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All sources NASA NTRS DOE OSTI

DOE OSTI2024

Realization of a two-dimensional Weyl semimetal and topological Fermi strings

A two-dimensional (2D) Weyl semimetal, akin to a spinful variant of graphene, represents a topological matter characterized by Weyl fermion-like quasiparticles in low dimensions. The spinful linear band structure in two dimensions gives rise to distinctive topological properties, accompanied by the emergence of Fermi string edge states. We report the experimental realization of a 2D Weyl semimetal, bismuthene monolayer grown on SnS(Se) substrates. Using spin and angle-resolved photoemission and scanning tunneling spectroscopies, we directly observe spin-polarized Weyl cones, Weyl nodes, and Fermi strings, providing consistent evidence of their inherent topological characteristics. Our work opens the door for the experimental study of Weyl fermions in low-dimensional materials.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Vibrational properties of CuInP 2 S 6 across the ferroelectric transition

In order to explore the properties of a two-sublattice ferroelectric, we measured the infrared and Raman scattering response of CuInP 2 S 6 across the ferroelectric and glassy transitions and compared our findings to a symmetry analysis, calculations of phase stability, and lattice dynamics. In addition to uncovering displacive character and a large hysteresis region surrounding the ferroelectric transition temperature T C , we identify the vibrational modes that stabilize the polar phase and confirm the presence of two ferroelectric variants with opposite polarizations. Below T C , a poorly understood relaxational or glassy transition at T g is characterized by local structure changes in the form of subtle peak shifting and activation of low frequency out-of-plane Cu- and In-containing modes. Here, the latter are due to changes in the Cu/In coordination environments and associated order-disorder processes. Moreover, T g takes place in two steps with another large hysteresis region and significant underlying scattering. Combined with imaging of the room temperature phase separation, this effort lays the groundwork for studying CuInP 2 S 6 under external stimuli and in the ultrathin limit.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Structural and functional validation of a highly specific Smurf2 inhibitor

Smurf1 and Smurf2 are two closely related member of the HECT (homologous to E6AP carboxy terminus) E3 ubiquitin ligase family and play important roles in the regulation of various cellular processes. Both were initially identified to regulate transforming growth factor‐β and bone morphogenetic protein signaling pathways through regulating Smad protein stability and are now implicated in various pathological processes. Generally, E3 ligases, of which over 800 exist in humans, are ideal targets for inhibition as they determine substrate specificity; however, there are few inhibitors with the ability to precisely target a particular E3 ligase of interest. In this work, we explored a panel of ubiquitin variants (UbVs) that were previously identified to bind Smurf1 or Smurf2. In vitro binding and ubiquitination assays identified a highly specific Smurf2 inhibitor, UbV S2.4, which was able to inhibit ligase activity with high potency in the low nanomolar range. Orthologous cellular assays further demonstrated high specificity of UbV S2.4 toward Smurf2 and no cross‐reactivity toward Smurf1. Structural analysis of UbV S2.4 in complex with Smurf2 revealed its mechanism of inhibition was through targeting the E2 binding site. In summary, we investigated several protein‐based inhibitors of Smurf1 and Smurf2 and identified a highly specific Smurf2 inhibitor that disrupts the E2–E3 protein interaction interface.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer

Neurofibromin is a tumor suppressor encoded by the NF1 gene, which is mutated in Rasopathy disease neurofibromatosis type I. Defects in NF1 lead to aberrant signaling through the RAS–mitogen-activated protein kinase pathway due to disruption of the neurofibromin GTPase-activating function on RAS family small GTPases. Very little is known about the function of most of the neurofibromin protein; to date, biochemical and structural data exist only for its GAP domain and a region containing a Sec-PH motif. To better understand the role of this large protein, here we carried out a series of biochemical and biophysical experiments, including size-exclusion chromatography–multiangle light scattering (SEC-MALS), small-angle X-ray and neutron scattering, and analytical ultracentrifugation, indicating that full-length neurofibromin forms a high-affinity dimer. We observed that neurofibromin dimerization also occurs in human cells and likely has biological and clinical implications. Analysis of purified full-length and truncated neurofibromin variants by negative-stain EM revealed the overall architecture of the dimer and predicted the potential interactions that contribute to the dimer interface. We could reconstitute structures resembling high-affinity full-length dimers by mixing N- and C-terminal protein domains in vitro. The reconstituted neurofibromin was capable of GTPase activation in vitro, and co-expression of the two domains in human cells effectively recapitulated the activity of full-length neurofibromin. Taken together, these results suggest how neurofibromin dimers might form and be stabilized within the cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Trigonal polymorph of Li 2 MnO 3

