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DOE OSTI2020

Graph-Directed Approach for Downselecting Toxins for Experimental Structure Determination

Conotoxins are short, cysteine-rich peptides of great interest as novel therapeutic leads and of great concern as lethal biological agents due to their high affinity and specificity for various receptors involved in neuromuscular transmission. Currently, of the approximately 6000 known conotoxin sequences, only about 3% have associated structural characterization, which leads to a bottleneck in rapid high-throughput screening (HTS) for identification of potential leads or threats. In this work, we combine a graph-based approach with homology modeling to expand the library of conotoxin structures and to identify those conotoxin sequences that are of the greatest value for experimental structural characterization. The latter would allow for the rapid expansion of the known structural space for generating high quality template-based models. Our approach generalizes to other evolutionarily-related, short, cysteine-rich venoms of interest. Overall, we present and validate an approach for venom structure modeling and experimental guidance and employ it to produce a 290%-larger library of approximate conotoxin structures for HTS. We also provide a set of ranked conotoxin sequences for experimental structure determination to further expand this library.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Effect of Micro-Structural Dispersity of SiMo Ductile Iron on High Temperature Performance during Static Oxidation

High silicon and molybdenum (SiMo) ductile iron is commonly used for car exhaust systems, and its micro-structural dispersity depends on intrinsic parameters, which include alloy composition and inoculation efficiency, as well as extrinsic factors, such as casting wall thickness and molding material, which define cooling rate during solidification. Micro-structural dispersity is referred to as the degree of heterogeneity of sizes of structural constituencies within the microstructure. A variation in the micro-structural dispersity could impact the high temperature performance of SiMo ductile iron during static oxidation and transient thermo-mechanical loading conditions. In this study, static high temperature tests were performed on SiMo ductile iron solidified in a casting with varying wall thicknesses from 5 mm to 100 mm. The faster solidified specimens (taken from near chilled casting surfaces) had extremely high micro-structural dispersity as compared to the thicker section samples. After thermal exposure, each of the samples were characterized using 2D sections and 3D µCT images, and the results indicated an order of magnitude difference in graphite phase dispersity. The surface degradation was quantified after static oxidation experiments were implemented at temperature intervals between 650 °C and 800 °C. Non-destructive µCT 3D analysis and SEM/EDS were performed on cross sections and used to quantify the scale topology and structure. Carbon analysis was used to decouple the scale formation and decarburization phenomena that occurred within the samples. These methods enabled the quantification of the oxidation of the SiMo cast iron with different micro-structural dispersity levels after being exposed to high temperature static oxidation. Additionally, the complex material behavior during oxidation-assisted transient thermo-mechanical loading will be presented in a separate article.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Sparse and Random Sampling Techniques for High-Resolution, Full-Field, BSS-Based Structural Dynamics Identification from Video

Video-based techniques for identification of structural dynamics have the advantage that they are very inexpensive to deploy compared to conventional accelerometer or strain gauge techniques. When structural dynamics from video is accomplished using full-field, high-resolution analysis techniques utilizing algorithms on the pixel time series such as principal components analysis and solutions to blind source separation the added benefit of high-resolution, full-field modal identification is achieved. An important property of video of vibrating structures is that it is particularly sparse. Typically video of vibrating structures has a dimensionality consisting of many thousands or even millions of pixels and hundreds to thousands of frames. However the motion of the vibrating structure can be described using only a few mode shapes and their associated time series. As a result, emerging techniques for sparse and random sampling such as compressive sensing should be applicable to performing modal identification on video. This work presents how full-field, high-resolution, structural dynamics identification frameworks can be coupled with compressive sampling. The techniques described in this work are demonstrated to be able to recover mode shapes from experimental video of vibrating structures when 70% to 90% of the frames from a video captured in the conventional manner are removed.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Ab Initio Study of Atomic and Electronic Structure of Promising Ba4XMn3O12 (X = Nb, Ce, Pr) Oxides for Solar Thermochemical Hydrogen Production

