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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Ferromagnets, a new anomaly, instantons, and (noninvertible) continuous translations

We discuss a large class of classical field theories with continuous translation symmetry. In the quantum theory, a new anomaly explicitly breaks this translation symmetry to a discrete symmetry. Furthermore, this discrete translation symmetry is extended by a d – 2-form global symmetry. All these theories can be described as U(1) gauge theories where Gauss law states that the system has nonzero charge density. Special cases of such systems can be phrased as theories with a compact phase space. Examples are ferromagnets and lattices in the lowest Landau level. In some cases, the broken continuous translation symmetry can be resurrected as a noninvertible symmetry. We clarify the relation between the discrete translation symmetry of the continuum theory and the discrete translation symmetry of an underlying lattice model. Our treatment unifies, clarifies, and extends earlier works on the same subject.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Circadian clock control of ribosome composition promotes rhythmic translation and termination fidelity

Ribosome composition is dynamic, shifting with cell state and stress, but whether it varies with circadian time is unknown. Here, we uncover circadian clock-driven changes in ribosome composition in Neurospora crassa . Mass spectrometry of ribosomes across circadian time identified six ribosomal proteins and one associated factor under clock control. Rhythms in eL31 abundance were validated in purified ribosomes, and deletion of el31 disrupted translation rhythms in nearly half of rhythmically translated mRNAs. N. crassa eL31 promotes circadian control of translation termination and impacts elongation fidelity while maintaining Mg homeostasis, a key determinant of translational accuracy. These findings reveal that the circadian clock reprograms ribosome composition to orchestrate rhythmic translation and fidelity, temporally expanding the proteome beyond the static genome to align cellular function with time of day.

circadian clock↗
DOE OSTI2024

Structure of saguaro cactus virus 3′ translational enhancer mimics 5′ cap for eIF4E binding

The genomes of several plant viruses contain RNA structures at their 3' ends called cap-independent translation enhancers (CITEs) that bind the host protein factors such as mRNA 5' cap-binding protein eIF4E for promoting cap-independent genome translation. However, the structural basis of such 5' cap-binding protein recognition by the uncapped RNA remains largely unknown. Here, we have determined the crystal structure of a 3' CITE, panicum mosaic virus-like translation enhancer (PTE) from the saguaro cactus virus (SCV), using a Fab crystallization chaperone. The PTE RNA folds into a three-way junction architecture with a pseudoknot between the purine-rich R domain and pyrimidine-rich Y domain, which organizes the overall structure to protrude out a specific guanine nucleotide, G18, from the R domain that comprises a major interaction site for the eIF4E binding. The superimposable crystal structures of the wild-type, G18A, G18C, and G18U mutants suggest that the PTE scaffold is preorganized with the flipped-out G18 ready to dock into the eIF4E 5' cap-binding pocket. The binding studies with wheat and human eIF4Es using gel electrophoresis and isothermal titration calorimetry, and molecular docking computation for the PTE–eIF4E complex demonstrated that the PTE structure essentially mimics the mRNA 5' cap for eIF4E binding. Such 5' cap mimicry by the uncapped and structured viral RNA highlights how viruses can exploit RNA structures to mimic the host protein-binding partners and bypass the canonical mechanisms for their genome translation, providing opportunities for a better understanding of virus-host interactions and non-canonical translation mechanisms found in many pathogenic RNA viruses.

3' cap-independent translation enhancers↗
DOE OSTI2025

Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae

Advances in sequencing technology have unveiled examples of nucleus-encoded polycistrons, once considered rare. Exclusively polycistronic transcripts are prevalent in green algae, although the mechanism by which multiple polypeptides are translated from a single transcript is unknown. Here, we used bioinformatic and in vivo mutational analyses to evaluate competing mechanistic models for translation of bicistronic mRNAs in green algae. High-confidence manually curated datasets of bicistronic loci from two divergent green algae, Chlamydomonas reinhardtii and Auxenochlorella protothecoides, revealed a preference for weak Kozak-like sequences for ORF 1 and an underrepresentation of potential initiation codons before the ORF 2 start codon, which are suitable conditions for leaky ribosome scanning to allow ORF 2 translation. We used mutational analysis in A. protothecoides to test the mechanism. In vivo manipulation of the ORF 1 Kozak-like sequence and start codon altered reporter expression at ORF 2, with a weaker Kozak-like sequence enhancing expression and a stronger one diminishing it. A synthetic bicistronic dual reporter demonstrated inversely adjustable activity of green fluorescent protein expressed from ORF 1 and luciferase from ORF 2, depending on the strength of the ORF 1 Kozak-like sequence. Our findings demonstrate that translation of multiple ORFs in green algal bicistronic transcripts is consistent with episodic leaky scanning of ORF 1 to allow translation at ORF 2. This work has implications for the potential functionality of upstream open reading frames (uORFs) found across eukaryotic genomes and for transgene expression in synthetic biology applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Uncovering translation roadblocks during the development of a synthetic tRNA

