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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2018

Real-space refinement in PHENIX for cryo-EM and crystallography

This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Impulse Response Functions for Characterizing Pulse-to-Pulse Junction Temperature Behavior in Laser Diode Pulse Trains

A method is proposed for determination of the pulse-to-pulse variation in junction temperature and emission wavelength of a semiconductor laser diode during a train of pulses. Here, this approach, based on impulse response functions, enables predictions for pulse trains with arbitrary pulse-to-pulse variations in output power, pulse width, and pulse delay using a limited set of experimental characterization data. The use of this approach is illustrated by application to a particular device structure.

Deri, Robert J. [Lawrence Livermore National Labor↗

DOE OSTI2023

Using an Analytic-Based Magnetic Charge Fourier Series Model to Study a Magnetic Lead Screw when Operating as a Magnetic Spring

A magnetic charge field analysis approach is presented that models an array of magnets by using a magnetic vector Fourier series representation. Using a Fourier series function enables the magnets' relative permeability to be accounted for and also reduces the computational burden. The accuracy of the presented modelling approach is validated by studying the fields and forces created by a magnetic lead screw when acting as a magnetic spring

Kouhshahi, Mojtaba Bahrami↗

DOE OSTI2018

An updated gene atlas for maize reveals organ-specific and stress-induced genes

Maize (Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide. The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long-read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA-sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36 207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4154 organ-specific and 7704 differentially expressed (DE) genes following stress treatment. Gene co-expression network analyses revealed 12 modules associated with distinct biological processes containing 13 590 genes providing a resource for further association of gene function based on co-expression patterns. Presence–absence variants (PAVs) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ-specific and stress-induced DE genes suggesting that PAVs may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds, PAVs have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average have significantly fewer co-expression network connections suggesting that a subset of PAVs may be on an evolutionary path to pseudogenization. Here, to facilitate use by the community, we developed the Maize Genomics Resource website (maize.plantbiology.msu.edu) for viewing and data-mining these resources and deployed two new views on the maize electronic Fluorescent Pictograph Browser (bar.utoronto.ca/efp_maize).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

SU-E-T-406: Use of TrueBeam Developer Mode and API to Increase the Efficiency and Accuracy of Commissioning Measurements for the Varian EDGE Stereotactic Linac

Purpose: The Varian EDGE machine is a new stereotactic platform, combining Calypso and VisionRT localization systems with a stereotactic linac. The system includes TrueBeam DeveloperMode, making possible the use of XML-scripting for automation of linac-related tasks. This study details the use of DeveloperMode to automate commissioning tasks for Varian EDGE, thereby improving efficiency and measurement consistency. Methods: XML-scripting was used for various commissioning tasks,including couch model verification,beam-scanning,and isocenter verification. For couch measurements, point measurements were acquired for several field sizes (2×2,4×4,10×10cm{sup 2}) at 42 gantry angles for two couch-models. Measurements were acquired with variations in couch position(rails in/out,couch shifted in each of motion axes) compared to treatment planning system(TPS)-calculated values,which were logged automatically through advanced planning interface(API) scripting functionality. For beam scanning, XML-scripts were used to create custom MLC-apertures. For isocenter verification, XML-scripts were used to automate various Winston-Lutz-type tests. Results: For couch measurements, the time required for each set of angles was approximately 9 minutes. Without scripting, each set required approximately 12 minutes. Automated measurements required only one physicist, while manual measurements required at least two physicists to handle linac positions/beams and data recording. MLC apertures were generated outside of the TPS,and with the .xml file format, double-checking without use of TPS/operator console was possible. Similar time efficiency gains were found for isocenter verification measurements Conclusion: The use of XML scripting in TrueBeam DeveloperMode allows for efficient and accurate data acquisition during commissioning. The efficiency improvement is most pronounced for iterative measurements, exemplified by the time savings for couch modeling measurements(approximately 10 hours). The scripting also allowed for creation of the files in advance without requiring access to TPS. The API scripting functionality enabled efficient creation/mining of TPS data. Finally, automation reduces the potential for human error in entering linac values at the machine console,and the script provides a log of measurements acquired for each session. This research was supported in part by a grant from Varian Medical Systems, Palo Alto, CA.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

