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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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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Domain-specific compilers for dynamic simulations of quantum materials on quantum computers

Abstract Simulation of the dynamics of quantum materials is emerging as a promising scientific application for noisy intermediate-scale quantum (NISQ) computers. Due to their high gate-error rates and short decoherence times, however, NISQ computers can only produce high-fidelity results for those quantum circuits smaller than some given circuit size. Dynamic simulations, therefore, pose a challenge as current algorithms produce circuits that grow in size with each subsequent time-step of the simulation. This underscores the crucial role of quantum circuit compilers to produce executable quantum circuits of minimal size, thereby maximizing the range of physical phenomena that can be studied within the NISQ fidelity budget. Here, we present two domain-specific (DS) quantum circuit compilers for the Rigetti and IBM quantum computers, specifically designed to compile circuits simulating dynamics under a special class of time-dependent Hamiltonians. The compilers outperform state-of-the-art general-purpose compilers in terms of circuit size reduction by around 25%–30% as well as wall-clock compilation time by around 40% (dependent on system size and simulation time-step). Drawing on heuristic techniques commonly used in artificial intelligence, both compilers scale well with simulation time-step and system size. Code for both compilers is open-source and packaged into a full-stack quantum simulation software with tutorials included for ease of use for future researchers wishing to perform dynamic simulations of quantum materials on quantum computers. As our DS compilers provide significant improvements in both compilation time and simulation fidelity, they provide a building block for accelerating progress toward physical quantum supremacy.

Physics↗
DOE OSTI2020

Species-specific flowering phenology responses to experimental warming and drought alter herbaceous plant species overlap in a temperate–boreal forest community

Abstract Background and Aims Warmer temperatures and altered precipitation patterns are expected to continue to occur as the climate changes. How these changes will impact the flowering phenology of herbaceous perennials in northern forests is poorly understood but could have consequences for forest functioning and species interactions. Here, we examine the flowering phenology responses of five herbaceous perennials to experimental warming and reduced summer rainfall over 3 years. Methods This study is part of the B4WarmED experiment located at two sites in northern Minnesota, USA. Three levels of warming (ambient, +1.6 °C and +3.1 °C) were crossed with two rainfall manipulations (ambient and 27 % reduced growing season rainfall). Key Results We observed species-specific responses to the experimental treatments. Warming alone advanced flowering for four species. Most notably, the two autumn blooming species showed the strongest advance of flowering to warming. Reduced rainfall alone advanced flowering for one autumn blooming species and delayed flowering for the other, with no significant impact on the three early blooming species. Only one species, Solidago spp., showed an interactive response to warming and rainfall manipulation by advancing in +1.6 °C warming (regardless of rainfall manipulation) but not advancing in the warmest, driest treatment. Species-specific responses led to changes in temporal overlap between species. Most notably, the two autumn blooming species diverged significantly in their flowering timing. In ambient conditions, these two species flowered within the same week. In the warmest, driest treatment, flowering occurred over a month apart. Conclusions Herbaceous species may differ in how they respond to future climate conditions. Changes to phenology may lead to fewer resources for insects or a mismatch between plants and pollinators.

Plant Sciences↗
DOE OSTI2023

AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes

Microbial natural products represent a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class that include antibiotics, immunosuppressants, anticancer agents, toxins, siderophores, pigments, and cytostatics. The discovery of novel NRPs remains a laborious process because many NRPs consist of nonstandard amino acids that are assembled by nonribosomal peptide synthetases (NRPSs). Adenylation domains (A-domains) in NRPSs are responsible for selection and activation of monomers appearing in NRPs. During the past decade, several support vector machine-based algorithms have been developed for predicting the specificity of the monomers present in NRPs. These algorithms utilize physiochemical features of the amino acids present in the A-domains of NRPSs. In this article, we benchmarked the performance of various machine learning algorithms and features for predicting specificities of NRPSs and we showed that the extra trees model paired with one-hot encoding features outperforms the existing approaches. Moreover, we show that unsupervised clustering of 453560 A-domains reveals many clusters that correspond to potentially novel amino acids. While it is challenging to predict the chemical structure of these amino acids, we developed novel techniques to predict their various properties, including polarity, hydrophobicity, charge, and presence of aromatic rings, carboxyl, and hydroxyl groups.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

