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At least 1,675 records · Page 93
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps

Abstract The information about the domain architecture of proteins is useful for studying protein structure and function. However, accurate prediction of protein domain boundaries (i.e., sequence regions separating two domains) from sequence remains a significant challenge. In this work, we develop a deep learning method based on multi-head U-Nets (called DistDom) to predict protein domain boundaries utilizing 1D sequence features and predicted 2D inter-residue distance map as input. The 1D features contain the evolutionary and physicochemical information of protein sequences, whereas the 2D distance map includes the structural information of proteins that was rarely used in domain boundary prediction before. The 1D and 2D features are processed by the 1D and 2D U-Nets respectively to generate hidden features. The hidden features are then used by the multi-head attention to predict the probability of each residue of a protein being in a domain boundary, leveraging both local and global information in the features. The residue-level domain boundary predictions can be used to classify proteins as single-domain or multi-domain proteins. It classifies the CASP14 single-domain and multi-domain targets at the accuracy of 75.9%, 13.28% more accurate than the state-of-the-art method. Tested on the CASP14 multi-domain protein targets with expert annotated domain boundaries, the average per-target F1 measure score of the domain boundary prediction by DistDom is 0.263, 29.56% higher than the state-of-the-art method.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Magnetic Helicity in a Chiral-Polar Magnet Ni 2 InSbO 6

The class of chiral-polar magnets has recently captured significant interest in scientific study due to their intriguing physical phenomena. Among all the chiral-polar magnets, Ni 2 InSbO 6 stands out because of its unique attributes, such as the emergence of the topological chiral soliton lattice in the presence of an external magnetic field perpendicular to the chiral-polar axis. However, the magnetic structure of Ni 2 InSbO 6 at zero field has not been well understood yet. This work presents an analysis including polarized optical microscopy and polarized neutron diffraction on a carefully chosen Ni 2 InSbO 6 crystal. Here, results confirm the predominance of a single chiral-polar domain within the crystal and indicate the likelihood of cycloidal magnetic ordering under zero magnetic field, alongside the observation of net magnetic helicity. The existence of both a dominant chiral-polar domain and a dominant cycloidal magnetic domain within Ni 2 InSbO 6 provides an excellent platform for further exploration of its unconventional physical attributes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

In-plane current induced domain wall nucleation and its stochasticity in perpendicular magnetic anisotropy Hall cross structures

Hall cross structures in magnetic nanowires are commonly used for electrical detection of magnetization reversal in which a domain wall (DW) is conventionally nucleated by a local Oersted field. In this letter, we demonstrate DW nucleation in Co/Ni perpendicular magnetic anisotropy nanowire at the magnetic Hall cross junction. The DWs are nucleated by applying an in-plane pulsed current through the nanowire without the need of a local Oersted field. The change in Hall resistance, detected using anomalous Hall effect, is governed by the magnetic volume switched at the Hall junction, which can be tuned by varying the magnitude of the applied current density and pulse width. The nucleated DWs are driven simultaneously under the spin transfer torque effect when the applied current density is above a threshold. The possibility of multiple DW generation and variation in magnetic volume switched makes nucleation process stochastic in nature. The in-plane current induced stochastic nature of DW generation may find applications in random number generation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Structural analysis of nested neutralizing and non-neutralizing B cell epitopes on ricin toxin's enzymatic subunit

In this report, we describe the X–ray crystal structures of two single domain camelid antibodies (V H H), F5 and F8, each in complex with ricin toxin's enzymatic subunit (RTA). F5 has potent toxin–neutralizing activity, while F8 has weak neutralizing activity. F5 buried a total of 1760 Å 2 in complex with RTA and made contact with three prominent secondary structural elements: α–helix B (Residues 98–106), β–strand h (Residues 113–117), and the C–terminus of α–helix D (Residues 154–156). F8 buried 1103 Å 2 in complex with RTA that was centered primarily on β–strand h. As such, the structural epitope of F8 is essentially nested within that of F5. All three of the F5 complementarity determining regions CDRs were involved in RTA contact, whereas F8 interactions were almost entirely mediated by CDR3, which essentially formed a seventh β–strand within RTA's centrally located β–sheet. A comparison of the two structures reported here to several previously reported (RTA–VHH) structures identifies putative contact sites on RTA, particularly α–helix B, associated with potent toxin–neutralizing activity. Here, this information has implications for rational design of RTA–based subunit vaccines for biodefense.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Exploration of High-Dimensional Scalar Function for Nuclear Reactor Safety Analysis and Visualization

