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Results for “3D Modeling”

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 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Selection of nanobodies with broad neutralizing potential against primary HIV-1 strains using soluble subtype C gp140 envelope trimers

Broadly neutralizing antibodies (bnAbs) against HIV-1 protect from infection and reduce viral load upon therapeutic applications. However no vaccine was able so far to induce bnAbs demanding their expensive biotechnological production. For clinical applications, nanobodies (VHH) derived from heavy chain only antibodies from Camelidae, may be better suited due to their small size, high solubility/stability and extensive homology to human VH3 genes. Here we selected broadly neutralizing nanobodies by phage display after immunization of dromedaries with different soluble trimeric envelope proteins derived from HIV-1 subtype C. We identified 25 distinct VHH families binding trimeric Env, of which 6 neutralized heterologous primary isolates of various HIV-1 subtypes in a standardized in vitro neutralization assay. The complementary neutralization pattern of two selected VHHs in combination covers 19 out of 21 HIV-1 strains from a standardized panel of epidemiologically relevant HIV-1 subtypes. The CD4 binding site was preferentially targeted by the broadly neutralizing VHHs as determined by competition ELISAs and 3D models of VHH-Env complexes derived from negative stain electron microscopy. The nanobodies identified here are excellent candidates for further preclinical/clinical development for prophylactic and therapeutic applications due to their potency and their complementary neutralization patterns covering the majority of epidemiologically relevant HIV-1 subtypes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Electron tomography unravels new insights into fiber cell wall nanostructure; exploring 3D macromolecular biopolymeric nano-architecture of spruce fiber secondary walls

Lignocellulose biomass has a tremendous potential as renewable biomaterials for fostering the “bio-based society” and circular bioeconomy paradigm. It requires efficient use and breakdown of fiber cell walls containing mainly cellulose, hemicellulose and lignin biopolymers. Despite their great importance, there is an extensive debate on the true structure of fiber walls and knowledge on the macromolecular nano-organization is limited and remains elusive in 3D. We employed dual-axis electron tomography that allows visualization of previously unseen 3D macromolecular organization/biopolymeric nano-architecture of the secondary S2 layer of Norway spruce fiber wall. Unprecedented 3D nano-structural details with novel insights into cellulose microfibrils (~2 nm diameter), macrofibrils, nano-pore network and cell wall chemistry (volume %) across the S2 were explored and quantified including simulation of structure related permeability. Matrix polymer association with cellulose varied between microfibrils and macrofibrils with lignin directly associated with MFs. Simulated bio-nano-mechanical properties revealed stress distribution within the S2 and showed similar properties between the idealized 3D model and the native S2 (actual tomogram). Present work has great potential for significant advancements in lignocellulose research on nano-scale understanding of cell wall assembly/disassembly processes leading to more efficient industrial processes of functionalization, valorization and target modification technologies.

3-D reconstruction↗
DOE OSTI2014

An automated miniature robotic vehicle inspection system

A novel, autonomous reconfigurable robotic inspection system for quantitative NDE mapping is presented. The system consists of a fleet of wireless (802.11g) miniature robotic vehicles, each approximately 175 × 125 × 85 mm with magnetic wheels that enable them to inspect industrial structures such as storage tanks, chimneys and large diameter pipe work. The robots carry one of a number of payloads including a two channel MFL sensor, a 5 MHz dry coupled UT thickness wheel probe and a machine vision camera that images the surface. The system creates an NDE map of the structure overlaying results onto a 3D model in real time. The authors provide an overview of the robot design, data fusion algorithms (positioning and NDE) and visualization software.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Numerical study on microwave-sustained argon discharge under atmospheric pressure

A numerical study on microwave sustained argon discharge under atmospheric pressure is reported in this paper. The purpose of this study is to investigate both the process and effects of the conditions of microwave-excited gas discharge under atmospheric pressure, thereby aiding improvements in the design of the discharge system, setting the appropriate working time, and controlling the operating conditions. A 3D model is presented, which includes the physical processes of electromagnetic wave propagation, electron transport, heavy species transport, gas flow, and heat transfer. The results can be obtained by means of the fluid approximation. The maxima of the electron density and gas temperature are 4.96 × 10{sup 18} m{sup −3} and 2514.8 K, respectively, and the gas pressure remains almost unchanged for typical operating conditions with a gas flow rate of 20 l/min, microwave power of 1000 W, and initial temperature of 473 K. In addition, the conditions (microwave power, gas flow rate, and initial temperature) of discharge are varied to obtain deeper information about the electron density and gas temperature. The results of our numerical study are valid and clearly describe both the physical process and effects of the conditions of microwave-excited argon discharge.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Plasma asymmetry due to the magnetic filter in fusion-type negative ion sources: Comparisons between two and three-dimensional particle-in-cell simulations

