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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 955 records · Page 53
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Red algal Rubisco fails to accumulate in transplastomic tobacco expressing Griffithsia monilis RbcL and RbcS genes

Abstract In C 3 plants, the carbon fixation step catalyzed by ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) represents a major rate‐limiting step due to the competing oxygenation reaction, which leads to the energy‐intensive photorespiration and lowers the overall photosynthetic efficiency. Hence, there is great biotechnological interest in replacing the Rubisco in C 3 crops with a more efficient enzyme. The Rubisco enzymes from red algae are among the most attractive choices due to their remarkable preference for carboxylation over oxygenation reaction. However, the biogenesis of Rubisco is extremely complex. The Rubisco enzymes in plants, algae, and cyanobacteria are made up of eight large and eight small subunits. The folding of the large subunits and the assembly of the large subunits with the small subunits to form a functional holoenzyme require specific chaperonin complexes and assembly factors. As a result, previous success in expressing foreign Rubisco in plants has been limited to Rubisco large subunits from closely related plant species and simpler bacterial enzymes. In our previous work, we successfully replaced the Rubisco in tobacco with a cyanobacterial enzyme, which was able to support the phototrophic growth of the transgenic plants. In this work, we used the same approach to express the Rubisco subunits from the red alga Griffithsia monilis in tobacco chloroplasts in the absence of the tobacco Rubisco large subunit. Although the red algal Rubisco genes are being transcribed in tobacco chloroplasts, the transgenic plants lack functional Rubisco and can only grow in a medium containing sucrose. Our results suggest that co‐expression of compatible chaperones will be necessary for successful assembly of red algal Rubisco in plants.

Plant Sciences↗
DOE OSTI2023

Dissecting the structural heterogeneity of proteins by native mass spectrometry

Abstract A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher‐order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the “bottom‐up” approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher‐order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the “top‐down” approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in‐depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero‐complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near‐native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding the molecular heterogeneity of proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Non-standard axion electrodynamics and the dual Witten effect

Standard axion electrodynamics has two closely related features. First, the coupling of a massless axion field to photons is quantized, in units proportional to the electric gauge coupling squared. Second, the equations of motion tell us that a time-dependent axion field in a background magnetic field sources an effective electric current, but a time-dependent axion field in a background electric field has no effect. These properties, which manifestly violate electric-magnetic duality, play a crucial role in experimental searches for axions. Recently, electric-magnetic duality has been used to motivate the possible existence of non-standard axion couplings, which can both violate the usual quantization rule and exchange the roles of electric and magnetic fields in axion electrodynamics. We show that these non-standard couplings can be derived from SL(2,Z) duality, but that they come at a substantial cost: in non-standard axion electrodynamics, all electrically charged particles become dyons when the axion traverses its field range, in a dual form of the standard Witten effect monodromy. This implies that there are dyons near the weak scale, leads to a large axion mass induced by Standard Model fermion loops, and dramatically alters Higgs physics. We conclude that non-standard axion electrodynamics, although interesting to consider in abstract quantum field theory, is not phenomenologically viable.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2013

Six novel transition-metal phosphite compounds, with structure related to yavapaiite: Crystal structures and magnetic and thermal properties of A{sup I}[M{sup III}(HPO{sub 3}){sub 2}] (A=K, NH{sub 4}, Rb and M=V, Fe)