The two-step metal oxide water-splitting cycle is one of the most viable approach for Solar Thermochemical Hydrogen (STCH) production. Challenges exist in finding suitable oxides that can satisfy thermodynamics of the STCH redox cycle under viable range of temperatures and partial pressures. Recently, BXM family members, i.e., Ba4NbMn3O12 (BNM), Ba4CeMn3O12 (BCM), Ba4PrMn3O12 (BPM) are discovered to exhibit promising STCH performance. However, the magnetic degrees of freedom of their experimental crystal structures is not characterized, and only hypothetical models exist for their electronic structure. We performed Monte-Carlo sampling for the magnetic spin arrangement of Mn atoms to provide explicit atomic structure models for their ground state 12R polytype and determined the most stable spin configuration for each member after structure relaxation using density functional theory (DFT) calculations. We also elucidate the most stable charge configuration (Mn3+/Mn4+ arrangement) for BNM among the existing hypothesis in literature. We investigate these strongly correlated oxides using different levels of theory (DFT+U, Hybrid-DFT) to develop better understanding of their electronic structure. These calculations allowed us to develop a model based on molecular orbital interactions that help explain the observed changes in their experimental x-ray spectroscopy measurements. Thereby, help link differences in electronic structure of BXM family members to their varying water-splitting behavior. These structure models will further facilitate future in-depth defect studies to model STCH redox cycle of these oxides.

atomic and magnetic structure↗

DOE OSTI2022

Subcomponent Validation of Composite Joints for Marine Energy Structures

The Marine Energy Advanced Materials project addresses the barriers and uncertainties facing marine renewable energy developers in using composite materials for load-bearing structures. Sponsored by the U.S. Department of Energy's Water Power Technologies Office, the multiyear project comprises of collaborators from the National Renewable Energy Laboratory (NREL), Sandia National Laboratories, Pacific Northwest National Laboratory (PNNL), Montana State University (MSU), Florida Atlantic University (FAU), and industry stakeholders. As part of the Marine Energy Advanced Materials project, marine renewable energy industry surveys and assessments were conducted to identify key materials and knowledge gaps that hinder the adoption of composite materials in marine renewable energy structures. Specific knowledge gaps highlighted for composite materials were environmental effects, fatigue strengths, and bonded and bolted interconnects (composite/composite and composite/metal). It was concluded that many of these gaps could be addressed through subcomponent validation; consequently, a program was developed at NREL with the goals of developing subcomponent validation methods for appropriate marine energy materials, which would improve the understanding of design allowables for full-scale structural components and joints. Ultimately, the aim is to reduce timelines and costs associated with full-scale structural validation efforts while also providing near-net-scale static and fatigue data of composite/metal subcomponents for marine renewable energy systems. To approach these goals, a testing program was developed at NREL to investigate a variety of materials and structural design details at the subcomponent scale to understand (a) the effects of harsh and corrosive marine energy environments and (b) the static and fatigue strengths of the complex geometries. The recent study from this testing program is perhaps the largest that has ever been conducted with respect to specimen scale and geographic diversity of underwater environmental conditions that the specimens were subjected to. A variety of specimen geometries were designed by NREL to highlight key features of multimaterial (composite/composite or metal/composite) interconnects that may be used in marine renewable energy structural designs. The designs used several different composite matrices, adhesives, and marine-grade steels, which were highlighted in the surveys as being the most appropriate for harsh marine environments. Composite panels were then manufactured at MSU, and were subsequently manufactured into test specimens by NREL. The specimens were shipped to FAU and PNNL for conditioning in ocean water tanks at various temperatures for an extended period. The specimens were then returned to NREL for structural validation. This presentation will provide an overview of recent advances within the testing program in terms of specimen design and test methods, and will discuss results and key findings of the subcomponent testing program to date at NREL.

adhesives↗

DOE OSTI2025

Standardized Residue Numbering and Secondary Structure Nomenclature in the Class D β-Lactamases

