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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3

Abstract Replication of the coronavirus genome starts with the formation of viral RNA-containing double-membrane vesicles (DMV) following viral entry into the host cell. The multi-domain nonstructural protein 3 (nsp3) is the largest protein encoded by the known coronavirus genome and serves as a central component of the viral replication and transcription machinery. Previous studies demonstrated that the highly-conserved C-terminal region of nsp3 is essential for subcellular membrane rearrangement, yet the underlying mechanisms remain elusive. Here we report the crystal structure of the CoV-Y domain, the most C-terminal domain of the SARS-CoV-2 nsp3, at 2.4 Å-resolution. CoV-Y adopts a previously uncharacterized V-shaped fold featuring three distinct subdomains. Sequence alignment and structure prediction suggest that this fold is likely shared by the CoV-Y domains from closely related nsp3 homologs. NMR-based fragment screening combined with molecular docking identifies surface cavities in CoV-Y for interaction with potential ligands and other nsps. These studies provide the first structural view on a complete nsp3 CoV-Y domain, and the molecular framework for understanding the architecture, assembly and function of the nsp3 C-terminal domains in coronavirus replication. Our work illuminates nsp3 as a potential target for therapeutic interventions to aid in the on-going battle against the COVID-19 pandemic and diseases caused by other coronaviruses.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Voltage-induced magnetic domain evolution in a phase-change material

Applying voltage to metal–insulator transition (MIT) materials allows electrical actuation of the local electronic phase state. In MIT systems that have the electronic order coupled with the magnetic order, voltage switching of the electronic phase state can also enable the electrical manipulation of magnetic properties. In this work, we utilized x-ray magnetic circular dichroism photoemission electron microscopy (XMCD-PEEM) to investigate the control of magnetic domain configurations in ferromagnetic MIT electrical switches. For applied voltages above a threshold value, the XMCD-PEEM images show that the magnetic domains separate into two distinct regions: one with a high contrast (white/black), indicating well-defined micrometer-scale magnetic domains with a component of their magnetization aligned parallel/antiparallel to the x-ray helicity, and the other with different shades of intermediate contrast (gray). Significant changes in magnetic domain configurations upon voltage biasing were only observed in these gray regions. Furthermore, the voltage-induced magnetic domain separation was found to be bias polarity-dependent, with the gray regions expanding from the opposite sample edge when the applied voltage polarity was reversed. This polarity-dependent electrical control of magnetic domain configurations during the MIT switching opens alternative opportunities in memory applications for magnetic MIT switching materials.

42 ENGINEERING↗
DOE OSTI2024

Quantum Barkhausen noise induced by domain wall cotunneling

Most macroscopic magnetic phenomena (including magnetic hysteresis) are typically understood classically. Here, we examine the dynamics of a uniaxial rare-earth ferromagnet deep within the quantum regime, so that domain wall motion, and the associated hysteresis, is initiated by quantum nucleation, which then grows into large-scale domain wall motion, which is observable as an unusual form of Barkhausen noise. We observe noncritical behavior in the resulting avalanche dynamics that only can be explained by going beyond traditional renormalization group methods or classical domain wall models. We find that this “quantum Barkhausen noise” exhibits two distinct mechanisms for domain wall movement, each of which is quantum-mechanical, but with very different dependences on an external magnetic field applied transverse to the spin (Ising) axis. These observations can be understood in terms of the correlated motion of pairs of domain walls, nucleated by cotunneling of plaquettes (sections of domain wall), with plaquette pairs correlated by dipolar interactions; this correlation is suppressed by the transverse field. Similar macroscopic correlations may be expected to appear in the hysteresis of other systems with long-range interactions.

Science & Technology - Other Topics↗
DOE OSTI2021

Unusual dynamic susceptibility arising from soft ferromagnetic domains in MnBi 8 Te 13 and Sb-doped MnBi 2n Te 3n+1 (n = 2, 3)

