Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Translational”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

From photosynthetic electron flow to gene regulation: redox signal transduction in cyanobacteria

In cyanobacteria, the free-living ancestors of chloroplasts, photosynthesis simultaneously sustains growth and generates reactive oxygen species (ROS) that damage proteins, lipids, and DNA when light capture outpaces carbon fixation. Maintaining redox balance, therefore, requires cells to read photosynthetic electron flow as a signal that continuously tunes gene expression and protein activity. This review traces how these redox signals are transduced to transcription machinery through three routes: membrane-localized sensors, cytoplasmic redox sensors downstream of photosystem I, and ROS generated when electron sinks are saturated. Membrane-bound histidine kinases (two-component systems) relay the redox state of the plastoquinone pool to control photosystem remodeling, pigment biosynthesis, and circadian timing. Cytoplasmic one-component regulators, by contrast, sense redox directly through thiol-disulfide switches, glutathionylation, iron-sulfur clusters, and metal-catalyzed oxidation to control photosystem-cofactor, electron-carrier, and transition-metal homeostasis. Because many of these regulators persist in algal and plant chloroplasts, cyanobacteria illuminate principles of redox control across photosynthetic eukaryotes. Post-transcriptional and translational control further shapes redox-dependent gene expression programs through transcript stability, ribosome assembly, and translation initiation, extending redox regulation beyond transcription to every step of protein synthesis and even activity modulation. Finally, we connect redox regulation to photosynthetic physiology, stress resilience, and the rational engineering of cyanobacteria for sustainable bioproduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genomic factors shaping codon usage across the Saccharomycotina subphylum

Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. It has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. We characterized codon usage across 1,154 strains from 1,051 species from the fungal subphylum Saccharomycotina to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns. We found a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is distinct between the 12 orders to such a degree that yeasts can be classified with an accuracy >90% using a machine learning algorithm. We also characterized the degree to which codon usage bias is impacted by translational selection. We found it was influenced by a combination of features, including the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that avoidance of the CGN codons is associated with a decline in arginine tRNA function. Consistent with previous findings, codon usage bias within the Saccharomycotina is shaped by genomic features and GC bias. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Cytochromes P450 involved in bacterial RiPP biosyntheses

Abstract Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of secondary metabolites that have garnered scientific attention due to their complex scaffolds with potential roles in medicine, agriculture, and chemical ecology. RiPPs derive from the cleavage of ribosomally synthesized proteins and additional modifications, catalyzed by various enzymes to alter the peptide backbone or side chains. Of these enzymes, cytochromes P450 (P450s) are a superfamily of heme-thiolate proteins involved in many metabolic pathways, including RiPP biosyntheses. In this review, we focus our discussion on P450 involved in RiPP pathways and the unique chemical transformations they mediate. Previous studies have revealed a wealth of P450s distributed across all domains of life. While the number of characterized P450s involved in RiPP biosyntheses is relatively small, they catalyze various enzymatic reactions such as C–C or C–N bond formation. Formation of some RiPPs is catalyzed by more than one P450, enabling structural diversity. With the continuous improvement of the bioinformatic tools for RiPP prediction and advancement in synthetic biology techniques, it is expected that further cytochrome P450-mediated RiPP biosynthetic pathways will be discovered. Summary The presence of genes encoding P450s in gene clusters for ribosomally synthesized and post-translationally modified peptides expand structural and functional diversity of these secondary metabolites, and here, we review the current state of this knowledge.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Expanding the genetic toolset: using serine recombinases to integrate riboregulatory elements into industrially relevant microbial chassis

To realize the full potential of biomanufacturing, the breadth of industrial microbes used to consume diverse feedstock and generate bioproducts needs to expand. As such, portable tools are required that can be used by multiple hosts for straightforward genomic manipulation and precise gene expression. Here, we demonstrate the co-utilization of two synthetic biology tools to achieve these goals: cis-repressors (CRs) and serine recombinase-assisted genome engineering (SAGE). CRs are small, noncoding RNAs that are placed upstream of the target gene to modulate bacterial translation rates at varying, discrete levels. SAGE uses site-specific serine recombinases to catalyze highly efficient, unidirectional insertion of DNA into the chromosome of diverse organisms. We used SAGE to integrate a suite of CRs into the industrially relevant hosts Pseudomonas putida, Corynebacterium glutamicum, and Cupriavidus necator. Using a fluorescent reporter as a readout of CR functionality, we found that CR performance across these backgrounds was similar—providing a range of translational repression up to 100-fold. Overall, these results demonstrate the high portability of CRs across bacterial genetic backgrounds, which ideally can be used in future microbial engineering efforts pertinent to biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

