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DOE OSTI2023

X-ray diffraction reveals two structural transitions in szomolnokite

Hydrated sulfates have been identified and studied in a wide variety of environments on Earth, Mars, and the icy satellites of the solar system. The subsurface presence of hydrous sulfur-bearing phases to any extent necessitates a better understanding of their thermodynamic and elastic properties at pressure. End-member experimental and computational data are lacking and are needed to accurately model hydrous, sulfur-bearing planetary interiors. In this work, high-pressure X-ray diffraction (XRD) and synchrotron Fourier-transform infrared (FTIR) measurements were conducted on szomolnokite (FeSO 4 ·H 2 O) up to ~83 and 24 GPa, respectively. This study finds a monoclinic-triclinic (C2/c to P1¯) structural phase transition occurring in szomolnokite between 5.0(1) and 6.6(1) GPa and a previously unknown triclinic-monoclinic (P1¯ to P2 1 ) structural transition occurring between 12.7(3) and 16.8(3) GPa. The high-pressure transition was identified by the appearance of distinct reflections in the XRD patterns that cannot be attributed to a second phase related to the dissociation of the P1¯ phase, and it is further characterized by increased H 2 O bonding within the structure. We fit third-order Birch-Murnaghan equations of state for each of the three phases identified in our data and refit published data to compare the elastic parameters of szomolnokite, kieserite (MgSO 4 ·H 2 O), and blödite (Na 2 Mg(SO 4 ) 2 ·4H 2 O). At ambient pressure, szomolnokite is less compressible than blödite and more than kieserite, but by 7 GPa both szomolnokite and kieserite have approximately the same bulk modulus, while blödite’s remains lower than both phases up to 20 GPa. Furthermore, these results indicate the stability of szomolnokite’s high-pressure monoclinic phase and the retention of water within the structure up to pressures found in planetary deep interiors.

58 GEOSCIENCES↗

DOE OSTI2021

Interpolated Sounding and Gridded Sounding Value-Added Products

Standard Atmospheric Radiation Measurement (ARM) Climate Research Facility sounding files provide atmospheric state data in one dimension of increasing time and height per sonde launch. Many applications require a quick estimate of the atmospheric state at higher time resolution. The INTERPOLATEDSONDE (i.e., Interpolated Sounding) Value-Added Product (VAP) transforms sounding data into continuous daily files on a fixed time-height grid, at 1-minute time resolution, on 332 levels, from the surface up to a limit of approximately 40 km. The grid extends that high so the full height of soundings can be captured; however, most soundings terminate at an altitude between 25 and 30 km, above which no data is provided. Between soundings, the VAP linearly interpolates atmospheric state variables in time for each height level. In addition, INTERPOLATEDSONDE provides relative humidity scaled to microwave radiometer (MWR) observations.The INTERPOLATEDSONDE VAP, a continuous time-height grid of relative humidity-corrected sounding data, is intended to provide input to higher-order products, such as the Merged Soundings (MERGESONDE; Troyan 2012) VAP, which extends INTERPOLATEDSONDE by incorporating model data. The INTERPOLATEDSONDE VAP also is used to correct gaseous attenuation of radar reflectivity in products such as the KAZRCOR VAP.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

2019 Computing Sciences Strategic Plan

Computing has transformed nearly every aspect of scientific inquiry — across disciplines and across scales — from the behavior of subatomic particles to the formation of structures in the early universe, from the assembly of the human genome to the evolution of earth systems. Over the past two decades, computing has become an integral part of how Berkeley Lab is “Bringing Science Solutions to the World.” Advances in computing and mathematics have been key, with new mathematical models of complex physical phenomena, new methods for analyzing complex data, new algorithms for accuracy and scaling and sophisticated software systems that encapsulate these techniques into open, reusable tools. The performance of NERSC computers and the ESnet network have grown by several orders of magnitude, along with our understanding of how to map scientific computations and workflows onto these systems. From research to facility operations, the passion, talent and dedication of the Computing Sciences Area staff has been the cornerstone of our success. The plan outlined in this document describes the next step in a journey to expand the influence and impact of our efforts, building an increasingly connected global enterprise for science that places more powerful instruments in the hands of scientists, along with more powerful methods and tools for modeling, analysis and prediction.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Adaptive Patching for High-resolution Image Segmentation with Transformers

