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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Post-translational modifications: emerging directors of cell-fate decisions during endoplasmic reticulum stress in Arabidopsis thaliana

Homeostasis of the endoplasmic reticulum (ER) is critical for growth, development, and stress responses. Perturbations causing an imbalance in ER proteostasis lead to a potentially lethal condition known as ER stress. In ER stress situations, cell-fate decisions either activate pro-life pathways that reestablish homeostasis or initiate pro-death pathways to prevent further damage to the organism. Understanding the mechanisms underpinning cell-fate decisions in ER stress is critical for crop development and has the potential to enable translation of conserved components to ER stress-related diseases in metazoans. Post-translational modifications (PTMs) of proteins are emerging as key players in cell-fate decisions in situations of imbalanced ER proteostasis. In this review, we address PTMs orchestrating cell-fate decisions in ER stress in plants and provide evidence-based perspectives for where future studies may focus to identify additional PTMs involved in ER stress management.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Hijacking Translation Initiation for Synthetic Biology

Genetic code expansion (GCE) has revolutionized the field of protein chemistry. Over the past several decades more than 150 different noncanonical amino acids (ncAAs) have been co-translationally installed into proteins within various host organisms. Further, the vast majority of these ncAAs have been incorporated between the start and stop codons within an open reading frame. This requires that the ncAA be able to form a peptide bond at the α-amine, limiting the types of molecules that can be genetically encoded. In contrast, the α-amine of the initiating amino acid is not required for peptide bond formation. Therefore, including the initiator position in GCE allows for co-translational insertion of more diverse molecules that are modified, or completely lacking an α-amine. This review explores various methods which have been used to initiate protein synthesis with diverse molecules both in vitro and in vivo.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Solving a class of infinite-dimensional tensor eigenvalue problems by translational invariant tensor ring approximations

Here, we examine a method for solving an infinite-dimensional tensor eigenvalue problem Hx = λx, where the infinite-dimensional symmetric matrix H exhibits a translational invariant structure. We provide a formulation of this type of problem from a numerical linear algebra point of view and describe how a power method applied to e -Ht is used to obtain an approximation to the desired eigenvector. This infinite-dimensional eigenvector is represented in a compact way by a translational invariant infinite Tensor Ring (iTR). Low rank approximation is used to keep the cost of subsequent power iterations bounded while preserving the iTR structure of the approximate eigenvector. We show how the averaged Rayleigh quotient of an iTR eigenvector approximation can be efficiently computed and introduce a projected residual to monitor its convergence. In the numerical examples, we illustrate that the norm of this projected iTR residual can also be used to automatically modify the time step to ensure accurate and rapid convergence of the power method.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Translational research in the MPICH project

The MPICH project is an example of translational research in computer science before that term was well known or even coined. The project began in 1992 as an effort to develop a portable, high-performance implementation of the emerging Message-Passing Interface (MPI) Standard. It has enabled the widespread adoption of MPI as a way to write scalable parallel applications on systems of all sizes including upcoming exascale supercomputers. In this paper, we describe how the translational research process was used in MPICH, how that led to its success, the challenges encountered and lessons learned, and how the process could be applied to other similar projects.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Antibiotic that inhibits trans -translation blocks binding of EF-Tu to tmRNA but not to tRNA

trans-Translation is conserved throughout bacteria and is essential in many species. High-throughput screening identified a tetrazole-based trans-translation inhibitor, KKL-55, that has broad-spectrum antibiotic activity. A biotinylated version of KKL-55 pulled down elongation factor thermo-unstable (EF-Tu) from bacterial lysates. Purified EF-Tu bound KKL-55 in vitro with a K d = 2 µM, confirming a high-affinity interaction. An X-ray crystal structure showed that KKL-55 binds in domain 3 of EF-Tu, and mutation of residues in the binding pocket abolished KKL-55 binding. RNA-binding assays in vitro showed that KKL-55 inhibits binding between EF-Tu and transfer-messenger RNA (tmRNA) but not between EF-Tu and tRNA. These data demonstrate a new mechanism for the inhibition of EF-Tu function and suggest that this specific inhibition of EF-Tu•tmRNA binding is a viable target for antibiotic development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enhancing chemical bioproduction with rational control of bacterial post-translational modifications