Over 1370 class D β-lactamases are currently known, and they pose a serious threat to the effective treatment of many infectious diseases, particularly in some pathogenic bacteria where evolving carbapenemase activity has been reported. Detailed understanding of their molecular biology, enzymology, and structural biology are critically important, but the lack of a standardized residue numbering scheme and inconsistent secondary structure annotation has made comparative analyses sometimes difficult and cumbersome. Compounding this, in the post-AlphaFold world where we currently find ourselves, an extraordinary wealth of detailed structural information on these enzymes is literally at our fingertips; therefore it is vitally important that a standard numbering system is in place to facilitate the accurate and straightforward analysis of their structures. In conclusion, here we present a residue numbering and secondary structure scheme for the class D enzymes based on the sequence and structure of OXA-48 and apply it to test targets to demonstrate the ease with which it can be used.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Differentiating Three-Dimensional Molecular Structures Using Laser-Induced Coulomb Explosion Imaging

Coulomb explosion imaging (CEI) with x-ray free electron lasers has recently been shown to be a powerful method for obtaining detailed structural information of gas-phase planar ring molecules [R. Boll et al., X-ray multiphoton-induced Coulomb explosion images complex single molecules, Nat. Phys. 18, 423 (2022).]. In this Letter, we investigate the potential of CEI driven by a tabletop laser and extend this approach to differentiating three-dimensional structures. We study the static CEI patterns of planar and nonplanar organic molecules that resemble the structures of typical products formed in ring-opening reactions. Here, our results reveal that each molecule exhibits a well-localized and distinctive pattern in three-dimensional fragment-ion momentum space. We find that these patterns yield direct information about the molecular structures and can be qualitatively reproduced using a classical Coulomb explosion simulation. Our findings suggest that laser-induced CEI can serve as a robust method for differentiating molecular structures of organic ring and chain molecules. As such, it holds great promise as a method for following ultrafast structural changes, e.g., during ring-opening reactions, by tracking the motion of individual atoms in pump-probe experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Structure of the T. brucei kinetoplastid RNA editing substrate-binding complex core component, RESC5

Kinetoplastid protists such as Trypanosoma brucei undergo an unusual process of mitochondrial uridine (U) insertion and deletion editing termed kinetoplastid RNA editing (kRNA editing). This extensive form of editing, which is mediated by guide RNAs (gRNAs), can involve the insertion of hundreds of Us and deletion of tens of Us to form a functional mitochondrial mRNA transcript. kRNA editing is catalyzed by the 20 S editosome/RECC. However, gRNA directed, processive editing requires the RNA editing substrate binding complex (RESC), which is comprised of 6 core proteins, RESC1-RESC6. To date there are no structures of RESC proteins or complexes and because RESC proteins show no homology to proteins of known structure, their molecular architecture remains unknown. RESC5 is a key core component in forming the foundation of the RESC complex. To gain insight into the RESC5 protein we performed biochemical and structural studies. We show that RESC5 is monomeric and we report the T . brucei RESC5 crystal structure to 1.95 Å. RESC5 harbors a dimethylarginine dimethylaminohydrolase-like (DDAH) fold. DDAH enzymes hydrolyze methylated arginine residues produced during protein degradation. However, RESC5 is missing two key catalytic DDAH residues and does bind DDAH substrate or product. Implications of the fold for RESC5 function are discussed. This structure provides the first structural view of an RESC protein.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Wind and Structural Loads on Parabolic Trough Solar Collectors at Nevada Solar One

Wind loading is a main contributor to structural design costs of Concentrating Solar Power (CSP) collectors, such as heliostats and parabolic troughs. These structures must resist the mechanical forces generated by turbulent wind. At the same time, the reflector surfaces must exhibit the necessary rigidity to maintain their optimal optical performance in windy conditions. Over two years, NREL conducted comprehensive field measurements of the atmospheric turbulent wind conditions and the resulting structural wind loads on parabolic troughs at the Nevada Solar One (NSO) plant. The measurement set-up included meteorological masts and structural load sensors on four trough rows. Additionally, we commissioned a lidar scanning the horizontal plane over the trough field. This data set catalogs the high-resolution data set characterizing the complex flow field and resulting structural loads on parabolic trough collectors. By providing this first-of-its-kind data set to the CSP community, we aim to enhance the community's understanding of wind-loading experienced by CSP collector structures. This data set will also help design next-generation solar collectors and photovoltaic trackers.

