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DOE OSTI2020

TDP-43 α-helical structure tunes liquid–liquid phase separation and function

Liquid–liquid phase separation (LLPS) is involved in the formation of membraneless organelles (MLOs) associated with RNA processing. The RNA-binding protein TDP-43 is present in several MLOs, undergoes LLPS, and has been linked to the pathogenesis of amyotrophic lateral sclerosis (ALS). While some ALS-associated mutations in TDP-43 disrupt self-interaction and function, here we show that designed single mutations can enhance TDP-43 assembly and function via modulating helical structure. Using molecular simulation and NMR spectroscopy, we observe large structural changes upon dimerization of TDP-43. Two conserved glycine residues (G335 and G338) are potent inhibitors of helical extension and helix–helix interaction, which are removed in part by variants at these positions, including the ALS-associated G335D. Substitution to helix-enhancing alanine at either of these positions dramatically enhances phase separation in vitro and decreases fluidity of phase-separated TDP-43 reporter compartments in cells. Furthermore, G335A increases TDP-43 splicing function in a minigene assay. Therefore, the TDP-43 helical region serves as a short but uniquely tunable module where application of biophysical principles can precisely control assembly and function in cellular and synthetic biology applications of LLPS.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Effects of baryonic feedback on the cosmic web

Here, we study the effect of baryons on the cosmic web—halos, filaments, walls, and voids. To do so, we apply a modified version of NEXUS, a cosmic web morphological analysis algorithm, to the IllustrisTNG simulations. We find that halos lose more than 10% of their mass due to baryons, mostly to filaments and a small portion to walls and voids. However, the mass transfer does not significantly shift the boundaries of structures, leaving the volume fractions of the cosmic structures largely unaffected. We quantify the effects of baryonic feedback on the power spectrum and the probability density function of the density field for individual cosmic structures. For the power spectrum, most suppression due to feedback can be accounted for by including M ≥ 10 12 M ⊙ /h halos, without considering other cosmic structures. However, when examining the probability density function of the density field, we find nearly 100% suppression of the emptiest regions and 10%-level effects (boost or suppression) in the remaining regions of filaments, walls, and voids. Our results indicate the importance of modeling the effects of baryons in the whole cosmic web, not just halos, for cosmological analysis beyond two-point statistics or field-based inferences.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Evaluation of the Function of the ASFV KP177R Gene, Encoding for Structural Protein p22, in the Process of Virus Replication and in Swine Virulence

African swine fever virus (ASFV) causes a devastating disease of swine that has caused outbreaks in Central Europe since 2007, spreading into Asia in 2018. ASFV is a large, structurally complex virus with a large dsDNA genome encoding for more than 160 genes, most of them still uncharacterized. p22, encoded by the ASFV gene KP177R, is an early transcribed, structural virus protein located in the ASFV particle. Although its exact function is unknown, p22 has recently been identified as an interacting partner of several host proteins. Here, we describe the development of a recombinant ASFV (ASFV-G-ΔKP177R) lacking the KP177R gene as a tool to evaluate the role of p22 in virus replication and virulence in swine. The recombinant ASFV-G-ΔKP177R demonstrated that the KP177R gene is non-essential for ASFV replication in primary swine macrophages, with virus yields similar to those of the parental, highly virulent field isolate Georgia2010 (ASFV-G). In addition, experimental infection of domestic pigs with ASFV-G-ΔKP177R produced a clinical disease similar to that caused by the parental ASFV-G. Therefore, and surprisingly, p22 does not seem to be involved in virus replication or virulence in swine.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

There’s plenty of room at the top

Richard Feynman’s famous words, “there’s plenty of room at the bottom,” referred to the opportunities for revolutionizing the electronics industry by developing the science and technology of how to manufacture very small components (sub-micron to nanometer sized features). In additive manufacturing (AM), the opposite may be true: There’s plenty of room at the top. AM’s strength is in the low volume production of complex components, which is demanded in big industries such as oil and gas, construction, tooling, wind and water turbines, and infrastructure. Is AM’s ‘big’ future in the manufacture of large structures? Here, this special issue surveys the technical challenges and enormous opportunities associated with large scale additive manufacturing while discussing the materials, processes and applications that are enabled by scaling to much larger structures, much faster speeds and lower manufacturing costs. The authors believe that, if Professor Feynman was alive, he’d say “There’s plenty of room at the top.”