Efficient conversion of inexpensive feedstocks to valuable chemicals by microbes is critical for a robust bioeconomy, but the ability to rationally design bacteria is hampered by insufficient knowledge of how post translational modifications (PTMs) control bacterial protein function and thus bioproduction phenotypes. Our study will focus on the lysine acetylation, a ubiquitous bacterial PTM that can affect the function of enzymes in central metabolism that are often critical for bioproduction processes, disrupt transcriptional regulation, and reduce translation. However, most lysine acetylation data is observational, which means that we do not know when, how, and what specific acetylated residues affect protein function and bacterial physiology. For our model host, we will use a Pseudomonas putida strain that we previously engineered to convert lignocellulosic feedstocks into chemicals such as itaconic acid (ITA). With this strain, we use a dynamic two-stage bioproduction process in which ITA is produced during a non-growth associated production phase. Production is highest during growth stages when lysine acetylation is low in other organisms (early stationary phase) and stalls in conditions where acetylation is highest (late stationary phase). The switch from high to stalled ITA production is also correlated with an unexpected increase in acetate levels – the precursor to non-enzymatic lysine acetylation. As such, we predict that lysine acetylation plays a substantial role in regulating the metabolic pathways required for ITA production. We will develop a generalizable approach that combines high-throughput genetic screens and cutting-edge genome engineering with state-of-the-art proteomics, metabolomics, and genetic code expansion methods to identify and modulate lysine acetylation patterns in bacteria. Ultimately, these strategies aim to manipulate protein expression and acetylation patterns to enhance bioproduction phenotypes (e.g., sustained ITA production in late stationary phase).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has provided some of the most in-depth analyses of the phenotypes of human tumors ever constructed. Today, the majority of proteomic data analysis is still performed using software housed on desktop computers which limits the number of sequence variants and post-translational modifications that can be considered. The original CPTAC studies limited the search for PTMs to only samples that were chemically enriched for those modified peptides. Similarly, the only sequence variants considered were those with strong evidence at the exon or transcript level. In this multi-institutional collaborative reanalysis, we utilized unbiased protein databases containing millions of human sequence variants in conjunction with hundreds of common post-translational modifications. Using these tools, we identified tens of thousands of high-confidence PTMs and sequence variants. We identified 4132 phosphorylated peptides in nonenriched samples, 93% of which were confirmed in the samples which were chemically enriched for phosphopeptides. In addition, our results also cover 90% of the high-confidence variants reported by the original proteogenomics study, without the need for sample specific next-generation sequencing. Finally, we report fivefold more somatic and germline variants that have an independent evidence at the peptide level, including mutations in ERRB2 and BCAS1. In this reanalysis of CPTAC proteomic data with cloud computing, we present an openly available and searchable web resource of the highest-coverage proteomic profiling of human tumors described to date.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Calibration and Validation of a Mechanistic COVID-19 Model for Translational Quantitative Systems Pharmacology – A Proof-of-Concept Model Development for Remdesivir

With the ongoing global pandemic of coronavirus disease 2019 (COVID-19), there is an urgent need to accelerate the traditional drug development process. Many studies identified potential COVID-19 therapies based on promising nonclinical data. However, the poor translatability from nonclinical to clinical settings has led to failures of many of these drug candidates in the clinical phase. In this study, we propose a mechanism-based, quantitative framework to translate nonclinical findings to clinical outcome. Adopting a modularized approach, this framework includes an in silico disease model for COVID-19 (virus infection and human immune responses) and a pharmacological component for COVID-19 therapies. Here, the disease model was able to reproduce important longitudinal clinical data for patients with mild and severe COVID-19, including viral titer, key immunological cytokines, antibody responses, and time courses of lymphopenia. Using remdesivir as a proof-of-concept example of model development for the pharmacological component, we developed a pharmacological model that describes the conversion of intravenously administered remdesivir as a prodrug to its active metabolite nucleoside triphosphate through intracellular metabolism and connected it to the COVID-19 disease model. After being calibrated with the placebo arm data, our model was independently and quantitatively able to predict the primary endpoint (time to recovery) of the remdesivir clinical study, Adaptive Covid-19 Clinical Trial (ACTT). Our work demonstrates the possibility of quantitatively predicting clinical outcome based on nonclinical data and mechanistic understanding of the disease and provides a modularized framework to aid in candidate drug selection and clinical trial design for COVID-19 therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational Modifications under Light Disturbance