We report the discovery of a trigonal polymorph of the prospective Li ion battery material Li 2 MnO 3 and its synthesis in bulk, single crystal form. Crystal growth of trigonal Li 2 MnO 3 is strongly dependent upon the quality of a polycrystalline LiMnO 2 precursor consumed in the synthesis process. The crystal structure of the new trigonal phase is composed of ordered honeycomb layers of LiO 6 and MnO 6 octahedra segregated by layers of LiO 6 octahedra and represents an ordered stacking variant of the known monoclinic polymorph. Diffuse reflectance spectroscopy reveals a direct optical gap of 2.47 ± 0.11 eV and a series of charge excitations that are well explained by the expected Mn 4+ 3d 3 valence. Density functional theory calculations are in excellent agreement with the spectroscopic measurements and find a near degeneracy in the formation energies of the two polymorphs. Furthermore, our results suggest that the trigonal structure resolves the compositional and structural disorder often manifested in the monoclinic phase.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography

Single-domain Variable New Antigen Receptors (VNARs) from the immune system of sharks are the smallest naturally occurring binding domains found in nature. Possessing flexible paratopes that can recognize protein motifs inaccessible to classical antibodies, VNARs have yet to be exploited for the development of SARS-CoV-2 therapeutics. Here, we detail the identification of a series of VNARs from a VNAR phage display library screened against the SARS-CoV-2 receptor binding domain (RBD). The ability of the VNARs to neutralize pseudotype and authentic live SARS-CoV-2 virus rivalled or exceeded that of full-length immunoglobulins and other single-domain antibodies. Crystallographic analysis of two VNARs found that they recognized separate epitopes on the RBD and had distinctly different mechanisms of virus neutralization unique to VNARs. Structural and biochemical data suggest that VNARs would be effective therapeutic agents against emerging SARS-CoV-2 mutants, including the Delta variant, and coronaviruses across multiple phylogenetic lineages. This study highlights the utility of VNARs as effective therapeutics against coronaviruses and may serve as a critical milestone for nearing a paradigm shift of the greater biologic landscape.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Customizable wave tailoring nonlinear materials enabled by bilevel inverse design

Abstract Passive wave transformation via nonlinearity is ubiquitous in settings from acoustics to optics and electromagnetics. It is well known that different nonlinearities yield different effects on propagating signals, which raises the question of “what precise nonlinearity is the best for a given wave tailoring application?” In this work, considering a one-dimensional spring-mass chain connected by polynomial springs (a variant of the Fermi-Pasta-Ulam-Tsingou system), we introduce a bilevel inverse design method which couples the shape optimization of structures for tailored constitutive responses with reduced-order nonlinear dynamical inverse design. We apply it to two qualitatively distinct problems—minimization of peak transmitted kinetic energy from impact, and pulse shape transformation—demonstrating our method’s breadth of applicability. For the impact problem, we obtain two fundamental insights. First, small differences in nonlinearity can drastically change the dynamic response of the system, from severely under- to outperforming a comparative linear system. Second, the oft-used strategy of impact mitigation via “energy locking” bistability can be significantly outperformed by our optimal nonlinearity. We validate this case with impact experiments and find excellent agreement. This study establishes a framework for broader passive nonlinear mechanical wave tailoring material design, with applications to computing, signal processing, shock mitigation, and autonomous materials.

Science & Technology - Other Topics↗

DOE OSTI2022

Photoinduced chemomimetic biocatalysis for enantioselective intermolecular radical conjugate addition

Exploiting nature’s catalysts for non-natural transformations that are inaccessible to chemocatalysis is highly desirable but challenging. On the one hand, the widespread nicotinamide-dependent oxidoreductases have not been utilized for single-electron-transfer-induced bimolecular cross-couplings; on the other, the addition of catalytic asymmetric radical con- jugate to terminal alkenes remains a challenge owing to strong racemic background reaction and unselective termination of prochiral radical species. Here we report a chemomimetic biocatalysitic approach for construction of alpha-carbonyl stereocentres via an unnatural intermolecular conjugate addition of N-(acyloxy)phthalimides-derived radicals with acceptor-substituted terminal alkenes, by combination of visible-light excitation and nicotinamide-dependent ketoreductases (KREDs). Based on protein crystal structure, we engineered KREDs via a semi-rational mutagenesis strategy to improve reaction outcomes with a small and high-quality variants library. Here, mechanistic investigations combining wet experiments, crystallographic studies and computational simulations demonstrate that the repurposed biocatalyst can suppress racemic background reaction and unselected side reactions, yielding enantioselectivity that is challenging to achieve by chemocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Rubisco Function, Evolution, and Engineering