Six new transition metal(III) phosphites A{sup I}[V{sup III}(HPO{sub 3}){sub 2}], where A=K (1), NH{sub 4} (2) and Rb (3) and A{sup I}[Fe{sup III}(HPO{sub 3}){sub 2}] where A=K (4), NH{sub 4} (5) and Rb (6) have been synthesized under hydrothermal conditions and the solid-state structures were solved from single-crystal X-ray diffraction data. These compounds crystallize in the hexagonal system, space group P6{sub 3}mc (no. 186), with a=5.3294(2) A and c=12.3130(5) A for 1, a=5.3330(2) A and c=12.8760(4) A for 2, a=5.3459(2) A and c=12.6850(8) A for 3, a=5.3256(1) A and c=12.2362(3) A for 4, a=5.3229(2) A and c=12.8562(4) A for 5, a=5.3393(2) A and c=12.6913(5) A for 6, with Z=2 in the six phases. The crystal structures of these compounds are isotypic and exhibit a layered structure stacked along the c-axis with the A{sup +} cations located in the interlayer space. The [M{sup III}(HPO{sub 3}){sub 2}]{sup -} sheets are formed by MO{sub 6} octahedra interconnected by HPO{sub 3} tetrahedral phosphite oxoanions through sharing vertices. Thermal analysis shows a large range of stability for compounds containing potassium and rubidium cations with decomposition starting around 550 K for stable compounds and above 840 K for the most stable compounds leading in general to pyrophosphate compounds. Triangular nets of metallic centers are observed within the layers in which antiferromagnetic interactions are evidenced by magnetic susceptibility measurements suggesting magnetic frustration. - Graphical abstract: Six new transition metal(III) phosphites A{sup I}[M{sup III}(HPO{sub 3}){sub 2}], where A=K, NH{sub 4}, Rb and M=V, Fe, have been synthesized. The crystal structures of these compounds are isotypic and exhibit a lamellar structure related to Yavapaiite. The M(HPO{sub 3}){sub 2} layers separated by cationic species present the metallic centers in a triangular arrangement. Bulk antiferromagnetic behavior is observed for all the studied compounds. Highlights: Black-Right-Pointing-Pointer A new family of transition metal phosphites has been prepared. Black-Right-Pointing-Pointer The structure of these compounds is related to layered minerals like Yavapaiite. Black-Right-Pointing-Pointer Antiferromagnetic coupling is evidenced suggesting possible magnetic frustration. Black-Right-Pointing-Pointer Thermal studies show, in general, oxidation of phosphites into pyrophosphates.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Selectivity trend of gas separation through nanoporous graphene

By means of molecular dynamics (MD) simulations, we demonstrate that porous graphene can efficiently separate gases according to their molecular sizes. The flux sequence from the classical MD simulation is H{sub 2}>CO{sub 2}≫N{sub 2}>Ar>CH{sub 4}, which generally follows the trend in the kinetic diameters. This trend is also confirmed from the fluxes based on the computed free energy barriers for gas permeation using the umbrella sampling method and kinetic theory of gases. Both brute-force MD simulations and free-energy calcualtions lead to the flux trend consistent with experiments. Case studies of two compositions of CO{sub 2}/N{sub 2} mixtures further demonstrate the separation capability of nanoporous graphene. - Graphical abstract: Classical molecular dynamics simulations show the flux trend of H{sub 2}>CO{sub 2}≫N{sub 2}>Ar>CH{sub 4} for their permeation through a porous graphene, in excellent agreement with a recent experiment. - Highlights: • Classical MD simulations show the flux trend of H{sub 2}>CO{sub 2}≫N{sub 2}>Ar>CH{sub 4} for their permeation through a porous graphene. • Free energy calculations yield permeation barriers for those gases. • Selectivities for several gas pairs are estimated from the free-energy barriers and the kinetic theory of gases. • The selectivity trend is in excellent agreement with a recent experiment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Magnetic and structural investigations on La{sub 0.6}Sr{sub 0.4}MnO{sub 3} nanostructured manganite: Evidence of a ferrimagnetic shell

This paper presents the structural and magnetic properties of La{sub 0.6}Sr{sub 0.4}MnO{sub 3} nanoparticles with sizes from 21 to 106 nm, which have been prepared using the sol–gel method. The reduction of the nanoparticles' size tends to broaden the paramagnetic to ferromagnetic transition, as well as to promote magnetic hysteresis and a remarkable change on the magnetic saturation. In order to better understand the magnetic behavior of those nanoparticles, a simple model based on a ferromagnetic core and a ferrimagnetic shell was considered, where the magnetization was described in terms of the standard mean-field Brillouin function. This model matches the experimental data, leading to conclusion the nanoparticles with size <40nm are single magnetic domain. In addition, the output fitting parameters give information on the Landé factor of the core and shell. - Graphical abstract: Core–shell model: The core has a ferromagnetic character, while the shell is ferrimagnetic. Each one has two sub-lattices (Mn{sup 3+} and Mn{sup 4+}) that interact through a mean-field (see Eq. (6)). Interactions strength and signals are also represented in this figure. In this figure the arrows (or vectors) represent the magnetic moment of ions Mn{sup 3+} (s=2) and Mn{sup 4+} (s=3/2). βλ's describe the ferromagnetic interaction between Mn{sup 4+} ions into the core (βλ{sub co}) and into the shell (βλ{sub sh}), while αλ's represent ferromagnetic interaction between Mn{sup 3+} ions into the core (αλ{sub co}) and into the shell (αλ{sub sh}). The −λ{sub sh} and +λ{sub co}co are associated to the mean field parameter of interaction between Mn{sup 3+} and Mn{sup 4+} sub-lattices in the shell (ferrimagnetic, negative sign) and core (ferromagnetic, positive sign), respectively. - Highlights: • Evidences of ferromagnetic shell in La{sub 0.6}Sr{sub 0.4}MnO{sub 3} ferromagnetic nanoparticles. • Core(ferromagnetic)–shell(ferromagnetic) model for nanostructured manganite. • Sol–gel method was successfully used to obtain nanostructured manganite.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Application of isotopic labeling, and gas chromatography mass spectrometry, to understanding degradation products and pathways in the thermal-oxidative aging of Nylon 6.6