In silico λ-dynamics predicts protein binding specificities to modified RNAs

Abstract RNA modifications shape gene expression through a variety of chemical changes to canonical RNA bases. Although numbering in the hundreds, only a few RNA modifications are well characterized, in part due to the absence of methods to identify modification sites. Antibodies remain a common tool to identify modified RNA and infer modification sites through straightforward applications. However, specificity issues can result in off-target binding and confound conclusions. This work utilizes in silico λ-dynamics to efficiently estimate binding free energy differences of modification-targeting antibodies between a variety of naturally occurring RNA modifications. Crystal structures of inosine and N6-methyladenosine (m6A) targeting antibodies bound to their modified ribonucleosides were determined and served as structural starting points. λ-Dynamics was utilized to predict RNA modifications that permit or inhibit binding to these antibodies. In vitro RNA-antibody binding assays supported the accuracy of these in silico results. High agreement between experimental and computed binding propensities demonstrated that λ-dynamics can serve as a predictive screen for antibody specificity against libraries of RNA modifications. More importantly, this strategy is an innovative way to elucidate how hundreds of known RNA modifications interact with biological molecules without the limitations imposed by in vitro or in vivo methodologies.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Self-energy dynamics and the mode-specific phonon threshold effect in Kekulé-ordered graphene

Abstract Electron-phonon interaction and related self-energy are fundamental to both the equilibrium properties and non-equilibrium relaxation dynamics of solids. Although electron-phonon interaction has been suggested by various time-resolved measurements to be important for the relaxation dynamics of graphene, the lack of energy- and momentum-resolved self-energy dynamics prohibits direct identification of the role of specific phonon modes in the relaxation dynamics. Here, by performing time- and angle-resolved photoemission spectroscopy measurements on Kekulé-ordered graphene with folded Dirac cones at the Γ point, we have succeeded in resolving the self-energy effect induced by the coupling of electrons to two phonons at Ω1 = 177 meV and Ω2 = 54 meV, and revealing its dynamical change in the time domain. Moreover, these strongly coupled phonons define energy thresholds, which separate the hierarchical relaxation dynamics from ultrafast, fast to slow, thereby providing direct experimental evidence for the dominant role of mode-specific phonons in the relaxation dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Specific Gamma-Ray Dose Constants with Current Emission Data

The specific gamma-ray dose constant represents the gamma effective dose rate due to a point source of unit activity of a given nuclide at 1 m. New tabulations of specific gamma-ray dose constants have been made using current gamma emission data from the SCALE 6.2.3 software package and International Commission on Radiological Protection Publication 107, combined with the effective dose per fluence conversion coefficients (antero-posterior orientation) of International Commission on Radiological Protection Publication 116. SCALE data cover 1,264 nuclides, and International Commission on Radiological Protection Publication 107 data include 1,192 nuclides, with only 777 nuclides in common between the two sets.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms,Drosophila melanogaster(fly) andCaenorhabditis elegans(worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Domain-specific text embedding model for accelerator physics

Accelerator physics presents unique challenges for natural language processing (NLP) due to its specialized terminology and complex concepts. A key component in overcoming these challenges is the development of robust text embedding models that transform textual data into dense vector representations, facilitating efficient information retrieval and semantic understanding. In this work, we introduce AccPhysBERT, a sentence embedding model fine-tuned specifically for accelerator physics. Our model demonstrates superior performance across a range of downstream NLP tasks, surpassing existing models in capturing the domain-specific nuances of the field. We further showcase its practical applications, including semantic paper-reviewer matching and integration into retrieval-augmented generation systems, highlighting its potential to enhance information retrieval and knowledge discovery in accelerator physics. Published by the American Physical Society 2025

Hellert, Thorsten (ORCID:0000000227970926)↗
DOE OSTI2021

Role of element-specific damping in ultrafast, helicity-independent, all-optical switching dynamics in amorphous (Gd,Tb)Co thin films