Carbon fixation is the process by which CO 2 is converted from a gas into biomass. The Calvin–Benson–Bassham cycle (CBB) is the dominant carbon-consuming pathway on Earth, driving >99.5% of the ~120 billion tons of carbon that are converted to sugar by plants, algae, and cyanobacteria. The carboxylase enzyme in the CBB, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco), fixes one CO 2 molecule per turn of the cycle into bioavailable sugars. Despite being critical to the assimilation of carbon, rubisco's kinetic rate is not very fast, limiting flux through the pathway. This bottleneck presents a paradox: Why has rubisco not evolved to be a better catalyst? Many hypothesize that the catalytic mechanism of rubisco is subject to one or more trade-offs and that rubisco variants have been optimized for their native physiological environment. Here, we review the evolution and biochemistry of rubisco through the lens of structure and mechanism in order to understand what trade-offs limit its improvement. We also review the many attempts to improve rubisco itself and thereby promote plant growth.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

fpikachu96/KRED-data

Exploiting nature’s catalysts for non-natural transformations that are inaccessible to chemocatalysis is highly desirable but challenging. On the one hand, the widespread nicotinamide-dependent oxidoreductases have not been utilized for single-electron-transfer-induced bimolecular cross-couplings; on the other, the addition of catalytic asymmetric radical conjugate to terminal alkenes remains a challenge owing to strong racemic background reaction and unselective termination of prochiral radical species. Here we report a chemomimetic biocatalysitic approach for construction of alpha-carbonyl stereocentres via an unnatural intermolecular conjugate addition of N-(acyloxy)phthalimides-derived radicals with acceptor-substituted terminal alkenes, by combination of visible-light excitation and nicotinamide-dependent ketoreductases (KREDs). Based on protein crystal structure, we engineered KREDs via a semi-rational mutagenesis strategy to improve reaction outcomes with a small and high-quality variants library. Mechanistic investigations combining wet experiments, crystallographic studies and computational simulations demonstrate that the repurposed biocatalyst can suppress racemic background reaction and unselected side reactions, yielding enantioselectivity that is challenging to achieve by chemocatalysis.

Huang, Xiaoqiang↗

DOE OSTI2021

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics

Background Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context. Results. Here, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity, and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have 4 to 16 copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis co-existed with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition. Conclusions The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1993

Optimization by decomposition

An algorithm is presented for solving the structural optimization problem as a set of smaller subproblems that correspond to levels of nested substructures. In all three of the algorithm variants presented, the matching was assisted by means of the behavior and optimum sensitivity derivatives. The algorithm is noted to be intrinsically germane to distributed computing, since the subproblems can be concurrently addressed; the algorithm can also be generalized to those multidisciplinary systems whose subsystems can be arranged into a hierarchy of substructure-like dependencies.

Sobieszczanski-Sobieski, Jaroslaw↗

NASA NTRS2003

A Time Integration Algorithm Based on the State Transition Matrix for Structures with Time Varying and Nonlinear Properties

A variable order method of integrating the structural dynamics equations that is based on the state transition matrix has been developed. The method has been evaluated for linear time variant and nonlinear systems of equations. When the time variation of the system can be modeled exactly by a polynomial it produces nearly exact solutions for a wide range of time step sizes. Solutions of a model nonlinear dynamic response exhibiting chaotic behavior have been computed. Accuracy of the method has been demonstrated by comparison with solutions obtained by established methods.

Bartels, Robert E.↗

NASA NTRS2012

Accelerated Creep Testing of High Strength Aramid Webbing

A series of preliminary accelerated creep tests were performed on four variants of 12K and 24K lbf rated Vectran webbing to help develop an accelerated creep test methodology and analysis capability for high strength aramid webbings. The variants included pristine, aged, folded and stitched samples. This class of webbings is used in the restraint layer of habitable, inflatable space structures, for which the lifetime properties are currently not well characterized. The Stepped Isothermal Method was used to accelerate the creep life of the webbings and a novel stereo photogrammetry system was used to measure the full-field strains. A custom MATLAB code is described, and used to reduce the strain data to produce master creep curves for the test samples. Initial results show good correlation between replicates; however, it is clear that a larger number of samples are needed to build confidence in the consistency of the results. It is noted that local fiber breaks affect the creep response in a similar manner to increasing the load, thus raising the creep rate and reducing the time to creep failure. The stitched webbings produced the highest variance between replicates, due to the combination of higher local stresses and thread-on-fiber damage. Large variability in the strength of the webbings is also shown to have an impact on the range of predicted creep life.

Jones, Thomas C.↗

NASA NTRS2022

NESC Peer Review of Exploration Systems Development (ESD) Integrated Vehicle Modal Test, Model Correlation, Development Flight Instrumentation (DFI) and Flight Loads Readiness; Uncertainty Propagation for Model Validation Sub-task

This report details a sub-task (regarding Uncertainty Propagation for Model Validation) from a NASA Engineering and Safety Center assessment that is a multi-year activity spanning the complete development of the Space Launch System integrated vehicle structural dynamic models, and the development of the certification of flight readiness for the Artemis 1 and Artemis 2 vehicles and their variants.

