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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Causal structure of interacting Weyl fermions in condensed matter systems

Abstract The spacetime light cone is central to the definition of causality in the theory of relativity. Recently, links between relativistic and condensed matter physics have been uncovered, where relativistic particles can emerge as quasiparticles in the energy-momentum space of matter. Here, we unveil an energy-momentum analogue of the spacetime light cone by mapping time to energy, space to momentum, and the light cone to the Weyl cone. We show that two Weyl quasiparticles can only interact to open a global energy gap if they lie in each other’s energy-momentum dispersion cones–analogous to two events that can only have a causal connection if they lie in each other’s light cones. Moreover, we demonstrate that the causality of surface chiral modes in quantum matter is entangled with the causality of bulk Weyl fermions. Furthermore, we identify a unique quantum horizon region and an associated ‘thick horizon’ in the emergent causal structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Gas–Phase Preparation of the 14π Hückel Polycyclic Aromatic Anthracene and Phenanthrene Isomers (C 14 H 10 ) via the Propargyl Addition–BenzAnnulation (PABA) Mechanism

Polycyclic aromatic hydrocarbons (PAHs) imply the missing link between resonantly stabilized free radicals and carbonaceous nanoparticles, commonly referred to as soot particles in combustion systems and interstellar grains in deep space. Whereas gas phase formation pathways to the simplest PAH – naphthalene (C 10 H 8 ) – are beginning to emerge, reaction pathways leading to the synthesis of the 14π Hückel aromatic PAHs anthracene and phenanthrene (C 14 H 10 ) are still incomplete. Here, by utilizing a chemical microreactor in conjunction with vacuum ultraviolet (VUV) photoionization (PI) of the products followed by detection of the ions in a reflectron time-of-flight mass spectrometer (ReTOF-MS), the reaction between the 1'- and 2'-methylnaphthyl radicals (C 11 H 9 •) with the propargyl radical (C 3 H 3 •) accesses anthracene (C 14 H 10 ) and phenanthrene (C 14 H 10 ) via the Propargyl Addition–BenzAnnulation (PABA) mechanism in conjunction with a hydrogen assisted isomerization. Furthermore, the preferential formation of the thermodynamically less stable anthracene isomer compared to phenanthrene suggests a kinetic, rather than a thermodynamics control of the reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Kinetics of amorphous defect phases measured through ultrafast nanocalorimetry

Recognition of the role of extended defects on local phase transitions has led to the conceptualization of the defect phase, localized thermodynamically stable interfacial states that have since been applied in a myriad of material systems to realize significant enhancements in material properties. Here, we explore the kinetics of grain boundary confined amorphous defect phases, utilizing the high temperature and scanning rates afforded by ultrafast differential scanning calorimetry to apply targeted annealing/quenching treatments at high rates capable of capturing the kinetic behavior. Four Al-based nanocrystalline alloys, including two binary systems, Al–Ni and Al–Y, and two ternary systems, Al–Mg–Y and Al–Ni–Y, are selected to probe the materials design space (enthalpy of mixing, enthalpy of segregation, chemical complexity) for amorphous defect phase formation and stability, with correlative transmission electron microscopy applied to link phase evolution and grain stability to nanocalorimetry signatures. A series of targeted isothermal annealing heat treatments is utilized to construct a Time–Temperature-Transformation curve for the Al–Ni system, from which a critical cooling rate of 2400 °C/s was determined for the grain boundary confined disordered-to-ordered transition. Finally, a thermal profile consisting of 1000 repeated annealing sequences was created to quantify the recovery of the amorphous defect phase following sequential annealing treatments, with results indicating remarkable microstructural stability after annealing at temperatures above 90% of the melting temperature. This work contributes to a deeper understanding of grain boundary localized thermodynamics and kinetics, with potential implications for the design and optimization of advanced materials with enhanced stability and performance.