DNA Breaks-Mediated Fitness Cost Reveals RNase HI as a New Target for Selectively Eliminating Antibiotic-Resistant Bacteria

Abstract Antibiotic resistance often generates defects in bacterial growth called fitness cost. Understanding the causes of this cost is of paramount importance, as it is one of the main determinants of the prevalence of resistances upon reducing antibiotics use. Here we show that the fitness costs of antibiotic resistance mutations that affect transcription and translation in Escherichia coli strongly correlate with DNA breaks, which are generated via transcription–translation uncoupling, increased formation of RNA–DNA hybrids (R-loops), and elevated replication–transcription conflicts. We also demonstrated that the mechanisms generating DNA breaks are repeatedly targeted by compensatory evolution, and that DNA breaks and the cost of resistance can be increased by targeting the RNase HI, which specifically degrades R-loops. We further show that the DNA damage and thus the fitness cost caused by lack of RNase HI function drive resistant clones to extinction in populations with high initial frequency of resistance, both in laboratory conditions and in a mouse model of gut colonization. Thus, RNase HI provides a target specific against resistant bacteria, which we validate using a repurposed drug. In summary, we revealed key mechanisms underlying the fitness cost of antibiotic resistance mutations that can be exploited to specifically eliminate resistant bacteria.

Balbontín, Roberto↗
DOE OSTI2021

Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication

Abstract Mosquito-borne flaviviruses (MBFVs) including dengue, West Nile, yellow fever, and Zika viruses have an RNA genome encoding one open reading frame flanked by 5′ and 3′ untranslated regions (UTRs). The 3′ UTRs of MBFVs contain regions of high sequence conservation in structured RNA elements known as dumbbells (DBs). DBs regulate translation and replication of the viral RNA genome, functions proposed to depend on the formation of an RNA pseudoknot. To understand how DB structure provides this function, we solved the x-ray crystal structure of the Donggang virus DB to 2.1Å resolution and used structural modeling to reveal the details of its three-dimensional fold. The structure confirmed the predicted pseudoknot and molecular modeling revealed how conserved sequences form a four-way junction that appears to stabilize the pseudoknot. Single-molecule FRET suggests that the DB pseudoknot is a stable element that can regulate the switch between translation and replication during the viral lifecycle by modulating long-range RNA conformational changes.

Akiyama, Benjamin M.↗
DOE OSTI2023

The Human Phenotype Ontology in 2024: phenotypes around the world

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut

Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating > 200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G–U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G–C base pairs (G3:C70 and G5:C68).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era

Abstract The aquatic Lemnaceae family, commonly called duckweed, comprises some of the smallest and fastest growing angiosperms known on Earth. Their tiny size, rapid growth by clonal propagation, and facile uptake of labeled compounds from the media were attractive features that made them a well-known model for plant biology from 1950 to 1990. Interest in duckweed has steadily regained momentum over the past decade, driven in part by the growing need to identify alternative plants from traditional agricultural crops that can help tackle urgent societal challenges, such as climate change and rapid population expansion. Propelled by rapid advances in genomic technologies, recent studies with duckweed again highlight the potential of these small plants to enable discoveries in diverse fields from ecology to chronobiology. Building on established community resources, duckweed is reemerging as a platform to study plant processes at the systems level and to translate knowledge gained for field deployment to address some of society’s pressing needs. This review details the anatomy, development, physiology, and molecular characteristics of the Lemnaceae to introduce them to the broader plant research community. We highlight recent research enabled by Lemnaceae to demonstrate how these plants can be used for quantitative studies of complex processes and for revealing potentially novel strategies in plant defense and genome maintenance.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Quantitative proteomics reveals extensive lysine ubiquitination and transcription factor stability states in Arabidopsis

Abstract Protein activity, abundance, and stability can be regulated by post-translational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function; yet, we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich ubiquitinated peptides coupled with isobaric labeling to enable quantification of up to 18-multiplexed samples. This approach identified 17,940 ubiquitinated lysine sites arising from 6,453 proteins from Arabidopsis (Arabidopsis thaliana) primary roots, seedlings, and rosette leaves. Gene ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and metabolism. We determined ubiquitinated lysine residues that directly regulate the stability of three transcription factors, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 (CIB1), CIB1 LIKE PROTEIN 2 (CIL2), and SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1) using in vivo degradation assays. Furthermore, codon mutation of CIB1 to create a K166R conversion to prevent ubiquitination, via CRISPR/Cas9-derived adenosine base editing, led to an early flowering phenotype and increased expression of FLOWERING LOCUS T (FT). These comprehensive site-level ubiquitinome profiles provide a wealth of data for future functional studies related to modulation of biological processes mediated by this post-translational modification in plants.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Electric field control of magnetism