Ultrafast control of the magnetization in ps timescales by fs laser pulses offers an attractive avenue for applications such as fast magnetic devices for logic and memory. However, ultrafast helicity-independent all-optical switching (HI-AOS) of the magnetization has thus far only been observed in Gd-based, ferrimagnetic amorphous (a-) rare earth-transition metal (a-RE-TM) systems, and a comprehensive understanding of the reversal mechanism remains elusive. Here, we report HI-AOS in ferrimagnetic a-Gd 22-x Tb x Co 78 thin films, from x=0 to 18, and elucidate the role of Gd in HI-AOS in a-RE-TM alloys and multilayers. Increasing Tb content results in increasing perpendicular magnetic anisotropy and coercivity, without modifying magnetization density, and slower remagnetization rates and higher critical fluences for switching but still shows picosecond HI-AOS. Simulations of the atomistic spin dynamics based on the two-temperature model reproduce these results qualitatively and predict that the lower damping on the RE sublattice arising from the small spin-orbit coupling of Gd (with L=0) is instrumental for the faster dynamics and lower critical fluences of the Gd-rich alloys. Annealing a-Gd 10 Tb 12 Co 78 leads to slower dynamics which we argue is due to an increase in damping. These simulations strongly indicate that accounting for element-specific damping is crucial in understanding HI-AOS phenomena. The results suggest that engineering the element-specific damping of materials can open up new classes of materials that exhibit low-energy, ultrafast HI-AOS.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

eCC++ : A Compiler Construction Framework for Embedded Domain-Specific Languages

eCC++ is a new compiler construction framework for embedding domain-specific programming languages within C++. That is, the host language is C++, the guest language is the DSL to be embedded in C++, and eCC++ is the tool that enables the embedding. The eCC++ framework is composed of three main components: a front-end, an API for program verification based on a functional and declarative intermediate representation (IR), and a Multi-Level Intermediate Representation (MLIR) code generator. The eCC++ front-end consists of a library of C++ classes and operators that can be used to define the guest language. Guest sources are compiled with any standard C++ compiler, and when run, the resulting executable generates an eCC++ IR representation of the program, which can be verified within the eCC++ framework. Finally, eCC++ allows for high-level and domain-specific optimizations before generating MLIR. In summary, eCC++ aims to act as a generic front-end that enables embedding guest languages into C++, and provides necessary compiler technology for program verification, targeting the existing capabilities in the MLIR infrastructure. The paper evaluates the eCC++ expressiveness and usability describing the process of embedding GraphIt, a high-performance graph language in C++.

Gonzalez Tallada, Marc↗
DOE OSTI2022

Assembly and Pre-Loading Specifications for the Series Production of the Nb 3 Sn MQXFA Quadrupole Magnets for the HL-LHC

We report the High Luminosity LHC (HL-LHC) Project is planning to install 16 cold-masses made with Nb 3 Sn quadrupole magnets in the LHC Interaction Regions to significantly increase its luminosity. Half of these cold masses are fabricated at BNL, FNAL, and LBNL under the US Accelerator Research Program (AUP). Each cold mass includes two identical Nb 3 Sn quadrupole magnets, called MQXFA with a magnetic length of 4.2 m. Currently, the AUP project has completed the fabrication and test of the first 5 pre-series magnets, and is working on the following 16 magnets for the series production. The brittleness and strain sensitivity of the Nb 3 Sn superconducting material requires a careful definition of the allowable maximum stress in the windings during magnet assembly and pre-load, and a tight control of their variation within the whole coil length. Therefore, a series of assembly and pre-load specifications have been defined with the goals of minimizing the risk of conductor degradation and providing the mechanical support required to reach the nominal current during powering. In this paper we present the specifications defined for the MQXFA magnets and applied during the different assembly phases and during the pre-load process of the first 5 pre-series magnets.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Amino acid substrate specificities and tissue expression profiles of the nine CYP79A encoding genes in Sorghum bicolor