Amorphous defect phases↗
DOE OSTI2025

Noncollinear ground states of solids with a source-free exchange correlation functional

In this paper, we expand upon the source-free (SF) exchange correlation (XC) functional developed by Sangeeta Sharma and coworkers to plane-wave density functional theory (DFT) based on the projector augmented wave (PAW) method. This constraint is implemented by the current authors within the VASP source code, using a fast Poisson solver that capitalizes on the parallel three-dimensional fast Fourier transforms (FFTs) implemented in VASP. Using this modified XC functional, we explore the improved convergence behavior that results from applying this constraint to the GGA-PBE+U+J functional. In the process, we compare the noncollinear magnetic ground state computed by each functional and their SF counterpart for a select number of magnetic materials in order to provide a metric for comparing with experimentally determined magnetic orderings. We observe significantly improved agreement with experimentally measured magnetic ground-state structures after applying the source-free constraint. Furthermore, we explore the importance of considering probability current densities in spin-polarized systems, even under no applied field. We analyze the XC torque as well, in order to provide theoretical and computational analyses of the net XC magnetic torque induced by the source-free constraint. Along these lines, we highlight the importance of properly considering the real-space integral of the source-free local magnetic XC field. Our analyses on probability currents, net torque, and constant terms draw additional links to the rich body of previous research on spin-current density functional theory (SCDFT), and pave the way for future extensions and corrections to the SF corrected XC functional.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Understanding Event Trajectories Across Massive Temporal Datasets with Word Embeddings and Visualization

In collaboration with researchers from Virginia Tech, Savannah River National Laboratory has continued development of a natural language processing pipeline to identify and extract events of interest from massive open data sources in the domain of worldwide state-sponsored civil nuclear energy. The foundation of the pipeline is built on compass aligned temporal word embedding models, whereby contextual shifts are automatically identified by comparing keyword embedding vectors across successive time windows. Within the approach, a contextual shift indicates the occurrence of a potential event of interest. However, in such a broad topical domain that captures events at a global scale, across various life cycle stages, and across numerous different technology types, a user that is monitoring events may have broad interests in capturing many different event types with varying degrees of signal. As such, the quantity of information that may be returned from an automated event extraction pipeline can be substantial, requiring manual effort to sift through the information to identify any relevant bits of information. Therefore, a more streamlined workflow that aids in directing a user toward specific information at different points in time is necessary. The workflow presented here has been developed with this concept in mind, built on top of the initial prototype event extraction pipeline, whereby a user can analyze temporal text-based data sources at multiple different contextual levels to isolate key points in time and key subdomains captured within a data corpus. Using multiple corpuses that consist of approximately 7 million Tweets and 7 million news articles, the team has extended compass aligned temporal word embedding models to establish an interconnected and hierarchical structure that relates known key words of interest to documents, local topics (i.e., within a time window), and global topics across the corpuses. All of this information is packaged into a visual analytics system that is linked to the information extraction pipeline and enables a user to identify contextual information that describes the evolution of a high dimensional embedding space across time to isolate changes of interest and explore associated events. This report demonstrates the use of these analytics and a means to fuse information across multiple datasets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

A restructured and updated global soil respiration database (SRDB-V5)

Field-measured soil respiration (R S , the soil-to-atmosphere CO 2 flux) observations were compiled into a global soil respiration database (SRDB) a decade ago, a resource that has been widely used by the biogeochemistry community to advance our understanding of R S dynamics. Novel carbon cycle science questions require updated and augmented global information with better interoperability among datasets. Here, we restructured and updated the global R S database to version SRDB-V5. The updated version has all previous fields revised for consistency and simplicity, and it has several new fields to include ancillary information (e.g., R S measurement time, collar insertion depth, collar area). The new SRDB-V5 includes published papers through 2017 (800 independent studies), where total observations increased from 6633 in SRDB-V4 to 10 366 in SRDB-V5. The SRDB-V5 features more R S data published in the Russian and Chinese scientific literature and has an improved global spatio-temporal coverage and improved global climate space representation. We also restructured the database so that it has stronger interoperability with other datasets related to carbon cycle science. For instance, linking SRDB-V5 with an hourly timescale global soil respiration database (HGRsD) and a community database for continuous soil respiration (COSORE) enables researchers to explore new questions. The updated SRDB-V5 aims to be a data framework for the scientific community to share seasonal to annual field R S measurements, and it provides opportunities for the biogeochemistry community to better understand the spatial and temporal variability in R S , its components, and the overall carbon cycle.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Ultra-power-efficient heterogeneous III–V/Si MOSCAP (de-)interleavers for DWDM optical links