Attention-based models are proliferating in the space of image analytics, including segmentation. The standard method of feeding images to transformer encoders is to divide the images into patches and then feed the patches to the model as a linear sequence of tokens. For high-resolution images, e.g. microscopic pathology images, the quadratic compute and memory cost prohibits the use of an attention-based model, if we are to use smaller patch sizes that are favorable in segmentation. The solution is to either use custom complex multi-resolution models or approximate attention schemes. We take inspiration from Adapative Mesh Refinement (AMR) methods in HPC by adaptively patching the images, as a pre-processing step, based on the image details to reduce the number of patches being fed to the model, by orders of magnitude. This method has a negligible overhead, and works seamlessly with any attention-based model, i.e. it is a pre-processing step that can be adopted by any attention-based model without friction. We demonstrate superior segmentation quality over SoTA segmentation models for realworld pathology datasets while gaining a geomean speedup of 6.9× for resolutions up to 64K2, on up to 2, 048 GPUs.

Zhang, Enzhi↗

DOE OSTI2025

Computational investigation of water glasses using machine-learning potentials

The molecular origins of water’s anomalous properties have long been a subject of scientific inquiry. The liquid–liquid phase transition hypothesis, which posits the existence of distinct low-density and high-density liquid states separated by a first-order phase transition terminating at a critical point, has gained increasing experimental and computational support and offers a thermodynamically consistent framework for many of water’s anomalies. However, experimental challenges in avoiding crystallization near the postulated liquid–liquid critical point have focused attention to water’s canonical glassy states: low-density and high-density amorphous ice. Here, we use two Deep Potential machine-learning models, trained on the Strongly Constrained and Appropriately Normed density functional and the highly accurate Many-Body Polarizable potential, to conduct an investigation of water’s glassy phenomenology based on quantum mechanical calculations. Despite not being explicitly trained on amorphous ices, both models accurately capture the structure and transformation of the water glasses, including their interconversion along different thermodynamic paths. Isobaric quenching of liquid water at various pressures generates a continuum of intermediate amorphous ices and density fluctuations increase near the liquid–liquid critical pressure. The glass transition temperatures of the amorphous ices produced at different pressures exhibit two distinct branches, corresponding to low-density and high-density amorphous ice behaviors, consistent with experiment and the liquid–liquid transition hypothesis. Extrapolating transformation pressures from isothermal compressions to experimental compression rates brings our simulations into excellent agreement with data. Our findings demonstrate that machine-learning potentials trained on equilibrium phases can effectively model nonequilibrium glassy behavior and pave the way for studying long-timescale, out-of-equilibrium processes with quantum mechanical accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

MEUMAPPS (C++ Version)

Many materials, metal alloys in particular, have features on the on micrometer or nanometer scale that have a large impact on the properties of the material. These features are known as the microstructure of the material. Understanding why and how the microstructure forms in a material is of fundamental scientific interest as well as of significant technological interest. The capability to predict microstructure evolution in a material allows the intentional design of microstructures and hence the intentional design of material properties. The phase-field method is one of the leading methods for predicting microstructure evolution. One of the most significant problems for phase-field models is their computational expense. Even limited phase-field simulations can easily require thousands of CPU core-hours to complete, which significantly limits their use. This code provides both a general framework for creating scalable, GPU-accelerated phase-field model applications as well as several applications themselves. The code is capable of using hundreds of GPUs efficiently, which greatly reduces the time required to perform simulations. The code is written with an emphasis on performance portability, that is the ability for the code to run efficiently on a number of different computing architectures without modification of the source code. The performance portability of this code is primarily enabled through the use of two libraries, Kokkos (performance portable data structures and execution patterns) and heFFTe (performance portable distributed 3D fast Fourier transforms). The code consists of a core library, applications, and tests. The core library includes shared functionality between applications. This includes interfaces with fast Fourier transform (FFT) libraries such as heFFTe, data structures based on Kokkos, file input and output capabilities, and a solver for infinitesimal strain mechanical equilibrium problems. Five applications are included in the code. The flagship application is the MEUMAPPS-SS application, which implements the Kim-Kim-Suzuki phase-field model for precipitation for an arbitrary number of phases and components in a metal alloy. Five simpler applications are also included that solve the Eshelby inclusion problem, Allen-Cahn equation, the coupled Allen-Cahn and diffusion equations, and the Cahn-Hilliard equation. The code includes two applications to solve the Cahn-Hilliard equation, one with constant-step-size first-order time integration and the second with adaptive high-order time integration.