MnBi$_{2n}$Te$_{3n+1}$ (MBT) is the first intrinsic magnetic topological insulator and is promising to host emergent phenomena such as quantum anomalous Hall effect. They can be made ferromagnetic by having n ≥ 4 or with Sb doping. In this work, we studied the magnetic dynamics in a few selected ferromagnetic (FM) MBT compounds, including MnBi 8 Te 13 and Sb doped MnBi$_{2n}$Te$_{3n+1}$ ($n = 2, 3)$ using AC susceptibility and magneto-optical imaging. Slow relaxation behavior is observed in all three compounds, suggesting its universality among FM MBT. We attribute the origin of the relaxation behavior to the irreversible domain movements since they only appear below the saturation fields when ferromagnetic domains form. The very soft ferromagnetic domain nature is revealed by the low-field fine-structured domains and high-field sea-urchin-shaped remanent-state domains imaged via our magneto-optical measurements. Finally, we ascribe the rare 'double-peak' behavior observed in the AC susceptibility under small DC bias fields to the very soft ferromagnetic domain formations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Disentangling ferroelectric domain wall geometries and pathways in dynamic piezoresponse force microscopy via unsupervised machine learning

In this work, domain switching pathways in ferroelectric materials visualized by dynamic piezoresponse force microscopy (PFM) are explored via variational autoencoder, which simplifies the elements of the observed domain structure, crucially allowing for rotational invariance, thereby reducing the variability of local polarization distributions to a small number of latent variables. For small sampling window sizes the latent space is degenerate, and variability is observed only in the direction of a single latent variable that can be identified with the presence of domain wall. For larger window sizes, the latent space is 2D, and the disentangled latent variables can be generally interpreted as the degree of switching and complexity of domain structure. Applied to multiple consecutive PFM images acquired while monitoring domain switching, the polarization switching mechanism can thus be visualized in the latent space, providing insight into domain evolution mechanisms and their correlation with the microstructure.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

High-resolution crystal structure of the Borreliella burgdorferi PlzA protein in complex with c-di-GMP: new insights into the interaction of c-di-GMP with the novel xPilZ domain

ABSTRACT In the tick-borne pathogens, Borreliella burgdorferi and Borrelia hermsii, c-di-GMP is produced by a single diguanylate cyclase (Rrp1). In these pathogens, the Plz proteins (PlzA, B and C) are the only c-di-GMP receptors identified to date and PlzA is the sole c-di-GMP receptor found in all Borreliella isolates. Bioinformatic analyses suggest that PlzA has a unique PilZN3-PilZ architecture with the relatively uncommon xPilZ domain. Here, we present the crystal structure of PlzA in complex with c-di-GMP (1.6 Å resolution). This is the first structure of a xPilz domain in complex with c-di-GMP to be determined. PlzA has a two-domain structure, where each domain comprises topologically equivalent PilZ domains with minimal sequence identity but remarkable structural similarity. The c-di-GMP binding site is formed by the linker connecting the two domains. While the structure of apo PlzA could not be determined, previous fluorescence resonance energy transfer data suggest that apo and holo forms of the protein are structurally distinct. The information obtained from this study will facilitate ongoing efforts to identify the molecular mechanisms of PlzA-mediated regulation in ticks and mammals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA

The recently characterized mammalian writer (methyltransferase) and eraser (demethylase) of the DNA N6-methyladenine (N6mA) methyl mark act on single-stranded (ss) and transiently-unpaired DNA. As YTH domain-containing proteins bind N6mA-containing RNA in mammalian cells, we investigated whether mammalian YTH domains are also methyl mark readers of N6mA DNA. Here, we show that the YTH domain of YTHDC1 (known to localize in the nucleus) binds ssDNA containing N6mA, with a 10 nM dissociation constant. This binding is stronger by a factor of 5 than in an RNA context, tested under the same conditions. However, the YTH domains of YTHDF2 and YTHDF1 (predominantly cytoplasmic) exhibited the opposite effect with ~1.5–2× stronger binding to ssRNA containing N6mA than to the corresponding DNA. We determined two structures of the YTH domain of YTHDC1 in complex with N6mA-containing ssDNA, which illustrated that YTHDC1 binds the methylated adenine in a single-stranded region flanked by duplexed DNA. We discuss the hypothesis that the writer-reader-eraser of N6mA-containining ssDNA is associated with maintaining genome stability. Structural comparison of YTH and SRA domains (the latter a DNA 5-methylcytosine reader) revealed them to be diverse members of a larger family of DNA/RNA modification readers, apparently having originated from bacterial modification-dependent restriction enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

N-Terminal domain homologs of the orange carotenoid protein increase quenching of cyanobacterial phycobilisomes

