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At least 757 records · Page 42

Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes

Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor’s chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.

59 BASIC BIOLOGICAL SCIENCES↗

The circular bioeconomy: a driver for system integration

Background: Human and earth system modeling, traditionally centered on the interplay between the energy system and the atmosphere, are facing a paradigm shift. The Intergovernmental Panel on Climate Change’s mandate for comprehensive, cross-sectoral climate action emphasizes avoiding the vulnerabilities of narrow sectoral approaches. Our study explores the circular bioeconomy, highlighting the intricate interconnections among agriculture, forestry, aquaculture, technological advancements, and ecological recycling. Collectively, these sectors play a pivotal role in supplying essential resources to meet the food, material, and energy needs of a growing global population. We pose the pertinent question of what it takes to integrate these multifaceted sectors into a new era of holistic systems thinking and planning. Results: The foundation for discussion is provided by a novel graphical representation encompassing statistical data on food, materials, energy flows, and circularity. This representation aids in constructing an inventory of technological advancements and climate actions that have the potential to significantly reshape the structure and scale of the economic metabolism in the coming decades. In this context, the three dominant mega-trends—population dynamics, economic developments, and the climate crisis—compel us to address the potential consequences of the identified actions, all of which fall under the four categories of substitution, efficiency, sufficiency, and reliability measures. Substitution and efficiency measures currently dominate systems modeling. Including novel bio-based processes and circularity aspects might require only expanded system boundaries. Conversely, paradigm shifts in systems engineering are expected to center on sufficiency and reliability actions. Effectively assessing the impact of sufficiency measures will necessitate substantial progress in inter- and transdisciplinary collaboration, primarily due to their non-technological nature. In addition, placing emphasis on modeling the reliability and resilience of transformation pathways represents a distinct and emerging frontier that highlights the significance of an integrated network of networks. Conclusions: Existing and emerging circular bioeconomy practices can serve as prime examples of system integration. These practices facilitate the interconnection of complex biomass supply chain networks with other networks encompassing feedstock-independent renewable power, hydrogen, CO 2 , water, and other biotic, abiotic, and intangible resources. Elevating the prominence of these connectors will empower policymakers to steer the amplification of synergies and mitigation of tradeoffs among systems, sectors, and goals.

09 BIOMASS FUELS↗

Pseudo-gray-scale halftone gratings for shearing and Hartmann wavefront sensors

Now in use on x-ray beamlines worldwide, shearing interferometry and Hartmann wavefront sensing provide effective feedback for measuring and optimizing high-quality beams. Conventionally, both approaches spatially modulate the beam properties (amplitude or phase) using two-tone, binary patterns, leading to deleterious diffraction effects that must be mitigated. In shearing, the presence of multiple diffraction orders affects measurement near boundaries. In Hartmann, diffraction limits the measurement point density. We demonstrate that the use of pseudo-gray-scale halftone patterns in the diffracting elements can improve the performance of both techniques.

47 OTHER INSTRUMENTATION↗

A computational study of turbulent separated flow over a wall-mounted cube at two different Reynolds numbers and incoming velocity profiles

Simulations of the canonical wall-mounted unit cube subjected to two distinct incident velocity profiles is performed at Reynolds numbers (Re) where the bulk flow characteristics are known to become relatively Re-insensitive using both direct numerical simulation (DNS) and wall-resolved large eddy simulation (WRLES). The aim of this work is to highlight the sensitivity of such bluff-body flows to mean shear and to provide a representative set of data for such flow scenarios where common turbulence modeling techniques often fail. Simple boundary conditions are selected to allow for easy comparisons for model development purposes and avoid confounding effects from freestream turbulence. In addition to mean velocity profiles, select turbulence statistics are presented in detail. We find that both mean velocity profiles and mean wake turbulence are Re-insensitive over the range examined here.

