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At least 469 records · Page 26

Increased enhancer–promoter interactions during developmental enhancer activation in mammals

Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here, in this study, we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer-promoter physical proximity for developmental gene activation in mammals.

59 BASIC BIOLOGICAL SCIENCES↗

Relevant Environment Additive Construction Technology (REACT)

Project Overview This project is focused on developing technologies that enable construction of a Lunar Safe Haven type structure on the moon. A full scale architectural and structural design will be completed based on lunar conditions and Artemis mission needs. A scaled structure will be 3D printed in simulated lunar environments. Technical Approach Polymer bound regolith composite materials will be developed and characterized for lunar additive construction applications. A full scale architectural and structural design will be completed based on the latest scientific data on lunar environments including radiation, meteoroids, thermal conditions, reduced gravity, and moonquakes. The project will culminate with a demonstration of additive construction in simulated lunar vacuum, thermal, regolith, and UV conditions. Results/Summary Preliminary material specifications have been developed and an initial batch has been produced. A first iteration of the architectural and structural designs have been completed. Hardware for 3D printing in simulated lunar conditions is under development. Contributing Partners AI Space Factory – Winner of the NASA 3D Printed Habitat Centennial Challenge Infusion and Transition Plan On-surface construction of infrastructure is a critical capability of the sustainable phase of the Artemis Program and eventual sustainable human presence on Mars. It provides the ability to create protective shelters on-demand using local resources. The 3D-printing technology will achieve TRL 6 in 1g/vacuum tests with thermal/UV exposure in this project. CLPS missions will be pursued for infusion to demonstrate vertical construction with lunar regolith and conditions. Modeling and simulation will be used to define the pilot-scale shelter construction mission for long-term exposure on the lunar surface to validate the system for Artemis operational deployment.

Lunar Construction↗

Three-dimensional super line-localization in low signal-to-noise microscope images via prior-apprised unsupervised learning (PAUL)

Biological processes such as processive enzyme turnover and intracellular cargo tracking involve the dynamic motion of a small "article" along a curvilinear biopolymer track. To understand these processes that occur across multiple length and time scales, one must acquire both the trajectory of the particle and the position of the track along which it moves, possibly by combining high-resolution single-particle tracking with conventional microscopy. Yet, usually there is a significant resolution mismatch between these modalities: while the tracked particle is localized with a precision of 10 nm, the image of the surroundings is limited by optical difraction, with 200 nm lateral and 500 nm axial resolutions. Compared to the particle's trajectory, the surrounding curvilinear structure appears as a blurred and noisy image. This disparity in the spatial resolutions of the particle trajectory and the surrounding curvilinear structure image makes data reconstruction, as well as interpretation, particularly challenging. Analysis is further complicated when the curvilinear structures are oriented arbitrarily in 3D space. Here, we present a prior-apprised unsupervised learning (PAUL) approach to extract information from 3D images where the underlying features resemble a curved line such as a filament or microtubule. This three-stage framework starts with a Hessian-based feature enhancement, which is followed by feature registration, where local line segments are detected on repetitively sampled subimage tiles. In the final stage, statistical learning, segments are clustered based on their geometric relationships. Principal curves are then approximated from each segment group via statistical tools including principal component analysis, bootstrap and kernel transformation. This procedure is characterized on simulated images, where sub-voxel medium deviations from true curves have been achieved. The 3D PAUL approach has also been implemented for successful line localization in experimental 3D images of gold nanowires obtained using a multifocal microscope. Lastly, this work not only bridges the resolution gap between two microscopy modalities, but also allows us to conduct 3D super line-localization imaging experiments, without using super-resolution techniques.

42 ENGINEERING↗

Discovering Planetary Nebula Geometries: Explorations with a Hierarchy of Models

Astronomical objects known as planetary nebulae (PNe) consist of a shell of gas expelled by an aging medium-sized star as it makes its transition from a red giant to a white dwarf. In many cases this gas shell can be approximately described as a prolate ellipsoid. Knowledge of the physics of ionization processes in this gaseous shell enables us to construct a model in three dimensions (3D) called the Ionization-Bounded Prolate Ellipsoidal Shell model (IBPES model). Using this model we can generate synthetic nebular images, which can be used in conjunction with Hubble Space Telescope (HST) images of actual PNe to perform Bayesian model estimation. Since the IBPES model is characterized by thirteen parameters, model estimation requires the search of a 13-dimensional parameter space. The 'curse of dimensionality,' compounded by a computationally intense forward problem, makes forward searches extremely time-consuming and frequently causes them to become trapped in local solutions. We find that both the speed and of the search can be improved by judiciously reducing the dimensionality of the search space. Our basic approach employs a hierarchy of models of increasing complexity that converges to the IBPES model. Earlier studies establish that a hierarchical sequence converges more quickly, and to a better solution, than a search relying only on the most complex model. Here we report results for a hierarchy of five models. The first three models treat the nebula as a 2D image, while the last two models explore its characteristics as a 3D object and enable us to characterize the physics of the nebula. This five-model hierarchy is applied to HST images of ellipsoidal PNe to estimate their geometric properties and gas density profiles.

