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DOE OSTI2019

Dynamics of Kondo voltage splitting after a quantum quench

We analyze the time-dependent formation of the spectral function of an Anderson impurity model in the Kondo regime within a numerically exact real-time quantum Monte Carlo framework. At steady state, splitting of the Kondo peak occurs with nontrivial dependence on voltage and temperature, and with little effect on the location or intensity of high-energy features. Examining the transient development of the Kondo peak after a quench from an initially uncorrelated state reveals a two-stage process where the initial formation of a single central Kondo peak is followed by splitting. We analyze the time dependence of splitting in detail and demonstrate a strong dependence of its characteristic timescale on the voltage. We expect both the steady state and the transient phenomenon to be experimentally observable.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Sensitivity calibration of a Carestream HPX-1 image plate scanner

There is a need to measure the sensitivity of the image plate scanners used to scan Z shot data. The Carestream HPX-1 image plate scanner was tested, and its performance was characterized to determine the system sensitivity in terms of signal per incident photon as a function of x-ray energy. A Manson source was used to simultaneously expose an Amptek x-ray multi-channel analyzer and image plates, allowing for a comparison of the counts as a function of energy to the signal recorded on the image plates. NIST-certified radioactive sources were used to assign an absolute sensitivity. Results indicate that the HPX-1 scanner response matches the shape of the modeled response, allowing for absolute scaling using NIST-certified radioisotope sources. The HPX-1 scanner shows a stable response with measurements taken over one week. In contrast, the sensitivity of the DITABIS scanner was characterized using the same approach, but it exhibits changes in its response that varied by more than 50% over the span of 4 days.

42 ENGINEERING↗

DOE OSTI2022

Memory forensic analysis of a programmable logic controller in industrial control systems

In industrial control systems (ICS), programmable logic controllers (PLCs) are used to automate physical processes such as nuclear plants and power grid stations, and are often subject to cyber attacks. As in conventional IT domain, the memory analysis of the PLCs can help answer important forensic questions about the attack, such as the presence of malicious firmware, injection of modified control logic (the program running on the PLC), and manipulation of I/O devices (e.g., sensors and actuators). Unlike conventional IT domain, PLCs have heterogeneous hardware architecture, proprietary firmware and control software, making it challenging to employ a unified framework for their memory forensics. For merely extracting artifacts of forensic importance, reverse-engineering the firmware is a tedious task, and the effort needs to be repeated for every PLC model. As a community, a step-wise approach to tackle this challenge is to analyze the memory of specific PLCs, and subsequently find a generic framework applicable to all PLCs. Our work is a step forward in this direction. By following a methodology that focuses on the functional layer of PLCs instead of reverse engineering the firmware, we analyze the digital forensic artifacts available in a common PLC, Allen-Bradley ControlLogix 1756-L61. Before diving into the memory dump, we analyze the PLC control software to create a list of important artifacts that are sure to exist in the PLC memory dump. The approach employs a setup where PLC control software RSLogix-5000 is connected to the PLC, and the memory dump can be obtained as and when needed. We create test cases that sequentially highlight each category of artifacts, followed by an examination of the resultant impact on memory. After attaining the listed artifacts, we employ conventional string and known data searches to extract interesting information present in this PLC's memory. The memory analysis profile, presented as a Python library and shared with the community, can help a forensic investigator to readily extract forensic artifacts from the same model's controller. The adopted approach may help researchers in creating memory profile of other PLCs, and ultimately formulating a generic PLC memory analysis framework.