The next generation of methodologies for nuclear reactor Probabilistic Risk Assessment (PRA) explicitly accounts for the time element in modeling the probabilistic system evolution and uses numerical simulation tools to account for possible dependencies between failure events. The Monte-Carlo (MC) and the Dynamic Event Tree (DET) approaches belong to this new class of dynamic PRA methodologies. A challenge of dynamic PRA algorithms is the large amount of data they produce which may be difficult to visualize and analyze in order to extract useful information. We present a software tool that is designed to address these goals. We model a large-scale nuclear simulation dataset as a high-dimensional scalar function defined over a discrete sample of the domain. First, we provide structural analysis of such a function at multiple scales and provide insight into the relationship between the input parameters and the output. Second, we enable exploratory analysis for users, where we help the users to differentiate features from noise through multi-scale analysis on an interactive platform, based on domain knowledge and data characterization. Our analysis is performed by exploiting the topological and geometric properties of the domain, building statistical models based on its topological segmentations and providing interactive visual interfaces to facilitate such explorations. We provide a user’s guide to our software tool by highlighting its analysis and visualization capabilities, along with a use case involving dataset from a nuclear reactor safety simulation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

Exploration of high-dimensional scalar function for nuclear reactor safety analysis and visualization

The next generation of methodologies for nuclear reactor Probabilistic Risk Assessment (PRA) explicitly accounts for the time element in modeling the probabilistic system evolution and uses numerical simulation tools to account for possible dependencies between failure events. The Monte-Carlo (MC) and the Dynamic Event Tree (DET) approaches belong to this new class of dynamic PRA methodologies. A challenge of dynamic PRA algorithms is the large amount of data they produce which may be difficult to visualize and analyze in order to extract useful information. We present a software tool that is designed to address these goals. We model a large-scale nuclear simulation dataset as a high-dimensional scalar function defined over a discrete sample of the domain. First, we provide structural analysis of such a function at multiple scales and provide insight into the relationship between the input parameters and the output. Second, we enable exploratory analysis for users, where we help the users to differentiate features from noise through multi-scale analysis on an interactive platform, based on domain knowledge and data characterization. Our analysis is performed by exploiting the topological and geometric properties of the domain, building statistical models based on its topological segmentations and providing interactive visual interfaces to facilitate such explorations. We provide a user's guide to our software tool by highlighting its analysis and visualization capabilities, along with a use case involving data from a nuclear reactor safety simulation. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Gcn2 structurally mimics and functionally repurposes the HisRS enzyme for the integrated stress response

Protein kinase Gcn2 attenuates protein synthesis in response to amino acid starvation while stimulating translation of a transcriptional activator of amino acid biosynthesis. Gcn2 activation requires a domain related to histidyl-tRNA synthetase (HisRS), the enzyme that aminoacylates tRNA His . While evidence suggests that deacylated tRNA binds the HisRS domain for kinase activation, ribosomal P-stalk proteins have been implicated as alternative activating ligands on stalled ribosomes. We report crystal structures of the HisRS domain ofChaetomium thermophilumGcn2 that reveal structural mimicry of both catalytic (CD) and anticodon-binding (ABD) domains, which in authentic HisRS bind the acceptor stem and anticodon loop of tRNA His . Elements for forming histidyl adenylate and aminoacylation are lacking, suggesting that Gcn2 HisRS was repurposed for kinase activation, consistent with mutations in the CD that dysregulate yeast Gcn2 function. Substituting conserved ABD residues well positioned to contact the anticodon loop or that form a conserved ABD–CD interface impairs Gcn2 function in starved cells. Mimicry in Gcn2 HisRS of two highly conserved structural domains for binding both ends of tRNA—each crucial for Gcn2 function—supports that deacylated tRNAs activate Gcn2 and exemplifies how a metabolic enzyme is repurposed to host new local structures and sequences that confer a novel regulatory function.