Huyser, Karen A.↗

Elastic plastic fracture mechanics methodology for surface cracks

The Elastic Plastic Fracture Mechanics (EPFM) Methodology has evolved significantly in the last several years. Nevertheless, some of these concepts need to be extended further before the whole methodology can be safely applied to structural parts. Specifically, there is a need to include the effect of constraint in the characterization of material resistance to crack growth and also to extend these methods to the case of 3D defects. As a consequence, this project was started as a 36 month research program with the general objective of developing an EPFM methodology to assess the structural reliability of pressure vessels and other parts of interest to NASA containing defects. This report covers a computer modelling algorithm used to simulate the growth of a semi-elliptical surface crack; the presentation of a finite element investigation that compared the theoretical (HRR) stress field to that produced by elastic and elastic-plastic models; and experimental efforts to characterize three dimensional aspects of fracture present in 'two dimensional', or planar configuration specimens.

Ernst, Hugo A.↗

Elastic plastic fracture mechanics methodology for surface cracks

The Elastic Plastic Fracture Mechanics Methodology has evolved significantly in the last several years. Nevertheless, some of these concepts need to be extended further before the whole methodology can be safely applied to structural parts. Specifically, there is a need to include the effect of constraint in the characterization of material resistance to crack growth and also to extend these methods to the case of 3D defects. As a consequence, this project was started as a 36 month research program with the general objective of developing an elastic plastic fracture mechanics methodology to assess the structural reliability of pressure vessels and other parts of interest to NASA which may contain flaws. The project is divided into three tasks that deal with (1) constraint and thickness effects, (2) three-dimensional cracks, and (3) the Leak-Before-Burst (LBB) criterion. This report period (March 1994 to August 1994) is a continuation of attempts to characterize three dimensional aspects of fracture present in 'two dimensional' or planar configuration specimens (Chapter Two), especially, the determination of, and use of, crack face separation data. Also, included, are a variety of fracture resistance testing results (J(m)R-curve format) and a discussion regarding two materials of NASA interest (6061-T651 Aluminum alloy and 1N718-STA1 nickel-base super alloy) involving a bases for like constraint in terms of ligament dimensions, and their comparison to the resulting J(m)R-curves (Chapter Two).

Ernst, Hugo A.↗

Higher-Order VLP-Based Protein Macromolecular Framework Structures Assembled via Coiled-Coil Interactions

Hierarchical organization is one of the fundamental features observed in biological systems that allows for efficient and effective functioning. Virus-like particles (VLPs) are elegant examples of a hierarchically organized supramolecular structure, where many subunits are self-assembled to generate the functional cage-like architecture. Utilizing VLPs as building blocks to construct two- and three-dimensional (3D) higher-order structures is an emerging research area in developing functional biomimetic materials. VLPs derived from P22 bacteriophages can be repurposed as nanoreactors by encapsulating enzymes and modular units to build higher-order catalytic materials via several techniques. In this study, we have used coiled-coil peptide interactions to mediate the P22 interparticle assembly into a highly stable, amorphous protein macromolecular framework (PMF) material, where the assembly does not depend on the VLP morphology, a limitation observed in previously reported P22 PMF assemblies. Many encapsulated enzymes lose their optimum functionalities under the harsh conditions that are required for the P22 VLP morphology transitions. Therefore, the coiled-coil-based PMF provides a fitting and versatile platform for constructing functional higher-order catalytic materials compatible with sensitive enzymes. Finally, we have characterized the material properties of the PMF and utilized the disordered PMF to construct a biocatalytic 3D material performing single- and multistep catalysis.