36 MATERIALS SCIENCE↗

DOE OSTI2024

Control over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning

The ability to program chain conformation and structure through control over the monomer sequence of synthetic polymers has broad implications for next-generation material design. While related problems of protein-folding and de novo design have generated accurate predictions of 3D folded chain structures, generalization to synthetic polymers remains intractable due to the requirement of large structural databases and the intrinsically disordered nature of polymer building blocks. In this work, polypeptoids, a class of peptidomimetic synthetic polymers, are utilized to build a general workflow for the study of relationships between monomer sequence and dynamic 3D chain structure in solution. Furthermore, this work demonstrates how control over the monomer sequence can alter the conformational landscape of synthetic polymers to deviate dramatically from classical chain statistics. Specifically, the distribution of end-to-end distances, as measured by double electron-electron resonance spectroscopy in dilute solvent, is systematically skewed towards shorter distances with an increasing number of hydrophobes and further refined by hydrophobe arrangement in amphiphilic polypeptoid chains.

36 MATERIALS SCIENCE↗

DOE OSTI2020

EPRI Demonstration of an Autonomous Site Characterization Vehicle - 20523

A substantial effort is applied in performing radiological characterization of structures and land areas during decommissioning of a nuclear facility. This includes multiple surveys of land areas and large structures to support eventual site release under the Multi Agency Survey and Site Investigation Manual (MARSSIM, Reference 1). These surveys are typically performed using manually delivered systems, which is time consuming and labor intensive. Radiological surveys intentionally follow a prescribed protocol with respect to areas covered, scan speeds, responses to elevated readings, required detector offsets, the need for repeat measurements, etc. Based on these attributes, combined with the repetitive effort of performing surveys over large areas, automation of radiological characterization techniques has a high potential to be successful and promises substantial benefit. EPRI has performed a project that resulted in the development and demonstration of an autonomous site characterization system. This EPRI project focused on building surfaces and the surfaces of large land areas as these configurations lend themselves more readily to automated survey. The project included: - Identification of the requirements for an autonomous site characterization system; - A survey of existing control systems that use automation to conduct characterization of structures and land areas. - As no fully adequate systems were identified, a complete system was developed that utilized commercially available detection and analysis systems and a self driving vehicle owned by EPRI. The system was demonstrated at the Kewaunee nuclear power plant site in the fall of 2019. The demonstration included: - Autonomous surveys of floor areas inside the Auxiliary Building at Kewaunee after manually controlled mapping of the survey areas. - For land areas, the vehicle autonomously surveyed areas using travel paths had been preprogrammed onto an internet available map of area. In this case, GPS coordinates from the preprogramming were used for navigation by the vehicles guidance system. This paper summarizes the characterization system development and system demonstration which will also be published in an EPRI report in the first half of 2020. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

Process-structure-property considerations for wire-based directed energy deposition of Ti-6Al-4V

Directed energy deposition (DED) is an attractive additive manufacturing (AM) process for large structural components. The rapid solidification and layer-by-layer process associated with DED results in non-ideal microstructures, such as large grains with strong crystallographic textures. These non-ideal microstructures can lead to severe anisotropy in the mechanical properties. Despite these challenges, DED has been identified as a potential solution for the manufacturing of near net shape Ti-6Al-4V preforms, replacing lost casting and forging capabilities. Two popular wire-based directed energy deposition (W-DED) processes were considered for the manufacturing of Ti-6Al-4V with assessments on their respective metallurgical and mechanical properties, as compared to a conventionally processed material. The two W-DED processes explored were wire arc additive manufacturing (WAAM) and electron beam additive manufacturing (EBAM). High throughput inspection and tensile testing procedures were utilized to generate statistically relevant data sets related to each process and sample orientation. The 2 AM technologies produced material with remarkably different microstructures and mechanical properties. Importantly, results revealed key differences in strength and ductility for the two disparate processes which were found to be related to differences in the metallurgical properties.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Density Functional Tight-Binding Models for Band Structures of Transition-Metal Alloys and Surfaces across the d -Block