Array↗

DOE OSTI2026

Proximity Ferroelectricity in Compositionally Graded Structures

Proximity ferroelectricity is a novel paradigm for inducing ferroelectricity in a non-ferroelectric polar material, such as AlN or ZnO that are typically unswitchable with an external field below their dielectric breakdown field. When placed in direct contact with a thin switchable ferroelectric layer (such as Al 1-x Sc x N or Zn 1-x Mg x O), they become a practically switchable ferroelectric. Using the thermodynamic Landau-Ginzburg-Devonshire theory, in this work, we perform the finite element modeling of the polarization switching in the compositionally graded AlN-Al 1-x Sc x N, ZnO-Zn 1-x Mg x O, and MgO-Zn 1-x Mg x O structures sandwiched in both a parallel-plate capacitor geometry as well as in a sharp probe-planar electrode geometry. We reveal that the compositionally graded structure allows the simultaneous switching of spontaneous polarization in the whole system by a coercive field significantly lower than the electric breakdown field of unswitchable polar materials. The physical mechanism is the depolarization electric field determined by the gradient of chemical composition “x”. The field lowers the steepness of the switching barrier in the otherwise unswitchable parts of the compositionally graded AlN-Al 1-x Sc x N and ZnO-Zn 1-x Mg x O structures. In the MgO-like regions of the compositionally graded MgO-Zn 1-x Mg x O structure, a shallow double-well free energy potential emerges. Proximity ferroelectric switching of the compositionally graded structures placed in the probe-electrode geometry occurs due to nanodomain formation under the tip. We predict that a gradient of chemical composition “x” significantly lowers effective coercive fields of the compositionally graded AlN-Al 1-x Sc x N and ZnO-Zn 1-x Mg x O structures compared to the coercive fields of the corresponding multilayers with a uniform chemical composition in each layer. A tip-induced switching further lowers the coercive field, enabling control of ferroelectric domains in otherwise unswitchable compositionally graded structures, which can provide nanoscale domain control for memory, actuation, sensing, and optical applications.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Crystal Structure of an i‐Motif from the HRAS Oncogene Promoter

Abstract An i‐motif is a non‐canonical DNA structure implicated in gene regulation and linked to cancers. The C‐rich strand of the HRAS oncogene, 5′‐CG CCC GTG CCC TGCG CCC GCAA CCC GA‐3′ (herein referred to as iHRAS), forms an i‐motif in vitro but its exact structure was unknown. HRAS is a member of the RAS proto‐oncogene family. About 19 % of US cancer patients carry mutations in RAS genes. We solved the structure of iHRAS at 1.77 Å resolution. The structure reveals that iHRAS folds into a double hairpin. The two double hairpins associate in an antiparallel fashion, forming an i‐motif dimer capped by two loops on each end and linked by a connecting region. Six C−C + base pairs form each i‐motif core, and the core regions are extended by a G−G base pair and a cytosine stacking. Extensive canonical and non‐canonical base pairing and stacking stabilizes the connecting region and loops. The iHRAS structure is the first atomic resolution structure of an i‐motif from a human oncogene. This structure sheds light on i‐motifs folding and function in the cell.

Li, Kevin S.↗

DOE OSTI2023

Crystal Structure of an i‐Motif from the HRAS Oncogene Promoter

Li, Kevin S.↗

DOE OSTI2021

Importance of Depth and Artificial Structure as Predictors of Female Red Snapper Reproductive Parameters