DeWitt, Stephen [Oak Ridge National Lab. (ORNL), O↗

DOE OSTI2025

Microreactor Automated Control System Test Bed Digital Architecture for Real-Time, Hardware-in-the-Loop Simulation

This work describes progress made towards the development of a real-time hardware-in-the-loop (HIL) test bed for non-nuclear testing of microreactor control schemes and failure modes. Non-nuclear testing is a crucial step in developing robust control algorithms for managing microreactor dynamics. The creation of an HIL simulation harnesses the realistic dynamics of physical analogue systems while additionally considering the challenges of variable communication delay. This collaborative effort between Oak Ridge National Laboratory and Idaho National Laboratory has resulted in a LabVIEW-based gRPC communication protocol which couples a TRANSFORM Modelica simulation of nuclear components to the ViBRANT physical hardware for realistic feedback and visual representation of control action in real time. A modular python client structure is developed to manage FMU-based Modelica simulation and real-time gRPC communication. HIL testing suggests that the modeled reactor with natural convection molten salt loop coolant configuration responds well to PID control of drum positioning for modulation of reactor core power, however, future efforts will be made to explore the added thermal inertial delay of system level control and downstream demand changes. Development of this platform with a generalized methodology provides a foundation for exploring a variety of reactor configurations and failure modes in rapid order to provide insight into the most effective avenues of study for further research and development.

McConnell, Jono [ORNL] (ORCID:0000000238984741)↗

DOE OSTI2022

An algorithmic approach to predicting mechanical draft cooling tower fan speeds from infrasound signals

Mechanical draft cooling towers (MDCTs) serve a critical heat management role in a variety of industries. For nuclear reactors in particular, the consistent, predictable operation of MDCTs is required to avoid damage to infrastructure and reduce the potential for catastrophic failure. Accurate, reliable measurement of MDCT fan speed is therefore an important maintenance and safety requirement. To that end, we have developed an algorithm for automatically predicting the rotational speeds of multiple, simultaneously operating fan rotors using contactless, infrasound measurements. The algorithm is based on identifying the blade passing frequencies (BPFs), their harmonics, as well as the motor frequencies (MFs) for each fan in operation. Using the algorithm, these frequencies can be automatically identified in the acoustic waveform’s short-time Fourier transform spectrogram. Attribution is aided by a set of filters that rely on the unique spectral and temporal characteristics of fan operation, as well as the intrinsic frequency ratios of the BPF harmonics and the BPF/MF signals. The algorithm was tested against infrasound data acquired from infrasound sensors deployed at two research reactors: the Advanced Test Reactor (ATR) located at Idaho National Laboratory (INL) and the High Flux Isotope Reactor (HFIR) located at Oak Ridge National Laboratory (ORNL). After manually identifying the MDCT gearbox ratio, the algorithm was able to quickly yield fan speeds at both reactors in good agreement with ground truth. Ultimately, this work demonstrates the ease by which MDCT fans may be monitored in order to optimize operational conditions and avoid infrastructure damage.

42 ENGINEERING↗

DOE OSTI2021

Directional amorphization of covalently-bonded solids: A generalized deformation mechanism in extreme loading

Shock compression subjects materials to a unique regime of high quasi-hydrostatic pressure and coupled shear stresses for durations on the order of 1–10 nanoseconds for laser-driven loading of samples. There is, additionally, an attendant temperature increase due to the shock and the mechanisms of plastic deformation in metals whereby dislocations, twins, and phase transitions nucleate and propagate at velocities near the sound speed. Covalently bonded materials have, by virtue of the directionality of their bonds, great difficulty in responding by conventional plastic deformation to this extreme regime of shock compression. Here, we propose that the shear from shock compression induces amorphization, as observed in Si, Ge, B4C, SiC, and olivine ((Mg, Fe) 2 SO 4 ) and that this is a general deformation mechanism in a broad class of covalently bonded materials. The crystalline structure transforms to amorphous along regions of maximum shear stress, forming nanoscale bands, and thereby relaxing the shear component of the imposed shock stress. This process is usually preceded by the emission and propagation of a critical concentration of dislocations.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Aromatic heterobicycle-fused porphyrins: impact on aromaticity and excited state electron transfer leading to long-lived charge separation