Ribosomes are remarkable in their malleability to accept diverse aminoacyl-tRNA substrates from both the same organism and other organisms or domains of life. This is a critical feature of the ribosome that allows the use of orthogonal translation systems for genetic code expansion. Optimization of these orthogonal translation systems generally involves focusing on the compatibility of the tRNA, aminoacyl-tRNA synthetase, and a non-canonical amino acid with each other. As we expand the diversity of tRNAs used to include non-canonical structures, the question arises as to the tRNA suitability on the ribosome. Specifically, we investigated the ribosomal translation of allo-tRNA UTu1 , a uniquely shaped (9/3) tRNA exploited for site-specific selenocysteine insertion, using single-molecule fluorescence. With this technique we identified ribosomal disassembly occurring from translocation of allo-tRNA UTu1 from the A to the P site. Using cryo-EM to capture the tRNA on the ribosome, we pinpointed a distinct tertiary interaction preventing fluid translocation. Through a single nucleotide mutation, we disrupted this tertiary interaction and relieved the translation roadblock. With the continued diversification of genetic code expansion, our work highlights a targeted approach to optimize translation by distinct tRNAs as they move through the ribosome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Majorana chain and Ising model - (non-invertible) translations, anomalies, and emanant symmetries

We study the symmetries of closed Majorana chains in 1+1d, including the translation, fermion parity, spatial parity, and time-reversal symmetries. The algebra of the symmetry operators is realized projectively on the Hilbert space, signaling anomalies on the lattice, and constraining the long-distance behavior. In the special case of the free Hamiltonian (and small deformations thereof), the continuum limit is the 1+1d free Majorana CFT. Its continuum chiral fermion parity (-1)^{F_L} ( − 1 ) F L emanates from the lattice translation symmetry. We find a lattice precursor of its mod 8 ’t Hooft anomaly. Using a Jordan-Wigner transformation, we sum over the spin structures of the lattice model (a procedure known as the GSO projection), while carefully tracking the global symmetries. In the resulting bosonic model of Ising spins, the Majorana translation operator leads to a non-invertible lattice translation symmetry at the critical point. The non-invertible Kramers-Wannier duality operator of the continuum Ising CFT emanates from this non-invertible lattice translation of the transverse-field Ising model.

Physics↗
DOE OSTI2022

Translator Plan: A Coordinated Vision for Fiscal Years 2023-2025

Translators serve a unique role in the U.S. Department of Energy (DOE)’s Atmospheric Radiation Measurement (ARM) user facility, offering scientific input through various leadership and service roles. The Translators direct the creation of value-added products (VAPs) and analysis tools that make ARM measurements more accessible to the scientific community. Translators also serve as liaisons between users and the ARM infrastructure, collecting information about priorities and communicating ARM data and services. A key group focus is supporting the DOE Atmospheric System Research (ASR) program scientists and ASR’s efforts towards a process-level understanding of cloud-aerosol interactions, and in reducing uncertainty in global climate model projections. The ARM Translator Group (Table 1) consists of the five Translators, a representative of software development, and one from the Data Quality Office (DQO). Additionally, the ARM Engineering and Process Manager participates in this group and provides input and direction from ARM and its programmatic priorities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin

Thermorubin (THR) is an aromatic anthracenopyranone antibiotic active against both Gram-positive and Gram-negative bacteria. It is known to bind to the 70S ribosome at the intersubunit bridge B2a and was thought to inhibit factor-dependent initiation of translation and obstruct the accommodation of tRNAs into the A site. Here, we show that thermorubin causes ribosomes to stall in vivo and in vitro at internal and termination codons, thereby allowing the ribosome to initiate protein synthesis and translate at least a few codons before stalling. Our biochemical data show that THR affects multiple steps of translation elongation with a significant impact on the binding stability of the tRNA in the A site, explaining premature cessation of translation. Our high-resolution crystal and cryo-EM structures of the 70S-THR complex show that THR can co-exist with P- and A-site tRNAs, explaining how ribosomes can elongate in the presence of the drug. Remarkable is the ability of THR to arrest ribosomes at the stop codons. Our data suggest that by causing structural re-arrangements in the decoding center, THR interferes with the accommodation of tRNAs or release factors into the ribosomal A site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structure of a cap-independent translation enhancer RNA