Abstract The Red Snapper Lutjanus campechanus is a structure‐associated species occurring across a wide depth range in the northern Gulf of Mexico. We used the random forest machine learning algorithm to understand which habitat and individual fish characteristics could predict reproductive parameters of female Red Snapper. We evaluated fish captured from 2016 to 2018 on three artificial structure types with various structure heights at depths of 100 m or less. Overall, we found that depth and month were important predictors for most reproductive parameters, but the type of structure (artificial reefs, oil platforms, and rigs‐to‐reefs structures) was not important. Maturity was correctly classified in 88.9% of the cases when using the random forest ensemble model, with important predictors including FL, depth, structure height, and month of collection. Spawning seasonality (measured as gonadosomatic index [GSI]) was correctly classified in 59.5% of the cases when using histology reproductive phase, FL, month, and depth variables. Reproductively active or inactive females were correctly classified in 89.3% of the cases using GSI, month, FL, and depth, while females in the developing versus spawning capable phases were correctly classified in 82.2% of the cases using GSI, FL, month, and depth. Histological indicators that show potential spawning within a 36‐h period were correctly classified 61.5% of the time, with the best predictors being depth, FL, GSI, and month. Stepwise regression indicated that month was the only factor that significantly predicted contrasts in relative batch fecundity, with significantly greater values in August compared to all other months. Our findings suggest that female Red Snapper reproductive effort is not consistently or well predicted by artificial structure type or height but that a combination of fish FL, month, and depth can predict reproductive characteristics of female Red Snapper.

Brown‐Peterson, Nancy J.↗

DOE OSTI2023

BaCu 2 SiS 4 : A New Member of the A II B I 2 M IV Q 4 Chalcogenide Family with a Chiral Crystal Structure

Abstract Noncentrosymmetric ternary and quaternary chalcogenides are studied as promising nonlinear optical (NLO) materials in the mid‐infrared region. Here, we report the synthesis of a new material BaCu 2 SiS 4 in the A II B I 2 M IV Q 4 family ( A =divalent metal; B =monovalent metal; M =tetrel, Q =chalcogen), and discuss its crystal structure, thermal stability, optical behavior, and electronic structure. BaCu 2 SiS 4 crystallizes in the noncentrosymmetric chiral space group P 3 2 21 with lattice parameters a =6.1440(3) Å, c =15.3542(8) Å, V =501.95(6) Å 3 , Z =3. The structure features helical channels formed by corner‐sharing [CuS 4 ] and [SiS 4 ] tetrahedral units. Synthesis was carried out in a molten salt flux, as opposed to a traditional solid‐state route from elements, to minimize the formation of a competing ternary phase, Ba 2 SiS 4 . BaCu 2 SiS 4 is a semiconductor with an experimentally‐determined direct bandgap of ~2.2 eV. The material exhibits second harmonic generation (SHG) activity, confirming the noncentrosymmetric nature of the structure. Analysis of reported A II B I 2 M IV Q 4 crystal structures pointed out a correlation among potential structure types and the radii of the constituent elements. Total energy calculations were carried out to explore the relative stability of several reported crystal structures in this family of compounds.

Sarkar, Arka↗

DOE OSTI2020

Synchrotron CT imaging of lattice structures with engineered defects

Understanding mechanical failure, crack propagation, and compressive behavior at the micrometer scale is essential for tailoring material properties for structural performance in cellular materials. Typically, modeling of traditional polymer foam materials is clouded by the lack of control in material morphology and its inherent stochastic structure. Additive manufacturing with sub-micrometer resolution provides a direct path for experimenters to specifically tailor structures needed by modelers to explicitly probe mechanical performance. Using laboratory-based 3D X-ray computed tomographic imaging (CT), the examination of deformation and damage provides a critical path to understand how these soft materials behave. Additionally, synchrotron CT yields realistic information at higher strain rates to directly validate the robustness of our finite element modeling. For this study, nanolithographic printing was employed to generate a series of engineered lattices with increasing levels of defects through the random removal of ligaments. These structures were mechanically tested and imaged with laboratory-based microCT. Additionally, synchrotron experiments were conducted in which the structures were imaged in 3D at 14 Hz during compression at a 0.4 s –1 strain rate. These 3D images show the changes in the structure as the ligaments bend, buckle and fracture in real time. This technique provides a robust framework for developing our methodologies and future exploration of engineered structures.