Cytochrome P450s of the CYP79 family catalyze two N-hydroxylation reactions, converting a selected number of amino acids into the corresponding oximes. The sorghum genome (Sorghum bicolor) harbours nine CYP79A encoding genes, and here sequence comparisons of the CYP79As along with their substrate recognition sites (SRSs) are provided. The substrate specificity of previously uncharacterized CYP79As was investigated by transient expression in Nicotiana benthamiana and subsequent transformation of the oximes formed into the corresponding stable oxime glucosides catalyzed by endogenous UDPG-glucosyltransferases (UGTs). CYP79A61 uses phenylalanine as a substrate, whereas CYP79A91, CYP79A93, and CYP79A95 use valine and isoleucine as substrates, with CYP79A93 showing the ability also to use phenylalanine. CYP79A94 uses isoleucine as a substrate. Analysis of 249 sorghum transcriptomes from two different sorghum cultivars showed the expression levels and tissue-specific expression of the CYP79As. CYP79A1 is the committed gene in dhurrin formation and was the highest expressed gene in most tissues/organs. CYP79A61 was primarily expressed in fully developed leaf blades and leaf sheaths. CYP79A91 and CYP79A92 were expressed mainly in roots >200 cm below ground, while CYP79A93 and CYP79A94 were most highly expressed in the leaf collar and leaf sheath, respectively. Here, the possible signalling effects of the oximes and their metabolites produced in different sorghum tissues are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

OPEN leaf : an open‐source cloud‐based phenotyping system for tracking dynamic changes at leaf‐specific resolution in Arabidopsis

SUMMARY The first draft of the Arabidopsis genome was released more than 20 years ago and despite intensive molecular research, more than 30% of Arabidopsis genes remained uncharacterized or without an assigned function. This is in part due to gene redundancy within gene families or the essential nature of genes, where their deletion results in lethality (i.e., thedark genome). High‐throughput plant phenotyping (HTPP) offers an automated and unbiased approach to characterize subtle or transient phenotypes resulting from gene redundancy or inducible gene silencing; however, access to commercial HTPP platforms remains limited. Here we describe the design and implementation ofOPEN leaf, an open‐source phenotyping system with cloud connectivity and remote bilateral communication to facilitate data collection, sharing and processing.OPEN leaf, coupled with our SMART imaging processing pipeline was able to consistently document and quantify dynamic changes at the whole rosette level and leaf‐specific resolution when plants experienced changes in nutrient availability. Our data also demonstrate that VIS sensors remain underutilized and can be used in high‐throughput screens to identify and characterize previously unidentified phenotypes in a leaf‐specific time‐dependent manner. Moreover, the modular and open‐source design ofOPEN leafallows seamless integration of additional sensors based on users and experimental needs.

Plant Sciences↗
DOE OSTI2025

Untargeted metabolomics reveals anion and organ‐specific metabolic responses of salinity tolerance in willow

SUMMARY Willows can alleviate soil salinisation while generating sustainable feedstock for biorefinery, yet the metabolomic adaptations underlying their tolerance remain poorly understood.Salix miyabeanawas treated with two environmentally abundant salts, NaCl and Na 2 SO 4 , in a 12‐week pot trial. Willows tolerated salts across all treatments (up to 9.1 dS m −1 soil EC e ), maintaining biomass while selectively partitioning ions, confining Na + to roots and accumulating Cl − and in the canopy and adapting to osmotic stress via reduced stomatal conductance. Untargeted metabolomics captured >5000 putative compounds, including 278 core willow metabolome compounds constitutively produced across organs. Across all treatments, salinity drove widespread metabolic reprogramming, altering 28% of the overall metabolome, with organ‐tailored strategies. Comparing salt forms at equimolar sodium, shared differentially abundant metabolites were limited to 3% of the metabolome, representing the generalised salinity response, predominantly in roots. Anion‐specific metabolomic responses were extensive. NaCl reduced carbohydrates and tricarboxylic acid cycle intermediates, suggesting potential carbon and energy resource pressure, and accumulated root structuring compounds, antioxidant flavonoids, and fatty acids. Na 2 SO 4 salinity triggered accumulation of sulphur‐containing larger peptides, suggesting excess sulphate incorporation leverages ion toxicity to produce specialised salt‐tolerance‐associated metabolites. This high‐depth picture of the willow metabolome underscores the importance of capturing plant adaptations to salt stress at organ scale and considering ion‐specific contributions to soil salinity.