42 ENGINEERING↗

Microstructural Simulation of Ion-Irradiated Natural Rocks and Minerals

This report details the contribution of Oak Ridge National Laboratory to the Nuclear Energy University Program (NEUP) project, "Rapid Characterization of Concrete Mineralogy using Multi-Scale Tools" led by the University of Illinois at Urbana-Champaign. To support the subsequent license renewal (SLR) of the US nuclear power plants (NPPs) fleet, the performance of concrete-forming aggregates against neutron irradiation needs to be assessed. Ion irradiation is proposed as a rapid, cost-effective surrogate method to full neutron irradiation testing. To complement the characterization of ion-irradiated rock specimens, ORNL has run finite-elements and fast-Fourier transform (FFT-based) simulations using the codes MARS and Microstructure-Oriented Scientific Analysis of Irradiated Concrete (MOSAIC). The main conclusion of this analysis is that the apparent post–ion-irradiation step-height underestimates the accumulated free radiation-induced volumetric expansion (RIVE) in the ion-implanted depth by about 15% at full amorphization and about 25% toward the beginning of the ion irradiation experiment. The discrepancy is explained by the fact that the step height is proportional to the sum of the RIVE (i.e., one third of the RIVE) and the irradiation-assisted plastic strains in the vertical direction (lower than two thirds of the RIVE). Because of the large lateral compressive stresses caused by the restraining effect of the unirradiated substrate, the stress field in the mineral grains and at the grain boundary (GB) in the ion-implanted layer is much different than the comparable stress field occurring during neutron irradiation. Hence, the mismatch RIVE causing cracks in the rock-forming minerals leads to different cracking patterns. Ion irradiation continues to be used as a rapid technique to assess the RIVE potential of rocks.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Enhancing the Performance of Plasma-facing Materials Through Solute-stabilized Nanostructured Tungsten Alloys

This report is a summary of the work completed under the auspices of the Department of Energy Early Career Award DE-SC0017899 entitled “Enhancing the Performance of Plasma-facing Materials Through Solute-stabilized Nanostructured Tungsten Alloys”. Summaries of initiatives on computational thermodynamics modeling, experimental alloy synthesis including traditional and additive manufacturing routes, several ion irradiation studies, and plasma exposures are reported.

36 MATERIALS SCIENCE↗

A combined kinetic Monte Carlo and phase field approach to model thermally activated dislocation motion

In this work, a kinetic Monte Carlo (KMC) scheme is integrated into a phase field dislocation dynamics (PFDD) model to account for thermal activation. While the implementation is general and could be applied to many different thermally activated processes, we apply the model to simulate a dislocation transmitting through an interface. Two cases are analyzed: a dislocation transmitting through a strong interface, and a dislocation transmitting through a more realistic grain boundary in tungsten. In conclusion, results and trends for both cases are discussed in detail, and ultimately show that the combined KMC-PFDD algorithm is effective in capturing thermally activated dislocation processes.

36 MATERIALS SCIENCE↗

Turbulent kinetic energy over large offshore wind farms observed and simulated by the mesoscale model WRF (3.8.1)

Abstract. Wind farms affect local weather and microclimates;hence, parameterizations of their effects have been developed for numerical weather prediction models.While most wind farm parameterizations (WFPs) include drag effects of wind farms, models differ on whether or not an additionalturbulent kinetic energy (TKE) source should be included in theseparameterizations to simulate the impact of wind farms on the boundary layer.Therefore, we use aircraft measurements above large offshore wind farms in stable conditions to evaluateWFP choices. Of the three case studies we examine, we find the simulated ambient backgroundflow to agree with observations of temperature stratification and winds. This agreement allows us toexplore the sensitivity of simulated wind farm effects with respect to modeling choicessuch as whether or not to include a TKE source, horizontal resolution, vertical resolutionand advection of TKE. For a stably stratified marine atmospheric boundary layer (MABL), a TKE source and a horizontal resolutionon the order of 5 km or finer are necessary to represent the impact of offshore wind farms on the MABL.Additionally, TKE advection results in excessively reduced TKE over the wind farms, which in turn causesan underestimation of the wind speed deficit above the wind farm. Furthermore, using fine verticalresolution increases the agreement of the simulated wind speed with satellite observations of surface wind speed.