Nylon 6.6 containing 13 C isotopic labels at specific positions along the macromolecular backbone has been subjected to extensive thermal-oxidative aging at 138 °C for time periods up to 243 days. In complementary experiments, unlabeled Nylon 6.6 was subjected to the same aging conditions under an atmosphere of 18 O 2 . Volatile organic degradation products were analyzed by cryofocusing gas chromatography mass spectrometry (cryo-GC/MS) to identify the isotopic labeling. The labeling results, combined with basic considerations of free radical reaction chemistry, provided insights to the origin of degradation species, with respect to the macromolecular structure. A number of inferences on chemical mechanisms were drawn, based on 1) the presence (or absence) of the isotopic labels in the various products, 2) the location of the isotope within the product molecule, and 3) the relative abundance of products as indicated by large differences in peak intensities in the gas chromatogram. The overall degradation results can be understood in terms of free radical pathways originating from initial attacks on three different positions along the nylon chain which include hydrogen abstraction from: the (CH 2 ) group adjacent to the nitrogen atom, at the (CH 2 ) adjacent the carbonyl group, and direct radical attack on the carbonyl. Understanding the pathways which lead to Nylon 6.6 degradation ultimately provides new insight into changes that can be leveraged to detect and reduce early aging and minimize problems associated with material degradation.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Generating Protein Structures for Pathway Discovery Using Deep Learning

Resolving the intricate details of biological phenomena at the molecular level is fundamentally limited by both length- and time scales that can be probed experimentally. Molecular dynamics (MD) simulations at various scales are powerful tools frequently employed to offer valuable biological insights beyond experimental resolution. However, while it is relatively simple to observe long-lived, stable configurations of, for example, proteins, at the required spatial resolution, simulating the more interesting rare transitions between such states often takes orders of magnitude longer than what is feasible even on the largest supercomputers available today. One common aspect of this challenge is pathway discovery, where the start and end states of a scientific phenomenon are known or can be approximated, but the mechanistic details in between are unknown. Here, we propose a representation-learning-based solution that uses interpolation and extrapolation in an abstract representation space to synthesize potential transition states, which are automatically validated using MD simulations. The new simulations of the synthesized transition states are subsequently incorporated into the representation learning, leading to an iterative framework for targeted path sampling. Our approach is demonstrated by recovering the transition of a RAS-RAF protein domain (CRD) from membrane-free to interacting with the membrane using coarse-grain MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Large‐Scale Statistically Meaningful Patterns (LSMPs) Associated With Precipitation Extremes Over Northern California

Abstract We analyze large‐scale statistically meaningful patterns (LSMPs) that precede extreme precipitation (PEx) events over Northern California (NorCal). We find LSMPs by applying k‐means clustering to the two leading principal components of daily 500 hPa geopotential height anomalies two days before the onset, from October to March during 1948–2015. Statistical significance testing based on Monte Carlo simulations suggests a minimum of four statistically distinguished LSMP clusters. The four LSMP clusters are characterized as Northwest continental negative height anomaly, Eastward positive “Pacific‐North American Pattern (PNA),” Westward negative “PNA,” and Prominent Alaskan ridge. These four clusters, shown in multiple variables, evolve very differently and have differing links to the Arctic and tropical Pacific regions. Using binary forecast skill measures and a new copula‐based framework for predicting PEx events, we find LSMP indices that are useful predictors of NorCal PEx events, with moisture‐based variables being the best predictors of PEx events at least 6 days before the onset, and the lower atmospheric variables being better than their upper atmospheric counterparts any day in advance tested. To ensure statistical rigor, the LSMPs analyzed here (with the modified acronym) include local tests of both significance and consistency, which are not always featured in the literature on large‐scale meteorological patterns.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Decrypting bacterial polyphenol metabolism in an anoxic wetland soil

