetic Bottle above a Solar Flare Arcade

Where and how flares efficiently accelerate charged particles remains an unresolved question. Recent studies revealed that a “magnetic bottle” structure, which forms near the bottom of a large-scale reconnection current sheet above the flare arcade, is an excellent candidate for confining and accelerating charged particles. However, further understanding its role requires linking the various observational signatures to the underlying coupled plasma and particle processes. Here we present the first study combining multiwavelength observations with data-informed macroscopic magnetohydrodynamics and particle modeling in a realistic eruptive flare geometry. The presence of an above-the-loop-top magnetic bottle structure is strongly supported by the observations, which feature not only a local minimum of magnetic field strength but also abruptly slowing plasma downflows. It also coincides with a compact above-the-loop-top hard X-ray source and an extended microwave source that bestrides the flare arcade. Spatially resolved spectral analysis suggests that nonthermal electrons are highly concentrated in this region. Our model returns synthetic emission signatures that are well matched to the observations. The results suggest that the energetic electrons are strongly trapped in the magnetic bottle region due to turbulence, with only a small fraction managing to escape. The electrons are primarily accelerated by plasma compression and facilitated by a fast-mode termination shock via the Fermi mechanism. Our results provide concrete support for the magnetic bottle as the primary electron acceleration site in eruptive solar flares. They also offer new insights into understanding the previously reported small population of flare-accelerated electrons entering interplanetary space.

79 ASTRONOMY AND ASTROPHYSICS↗