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At least 1,333 records · Page 74

Structural analysis of the NifL-NifA complex reveals the molecular basis of anti-activation of nitrogen fixation gene expression in Azotobacter vinelandii

Understanding the molecular basis of regulated nitrogen (N 2 ) fixation is essential for engineering N 2 -fixing bacteria that fulfill the demand of crop plants for fixed nitrogen, reducing our reliance on synthetic nitrogen fertilizers. In Azotobacter vinelandii and many other members of Proteobacteria, the two-component system comprising the anti-activator protein (NifL) and the Nif-specific transcriptional activator (NifA)controls the expression of nif genes, encoding the nitrogen fixation machinery. The NifL-NifA system evolved the ability to integrate several environmental cues, such as oxygen, nitrogen, and carbon availability. The nitrogen fixation machinery is thereby only activated under strictly favorable conditions, enabling diazotrophs to thrive in competitive environments. While genetic and biochemical studies have enlightened our understanding of how NifL represses NifA, the molecular basis of NifA sequestration by NifL depends on structural information on their interaction. Here, we present mechanistic insights into how nitrogen fixation is regulated by combining biochemical and genetic approaches with a low-resolution cryo-electron microscopy (cryo-EM) map of the oxidized NifL-NifA complex. Our findings define the interaction surface between NifL and NifA and reveal how this interaction can be manipulated to generate bacterial strains with increased nitrogen fixation rates able to secrete surplus nitrogen outside the cell, a crucial step in engineering improved nitrogen delivery to crop plants.

59 BASIC BIOLOGICAL SCIENCES↗

Pseudoplasticity and Dynamic Interfacial Tension Relaxation Effects on Nucleate Pool Boiling in Aqueous Polymeric Liquids

Nucleate pool boiling heat transfer and its ebullient dynamics in polymeric solutions at atmospheric pressure saturated conditions are experimentally investigated. Three grades of hydroxyethyl cellulose (HEC) are used, which have intrinsic viscosity in the range 5.29 ≤ [ η ] ≤ 10.31 [dl/g]. Their aqueous solutions in different concentrations, with zero-shear viscosity in the range 0.0021 ≤ η 0 ≤ 0.0118 [N∙s/m 2 ], exhibit shear-thinning rheology in varying degrees, as well as gas–liquid interfacial tension relaxation and wetting. Boiling heat transfer in solutions with constant molar concentrations of each additive, which are greater than their respective critical polymer concentration C * , is seen to have anomalous characteristics. There is degradation in the heat transfer at low heat fluxes, relative to that in the solvent, where the postnucleation bubble dynamics in the partial boiling regime is dominated by viscous resistance of the polymeric solutions. At higher heat fluxes, however, there is enhancement of boiling heat transfer due to a complex interplay of pseudoplasticity and dynamic surface tension effects. The higher frequency vapor bubbling train with high interfacial shear rates in this fully developed boiling regime tends to be influenced by increasing shear-thinning and time-dependent differential interfacial tension relaxation at the dynamic gas–liquid interfaces.

Engineering↗

Volumetric additive manufacturing via tomographic reconstruction

Additive manufacturing promises enormous geometrical freedom and the potential to combine materials for complex functions. The speed, geometry, and surface quality limitations of additive processes are linked to their reliance on material layering. We demonstrated concurrent printing of all points within a three-dimensional object by illuminating a rotating volume of photosensitive material with a dynamically evolving light pattern. We printed features as small as 0.3 millimeters in engineering acrylate polymers and printed soft structures with exceptionally smooth surfaces into a gelatin methacrylate hydrogel. Our process enables us to construct components that encase other preexisting solid objects, allowing for multimaterial fabrication. We developed models to describe speed and spatial resolution capabilities and demonstrated printing times of 30 to 120 seconds for diverse centimeter-scale objects.