First-principles electronic structure simulations are an invaluable tool for understanding chemical bonding and reactions. While machine-learning models such as interatomic potentials significantly accelerate the exploration of potential energy surfaces, electronic structure information is generally lost. Particularly in the field of heterogeneous catalysis, simulated electron band structures provide fundamental insights into catalytic reactivity. This ab initio knowledge is preserved in semiempirical methods such as density functional tight binding (DFTB), which extend the accessible computational length and time scales beyond first-principles approaches. In this paper here we present Shell-Optimized Atomic Confinement (SOAC) DFTB electronic-part-only parametrizations for bulk and surface band structures of all d-block transition metals that enable efficient predictions of electronic descriptors for large structures or high-throughput studies on complex systems outside the computational reach of density functional theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

On the Mechanical Behavior of LP-DED C103 Thin-Wall Structures

Laser Powder Directed Energy Deposition (LP-DED) can produce thin-wall features on the order of 1 mm. These features are essential for large structures operating in extreme environments such as regeneratively cooled nozzles and heat exchangers, which often make use of refractory metals. In this work, the mechanical behavior of LP-DED C103 was investigated via quasi-static tensile testing and low cycle fatigue (LCF) testing. The effects of vacuum stress relief (SR) and hot isostatic pressing (HIP) heat treatments were investigated for specimens in the vertical and horizontal build orientations during tensile testing. The AB and SR properties were lower than literature values for wrought and laser powder bed fusion (L-PBF) bulk components but higher than electron beam powder bed fusion (EB-PBF). The application of a HIP cycle improved strength by 7% and ductility by 27% past the initial as-built condition. Fracture images reveal that interlayer stress concentration sites are responsible for fracture in specimens in the vertical orientation. Meanwhile, fracture in the horizontal specimens mainly propagates at a slanted angle typical of plane stress conditions. The LCF results show cycles to failure ranging from 100 cycles to 8000 cycles for max strain levels of 2% and 0.5%, respectively. Fractography on the fatigue specimens reveals an increasing propagation zone as max strain levels are increased. The impact of these findings and future work are discussed in detail.

36 MATERIALS SCIENCE↗

DOE OSTI2020

DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

DNA methylation maintenance by DNMT1 is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive. Here, we systematically analyzed the specificity of DNMT1, revealing a pronounced influence of the DNA sequences flanking the target CpG site on DNMT1 activity. We determined DNMT1 structures in complex with preferred DNA substrates revealing that DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrangements of the DNA correlating with low catalytic activity. Moreover, flanking sequences influence the conformational dynamics of the active site and cofactor binding pocket. Importantly, we show that the flanking sequence preferences of DNMT1 highly correlate with genomic methylation in human and mouse cells, and 5-azacytidine triggered DNA demethylation is more pronounced at CpG sites with flanks disfavored by DNMT1. Overall, our findings uncover the intricate interplay between CpG-flanking sequence, DNMT1-mediated base flipping and the dynamic landscape of DNA methylation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Folded network and structural transition in molten tin

The fundamental relationships between the structure and properties of liquids are far from being well understood. For instance, the structural origins of many liquid anomalies still remain unclear, but liquid-liquid transitions (LLT) are believed to hold a key. However, experimental demonstrations of LLTs have been rather challenging. Here, we report experimental and theoretical evidence of a second-order-like LLT in molten tin, one which favors a percolating covalent bond network at high temperatures. The observed structural transition originates from the fluctuating metallic/covalent behavior of atomic bonding, and consequently a new paradigm of liquid structure emerges. The liquid structure, described in the form of a folded network, bridges two well-established structural models for disordered systems, i.e., the random packing of hard-spheres and a continuous random network, offering a large structural midground for liquids and glasses. Our findings provide an unparalleled physical picture of the atomic arrangement for a plethora of liquids, shedding light on the thermodynamic and dynamic anomalies of liquids but also entailing far-reaching implications for studying liquid polyamorphism and dynamical transitions in liquids.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Recent Hydrodynamic Modeling Enhancements in OpenFAST