Rais, Muhammad Haris↗

DOE OSTI2022

Advanced Finite-Volume Numerics and Source Term Assumptions for Kernel and G-Equation Modelling of Propane/Air Flames

Here G-Equation models represent propagating flame fronts with an implicit two-dimensional surface representation (level-set). Level-set methods are fast, as transport source terms for the implicit surface can be solved with finite-volume operators on the finite-volume domain, without having to build the actual surface. However, they include approximations whose practical effects are not properly understood. In this study, we improved the numerics of the FRESCO CFD code’s G-Equation solver and developed a new method to simulate kernel growth using signed distance functions and the analytical sphere-mesh overlap. We analyzed their role for simulating propane/air flames, using three well-established constant-volume configurations: a one-dimensional, freely propagating laminar flame; a disc-shaped, constant-volume swirl combustor; and torch-jet flame development through an orifice from a two-chamber device. We tested the explicit (sub-cycled) vs. implicit formulation for the standard transport operators (advection, diffusion, compressibility). In addition to the accurate flame swept-volume method for chemistry and species source term, we developed a more accurate estimator for the burnt/unburnt split cell composition. Then, we developed a signed-distance-function (SDF) based method which provides a more stable reinitialization of the level-set field at every time-step. We found that simplifying assumptions common to several G-Equation implementations, for straightforward terms such as compressibility and advection, lead to large errors in predicting the propagation of even laminar flames, with deviations up to ~300% in simulated vs. formulated flame speed. Conversely, the enhanced numerics enabled through the SDF field reinitialization and improved chemistry source term improve simulation stability and smooth flame propagation even with significantly larger solver time-steps.

42 ENGINEERING↗

DOE OSTI2024

The effect of temperature on photosystem II efficiency across plant functional types and climate

Modeling terrestrial gross primary productivity (GPP) is central to predicting the global carbon cycle. Much interest has been focused on the environmentally induced dynamics of photosystem energy partitioning and how improvements in the description of such dynamics assist the prediction of light reactions of photosynthesis and therefore GPP. The maximum quantum yield of photosystem II (Φ PSIImax ) is a key parameter of the light reactions that influence the electron transport rate needed for supporting the biochemical reactions of photosynthesis. Φ PSIImax is generally treated as a constant in biochemical photosynthetic models even though a constant Φ PSIImax is expected only for non-stressed plants. We synthesized reported Φ PSIImax values from pulse-amplitude-modulated fluorometry measurements in response to variable temperatures across the globe. We found that Φ PSIImax is strongly affected by prevailing temperature regimes with declined values in both hot and cold conditions. To understand the spatiotemporal variability in Φ PSIImax , we analyzed the temperature effect on Φ PSIImax across plant functional type (PFT) and habitat climatology. The analysis showed that temperature's impact on Φ PSIImax is shaped more by climate than by PFT for plants with broad latitudinal distributions or in regions with extreme temperature variability. There is a trade-off between the temperature range within which Φ PSIImax remains maximal and the overall rate of decline of Φ PSIImax outside the temperature range such that species cannot be simultaneously tolerant and resilient to extreme temperatures. Our study points to a quantitative approach for improving electron transport and photosynthetic productivity modeling under changing climates at regional and global scales.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Ignition thresholds of aluminized HMX-based polymer-bonded explosives

Here, the ignition of aluminized HMX-based polymer-bonded explosives (PBXs) under shock loading is studied via mesoscale simulations. The conditions analyzed concern loading pulses of 20 nanoseconds to 0.8 microseconds in duration and impact piston velocities on the order of 400-1000 m/s or loading stresses on the order of 3-14 GPa. The sets of samples studied have stochastically similar microstructures consisting of a bimodal distribution of HMX grains, an Estane binder, and aluminum particles 50-100 µm in diameter. The computational model accounts for constituent elasto-viscoplasticity, viscoelasticity, bulk compressibility, fracture, interfacial debonding, internal contact, bulk and frictional heating, and heat conduction. The analysis focuses on the development of hotspots under different material settings and loading conditions. In particular, the ignition thresholds in the forms of the James relation and the Walker-Wasley relation and the corresponding ignition probability are calculated and expressed as functions of the aluminum volume fraction for the PBXs analyzed. Lastly, it is found that the addition of aluminum raises the ignition thresholds, causing the materials to be less sensitive. Dissipation and heating mechanism changes responsible for this trend are delineated.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Elucidating Instabilities Contributing to Capacity Fade in Bipyridine‐Based Materials for Non‐aqueous Flow Batteries