We discuss the design and demonstration of various III–V/Si asymmetric Mach–Zehnder interferometer (AMZI) and ring-assisted AMZI (de-)interleavers operating at O-band wavelengths with 65 GHz channel spacing. The wafer-bonded III–V/Si metal-oxide-semiconductor capacitor (MOSCAP) structure facilitates ultra-low-power phase tuning on a heterogeneous platform that allows for complete monolithic transceiver photonic integration. The second- and third-order MOSCAP AMZI (de-)interleavers exhibit cross-talk (XT) levels down to − 22 dB and − 32 dB with tuning powers of 83.0 nW and 53.0 nW, respectively. The one-, two-, and three-ring-assisted MOSCAP AMZI (de-)interleavers have XT levels down to − 27 dB, − 22 dB, and − 20 dB for tuning powers of 10.0 nW, 7220.0 nW, and 33.6 nW, respectively. The leakage current density is measured to be in the range of 1.6 – 27 μA / cm 2 . To the best of our knowledge, we have demonstrated for the first time, athermal III–V/Si MOSCAP (de-)interleavers with the lowest XT and reconfiguration power consumption on a silicon platform.

Cheung, Stanley (ORCID:0000000248860013)↗
DOE OSTI2026

Microstructure prediction for Ti-22Al-25Nb in laser powder bed fusion

This work presents a physics-informed framework for predicting solidification morphology and defect susceptibility in additively manufactured Ti–22Al–25Nb across a broad processing space. The framework integrates solidification microstructure selection (SMS) analysis with a single-track defect-based printability map to establish a unified methodology linking processing parameters to both interfacial morphology and manufacturability. Thermal gradients G and solidification rates R are first computed using the Thermo-Calc Additive Manufacturing (TC-AM) module, a finite-interface-dissipation (FID) phase-field (PF) model coupled with CALPHAD method is then employed to systematically distinguish planar and dendritic regimes as functions of $G$ and $R$. By superimposing the printability map onto the morphology projections, a comprehensive process–structure framework is obtained. Across most processing conditions, the predicted microstructure is predominantly dendritic, while planar growth emerges only under selected laser power $P$ and scan speed $v$ combinations. In addition to morphology classification, the framework quantifies the dendritic area fraction and introduces a width-based morphology descriptor to characterize the spatial extent of planar/dendritic regions within the melt pool. It provides mechanistic insight into the interplay between solidification physics and defect formation, offering practical guidance for parameter selection and microstructural control in Ti–22Al–25Nb additive manufacturing (AM).

36 MATERIALS SCIENCE↗
DOE OSTI2025

Interplay between Cation “Coloring” and Stereochemically Active Lone Pairs in AgBiS 2 Thin Films

Solution-processed AgBiS 2 thin films were fabricated using novel thiol− amine precursor inks to investigate the stereochemical activity of Bi 3+ 6s 2 lone pairs and their impact on the structure. A dual-space analysis combining Bragg diffraction and hard X-ray photoelectron spectroscopy (HAXPES) revealed a rock salt-like average structure with local distortions linked to cation coloring. Density functional theory (DFT) and crystal orbital Hamilton population (COHP) analyses confirmed that local Bi-rich and Ag-rich nanodomains amplify stereochemical activity, whereas more mixed and cation-order nanodomains are less stereochemically active. This local, nanoscopic mixing of segregated and ordered domains would indeed explain an average Fm3̅m structure that is rock salt-like and that does not manifest the full anharmonicity and noncentrosymmetry evidenced in canonical structures with stereochemical expression. These findings provide insights into the local structural and electronic complexities governing the optoelectronic properties of AgBiS 2 thin films.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Entanglement rearrangement in self-consistent nuclear structure calculations

