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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 1,387 records · Page 77
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2’-dG in aptamer folding

Recent advancements in RNA structural biology have focused on unraveling the complexities of non-coding mRNA elements like riboswitches. These cis-acting regulatory regions undergo structural changes in response to specific cellular metabolites, leading to up or downregulation of downstream genes. The purine riboswitch family regulates many prokaryotic genes involved in purine degradation and biosynthesis. They feature an aptamer domain organized around a 3-way helical junction, where ligand encapsulation occurs at the junctional core. In our study, we chemically probed the aptamer domain of the 2’-dG-sensing purine riboswitch from Mesoplasma florum (dGsw) under various solution conditions to understand how Mg²⁺ and 2’-dG influence riboswitch folding. Here, we find that efficient 2’-dG binding strongly depends on Mg²⁺, indicating that Mg²⁺ is essential for priming dGsw for ligand interactions. We identified a previously undescribed sequence in the 5’ tail of dGsw that is complementary to a conserved helix. The inclusion of this region in a construct led to intramolecular competition between the alternate helix, Palt, and P1. Mutational analysis confirmed that 5’ flanking end of the aptamer domain forms an alternate helix in the absence of ligand. Molecular dynamics simulations revealed that this alternative conformation is stable. This helix may, therefore, facilitate the formation of an anti-terminator helix by opening the 3-way junction surrounding the 2’-dG binding site. Our study further establishes the importance of a closed terminal P1 helix conformation for metabolite binding and suggests that the delicate interplay between P1 and Palt may fine-tune downstream gene regulation. These insights offer a new perspective on riboswitch structure and enhance our understanding of the role that a conformational ensemble plays in riboswitch activity and regulation.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Unraveling Hidden Order and Dynamics in a Heterogeneous Ferroelectric System Using Machine Learning

We uploaded two batches of datasets: Batch-a) Equilibrium dynamics at a constant temperature at zero electric-field, with one trajectory each for 4-different defect structures (i.e. SETs 1 to 4). Each trajectory has a time-step of 0.25 fs, and is run for 7775000 time-steps, with snapshots written out every 4 time-steps (i.e. every 1fs); and Batch-b) Non-Equilibrium dynamics at a constant temperature with the same 0.25 fs time-step, but data dumped every 500 times-steps (i.e. every 125fs) for each of the SETs. The total trajectory of each defect structure (i.e. each SETs 1 to 4) is 2800000 time-steps (5600 snapshots), with stepping of electric-field by 0.01 V/Ã…, after every 100,000 time-steps (i.e. every 200 snapshots), from E=0 to E=0.05 V/Ã… to E = -0.05 V/Ã… to E=0.05 V/Ã….

36 MATERIALS SCIENCE↗
DOE OSTI2022

Rapid simulations of hyperspectral near-field images of three-dimensional heterogeneous surfaces – part II

The modeling of the near-field interaction in the scattering-type scanning near-field optical microscope (s-SNOM) is rapidly advancing, although an accurate yet versatile modeling framework that can be easily adapted to various complex situations is still lacking. In this work, we propose a time-efficient numerical scheme in the quasi-electrostatic limit to capture the tip-sample interaction in the near field. This method considers an extended tip geometry, which is a significant advantage compared to the previously reported method based on the point-dipole approximation. Using this formalism, we investigate, among others, nontrivial questions such as uniaxial and biaxial anisotropy in the near-field interaction, the relationship between various experimental parameters (e.g. tip radius, tapping amplitude, etc.), and the tip-dependent spatial resolution. The demonstrated method further sheds light on the understanding of the contrast mechanism in s-SNOM imaging and spectroscopy, while also representing a valuable platform for future quantitative analysis of the experimental observations.

Chen, Xinzhong (ORCID:0000000261033848)↗
DOE OSTI2024

Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Using heterogeneous data to identify signatures of dengue outbreaks at fine spatio-temporal scales across Brazil