17 WIND ENERGY↗

Validation of Actuator Line and Actuator Disk Models with Filtered Lifting Line Corrections Implemented in Nalu-Wind Large Eddy Simulations of the Atmospheric Boundary Layer

Turbine generator power from simulations using Actuator Line Models and Actuator Disk Models with a Filtered Lifting Line Correction are compared to field data of a V27 turbine. Preliminary results of the wake characteristics are also presented. Turbine quantities of interest from traditional ALM and ADM with the Gaussian kernel (..epsilon..) set at the optimum value for matching power production and that resolve the kernel at all mesh sizes are also presented. The atmospheric boundary layer is simulated using Nalu-Wind, a Large Eddy Simulation code which is part of the ExaWind code suite. The effect of mesh resolution on quantities of interest is also examined.

Actuator Disk Models↗

Surfactants are Ineffective for Reducing Imbibition of Water-Based Fracturing Fluids in Deep Gas Reservoirs

Minimizing loss of injected hydraulic fracturing fluids into shale along fracture-matrix boundaries is desired because imbibed water restricts gas production and wastes valuable water resources. This problem has motivated the addition of surfactants into water-based hydraulic fracturing fluids in order to reduce the capillary driving force for imbibition. Here, we show that reduction in interfacial tension and wettability alteration has negligible ability to reduce imbibition in deep gas reservoirs. The effectiveness of altering capillary forces acting at the wetting front also depends on the injection pressure acting at the fracture-matrix boundary. The pressure at the interface between the fracture and the shale matrix is constrained between the reservoir pore pressure and formation pressure (rock fracture pressure, also known as breakdown pressure of the rock) and increases with depth to magnitudes that greatly exceed that of capillary pressures. Furthermore, the analyses presented here show that even maximum alteration of interfacial properties that result in strongly hydrophobic interactions between the fracturing fluid and reservoir rock is incapable of significantly reducing imbibition in deep reservoirs. Instead of using surfactants, this analysis points to decreases in wellbore shut-in pressures and shut-in times as practical options for reducing imbibition losses of water-based fluids.

03 NATURAL GAS↗

Holographic measurement and bulk teleportation

Holography has taught us that spacetime is emergent and its properties depend on the entanglement structure of the dual theory. In this paper, we describe how changes in the entanglement due to a local projective measurement (LPM) on a subregion A of the boundary theory modify the bulk dual spacetime. We find that LPMs destroy portions of the bulk geometry, yielding post-measurement bulk spacetimes dual to the complementary unmeasured region A c that are cut off by end-of-the-world branes. Using a bulk calculation in AdS 3 and tensor network models of holography (in particular, the HaPPY code and random tensor networks), we show that the portions of the bulk geometry that are preserved after the measurement depend on the size of A and the state we project onto. The post-measurement bulk dual to A c includes regions that were originally part of the entanglement wedge of A prior to measurement. This suggests that LPMs performed on a boundary subregion A teleport part of the bulk information originally encoded in A into the complementary region A c . In semiclassical holography an arbitrary amount of bulk information can be teleported in this way, while in tensor network models the teleported information is upper-bounded by the amount of entanglement shared between A and A c due to finite-N effects. When A is the union of two disjoint subregions, the measurement triggers an entangled/disentangled phase transition between the remaining two unmeasured subregions, corresponding to a connected/disconnected phase transition in the bulk description. Our results shed new light on the effects of measurement on the entanglement structure of holographic theories and give insight on how bulk information can be manipulated from the boundary theory. They could also represent a first step towards a holographic description of measurement-induced phase transitions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Section 110 Documentation of a Douglas AD-2 Skyraider Crash Site, Area 1, Nevada National Security Site, Nye County, Nevada

The National Nuclear Security Administration, Nevada Field Office has undertaken a Section 110 current condition assessment of the unanticipated discovery of an aviation crash site in Nye County, Nevada. Because no undertaking is planned, an area of potential effect (APE) was not defined. A study area of 0.55 acres was established to delineate the general extent of the debris scatter and establish a boundary for the cultural resource documentation of the site by Desert Research Institute (DRI). The Douglas AD-2 Skyraider drone crash site (26NY17011) is recommended eligible for the National Register of Historic Places (NRHP) under Significance Criterion A, as a physical remnant of Project 5.1 “Atomic Weapons Effects on AD Type Aircraft in Flight,” one of the series of military effects studies conducted as part of Shot Simon during Operation Upshot-Knothole in 1953. Furthermore, the site is eligible under Criterion D because closer examination of the debris could address research questions concerning the Type 1 Remote Control Equipment developed by the Naval Air Experimental Station that was onboard to remotely pilot the aircraft.

