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DOE OSTI2022

Nramp: Deprive and conquer?

Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H+)-dependent manganese (Mn2+) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)’s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries ‘eukaryotic signature’ marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H+-dependent Mn2+ acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn2+-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn2+ sequestering defense perhaps favoring intracellular growth-competent bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Cloning and Characterization of Aedes aegypti Trypsin Modulating Oostatic Factor (TMOF) Gut Receptor

Trypsin Modulating Oostatic Factor (TMOF) receptor was solubilized from the guts of female Ae. Aegypti and cross linked to His6-TMOF and purified by Ni affinity chromatography. SDS PAGE identified two protein bands (45 and 61 kDa). The bands were cut digested and analyzed using MS/MS identifying a protein sequence (1306 amino acids) in the genome of Ae. aegypti. The mRNA of the receptor was extracted, the cDNA sequenced and cloned into pTAC-MAT-2. E. coli SbmA− was transformed with the recombinant plasmid and the receptor was expressed in the inner membrane of the bacterial cell. The binding kinetics of TMOF-FITC was then followed showing that the cloned receptor exhibits high affinity to TMOF (KD = 113.7 ± 18 nM ± SEM and Bmax = 28.7 ± 1.8 pmol ± SEM). Incubation of TMOF-FITC with E. coli cells that express the receptor show that the receptor binds TMOF and imports it into the bacterial cells, indicating that in mosquitoes the receptor imports TMOF into the gut epithelial cells. A 3D modeling of the receptor indicates that the receptor has ATP binding sites and TMOF transport into recombinant E. coli cells is inhibited with ATPase inhibitors Na Arsenate and Na Azide.

Borovsky, Dov↗

DOE OSTI2024

Quantitative Analysis of Rhodobacter sphaeroides Storage Organelles via Cryo-Electron Tomography and Light Microscopy

Bacterial cytoplasmic organelles are diverse and serve many varied purposes. Here, we employed Rhodobacter sphaeroides to investigate the accumulation of carbon and inorganic phosphate in the storage organelles, polyhydroxybutyrate (PHB) and polyphosphate (PP), respectively. Using cryo-electron tomography (cryo-ET), these organelles were observed to increase in size and abundance when growth was arrested by chloramphenicol treatment. The accumulation of PHB and PP was quantified from three-dimensional (3D) segmentations in cryo-tomograms and the analysis of these 3D models. The quantification of PHB using both segmentation analysis and liquid chromatography and mass spectrometry (LCMS) each demonstrated an over 10- to 20-fold accumulation of PHB. The cytoplasmic location of PHB in cells was assessed with fluorescence light microscopy using a PhaP-mNeonGreen fusion-protein construct. The subcellular location and enumeration of these organelles were correlated by comparing the cryo-ET and fluorescence microscopy data. A potential link between PHB and PP localization and possible explanations for co-localization are discussed. Finally, the study of PHB and PP granules, and their accumulation, is discussed in the context of advancing fundamental knowledge about bacterial stress response, the study of renewable sources of bioplastics, and highly energetic compounds.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Optimization of Window Positions for Wind-Driven Natural Ventilation Performance

This paper optimizes opening positions on building facades to maximize the natural ventilation’s potential for ventilation and cooling purposes. The paper demonstrates how to apply computational fluid dynamics (CFD) simulation results to architectural design processes, and how the CFD-driven decisions impact ventilation and cooling: (1) background: A CFD helps predict the natural ventilation’s potential, the integration of CFD results into design decision-making has not been actively practiced; (2) methods: Pressure data on building facades were obtained from CFD simulations and mapped into the 3D modeling environment, which were then used to identify optimal positions of two openings of a zone. The effect of the selected opening positions was validated with building energy simulations; (3) results: The cross-comparison study of different window positions based on different geographical locations quantified the impact on natural ventilation effectiveness; and (4) conclusions: The optimized window position was shown to be effective, and some optimal solutions contradicted the typical cross-ventilation strategy.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