Dengue virus remains a significant public health challenge in Brazil, and seasonal preparation efforts are hindered by variable intra- and interseasonal dynamics. Here, we present a framework for characterizing weekly dengue activity at the Brazilian mesoregion level from 2010–2016 as time series properties that are relevant to forecasting efforts, focusing on outbreak shape, seasonal timing, and pairwise correlations in magnitude and onset. In addition, we use a combination of 18 satellite remote sensing imagery, weather, clinical, mobility, and census data streams and regression methods to identify a parsimonious set of covariates that explain each time series property. The models explained 54% of the variation in outbreak shape, 38% of seasonal onset, 34% of pairwise correlation in outbreak timing, and 11% of pairwise correlation in outbreak magnitude. Regions that have experienced longer periods of drought sensitivity, as captured by the “normalized burn ratio,” experienced less intense outbreaks, while regions with regular fluctuations in relative humidity had less regular seasonal outbreaks. Both the pairwise correlations in outbreak timing and outbreak trend between mesoresgions were best predicted by distance. Our analysis also revealed the presence of distinct geographic clusters where dengue properties tend to be spatially correlated. Forecasting models aimed at predicting the dynamics of dengue activity need to identify the most salient variables capable of contributing to accurate predictions. Our findings show that successful models may need to leverage distinct variables in different locations and be catered to a specific task, such as predicting outbreak magnitude or timing characteristics, to be useful. This advocates in favor of “adaptive models” rather than “one-size-fits-all” models. The results of this study can be applied to improving spatial hierarchical or target-focused forecasting models of dengue activity across Brazil.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Arctic sea ice albedo: Spectral composition, spatial heterogeneity, and temporal evolution observed during the MOSAiC drift

The magnitude, spectral composition, and variability of the Arctic sea ice surface albedo are key to understanding and numerically simulating Earth’s shortwave energy budget. Spectral and broadband albedos of Arctic sea ice were spatially and temporally sampled by on-ice observers along individual survey lines throughout the sunlit season (April–September, 2020) during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition. The seasonal evolution of albedo for the MOSAiC year was constructed from spatially averaged broadband albedo values for each line. Specific locations were identified as representative of individual ice surface types, including accumulated dry snow, melting snow, bare and melting ice, melting and refreezing ponded ice, and sediment-laden ice. The area-averaged seasonal progression of total albedo recorded during MOSAiC showed remarkable similarity to that recorded 22 years prior on multiyear sea ice during the Surface Heat Budget of the Arctic Ocean (SHEBA) expedition. In accord with these and other previous field efforts, the spectral albedo of relatively thick, snow-free, melting sea ice shows invariance across location, decade, and ice type. In particular, the albedo of snow-free, melting seasonal ice was indistinguishable from that of snow-free, melting second-year ice, suggesting that the highly scattering surface layer that forms on sea ice during the summer is robust and stabilizing. In contrast, the albedo of ponded ice was observed to be highly variable at visible wavelengths. Notable temporal changes in albedo were documented during melt and freeze onset, formation and deepening of melt ponds, and during melt evolution of sediment-laden ice. While model simulations show considerable agreement with the observed seasonal albedo progression, disparities suggest the need to improve how the albedo of both ponded ice and thin, melting ice are simulated.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Residue Specific Characterization of Electrostatics, Conformational Heterogeneity, and Dynamics of Electron Transfer Proteins with Linear and Nonlinear Infrared Spectroscopy. Final Report

The goal of this research project was to further our understanding of biological electron transfer through the development and application of new methods for studying proteins and their complexes with high spatial and temporal detail. The approach was based on incorporation of reporter bonds with distinct vibrational frequencies at specific locations in proteins and their characterization through the interaction of the bonds with pulses of infrared light. The project focused on the proteins plastocyanin (Pc) and cytochrome (cyt) f, two electron transfer partners in photosynthesis. The first thrust of the project was the incorporation of carbon deuterium bonds as non-perturbative probes at a ligand to the copper ion of Pc and their use to detect changes in the bonding due to the number of electrons at the metal and how the bonding changes upon association with cyt f. Toward developing more advanced approaches to characterize proteins, we incorporated a stronger reporter, the cyano group of cyanophenylalanine, at several locations in Pc and measured the frequency dynamics in the absence and presence of cyt f. The acquired data improved the current model for the protein complex. Notably, the data indicated that the majority of the population is involved in a loosely bound complex, providing insight into the nature of the ensembles formed by electron transfer protein complexes that is not available via other approaches. In addition to learning about the protein complex, we made strides toward developing and improving the new experimental approach to study highly dynamic behaviors of proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

New Architecture to Support Integration and Processing of Seismic Data from Heterogeneous Sources

The Geophysical Monitoring Program (GMP) at Lawrence Livermore National Lab (LLNL) maintains a database and supporting infrastructure for geophysical data used in support of the Nuclear Detonation Detection mission. This database includes data from multiple sources, many of which do not distribute data to the public or for which there is no automated means of access. For example, Figure 1 shows (left) the distribution of waveform data in our database by source. The Incorporated Research Institutions for Seismology Data Management Center (IRISDMC) is our major source of waveform data and those data may be retrieved at will using the Federated Digital Seismograph Networks FDSN web Application Programming Interface (API). However, the next 6 most important sources of waveform data have no or only limited automated access to waveforms. As Figure 1 (right) shows, it is very common for waveform records associate with an event in our database to come from two or more sources, and in some cases data come from 10 sources. This diversity of data sources drives our need for efficient and correct integration of metadata, parametric data, and waveform data.