Electroplating lithium transition metal oxides

Materials synthesis often provides opportunities for innovation. We demonstrate a general low-temperature (260°C) molten salt electrodeposition approach to directly electroplate the important lithium-ion (Li-ion) battery cathode materials LiCoO 2 , LiMn 2 O 4 , and Al-doped LiCoO 2 . The crystallinities and electrochemical capacities of the electroplated oxides are comparable to those of the powders synthesized at much higher temperatures (700° to 1000°C). In conclusion, this new growth method significantly broadens the scope of battery form factors and functionalities, enabling a variety of highly desirable battery properties, including high energy, high power, and unprecedented electrode flexibility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Neuromorphic ionic computing in droplet interface synapses

Ionic devices with memory capabilities can emulate neural functionality, enabling neuromorphic computing and biomedical applications. In this study, we report an ionic spiking synapse based on aqueous droplet interface bilayer assembly. Under stepwise triangular voltages, the device displays coupled memcapacitive-memristive behavior, showing noncrossing pinched hysteretic I-V loops. This hysteretic ion dynamics can be regulated by modifying bilayer components, reconstituting protein channels, or adjusting droplet assembly configuration. Droplet interface synapses (DIS) exhibit fundamental neuromorphic behaviors such as paired-pulse facilitation/depression, spike rate–dependent plasticity, Hebbian learning, and short-term associative learning under classical conditioning. We also used reservoir computing with DIS to implement two learning algorithms: a classification algorithm that recognizes handwritten digits and a reinforcement learning algorithm that learns to play a board game of tic-tac-toe.

Li, Zhongwu [Lawrence Livermore National Laborator↗

DOE OSTI2024

High-performance finite elements with MFEM

The MFEM (Modular Finite Element Methods) library is a high-performance C++ library for finite element discretizations. MFEM supports numerous types of finite element methods and is the discretization engine powering many computational physics and engineering applications across a number of domains. Furthermore, this paper describes some of the recent research and development in MFEM, focusing on performance portability across leadership-class supercomputing facilities, including exascale supercomputers, as well as new capabilities and functionality, enabling a wider range of applications. Much of this work was undertaken as part of the Department of Energy’s Exascale Computing Project (ECP) in collaboration with the Center for Efficient Exascale Discretizations (CEED).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2012

Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations

Background: The model bacterium Clostridium cellulolyticum efficiently hydrolyzes crystalline cellulose and hemicellulose, using cellulosomes to degrade lignocellulosic biomass. Although it imports and ferments both pentose and hexose sugars to produce a mixture of ethanol, acetate, lactate, H2 and CO2, the proportion of ethanol is low, which impedes its use in consolidated bioprocessing for biofuels. Therefore genetic engineering will likely be required to improve the ethanol yield. Random mutagenesis, plasmid transformation, and heterologous expression systems have previously been developed for C. cellulolyticum, but targeted mutagenesis has not been reported for this organism. Results: The first targeted gene inactivation system was developed for C. cellulolyticum, based on a mobile group II intron originating from the Lactococcus lactis L1.LtrB intron. This markerless mutagenesis system was used to disrupt both the paralogous L-lactate dehydrogenase (Ccel_2485; ldh) and L-malate dehydrogenase (Ccel_0137; mdh) genes, distinguishing the overlapping substrate specificities of these enzymes. Both mutations were then combined in a single strain. This double mutant produced 8.5-times more ethanol than wild-type cells growing on crystalline cellulose. Ethanol constituted 93% of the major fermentation products (by molarity), corresponding to a molar ratio of ethanol to organic acids of 15, versus 0.18 in wild-type cells. During growth on acid-pretreated switchgrass, the double mutant also produced four-times as much ethanol as wild-type cells. Detailed metabolomic analyses identified increased flux through the oxidative branch of the mutant s TCA pathway. Conclusions: The efficient intron-based gene inactivation system produced the first gene-targeted mutations in C. cellulolyticum. As a key component of the genetic toolbox for this bacterium, markerless targeted mutagenesis enables functional genomic research in C. cellulolyticum and rapid genetic engineering to significantly alter the mixture of fermentation products. The initial application of this system successfully engineered a strain with high ethanol productivity from complex biomass substrates.