Background: Entanglement plays a central role in a diverse array of increasingly important research areas, including quantum computation, simulation, measurement, sensing, and communication. Extensive suites of investigations have been performed to better understand entanglement in atomic and molecular quantum many-body systems, while the exploration of entanglement in the structure of nuclei and their reactions is presently in its infancy. Purpose: The goal of this work is to begin investigating the entanglement properties of nuclei from first-principles nuclear many-body calculations. We attempt to identify common features and emergent structures of entanglement that could ultimately lead to new and natural many-body schemes. With an eye toward quantum accelerators in future hybrid-supercomputers, criteria for partitioning nuclear many-body calculations into quantum and classical components may provide advantages in future large-scale computations. Along the way we look for explanations of the relative success of phenomenological models such as the nuclear shell model, and for better ways to match to low-energy nuclear effective field theories and lattice QCD calculations to nuclear many-body techniques that are based upon entanglement. Method: We explore the entanglement between single-particle states in 4 He and 6 He. The patterns of entanglement emerging from different single-particle bases are compared, and possible links with the convergence of observables are explored, in particular, ground-state energies. The nuclear wave functions are obtained by performing active-space no-core configuration-interaction calculations using a two-body nucleon-nucleon interaction derived from chiral effective field theory. Entanglement measures within single-particle bases exhibiting different degrees of complexity are determined, in particular, harmonic oscillator (HO), Hartree-Fock (HF), natural (NAT) and variational natural (VNAT) bases. Specifically, single-orbital entanglement entropy, two-orbital mutual information, and negativity are studied. Results: The entanglement structures in 4 He and 6 He are found to be more localized within NAT and VNAT bases than within a HO basis for the optimal HO parameters we have worked with. In particular a core-valence structure clearly emerges from the full no-core calculation of 6 He. Here, the two-nucleon mutual information shows that the VNAT basis, which typically exhibits good convergence properties, effectively decouples the active and inactive spaces. Conclusions: Measures of one- and two-nucleon entanglement are found to be useful in analyzing the structure of nuclear wave functions, in particular the efficacy of basis states, and may provide useful metrics toward developing more efficient schemes for ab initio computations of the structure and reactions of nuclei, and quantum many-body systems more generally.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Performance Characteristics of the BlueField-2 SmartNIC

High-performance computing (HPC) researchers have long envisioned scenarios where application workflows could be improved through the use of programmable processing elements embedded in the network fabric. Recently, vendors have introduced programmable Smart Network Interface Cards (SmartNICs) that enable computations to be offloaded to the edge of the network. There is great interest in both the HPC and high-performance data analytics (HPDA) communities in understanding the roles these devices may play in the data paths of upcoming systems. This paper focuses on characterizing both the networking and computing aspects of NVIDIA’s new BlueField-2 SmartNIC when used in a 100Gb/s Ethernet environment. For the networking evaluation we conducted multiple transfer experiments between processors located at the host, the SmartNIC, and a remote host. These tests illuminate how much effort is required to saturate the network and help estimate the processing headroom available on the SmartNIC during transfers. For the computing evaluation we used the stress-ng benchmark to compare the BlueField-2 to other servers and place realistic bounds on the types of offload operations that are appropriate for the hardware. Our findings from this work indicate that while the BlueField-2 provides a flexible means of processing data at the network’s edge, great care must be taken to not overwhelm the hardware. While the host can easily saturate the network link, the SmartNIC’s embedded processors may not have enough computing resources to sustain more than half the expected bandwidth when using kernel-space packet processing. From a computational perspective, encryption operations, memory operations under contention, and on-card IPC operations on the SmartNIC perform significantly better than the general-purpose servers used for comparisons in our experiments. Therefore, applications that mainly focus on these operations may be good candidates for offloading to the SmartNIC.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Mitochondrial Effects in the Liver of C57BL/6 Mice by Low Dose, High Energy, High Charge Irradiation

Galactic cosmic rays are primarily composed of protons (85%), helium (14%), and high charge/high energy ions (HZEs) such as 56 Fe, 28 Si, and 16 O. HZE exposure is a major risk factor for astronauts during deep-space travel due to the possibility of HZE-induced cancer. A systems biology integrated omics approach encompassing transcriptomics, proteomics, lipidomics, and functional biochemical assays was used to identify microenvironmental changes induced by HZE exposure. C57BL/6 mice were placed into six treatment groups and received the following irradiation treatments: 600 MeV/n 56 Fe (0.2 Gy), 1 GeV/n 16 O (0.2 Gy), 350 MeV/n 28 Si (0.2 Gy), 137 Cs (1.0 Gy) gamma rays, 137 Cs (3.0 Gy) gamma rays, and sham irradiation. Left liver lobes were collected at 30, 60, 120, 270, and 360 days post-irradiation. Analysis of transcriptomic and proteomic data utilizing ingenuity pathway analysis identified multiple pathways involved in mitochondrial function that were altered after HZE irradiation. Lipids also exhibited changes that were linked to mitochondrial function. Molecular assays for mitochondrial Complex I activity showed significant decreases in activity after HZE exposure. HZE-induced mitochondrial dysfunction suggests an increased risk for deep space travel. Microenvironmental and pathway analysis as performed in this research identified possible targets for countermeasures to mitigate risk.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Crosstalk between cyclophilins and T lymphocytes in coronary artery disease

