Search NASA⌕ Search

SEARCH · Search NASA

Results for “transfer line”

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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Cosmic Reionization on Computers: Statistics, Physical Properties, and Environments of Lyman Limit Systems at z ~ 6

Lyman limit systems (LLSs) are dense hydrogen clouds with high enough H i column densities to absorb Lyman continuum photons emitted from distant quasars. Their high column densities imply an origin in dense environments; however, the statistics and distribution of LLSs at high redshifts still remain uncertain. In this paper, we use self-consistent radiative transfer cosmological simulations from the Cosmic Reionization on Computers (CROC) project to study the physical properties of LLSs at the tail end of cosmic reionization at z ~ 6. We generate 3000 synthetic quasar sight lines to obtain a large number of LLS samples in the simulations. In addition, with the high physical fidelity and resolution of CROC, we are able to quantify the association between these LLS samples and nearby galaxies. Our results show that the fraction of LLSs spatially associated with nearby galaxies increases with H i column density. Moreover, we find that LLSs that are not near any galaxy typically reside in filamentary structures connecting neighboring galaxies in the intergalactic medium (IGM). This quantification of the distribution and association of LLSs to large-scale structure informs our understanding of the IGM–galaxy connection during the "Epoch of Reionization," and provides a theoretical basis for interpreting future observations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Enhancers are important non-coding elements, but they have traditionally been hard to characterize experimentally. The development of massively parallel assays allows the characterization of large numbers of enhancers for the first time. Here, we developed a framework using Drosophila STARR-seq to create shape-matching filters based on meta-profiles of epigenetic features. We integrated these features with supervised machine-learning algorithms to predict enhancers. We further demonstrated that our model could be transferred to predict enhancers in mammals. We comprehensively validated the predictions using a combination of in vivo and in vitro approaches, involving transgenic assays in mice and transduction-based reporter assays in human cell lines (153 enhancers in total). The results confirmed that our model can accurately predict enhancers in different species without re-parameterization. Finally, we examined the transcription factor binding patterns at predicted enhancers versus promoters. Here, we demonstrated that these patterns enable the construction of a secondary model that effectively distinguishes enhancers and promoters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Expression of a bacterial 3-dehydroshikimate dehydratase (QsuB) reduces lignin and improves biomass saccharification efficiency in switchgrass (Panicum virgatum L.)

Abstract Background Lignin deposited in plant cell walls negatively affects biomass conversion into advanced bioproducts. There is therefore a strong interest in developing bioenergy crops with reduced lignin content or altered lignin structures. Another desired trait for bioenergy crops is the ability to accumulate novel bioproducts, which would enhance the development of economically sustainable biorefineries. As previously demonstrated in the model plant Arabidopsis, expression of a 3-dehydroshikimate dehydratase in plants offers the potential for decreasing lignin content and overproducing a value-added metabolic coproduct (i.e., protocatechuate) suitable for biological upgrading. Results The 3-dehydroshikimate dehydratase QsuB from Corynebacterium glutamicum was expressed in the bioenergy crop switchgrass ( Panicum virgatum L.) using the stem-specific promoter of an O-methyltransferase gene ( pShOMT ) from sugarcane. The activity of pShOMT was validated in switchgrass after observation in-situ of beta-glucuronidase (GUS) activity in stem nodes of plants carrying a pShOMT::GUS fusion construct. Under controlled growth conditions, engineered switchgrass lines containing a pShOMT::QsuB construct showed reductions of lignin content, improvements of biomass saccharification efficiency, and accumulated higher amount of protocatechuate compared to control plants. Attempts to generate transgenic switchgrass lines carrying the QsuB gene under the control of the constitutive promoter pZmUbi-1 were unsuccessful, suggesting possible toxicity issues associated with ectopic QsuB expression during the plant regeneration process. Conclusion This study validates the transfer of the QsuB engineering approach from a model plant to switchgrass. We have demonstrated altered expression of two important traits: lignin content and accumulation of a co-product. We found that the choice of promoter to drive QsuB expression should be carefully considered when deploying this strategy to other bioenergy crops. Field-testing of engineered QsuB switchgrass are in progress to assess the performance of the introduced traits and agronomic performances of the transgenic plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Geospatial mapping of distribution grid with machine learning and publicly-accessible multi-modal data