Abstract Metal‐based non‐aqueous redox flow batteries have the potential for long‐term energy storage if stability requirements can be achieved. One such stability issue in metal coordination complexes arises from ligand shedding in the anolyte upon reduction. Recognizing that the free ligands are relatively more stable than the metal coordination complex under highly reducing conditions, we evaluated a family of metal‐free bipyridinium materials as flow battery anolytes with the corresponding iron coordination complex as the catholyte. Bipyridinium compounds were functionalized for increased electrochemical stability, cycled in flow cells to understand efficiencies, and analyzed for degradation products. Methylation of the bipyridine nitrogens increased electrochemical stability yet left the reduced molecule susceptible to radical‐induced bond cleavage. Subsequent functionalization of bipyridine with carbomethoxy groups resulted in good battery performance with 96 % Coulombic and 90 % voltage efficiency, and improved cycling stability over a methoxy‐substituted anolyte with 14 % vs 36 % capacity fade in the first charge‐discharge cycle.

Kolesnichenko, Claudina X.↗

DOE OSTI2021

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H 2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Heat rectification through single and coupled quantum dots

We study heat rectification through quantum dots in the Coulomb blockade regime using a master equation approach. We consider both cases of two-terminal and four-terminal devices. In the two-terminal configuration, we analyze the case of a single quantum dot with either a doubly-degenerate level or two non-degenerate levels. In the sequential tunneling regime we analyze the behaviour of heat currents and rectification as functions of the position of the energy levels and of the temperature bias. In particular, we derive an upper bound for rectification in the closed-circuit setup with the doubly-degenerate level. We also prove the absence of a bound for the case of two non-degenerate levels and identify the ideal system parameters to achieve nearly perfect rectification. The second part of the paper deals with the effect of second-order cotunneling contributions, including both elastic and inelastic processes. In all cases we find that there exists ranges of values of parameters (such as the levels' position) where rectification is enhanced by cotunneling. In particular, in the doubly-degenerate level case we find that cotunneling corrections can enhance rectification when they reduce the magnitude of the heat currents. For the four-terminal configuration, we analyze the non-local situation of two Coulomb-coupled quantum dots, each connected to two terminals: the temperature bias is applied to the two terminals connected to one quantum dot, while the heat currents of interest are the ones flowing in the other quantum dot. Remarkably, in this situation we find that non-local rectification can be perfect as a consequence of the fact that the heat currents vanish for properly tuned parameters.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Sennoside A protects mitochondrial structure and function to improve high-fat diet-induced hepatic steatosis by targeting VDAC1

Highlights: • SA inhibited VDAC1 expression in livers of HFD-induced hepatic steatosis mice. • SA suppressed the ATP surplus by inhibiting mitochondrial complex I in livers of HFD-induced hepatic steatosis mice. • SA protected mitochondrial function and structure in livers of HFD-induced hepatic steatosis mice. • SA improved HFD-induced hepatic steatosis and hepatomegaly. Mitochondrial dysfunction is mainly associated with high-fat-diet (HFD)-induced hepatic steatosis. Sennoside A (SA), a commonly used clinical stimulant laxative, is reported to improve energy metabolism and insulin resistance. However, the effect and mechanism of SA on HFD-induced hepatic steatosis remain largely unknown. The aim of this study was to determine the effect and mechanism of SA on HFD-induced hepatic steatosis in mice. We examined the liver and body weight of mice to evaluate the physical changes in the liver. Hematoxylin and eosin (H&E) and oil red O staining were used to detect the lipid accumulation. The mitochondrial structure and function were tested by transmission electron microscopy and the Seahorse XF24 Analyzer. Furthermore, mitochondrial complexes I, II, and IV and voltage-dependent anion channel 1 (VDAC1) protein activity were detected to understand the mechanism of the protective effect on mitochondria. As a result, damage to the structure and function in the hepatic mitochondria of HFD-induced hepatic steatosis was observed in mice. The structural damage was in the form of loss of cristae, mitochondrial swelling, vacuolization and even rupturing of the outer mitochondrial membrane (OMM). Functional alterations were found by activation of complex I and deficiency in complexes II and IV. The VDAC1 activity and the total ATP in the liver tissue was increased under hepatic steatosis conditions. The above effects were reversed by SA. These data suggest that inhibition of VDAC1 may be an underlying mechanism of SA for protecting mitochondria in HFD-induced hepatic steatosis in mice. Thus, VDAC1 may be a promising target for treating fatty liver disease.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Performance evaluation of the three-point angular correlation function