A new synthetic method to fuse benzo[4,5]imidazo[2,1-a]isoindole to the porphyrin periphery at the β,β-positions has been developed, and its impact on the aromaticity and electronic structures is investigated. Reactivity investigation of the fused benzoimidazo-isoindole component reveals fluorescence quenching of a zinc porphyrin (AMIm-2) upon treatment with a Brønsted acid. The reaction of the zinc porphyrin (AMIm-2) with methyl iodide initiated a new organic transformation, resulting in the ring-opening of isoindole with the formation of an aldehyde and dimethylation of the benzoimidazo component. The fused benzoimidazo-isoindole component acted as a good ligand to bind platinum(II), forming novel homobimetallic and heterobimetallic porphyrin complexes. The fusion of benzoimidazo-isoindole on the porphyrin ring resulted in bathochromically shifted absorptions and emissions, reflecting the extended conjugation of the porphyrin π-system. Time-resolved emission and transient absorption spectroscopy revealed stable excited state species of the benzoimidazo-isoindole fused porphyrins. Zinc porphyrin AMIm-2 promoted excited state electron transfer upon coordinating with an electron acceptor, C60, generating a long-lived charge-separated state, in the order of 37.4 μs. The formation of the exceptionally long-lived charge-separated state is attributed to the involvement of both singlet and triplet excited states of AMIm-2, which is rarely reported in porphyrins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Analysis of microplastics in bivalves along Fourmile Branch

Microplastics are commonly found near wastewater treatment facilities with the source originating typically from fibers associated with laundry detergents. Fourmile branch would have limited laundry associated effluent and does not receive any input from water originating from upstream industry sources, therefore microplastics would have originated from Site operations or through atmospheric deposition which are both unexplored pathways. In order to assess environmental inventory effects on the biota, water samples were collected from sampling locations along Fourmile Branch on the Savannah River Site using plankton nets and grab samples at Fourmile Branch locations (i.e., FM-2B, FM-A7, and FM6). Fourmile Branch has a long history of receiving industrial effluents from site operations as well effluent from the site’s wastewater treatment plant. Water samples and the debris collected in the nets were rinsed with deionized water and sieved to remove the larger fractions of plastics (4000-2000 µm) and retain fractions <500 µm. The water samples were analyzed for the type and size of plastics by μ-Raman, mass spectrometry, and Fourier Transform Infrared Spectroscopy (FTIR) methods. Previously collected bivalves were prepared into thin sections and analyzed using microscopy.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Catalytic Transformation of Positional Nitrophenol Isomers on Highly Active Ag/Linde‐Type A4 Zeolite: A Comparative Analysis

Abstract The catalytic transformation of ortho‐( o‐ NP), meta‐( m‐ NP) and para‐nitrophenols ( p‐ NP) by Ag nanoparticles (Ag‐NPs) stabilised on zeolite A4 (ZA4) is presented for the first time. The catalysts are prepared by microwave‐assisted synthesis (Ag/ZA4‐MW) or ion exchange (Ag/ZA4‐IE). The results indicate that the nitrophenol reduction rate depends on the molecule structure and the presence of low‐coordinated metallic Ag‐NPs (∼2 nm and sub nanometric species). Meanwhile, the reactivity tendency depends on the synthesis methodology ( m‐ NP> p‐ NP> o‐ NP and o‐ NP> m‐ NP> p‐ NP for Ag/ZA4‐MW and Ag/ZA4‐IE, respectively). The turnover frequency (TOF) values estimated for nitrophenols reduction are superior for Ag/ZA4‐MW catalyst by several orders of magnitude compared with those obtained for Ag/ZA4‐IE catalyst. In addition, the catalyst exhibits remarkable catalytic stability for the reduction of p‐ NP even after the fifth consecutive catalytic run. The presently prepared catalysts are characterised by superior catalytic activity for the reduction of nitroaromatic compounds than similar Ag‐based materials reported in the literature.