Abstract Detailed and location-aware distribution grid information is a prerequisite for various power system applications such as renewable energy integration, wildfire risk assessment, and infrastructure planning. However, a generalizable and scalable approach to obtain such information is still lacking. In this work, we develop a machine-learning-based framework to map both overhead and underground distribution grids using widely-available multi-modal data including street view images, road networks, and building maps. Benchmarked against the utility-owned distribution grid map in California, our framework achieves > 80% precision and recall on average in the geospatial mapping of grids. The framework developed with the California data can be transferred to Sub-Saharan Africa and maintain the same level of precision without fine-tuning, demonstrating its generalizability. Furthermore, our framework achieves a R 2 of 0.63 in measuring the fraction of underground power lines at the aggregate level for estimating grid exposure to wildfires. We offer the framework as an open tool for mapping and analyzing distribution grids solely based on publicly-accessible data to support the construction and maintenance of reliable and clean energy systems around the world.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Experimental and theoretical evidence of universality in superfluid vortex reconnections

The minimum separation between reconnecting vortices in fluids and superfluids obeys a universal scaling law with respect to time. The prereconnection and the postreconnection prefactors of this scaling law are different, a property related to irreversibility and to energy transfer and dissipation mechanisms. In the present work, we determine the temperature dependence of these prefactors in superfluid helium from experiments and a numeric model which fully accounts for the coupled dynamics of the superfluid vortex lines and the thermal normal fluid component. At all temperatures, we observe a pre- and postreconnection asymmetry similar to that observed in other superfluids and in classical viscous fluids, indicating that vortex reconnections display a universal behavior independent of the small-scale regularizing dynamics. We also numerically show that each vortex reconnection event represents a sudden injection of energy in the normal fluid. Finally we argue that in a turbulent flow, these punctuated energy injections can sustain the normal fluid in a perturbed state, provided that the density of superfluid vortices is large enough.

Reconnections↗
DOE OSTI2024

Predicting U.S. federal fleet electric vehicle charging patterns using internal combustion engine vehicle fueling transaction statistics

Utilizing fueling transactions from internal combustion engine vehicles (ICEVs), the authors estimated how frequently midday public charging would be required for U.S. federal fleet battery electric vehicles (BEVs). Fueling transaction summary statistics are more widely available than trip-level telematics data, making this methodology more accessible and transferable to other researchers and fleet managers considering BEV replacements. For example, readers can easily apply a linear model using only the count of back-to-back fueling events at gas stations over 57 straight-line miles apart to predict days exceeding range. This linear regression predicted binned days exceeding 250 miles at 80% accuracy on a hold-out test set from the same fleet as the training data and 66 % accuracy on a new fleet displaying different driving behaviors. The authors additionally provide linear equations for days exceeding 200 and 300 miles as alternative range estimates to account for differences in BEV range and temperature impacts. Beyond the single-feature linear models which readers can apply, the authors tuned and trained other machine learning models on a variety of fueling transaction statistics including consecutive transaction distances, transaction distance from garage, estimated miles traveled from fuel economy and fuel quantity, and transaction periodicity. Utilizing a subset of 1678 light-duty federal fleet vehicles which contained daily vehicle miles traveled (VMT) in addition to fueling statistics, the authors determined which fueling transaction statistics were most relevant in predicting driving days exceeding 250 miles (an approximation of BEV rated driving range). In support of the U.S. federal fleet transition to zero-emission vehicles (ZEVs), the authors used these statistics and machine learning models to predict the frequency of BEV midday charging. After training models on the subset with VMT, the authors predicted days exceeding rated range for 112,902 light-duty vehicles operating in similar circumstances in the federal fleet using a Support Vector Regressor (SVR). In conclusion, they then used the projections as part of the ZEV Planning and Charging (ZPAC) tool to identify optimal candidates for BEVs for the federal fleet. An anonymized version of ZPAC is included in the supplementary materials.