Machine Learning for Additive Manufacturing of Functionally Graded Materials

Additive Manufacturing (AM) is a transformative manufacturing technology enabling direct fabrication of complex parts layer-by-layer from 3D modeling data. Among AM applications, the fabrication of Functionally Graded Materials (FGMs) has significant importance due to the potential to enhance component performance across several industries. FGMs are manufactured with a gradient composition transition between dissimilar materials, enabling the design of new materials with location-dependent mechanical and physical properties. This study presents a comprehensive review of published literature pertaining to the implementation of Machine Learning (ML) techniques in AM, with an emphasis on ML-based methods for optimizing FGMs fabrication processes. Through an extensive survey of the literature, this review article explores the role of ML in addressing the inherent challenges in FGMs fabrication and encompasses parameter optimization, defect detection, and real-time monitoring. The article also provides a discussion of future research directions and challenges in employing ML-based methods in the AM fabrication of FGMs.

36 - MATERIALS SCIENCE↗

DOE OSTI2017

A Large-scale Plume in an X-class Solar Flare

Ever-increasing multi-frequency imaging of solar observations suggests that solar flares often involve more than one magnetic fluxtube. Some of the fluxtubes are closed, while others can contain open fields. The relative proportion of nonthermal electrons among those distinct loops is highly important for understanding energy release, particle acceleration, and transport. The access of nonthermal electrons to the open field is also important because the open field facilitates the solar energetic particle (SEP) escape from the flaring site, and thus controls the SEP fluxes in the solar system, both directly and as seed particles for further acceleration. The large-scale fluxtubes are often filled with a tenuous plasma, which is difficult to detect in either EUV or X-ray wavelengths; however, they can dominate at low radio frequencies, where a modest component of nonthermal electrons can render the source optically thick and, thus, bright enough to be observed. Here we report the detection of a large-scale “plume” at the impulsive phase of an X-class solar flare, SOL2001-08-25T16:23, using multi-frequency radio data from Owens Valley Solar Array. To quantify the flare’s spatial structure, we employ 3D modeling utilizing force-free-field extrapolations from the line of sight SOHO /MDI magnetograms with our modeling tool GX-Simulator. We found that a significant fraction of the nonthermal electrons that accelerated at the flare site low in the corona escapes to the plume, which contains both closed and open fields. We propose that the proportion between the closed and open fields at the plume is what determines the SEP population escaping into interplanetary space.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2017

Distortion of Magnetic Fields in a Starless Core II: 3D Magnetic Field Structure of FeSt 1-457

Three-dimensional (3D) magnetic field information on molecular clouds and cores is important for revealing their kinematical stability (magnetic support) against gravity, which is fundamental for studying the initial conditions of star formation. In the present study, the 3D magnetic field structure of the dense starless core FeSt 1-457 is determined based on the near-infrared polarimetric observations of the dichroic polarization of background stars and simple 3D modeling. With an obtained angle of line-of-sight magnetic inclination axis θ{sub inc} of 45{sup ∘}±10{sup ∘} and previously determined plane-of-sky magnetic field strength B{sub pol} of 23.8 ± 12.1 μG, the total magnetic field strength for FeSt 1-457 is derived to be 33.7 ± 18.0 μG. The critical mass of FeSt 1-457, evaluated using both magnetic and thermal/turbulent support is M{sub cr}=3.70±0.92 M{sub ⊙}, which is identical to the observed core mass, M{sub core}=3.55±0.75 M{sub ⊙}. We thus conclude that the stability of FeSt 1-457 is in a condition close to the critical state. Without infalling gas motion and no associated young stars, the core is regarded to be in the earliest stage of star formation, i.e., the stage just before the onset of dynamical collapse following the attainment of a supercritical condition. These properties could make FeSt 1-457 one of the best starless cores for future studies of the initial conditions of star formation.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