To improve the hydrodynamic modeling capabilities of the offshore wind design and modeling tool OpenFAST, a restructuring of the HydroDyn hydrodynamics module was undertaken with several new features implemented. The generation of the wave field is now separated from HydroDyn into a new module called SeaState. Unlike previous versions of HydroDyn, which precomputed the wave kinematics at the undisplaced positions of the hydrodynamic nodes, the new SeaState module computes the complete time history of the wave field at the vertices of a user-defined wave grid. During the simulation, the wave kinematics at any point within the grid can be efficiently interpolated, allowing the strip-theory wave loads to be evaluated based on the wave kinematics at the displaced structure position. A phase correction was also implemented for the potential-flow wave-exciting loads to account for large structure displacements. Several wave-stretching methods were implemented for the strip-theory solution along with a wave-load redistribution method that ensures smooth variation of the nodal loads as the nodes of a discrete hydrodynamic mesh enter and exit the water. The load smoothing is included to avoid the excitation of unphysical high-frequency structural vibration during hydroelastic simulations. The MacCamy-Fuchs diffraction correction for the strip-theory solution and the capability to insert a constrained NewWave into extreme stochastic sea states with directional spreading were also added. The present article documents the formulations of the new improvements to HydroDyn with example applications and numerical results.

constrained wave↗

DOE OSTI2022

Recent Hydrodynamic Modeling Enhancements in OpenFAST: Preprint

constrained wave↗

DOE OSTI2026

Additive Manufacturing of Cryogenic Austenitic Steel JK2LB via Wire-Fed Directed Energy Deposition (DED) for Fusion Energy Applications

This study explores the feasibility of fabricating cryogenic austenitic steel JK2LB via both laser-based directed energy deposition (laser-DED) and arc-based directed energy deposition (arc-DED) additive manufacturing processes for potential application in fusion reactors. JK2LB, a low-nickel, high-manganese stainless steel developed for ITER, offers excellent cryogenic toughness, radiation resistance, and decay-to-clearance characteristics. Although JK2LB was originally designed to endure cyclic stresses at cryogenic temperatures in tokamaks, its low-temperature mechanical integrity and radiation tolerance also make it a promising candidate for structural components, such as the coil case/support structure in nonplanar high-temperature superconducting magnet assemblies in stellarators. Directed energy deposition (DED) additive manufacturing was selected for this study due to its capability to fabricate large structures with complex geometries. Here, to address the long lead time and high cost associated with acquiring conventional JK2LB solid wire, JK2LB powder-cored wire was developed as the feedstock material. Testing blocks were then fabricated using both wire-fed laser-DED and arc-DED processes. Microstructural and compositional analyses revealed that both DED approaches yield fully austenitic phase and columnar grain structures. Mechanical testing at room temperature revealed that both DED routes achieved yield strength and elongation comparable to those of conventionally processed JK2LB via vacuum melting, electroslag remelting, extrusion, and drawing, though ultimate tensile strength was reduced due to Mn loss and large columnar grains. As a study mainly focusing on the additive manufacturing process, this work demonstrates the potential of additive manufacturing for fusion energy applications and provides a basis for optimization and future cryogenic mechanical evaluation.

Cryogenic steel↗

DOE OSTI2025

Orientation-Driven Chirality Funnels in Chiral Low-Dimensional Lead-Halide Perovskite Heterostructures

Chiral hybrid metal-halide perovskites show low-symmetry crystal structures, large Rashba splitting, spin-filtering, and strong chiroptical activity. Circular dichroism and circularly polarized photoluminescence have been investigated in chiral perovskites with increasingly distorted chiral structures. Here, we report the fabrication of chiral (R/S)-EBAPbI3 (EBA = α-ethylbenzylamine) single crystals, which possess highly distorted octahedral structures with a high angle variance value of ∼68 degree2. Using control in the fabrication conditions, we transfer chiral single crystals to thin films and achieve different crystal orientation preferences that induce tunable chiroptical properties to their heterostructures with PbI2 nanodomains, which we characterize with in situ X-ray diffraction and grazing-incidence wide-angle X-ray scattering measurements. Using transient chiroptical spectroscopies, we resolve photoexcited charge carrier dynamics and chirality transfer processes in such heterostructures down to cryogenic temperatures. We observe rapid carrier transfer along the in-plane (002) facets in chiral perovskite phases to PbI2 nanostructures within the initial few picoseconds, while carrier transfer along the out-of-plane (002) facets occurs at a slower rate. This fast transfer process leads to high photoluminescence intensities and large degrees of circular polarization in the emission from PbI2 nanodomains at cryogenic temperatures. Our findings report a multidimensional chiral-achiral heterostructure which takes advantage of controllable chirality transfer and offers new routes for future spintronic and chiroptical applications.