25 ENERGY STORAGE↗
DOE OSTI2021

Quantum communication with itinerant surface acoustic wave phonons

Abstract Surface acoustic waves are commonly used in classical electronics applications, and their use in quantum systems is beginning to be explored, as evidenced by recent experiments using acoustic Fabry–Pérot resonators. Here we explore their use for quantum communication, where we demonstrate a single-phonon surface acoustic wave transmission line, which links two physically separated qubit nodes. Each node comprises a microwave phonon transducer, an externally controlled superconducting variable coupler, and a superconducting qubit. Using this system, precisely shaped individual itinerant phonons are used to coherently transfer quantum information between the two physically distinct quantum nodes, enabling the high-fidelity node-to-node transfer of quantum states as well as the generation of a two-node Bell state. We further explore the dispersive interactions between an itinerant phonon emitted from one node and interacting with the superconducting qubit in the remote node. The observed interactions between the phonon and the remote qubit promise future quantum-optics-style experiments with itinerant phonons.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Integrated phononic waveguide on thin-film lithium niobate on diamond

Here, we demonstrate wavelength-scale phononic waveguides formed by transfer-printed thin-film lithium niobate (LN) on bulk diamond, a material stack that combines the strong piezoelectricity of LN with the high acoustic velocity and color-center compatibility of diamond. We characterize a delay line based on a 100 μm long phononic waveguide at room and cryogenic temperatures. The total insertion loss through the device at 4 K is −5.8 dB, corresponding to a $>$ 50 % transducer efficiency, at a frequency of 2.8 GHz. Our work represents a step toward phonon-mediated hybrid quantum systems consisting of strain-sensitive color centers in diamond.

Malik, Sultan [Stanford Univ., CA (United States)]↗
DOE OSTI2020

Multitask Recommender Systems for Cancer Drug Response

The problem we are currently trying to address is that there are many types of cancer drugs and many types of cancers and there is not always experimental data for a specific cancer type and cancer drug interaction. While there is a large possible set of feasible drug and cancer combinations, testing each pair is not realistic due to the high monetary cost of cell-based assays. Thus, this leaves researchers with a difficult choice of what drugs they should test on specific cancer types. This issue is known as the cold-start problem. Our focus is on developing recommender systems capable of addressing the cold-start problem as it relates to interaction between cancer types and cancer drugs. One of the most effective ways to address the cold-start problem is through large data analysis, however due to the cost prohibitive nature of cancer research the largest available data set size is the Genomics of Drug Sensitivity in Cancer with 494,973 genomic associations. To achieve optimal model performance on the cold-start problem, it is advantageous to employ multitask algorithms that are capable of transferring information between cancer datasets. The aim of this report is to draw from adaptations and state of the art developments in both algorithms for recommender systems and multitask learning to model the interaction between cancer cell lines and cancer drugs. Cancer cell lines are defined by the US National Cancer Institute as "cancer cells that keep dividing and growing over time, under certain conditions in a laboratory". This paper will focus on evaluating the performance of Neural Collaborative Filtering and Gaussian Processes, as well as their multitask adaptations, on cancer datasets from CCLE, NCI60, GDSC and CTRP. These methods will be evaluated on model performance in regression prediction but also in interpretability.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Development of Digital Twin Predictive Model for PWR Components: Updates on Multi Times Series Temperature Prediction Using Recurrent Neural Network, DMW Fatigue Tests, System Level Thermal-Mechanical-Stress Analysis