Highlights: • CD147 receptor expression is elevated in T lymphocytes from CAD patients. • Intracellular CypA and B expression are augmented in T lymphocytes from CAD patients. • CypA, B and C, and IL-1β and IL-6 serum levels are increased in patients with CAD. • CypA and B levels in T lymphocytes are correlated with CypA and B serum levels, respectively. Cardiovascular diseases and atherosclerosis are currently some of the most widespread diseases of our time. Within cardiovascular disease, coronary artery disease and underlying atherosclerosis were recently linked with systemic and local inflammation. Cyclophilins participate in the initiation and progression of these inflammatory-related diseases. Cyclophilins are released into the extracellular space upon inflammatory stimuli and participate in the pathology of cardiovascular diseases. The cell surface receptor for extracellular cyclophilins, the CD147 receptor, also contributes to coronary artery disease pathogenesis. Nevertheless, the physiological relevance of cyclophilin's family and their receptor in cardiovascular diseases remains unclear. The present study aimed to better understand the role of cyclophilins in cardiovascular artery disease and their relationship with inflammation. Hence, cyclophilins and pro-inflammatory interleukins were measured in the serum of 30 subjects (divided into three groups according to coronary artery disease status: 10 patients with acute coronary syndrome, 10 patients with chronic coronary artery disease, and 10 control volunteers). In addition, cyclophilin levels and CD147 receptor expression were measured in T lymphocytes purified from these subjects. Cyclophilin A, B, and C, pro-inflammatory interleukins, and CD147 membrane expression were significantly elevated in patients with coronary artery disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Monomer-dimer tensor-network basis for qubit-regularized lattice gauge theories

Traditional SU⁡(𝑁) lattice gauge theories (LGTs) can be formulated using an orthonormal basis constructed from the irreducible representations (irreps) 𝑉 𝜆 of the SU⁡(𝑁) gauge symmetry. On a lattice, the elements of this basis are tensor networks comprising dimer tensors on the links labeled by a set of irreps {𝜆 ℓ } and monomer tensors on sites labeled by {𝜆 𝑠 }. These tensors naturally define a local site Hilbert space, ℋ$^𝑔_𝑠$, on which gauge transformations act. Gauss’s law introduces an additional index 𝛼 𝑠 =1,2,…,𝒟⁡(ℋ$^𝑔_𝑠$) that labels an orthonormal basis of the gauge-invariant subspace of ℋ$^𝑔_𝑠$. This monomer-dimer tensor-network (MDTN) basis, |{𝜆 𝑠 },{𝜆 ℓ },{𝛼 𝑠 }⟩, of the physical Hilbert space enables the construction of new qubit-regularized SU⁡(𝑁) gauge theories that are free of sign problems while preserving key features of traditional LGTs. Here, we investigate finite-temperature confinement-deconfinement transitions in a simple qubit-regularized SU(2) and SU(3) gauge theory in 𝑑 =2 and 𝑑 =3 spatial dimensions, formulated using the MDTN basis, and show that they reproduce the universal results of traditional LGTs at these transitions. Additionally, in 𝑑 =1, we demonstrate using a plaquette chain that the string tension at zero temperature can be continuously tuned to zero by adjusting a model parameter that plays the role of the gauge coupling in traditional LGTs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

A Blueprint for the Milky Way’s Stellar Populations. IV. A String of Pearls—the Galactic Starburst Sequence