59 BASIC BIOLOGICAL SCIENCES↗

Rendering Three-Dimensional Solar Coronal Structures

An X-ray or EUV image of the corona or chromosphere is a 2D representation of an extended 3D complex for which a general inversion process is impossible. A specific model must be incorporated in order to understand the full 3D structure. We approach this problem by modeling a set of optically-thin 3D plasma flux tubes which we render these as synthetic images. The resulting images allow the interpretation of the X-ray/EUV observations to obtain information on (1) the 3D structure of X-ray images, i.e., the geometric structure of the flux tubes, and on (2) the internal structure using specific plasma characteristics, i.e., the physical structure of the flux tubes. The data-analysis technique uses magnetograms to characterize photospheric magnetic fields and extrapolation techniques to form the field lines. Using a new set of software tools, we have generated 3D flux tube structures around these field lines and integrated the plasma emission along the line of sight to obtain a rendered image. A set of individual flux-tube images is selected by a non-negative least-squares technique to Provide a match with an observed X-ray image. The scheme minimizes the squares of the differences between the synthesized image and the observed image with a non-negative constraint on the coefficients of the brightness of the individual flux-tube loops. The derived images are used to determine the specific photospheric foot points and physical data, i.e., scaling laws for densities and loop lengths. The development has led to Computer efficient integration and display software that is compatible for comparison with observations (e.g., Yohkoh SXT data, NIXT, or EIT). This analysis is important in determining directly the magnetic field configuration, which provides the structure of coronal loops, and indirectly the electric currents or waves, which provide the energy for the heating of the plasma. We have used very simple assumptions (i.e., potential magnetic fields and isothermal corona) to provide an initial test of the techniques before complex models are introduced. We have separated the physical and geometric contributions of the emission for a set of flux tubes and concentrated, in this initial study, on the geometric contributions by making approximations to the physical contributions. The initial results are consistent with the scaling laws derived from Yohkoh SXT data.

Gary, G. Allen↗

Reconnection and particle acceleration in 3D current sheet evolution in moderately-magnetized astrophysical pair plasma

Magnetic reconnection, a plasma process converting magnetic energy to particle kinetic energy, is often invoked to explain magnetic energy releases powering high-energy flares in astrophysical sources including pulsar wind nebulae and black hole jets. Reconnection is usually seen as the (essentially 2D) nonlinear evolution of the tearing instability disrupting a thin current sheet. To test how this process operates in 3D, we conduct a comprehensive particle-in-cell simulation study comparing 2D and 3D evolution of long, thin current sheets in moderately-magnetized, collisionless, relativistically-hot electron- positron plasma, and find dramatic differences. We first systematically characterize this process in 2D, where classic, hierarchical plasmoid-chain reconnection determines energy release, and explore a wide range of initial configurations, guide magnetic field strengths, and system sizes. We then show that 3D simulations of similar configurations exhibit a diversity of behaviours, including some where energy release is determined by the nonlinear relativistic drift-kink instability. Thus, 3D current-sheet evolution is not always fundamentally classical reconnection with perturbing 3D effects, but, rather, a complex interplay of multiple linear and nonlinear instabilities whose relative importance depends sensitively on the ambient plasma, minor configuration details, and even stochastic events. It often yields slower but longer-lasting and ultimately greater magnetic energy release than in 2D. Intriguingly, nonthermal particle acceleration is astonishingly robust, depending on the upstream magnetization and guide field, but otherwise yielding similar particle energy spectra in 2D and 3D. Though the variety of underlying current-sheet behaviours is interesting, the similarities in overall energy release and particle spectra may be more remarkable.

Gregory R. Werner↗

Going Off Grid: A Comparative Study of the Lagrangian and Eulerian Perspectives of New Particle Formation Events

New particle formation and growth (NPF&G) is the process by which ultrafine particles are formed from gas-phase precursors. NPF&G is the dominant source of global aerosol number with important influences on climate. Most observations of NPF&G events are conducted at stationary sites; however, NPF&G observed from stationary sites is influenced by gradual or rapid changes in the air masses passing over the site, complicating NPF&G analysis. In this work, we use observations and a 3D aerosol model to compare aerosol size distributions at a stationary site (Southern Great Plains [SGP] observatory, Oklahoma, USA) and along Lagrangian trajectories crossing the site. The model simulates the NPF&G events reasonably well at SGP. Using the model to compare the Lagrangian and stationary perspectives, we can explain previously unanalyzable days with some evidence of NPF&G as either non-event or analyzable NPF&G days. We find most of the unanalyzable NPF&G days are due to isolated and inhomogeneous NPF&G occurring upwind of the stationary site, often in the outflow of urban regions. Finally, we compare formation rates of 3 nm particles, growth rates, and the survival probability of 3 nm particles growing to 25 nm between the stationary and Lagrangian perspectives. Because of the much larger number of analyzable days along the Lagrangian trajectories, this perspective potentially provides more robust statistics and better characterization of NPF&G event extremes. Our method for extracting chemical/physical properties along Lagrangian trajectories from 3D models can be applied to a wide range of science questions.