42 ENGINEERING↗

Time-Based CAN IDS Paper Results Code

Modern vehicles are complex cyber-physical systems made of hundreds of electronic control units (ECUs) that communicate over controller area networks (CANs). This inherited complexity has expanded the CAN attack surface which is vulnerable to message injection attacks. These injections change the overall timing characteristics of messages on the bus, and thus, to detect these malicious messages, time-based intrusion detection systems (IDSs) have been proposed. However, time-based IDSs are usually trained and tested on low-fidelity datasets with unrealistic, labeled attacks. This makes difficult the task of evaluating, comparing, and validating IDSs. Here we detail and benchmark four time-based IDSs against the newly published ROAD dataset, the first open CAN IDS dataset with real (non-simulated) stealthy attacks with physically verified effects. We found that methods that perform hypothesis testing by explicitly estimating message timing distributions have lower performance than methods that seek anomalies in a distribution related statistic. In particular, these “distribution-agnostic” based methods outperform “distribution-based” methods by at least 55% in area under the precision-recall curve (AUC-PR). Our results expand the body of knowledge of CAN time-based IDSs by providing details of these methods and reporting their results when tested on datasets with real advanced attacks. Finally, we develop an after-market plug-in detector using lightweight hardware, which can be used to deploy the best performing IDS method on nearly any vehicle.

Moriano, Pablo [Oak Ridge National Lab. (ORNL), Oa↗

“Gray Zone” Simulations Using a Three-Dimensional Planetary Boundary Layer Parameterization in the Weather Research and Forecasting Model

Abstract Generating accurate weather forecasts of planetary boundary layer (PBL) properties is challenging in many geographical regions, oftentimes due to complex topography or horizontal variability in, for example, land characteristics. While recent advances in high-performance computing platforms have led to an increase in the spatial resolution of numerical weather prediction (NWP) models, the horizontal gridcell spacing (Δ x ) of many regional-scale NWP models currently fall within or are beginning to approach the gray zone (i.e., Δ x ≈ 100–1000 m). At these gridcell spacings, three-dimensional (3D) effects are important, as the most energetic turbulent eddies are neither fully parameterized (as in traditional mesoscale simulations) nor fully resolved [as in traditional large-eddy simulations (LES)]. In light of this modeling challenge, we have implemented a 3D PBL parameterization for high-resolution mesoscale simulations using the Weather Research and Forecasting Model. The PBL scheme, which is based on the algebraic model developed by Mellor and Yamada, accounts for the 3D effects of turbulence by calculating explicitly the momentum, heat, and moisture flux divergences in addition to the turbulent kinetic energy. In this study, we present results from idealized simulations in the gray zone that illustrate the benefit of using a fully consistent turbulence closure framework under convective conditions. While the 3D PBL scheme reproduces the evolution of convective features more appropriately than the traditional 1D PBL scheme, we highlight the need to improve the turbulent length scale formulation. Significance Statement The spatial resolution of weather models continues to increase at a rapid rate in accordance with the enhancement of computing power. As a result, smaller-scale atmospheric features become more explicitly resolved. However, most numerical models still ignore the impact of horizontal weather variations on boundary layer flows, which becomes more important at these smaller spatial scales. To address this issue, we have implemented a new modeling approach, using fundamental principles, which accounts for horizontal variability. Our results show that including three-dimensional effects of turbulence is necessary to achieve realistic boundary layer characteristics. This novel technique may be useful for many applications including complex terrain flows, pollutant dispersion, and surface–atmosphere interaction studies.

Juliano, Timothy W.↗

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station

The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months. Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results. Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 10 5 cfu/m 2 . Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity.

59 BASIC BIOLOGICAL SCIENCES↗

Time-Based CAN Intrusion Detection Benchmark

Modern vehicles are complex cyber-physical systems made of hundreds of electronic control units (ECUs) that communicate over controller area networks (CANs). This inherited complexity has expanded the CAN attack surface by the injection of malicious messages that vary their time-based characteristics. To detect these malicious messages, time-based intrusion detection systems (IDS) have been proposed. However, time-based IDS are usually trained and tested on low-fidelity datasets with unrealistic labeled attacks. This makes difficult the task of evaluating, comparing, and validating IDS. Here we detail and benchmark four time-based IDS in a dataset with real and advanced attacks. We found that methods with strong assumptions regarding the distribution of inter-arrival times have lower performance than distribution agnostic based methods. In particular, distribution agnostic based methods outperform distribution based methods at least on $55\%$ in area under the precision-recall (AUC-PR) curve. Our results expand the body of knowledge of CAN time-based IDS by providing details of these methods and reporting their results when tested on datasets with real and advanced attacks. We describe limitations, open challenges, and how lessons learnt from this research can inform the design of deployable time-based IDS in modern vehicles.