36 MATERIALS SCIENCE↗

DOE OSTI2020

The relation between lignin sequence and its 3D structure

Background: Lignin, the second most abundant biopolymer on earth, plays a major structural role in plants, conferring mechanical strength and regulating water conduction. Understanding the three-dimensional structure of lignin is important for fundamental reasons as well as engineering plants towards lignin valorization. Lignin lacks a specific primary sequence, making its average chemical composition the focus of most recent studies. However, it remains unclear whether the 3D structure of lignin molecules depends on their sequence. Methods: In this work, we performed all-atom molecular dynamics simulation of three S/G-lignin molecules with the same average composition but different sequence. Results: A detailed statistical analysis of the radius of gyration and relative shape anisotropy reveals that the lignin sequence has no statistically significant effect on the global three-dimensional structure. We found however, that homopolymers of C-lignin with the same molecular weight have smaller radii of gyration than S/G-lignin. We attribute this to lower hydroxyl content of C-lignin, which makes it more compact and rigid. Conclusions: The 3D structure of lignin is influenced by the overall content of monomeric units and interunit linkages and not by its precise primary sequence. General Significance: Lignin is assumed to not have a well-defined primary structure. The results presented here demonstrate there are no significant differences in the global 3D structure of lignin molecules with the same average composition but different primary sequence.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Predicting RNA structure and dynamics with deep learning and solution scattering

Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce conformational changes. Small-angle x-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures. There are two main challenges in comparing SAXS profiles to RNA structures: the absence of cations essential for stability and charge neutralization in predicted structures and the inadequacy of a single structure to represent RNA’s conformational plasticity. We introduce a solution conformation predictor for RNA (SCOPER) to address these challenges. This pipeline integrates kinematics-based conformational sampling with the innovative deep learning model, IonNet, designed for predicting Mg 2+ ion binding sites. Validated through benchmarking against 14 experimental data sets, SCOPER significantly improved the quality of SAXS profile fits by including Mg 2+ ions and sampling of conformational plasticity. We observe that an increased content of monovalent and bivalent ions leads to decreased RNA plasticity. Therefore, carefully adjusting the plasticity and ion density is crucial to avoid overfitting experimental SAXS data. SCOPER is an efficient tool for accurately validating the solution state of RNAs given an initial, sufficiently accurate structure and provides the corrected atomistic model, including ions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Contrasting thermally-induced structural and microstructural evolution of alumino-silicates with tubular and planar arrangements: Case study of halloysite and kaolinite

Materials with the similar chemical structures but different morphological organization exhibit considerable differences in thermally induced chemo-morphological evolution. With recent advancements in multi-scale X-ray scattering measurements, it is now possible to non-invasively probe the structural and microstructural evolution of such materials. In this study, we investigate the chemo-morphological evolution of halloysite and contrast the results with those for kaolinite. Halloysite and kaolinite have tubular and planar morphologies, respectively. Both materials are alumino-silicates comprising silica tetrahedra (T) and alumina octahedra (O) organized in a TO structure. Four distinct stages in the structural evolution were identified. Stages I, II, III, and IV correspond to temperature ranges of 25 to 125 °C, 125 to 400 °C, 400 to 625 °C, and 625 to 875 °C. Major structural changes correspond to the removal of interlayer/adsorbed water in stage I, the existence of the halloysite structure without interlayer water in stage II, dehydroxylation of halloysite in stage III, and the conversion of ordered halloysite to amorphous meta-halloysite in stage IV. Additionally, heating halloysite up to 875 °C resulted in slight widening of the nanotubes, as the average pore radius increased from 6.4 nm to 6.6 nm. Heating also resulted in an increase of wall thickness of the nanotubes from ~120 nm (25 °C) to 161 nm (875 °C). The increase in the halloysite nanotube diameter was attributed to the expansion of the structure and an increase in the surface roughness. The pore sizes in halloysite nanotubes were also confirmed using N 2 adsorption-desorption and nano-X-ray computed tomography (nano-XCT) measurements. The interlayer basal spacing in halloysite changed from 9.8 Å to 7.2 Å after the removal of interlayer water. At temperatures in the range of 625 to 875 °C, heating halloysite causes a small widening of nanotube pores and a minor increase in the surface area. In contrast, the interlayer spacing in kaolinite collapses on heating which reduces the nanoscale porosity. Furthermore, these studies demonstrate the differences in the chemo-morphological evolution of alumino-silicates with tubular and planar morphologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