Plant Sciences↗
DOE OSTI2021

Comparison of Rotary and Linear Cutting Methodology in Determining Specific Cutting Energy of Granite

Abstract Single polycrystalline diamond compact (PDC) cutting is a practical technique to understand the rock–tool interactions in drag-bit-type geothermal drilling operations. This paper introduces a rotary cutting method to determine specific cutting energy (SCE) and compares it with the conventional linear cutting method. In this work, granite is selected to represent hard rock formations in geothermal drilling. Cutting tests are conducted on a Computer Numerical Control (CNC) machine with a realistic cutting speed of 12.7 m/min and several chip loads ranging from 0.08 to 0.25 mm. The cutting force is measured using a dynamometer and then converted to specific cutting energy (SCE). The results show that the rotary method produces an inverse relationship between SCE and chip load, whereas the linear method shows the opposite. As a result, the produced SCE by the rotary method tends to be lower than that of the linear method at a higher chip load at and over 0.16 mm. The difference may be attributed to the cutting configuration and associated force components.

Engineering↗
DOE OSTI2020

Synthesis of site-specific antibody-drug conjugates by ADP-ribosyl cyclases

Most of the current antibody-drug conjugates (ADCs) in clinic are heterogeneous mixtures. To produce homogeneous ADCs, established procedures often require multiple steps or long reaction times. The introduced mutations or foreign sequences may cause high immunogenicity. Here, we explore a new concept of transforming CD38 enzymatic activity into a facile approach for generating site-specific ADCs. This was achieved through coupling bifunctional antibody-CD38 fusion proteins with designer dinucleotide-based covalent inhibitors with stably attached payloads. The resulting adenosine diphosphate–ribosyl cyclase–enabled ADC (ARC-ADC) with a drug-to-antibody ratio of 2 could be rapidly generated through single-step conjugation. The generated ARC-ADC targeting human epidermal growth factor receptor 2 (HER2) displays excellent stability and potency against HER2-positive breast cancer both in vitro and in vivo. This proof-of-concept study demonstrates a new strategy for production of site-specific ADCs. It may provide a general approach for the development of a novel class of ADCs with potentially enhanced properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Egr1 is a 3D matrix–specific mediator of mechanosensitive stem cell lineage commitment

While extracellular matrix (ECM) mechanics strongly regulate stem cell commitment, the field’s mechanistic understanding of this phenomenon largely derives from simplified two-dimensional (2D) culture substrates. Here, we found a 3D matrix–specific mechanoresponsive mechanism for neural stem cell (NSC) differentiation. NSC lineage commitment in 3D is maximally stiffness sensitive in the range of 0.1 to 1.2 kPa, a narrower and more brain-mimetic range than we had previously identified in 2D (0.75 to 75 kPa). Transcriptomics revealed stiffness-dependent up-regulation of early growth response 1 (Egr1) in 3D but not in 2D. Egr1 knockdown enhanced neurogenesis in stiff ECMs by driving β-catenin nuclear localization and activity in 3D, but not in 2D. Mechanical modeling and experimental studies under osmotic pressure indicate that stiff 3D ECMs are likely to stimulate Egr1 via increases in confining stress during cell volumetric growth. To our knowledge, Egr1 represents the first 3D-specific stem cell mechanoregulatory factor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Time-resolving state-specific molecular dissociation with XUV broadband absorption spectroscopy

The electronic and nuclear dynamics inside molecules are essential for chemical reactions, where different pathways typically unfold on ultrafast timescales. Extreme ultraviolet (XUV) light pulses generated by free-electron lasers (FELs) allow atomic-site and electronic-state selectivity, triggering specific molecular dynamics while providing femtosecond resolution. Yet, time-resolved experiments are either blind to neutral fragments or limited by the spectral bandwidth of FEL pulses. Here, we combine a broadband XUV probe pulse from high-order harmonic generation with an FEL pump pulse to observe dissociation pathways leading to fragments in different quantum states. We temporally resolve the dissociation of a specific O 2 + state into two competing channels by measuring the resonances of ionic and neutral fragments. This scheme can be applied to investigate convoluted dynamics in larger molecules relevant to diverse science fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