Abstract Microorganisms play vital roles in modulating organic matter decomposition and nutrient cycling in soil ecosystems. The enzyme latch paradigm posits microbial degradation of polyphenols is hindered in anoxic peat leading to polyphenol accumulation, and consequently diminished microbial activity. This model assumes that polyphenols are microbially unavailable under anoxia, a supposition that has not been thoroughly investigated in any soil type. Here, we use anoxic soil reactors amended with and without a chemically defined polyphenol to test this hypothesis, employing metabolomics and genome-resolved metaproteomics to interrogate soil microbial polyphenol metabolism. Challenging the idea that polyphenols are not bioavailable under anoxia, we provide metabolite evidence that polyphenols are depolymerized, resulting in monomer accumulation, followed by the generation of small phenolic degradation products. Further, we show that soil microbiome function is maintained, and possibly enhanced, with polyphenol addition. In summary, this study provides chemical and enzymatic evidence that some soil microbiota can degrade polyphenols under anoxia and subvert the assumed polyphenol lock on soil microbial metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Assessing the impact of human mobility to predict regional excess death in Ecuador

Abstract COVID-19 outbreaks have had high mortality in low- and middle-income countries such as Ecuador. Human mobility is an important factor influencing the spread of diseases possibly leading to a high burden of disease at the country level. Drastic control measures, such as complete lockdown, are effective epidemic controls, yet in practice one hopes that a partial shutdown would suffice. It is an open problem to determine how much mobility can be allowed while controlling an outbreak. In this paper, we use statistical models to relate human mobility to the excess death in Ecuador while controlling for demographic factors. The mobility index provided by GRANDATA, based on mobile phone users, represents the change of number of out-of-home events with respect to a benchmark date (March 2nd, 2020). The study confirms the global trend that more men are dying than expected compared to women, and that people under 30 show less deaths than expected, particularly individuals younger than 20 with a death rate reduction between 22 and 27%. The weekly median mobility time series shows a sharp decrease in human mobility immediately after a national lockdown was declared on March 17, 2020 and a progressive increase towards the pre-lockdown level within two months. Relating median mobility to excess deaths shows a lag in its effect: first, a decrease in mobility in the previous two to three weeks decreases excess death and, more novel, we found an increase of mobility variability four weeks prior increases the number of excess deaths.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Long-term survival and second malignant tumor prediction in pediatric, adolescent, and young adult cancer survivors using Random Survival Forests: a SEER analysis

Abstract Survival and second malignancy prediction models can aid clinical decision making. Most commonly, survival analysis studies are performed using traditional proportional hazards models, which require strong assumptions and can lead to biased estimates if violated. Therefore, this study aims to implement an alternative, machine learning (ML) model for survival analysis: Random Survival Forest (RSF). In this study, RSFs were built using the U.S. Surveillance Epidemiology and End Results to (1) predict 30-year survival in pediatric, adolescent, and young adult cancer survivors; and (2) predict risk and site of a second tumor within 30 years of the first tumor diagnosis in these age groups. The final RSF model for pediatric, adolescent, and young adult survival has an average Concordance index (C-index) of 92.9%, 94.2%, and 94.4% and average time-dependent area under the receiver operating characteristic curve (AUC) at 30-years since first diagnosis of 90.8%, 93.6%, 96.1% respectively. The final RSF model for pediatric, adolescent, and young adult second malignancy has an average C-index of 86.8%, 85.2%, and 88.6% and average time-dependent AUC at 30-years since first diagnosis of 76.5%, 88.1%, and 99.0% respectively. This study suggests the robustness and potential clinical value of ML models to alleviate physician burden by quickly identifying highest risk individuals.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Non-reciprocal acoustoelectric microwave amplifiers with net gain and low noise in continuous operation