Photosynthetic microorganisms rely on multiple pathways in central carbon metabolism to adapt to fluctuating light and energy availability across diel cycles. Mechanistic insight into the regulatory dynamics of this adaptation requires integrating processes spanning disparate timescales, from rapid redox-dependent post-translational modifications (PTMs) to slower changes in protein expression and metabolic pathway usage. To address this complexity beyond genome-based inference and traditional modeling, we develop a whole-cell four-dimensional (3D + time) model of the marine cyanobacterium Prochlorococcus marinus MED4 that explicitly represents the spatial organization of enzymatic and molecular processes in central carbon metabolism under light perturbation. We employ a perturbation-based research design to experimentally generate time-series, multi-omics measurements that provide molecular descriptors and cryo-ET derived 3D segmented volumes as constraints for this dynamic 4D framework. The integration of experiments and modeling across defined light regimes enables quantitative validation of system-level responses and forecasting under distinct light disturbances. We test the hypothesis that light-dependent redox PTMs regulating the structural assembly of a protein megacomplex, the “dark complex,” modulate metabolic flux at a conserved regulatory node of the Calvin–Benson cycle (CBC) in cyanobacteria. Our model shows that subcellular spatial organization buffers rapid light-induced changes in thylakoid reaction rates, which are followed by redox-PTM-mediated sequestration or release of CBC enzymes in the dark complex, ultimately impacting carbon fixation dynamics within carboxysomes. Comparison with an equivalently parameterized well-mixed stochastic model demonstrates that post-translational regulation not only buffers transcriptional noise and diffusion-driven fluctuations but also stabilizes phenotypic outcomes, underscoring the importance of spatial heterogeneity in phenotypic robustness. This ability to probe adaptive, spatiotemporally resolved mechanisms in photosynthetic machinery and central carbon metabolism addresses a critical gap in genotype-to-phenotype inference and expands modeling and design capabilities for understudied or genetically intractable autotrophs such as P. marinus MED4.

Johnson, Connah G.↗
DOE OSTI2023

TRANSLATE - a Monte Carlo simulation of electron transport in liquid argon

Here, the microphysics of electron and photon propagation in liquid argon is a key component of detector design and calibrations needed to construct and perform measurements within a wide range of particle physics experiments. As experiments grow in scale and complexity, and as the precision of their intended measurements increases, the development of tools to investigate important microphysics effects impacting such detectors becomes necessary. In this paper we present a new time-domain Monte Carlo simulation of electron transport in liquid argon. The simulation models the TRANSport in Liquid Argon of near-Thermal Electrons (TRANSLATE) with the aim of providing a multi-purpose software package for the study and optimization of detector environments, with a particular focus on ongoing and next generation liquid argon neutrino experiments utilizing the time projection chamber technology. TRANSLATE builds on previous work of Wojcik and Tachiya, amongst others, introducing additional processes, including ionization, thus modeling the full range of drift electron scattering interactions. The simulation is validated by benchmarking its performance with swarm parameters from data collected in experimental setups operating in gas and liquid.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Translating nanoparticle dosimetry from conventional in vitro systems to occupational inhalation exposures

As encouraged by Toxicity Testing in the 21st Century, researchers increasingly apply high-throughput in vitro approaches to identify and characterize nanoparticle hazards, including conventional aqueous cell culture systems to assess respiratory hazards. Translating nanoparticle dose from conventional toxicity testing systems to relevant human exposures remains a major challenge for assessing occupational risk of nanoparticle exposures. Here, we explored existing computational tools and data available to translate nanoparticle dose metrics from cellular test systems to inhalation exposures of silver nanoparticles in humans. We used the Multiple-Path Particle Dosimetry (MPPD) Model to predict deposition of humans exposed to 20 and 110 nm silver nanoparticles at 0.9 µg/m3 over an 8 hr period, the proposed a National Institute of Occupational Safety and Health (NIOSH) recommended exposure limit (REL). MPPD predicts 1.88 and 0.98 µg of silver deposited in an 8 hr period for 20 and 110 nm nanoparticles, respectively, with 20 nm particles displaying nearly 11-fold higher total surface area deposited. Peak nanoparticle concentrations occurred more proximal in the pulmonary tract compared to mass deposition patterns (generation 5 vs. generations 20-21, respectively) due to regional differences in lung lining fluid volumes. Assuming 0.4% nanoparticle dissolution by mass as previously measured, we predict peak concentrations of silver ions in cells of 0.24 and 0.17 µg/mL for 20 and 110 nm particles, respectively. Both predicted concentrations are below the measured toxic threshold of 1.7 µg/mL of silver ions in cells from in vitro assessments. Assuming 4% dissolution by mass, we predict 10-fold higher silver concentrations in tissues, peaking at 2.4 and 1.7 µg/mL, for 20 and 110 nm nanoparticles respectively, exceeding the observed in vitro toxic threshold and highlighting the importance and sensitivity of dissolution rates. Overall, this approach offers a framework for extrapolating nanotoxicity results from in vitro cell culture systems to human exposures. Aligning appropriate dose metrics from in vitro and in vivo hazard characterizations and human pulmonary doses from occupational exposures are critical components for successful nanoparticle risk assessment and worker protection and provide guidance for designing future in vitro studies aimed at relevant human exposures.