O’Donnell, Samuel E. [Colorado State Univ., Fort C↗

Characterization, comparison, and optimization of lattice light sheets

Lattice light sheet microscopy excels at the noninvasive imaging of three-dimensional (3D) dynamic processes at high spatiotemporal resolution within cells and developing embryos. Recently, several papers have called into question the performance of lattice light sheets relative to the Gaussian sheets most common in light sheet microscopy. Here, we undertake a theoretical and experimental analysis of various forms of light sheet microscopy, which demonstrates and explains why lattice light sheets provide substantial improvements in resolution and photobleaching reduction. The analysis provides a procedure to select the correct light sheet for a desired experiment and specifies the processing that maximizes the use of all fluorescence generated within the light sheet excitation envelope for optimal resolution while minimizing image artifacts and photodamage. We also introduce a new type of “harmonic balanced” lattice light sheet that improves performance at all spatial frequencies within its 3D resolution limits and maintains this performance over lengthened propagation distances allowing for expanded fields of view.

59 BASIC BIOLOGICAL SCIENCES↗

Reconfigurable plasma-dielectric hybrid photonic crystal as a platform for electromagnetic wave manipulation and computing

The introduction of 3D printing has enabled fabrication of photonic crystal devices with complex crystal structures that would be challenging to construct using other fabrication methods. In this paper, we construct and characterize a photonic crystal consisting of two 4 x 8 x 8 cubic lattices composed of spherical silicon nitride elements straddling a layer of 8 plasma discharge tubes, creating a 3D hybrid plasma photonic crystal device. Integrating under-dense gaseous plasma elements provides a unique coupling dynamic between the dielectric spheres and the cylindrical plasma discharges, creating a monolithic hybrid photonic crystal with solid state and reconfigurable elements. The device has resonant modes that have attenuation peaks that are either switchable, tunable in amplitude, or tunable in frequency with variations in plasma density. The response of these bands seen with varying plasma density is confirmed through simulations when effects due to the heating of the photonic crystal from the gaseous plasma elements are accounted for in the experiments. We discuss how this reconfigurable device may be used and expanded upon for applications in photonic artificial neural networks and optical computing systems.

3D printing↗

Effect of tow alignment on the mechanical performance of 3D woven textile composites

Three-dimensional (3D) woven preforms are currently being considered for use as primary structural components. Lack of technology to properly manufacture, characterize and predict mechanical properties, and predict damage mechanisms leading to failure are problems facing designers of textile composite materials. Two material systems with identical specifications but different manufacturing approaches are investigated. One manufacturing approach resulted in an irregular (nonuniform) preform geometry. The other approach yielded the expected preform geometry (uniform). The objectives are to compare the mechanical properties of the uniform and nonuniform angle interlock 3D weave constructions. The effect of adding layers of laminated tape to the outer surfaces of the textile preform is also examined. Damage mechanisms are investigated and test methods are evaluated.

Norman, Timothy L.↗

Markforged Continuous Fiber Composite Material Testing

Continuous fiber composite 3D printing promises to greatly expand the design space of polymer additive manufacturing (AM). A series of mechanical tests were performed to attempt to fully characterize the composite materials built from feedstock provided by the Markforged company. These tests included tensile, compression, Charpy impact, three point bending, coefficient of thermal expansion, and calorimetry tests. Specimens were prepared on the Mark Two 3D printer at LANL during the spring and summer of 2019. These samples were then shipped to New Mexico Institute of Mining and Technology’s Thermo-Mechanical Lab for testing during the summer and fall of 2019. Test data are reported and analyzed for each of the tests.

36 MATERIALS SCIENCE↗

Iterative Stress Reconstruction Algorithm to Estimate Three-Dimensional Residual Stress Fields in Manufactured Components

Residual stress (RS) significantly impacts the mechanical performance of components. Measurement of RS often provides incomplete data in terms of components of stress and spatial density. Employing such fields in finite element simulations results in significant modification of the field to achieve equilibrium and compatibility among strains. To overcome this, an iterative stress reconstruction algorithm (ISRA) is developed to estimate 3D RS fields that satisfy equilibrium, are stress component-wise complete, and represent the characterized data sampled. An Al 7075-T651 plate and an additively manufactured (AM) A36 steel wall are considered for RS reconstruction using measurement data from the literature. A maximum variation of ~2.5 MPa in the Al plate, and ~10 MPa in the steel wall are observed between the reconstructed and measured stresses. Furthermore, unknown stress components emerge and reach significant magnitudes (upto ~2.3 MPa in the Al plate and ~45 MPa in the AM wall) during ISRA. Indeed, it is found that minor errors in measurement or data processing are eliminated through the physical requirements during ISRA. Employing a reconstructed RS field is hence not just more accurate given its compatibility, but it additionally corrects for minor errors in measurement. Furthermore, it is found that spatially dense measurement data result in convergence with fewer iterations. Finally, although ISRA yields a nonunique solution dependent on boundary conditions, measurement errors, fitting errors, and mesh density, it accommodates for uncertainties and inaccuracies in measurement, as opposed to failing to reach a physically realistic converged solution.