Previously reported 2D Particle-In-Cell Monte Carlo Collisions (PIC-MCC) simulations of negative ion sources under conditions similar to those of the ITER neutral beam injection system have shown that the presence of the magnetic filter tends to generate asymmetry in the plasma properties in the extraction region. In this paper, we show that these conclusions are confirmed by 3D PIC-MCC simulations and we provide quantitative comparisons between the 2D and 3D model predictions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Numerical simulation of transient moisture transfer into an electronic enclosure

Electronic systems are sometimes exposed to harsh environmental conditions of temperature and humidity. Moisture transfer into electronic enclosures and condensation can cause several problems such as corrosion and alteration in thermal stresses. It is therefore essential to study the local climate inside the enclosures to be able to protect the electronic systems. In this work, moisture transfer into a typical electronic enclosure is numerically studied using CFD. In order to reduce the CPU-time and make a way for subsequent factorial design analysis, a simplifying modification is applied in which the real 3D geometry is approximated by a 2D axial symmetry one. The results for 2D and 3D models were compared in order to calibrate the 2D representation. Furthermore, simulation results were compared with experimental data and good agreement was found.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Design of novel dual-port tapered waveguide plasma apparatus by numerical analysis

Microwave plasma apparatus is often of particular interest due to their superiority of low cost, electrode contamination free, and suitability for industrial production. However, there exist problems of unstable plasma and low electron density in conventional waveguide apparatus based on single port, due to low strength and non-uniformity of microwave field. This study proposes a novel dual-port tapered waveguide plasma apparatus based on power-combining technique, to improve the strength and uniformity of microwave field for the applications of plasma. A 3D model of microwave-induced plasma (field frequency 2.45 GHz) in argon at atmospheric pressure is presented. On the condition that the total input power is 500 W, simulations indicate that coherent power-combining will maximize the electric-field strength to 3.32 × 10{sup 5 }V/m and improve the uniformity of distributed microwave field, which raised 36.7% and 47.2%, respectively, compared to conventional waveguide apparatus of single port. To study the optimum conditions for industrial application, a 2D argon fluid model based on above structure is presented. It demonstrates that relatively uniform and high-density plasma is obtained at an argon flow rate of 200 ml/min. The contrastive result of electric-field distribution, electron density, and gas temperature is also valid and clearly proves the superiority of coherent power-combining to conventional technique in flow field.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

A numerical study of latent thermal energy storage in a phase change material/carbon panel

To reduce the energetic dependence of building, it has become necessary to explore and develop new materials promoting energy conservation. Because of their high storage capacity, phase change materials (PCMs) are efficient to store thermal energy. In this paper, a 3D model was studied for simulation of energy storing cycles to predict the performances of PCM loaded panels. Carbon was used as supporting material for the PCM. The simulation was based on the enthalpy method using Ansys Fluent software. The panel was exposed to a daily heat flow including the effects of convection and radiation. The results show that the temperature decreased of approximately 2.5°C with a time shift about 2 hours. The steady state was reached after four cycles. Thus, after four cycles the PCM showed its effects on the temperature conditioning.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Improving ICF implosion performance with alternative capsule supports

The thin membrane that holds the capsule in-place in the hohlraum is recognized as one of the most significant contributors to reduced performance in indirect drive inertial confinement fusion (ICF) experiments on the National Ignition Facility. This membrane, known as the “tent,” seeds a perturbation that is amplified by Rayleigh-Taylor and can rupture the capsule. A less damaging capsule support mechanism is under development. Possible alternatives include the micron-scale rods spanning the hohlraum width and supporting either the capsule or stiffening the fill-tube, a larger fill-tube to both fill and support the capsule, or a low-density foam layer that protects the capsule from the tent impact. Experiments are testing these support features to measure their imprint on the capsule. These experiments are revealing unexpected aspects about perturbation development in indirect drive ICF, such as the importance of shadows coming from bright spots in the hohlraum. Two dimensional and 3D models are used to explain these features and assess the impact on implosion performance. Experiments and modeling suggest that the fill-tube supported by a perpendicular rod can mount the capsule without any additional perturbation beyond that of the fill tube.