Smith, Jordan N.↗
DOE OSTI2026

Insights into Rotational and Translational Dynamics in Mixtures of Ethylene Glycol and Choline Chloride Using Nuclear Magnetic Resonance Techniques

This work examines molecular dynamics and interactions in ethylene glycol–choline chloride (EG–ChCl) mixtures across 0–33 mol % ChCl, spanning the true eutectic region near 17–20 mol % and the commonly used 1:2 formulation. We combine pulsed-field-gradient (PFG) diffusion, fast-field-cycling (FFC) relaxometry, temperature-dependent 13 C T 1 , and nuclear Overhauser effect spectroscopy (NOESY) to disentangle local from macroscopic dynamics. PFG and FFC show that both translational and average rotational motions largely track the strong increase in viscosity with ChCl content, with ethylene glycol consistently diffusing faster than the choline cation and no global dynamical anomaly at the eutectic composition. More subtle, site-specific composition effects nevertheless emerge. The ratio of the diffusion coefficient of the hydroxyl group of choline to the diffusion coefficient of the methyl group of choline displays a shallow minimum in the 17–25 mol % region, indicating a modest change in how the hydroxyl-bearing end of choline samples the underlying translational motion relative to the methyl groups. 13 C T 1 analysis shows that rotational correlation times at 25 °C generally increase with ChCl, reflecting viscosity-coupled slowing, while the CH 2 –N α site exhibits a small but reproducible deviation from this monotonic trend near the eutectic. NOESY spectra at similar compositions reveal enhanced cross-relaxation between EG and choline protons, consistent with increased headgroup–solvent contact density rather than a wholesale structural rearrangement. Overall, our multitechnique study demonstrates that EG–ChCl dynamics are predominantly viscosity-dominated, with the eutectic region acting as a subtle dynamical crossover where specific choline segments become maximally coupled to the hydrogen-bond network. These insights refine the structure–dynamics picture of choline-chloride DESs and provide practical guidance for tuning composition in electrochemical, separation, and catalytic applications.

diffusion↗
DOE OSTI2022

Rotational and translational diffusion of liquid n-hexane: EFP-based molecular dynamics analysis

Molecular Dynamics (MD) simulations based on the Effective Fragment Potential (EFP) method are utilized to provide a comprehensive assessment of diffusion in liquid n-hexane. We decompose translational diffusion into components along and orthogonal to the long axis of the molecule. Rotational diffusion is decomposed into tumbling and spinning motions about this axis. Our analysis yields four corresponding diffusion coefficients which are related to diagonal entries in the complete 6 × 6 diffusion tensor accounting for the three rotational and three translational degrees of freedom and for the potential coupling between them. However, coupling between different degrees of freedom is expected to be minimal for a natural choice of the molecular body-fixed axis, so then off-diagonal entries in the tensor are negligible. This expectation is supported by a hydrodynamic analysis of the diffusion tensor which treats the liquid surrounding the molecule being tracked as a viscous continuum. Thus, the EFP MD analysis provides a comprehensive characterization of diffusion and also reveals expected shortcomings of the hydrodynamic treatment, particularly for rotational diffusion, when applied to neat liquids.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Translational diffusion in supercooled water at and near the glass transition temperature—136 K

The properties of amorphous solid water at and near the calorimetric glass transition temperature, T g , of 136 K have been debated for years. One hypothesis is that water turns into a “true” liquid at T g (i.e., it becomes ergodic) and exhibits all the characteristics of an ergodic liquid, including translational diffusion. A competing hypothesis is that only rotational motion becomes active at T g , while the “real” glass transition in water is at a considerably higher temperature. To address this dispute, we have investigated the diffusive mixing in nanoscale water films, with thicknesses up to ∼100 nm, using infrared (IR) spectroscopy. The experiments used films that were composed of at least 90% H 2 O with D 2 O making up the balance and were conducted under conditions where H/D exchange was essentially eliminated. Because the IR spectra of multilayer D 2 O films (e.g., thicknesses of ∼3–6 nm) embedded within thick H 2 O films are distinct from the spectrum of isolated D 2 O molecules within H 2 O, the diffusive mixing of (initially) isotopically layered water films could be followed as a function of annealing time and temperature. The results show that water films with total thicknesses ranging from ∼20 to 100 nm diffusively mixed prior to crystallization for temperatures between 120 and 144 K. The translational diffusion had an Arrhenius temperature dependence with an activation energy of 40.8 ± 3.5 kJ/mol, which indicates that water at and near T g is a strong liquid. The measured diffusion coefficient at 136 K is 6.25 ± 1.4 × 10 −21 m 2 /s.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The role of non-standard translation in Candida albicans pathogenesis