In recent years, we have observed an increase in the diversity of the processors ecosystem. Different designs and architectures are being studied based on their performance and power characteristics. While using benchmarks for this purpose allows for reproducibility and easy understanding of the results, using real scientific applications allows researchers to realize the actual implications of each design on the overall performance of their codes. This paper analyzes the performance of different implementations of a three-point angular correlation function. This function is used in the study of Large-Scale Distribution of galaxies in a variety of computational platforms. The function is based on histogram construction and presents a large computational cost. This cost dramatically increases with the size of the datasets. We have considered two different GPUs, a set of x86 Intel machines (multi- and many-core), ARM chipsets, as well as an FPGA. We first study the best possible implementation for each platform in terms of time to solution. We then compare the power used by those platforms for a predefined number of datasets. Energy is one of the main constraints that computer architects are facing nowadays. The results will be used to evaluate the performance of this function considering those two targets – time and energy – for those platforms and to analyze the suitability of each of those platforms for this specific problem.

Computer Science↗

DOE OSTI2022

Stability margin analysis of the Holos-quad microreactor design

A simplified point model of the Holos-Quad microreactor is introduced. The model is based on the point kinetics equations coupled to three heat balance equations, representing the mean temperatures of the fuel particles, the graphite moderator and the helium coolant. The differential equations are converted to the frequency domain, enabling the construction of the closed-loop reactor transfer function. Using this function the stability margins of the core design is analyzed for various power levels. It is shown that the gain margins approaches infinity, demonstrating the stability of the reactor for all power levels. The phase margin at nominal power is about 60 degrees, however it shows a non-monotonous dependence on power, with minimal value obtained for about 10% of nominal power. As power level is further increased, the phase margin also increases, demonstrating the reactor becomes more stable. This behavior may be of high importance in load-follow scenarios, where the power level of the reactor changes with time. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2023

Review of Current Software for Analyzing Total X-ray Scattering Data from Liquids

The popularity of the pair distribution function (PDF) analysis of X-ray total scattering data has steadily grown as access to ex situ synchrotron data has expanded. Due to the broadening of the PDF user community, there is a growing demand for software that can be used to extract PDFs and is accessible to non-expert users. While user-friendly options have been developed over the past decade for fast, streamlined data analysis, care must be taken in both processing the data and understanding any limitations, especially in the case of liquids. In this review, the same scattering data are analyzed using different total X-ray scattering software, in order to compare the accuracy of the extracted structure factors and associated pair distribution functions. The goal is to assess the best practices for extracting the most accurate liquid data for each software package. The importance of absolute normalization and the application of the most appropriate corrections are emphasized via quantitative comparisons between liquid sulfur and water. Additionally, an awareness of the competing conventions used to define the PDF in crystallography and liquids/glasses is crucial for both the downstream analyses of the data and a comparison with the previous results in the literature.