The long-term operation (LTO) of nuclear power plant (NPP) beyond their original design life of 40 years, can lead to more material damage associated with cyclic fatigue under thermal-mechanical loading cycles and associated long-term exposure of reactor material to the deleterious reactor-coolant environments. However, under this LTO condition the reactor components can still safely operate but may require more frequent Nondestructive Evaluation (NDE) of reactor components. Frequent NDE requirement may lead to frequent shutdown of the NPP. This in turn can lead to power outage and additional NDE-inspection-cost related economic loss. The economic loss can be minimized by reducing uncertainty in life estimation of safety-critical pressure boundary components and by implementing more digital approach such as by using upcoming digital-twin (DT) technology for predicting the structural states (e.g., time and location dependent inside/outside thickness temperature, stress, strain, plastic deformation, etc.) and associated fatigue life of a component in real time. Towards this goal Argonne National Laboratory (ANL) with the sponsorship of DOE Light Water Reactor Sustainability (LWRS) program is working on the development of a DT framework that can be used for real time environmental fatigue prediction of reactor components. The DT framework is based on limited experiment-data, Artificial-intelligence (AI) – Machine-Learning (ML) - Deep-Learning (DL) based techniques and Multiphysics-computational-mechanics such as finite element (FE) based modeling tools. Towards this overall goal, following are some of the major contributions made during the FY21: 1) Multiple 82/182 dissimilar metal weld (DMW) specimens (both solid-weld and joint-weld representing the actual reactor multi-metal nozzles) were fatigue tested. The resulting fatigue lives were compared to the NUREG-6909 based best-fit and design fatigue curves. Additionally, the results of 52/152 DMW fatigue specimens (which were recently tested at Republic of Korea under the sponsorship of International Nuclear Energy Research Initiative - INERI program) were compared to the NUREG-6909 based best-fit and design fatigue curves. From the comparison of 82/182 and 52/152 DMW test data with NUREG-6909 best-fit curve, most of the reported test data fall way away from the NUREG-6909 suggested best-fit or mean curve. The NUREG-6909 suggested best-fit curve is the best-fit curve of austenitic stainless steel and due to lack of enough data on Nickel-based welds, this is currently being used for predicting the life of Nickel-alloy-based welded components. However, the above observation may require higher scaling factor (e.g., ASME suggested factor of 20 on cycles rather than the current NUREG-6909 suggested factor of 12 on cycles) for scaling the austenitic-stainless-steel best-fit-curve for estimating the design or safe-life of a welded component. Accordingly, for example, if a DMW component experience a strain amplitude of 0.6% the PWR-water life of the component would be 52 cycles instead of 85 cycles. However, more DMW tests are required to further ascertain the above-mentioned observations. 2) A system level CAD and finite element model were developed which consists of reactor pressure vessel (RPV), part of steam generator (SG), part of pressurizer (PRZ), hot leg (HL), and surge line (SL). This is with detailed nozzle geometry and thermal-mechanical material properties of different metals to simulate realistic thermal-mechanical stress under connected system global thermal-mechanical boundary conditions. 3) Different system level heat transfer analyses were performed with estimation of relevant heat transfer coefficients. The resulting data were used in subsequent system level thermal-mechanical stress analysis and for generating spatial-temporal training and validation data for a system level digital-twin based temperature predictor. Transient heat transfer analyses were performed considering thermal boundary condition under design-basis (DB) loading and EDF (Électricité de France) data-based grid-load-following (EDF-GLF) loading cycles. 4) System level thermal-mechanical stress analysis was performed for identifying damage-prone hotspots and for future extension of the model for cyclic state prediction. From the system-level model simulation under DB loading cycle it is found that HL and the SL nozzle that connect to the HL can experience significant stress and strain and could be one of the weakest links in the overall reactor coolant system (RCS). 5) An AI/ML based DT model was developed for multi-time-series temperature prediction at any inside/outside thickness locations of PWR pressure boundary components. This is by using Recurrent-neural-network (RNN) and keras machine learning libraries. The RNN model was validated against two laboratory test-based data sets with one obtained through ANL’s in-air fatigue test system and other through PWR-water test loop. The experimentally validated DT model further validated against FE model results to predict thermal scarification related spatialtemporal temperatures at random locations of a component. The well validated DT model was then used for demonstrating spatial-temporal temperature prediction under 100+ years of reactor operation subjected to combined DB, EDF-GLF and randomized grid-load-following (RANDOMGLF) loading Cycles. The expert-elicitation DT model framework was developed assuming field/input/process measurements can be available from a few existing plant sensors and can readily be used by the NPP operators. The above temperature prediction model will feed to the next-step stress analysis model based on which the life of a component can be predicted in realtime, which is one of our future works.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Aqueous TiO 2 Nanoparticles React by Proton-Coupled Electron Transfer