42 ENGINEERING↗

Li 7 P 2 S 8 Br 0.5 I 0.5 (LPSBI) solid state electrolyte by XPS

There have been increasing surface characterization studies of battery materials specifically in the context of before and after cell operation to determine any chemical changes. Therefore, providing reliable reference spectra of battery-related materials is important. In this paper, survey and high-energy resolution data are reported for the solid-state electrolyte Li 7 P 2 S 8 Br 0.5 I 0.5 (LPSBI), which has been synthesized and characterized at Pacific Northwest National Laboratory. The current data presents narrow scan regions of I 3d, I 4d, Br 3d, O 1s, P 2p, S 2p, and C 1s core level spectra as well as wide-scan survey data that was obtained using Al K a x-ray source with a Thermo Fisher Nexsa instrument.

25 ENERGY STORAGE↗

Continuous surface-to-distributed acoustic sensor snapshots explain reactivation of individual natural fractures during an unconventional reservoir stimulation

ABSTRACT Fiber-optic sensing technologies allow petroleum engineering teams to detect hydraulic fracture interaction with boreholes during unconventional reservoir stimulation. In combination with high-repeatability seismic sources, the same distributed acoustic sensors (DASs) enable vertical seismic profiling (VSP) of the fracture evolution away from the boreholes. We discovered clear signatures of seismic scattering on activated fractures during nine days of continuous seismic monitoring of the fracturing stages at the Austin Chalk/Eagle Ford Field Laboratory. The present study applies a novel approach for quantitative analysis of the scattering events in terms of the evolution of the geometry and elastic stiffness of individual fractures. Our characterization strategy sequentially refines the fracture models: from a stack of 1D soft layers to 3D rectangular inclusions. First, we estimate the number of fracture locations and reflectivity using a modified sparse-spike deconvolution of the stacked VSP traces. The fracture set consists of five fractures spaced by 15–30 m with a reflectivity of approximately 1%. Then, we develop a scattering integral method to refine these estimates along with an inversion of the fracture top and bottom for each monitoring vintage. We find that, initially, some of the fractures are located above the monitoring fiber with the height of approximately 100 m. Then we integrate the seismic interpretation with the low-frequency DAS and pressure and microseismic monitoring to reconstruct the activation process of the fractures. Most likely, some of the natural fractures slowly grew downward to the monitoring fiber as a result of fluid injections in the stimulated well. This led to bright strain anomalies but did not trigger seismicity. The top of the fractures remained almost constant and were limited by a lithologic boundary/stress barrier. To our knowledge, this is the first time VSP data enabled tracking of the fracture evolution with such high spatial and temporal resolution, which was previously only available for crosswell surveys and at a much smaller scale.

Glubokovskikh, Stanislav↗

Keyhole-mode Microscopy Dataset for Laser Powder-bed Fusion Modeling

Laser powder-bed fusion (LPBF) is an additive manufacturing (AM) technology that uses high-power sintering lasers to precisely construct metal designs. Material is accumulated by selectively sintering regions of a metal powder layer to a growing structure underneath forming a 3D geometry. Certain conditions make fusion in this process to operate in "keyhole-mode," characterized by targeted materials evaporating as plasma. While keyhole-mode operations can produce deeper molten pools than that observed in "conduction-mode", this mode of operation is often undesirable, as its molten regions can collapse on themselves, encapsulating metal vapors and forming cavities. The formation of such cavities negatively affects strength and consistency of the fused materials. To identify and avoid these detrimental effects of keyhole-mode operation, considerable data collection and analysis regarding this mode of operation is needed. Therefore, under the support of the "Open Data Initiative," Lawrence Livermore National Lab is releasing a dataset for analysis of this keyhole effect, and the conditions which transition operation from conduction-mode to keyhole-mode melting. This dataset consists of 600+ micrographs from laser powder-bed single track runs, with differing cross-section angles and input parameters, operating under both normal and keyhole mode operations. This journal documents the collection, organization, and usage of this dataset.

36 MATERIALS SCIENCE↗