Stress exerted by excess captured light energy in cyanobacteria is prevented by the photoprotective activity of the orange carotenoid protein (OCP). Under high light, the OCP converts from an orange, inactive form (OCP O ) into the red form (OCP R ) that binds to and quenches the phycobilisome (PBS). Structurally, the OCP consists of 2 domains: the N-terminal effector domain and a C-terminal regulatory domain. Structural analysis of the OCP-PBS complex showed that the N-terminal domains of an OCP dimer interact with the PBS core. These N-terminal OCP domains have single-domain protein paralogs known as helical carotenoid proteins (HCPs). Using PBS quenching assays, we show that the HCP4 and HCP5 homologs efficiently quench PBS fluorescence in vitro, surpassing the quenching ability of the OCP. This is consistent with computational quantum mechanics/molecular mechanics results. Interestingly, when using a maximum quenching concentration of OCP with PBSs, HCP5 addition further increases PBS quenching. Our results provide mechanistic insight into the quenching capacity and roles of HCP4 and HCP5 in cyanobacteria, suggesting that they are more than simply functionally redundant to the OCP.

Sheppard, Damien I.↗
DOE OSTI2020

Stacking Domain Wall Magnons in Twisted van der Waals Magnets

In this report using bilayer CrI 3 as an example, we demonstrate that stacking domain walls in van der Waals magnets can host one-dimensional (1D) magnon channels, which have lower energies than bulk magnons. Interestingly, some magnon channels are hidden in magnetically homogeneous background and can only be inferred with the knowledge of stacking domain walls. Compared to 1D magnons confined in magnetic domain walls, 1D magnons in stacking domain walls are more stable against external perturbations. We show that the relaxed moiré superlattices of small-angle twisted bilayer CrI 3 is a natural realization of stacking domain walls and host interconnected moiré magnon network. Our Letter reveals the importance of stacking domain walls in understanding magnetic properties of van der Waals magnets and extends the scope of stacking engineering to magnetic dynamics.

2-dimensional system↗
DOE OSTI2025

Enhanced domain dynamics in alternating current poled rhombohedral Pb(Mg 1/3 Nb 2/3 )O 3 –PbTiO 3 single crystals

Abstract The understanding of domain dynamics in ferroelectric materials is crucial for optimizing their performance in piezoelectric and electro‐optic applications. Although previous studies have focused on static domain structures and macroscopic characteristics, the time‐resolved approach of domains remains largely unexplored. In this study, we compare the dynamic responses of direct current (DC) and alternating current (AC) poled [001]‐oriented rhombohedral Pb(Mg 1/3 Nb 2/3 )O 3 –PbTiO 3 (PMN–PT) single crystals using X‐ray photon correlation spectroscopy (XPCS) during the application of external electric fields. Our results demonstrate that the AC‐poled sample exhibit enhanced reconfiguration of domain variants in response to driving fields compared to the DC‐poled counterpart, as evidenced by accelerated correlation decay and faster relaxation time. This phenomenon is attributed to enhanced reversible domain wall motion achieved through AC poling, which facilitates field‐induced domain realignment. These findings provide insight into the relationship between dynamics and macroscopic properties in relaxor‐PT single crystals for high‐performance applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Temperature modulation of CAMTA3 gene induction activity is mediated through the DNA binding domain

The calmodulin-binding transcription activator (CAMTA) proteins of Arabidopsis thaliana play a major role in cold acclimation, contributing to the rapid induction of the C-REPEAT BINDING FACTOR (CBF) genes and other genes that impart freezing tolerance in plants exposed to cold temperature (4°C). The goal of this study was to better understand how the gene induction activity of CAMTA3 is modulated by temperature. Our results indicate that a severely truncated version of CAMTA3, CAMTA3 334 , which includes the N-terminal CG-1 DNA binding domain and a newly identified transcriptional activation domain (TAD), was able to rapidly induce the expression of CBF2 and two newly identified target genes, EXPANSIN-LIKE A1 (EXPL1) and NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3), in response to cold temperature. Additionally, CAMTA3 334 was able to restore freezing tolerance when expressed in a camta23 double mutant. The ability of CAMTA3 and CAMTA3 334 to induce target genes at cold temperature did not involve increased levels of these proteins or increased binding of these proteins to target gene promoters in cold-treated plants. Rather, domain-swapping experiments indicated that the CAMTA3 CG-1 domain conferred temperature dependence to the ability of the CAMTA3 TAD to induce gene expression. The CG-1 domain also enabled the TAD to induce the expression of target genes at a moderate temperature (22°C) in response to cycloheximide treatment, consistent with the TAD activity not being intrinsically temperature dependent. We propose a working model in which the temperature modulation of CAMTA3 gene induction activity occurs independently from the C-terminal calmodulin-binding domains that previously have been proposed to activate CAMTA3 transcriptional activity in response to cold temperature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Real-space observation of fluctuating antiferromagnetic domains