09 BIOMASS FUELS↗

DOE OSTI2011

Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium

Background: Two component regulatory systems are the primary form of signal transduction in bacteria. Although genomic binding sites have been determined for several eukaryotic and bacterial transcription factors, comprehensive identification of gene targets of two component response regulators remains challenging due to the lack of knowledge of the signals required for their activation. We focused our study on Desulfovibrio vulgaris Hildenborough, a sulfate reducing bacterium that encodes unusually diverse and largely uncharacterized two component signal transduction systems. Results: We report the first systematic mapping of the genes regulated by all transcriptionally acting response regulators in a single bacterium. Our results enabled functional predictions for several response regulators and include key processes of carbon, nitrogen and energy metabolism, cell motility and biofilm formation, and responses to stresses such as nitrite, low potassium and phosphate starvation. Our study also led to the prediction of new genes and regulatory networks, which found corroboration in a compendium of transcriptome data available for D. vulgaris. For several regulators we predicted and experimentally verified the binding site motifs, most of which were discovered as part of this study. Conclusions: The gene targets identified for the response regulators allowed strong functional predictions to be made for the corresponding two component systems. By tracking the D. vulgaris regulators and their motifs outside the Desulfovibrio spp. we provide testable hypotheses regarding the functions of orthologous regulators in other organisms. The in vitro array based method optimized here is generally applicable for the study of such systems in all organisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations

Abstract Background Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. Results In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resulting functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Conclusions PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/ . PSAT stands apart from other sequence-based genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Beta Test Plan for Advanced Inverters Interconnecting Distributed Resources with Electric Power Systems

This document provides a preliminary (beta) test plan for grid interconnection systems of advanced inverter-based DERs. It follows the format and methodology/approach established by IEEE Std 1547.1, while incorporating: 1. Upgraded tests for responses to abnormal voltage and frequency, and also including ride-through. 2. A newly developed test for voltage regulation, including dynamic response testing. 3. Modified tests for unintentional islanding, open phase, and harmonics to include testing with the advanced voltage and frequency response functions enabled. Two advanced inverters, one single-phase and one three-phase, were tested under the beta test plan. These tests confirmed the importance of including tests for inverter dynamic response, which varies widely from one inverter to the next.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

Mojave firmware 1.09 FW valuation- Firmware 1.09 Results

This quick note outlines what we found after our conversion with you and your team. As suggested, we loaded 1547-2003 source requirements document (SRD) and then went back and loaded 1547-2018 SRD. This did result in implementing the new 1547-2018 settings. This short report focuses on the frequency-watt function and shows a couple of screen shots of the parameter settings via the Mojave HMI interface and plots of the results of the inverter with FW function enabled in both default and most aggressive settings response to frequency events. The first screen shot shows the 1547-2018 selected after selecting 1547-2003.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Modular Control Architecture for Scalable, Resilient, and Cybersecure Microgrids Test Results [Mojave firmware 1.09 FW valuation]

42 ENGINEERING↗

DOE OSTI2026

Bioinspired Design of Dissipative Self-Assembly of Active Materials (Final Technical Report)