Weber, C. R.↗
DOE OSTI2017

Laser beam coupling with capillary discharge plasma for laser wakefield acceleration applications

One of the most robust approaches, demonstrated to date, of accelerating electron beams by laser-plasma sources is the utilization of plasma channels generated by the capillary discharges. Although the spatial structure of the installation is simple in principle, there may be some important effects caused by the open ends of the capillary, by the supplying channels etc., which require a detailed 3D modeling of the processes. In the present work, such simulations are performed using the code MARPLE. First, the process of capillary filling with cold hydrogen before the discharge is fired, through the side supply channels is simulated. Second, the simulation of the capillary discharge is performed with the goal to obtain a time-dependent spatial distribution of the electron density near the open ends of the capillary as well as inside the capillary. Lastly, to evaluate the effectiveness of the beam coupling with the channeling plasma wave guide and of the electron acceleration, modeling of the laser-plasma interaction was performed with the code INF&RNO.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome

Significance Breakthrough technological advances such as Hi-C have enabled large-scale sequencing of pairwise genomic contacts. However, translating the 2D contacts to 3D spatial models remains challenging. Here we develop the “4DHiC” modeling method to infer 3D information from 2D datasets across time and construct a 3D model of the inactive X-chromosome (Xi). Our model not only demonstrates a spatial phase-separation between A/B and S1/S2 compartments to form “hemispheres,” but also reveals persistent smaller-scale structures hidden under the Xi superstructure. We also simulate Xist RNA spreading dynamics and deduce that the RNA spreads between hemispheres via both surface and core to establish the Xi. Our 4DHiC will serve a growing demand for data-driven methodologies that extract spatial information from biochemical interaction data.

Lappala, Anna↗
DOE OSTI2015

INTERNAL PROPER MOTIONS IN THE ESKIMO NEBULA

We present measurements of internal proper motions at more than 500 positions of NGC 2392, the Eskimo Nebula, based on images acquired with WFPC2 on board the Hubble Space Telescope at two epochs separated by 7.695 yr. Comparisons of the two observations clearly show the expansion of the nebula. We measured the amplitude and direction of the motion of local structures in the nebula by determining their relative shift during that interval. In order to assess the potential uncertainties in the determination of proper motions in this object, in general, the measurements were performed using two different methods, used previously in the literature. We compare the results from the two methods, and to perform the scientific analysis of the results we choose one, the cross-correlation method, because it is more reliable. We go on to perform a ''criss-cross'' mapping analysis on the proper motion vectors, which helps in the interpretation of the velocity pattern. By combining our results of the proper motions with radial velocity measurements obtained from high resolution spectroscopic observations, and employing an existing 3D model, we estimate the distance to the nebula to be 1.3 kpc.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

EMERGENCE OF GRANULAR-SIZED MAGNETIC BUBBLES THROUGH THE SOLAR ATMOSPHERE. II. NON-LTE CHROMOSPHERIC DIAGNOSTICS AND INVERSIONS

Magnetic flux emergence into the outer layers of the Sun is a fundamental mechanism for releasing energy into the chromosphere and the corona. In this paper, we study the emergence of granular-sized flux concentrations and the structuring of the corresponding physical parameters and atmospheric diagnostics in the upper photosphere and in the chromosphere. We make use of a realistic 3D MHD simulation of the outer layers of the Sun to study the formation of the Ca ii 8542 line. We also derive semi-empirical 3D models from non-LTE inversions of our observations. These models contain information on the line-of-sight stratifications of temperature, velocity, and the magnetic field. Our analysis explains the peculiar Ca ii 8542 Å profiles observed in the flux emerging region. Additionally, we derive detailed temperature and velocity maps describing the ascent of a magnetic bubble from the photosphere to the chromosphere. The inversions suggest that, in active regions, granular-sized bubbles emerge up to the lower chromosphere where the existing large-scale field hinders their ascent. We report hints of heating when the field reaches the chromosphere.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Connection between plasma response and resonant magnetic perturbation (RMP) edge localized mode (ELM) suppression in DIII-D [Connection between plasma response and RMP ELM suppression in DIII-D]

Calculations of the plasma response to applied non-axisymmetric fields in several DIII-D discharges show that predicted displacements depend strongly on the edge current density. This result is found using both a linear two-fluid-MHD model (M3D-C1) and a nonlinear ideal-MHD model (VMEC). Furthermore, it is observed that the probability of a discharge being edge localized mode (ELM)-suppressed is most closely related to the edge current density, as opposed to the pressure gradient. It is found that discharges with a stronger kink response are closer to the peeling–ballooning stability limit in ELITE simulations and eventually cross into the unstable region, causing ELMs to reappear. Thus for effective ELM suppression, the RMP has to prevent the plasma from generating a large kink response, associated with ELM instability. Experimental observations are in agreement with the finding; discharges which have a strong kink response in the MHD simulations show ELMs or ELM mitigation during the RMP phase of the experiment, while discharges with a small kink response in the MHD simulations are fully ELM suppressed in the experiment by the applied resonant magnetic perturbation. The results are cross-checked against modeled 3D ideal MHD equilibria using the VMEC code. The procedure of constructing optimal 3D equilibria for diverted H-mode discharges using VMEC is presented. As a result, kink displacements in VMEC are found to scale with the edge current density, similar to M3D-C1, but the displacements are smaller. A direct correlation in the flux surface displacements to the bootstrap current is shown.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