Redox reactions of aqueous colloidal TiO 2 4 nm nanoparticles (NPs) have been examined, including both citratecapped and uncapped NPs (c-TiO 2 and uc-TiO 2 ). Photoreduction gave stable blue colloidal c-TiO 2 R NPs with 10–60 electrons per particle. Equilibration of these reduced NPs with soluble redox reagents such as methylviologen (MV 2+ ) provided measurements of the colloid reduction potential as a function of pH. The potentials of c-TiO 2 from pH 2–9 varied linearly with pH, with a slope of –60 ± 5 mV/pH. Estimates of the potential at pH 12 were consistent with extrapolating that line to high pH. The reduction potentials did not correlate with the zeta potentials (ζ) or the surface charge of the NPs across this pH range. Similar reduction potentials were observed for c- and uc-TiO 2 at low pH even though they have quite different ζ potentials. These results show that the common surface-charging explanation of the pH dependence is not tenable in these systems. Oxidation of reduced c-TiO 2 R with the electron-transfer oxidant potassium triiodide (KI 3 ) occurred with a significant drop in pH, showing that protons were released when the electrons were removed from the NPs. Smaller pH drops were observed for the proton-coupled electron transfer (PCET) reagents O 2 (air) and 4-MeO-TEMPO (4-methoxy-2,2,6,6-tetramethylpiperine-1-oxy radical). The difference in the number of protons released with KI 3 vs O 2 and 4-MeO-TEMPO was roughly one proton per electron removed. Thus, the thermodynamically preferred reactivity of these colloidal TiO 2 NPs is PCET over the pH 2–13 range studied. The measured redox potentials refer to the chemical process TiO 2 + H + + e – → TiO 2 ·e – ,H + ; and therefore they do not correspond with an electronic energy such as a conduction band edge or flat band potential. The 1e – /1H + stoichiometry means that the TiO 2 reduction potentials correspond to a TiO 2 –H bond dissociation free energy (BDFE), determined to be 49 ± 2 kcal mol –1 . The PCET description is consistent with the pH dependence of E(TiO 2 /TiO 2 ·e – ,H + ), the release of protons upon oxidation, the lack of correlation with ζ potentials, the similarity of capped and uncapped NPs, and the small change in the potential and BDFE from the first to the last electron/proton pair (H atom) removed. Furthermore, this behavior is suggested to be the norm for redox-active oxide/water interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Sensitivity Analyses of Natural Convection in the AP1000 Passive Containment Cooling System Following LBLOCA Using CFD

The AP1000 power plant has implemented multiple layers of passive safety systems to enhance reactor safety and ensure system integrity during postulated scenarios, such as loss of coolant accident (LOCA) and main steam line break (MSLB). Among these, the passive containment cooling system (PCCS) is a safety-related system designed to prevent the containment from exceeding the design limits of both pressure and temperature following a postulated design basis accident, by transferring heat from the steel containment vessel to the atmosphere. During LOCA, natural air convection plays a vital role in removing heat from the steel containment vessel to the atmosphere. This is integrated with the condensate film from the Passive Containment Cooling Water Storage Tank (PCCWST). Air natural convection is also the only heat removal mechanism after the dry-out of the PCCWST and during the loss of shutdown decay heat removal (LOSDHR) event. Therefore, it is essential to investigate the thermal hydraulics behavior of the containment under transient conditions to ensure its safety and integrity. This paper presents a simplified CFD/ANSYS FLUENT model developed to analyze the impact of different parameters, such as air relative humidity, air temperature, and steel containment temperature, on the natural convection capability to remove the decay heat following LOCA. The model aims to examine the thermal behavior of the containment and provides a comprehensive understanding of the system's natural convection capability during postulated accidents. The results obtained from the model can be used to improve the safety and integrity of the containment system and provide valuable insights for future research in the field.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2023

Observational signatures of circumbinary discs – I. Kinematics

We present five morphological and kinematic criteria to aid in asserting the binary nature of a protoplanetary disc, based on 3D hydrodynamical simulations of circumbinary discs post-processed with Monte Carlo radiative transfer. We find that circumbinary discs may be identified by (i) a central cavity, (ii) spiral arms both in and outside of their central cavities, (iii) non-localized perturbations in their iso-velocity curves, (iv) asymmetry between the lines of maximum speed of the blue shifted and redshifted wings, and (v) asymmetry between the area of the blue shifted and redshifted wings. In this study, we provide quantitative metrics for the last two criteria that can be used, in conjunction with the morphological criteria, to signal whether a protoplanetary disc is likely to be a circumbinary disc.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Hybrid Solar System (Final Scientific/Technical Report)