Horta‐Fraijo, Patricia↗

DOE OSTI2021

A critical dislocation velocity for serration mechanism transition in a nickel-chromium solid solution alloy

Here, the influence of strain rate across three orders of magnitude (1.70 × 10 –5 /s to 1.43 × 10 –2 /s) along with the effect of the plastic strain accumulation (up to 10%) on the serrated plastic flow were investigated in the nickel-chromium (Ni-Cr) solid solution alloy Nimonic 75 by performing constant-strain-rate tension testing at 600 °C. As the strain rate decreased, the critical strain for the onset of serrations transitioned from normal behavior to inverse behavior. The serrated flow was characterized as Type A+B serration at high strain rate (1.43 × 10 –2 /s). In the intermediate strain-rate regime (1.43 × 10 –3 /s and 1.45 × 10 –4 /s), Type B serrations were observed and followed by a transformation to Type C+B serrations. At the low strain rate (1.70 × 10 –5 /s), the plastic flow immediately displayed Type C serrations, which later evolved into Type C+B serrations. Regardless of the strain rate, plastic strain, or dislocation density, a critical dislocation velocity falling in the range of 1.2 × 10 –6 – 2.2 × 10 –6 m/s was identified to signify the onset of Type C serration, whereby the mobile dislocations break free from the solute cloud for short bursts of deformation. Finally, a novel model by solute rearrangement across dislocation cores was used to understand how the critical dislocation velocity is quantitatively determined by the rate at which solute atoms are able to hop across the glide plane as a partial dislocation core moves through the lattice.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Models and Strategies for Optimal Demand Side Management in the Chemical Industries

Deregulation and the increase of renewable electricity generation from wind and solar photovoltaics have transformed the U.S. electricity market. Economic and environmental benefits notwithstanding, the presence of renewables has increased variability and uncertainty on the supply side of the grid. Managing demand, rather than generation – a strategy referred to as “demand response (DR)” – is an attractive approach for mitigating this imbalance. DR efforts aim to reduce electricity usage during peak demand times, lessening stress on the grid. Industrial users are particularly attractive entities for DR participation since they present large, localized loads that can provide significant relief on grid demand and –unlike other large loads, such as buildings – are minimally dependent on human needs and preferences. In this project, we accomplished three main objectives. (1) We developed data-driven low-order DR scheduling-relevant dynamic models of chemical processes. Concurrently, we studied the formulation and solution of the associated optimal DR production scheduling problems. (a) A prototype air separation unit (ASU) model was used to generate simulated operating data for initial modeling efforts, which enabled the later use of industrial data for data-driven modeling. (b) We utilized Hammerstein-Wiener (HW) and Finite Step Response (FSR) models to represent nonlinear plant dynamics. (c) The HW models were linearized using exact linearization so they could potentially be embedded in power system models, which are formulated as mixed integer linear programs (MILPs). (d) We solved DR optimization problems under uncertainty and found that even naïve predictions of electricity price and product demand led to significant cost savings benefits. (2) Our DR scheduling optimization problem formulations are amenable to real-time solution. (a) We utilized Lagrangian Relaxation (LR) to efficiently solve the optimization problem by decoupling subproblems linked by complicating constraints. (b) We have achieved computation times for the 3-day DR scheduling problem of an ASU as low as 1.88 minutes. (3) Our representations of the DR behavior of chemical process as grid-level batteries were embedded in power system models. (a) For a small-scale grid, we found that incorporating the dynamics of the chemical plant in the optimal power flow calculations resulted in better resource management leading to up to 15% and 46% cost reduction for the grid and chemical plant operations, respectively, during periods of power line congestion. We have published several works dedicated to modeling and solving DR optimization problems from the user side. These were published in top peer-reviewed journals and are summarized in this report. The most recent work (and papers in preparation) considers DR scheduling from the grid side. Future efforts will consider networked plants (e.g., air separation units operating on a common pipeline) for DR participation, which is expected to amplify the capabilities of industrial DR participants to perform load-shifting. Our consideration of uncertainty in DR has inspired future directions in this area as well: we plan to develop multistage methods to fully account for the effects of uncertainty in DR scheduling.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

Far-infrared absorption of undoped and Br-doped carbon nanofiber powder in stacked-cup cone configuration

In this study, we performed room-temperature far-infrared (40–650cm –1 ) transmission measurements on undoped and bromine-doped powder samples of carbon nanofibers in stacked-cup cone geometry. The transmission spectra show enhanced transmittance after bromine doping and all spectra were fit to a Drude-Lorentz (DL) model. A decreased metallic conductivity along with a redshift of the lowest semiconducting gap was found with doped samples. A significant decrease in the scattering rate upon heavy doping has been qualitatively explained as partial ordering of intercalated dopant ions. Absorption spectra were derived from the transmission spectra under the assumption of nondispersive reflectance and subsequently compared with DL-model-derived spectra. The free-carrier density of the n -type powder and the electronic mean free path were estimated and compared with reported values for single-walled nanotubes and pyrolytic graphite.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Use of Stable Mercury Isotopes to Assess Mercury and Methylmercury Transformation and Transport across Critical Interfaces from the Molecular to the Watershed Scale (Final Report)