54 ENVIRONMENTAL SCIENCES↗

The role of UC inclusions in the development of fission gas bubble superlattice neutron-irradiated monolithic U-10Mo fuels

Uranium Carbide (UC) inclusions are the most prevalent impurities in Uranium-Molybdenum (U-Mo) fuel and are considered undesirable because they could potentially affect fuel performance. This work revealed that, like grain boundaries (gBs), UC inclusions could help facilitate the formation of the fission gas bubble superlattice (GBS). The GBS is a highly organized complex defect structure that can effectively store fission gases, thereby inhibiting fuel swelling. Transmission electron microscopy (TEM) showed that GBS self-organization can initiate at the UC/U-Mo interfaces in U-10Mo fuel irradiated to low fission density. Furthermore, this study also revealed that the UC boundary in U-10Mo irradiated to low fission density is wavy and periodic in morphology and that GBS formation is semi-coherent with the UC boundary. Because the initiation of GBS occurs at gBs and UC/U-Mo interfaces, the fission gas inventory is always highest at those regions compared to the U-Mo grain interior. Consequently, at higher fission densities, it is likely that high burnup structure (HBS) development via grain refinement will begin at gBs and UC/U-Mo interfaces.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Effects of temperature and dose rate on ion-irradiated γ-LiAlO 2 pellets

Defect accumulation and microstructural evolution during ion irradiation at elevated temperatures are governed by competing processes of defect production, driven by the dose rate, and defect recovery, controlled by diffusion, interaction, and annihilation. Here, this study investigates the effects of irradiation temperature and the dose rate on microstructural evolution, deuterium retention, and lithium volatilization in γ-LiAlO 2 pellets subjected to sequential He + and D + ion irradiation. Experiments were performed to a total fluence of 3 × 10 17 (He + + D + )/cm 2 at 623, 673, 723, and 773 K with an average He + dose rate of 7.7 × 10 −4 dpa/s, and to 2 × 10 17 (He + + D + )/cm 2 at 773 K with dose rates of 6.8 × 10 −5 , 2.9 × 10 −4 , and 7.3 × 10 −4 dpa/s. At 623 K, the microstructure was dominated by cavities and fractures with no observable precipitate formation, while small precipitates emerged at 673 K. Increasing the irradiation temperature to 723–773 K promoted the formation of larger, faceted LiAl 5 O 8 precipitates, and surface amorphization, accompanied by pronounced lithium depletion and H–D isotopic exchange. At 773 K, medium and high dose rates produced an amorphized surface layer over a crystalline subsurface containing LiAl 5 O 8 precipitates and blisters at the crystalline–amorphous interface, whereas low-dose-rate irradiation preserved surface crystallinity with cavities distributed in the matrix, around precipitates, and along grain boundaries. Precipitate morphology was anisotropic with limited size dependence on the dose rate. These results elucidate the coupled effects of temperature and the dose rate and demonstrate that sequential He + and D 2 + irradiation at 773 K reproduces key microstructural features and H isotope behavior observed in neutron-irradiated γ-LiAlO 2 at 573 K.

dose rate effects↗

A predictive strain-gradient model with no undetermined constants or length scales

A general meso–scale (GM) crystal plasticity (CP) model was developed that accounts for lower-order (strain hardening) and higher-order (internal stress) effects of geometrically necessary dislocations (GNDs). It is predictive: no arbitrary parameters or length scales were invoked and no ad hoc numerical techniques were employed. It uses general stress field equations for GND content and a novel harmonization technique to enforce consistency of elastic long-range singular defect fields with applied elastic-plastic fields. The model facilitates implementation in commercial finite element programs without requiring special elements, special boundary conditions, or access to element shape functions. GM simulations confirmed, with improved accuracy, previously published predictions of the Hall-Petch effect, Bauschinger effect, and anelasticity. Previously unpredicted phenomena were also predicted: anelasticity and hysteresis for single Ta crystals and strain-hardening stagnation. The internal stresses (higher-order effect) dominate at large length scales, while at small length scales, the GND density hardening (lower-order effect) dominates. As a result, GM predicts that strain heterogeneity and consequent GND internal stresses are important factors in anelasticity.