ABSTRACT Candida albicans typically resides in the human gastrointestinal tract and mucosal membranes as a commensal organism. To adapt and cope with the host immune system, it has evolved a variety of mechanisms of adaptation such as stress-induced mutagenesis and epigenetic regulation. Niche-specific patterns of gene expression also allow the fungus to fine-tune its response to specific microenvironments in the host and switch from harmless commensal to invasive pathogen. Proteome plasticity produced by CUG ambiguity, on the other hand is emerging as a new layer of complexity in C. albicans adaptation, pathogenesis, and drug resistance. Such proteome plasticity is the result of a genetic code alteration where the leucine CUG codon is translated mainly as serine (97%), but maintains some level of leucine (3%) assignment. In this review, we dissect the link between C. albicans non-standard CUG translation, proteome plasticity, host adaptation and pathogenesis. We discuss published work showing how this pathogen uses the fidelity of protein synthesis to spawn novel virulence traits.

Bezerra, Ana Rita (ORCID:0000000346131711)↗
DOE OSTI2022

Translation and rotation equivariant normalizing flow (TRENF) for optimal cosmological analysis

ABSTRACT Our Universe is homogeneous and isotropic, and its perturbations obey translation and rotation symmetry. In this work, we develop translation and rotation equivariant normalizing flow (TRENF), a generative normalizing flow (NF) model which explicitly incorporates these symmetries, defining the data likelihood via a sequence of Fourier space-based convolutions and pixel-wise non-linear transforms. TRENF gives direct access to the high dimensional data likelihood p(x|y) as a function of the labels y, such as cosmological parameters. In contrast to traditional analyses based on summary statistics, the NF approach has no loss of information since it preserves the full dimensionality of the data. On Gaussian random fields, the TRENF likelihood agrees well with the analytical expression and saturates the Fisher information content in the labels y. On non-linear cosmological overdensity fields from N-body simulations, TRENF leads to significant improvements in constraining power over the standard power spectrum summary statistic. TRENF is also a generative model of the data, and we show that TRENF samples agree well with the N-body simulations it trained on, and that the inverse mapping of the data agrees well with a Gaussian white noise both visually and on various summary statistics: when this is perfectly achieved the resulting p(x|y) likelihood analysis becomes optimal. Finally, we develop a generalization of this model that can handle effects that break the symmetry of the data, such as the survey mask, which enables likelihood analysis on data without periodic boundaries.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Fractonic coset construction for spontaneously broken translations

We study the homogeneous breaking of spatial translation symmetry concomitantly with the spontaneous breaking of other internal and spacetime symmetries, including dilations. We use the symmetry-breaking pattern as the only input to derive, via the coset construction, general effective field theories for the symmetry-originated modes associated with Goldstone’s theorem, namely the Nambu-Goldstone candidates. Through explicit computations, we show that integrating out the explicit massive Nambu-Goldstone candidates or imposing symmetric constraints, namely the inverse Higgs constraints, to express massive modes in terms of the massless ones leads to physically distinct effective field theories. This sensitivity to the chosen method can be traced back to the homogeneous breaking of translations, the homogeneous aspect of the breaking induces a mixing between internal and spacetime symmetries at the level of the Lie algebra. This, in turn, leads to subtle discussions about the inverse Higgs constraints, in particular that they lead to a loss of generality in our specific examples. The derived general effective field theories also give rise to a broad class of theories exhibiting emergent enhanced shift symmetries, which constrain the mobility of the modes. The latter are referred to as fractonic modes. Published by the American Physical Society 2025

Chavda, Ameya (ORCID:0000000211731605)↗
DOE OSTI2020

ACTT: Automotive CAN Tokenization and Translation

Modern vehicles contain scores of Electrical Control Units (ECUs) that broadcast messages over a Controller Area Network (CAN). Vehicle manufacturers rely on security through obscurity by concealing their unique mapping of CAN messages to vehicle functions which differs for each make, model, year, and even trim. This poses a major obstacle for after-market modifications notably performance tuning and in-vehicle network security measures. We present ACTT: Automotive CAN Tokenization and Translation, a novel, vehicle-agnostic, algorithm that leverages available diagnostic information to parse CAN data into meaningful messages, simultaneously cutting binary messages into tokens, and learning the translation to map these contiguous bits to the value of the vehicle function communicated.

Verma, Miki↗