Magnetic domains play a fundamental role in physics of magnetism and its technological applications. Dynamics of antiferromagnetic domains is poorly understood, although antiferromagnets are expected to be extensively used in future electronic devices wherein it determines the stability and operational speed. Dynamics of antiferromagnets also features prominently in the studies of topological quantum matter. Real-space imaging of fluctuating antiferromagnetic domains is therefore highly desired but has never been demonstrated. We use coherent x-ray diffraction to obtain videos of fluctuating micrometer-scale antiferromagnetic domains in Ni 2 MnTeO 6 on time scales from 10 -1 to 10 3 s. In the collinear phase, thermally activated domain wall motion is observed in the vicinity of the Néel temperature. Unexpectedly, the fluctuations persist through the full range of the higher-temperature helical phase. These observations illustrate the high potential significance of the dynamic domain imaging in phase transition studies and in magnetic device research.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Multi-domain automated patterning of DNA-functionalized hydrogels

DNA-functionalized hydrogels are capable of sensing oligonucleotides, proteins, and small molecules, and specific DNA sequences sensed in the hydrogels’ environment can induce changes in these hydrogels’ shape and fluorescence. Fabricating DNA-functionalized hydrogel architectures with multiple domains could make it possible to sense multiple molecules and undergo more complicated macroscopic changes, such as changing fluorescence or changing the shapes of regions of the hydrogel architecture. However, automatically fabricating multi-domain DNA-functionalized hydrogel architectures, capable of enabling the construction of hydrogel architectures with tens to hundreds of different domains, presents a significant challenge. We describe a platform for fabricating multi-domain DNA-functionalized hydrogels automatically at the micron scale, where reaction and diffusion processes can be coupled to program material behavior. Using this platform, the hydrogels’ material properties, such as shape and fluorescence, can be programmed, and the fabricated hydrogels can sense their environment. DNA-functionalized hydrogel architectures with domain sizes as small as 10 microns and with up to 4 different types of domains can be automatically fabricated using ink volumes as low as 50 μL. We also demonstrate that hydrogels fabricated using this platform exhibit responses similar to those of DNA-functionalized hydrogels fabricated using other methods by demonstrating that DNA sequences can hybridize within them and that they can undergo DNA sequence-induced shape change.

Rubanov, Moshe (ORCID:0000000180507407)↗
DOE OSTI2024

CFT and lattice correlators near an RG domain wall between minimal models

Conformal interfaces separating two conformal field theories (CFTs) provide maps between different CFTs, and naturally exist in nature as domain walls between different phases. One particularly interesting construction of a conformal interface is the renormalization group (RG) domain wall between CFTs. For a given Virasoro minimal model \mathcal{M}_{k+3,k+2} ℳ k + 3 , k + 2 , an RG domain wall can be generated by a specific deformation which triggers an RG flow towards its adjacent Virasoro minimal model \mathcal{M}_{k+2,k+1} ℳ k + 2 , k + 1 with the deformation turned on over part of the space. An algebraic construction of this domain wall was proposed by Gaiotto in [J. High Energy Phys. 12, 103 (2012)]. In this paper, we will provide a study of this RG domain wall for the minimal case k=2 k = 2 , which can be thought of as a nonperturbative check of the construction. In this case the wall is separating the Tricritical Ising Model (TIM) CFT and the Ising Model (IM) CFT. We will check the analytical results of correlation functions from the RG brane construction with the numerical density matrix renormalization group (DMRG) calculation using a lattice model proposed in [arXiv.1206.1332, Science 344, 280 (2014)], and find a perfect agreement. We comment on possible experimental realizations of this RG domain wall.