The discrete-continuum connection in dislocation dynamics: I. Time coarse graining of cross slip

A recent continuum dislocation dynamics formalism (Xia and El-Azab 2015 Model. Simul. Mater. Sci. Eng. 23 055009) has been enriched by incorporating an improved cross slip model. 3D discrete dislocation dynamics simulations were used to collect cross slip rate data in the form of time series that were analysed to estimate the correlation time for cross slip, which was subsequently used as a time scale for local window averaging of the collected cross slip rate data. This time averaging filters out the cross slip rate fluctuations over time intervals less than the correlation time, thus resulting in relatively smoother time series for the cross slip rates. The coarse grained series were further cast in the form of smooth trends with superposed fluctuations and implemented in continuum dislocation dynamics simulations using a Monte Carlo scheme. Here, this approach resulted in a significant improvement of the predicted stress–strain response and a more realistic dislocation cell structure evolution. The similitude law for the average cell size evolution with inverse of stress, however, remains unaffected by the cross slip rates used in continuum dislocation dynamics.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Features of near and far scrape-off layer heat fluxes on the Wendelstein 7-X inboard limiters

The power fall-off length is used as a characteristic dimension to describe the power exhaust in the scrape-off layer (SOL) in magnetic confinement fusion devices. Measurements from the limiter campaign of the stellarator Wendelstein 7-X with inboard limiters are presented with the first-time characterization of the limiter heat loads. Two fall-off regimes are found with a narrow near SOL with power fall-off length in millimeters and a wider far SOL with fall-off lengths of several centimeters. An attempt is made to describe both regimes with a scaling law for plasma with different heating powers and densities. Finally, the results confirm the major geometry effects of the connection length on the heat transport predicted by 3D modeling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Evolutionary engineering reveals amino acid substitutions in Ato2 and Ato3 that allow improved growth of Saccharomyces cerevisiae on lactic acid

ABSTRACT In Saccharomyces cerevisiae, the complete set of proteins involved in transport of lactic acid across the cell membrane has not been determined. In this study, we aimed to identify transport proteins not previously described to be involved in lactic acid transport via a combination of directed evolution, whole-genome resequencing and reverse engineering. Evolution of a strain lacking all known lactic acid transporters on lactate led to the discovery of mutated Ato2 and Ato3 as two novel lactic acid transport proteins. When compared to previously identified S. cerevisiae genes involved in lactic acid transport, expression of ATO3T284C was able to facilitate the highest growth rate (0.15 ± 0.01 h-1) on this carbon source. A comparison between (evolved) sequences and 3D models of the transport proteins showed that most of the identified mutations resulted in a widening of the narrowest hydrophobic constriction of the anion channel. We hypothesize that this observation, sometimes in combination with an increased binding affinity of lactic acid to the sites adjacent to this constriction, are responsible for the improved lactic acid transport in the evolved proteins.

Baldi, Nicolò↗
DOE OSTI2025

Viroid-like “obelisk” agents are widespread in the ocean and exceed the abundance of RNA viruses in the prokaryotic fraction

Abstract “Obelisks” are recently discovered ribonucleic acid (RNA) viroid-like elements present in diverse environments with no phylogenetic similarity to any known biological agent. obelisks were first identified in the human gut and in a commensal bacterium acting as a replicative host. They have a circular ∼1 kb RNA genome, rod-like secondary structures, and the encoding of a protein superfamily called “Oblins”. We performed a large-scale search of obelisks in the ocean using the Pebblescout program and the transcriptomic Sequence Archive Read databases, revealing the biogeography and abundance of these viroid-like RNA elements. We detected 55 obelisk genomes resulting in 35 marine clusters at the species level. These obelisks were detected in the prokaryotic fraction and to a lesser extent in the eukaryotic fraction, and distributed across all the oceans from surface to mesopelagic including the Arctic, and even in the coldest seawater of Earth beneath the Antarctic Ross Ice Shelf. The obelisk hallmark protein Oblin-1 confirmed by 3D models was found in various marine samples. Some of the detected marine obelisks harbor hammerhead self-cleaving ribozymes in both polarities. In the prokaryotic, but not the eukaryotic, fraction of the Tara Ocean dataset, relative abundance of obelisks calculated by transcriptomic fragment recruitment indicated that they are abundant in marine samples, reaching or even exceeding the relative abundance of the previously discovered uncultured RNA viruses. In conclusion, obelisks are abundant and widespread viroid-like elements that should be included in ocean biogeochemical models.

Environmental Sciences & Ecology↗