We continue our series of papers on phase-space distributions of stars in the Milky Way based on photometrically derived metallicities and Gaia astrometry, with a focus on the halo-disk interface in the local volume. To exploit various photometric databases, we develop a method of empirically calibrating synthetic stellar spectra based on a comparison with observations of stellar sequences and individual stars in the Sloan Digital Sky Survey, the SkyMapper Sky Survey, and the Pan-STARRS1 surveys, overcoming band-specific corrections employed in our previous work. In addition, photometric zero-point corrections are derived to provide an internally consistent photometric system with a spatially uniform metallicity zero-point. Using our phase-space diagrams, we find a remarkably narrow sequence in the rotational velocity (v $\phi$ ) versus metallicity ([Fe/H]) space for a sample of high proper-motion stars (>25 mas yr -1 ), which runs along Gaia Sausage/Enceladus (GSE) and the Splash substructures and is linked to the disk, spanning nearly 2 dex in [Fe/H]. Notably, a rapid increase of v $\phi$ from a nearly zero net rotation to ~180 km s -1 in a narrow metallicity interval (-0.6 ≲ [Fe/H] ≲ -0.4) suggests that some of these stars emerged quickly on a short gas-depletion timescale. Through measurements of a scale height and length, we argue that these stars are distinct from those heated dynamically by mergers. This chain of high proper-motion stars provides additional support for recent discoveries suggesting that a starburst took place when the young Milky Way encountered the gas-rich GSE progenitor, which eventually led to the settling of metal-enriched gas onto the disk.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Orientation dependence of the effect of short-range ordering on the plastic deformation of a medium entropy alloy

Multi-principal-element alloys (also known as medium and high entropy alloys) offer a much larger and richer design space than conventional alloys, providing opportunities for discovering new functionalities and their governing physics. Some of these alloys exhibit an outstanding combination of high strength and ductility, linked to the activation of various deformation modes triggered by low-energy stacking faults. However, a pressing question remains: Is the plasticity of medium- and high-entropy alloys governed only by stacking fault energy, or does atomic short-range order (SRO) play a role? Here, to answer this, we investigated how SRO affects the deformation in single-crystalline NiCoCr, with previous contradictory findings. First, we established unique experimental evidence for SRO formation in bulk single crystals using high-energy synchrotron transmission X-Ray Diffraction. By tuning the degree of SRO by aging at high temperatures, twinning density and strain-induced martensitic phase transformation can be significantly increased in the [110] and [111] orientations under tension, increasing the tensile ductility; yet, no increase was observed along the [001] orientation due to lack of TWinning-Induced Plasticity (TWIP) or TRansformation-Induced Plasticity (TRIP), indicating a strong crystallographic orientation dependence. Our first-principles thermodynamic calculations unequivocally show SRO exists and governs the observed microstructural evolution and deformation hardening behavior. Here we find direct proof that SRO triggers a simultaneous TWIP and TRIP in NiCoCr, a rare microstructural evolution path. Our findings establish that the interplay of SRO and plasticity could be exploited to alter deformation modes and yield unprecedented mechanical response in medium- and high-entropy alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture

Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, a conditional fluorophore derived from GFP. It is 70% sequence-identical to the previously characterized homodimeric aptamer Corn, which binds one molecule of its cognate fluorophore DFHO at its interprotomer interface. We have now determined the Beetroot-DFAME co-crystal structure at 1.95 Å resolution, discovering that this RNA homodimer binds two molecules of the fluorophore, at sites separated by ~30 Å. In addition to this overall architectural difference, the local structures of the non-canonical, complex quadruplex cores of Beetroot and Corn are distinctly different, underscoring how subtle RNA sequence differences can give rise to unexpected structural divergence. Through structure-guided engineering, we generated a variant that has a 12-fold fluorescence activation selectivity switch toward DFHO. Beetroot and this variant form heterodimers and constitute the starting point for engineered tags whose through-space inter-fluorophore interaction could be used to monitor RNA dimerization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Protected fermionic zero modes in periodic gauge fields

It is well known that macroscopically normalizable zero-energy wave functions of spin-$\frac{1}{2}$ particles in a two-dimensional inhomogeneous magnetic field are spin-polarized and exactly calculable with degeneracy equaling the number of flux quanta linking the whole system. Here, extending this argument to massless Dirac fermions subjected to magnetic fields that have zero net flux but are doubly periodic in real space, we show that there exist only two Bloch-normalizable zero-energy eigenstates, one for each spin flavor. This result is immediately relevant to graphene multilayer systems subjected to doubly periodic strain fields, which at low energies enter the Hamiltonian as periodic pseudogauge vector potentials. Furthermore, we explore various related settings including nonlinearly dispersing band structure models and systems with singly periodic magnetic fields.

36 MATERIALS SCIENCE↗