Blevins, Deborah↗

Understanding of catalytic transformation of shale gas and development of catalysts with high activity and selectivity through experimental exploration and theoretical simulation

Catalysis on transition metal oxides is equivalently important in contrast to that on metal catalysts in chemical and energy transformations. Understanding of catalytic reactions on early transition metal oxide catalysts is fundamentally intriguing and of great practical interest in efficient production of chemical and fuel feedstocks. Fundamental understanding of catalysis on transition metal oxide-based catalysts has been lagged behind catalysis on metals due to the complexity of chemistry and structure of surface and bulk of oxide catalysts and their structural flexibility in reactive environment at high temperatures. The funded DOE project explored surface chemistry of a few reducible oxides including CeO 2 - based, Co 3 O 4 -based, and CoO-based which are significant for heterogeneous catalysis. Through in-situ studies using ambient pressure X-ray photoelectron spectroscopy and high pressure scanning tunneling microscopy, we revealed phase transformation, the accompanying changes of surface chemistry and structure, and uncovered their correlations with catalytic activity and selectivity in catalytic reactions including reduction of NO with CO, water-gas shift, and chemical transformations of methane to methanol and acetic acid under mild conditions. Driven by the following two facts, we propose to pursue fundamental understanding of oxidative dehydrogenation of ethane and oxidative coupling of methane on oxide catalysts through both in-situ studies of catalyst surfaces during catalysis and computational studies in the renewal proposal. One driving force is the significance of oxidative dehydrogenation of ethane and oxidative coupling of methane for utilization of earth-abundant, relatively inexpensive energy resource and the urgent needs of efficient chemical processes to generate ethylene from shale gas. The other is that exploration of surface chemistry of oxide catalysts during catalysis has remained challenging though it is critical in deeply understanding catalysis on oxide catalysts and developing oxide-based catalysts toward high selectivity and activity. Therefore, the overall objective of the renewal proposal is to mechanistically understand the oxidative dehydrogenation of ethane and oxidative coupling of methane at a molecular level through building correlations between surface chemistry of catalysts during catalysis and the corresponding catalytic performances, and thus design catalysts with high selectivity and activity for production of ethylene with the guidance achieved from these fundamental studies. Experiments were designed to explore the influences of electronic states of cations supported on substrate oxides, cations of surface of the substrate oxides, and surface lattice oxygen atoms of the substrate oxides on their catalytic selectivity and activity. Surface chemistry, including oxidation state of the surface monomers and cations of substrate oxides and density of oxygen vacancies during catalysis, will be tracked with AP-XPS during catalysis. A correlation between surface chemistry of these catalysts at different temperatures and their corresponding catalytic selectivity for production of ethylene and activity will be built. Computational studies will calculate adsorption energies of reactant molecules and their dissociated species and intermediates on the catalyst surface, search transition states, and simulate reaction pathway close to experimental studies. By integrating the computational studies into these correlations to be built from experimental studies, fundamental understanding of the catalytic mechanisms of oxidative dehydrogenation of ethane and oxidative coupling of methane at a molecular level will be achieved. With these insights, new catalysts with high selectivity and activity will be developed.

36 MATERIALS SCIENCE↗

Corrected Moments in Antenna Coordinates (CMAC) Technical Report

Various corrections are needed in order to extract the best value of the measurements from the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) User Facility’s scanning precipitation radars. The Corrected Moments in Antenna Coordinates (CMAC) Value-Added Product provides an application chain for providing radar moments that are corrected for artifacts such as aliasing, attenuation, multi-trip echoes, and beam blockage. This technical report provides details on the entire process of correcting the ARM scanning precipitation radar data using CMAC. CMAC has been used at multiple ARM sites and ARM Mobile Facility deployments including the Tracking Aerosol Convection Interactions Experiment (TRACER), Cloud, Aerosol, and Complex Terrain Interactions (CACTI), and the Surface Atmosphere Integrated Laboratory (SAIL).

54 ENVIRONMENTAL SCIENCES↗

Controlling Oxidation of Nb in Oxygen Abundant Environments

Modern particle accelerators depend on Superconducting Radio Frequency (SRF) cavities made from high-purity niobium (Nb) to achieve optimal performance, including high quality factors and strong accelerating gradients. However, when exposed to air, niobium naturally forms a complex oxide layer that can introduce surface imperfections and carbon contamination. This work examines an alternative oxidation strategy under oxygen-rich conditions to better regulate the oxide formation process. The ultimate objective is to improve surface uniformity and cleanliness, thereby reducing defect density and enhancing performance. We used Confocal Microscopy, Scanning Electron Microscopy (SEM), and X-Ray Photoelectron Spectroscopy (XPS) to analyze surface changes. We used standard metrics, like Arithmetic Average Roughness (Ra) and Root Mean Square (Rq). Three oxidation methods were applied: short, extended, and a repeated HF and H₂O₂ oxidation process. Preliminary results show promising reductions in carbon contamination and surface defects.