Electric field control of magnetism is an extremely exciting area of research, from both a fundamental science and an applications perspective and has the potential to revolutionize the world of computing. To realize this will require numerous further innovations, both in the fundamental science arena as well as translating these scientific discoveries into real applications. Thus, this article will attempt to bridge the gap between condensed matter physics and the actual manifestations of the physical concepts into applications. We have attempted to paint a broad-stroke picture of the field, from the macroscale all the way down to the fundamentals of spin–orbit coupling that is a key enabler of the physics discussed. Here, we hope it will help spur more translational research within the broad materials physics community. Needless to say, this article is written on behalf of a large number of colleagues, collaborators and researchers in the field of complex oxides as well as current and former students and postdocs who continue to pursue cutting-edge research in this field.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Reconstruction of beam parameters and betatron radiation spectra measured with a Compton spectrometer

The photon flux resulting from high-energy electron beam interactions with high-field systems, such as those found in the upcoming FACET-II experiments at the SLAC National Accelerator Laboratory, yields deep insight into the electron beam’s underlying dynamics during the interaction. However, extracting this information is an intricate process. To demonstrate how to approach this challenge using modern methods, this paper utilizes simulated data that models plasma wakefield acceleration-derived betatron radiation in experiments to determine reliable methods of reconstructing key beam and beam-plasma interaction properties. For betatron radiation measurements, translating the observed 200⁢ keV to 30⁢ MeV photon double-differential energy-angle spectra obtained from an advanced Compton spectrometer requires testing multiple methods to optimize the pipeline from its response to incident electron beam information. The paper compares maximum likelihood estimation and machine learning to refine the translation of photon spectra into precise electron beam metrics, such as spot size, energy, and emittance, enhancing the understanding of beam behavior within these dense, high-field environments. We also introduce machine learning and the expected maximization algorithm to reconstruct the primary photon spectrum, employing a multilayer neural network for regression analysis of the energy and angle spectra. With appropriate modifications, the advanced methods reproduce relevant incident beam parameters with high accuracy, even for beam sizes in the <10 μ⁢m range. This capacity is critical to understanding intense beam propagation and its optimization in plasma.

Beam code development & simulation techniques↗
DOE OSTI2023

Triplet pair density wave superconductivity on the π -flux square lattice

Pair-density waves (PDWs) are superconducting states that spontaneously break translation symmetry in systems with time-reversal symmetry (TRS). Evidence for PDWs has been seen in several recent experiments, as well as in the pseudogap regime in cuprates. Theoretical understanding of PDWs has been largely restricted to phenomenological and numerical studies, while microscopic theories typically require strong coupling or fine tuning. In this work, we provide a symmetry-based mechanism under which PDWs emerge as a weak-coupling instability of a two-dimensional TRS metal. Combining mean-field and renormalization-group analyses, we identify a weak-coupling instability towards a triplet PDW realized in the π-flux square lattice model with on-site repulsion and moderate nearest-neighbor attraction when the Fermi level crosses Van Hove singularities at 1/4 and 3/4 fillings. Further, this PDW is protected by the magnetic translation symmetries characteristic of Hofstadter systems, of which the π-flux lattice is a special time-reversal-symmetric case.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Ab initio leading order effective potential for elastic proton scattering based on the symmetry-adapted no-core shell model

Calculating microscopic optical potentials for elastic scattering at intermediate energies from light nuclei in an ab initio fashion within the Watson expansion has been established within the last few years. Based on the Watson expansion of the multiple scattering series, we employ a nonlocal translationally invariant nuclear density derived within the symmetry-adapted no-core shell model (SA-NCSM) framework from a chiral next-to-next-to-leading order (NNLO) nucleon-nucleon interaction and the very same interaction for a consistent full-folding calculation of the effective (optical) potential for nucleon-nucleus scattering for medium-heavy nuclei. The leading order effective (optical) folding potential is computed by integrating over a translationally invariant SA-NCSM one-body scalar density, spin-projected momentum distribution, and the Wolfenstein amplitudes 𝐴, 𝐶, and 𝑀. The resulting nonlocal potentials serve as input for a momentum space Lippmann-Schwinger equation. In the SA-NCSM, the model space is systematically up-selected using Sp⁡(3,ℝ) symmetry considerations. For the light nucleus of 6 He, we establish a systematic selection scheme in the SA-NCSM for scattering observables. Then, we apply this scheme to calculations of scattering observables, such as differential cross sections, analyzing powers, and spin rotation functions for elastic proton scattering from 20 Ne and 40 Ca in the energy regime between 65 and 200 MeV, and compare to available data. Furthermore, our calculations show that the leading order effective nucleon-nucleus potential in the Watson expansion of multiple scattering theory obtained from an up-selected SA-NCSM model space describes 40 Ca elastic scattering observables reasonably well to about 60 degrees in the center-of-mass frame, which coincides roughly with the validity of the NNLO chiral interaction used to calculate both the nucleon-nucleon amplitudes and the one-body scalar and spin nuclear densities.