GTI Energy (GTI) teamed with the University of California at Merced (UCM) to scaleup the hybrid solar system (HSS) technology for demonstrating its performance at the US Gypsum (USG) plant in Plaster City, California. The technology integrates two-stage concentrating solar collector with matching particle thermal transport and storage (TSS) system to deliver cost-effective, and on-demand distributed high temperature industrial process heat up to 600°C with solar thermal, in this case to a gypsum kettle, to reduce its fuel use and carbon footprint. Current solar technologies, which reach these temperatures, are not distributable (towers) or cost-effective (dish). The research team developed a conceptual system design for host site retrofit, including preliminary heat balance, process flow diagram, particle to process heat exchanger and equipment placements at the site. Subsequently, parallel efforts were carried out at UCM to design, build and test a 12 m long commercial scale prototype concentrating thermal-only collector system and at GTI to design, build and test a matching 650°C capable particle TTS system. The nominal 50 kWth collector consists of a parabolic trough and three 4 m long two-stage receivers in series. Prior to on-sun testing, a 4 m long receiver was fabricated and successfully tested at 650 °C in a laboratory setting for 100 hrs of continuous operation showing less than 15% radiation loss. A 7 m wide x 17 m long parabolic trough was then installed at UCM for on-sun testing of the 12 m long receiver, and concurrently several 4 m long receivers were built. The optics of the parabolic trough were calibrated, and on-sun test were carried out on 12 m long receivers. During tests, the intense solar radiation (53x) caused the absorber tubes in the receivers to bend, reducing the overall optical efficiency. To address the bending issue, a self-consistent algorithm that includes ray tracing, thermal and deformation models was developed to perform thermal stress analysis on absorbers for parabolic solar collectors. Results obtained with this algorithm showed a dramatic rise in deformation as absorber tube length increases. A combined efficiency parameter that includes the occluded area for the mounts was developed to obtain an optimized tube length obtained. Based on the results, a length of 2.7 m for the absorber + 0.2 m for the coupler was chosen to minimize any bending and optimize optical efficiency while maintaining ease of mounting. The associated particle TTS system was designed, built and successfully tested at GTI. It includes storage, receiving and lock hoppers and piping that simulates the transfer of captured solar energy to an actual industrial furnace. Tests over 77 charge-discharge cycles demonstrated <2% particle degradation, with no problematic particle accumulations and no flow interruptions. The piping pressure drop was about 5 psi. The team also worked with Stanley Consultants (Stanley) to prepare conceptual and preliminary engineering packages to facilitate follow-on development and commercialization efforts. These include process and instrumentation diagram’s (P&ID’s), general arrangements, electrical one-line, project definitions document, equipment data sheets, schedule, and construction cost estimate for 2 MWth system. Updated HSS technology commercialization and customer engagement plans and detailed costs and evaluated market trade-offs and manufacturing.

03 NATURAL GAS↗
DOE OSTI2026

Human RNome Project draft human RNome sequence of GM12878, B-cell line, obtained by mass-spectrometry sequencing, long-read sequencing and short-read sequencing.

Here we report the first draft of the human RNome sequence, a reference map of RNA chemical modifications in a human B-cell line. RNA carries a diverse repertoire of chemical modifications that regulate gene expression, cellular function, and responses to physiological and pathological cues. Yet, unlike the genome, no reference map of RNA modifications is available for any human cell. To generate this resource, the Human RNome Project Consortium analyzed a shared RNA preparation from the well-characterized GM12878 B-cell line using short-read sequencing, long-read direct RNA sequencing, and mass spectrometry, generating more than 7.1 billion sequencing reads spanning approximately 1.2 trillion nucleotides. The resulting maps of the human RNome reveal that RNA modifications are organized according to function, transcript architecture, and cellular identity. Modifications concentrate at functional centers of ribosomal and transfer RNAs, follow the canonical topology of N6-methyladenosine in coding transcripts, and form coordinated hotspots in immune regulatory genes. This first reference human RNome provides a foundation for understanding how RNA chemistry shapes cellular identity, human disease, and the development of RNA-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Effect of Cu on the passivity of Ti–xCu (x = 0, 3 and 5 wt%) alloy in phosphate-buffered saline solution within the framework of PDM-II