Exploration Systems Development; Development Fligh↗

NASA NTRS2019

Common Habitat for Long Duration Transit and Surface Operations

This concept is based on the Skylab II concept, which proposes using a SLS propellant tank as the primary structure of a habitat. Common Habitat takes this a step further, proposing an interior architecture that is equally viable as a lunar surface hab, transit hab, and Mars surface hab, thus enabling a single development to support all three long duration habitat roles. Common Habitat has been pursued by the PI and co-investigators at MSFC and other centers in a spare time / funding available basis, often with heavy student intern support. Student resources have developed preliminary concepts, but these models must be refined to reflect accurate vehicle subsystems, utilities, stowage, workstations, and other crew systems. This investigation applies NASA civil servant and contractor expertise to correct errors in the most recent student concepts in order to prepare them for future human-in-the-loop evaluations to determine the most viable configuration for a Common Habitat. In prior studies there was never an opportunity to trade both crew size and internal orientation. Prior work has been a series of point designs with inconsistent design constraints, making apples to apples comparisons impossible. The most recent student work produced CAD models of four habitat variants for future use in a trade study, but the student products contain model construction and geometry errors, inaccurate subsystems design and placement, and unrealistic structural elements and outfitting. These must be corrected before the models can be moved into a VR environment for humanin- the-loop testing. Through consultation with SMEs throughout the Agency, the fidelity of these designs will be upgraded to a level of quality sufficient to make a comparative analysis of crew size sensitivity and internal orientation. The product of this activity is four upgraded CAD models, each reflecting a different configuration of the Common Habitat. One is a horizontal configuration using the full length of the SLS LOX tank. One is a vertical configuration using the same tank dimensions. The third is a horizontal configuration using a truncated SLS LOX tank (half the barrel length). The fourth is a vertical configuration of the half-length SLS LOX tank.

Howard, Robert L.↗

DOE OSTI2022

Crystal structure of ultra-humanized anti-pTau Fab reveals how germline substitutions humanize CDRs without loss of binding’

Administration of therapeutic antibodies can elicit adverse immune responses in patients through the generation of anti-drug antibodies that, in turn, reduce the efficacy of the therapeutic. Removal of foreign amino acid content by humanization can lower the immunogenic risk of the therapeutic mAb. We previously developed the ultra-humanization technology “Augmented Binary Substitution” (ABS) which enables single-step CDR germlining of antibodies. The application of ABS to a chicken anti-pTau antibody generated an ultra-humanized variant, anti-pTau C21-ABS, with increased human amino acid content in the CDRs and reduced in-silico predicted immunogenicity risk. Here, we report the high-resolution crystal structure of anti-pTau C21-ABS Fab in complex with the pTau peptide (7KQK). This study examines how ultra-humanization, via CDR germlining, is facilitated while maintaining near-identical antigen affinity (within 1.6-fold). The co-complex structure reveals that the ABS molecule targets the same antigenic epitope, accommodated by structurally-similar changes in the paratope. These findings confirm that ABS enables the germlining of amino acids within CDRs by exploiting CDR plasticity, to reduce non-human amino acid CDR content, with few alterations to the overall mechanism of binding.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

PRISMS-PF: A general framework for phase-field modeling with a matrix-free finite element method

Abstract A new phase-field modeling framework with an emphasis on performance, flexibility, and ease of use is presented. Foremost among the strategies employed to fulfill these objectives are the use of a matrix-free finite element method and a modular, application-centric code structure. This approach is implemented in the new open-source PRISMS-PF framework. Its performance is enabled by the combination of a matrix-free variant of the finite element method with adaptive mesh refinement, explicit time integration, and multilevel parallelism. Benchmark testing with a particle growth problem shows PRISMS-PF with adaptive mesh refinement and higher-order elements to be up to 12 times faster than a finite difference code employing a second-order-accurate spatial discretization and first-order-accurate explicit time integration. Furthermore, for a two-dimensional solidification benchmark problem, the performance of PRISMS-PF meets or exceeds that of phase-field frameworks that focus on implicit/semi-implicit time stepping, even though the benchmark problem’s small computational size reduces the scalability advantage of explicit time-integration schemes. PRISMS-PF supports an arbitrary number of coupled governing equations. The code structure simplifies the modification of these governing equations by separating their definition from the implementation of the numerical methods used to solve them. As part of its modular design, the framework includes functionality for nucleation and polycrystalline systems available in any application to further broaden the phenomena that can be used to study. The versatility of this approach is demonstrated with examples from several common types of phase-field simulations, including coarsening subsequent to spinodal decomposition, solidification, precipitation, grain growth, and corrosion.

36 MATERIALS SCIENCE↗