Science & Technology - Other Topics↗
DOE OSTI2024

Atomic-Scale Scanning of Domain Network in the Ferroelectric HfO 2 Thin Film

Ferroelectric HfO 2 -based thin films have attracted much interest in the utilization of ferroelectricity at the nanoscale for next-generation electronic devices. However, the structural origin and stabilization mechanism of the ferroelectric phase are not understood because the film is typically nanocrystalline with active yet stochastic ferroelectric domains. Here, in this study, electron microscopy is used to map the in-plane domain network structures of epitaxially grown ferroelectric Y:HfO 2 films in atomic resolution. The ferroelectricity is confirmed in free-standing Y:HfO 2 films, allowing for investigating the structural origin for their ferroelectricity by 4D-STEM, high-resolution STEM, and iDPC-STEM. At the grain boundaries of <111>-oriented Pca2 1 orthorhombic grains, a high-symmetry mixed-(R3m, Pnm2 1 ) phase is induced, exhibiting enhanced polarization due to in-plane compressive strain. Nanoscale Pca2 1 orthorhombic grains and their grain boundaries with mixed-(R3m, Pnm2 1 ) phases of higher symmetry cooperatively determine the ferroelectricity of the Y:HfO 2 film. It is also found that such ferroelectric domain networks emerge when the film thickness is beyond a finite value. Furthermore, in-plane mapping of oxygen positions overlaid on ferroelectric domains discloses that polarization is suppressed at vertical domain walls, while it is active when domains are aligned horizontally with subangstrom domain walls. In addition, randomly distributed 180° charged domain walls are confined by spacer layers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Distinct Mechanisms of Recognizing Endosomal Sorting Complex Required for Transport III (ESCRT-III) Protein IST1 by Different Microtubule Interacting and Trafficking (MIT) Domains

The endosomal sorting complex required for transport (ESCRT) machinery is responsible for membrane remodeling in a number of biological processes including multivesicular body biogenesis, cytokinesis, and enveloped virus budding. In mammalian cells, efficient abscission during cytokinesis requires proper function of the ESCRT-III protein IST1, which binds to the microtubule interacting and trafficking (MIT) domains of VPS4, LIP5, and Spartin via its C-terminal MIT-interacting motif (MIM). In this paper, we studied the molecular interactions between IST1 and the three MIT domain-containing proteins to understand the structural basis that governs pairwise MIT-MIM interaction. Crystal structures of the three molecular complexes revealed that IST1 binds to the MIT domains of VPS4, LIP5, and Spartin using two different mechanisms (MIM1 mode versus MIM3 mode). Structural comparison revealed that structural features in both MIT and MIM contribute to determine the specific binding mechanism. Within the IST1 MIM sequence, two phenylalanine residues were shown to be important in discriminating MIM1 versus MIM3 binding. Finally, these observations enabled us to deduce a preliminary binding code, which we applied to provide CHMP2A, a protein that normally only binds the MIT domain in the MIM1 mode, the additional ability to bind the MIT domain of Spartin in the MIM3 mode.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Structure of human Niemann–Pick C1 protein

Niemann–Pick C1 protein (NPC1) is a late-endosomal membrane protein involved in trafficking of LDL-derived cholesterol, Niemann–Pick disease type C, and Ebola virus infection. NPC1 contains 13 transmembrane segments (TMs), five of which are thought to represent a “sterol-sensing domain” (SSD). Although present also in other key regulatory proteins of cholesterol biosynthesis, uptake, and signaling, the structure and mechanism of action of the SSD are unknown. Here we report a crystal structure of a large fragment of human NPC1 at 3.6 Å resolution, which reveals internal twofold pseudosymmetry along TM 2–13 and two structurally homologous domains that protrude 60 Å into the endosomal lumen. Strikingly, NPC1's SSD forms a cavity that is accessible from both the luminal bilayer leaflet and the endosomal lumen; computational modeling suggests that this cavity is large enough to accommodate one cholesterol molecule. In conclusion, we propose a model for NPC1 function in cholesterol sensing and transport.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Calsyntenin-3 Molecular Architecture and Interaction with Neurexin 1α

Calsyntenin 3 (Cstn3 or Clstn3), a recently identified synaptic organizer, promotes the development of synapses. Cstn3 localizes to the postsynaptic membrane and triggers presynaptic differentiation. Calsyntenin members play an evolutionarily conserved role in memory and learning. Cstn3 was recently shown in cell-based assays to interact with neurexin 1α (n1α), a synaptic organizer that is implicated in neuropsychiatric disease. Interaction would permit Cstn3 and n1α to form a trans-synaptic complex and promote synaptic differentiation. Here, it is contentious whether Cstn3 binds n1α directly. To understand the structure and function of Cstn3, we determined its architecture by electron microscopy and delineated the interaction between Cstn3 and n1α biochemically and biophysically. We show that Cstn3 ectodomains form monomers as well as tetramers that are stabilized by disulfide bonds and Ca 2+ , and both are probably flexible in solution. We show further that the extracellular domains of Cstn3 and n1α interact directly and that both Cstn3 monomers and tetramers bind n1α with nanomolar affinity. The interaction is promoted by Ca 2+ and requires minimally the LNS domain of Cstn3. Furthermore, Cstn3 uses a fundamentally different mechanism to bind n1α compared with other neurexin partners, such as the synaptic organizer neuroligin 2, because Cstn3 does not strictly require the sixth LNS domain of n1α. Our structural data suggest how Cstn3 as a synaptic organizer on the postsynaptic membrane, particularly in tetrameric form, may assemble radially symmetric trans-synaptic bridges with the presynaptic synaptic organizer n1α to recruit and spatially organize proteins into networks essential for synaptic function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