A Theory for Neutron Star and Black Hole Kicks and Induced Spins

Abstract Using 20 long-term 3D core-collapse supernova simulations, we find that lower compactness progenitors that explode quasi-spherically due to the short delay to explosion experience smaller neutron star recoil kicks in the ∼100−200 km s −1 range, while higher compactness progenitors that explode later and more aspherically leave neutron stars with kicks in the ∼300−1000 km s −1 range. In addition, we find that these two classes are correlated with the gravitational mass of the neutron star. This correlation suggests that the survival of binary neutron star systems may in part be due to their lower kick speeds. We also find a correlation between the kick and both the mass dipole of the ejecta and the explosion energy. Furthermore, one channel of black hole birth leaves masses of ∼10 M ⊙ , is not accompanied by a neutrino-driven explosion, and experiences small kicks. A second channel is through a vigorous explosion that leaves behind a black hole with a mass of ∼3.0 M ⊙ kicked to high speeds. We find that the induced spins of nascent neutron stars range from seconds to ∼10 ms, but do not yet see a significant spin/kick correlation for pulsars. We suggest that if an initial spin biases the explosion direction, a spin/kick correlation would be a common byproduct of the neutrino mechanism of core-collapse supernovae. Finally, the induced spin in explosive black hole formation is likely large and in the collapsar range. This new 3D model suite provides a greatly expanded perspective and appears to explain some observed pulsar properties by default.

Astronomy & Astrophysics↗

NASA NTRS1991

Structure and particle properties of Saturn's E Ring

The present systematic reanalysis of a substantial portion of extant photometric data on the Saturn E Ring has calibrated every observation on the basis of a common 3D model. A simple power-law model is found to describe the ring's normal optical depth profile with orbital radius; this trend is departed from, however, near the density peak, where there emerges a 30-percent localized decrease in thickness. No power-law size distribution is found to be compatible with available photometry. The peculiar size distribution points to a ring origin in a process that was not collisional or disruptive.

Showalter, Mark R.↗

NASA NTRS1990

Numerical simulations of solar disturbances and their interplanetary consequences

Time-dependent MHD numerical simulations are used to study responses of the solar atmosphere and interplanetary medium to simulated solar disturbances. A number of 2D and 3D examples of coronal mass ejection (CME) simulations and some current controversies concerning the basic processes of CME initiation are discussed. Footpoint shearing motion is tested to determine whether it can provide a reasonable mechanism for CME development from arch filament configurations. Possible interplanetary consequences to CME-like disturbances are demonstrated by using 3D simulations to determine the dynamic response of the solar wind to a plasmoid injection from an eruptive filament or prominence. The possibility that a plasmoid may be generated in the interplanetary medium by a solar-generated shock that propagates through a heliospheric current sheet is discussed. Application of the 3D model for the interpretation of interplanetary scintillation observations is addressed.

Dryer, M.↗

NASA NTRS1992

Magnetic resonance imaging as a tool for extravehicular activity analysis

The purpose of this research is to examine the value of magnetic resonance imaging (MRI) as a means of conducting kinematic studies of the hand for the purpose of EVA capability enhancement. After imaging the subject hand using a magnetic resonance scanner, the resulting 2D slices were reconstructed into a 3D model of the proximal phalanx of the left hand. Using the coordinates of several landmark positions, one is then able to decompose the motion of the rigid body. MRI offers highly accurate measurements due to its tomographic nature without the problems associated with other imaging modalities for in vivo studies.

Dickenson, R.↗

NASA NTRS1993

Operation of the helicopter antenna radiation prediction code

HARP is a front end as well as a back end for the AMC and NEWAIR computer codes. These codes use the Method of Moments (MM) and the Uniform Geometrical Theory of Diffraction (UTD), respectively, to calculate the electromagnetic radiation patterns for antennas on aircraft. The major difficulty in using these codes is in the creation of proper input files for particular aircraft and in verifying that these files are, in fact, what is intended. HARP creates these input files in a consistent manner and allows the user to verify them for correctness using sophisticated 2 and 3D graphics. After antenna field patterns are calculated using either MM or UTD, HARP can display the results on the user's screen or provide hardcopy output. Because the process of collecting data, building the 3D models, and obtaining the calculated field patterns was completely automated by HARP, the researcher's productivity can be many times what it could be if these operations had to be done by hand. A complete, step by step, guide is provided so that the researcher can quickly learn to make use of all the capabilities of HARP.

Braeden, E. W.↗

NASA NTRS1993

Ionization and expansion of barium clouds in the ionosphere

A recently envelope 3D model is used here to study the motion of the barium clouds released in the ionosphere, including the ionization stage. The ionization and the expansion of the barium clouds and the interaction between the clouds and the background ions are investigated using three simulations: a cloud without a directional velocity, a cloud with an initial velocity of 5 km/s across the B field, and a cloud with initial velocity components of 2 km/s both along and across the B field.