The major objective of this DOE-funded research program was to establish general, experimentally validated design principles for dissipative, out-of-equilibrium self-assembly of synthetic active materials. In living systems, structures such as actin filaments and microtubules are maintained far from thermodynamic equilibrium through continuous energy consumption. This persistent nonequilibrium operation enables functions including adaptability, self-healing, directed motion, and force generation—properties that are largely absent in traditional equilibrium soft materials.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Metasurfaces with Multipolar Resonances and Enhanced Light–Matter Interaction

Metasurfaces, composed of engineered nanoantennas, enable unprecedented control over electromagnetic waves by leveraging multipolar resonances to tailor light–matter interactions. This review explores key physical mechanisms that govern their optical properties, including the role of multipolar resonances in shaping metasurface responses, the emergence of bound states in the continuum (BICs) that support high-quality factor modes, and the Purcell effect, which enhances spontaneous emission rates at the nanoscale. These effects collectively underpin the design of advanced photonic devices with tailored spectral, angular, and polarization-dependent properties. This review discusses recent advances in metasurfaces and applications based on them, highlighting research that employs full-wave numerical simulations, analytical and semi-analytic techniques, multipolar decomposition, nanofabrication, and experimental characterization to explore the interplay of multipolar resonances, bound and quasi-bound states, and enhanced light–matter interactions. A particular focus is given to metasurface-enhanced photodetectors, where structured nanoantennas improve light absorption, spectral selectivity, and quantum efficiency. By integrating metasurfaces with conventional photodetector architectures, it is possible to enhance responsivity, engineer photocarrier generation rates, and even enable functionalities such as polarization-sensitive detection. The interplay between multipolar resonances, BICs, and emission control mechanisms provides a unified framework for designing next-generation optoelectronic devices. This review consolidates recent progress in these areas, emphasizing the potential of metasurface-based approaches for high-performance sensing, imaging, and energy-harvesting applications.

Kerker effect↗

DOE OSTI2025

Instant Folded Strings, Dark Energy and a Cyclic Bouncing Universe

We present a wholly self-consistent, complete cyclic bouncing cosmology based on components drawn from string theory and constructed in a way that is under perturbative control throughout (e.g., with temperature much less than the string scale and string coupling $g_s \ll 1$ at all times). The cyclic evolution is governed by standard dilaton-gravity in $(3+1)$-dimensions with a perturbatively generated potential and a coupling between the dilaton and a second field that becomes massless at $ϕ= ϕ_{ESP}$, resulting in an enhanced symmetry point (ESP) that prevents the dilaton from running all the way to zero coupling. A central role is played by instant folded strings (IFSs) - fundamental strings with the unusual property of being much lighter than the string mass while extending far beyond the string length, and violating the Null Energy Condition (NEC). IFSs are produced classically when the string coupling grows with time, which occurs at two critical points in each cycle. In turn, they fulfill a dual function: enabling cosmological bounces and initiating transient epochs of dark-energy domination that naturally transition into slow contraction. The resulting cosmology eliminates the cosmic singularity and multiverse problems of big bang inflationary models and robustly predicts time-varying IFS-induced dark energy and the absence of primordial B-mode polarization in the cosmic microwave background.

Cosmology and Nongalactic Astrophysics (astro-ph.C↗

DOE OSTI2018

Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes

Maize(Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide.The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long‐read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA‐sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36,207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4,154 organ‐specific and 7,704 differentially expressed genes following stress treatment. Gene co‐expression network analyses revealed 12 modules associated with distinct biological processes containing 13,590 genes providing a resource for further association of gene function based on co‐expression patterns. Presence/absence variants (PAVs) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ‐specific and stress‐induced differentially expressed genes, suggesting PAVs may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds, PAVs have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average, have significantly fewer co‐expression network connections suggesting that a subset of PAVs may be on an evolutionary path to pseudogenization. To facilitate use by the community, we developed the Maize Genomics Resource website(maize.plantbiology.msu.edu) for viewing and data‐mining these resources and deployed two new views on the Maize electronic Fluorescent Pictograph Browser (bar.utoronto. ca/efp_maize)

59 BASIC BIOLOGICAL SCIENCES↗