This project titled “Use of Stable Mercury Isotopes to Assess Mercury and Methylmercury Transformation and Transport across Critical Interfaces from the Molecular to the Watershed Scale” represents a collaborative effort between the University of Michigan (Jason Demers, PI) and Oak Ridge National Laboratory (Scott Brooks, co-I). Much has been learned about mercury (Hg) cycling in stream ecosystems, and East Fork Poplar Creek (EFPC) in particular, through decades of previous research. Nevertheless, some of the most fundamental questions regarding the sources of bioavailable Hg and its transformation to toxic methylmercury (MeHg) have remained unanswered. These fundamental questions include: (1) what are the sources and biogeochemical processes that lead to the input of dissolved Hg to stream water across critical subsurface interfaces within stream ecosystems, and EFPC in particular? and (2) what are the sources and biogeochemical processes that control the production and fate of bioaccumulative MeHg within stream ecosystems, and in EFPC in particular? To address these fundamental questions, our project aimed to couple laboratory experiments and field observations, both utilizing natural abundance Hg stable isotope techniques, to identify the processes responsible for generating mobile, bioavailable dissolved Hg from recalcitrant legacy sources within critical subsurface zones (e.g., streambed hyporheic zone, riparian floodplain subsurface). We used the isotopic signature of this bioavailable dissolved Hg to track its mobilization across these critical interfaces in order to link diffuse subsurface sources of dissolved Hg with increases in surface water dissolved Hg flux measured at the watershed scale. Additionally, our research aimed to determine the isotopic composition of MeHg within these same critical subsurface zones. We directly assessed the isotopic composition of MeHg within biota in order to gain insight into which subsurface sources of inorganic Hg and toxic MeHg are available for bioaccumulation within the EFPC ecosystem. Net fluxes of dissolved Hg along the flow path of EFPC were shown to vary spatially and temporally. In the Upper EFPC, within the Y12 boundary, stream water flux of dissolved Hg consistently decreased between the outfall and the downstream boundary of Y12 (57% ± 29%, 1SD). Within the Upper EFPC, an assessment of Hg isotopic composition suggested that losses were strongly reaction-driven, although isotopic diagnostics did not conform to any known processes. Downstream of Y12, in the upper reach of the Lower EFPC, dissolved Hg fluxes tended to increase during the dormant season (net gain of 11-120%), and decrease during the growing season (net loss of 23% +/- 18%, 1SD). In the downstream-most reach of Lower EFPC, dissolved Hg fluxes increased by 12-108% in 9 out of 10 monthly assessments. Overall, diffuse fluxes from the non-Y12 watershed accounted for 34% (+/- 17%, 1SD) of all dissolved Hg exported during base flow. Within Lower EFPC, an assessment of Hg isotopic composition was consistent with the contribution of diffuse Hg inputs from high-concentration hotspots within riparian floodplains and streambed hyporheic pore water. To investigate remobilization of recalcitrant Hg from legacy sediment sources, we developed procedures that coupled isotopic analysis with sequential extractions of streambed sediment. We found that the proportion of weakly-bound Hg within EFPC streambed sediment was relatively small, but could still account for a large proportion of the annual flux of dissolved Hg from EFPC. These sequential extractions also showed that this weakly-bound Hg fraction could be replenished from the much larger fraction of recalcitrant Hg in sediment. The isotopic composition of these weakly-bound and remobilized recalcitrant Hg fractions within the sediment was consistent with high-concentration dissolved Hg hotspots within hyporheic pore water. Thus, this research provided novel evidence that legacy mercury sources within streambed sediment could provide an ongoing contribution of dissolved Hg to surface waters. Finally, we developed new methods for the direct determination of the MeHg isotopic composition of organisms, which allowed a more direct evaluation of inorganic Hg and MeHg sources accumulating in the food web. We found that fish and aquatic invertebrates in both EFPC and a regional background site obtained inorganic Hg and MeHg from multiple isotopically distinct sources, including sediment, suspended particulates, and periphyton. Photodemethylation was found to be an important reaction influencing MeHg dynamics at both sites. However, the balance of microbial methylation and demethylation processes differed between the two streams, with fractionation resulting from methylation and demethylation processes being relatively in balance within the regional background site, whereas microbial methylation appeared to be dominant over microbial demethylation within the EFPC ecosystem. Broadly, the application of Hg isotopic analysis in this study led to numerous novel insights regarding the biogeochemical cycling of Hg in stream ecosystems. This research project promoted the development of two new approaches, including the coupling of sequential extractions with Hg isotopic analysis to assess remobilization of recalcitrant Hg within sediments, and a new method for the isotopic analysis of MeHg isolated from environmental samples. Both of these efforts represent advances in capacity for the field of mercury isotopic analysis and environmental assessment. Overall, this study demonstrates that the application of Hg stable isotope techniques continues to provide new insights into the biogeochemical cycling of Hg in complex aquatic environments, both within the EFPC and beyond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗

DOE OSTI2021

Phasor-Measurement-Unit-Based Data Analytics Using Digital Twin and PhasorAnalytics Software

A major objective of this project was to apply GE’s commercial machine learning and data analytics toolsets to large-scale, real-world, anonymized Phasor Measurement Unit (PMU) datasets in order to extract signatures, correlated and/or causal factors, and precursor patterns associated with significant power system phenomena. The project had a particular emphasis on extraction of insights relevant to asset health monitoring, real-time load modeling and cybersecurity monitoring. Additionally, the team was directed to undertake a comprehensive data quality analysis for the provided datasets and encouraged to estimate the ‘machine-learning readiness’ of the datasets by documenting any major obstacles to the application of commercial machine learning algorithms. To accomplish the aforementioned objectives, the project team’s work centered around the identification of key event signatures and application of the identified event signatures for event detection and event classification. The industry-validated, semi-supervised machine learning strategy employed for event signature identification involved several major tasks, including data-preprocessing, generation of an overabundance of features, normal data identification, normality modeling, and event signature identification through a methodical, quantitative ranking of features in order of relevance to each studied event type. Throughout the project, data quality issues and mitigation techniques were investigated. In this report, insights are provided regarding the readiness of the provided synchrophasor datasets for application of machine learning and data analytics. The methodologies employed for this technical strategy are summarized in this report. With regards to data preprocessing and feature generation, the provided Training and Test Datasets were ingested into GE’s big data environment. Subsequently, the team applied bad data cleansing and data imputation scripts, event detection scripts, and application programming interfaces (APIs) to the datasets for convenient data access. The project team completed development and validation of dozens of physics-based, statistics-based and transformation-based feature functions used for the extraction of over 60 synchrophasor features. Using a new parallel feature generation technology developed on this project, over 60 features have been rapidly generated for the full two years’ worth of Training and Test Dataset data associated with both the Eastern and Western interconnects. Even accommodating for temporal down-sampling inherent to the feature extraction procedure, this parallel feature generation activity resulted in a massive feature set with a storage requirement approximately equal to that of the raw training dataset itself. With regards to normal data identification and normality modeling, a normality model was built using the feature data extracted from the Training Dataset and iteratively refined subsequent to incremental adjustments and expansions of the Training Dataset feature data. With respect to event characterization and signature identification, an event signature identification pipeline was developed and used in conjunction with the normality model to identify over 15 event signatures for key event categories within the Training Dataset. The identified event signatures were used to characterize hundreds of key events in terms of relative severity, duration, and location of the event. An investigation was undertaken to identify correlated and causal factors involved in transformer events. A separate investigation into temporal trends in ring-down analysis results was undertaken to determine possible associations between system dynamics and various other factors such as loading, season or year. To validate the identified event signatures, additional work was undertaken to develop signature-based anomaly detection and classification tools suitable for convenient application to the synchrophasor datasets. The anomaly detection and classification tools, suitable for online application, were then applied to the entirety of the Eastern Interconnect Training and Test Datasets. Performance of the event detection and classification tools was evaluated upon receipt of the Test Dataset event logs (i.e., the labels for events contained in the Test Dataset), and promising results were obtained despite several challenges (documented herein) associated with application of supervised or semi-supervised machine learning methods to large-scale, anonymized datasets. Finally, the detection and classification tools were used to detect, classify, and characterize thousands of new events not included in the original event logs provided by the DOE within both the Training and Test Datasets.

24 POWER TRANSMISSION AND DISTRIBUTION↗