Romero, Juan [Fermilab]↗

Methanol Formation via Oxygen Insertion Chemistry in Ices

We present experimental constraints on the insertion of oxygen atoms into methane to form methanol in astrophysical ice analogs. In gas-phase and theoretical studies this process has previously been demonstrated to have a very low or nonexistent energy barrier, but the energetics and mechanisms have not yet been characterized in the solid state. We use a deuterium UV lamp filtered by a sapphire window to selectively dissociate O{sub 2} within a mixture of O{sub 2}:CH{sub 4} and observe efficient production of CH{sub 3}OH via O({sup 1}D) insertion. CH{sub 3}OH growth curves are fit with a kinetic model, and we observe no temperature dependence of the reaction rate constant at temperatures below the oxygen desorption temperature of 25 K. Through an analysis of side products we determine the branching ratio of ice-phase oxygen insertion into CH{sub 4}: ∼65% of insertions lead to CH{sub 3}OH, with the remainder leading instead to H{sub 2}CO formation. There is no evidence for CH{sub 3} or OH radical formation, indicating that the fragmentation is not an important channel and that insertions typically lead to increased chemical complexity. CH{sub 3}OH formation from O{sub 2} and CH{sub 4} diluted in a CO-dominated ice similarly shows no temperature dependence, consistent with expectations that insertion proceeds with a small or nonexistent barrier. Oxygen insertion chemistry in ices should therefore be efficient under low-temperature ISM-like conditions and could provide an important channel to complex organic molecule formation on grain surfaces in cold interstellar regions such as cloud cores and protoplanetary disk midplanes.

79 ASTRONOMY AND ASTROPHYSICS↗

A parameterization of sub-grid topographical effects on solar radiation in the E3SM Land Model (version 1.0): implementation and evaluation over the Tibetan Plateau

Abstract. Topography exerts significant influences on the incoming solar radiation at the land surface. A few stand-alone regional and global atmospheric models have included parameterizations for sub-grid topographic effects on solar radiation. However, nearly all Earth system models (ESMs) that participated in the Coupled Model Intercomparison Project (CMIP6) use a plane-parallel (PP) radiative transfer scheme that assumes that the terrain is flat. In this study, we incorporated a well-validated sub-grid topographic (TOP) parameterization in the Energy Exascale Earth System Model (E3SM) Land Model (ELM) version 1.0 to quantify the effects of sub-grid topography on solar radiation flux, including the shadow effects and multi-scattering between adjacent terrain. We studied the role of sub-grid topography by performing ELM simulations with the PP and TOP schemes over the Tibetan Plateau (TP). Additional ELM simulations were performed at multiple spatial resolutions to investigate the role of spatial scale on sub-grid topographic effects on solar radiation. The Moderate Resolution Imaging Spectroradiometer (MODIS) data was used to compare with the ELM simulations. The results show that topography has non-negligible effects on surface energy budget, snow cover, snow depth, and surface temperature over the TP. The absolute differences in surface energy fluxes for net solar radiation, latent heat flux, and sensible heat flux between TOP and PP exceed 20, 10, and 5 W m−2, respectively. The differences in land surface albedo, snow cover fraction, snow depth, and surface temperature between TOP and PP exceed 0.1, 0.1, 10 cm, and 1 K, respectively. The magnitude of the sub-grid topographic effects is dependent on seasons and elevations and is also sensitive to the spatial scales. Although the sub-grid topographic effects on solar radiation are larger with more spatial details at finer spatial scales, they cannot be simply neglected at coarse spatial scales. When compared to MODIS data, incorporating the sub-grid topographic effects overall reduces the biases of ELM in simulating surface energy balance, snow cover, and surface temperature, especially in the high-elevation and snow-covered regions over the TP. The inclusion of sub-grid topographic effects on solar radiation parameterization in ELM will contribute to advancing our understanding of the role of the surface topography on terrestrial processes over complex terrain.