58 GEOSCIENCES↗
DOE OSTI2020

HePHAESTUS: Heat Pipe Heterogeneous Approximation of Energy and Navier-Stokes Equations, Transience, and Non-Uniform Surface Heating [Slides]

A heat pipe is a liquid/vapor filled metal pipe capable of transporting large amounts of heat through evaporation of a liquid at one end and condensation of vapor at the other end creating a closed fluid loop. Heat pipes are widely used in the cooling of electronics and in space applications. Heat pipes are typically composed of a pipe wall, a wick material, a working fluid, and a central vapor channel. Heat is transferred into the working fluid at the “evaporator” end, through an adiabatic section, and heat is removed at the opposite end at the “condenser.” If no wick is used, gravitational acceleration can circulate the fluid due to the buoyancy of the vapor in the central core and a falling film of liquid at the pipe wall forming a “thermosyphon."

42 ENGINEERING↗
DOE OSTI2020

Evaluation of PETSc on a Heterogeneous Architecture, the OLCF Summit System: Part II - Basic Communication Performance

Nearest-neighbor communication is at the heart of many high-performance parallel computations. We report on the performance of such communication on the Oak Ridge Leadership Computing Facility system Summit in the context of the PETSc communication module. The analysis in this report includes basic Ping-Pong point-to-point communication and regular and irregular nearest-neighbor communication.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Boosting Energy Efficiency of Heterogeneous Connected Automated Vehicle (CAV) Fleets via Anticipative and Cooperative Vehicle Guidance

In 2017, the Department of Energy funded a team at Clemson University and Argonne National Laboratory to develop collaborative perception and anticipative/predictive vehicle guidance schemes for Connected and Automated Vehicles (CAVs) and to quantify the energy saving potential of this technology in large scale traffic microsimulations at different levels of technology penetration and also experimentally. The project goal was demonstrating up to a 10% energy saving potential from different aspects of the implementation with a focus on reducing unnecessary braking events by anticipatory speed and lane selection. This project introduced novel anticipative car following and lane selection schemes for Connected and Automated Vehicles (CAVs). Our control schemes benefited from prediction of human driver behavior, information exchange between CAVs, and sometimes from collaboration to save energy, reduce braking events, and harmonize traffic. The energy savings was first demonstrated by traffic micro-simulations and then via a novel Vehicle-In-the-Loop (VIL) experimental testbed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Nanostructured, Targeted Layered Metal Oxides as Active and Selective Heterogeneous Electrocatalysts for Oxygen Evolution

Oxygen evolution reaction (OER) is an important chemical transformation that governs the performance of technologically relevant energy conversion and storage processes, such as electrochemical water splitting in electrolyzers and metal-air batteries. This reaction involves the evolution of oxygen gas from (i) oxygen ions formed from water splitting at high temperatures, (ii) oxygen containing species (i.e., OH, OOH) formed from water splitting at low temperatures, and (iii) metal-oxide discharge products (M x O 2 ) in metal-air batteries. One of the main challenges with OER is that it is catalyzed at low temperatures by noble metal-based electrocatalysts, which are expensive (making this process economically unviable), or at high temperatures by metal-oxide based electrocatalysts that are inefficient and lead to high overpotential losses. Our preliminary results, as well as other results in the literature, show that non-noble metal-based oxide electrocatalysts with layered structures, known as nickelate oxides, exhibit promising OER activity. Nickelate oxides (A 2 MO 4+δ ) belong to the Ruddlesden-Popper series composed of alternating perovskite-like and rocksalt-like layers. They are promising OER electrocatalysts due to their high oxygen transport/exchange properties compared to the state-of-the-art perovskite-type oxides. Unfortunately, these materials are fairly unexplored and little is known about the properties that govern their OER activity. Our preliminary studies, where we combine density functional theory (DFT) calculations, selective synthesis and characterization, show that engineering their nanocrystalline structure can significantly impact their catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