In eukaryotic messenger RNAs, the 5' cap structure binds to the translation initiation factor 4E to facilitate early stages of translation. Although many plant viruses lack the 5' cap structure, some contain cap-independent translation elements (CITEs) in their 3' untranslated region. The PTE (Panicum mosaic virus translation element) class of CITEs contains a G-rich asymmetric bulge and a C-rich helical junction that were proposed to interact via formation of a pseudoknot. SHAPE analysis of PTE homologs reveals a highly reactive guanosine residue within the G-rich region proposed to mediate eukaryotic initiation factor 4E (eIF4E) recognition. Here we have obtained the crystal structure of the PTE from Pea enation mosaic virus 2 (PEMV 2 ) RNA in complex with our structural chaperone, Fab BL3–6. The structure reveals that the G-rich and C-rich regions interact through a complex network of interactions distinct from those expected for a pseudoknot. The motif, which contains a short parallel duplex, provides a structural mechanism for how the guanosine is extruded from the core stack to enable eIF4E recognition. Homologous PTE elements harbor a G-rich bulge and a three-way junction and exhibit covariation at crucial positions, suggesting that the PEMV 2 tertiary architecture is conserved among these homologs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Abstract Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Robust T cell activation requires an eIF3-driven burst in T cell receptor translation

Activation of T cells requires a rapid surge in cellular protein synthesis. However, the role of translation initiation in the early induction of specific genes remains unclear. Here, we show human translation initiation factor eIF3 interacts with select immune system related mRNAs including those encoding the T cell receptor (TCR) subunits TCRA and TCRB. Binding of eIF3 to the TCRA and TCRB mRNA 3’-untranslated regions (3’-UTRs) depends on CD28 coreceptor signaling and regulates a burst in TCR translation required for robust T cell activation. Use of the TCRA or TCRB 3’-UTRs to control expression of an anti-CD19 chimeric antigen receptor (CAR) improves the ability of CAR-T cells to kill tumor cells in vitro. These results identify a new mechanism of eIF3-mediated translation control that can aid T cell engineering for immunotherapy applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Particle removal from a flat surface using a translating bounded vortex flow

A bounded vortex flow is a hydrodynamic approach for removal of particles from a surface without scattering the particles onto nearby surfaces. The bounded vortex flow field is generated by a nozzle that combines azimuthally tilted jets arranged in a circular pattern and a central suction port. When the nozzle face is directed toward an ‘impingement surface’, the flow develops a wall-normal intake vortex below the suction outlet, which causes high shear stress on the impingement surface. When particles are present on the impingement surface, the high shear stress causes particles to roll along the surface and to be lifted off the surface and transported up the core of the wall-normal vortex into the suction outlet. In typical applications, the nozzle would be translated along the impingement surface to clean particles from the surface. The current paper reports on an experimental study of the effect of nozzle translation on the effectiveness of the bounded vortex flow field for particle mitigation. The effectiveness of particle mitigation was examined as a function of flow rate through the nozzle, particle size, and nozzle translation velocity relative to the impingement surface. As a result, numerical computations are used to relate the flow rate to the maximum shear stress on the impingement surface, which is then used to theoretically predict onset of particle motion.

42 ENGINEERING↗
DOE OSTI2021

2D-to-3D image translation of complex nanoporous volumes using generative networks

Image-based characterization offers a powerful approach to studying geological porous media at the nanoscale and images are critical to understanding reactive transport mechanisms in reservoirs relevant to energy and sustainability technologies such as carbon sequestration, subsurface hydrogen storage, and natural gas recovery. Nanoimaging presents a trade off, however, between higher-contrast sample-destructive and lower-contrast sample-preserving imaging modalities. Furthermore, high-contrast imaging modalities often acquire only 2D images, while 3D volumes are needed to characterize fully a source rock sample. In this work, we present deep learning image translation models to predict high-contrast focused ion beam-scanning electron microscopy (FIB-SEM) image volumes from transmission X-ray microscopy (TXM) images when only 2D paired training data is available. We introduce a regularization method for improving 3D volume generation from 2D-to-2D deep learning image models and apply this approach to translate 3D TXM volumes to FIB-SEM fidelity. We then segment a predicted FIB-SEM volume into a flow simulation domain and calculate the sample apparent permeability using a lattice Boltzmann method (LBM) technique. Results show that our image translation approach produces simulation domains suitable for flow visualization and allows for accurate characterization of petrophysical properties from non-destructive imaging data.