The polarized Debye sheath effect on Kadomtsev-Petviashvili electrostatic structures in strongly coupled dusty plasma

We give a theoretical investigation on the dynamics of nonlinear electrostatic waves in a strongly coupled dusty plasma with strong electrostatic interaction between dust grains in the presence of the polarization force (i.e., the force due to the polarized Debye sheath). Adopting a reductive perturbation method, we derived a three-dimensional Kadomtsev-Petviashvili equation that describes the evolution of weakly nonlinear electrostatic localized waves. The energy integral equation is used to study the existence domains of the localized structures. The analysis provides the localized structure existence region, in terms of the effects of strong interaction between the dust particles and polarization force.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Processing-Dependent Structure and Poroelasticity of Nafion in Liquid Water

Ionomers act as the solid polymer electrolyte membrane in many modern electrochemical devices, yet the role of their nanostructure in modulating the poroelastic response remains poorly understood, especially in liquid water, where few techniques can measure simultaneous transport-mechanical properties. Poroelastic Relaxation Indentation (PRI) is uniquely suited for measuring time-dependent transport-mechanical properties of porous solids, specifically hydraulic diffusivity, elastic modulus, Poisson’s ratio, and intrinsic permeability, for porous solids. While ionomers such as Nafion are not porous in the typical sense, Nafion has a nanophase-segregated structure that, when fully swollen in liquid water, behaves as a poroelastic solid with a coupled mechanical-transport response. Using a poroelastic framework, we investigate how casting and pretreatment of Nafion membranes alter their poroelastic response in liquid environments. We characterize both extruded and dispersion-cast Nafion membranes pretreated in water at 25 or 100 °C and relate the mechanical-transport properties to the ionomer structure via hydrophilic and intercrystalline domain spacing measured using Small-Angle X-ray Scattering (SAXS). At 25 °C, dispersion-cast membranes exhibit distinctly lower hydraulic diffusivity and intrinsic permeability than extruded membranes but with comparable mechanical properties. Pretreatment at 100 °C increases hydrophilic domain spacing, improving transport but at the expense of mechanical stiffness. Dispersion-cast membranes respond more strongly to pretreatment than extruded membranes. Using the Carman-Kozeny pore network model and the hydrophilic domain-spacing, we estimate the pore radius and tortuosity to show how pretreatment reduces structure-related tortuosity differences between dispersion-cast and extruded membranes. Here, in this work, we show that nanophase-segregated materials such as Nafion can be rigorously characterized using poroelasticity, resulting in physically meaningful transport-mechanical properties. Coupling PRI with SAXS provides insights into the nanostructural features that govern the coupled mechanical-transport response. By establishing PRI for a nanophase-segregated material, this approach opens avenues for this technique’s application in other hydrated polymeric materials not typically considered to be poroelastic.

Shen, Margaret [University of California, Berkeley↗
DOE OSTI2014

A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore

Spinach is an in vitro–selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-Å and 2.4-Å resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers.

Huang, Hao↗
DOE OSTI2016

Direct observation of B-site ordering in LSAT: (La{sub 0.3}Sr{sub 0.7})(Al{sub 0.65}Ta{sub 0.35})O{sub 3} single crystal

B-site atomic column regularity was directly observed in (La{sub 0.3}Sr{sub 0.7})(Al{sub 0.65}Ta{sub 0.35})O{sub 3} single crystals by Z-contrast imaging during high-angle annular dark-field scanning transmission electron microscopy. Two types of areas with different B-site regularity were found. One of the ordered structures, which was similar to a previously reported structure, was several tens of nanometers in size and had a rock salt-like regularity owing to variation in the B-site Al/Ta ratio. The other structure existed as disordered-like domains in the (La{sub 0.3}Sr{sub 0.7})(Al{sub 0.65}Ta{sub 0.35})O{sub 3} crystal. Fourier transform processing revealed that the disordered-like domains consisted of very fine ordered domains of several nanometers in size. These very fine ordered structures had a different B-site Al/Ta ratio variation with a rock salt-like regularity.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A Block-Structured Adaptive Mesh Framework to Solve Radiation Transfer Equation in Irregular Embedded Geometries