Abstract Piezoelectric acoustic devices that are integrated with semiconductors can leverage the acoustoelectric effect, allowing functionalities such as gain and isolation to be achieved in the acoustic domain. This could lead to performance improvements and miniaturization of radio-frequency electronic systems. However, acoustoelectric amplifiers that offer a large acoustic gain with low power consumption and noise figure at microwave frequencies in continuous operation have not yet been developed. Here we report non-reciprocal acoustoelectric amplifiers that are based on a three-layer heterostructure consisting of an indium gallium arsenide (In 0.53 Ga 0.47 As) semiconducting film, a lithium niobate (LiNbO 3 ) piezoelectric film, and a silicon substrate. The heterostructure can continuously generate 28.0 dB of acoustic gain (4.0 dB net radio-frequency gain) for 1 GHz phonons with an acoustic noise figure of 2.8 dB, while dissipating 40.5 mW of d.c. power. We also create a device with an acoustic gain of 37.0 dB (11.3 dB net gain) at 1 GHz with 19.6 mW of d.c. power dissipation and a non-reciprocal transmission of over 55 dB.

42 ENGINEERING↗
DOE OSTI2020

Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins

Abstract The accurate assignment of cofactors in cryo-electron microscopy maps is crucial in determining protein function. This is particularly true for chlorophylls (Chls), for which small structural differences lead to important functional differences. Recent cryo-electron microscopy structures of Chl-containing protein complexes exemplify the difficulties in distinguishing Chl b and Chl f from Chl a . We use these structures as examples to discuss general issues arising from local resolution differences, properties of electrostatic potential maps, and the chemical environment which must be considered to make accurate assignments. We offer suggestions for how to improve the reliability of such assignments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Use of differential plasma rotation to prevent disruptive tearing mode onset from 3-wave coupling

Abstract Plasma differential rotation is found to be capable of preventing disruptive neoclassical tearing modes (NTMs) seeded by nonlinear three-wave coupling. As tearing modes degrade confinement and can lead to disruptions, stabilization strategies are crucial to the successful operation of future devices. In ITER-relevant scenarios on DIII-D, rotationally coupled m / n = 1/1 and 3/2 modes have been observed to drive 2/1 islands through three-wave coupling. The frequency of the driven 2/1 mode is set by matching conditions and the frequencies of the driving modes. When the driven mode frequency matches the local plasma rotation frequency, e.g. at low differential rotation, the driven 2/1 island can grow into a disruptive NTM. Using neutral beam torque as an actuator to scan the differential rotation, these experiments demonstrate that a sufficiently large frequency mismatch prevents destabilization of disruptive 2/1 NTMs by three-wave coupling. This work indicates that differential rotation can be used as an actuator to prevent NTMs seeded by three-wave coupling.

Richner, N. J. (ORCID:0000000155443915)↗
DOE OSTI2018

Sources of Intermodel Spread in the Lapse Rate and Water Vapor Feedbacks

Abstract Sources of intermodel differences in the global lapse rate (LR) and water vapor (WV) feedbacks are assessed using CO2 forcing simulations from 28 general circulation models. Tropical surface warming leads to significant warming and moistening in the tropical and extratropical upper troposphere, signifying a nonlocal, tropical influence on extratropical radiation and feedbacks. Model spread in the locally defined LR and WV feedbacks is pronounced in the Southern Ocean because of large-scale ocean upwelling, which reduces surface warming and decouples the surface from the tropospheric response. The magnitude of local extratropical feedbacks across models and over time is well characterized using the ratio of tropical to extratropical surface warming. It is shown that model differences in locally defined LR and WV feedbacks, particularly over the southern extratropics, drive model variability in the global feedbacks. The cross-model correlation between the global LR and WV feedbacks therefore does not arise from their covariation in the tropics, but rather from the pattern of warming exerting a common control on extratropical feedback responses. Because local feedbacks over the Southern Hemisphere are an important contributor to the global feedback, the partitioning of surface warming between the tropics and the southern extratropics is a key determinant of the spread in the global LR and WV feedbacks. It is also shown that model Antarctic sea ice climatology influences sea ice area changes and southern extratropical surface warming. As a result, model discrepancies in climatological Antarctic sea ice area have a significant impact on the intermodel spread of the global LR and WV feedbacks.

54 ENVIRONMENTAL SCIENCES↗