58 GEOSCIENCES↗
DOE OSTI2022

Pseudomonas response regulators produced in an E. coli heterologous expression host exhibit host-derived post-translational phosphorylation

Abstract In this report, we systematically characterize 32 response regulators (RRs) from a metal tolerant groundwater isolate, Pseudomonas stutzeri RCH2 to assess the impact of host-derived post-translational phosphorylation. As observed by distinct shifted bands in a phos-tag gel, 12 of the 24 detected RRs show homogenous mixtures of phosphorylated proteins or heterogenous mixtures of unphosphorylated and phosphorylated proteins. By evaluating the phosphorylation state of CzcR and CopR II under varying assay parameters, we found that changes to pH and exogenous addition of phospho-donors (e.g. acetyl phosphate) have little to no effect on phosphorylation state. By applying protein production conditions that decrease the pool of intracellular acetyl-phosphate in E. coli , we found a reduction in the phosphorylated population of CopR II when magnesium was added to the medium, but observed no change in phosphorylated population when CopR II is expressed in E. coli BL21 (DE3) ∆pta , a mutant with a metabolic disruption to the acetyl-phosphate pathway. Therefore, the specific mechanism of post-translational phosphorylation of RRs in E. coli remains obscure. These findings show the importance of characterizing the phosphorylation state of proteins when heterologously expressed, since their biochemical and physiological properties can be dependent on post-translational modification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A riboswitch separated from its ribosome-binding site still regulates translation

Abstract Riboswitches regulate downstream gene expression by binding cellular metabolites. Regulation of translation initiation by riboswitches is posited to occur by metabolite-mediated sequestration of the Shine-Dalgarno sequence (SDS), causing bypass by the ribosome. Recently, we solved a co-crystal structure of a prequeuosine1-sensing riboswitch from Carnobacterium antarcticum that binds two metabolites in a single pocket. The structure revealed that the second nucleotide within the gene-regulatory SDS, G34, engages in a crystal contact, obscuring the molecular basis of gene regulation. Here, we report a co-crystal structure wherein C10 pairs with G34. However, molecular dynamics simulations reveal quick dissolution of the pair, which fails to reform. Functional and chemical probing assays inside live bacterial cells corroborate the dispensability of the C10–G34 pair in gene regulation, leading to the hypothesis that the compact pseudoknot fold is sufficient for translation attenuation. Remarkably, the C. antarcticum aptamer retained significant gene-regulatory activity when uncoupled from the SDS using unstructured spacers up to 10 nucleotides away from the riboswitch—akin to steric-blocking employed by sRNAs. Accordingly, our work reveals that the RNA fold regulates translation without SDS sequestration, expanding known riboswitch-mediated gene-regulatory mechanisms. The results infer that riboswitches exist wherein the SDS is not embedded inside a stable fold.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Anomalous strain-energy-driven macroscale translation of grains during nonisothermal annealing

We report a mode of grain growth, involving the macroscopic translation of grain centers during nonisothermal annealing. Through synchrotron high-energy x-ray diffraction microscopy, we find dissolution of semicoherent precipitates generates dislocations, thereby raising the stored strain energy within grains. Here, the subsequent evolution of grains shows unexpected grain translations over length scales of 10-100 mu m. Phase-field simulations reveal that such translations are not uncommon in strain-energy-driven grain growth, wherein different regions of a grain may grow and shrink simultaneously.

36 MATERIALS SCIENCE↗
DOE OSTI2023

UVCGAN: UNet Vision Transformer cycle-consistent GAN for unpaired image-to-image translation

Unpaired image-to-image translation has broad applications in art, design, and scientific simulations. One early breakthrough was CycleGAN that emphasizes one-to-one mappings between two unpaired image domains via generative-adversarial networks (GAN) coupled with the cycle-consistency constraint, while more recent works promote one-to-many mapping to boost diversity of the translated images. Motivated by scientific simulation and one-to-one needs, this work revisits the classic CycleGAN framework and boosts its performance to outperform more contemporary models without relaxing the cycle-consistency constraint. To achieve this, we equip the generator with a Vision Transformer (ViT) and employ necessary training and regularization techniques. Compared to previous best-performing models, our model performs better and retains a strong correlation between the original and translated image. An accompanying ablation study shows that both the gradient penalty and self-supervised pre-training are crucial to the improvement. To promote reproducibility and open science, the source code, hyperparameter configurations, and pre-trained model are available at https: //github.com/LS4GAN/uvcgan.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Quantitative cross-species translators of cardiac myocyte electrophysiology: Model training, experimental validation, and applications

Animal experimentation is key in the evaluation of cardiac efficacy and safety of novel therapeutic compounds. However, interspecies differences in the mechanisms regulating excitation-contraction coupling can limit the translation of experimental findings from animal models to human physiology and undermine the assessment of drugs’ efficacy and safety. Here, we built a suite of translators for quantitatively mapping electrophysiological responses in ventricular myocytes across species. We trained these statistical operators using a broad dataset obtained by simulating populations of our biophysically detailed computational models of action potential and Ca 2+ transient in mouse, rabbit, and human. We then tested our translators against experimental data describing the response to stimuli, such as ion channel block, change in beating rate, and β-adrenergic challenge. We demonstrate that this approach is well suited to predicting the effects of perturbations across different species or experimental conditions and suggest its integration into mechanistic studies and drug development pipelines.

60 APPLIED LIFE SCIENCES↗