Radiation transport arises in various scientific, industrial, and medical fields, and understanding its effect in applications is needed to make accurate predictions, safety assessments and performance optimizations. Solving the Radiation Transport Equation (RTE) is challenging due to its integro-differential nature, which involves both differential and integral terms. The differential term describes the change in radiation intensity due to absorption and emission, while the integral term accounts for scattering. The accurate modeling of radiation is further complicated in many applications due to the complex, irregular geometries. Various methods exist for solving the RTE, including the zonal, Monte Carlo, spherical harmonics, discrete ordinates, and finite volume methods. Traditional mesh-based approaches, which rely on structured or unstructured meshes, struggle with irregular geometries due to: a) the difficulty of conforming structured grids to irregular domains, b) challenges in enforcing boundary conditions correctly, and c) the additional computational cost of unstructured mesh methods. This work presents a second-order accurate method for solving the RTE in irregular geometries. The radiation intensity is discretized using the finite-volume method in both spatial and angular directions on regular Cartesian grid blocks. Leveraging the block-structured adaptive mesh refinement (AMR) framework provided by AMReX, our method refines the grid locally to reduce spatial discretization error, ensuring a converged numerical solution while minimizing computational costs elsewhere. A two-stage deferred correction approach is employed: First, a first-order discretization on grid blocks is solved using an algebraic multigrid method in HYPRE. Second, a correction term is applied explicitly to achieve second-order accuracy. The correction term is calculated by approximating the radiation flux on cell faces using a Total Variation Diminishing (TVD) scheme. This approach ensures quick convergence of the multigrid method while preserving higher-order accuracy of the numerical solution. Irregular geometries are resolved as embedded boundaries (EB), resulting in both cut cells and regular cells. In cut cells, we modify the fluxes using face fractions and incorporate additional contributions from EB boundary conditions. To ensure higher-order convergence near the EB interface, the correction term is modified by interpolating the radiation intensity to fictitious ghost points. The implementation takes advantage of modern supercomputers by leveraging AMReX’sMPI/X parallelization strategy where X can be MPI or a GPU accelerator including CUDA, HIP and DPC++. We validate our solver using classical test cases, both with and without EB, demonstrating accuracy and efficiency. Additionally, we analyze the impact of adaptive mesh refinement on solution accuracy and computational cost, highlighting the advantages of our approach for high-resolution radiation transport simulations.

computational fluid dynamics (CFD)↗
DOE OSTI2025

Diversity in the Common Fold: Structural Insights into Class D β-Lactamases from Gram-Negative Pathogens

Class D β-lactamases (DBLs) represent a major threat to antibiotic efficacy by hydrolyzing β-lactam drugs, including last-resort carbapenems, thereby driving antimicrobial resistance in Gram-negative bacteria. The enzymes share a structurally conserved two-domain α/β architecture with seven active-site motifs and three flexible extended loops (the P-loop, Ω-loop, and newly designated B-loop) that surround the active site. While each of these loops is known to influence enzyme function, their coordinated roles have not been fully elucidated. To investigate the significance of their interplay, we compared the sequences and crystal structures of 40 DBLs from clinically relevant Gram-negative pathogens and performed molecular dynamics simulations on selected representatives. Combined structural and dynamical analyses revealed a strong correlation between B-loop architecture and carbapenemase activity in the pathogens Klebsiella and Acinetobacter, particularly regarding loop length and spatial organization. These findings emphasize the B-loop’s critical contribution, in concert with the P- and Ω-loops, in tuning active site versatility, substrate recognition, catalytic activity, and structural stability. A deeper understanding of how these motifs and loops govern DBL function may inform the development of novel antibiotics and inhibitors targeting this class of enzymes.

antibiotic resistance↗
DOE OSTI2013

Structural analyses at pseudo atomic resolution of Chikungunya virus and antibodies show mechanisms of neutralization

A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 glycoprotein heterodimer. The heterodimer structure was divided into domains to obtain a good fit to the cryoEM density. Differences in the T = 4 quasi-equivalent heterodimer components show their adaptation to different environments. The spikes on the icosahedral 3-fold axes and those in general positions are significantly different, possibly representing different phases during initial generation of fusogenic E1 trimers. CryoEM maps of neutralizing Fab fragments complexed with VLPs have been interpreted using the crystal structures of the Fab fragments and the VLP structure. Based on these analyses the CHK-152 antibody was shown to stabilize the viral surface, hindering the exposure of the fusion-loop, likely neutralizing infection by blocking fusion. The CHK-9, m10 and m242 antibodies surround the receptor-attachment site, probably inhibiting infection by blocking cell attachment.

59 BASIC BIOLOGICAL SCIENCES↗