Cogburn, Cameron V.↗
DOE OSTI2020

A general framework for substructuring-based domain decomposition methods for models having nonlocal interactions [minus appendix B]

A rigorous mathematical framework is provided for a substructuring-based domain-decomposition approach for nonlocal problems that feature interactions between points separated by a finite distance. Here, by substructuring it is meant that a traditional geometric configuration for local partial differential equation problems is used in which a computational domain is subdivided into non-overlapping subdomains. In the nonlocal setting, this approach is substructuring-based in the sense that those subdomains interact with neighboring domains over interface regions having finite volume, in contrast to the local PDE setting in which interfaces are lower dimensional manifolds separating abutting subdomains Key results include the equivalence between the global, single-domain nonlocal problem and its multi-domain reformulation, both at the continuous and discrete levels. These results provide the rigorous foundation necessary for the development of efficient solution strategies for nonlocal domain-decomposition methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization

Introduction: Numerous X-ray crystal structures of the c-Src SH3 domain have provideda large sampling of atomic-level information for this important signaling domain. Multiple crystalforms have been reported, with variable crystal lattice contacts and chemical crystallizationconditions. Materials and Methods: We crystallized the c-Src SH3 domain in a crystallization buffercontaining NiCl2. Results: A unique crystal structure of the Src SH3 domain in the trigonal space group H32 isdetermined to 1.45 Å resolution. Crystal packing and anomalous scattering reveal that this crystalform is mediated by two ordered nickel ions provided by the crystallization buffer. Nickelcoordination occurs in a 2:2 stoichiometry, which dimerizes two SH3 domain monomers across apseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, asurface-exposed histidine residue, and ordered water molecules. Discussion: This study provides an example of metal-mediated crystallization and metal binding byN-terminal protein residues, contrasting with the Amino-Terminal Copper and Nickel Binding(ATCUN) motif. Conclusion: Alternative avenues help widen the potential for future crystallography-based studiesof the c-Src SH3 domain.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Modeling of Induction Motors and Variable Speed Drives for Multi-Domain System Simulations Using Modelica and the OpenIPSL Library

This paper introduces an innovative method for characterizing, implementing, and validating both three-phase and single-phase induction motor models, accompanied by a variable speed drive model. The primary goal is to investigate interactions between the electrical power grid and other dynamic domains (e.g., thermofluidic) that impact motor/load drive behavior. Our approach involves establishing a mechanical interface based on a physically meaningful equation linking motor torque/speed to the electrical model in the phasor domain. This allows seamless integration of diverse domain subsystems into a unified multi-domain model using Modelica v4.0.0 and the OpenIPSL library v3.0.1, overcoming co-simulation limitations. The proposed model, which requires only one Modelica-compliant tool for simulation, introduces additional dynamics through the mechanical interface, enabling explicit simulation of load disturbances based on constitutive physics. This deepens our understanding of dynamic interactions between the electrical power domain and other subsystems connected through the motor. We detail the modeled components using mathematical equations and textual descriptions, emphasizing the Modelica modeling approach. Simulation examples validate the implementation, demonstrating the multi-domain modeling capabilities of the newly developed components.

Computer Science↗
DOE OSTI2020

Structure of the Diphtheria Toxin at Acidic pH: Implications for the Conformational Switching of the Translocation Domain

Diphtheria toxin, an exotoxin secreted by Corynebacterium that causes disease in humans by inhibiting protein synthesis, enters the cell via receptor-mediated endocytosis. The subsequent endosomal acidification triggers a series of conformational changes, resulting in the refolding and membrane insertion of the translocation (T-)domain and ultimately leading to the translocation of the catalytic domain into the cytoplasm. Here, we use X-ray crystallography along with circular dichroism and fluorescence spectroscopy to gain insight into the mechanism of the early stages of pH-dependent conformational transition. For the first time, we present the high-resolution structure of the diphtheria toxin at a mildly acidic pH (5–6) and compare it to the structure at neutral pH (7). We demonstrate that neither catalytic nor receptor-binding domains change their structure upon this acidification, while the T-domain undergoes a conformational change that results in the unfolding of the TH2–3 helices. Surprisingly, the TH1 helix maintains its conformation in the crystal of the full-length toxin even at pH 5. This contrasts with the evidence from the new and previously published data, obtained by spectroscopic measurements and molecular dynamics computer simulations, which indicate the refolding of TH1 upon the acidification of the isolated T-domain. The overall results imply that the membrane interactions of the T-domain are critical in ensuring the proper conformational changes required for the preparation of the diphtheria toxin for the cellular entry.

59 BASIC BIOLOGICAL SCIENCES↗