Ma, T.-Z.↗

NASA NTRS1993

Plume structures in the hard-turbulent regime of three-dimensional infinite Prandtl number convection

Numerical simulations of three-dimensional infinite Prandtl number thermal convection with Rayleigh number (Ra) up to 10 exp 8 are reported. Convection with Ra higher than 10 exp 7 is characterized by the appearance of disconnected thermal plumes. The smaller plumes are detached by the currents produced by the larger plumes. The low wavenumber portion of a thermal power spectrum near the boundary layer becomes flat at high Ra, while the spectrum measured in the interior shows a positive slope for low wavenumbers. Differences are found in the thermal spectra between 2D and 3D models.

Malevsky, A. V.↗

NASA NTRS1993

Finite element analysis of the Space Shuttle Main Engine (SSME) alternate turbopump development (ATD) high pressure oxydizer turbopump (HPOTP)

A 3D model of all stationary components of the ATD HPOTP is analyzed using a superelement solution technique to obtain a better understanding of the pump behavior and to support pump testing. Emphasis is place on the methods used for determining deflections. As part of the model verification, analyses were conducted on the main housing model under proof-pressure and push-test loading conditions. The analysis at 109 percent rate power level resulted in asymmetric deformation patterns which were used to calculate operating and rub clearances. The present analysis is considered to provide the most realistic representation of the ATD HPOTP to date.

Ham-Battista, G. L.↗

NASA NTRS1992

Viewing analyses for the assembly of Space Station Freedom (SSF)

Analyses are currently being conducted in the Man-Systems Division of the NASA Johnson Space Center, on the restructured Space Station Freedom configuration to determine viewing requirements for both robotic tasks and for extravehicular crew activities. The use of the PLAID software, a 3D modeling simulation tool, provides a simulation of the environment and the system hardware to identify potential problem areas needing further refinement in design development. This process enables human factor considerations and issues to be explored during the design process to identify and correct problems before hardware is actually constructed. Preliminary results have identified several potential viewing problem areas with the available lighting for both robotic and EVA tasks. To rectify the potential viewing problems identified through simulation, additional cameras and lighting enhancements are being proposed at various sites along the truss and on the Shuttle to provide more complete coverage of work task sites. Supplementing the existing cameras with color coded alignment aids will also help reduce the workload involved with robotic tasks.

Stealey, Sheryl↗

NASA NTRS1994

SAVA 3: A testbed for integration and control of visual processes

The development of an experimental test-bed to investigate the integration and control of perception in a continuously operating vision system is described. The test-bed integrates a 12 axis robotic stereo camera head mounted on a mobile robot, dedicated computer boards for real-time image acquisition and processing, and a distributed system for image description. The architecture was designed to: (1) be continuously operating, (2) integrate software contributions from geographically dispersed laboratories, (3) integrate description of the environment with 2D measurements, 3D models, and recognition of objects, (4) capable of supporting diverse experiments in gaze control, visual servoing, navigation, and object surveillance, and (5) dynamically reconfiguarable.

Crowley, James L.↗

NASA NTRS1993

Virtual egocenters as a function of display geometric field of view and eye station point

The accurate location of one's virtual egocenter in a geometric space is of critical importance for immersion technologies. This experiment was conducted to investigate the role of field of view (FOV) and observer station points in the perception of the location of one's egocenter (the personal viewpoint) in virtual space. Rivalrous cues to the accurate location of one's egocenter may be one factor involved in simulator sickness. Fourteen subjects viewed an animated 3D model, of the room in which they sat, binocularly, from Eye Station Points (ESP) of either 300 or 800 millimeters. The display was on a 190 by 245 mm monitor, at a resolution of 320 by 200 pixels with 256 colors. They saw four models of the room designed with four geometric field of view (FOVg) conditions of 18, 48, 86, and 140 degrees. They drew the apparent paths of the camera in the room on a bitmap of the room as seen from infinity above. Large differences in the paths of the camera were seen as a function of both FOVg and ESP. Ten of the subjects were then asked to find the position for each display that minimized camera motion. The results fit well with predictions from an equation that took the ratio of human FOV (roughly 180 degrees) to FOVg times the Geometric Eye Point (GEP) of the imager: Zero Station Point = (180/FOVg)*GEP

Psotka, Joseph↗