36 MATERIALS SCIENCE↗

Stress-dominated growth of two-dimensional materials on nonplanar substrates

Curved features are ubiquitous on solid surfaces, but the effect of surface curvatures on growth of two-dimensional (2D) materials has not yet been established. Using a newly developed method based on the Metropolis algorithm and taking graphene as a prototype, we find that a curved feature on substrates can result in a variety of topological defects in 2D materials. As the feature's size increases by just nanometers, the defects can vary from adatoms, dislocation pairs, and grain boundary scars to long-range grain boundaries, in contrast to previously reported defect-free modes of rigid colloidal crystals growing on spheres. We identify an important role of curvature-induced lattice stress in lowering the growth rate over the curved features and driving a plastic instability in the materials. When the feature's size increases to several nanometers, the stress effect is compromised by an enhanced effect of geodesic curvature, yielding long-range grain boundaries as a result of increased local growth rate on the feature with respect to that on flat regions. Here we further provide a ‘phase diagram’ of defects that helps to guide a rational choice of geometrical parameters of features towards the growth of high-quality 2D materials as well as controllable creation of topological defects.

36 MATERIALS SCIENCE↗

Effect of grain size on iron-boride nanoglasses

Metallic nanoglasses are made of amorphous grains that are separated by lower-density amorphous boundaries, which have been proposed to enhance plasticity through the deflection of cracks and shear bands at interfaces. It has been difficult to experimentally control grain size and interfacial structure to understand their roles in plastic deformation. Here, we fabricate bulk nanoglasses via compaction and sintering of colloidally synthesized amorphous iron-boride nanoparticles. These nanoglasses have amorphous grains with diameters from 116nm to 576nm and were tested using nanoindentation and micropillar compressions. The nanoglass with a grain size of 576 nm shows the highest elastic modulus and hardness of 101 GPa and 7.4GPa, respectively. Transmission electron microscopy reveals that nanocrystals form within the nanoglasses during compaction. Higher nanocrystal density correlates with higher nanoparticle crystallization enthalpy, an increase in plasticity, and a decrease in yield strength. Plastic strain of 5.0%, yield strength of 3.8GPa, and ultimate compressive strength of 2.7–3.8GPa were achieved. Here we show that the compaction of colloidal metallic glass nanoparticles results in robust bulk samples, with mechanical properties similar to that of other iron-based bulk metallic glasses.

36 MATERIALS SCIENCE↗

Electronic coherence evolution at the nearly commensurate-incommensurate CDW boundary of 1⁢T−TaS 2

Transition-metal dichalcogenides host a variety of charge-density-wave phases that couple lattice, charge, and correlation effects. In 1⁢𝑇−TaS 2 , the commensurate and nearly commensurate states are well characterized, yet the transition near 350 K into the incommensurate phase has lacked direct momentum-resolved insight. In this work, we use temperature-dependent angle-resolved photoemission spectroscopy to track the electronic structure across this transition. We observe a suppression of quasiparticle spectral weight at the Brillouin-zone center, coincident with the transport anomaly, but without clear evidence of a full band-gap opening. The transition appears to involve momentum-dependent redistribution of spectral weight, consistent with a loss of coherence that reshapes the Fermi surface while leaving conduction dispersions largely intact. These results suggest that the nearly commensurate–incommensurate transition may not align with a conventional metal-insulator transition picture, but rather as an electronic reconstruction driven by loss of coherence. Our work provides new microscopic insight into the resistivity anomaly near room temperature and may guide design principles for collective electronic switching in transition-metal dichalcogenides.

36 MATERIALS SCIENCE↗