The effect of copper content on the passivity of Ti–xCu alloys in a phosphate-buffered saline electrolyte (pH 7.4), in the steady-state condition, was examined using potentiostatic polarization, electrochemical impedance spectroscopy, and Mott-Schottky analysis. The study demonstrates that the oxide layer forms on the Ti–xCu alloys surface have n-type semiconducting character, and the steady-state thickness of the oxide layer is observed linearly and depends on the applied potential. The study observations are in line with the predictions of the Point Defect Model (PDM-II), which provides a physiochemically realistic description of the oxide layer formation on Ti–xCu alloys. The observations reveal that the Cu additions result in a decrease in the charge transfer resistance and capacitances associated with the hydroxide and barrier layer, an increase in the donor density, and reduce the electrochemical resistance of the Ti–xCu alloys. The study also exhibits that the decrease in the steady-state current density after the initial addition of 3 wt% of Cu is attributed to the progressive substitution of copper on the cation sublattice of the film resulting in enhanced electrostatic interaction between the immobilized copper $Cu^{x'}_{Ti}$, and the mobile cation interstitials $Cu^{+}_{i}$, which carries the excess current over and that conveyed by oxygen vacancies $V^{••}_o$ in the barrier layer. Moreover, it is also observed that over a hundred-year implant period, about 0.006 cm (0.06 mm) of Ti–3Cu alloy is predicted to lose due to steady-state corrosion in the PBS solution under the given set of conditions, it is further seen that, as the Cu amount increased from 3 wt% to 5 wt% in the Ti–xCu alloys, the steady-state corrosion rate decreases.

Electrochemical Impedance Spectroscopy↗
DOE OSTI2023

Orbital polarization, charge transfer, and fluorescence in reduced-valence nickelates

Herein this paper presents a simple formalism for calculating X-ray absorption (XAS) and resonant inelastic x-ray scattering (RIXS) that has as input orbital-resolved density of states from a single particle or many-body ab initio calculation and is designed to capture itinerant-like features. We use this formalism to calculate both the XAS and RIXS with input from DFT and DFT + DMFT for the recently studied reduced valence nickelates R 4 Ni 3 O 8 and RNiO 2 (R = rare earth), and these results are then contrasted with those for the cuprate CaCuO 2 and the unreduced nickelate R 4 Ni 3 O 10 . In contrast to the unreduced R 4 Ni 3 O 10 , the reduced valence nickelates as well as the cuprate show strong orbital polarization due to the dominance of x 2 – y 2 orbitals for the unoccupied 3d states. We also reproduce two key aspects of a recent RIXS experiment for R 4 Ni 3 O 8 : (i) a charge transfer feature between 3d and oxygen 2p states whose energy we find to decrease as one goes from RNiO 2 to R 4 Ni 3 O 8 to the cuprate, and (ii) an energy-dependent polarization reversal of the fluorescence line that arises from hybridization of the unoccupied 3z 2 –r 2 states with R 5d states. We end with some implications of our results for the nature of the 3d electrons in reduced valence nickelates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Passivating Nucleobases Bring Charge Transfer Character to Optically Active Transitions in Small Silver Nanoclusters

DNA-wrapped silver nanoclusters (DNA–AgNCs) are known for their efficient luminescence. However, their emission is highly sensitive to the DNA sequence, the cluster size, and its charge state. To get better insights into photophysics of these hybrid systems, simulations based on density functional theory (DFT) are performed. Our calculations elucidate the effect of the structural conformations, charges, solvent polarity, and passivating bases on optical spectra of DNA–AgNCs containing five and six Ag atoms. It is found that inclusion of water in calculations as a polar solvent media results in stabilization of nonplanar conformations of base-passivated clusters, while their planar conformations are more stable in vacuum, similar to the bare Ag5 and Ag6 clusters. Cytosines and guanines interact with the cluster twice stronger than thymines, due to their larger dipole moments. In addition to the base–cluster interactions, hydrogen bonds between bases notably contribute to the structure stabilization. While the relative intensity, line width, and the energy of absorption peaks are slightly changing depending on the cluster charge, conformations, and base types, the overall spectral shape with five well-resolved bands at 2.5–5.5 eV is consistent for all structures. Independent of the passivating bases and the cluster size and charge, the low energy optical transitions at 2.5–3.5 eV exhibit a metal to ligand charge transfer (MLCT) character with the main contribution emerging from Ag-core to the bases. Cytosines facilitate the MLCT character to a larger degree comparing to the other bases. However, the doublet transitions in clusters with the open shell electronic structure (Ag5 and Ag6 + ) result in appearance of additional red-shifted (<2.5 eV) and optically weak band with negligible MLCT character. The passivated clusters with the closed shell electronic structure (Ag5 + and Ag6) exhibit higher optical intensity of their lowest transitions with much higher MLCT contribution, thus having better potential for emission, than their open shell counterparts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