Liu, Shangpu↗

DOE OSTI2025

Modeling the effects of active wake mixing on wake behavior through large-scale coherent structures

The use of active wake mixing (AWM) to mitigate downstream turbine wakes has created new opportunities for reducing power losses in wind farms. However, many current analytical or semi-empirical wake models do not capture the flow instabilities that are excited through the blade pitch actuation. In this work, we develop a framework, which accounts for the impacts of the large-scale coherent structures and turbulence on the mean flow, for modeling AWM. The framework uses a triple-decomposition approach for the unsteady flow field and models the mean flow and fine-scale turbulence with a parabolized Reynolds-averaged Navier–Stokes (RANS) system. The wave components are modeled using a simplified spatial linear stability formulation that captures the growth and evolution of the coherent structures. Comparisons with high-fidelity large eddy simulations (LESs) of the turbine wakes showed that this framework was able to capture the additional wake mixing and faster wake recovery in the far-wake regions for both the pulse and helix AWM strategies with minimal computational expense. In the near-wake region, some differences are observed in both the RANS velocity profiles and initial growth of the large-scale structures, which may be due to some simplifying assumptions used in the model.

17 WIND ENERGY↗

DOE OSTI2020

Predicting Volume of Distribution in Humans: Performance of In Silico Methods for a Large Set of Structurally Diverse Clinical Compounds

Volume of distribution at steady state (V D,ss ) is one of the key pharmacokinetic parameters estimated during the drug discovery process. Despite considerable efforts to predict V D,ss , accuracy and choice of prediction methods remain a challenge, with evaluations constrained to a small set (<150) of compounds. To address these issues, a series of in silico methods for predicting human V D,ss directly from structure were evaluated using a large set of clinical compounds. Machine learning (ML) models were built to predict V D,ss directly and to predict input parameters required for mechanistic and empirical V D,ss predictions. In addition, log D, fraction unbound in plasma (fup), and blood-to-plasma partition ratio (BPR) were measured on 254 compounds to estimate the impact of measured data on predictive performance of mechanistic models. Furthermore, the impact of novel methodologies such as measuring partition (Kp) in adipocytes and myocytes (n = 189) on V D,ss predictions was also investigated. In predicting V D,ss directly from chemical structures, both mechanistic and empirical scaling using a combination of predicted rat and dog V D,ss demonstrated comparable performance (62%–71% within 3-fold). The direct ML model outperformed other in silico methods (75% within 3-fold, r 2 = 0.5, AAFE = 2.2) when built from a larger data set. Scaling to human from predicted V D,ss of either rat or dog yielded poor results (<47% within 3-fold). Measured fup and BPR improved performance of mechanistic V D,ss predictions significantly (81% within 3-fold, r 2 = 0.6, AAFE = 2.0). Adipocyte intracellular Kp showed good correlation to the V D,ss but was limited in estimating the compounds with low V D,ss .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

In-Process Monitoring and Structural Health Monitoring of Large-Scale Additive Manufacturing Using Acoustic Emission Technique

ORNL collaborated with MISTRAS Group, Inc. to investigate acoustic emission (AE) as a structural health monitoring (SHM) method for large-scale additive manufacturing (AM). Large-scale AM is being adapted as method of producing large structures in a short lead time and cost-effective way. With the growing advancement in AM techniques and application, machine monitoring and part qualification is highly needed. There has been leading research focused on the manufacturing, feedstock material but minimum research on the SHM, defect detection, and nondestructive evaluation (NDE) for AM. Scanning large structure using conventional nondestructive testing (NDT) techniques, such as ultrasound or X-ray, and searching for potential defects can be very time consuming, challenging and cost prohibitive. AE is a passive technique that can be used to monitor and locate defect progression in large structure by distributing group of sensors around the part. This project utilized AE technique and system manufactured/designed by MISTRAS Group to monitor large-scale AM equipment (i.e. Big Area Additive Manufacturing (BAAM) system located at the Oak Ridge National Laboratory – Manufacturing Demonstration Facility (ORNL-MDF) and the printed parts it produces. The AE system provided valuable insight on defect development/progression during and post-printing process.

36 MATERIALS SCIENCE↗