Ab initio calculations↗
DOE OSTI2024

Gauging staggered fermion shift symmetries

Staggered fermion shift symmetries correspond to translations of the fermion field within the unit cell of a hypercubic lattice. They satisfy an algebra and in four Euclidean dimensions can be related to a discrete subgroup of an S U ( 4 ) flavor symmetry which plays a crucial role in showing that staggered fermions lead to a theory of four degenerate Dirac fermions in the continuum limit. They are associated with the appearance of certain Z 2 valued global parameters. We propose a strategy to try to partially gauge these translation symmetries by allowing these parameters to vary locally in the lattice. To maintain invariance of the action requires the addition of Z 2 valued higher form lattice gauge fields. An analogous procedure can be carried out for reduced staggered fermions where the shifts correspond to a discrete subgroup of an S O ( 4 ) flavor symmetry. Published by the American Physical Society 2024

Catterall, Simon (ORCID:0000000327352682)↗
DOE OSTI2020

Fractional Quantum Hall Effect in Weyl Semimetals

Weyl semimetal may be thought of as a gapless topological phase protected by the chiral anomaly, where the symmetries involved in the anomaly are the U(1) charge conservation and the crystal translational symmetry. The absence of a band gap in a weakly interacting Weyl semimetal is mandated by the electronic structure topology and is guaranteed as long as the symmetries and the anomaly are intact. The nontrivial topology also manifests in the Fermi arc surface states and topological response, in particular taking the form of an anomalous Hall effect in magnetic Weyl semimetals, whose magnitude is only determined by the location of the Weyl nodes in the Brillouin zone. In this work, we consider the situation when the interactions are not weak and ask whether it is possible to open a gap in a magnetic Weyl semimetal while preserving its nontrivial electronic structure topology along with the translational and the charge conservation symmetries. Surprisingly, the answer turns out to be yes. The resulting topologically ordered state provides a nontrivial realization of the fractional quantum Hall effect in three spatial dimensions in the absence of an external magnetic field, which cannot be viewed as a stack of two dimensional states. Our state contains loop excitations with nontrivial braiding statistics when linked with lattice dislocations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Nondispersing Wave Packets in Lattice Floquet Systems

We show that in a one-dimensional translationally invariant tight binding chain, nondispersing wave packets can in general be realized as Floquet eigenstates—or linear combinations thereof—using a spatially inhomogeneous drive, which can be as simple as modulation on a single site. The recurrence time of these wave packets (their “round-trip” time) locks in at rational ratios sT/r of the driving period T, where s, r are coprime integers. Wave packets of different s / r can coexist under the same drive, yet travel at different speeds. They retain their spatial compactness either infinitely (s/r = 1) or over a long time (s/r ≠ 1). Discrete time translation symmetry is manifestly broken for s ≠ 1, reminiscent of integer and fractional Floquet time crystals. We further demonstrate how to reverse engineer a drive protocol to reproduce a target Floquet micromotion, such as the free propagation of a wave packet, as if coming from a strictly linear energy spectrum. The variety of control schemes open up a new avenue for Floquet engineering in quantum information sciences.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Strange Metals as Ersatz Fermi Liquids

Here, a long-standing mystery of fundamental importance in correlated electron physics is to understand strange non-Fermi liquid metals that are seen in diverse quantum materials. A striking experimental feature of these metals is a resistivity that is linear in temperature (T). In this Letter we ask what it takes to obtain such non-Fermi liquid physics down to zero temperature in a translation invariant metal. If in addition the full frequency (ω) dependent conductivity satisfies ω/T scaling, we argue that the T-linear resistivity must come from the intrinsic physics of the low energy fixed point. Combining with earlier arguments that compressible translation invariant metals are “ersatz Fermi liquids” with an infinite number of emergent conserved quantities, we obtain powerful and practical conclusions. We show that there is necessarily a diverging susceptibility for an operator that is odd under inversion and time reversal symmetries, and has zero crystal momentum. We discuss a few other experimental consequences of our arguments, as well as potential loopholes, which necessarily imply other exotic phenomena.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