Hao, Dalei (ORCID:0000000334979774)↗

A Parameterization of Sub-grid Topographical Effects on Solar Radiation in the E3SM Land Model (Version 1.0): Implementation and Evaluation Over the Tibetan Plateau

Topography exerts significant influences on the incoming solar radiation at the land surface. A few stand-alone regional and global atmospheric models have included parameterizations for sub-grid topographic effects on solar radiation. However, nearly all Earth System Models (ESMs) that participated in the Coupled Model Intercomparison Project (CMIP6) use a plane-parallel (PP) radiative transfer scheme that assumes the terrain is flat. In this study, we incorporated a well-validated sub-grid topographic (TOP) parameterization in the Energy Exascale Earth System Model (E3SM) Land Model (ELM) version 1.0 to quantify the effects of sub-grid topography on solar radiation flux, including the shadow effects and multi-scattering between adjacent terrain. The Moderate Resolution Imaging Spectroradiometer (MODIS) data was used to evaluate the performance of ELM. We studied the role of sub-grid topography by performing ELM simulations with the PP and TOP schemes over the Tibetan Plateau (TP). Additional ELM simulations were performed at multiple spatial resolutions to investigate the role of spatial scale on sub-grid topographic effects on solar radiation. When compared to MODIS data, incorporating the sub-grid topographic effects overall reduces the biases of ELM in simulating surface energy balance, snow cover and surface temperature especially in the high-elevation and snow-cover regions over the TP. Topography has non-negligible effects on surface energy budget, snow cover, and surface temperature over the TP. The absolute differences in surface energy fluxes for net solar radiation, latent heat flux, and sensible heat flux between TOP and PP exceed 20 W/m 2 , 10 W/m 2 , and 5 W/m 2 , respectively. The differences in land surface albedo, snow cover fraction, and surface temperature between TOP and PP exceed 0.1, 20%, and 1K, respectively. The magnitude of the sub-grid topographic effects is dependent on seasons and elevations, and is also sensitive to the spatial scales. Although the sub-grid topographic effects on solar radiation are more significant with more spatial details at finer spatial scales, they cannot be simply neglected at coarse spatial scales. The inclusion of sub-grid topographic effects on solar radiation parameterization in ELM will contribute to advancing our understanding of the role of the surface topography on terrestrial processes over complex terrain.

58 GEOSCIENCES↗

Spread spectrum communication link using surface wave devices

A fast lock-up, 8-MHz bandwidth 8,000 bit per second data rate spread spectrum communication link breadboard is described that is implemented using surface wave devices as the primary signal generators and signal processing elements. It uses surface wave tapped delay lines in the transmitter to generate the signals and in the receiver to detect them. The breadboard provides a measured processing gain for Gaussian noise of 31.5 dB which is within one dB of the theoretical optimum. This development demonstrates that spread spectrum receivers implemented with surface wave devices have sensitivities and complexities comparable to those of serial correlation receivers, but synchronization search times which are two to three orders of magnitude smaller.

Hunsinger, B. J.↗

Application of the chromospheric magnetograph to active regions.

It is shown how to determine the magnetic field structure in active regions from the H-alpha morphology. The role of EFR (emerging flux region) as a bipolar region of velocity downflow is also shown. It is pointed out that, since all new magnetic flux emerges in strictly bipolar form, complex spot groups must result from surface interaction, hence most of the solar surface field may be produced on the surface.

Zirin, H.↗

Axial fatigue of /0, +30, and -30 deg/6s graphite/epoxy

Results are presented for an investigation carried out on a /0, +30, and -30 deg/6s graphite/epoxy angle-ply laminate in order to characterize the overall fatigue behavior, to evaluate strength/moduli degradation due to cyclic loading, and to identify the failure modes and mechanisms. The specimen life determined from fatigue tests is measured as a function of cyclic stress amplitude for various stress ratios. Fractured specimens are sectioned and examined by conventional metallography and SEM to reveal failure modes and mechanisms. It is shown that the laminate studied is susceptible to axial fatigue failures under cyclic loading which involves both tensile and compressive mean stresses. Fracture surface observations indicate the occurrence of complex failure modes. A variety of local failure mechanisms are identified.

Ramani, S. V.↗

Offset weap rib concept and development

The applicability of the Wrap rib antenna design for offset feed configurations for antennas up to 300 m in diameter was assessed. The antenna design was defined for both symmetric and offset configurations in terms of surface quality, cost, weight, and mechanical complexity. A supporting deployable feed support structure was developed and characterized.

Woods, A. A., Jr.↗