Gallington, Leighanne C. (ORCID:0000000203837522)↗

DOE OSTI2018

Theoretical Investigations of Properties of New Half-Heusler Compounds NiFeZ (Z = Si, Ge)

The half-Heusler alloys NiFeZ (Z = Si, Ge) are investigated theoretically in the general framework of Density Functional Theory (DFT). We have calculated structural, mechanical, elastic, electronic, magnetic, and optical properties using WIEN2k simulation package. To incorporate the electronic exchange-correlation energy we have used the GGA+U approximation. Both the compounds are found structurally stable, however, elastic properties show that NiFeSi is ductile while NiFeGe is brittle. Electronically, the compounds are found to be half-metals with small band gaps in the spin-down channels whereas spin-up channels are conducting. The total magnetic moments for both the compounds are ≈ 2μ{sub B}. Optical properties including dielectric function, refractive index, extinction coefficient, reflectivity, conductivity, and absorption coefficient are also calculated and analyzed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Putting error bars on density functional theory dataset

This dataset contains submission files and raw output files from high-throughput DFT simulations to analyze the systemic errors in lattice constant, bulk moduli and formation energy predictions for a range of binary and ternary oxides using four exchange correlation functionals (LDA, PBE, PBEsol and vdW-DF-C09). This data was then used as the basis for employing materials informatics methods to predict the expected errors in the lattice constants of the studied compounds. Predicted errors were also used to better the DFT-predicted lattice parameters. Our results emphasize the link between the computed errors and the electron density and hybridization errors of a functional. In essence, these results provide “error bars” for choosing a functional for the creation of high-accuracy, high-throughput datasets as well as avenues for the development of XC functionals with enhanced performance, thereby enabling the accelerated discovery and design of new materials.

36 MATERIALS SCIENCE↗

DOE OSTI2025

The developments in modifying functionality of lignin and its application in biocomposites

With the advancement of sustainable material innovations, renewable natural biopolymers are gradually replacing traditional metal and petroleum-based synthetic materials due to their environmental friendliness, biodegradability, and economic advantages. Lignin, the second most abundant natural aromatic polymer in the plant kingdom, has emerged as a key candidate raw material for the development of green polymer systems because of its unique phenylpropane unit network structure, high carbon content, and rich functional group characteristics. However, challenges such as the inherent structural complexity, chemical inertness, and uneven molecular weight distribution of lignin limit its direct application. By employing modification strategies such as chemical functionalization and physical regulation, researchers can precisely control its reactivity, thermal stability, and interfacial compatibility, enabling the preparation of high-performance lignin-based functional composites. Here, this paper systematically reviews the principles and methodological advancements in lignin's multi-dimensional modification technology. It analyzes the mechanisms by which various chemical and physical modification techniques enhance the mechanical properties, functional responsiveness, and environmental adaptability of materials, and discusses innovative applications in fields such as intelligent packaging, biomedical materials, and energy storage devices. Furthermore, this review addresses the key challenges encountered in the high-value transformation of lignin, with the aim of offering a theoretical framework and technical pathway for the transformative development of lignin from agricultural and forestry by-products to functional material platforms.

Functional composites↗

DOE OSTI2022

Comparison of the canonical transformation and energy functional formalisms for ab initio calculations of self-localized polarons

In materials with strong electron-phonon (e-ph) interactions, charge carriers can distort the surrounding lattice and become trapped, forming self-localized (small) polarons. We recently developed an ab initio approach based on canonical transformations to efficiently compute the formation and energetics of small polarons A different approach based on a Landau-Pekar energy functional has been proposed in the recent literature. Here in this work, we analyze and compare these two methods in detail. We show that the small polaron energy is identical in the two formalisms when using the same polaron wave function. We also show that our canonical transformation formalism can predict polaron band structures and can properly treat zero- and finite-temperature lattice vibration effects, although at present using a fixed polaron wave function. Conversely, the energy functional approach can compute the polaron wave function, but as we show here, it neglects lattice vibrations and cannot address polaron self-localization and thermal band narrowing. Taken together, this work relates two different methods developed recently to study polarons from first-principles, highlighting their merits and shortcomings and discussing them both in a unified formalism.

36 MATERIALS SCIENCE↗