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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

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

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

59 BASIC BIOLOGICAL SCIENCES↗
DOE 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 OSTI2026

The Novel Carbapenem, JDB/PQ-1-219, Has Potent Broad Spectrum Activity against Multi-Drug Resistant Acinetobacter baumannii

Carbapenem resistance in Acinetobacter baumannii, driven largely by class D, along with class A and class B β- lactamases, has severely compromised the utility of these last resort antibiotics. As a result, infections caused by such pathogens are characterized by extremely high mortality rates. Here we describe the antimicrobial activity of the novel C5 methyl-substituted carbapenem JDB/PQ-1−219 against multidrug resistant A. baumannii and the mechanism of its interaction with its major carbapenemase, OXA-23. JDB/PQ-1-219 exhibits potent antimicrobial activity against A. baumannii producing various carbapenemases, with MICs that are all in the clinically susceptible range. The compound has unrestricted ingress through porins and avoids egress by efflux pumps, a unique property when compared to all commercial carbapenems. Kinetic experiments demonstrated that unlike for other carbapenems, acylation of OXA-23 by JDB/ PQ-1-219 is monophasic, and mass spectrometry studies showed that this results from the conversion of all enzyme into a reversible tetrahedral intermediate which gradually transitions into the stable acyl-enzyme complex. No deacylation of this complex is observed over a physiologically relevant time period, making JDB/PQ-1−219 an extremely potent inhibitor of OXA-23. Time-resolved crystallography revealed fine details of active site dynamics, leading to complete inhibition of the enzyme. Together, these studies identify JDB/PQ-1-219 as a uniquely effective novel carbapenem with clinically significant levels of activity against multidrug resistant A. baumannii.

Acinetobacter baumannii↗
DOE OSTI2025

Dual mechanism of the OXA-23 carbapenemase inhibition by the carbapenem NA-1-157

Carbapenem-resistant Acinetobacter baumannii continues to be a leading cause of life-threatening infections that result in high mortality rates. The major cause of carbapenem resistance in this pathogen is the production of class D carbapenemases, enzymes that inactivate the last resort carbapenem antibiotics, thus significantly diminishing the available therapeutic options. In this study, we evaluated the interaction of OXA-23, the most widely disseminated class D carbapenemase in A. baumannii clinical isolates, with the atypically modified carbapenem, NA-1-157. The MICs of this compound against strains producing OXA-23 were reduced from highly resistant levels observed for the commercial carbapenems meropenem and imipenem (16–128 µg/mL) to sensitive or intermediate levels (2–4 µg/mL). Kinetic studies showed that NA-1-157 inhibits the enzyme due to a significant decrease (>2,000-fold) in the deacylation rate relative to its closest structural analog, meropenem. Structural studies and molecular dynamics simulations demonstrated that inhibition is caused by both the inability of a water molecule to get close enough to the scissile bond to perform deacylation and by partial decarboxylation of the catalytic lysine residue upon formation of the acyl-enzyme intermediate.

Acinetobacter baumannii↗
DOE OSTI2024

Decarboxylation of the Catalytic Lysine Residue by the C5α-Methyl-Substituted Carbapenem NA-1-157 Leads to Potent Inhibition of the OXA-58 Carbapenemase

Antibiotic resistance in bacteria is a major global health concern. The wide spread of carbapenemases, bacterial enzymes that degrade the last-resort carbapenem antibiotics, is responsible for multidrug resistance in bacterial pathogens and has further significantly exacerbated this problem. Acinetobacter baumannii is one of the leading nosocomial pathogens due to the acquisition and wide dissemination of carbapenem-hydrolyzing class D β-lactamases, which have dramatically diminished available therapeutic options. Thus, new antibiotics that are active against multidrug-resistantA. baumannii and carbapenemase inhibitors are urgently needed. Here we report characterization of the interaction of the C5α-methyl-substituted carbapenem NA-1-157 with one of the clinically important class D carbapenemases, OXA-58. Antibiotic susceptibility testing shows that the compound is more potent than commercial carbapenems against OXA-58-producingA. baumannii, with a clinically sensitive MIC value of 1 μg/mL. Kinetic studies demonstrate that NA-1-157 is a very poor substrate of the enzyme due mainly to a significantly reduced deacylation rate. Mass spectrometry analysis shows that inhibition of OXA-58 by NA-1-157 proceeds through both the classical acyl-enzyme intermediate and a reversible covalent species. Time-resolved X-ray crystallographic studies reveal that upon acylation of the enzyme, the compound causes progressive decarboxylation of the catalytic lysine residue, thus severely impairing deacylation. Overall, this study demonstrates that the carbapenem NA-1-157 is highly resistant to degradation by the OXA-58 carbapenemase.

Acinetobactor↗
DOE OSTI2024

Quantum criticality in the anisotropic spin-chain antiferromagnet Ca 2 ⁢CoH 2 ⁢(SeO 3 ) 4

Here, the quantum criticality of an XXZ-type spin chain antiferromagnet Ca 2 ⁢CoH 2 ⁢(SeO 3 ) 4 , subjected to an external magnetic field, was investigated through ultralow-temperature specific heat, magnetocaloric effect, and magnetic susceptibility measurements. In the absence of an external magnetic field, the system undergoes an antiferromagnetic phase transition at T N = 1.42K. The application of an external field gradually suppresses the antiferromagnetic order. Furthermore, an additional phase emerges in the intermediate field range when the zero-field antiferromagnetic order is suppressed, resulting in a quantum critical point at B s ≈ 2.55T. Near this field-induced quantum critical point, universal scaling behaviors are observed, characterized by the universality class parameters d=1, v=1/2, and z=2.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Evolution of carbapenemase activity in the class C β-lactamase ADC-1

Antibiotic resistance in bacteria poses a significant threat to public health. Among dozens of available antimicrobial agents, carbapenems are used as drugs of choice for the treatment of serious infections caused by pathogens resistant to other antibiotics. However, their usefulness has been severely compromised due to the emergence and wide spread of carbapenem-resistant clinical isolates worldwide. High-level resistance to carbapenems in bacteria is mediated by the production of β-lactamases from three molecular classes, A, B, and D, but not by class C enzymes. In this study, we selected a triple mutant of the intrinsic class C Acinetobacter-derived cephalosporinase ADC-1 (ADC-1 TM ) that confers high-level resistance to the carbapenems meropenem, ertapenem, and doripenem. Kinetic experiments demonstrated that the apparent binding affinity, along with the acylation and deacylation rates, were all improved for the mutant enzyme. X-ray crystallography, molecular docking, and molecular dynamics simulations revealed that the amino acid substitutions in ADC-1 TM produce significant changes in the enzyme active site architecture and binding mode of the carbapenem ertapenem. These changes allow for better positioning of a deacylating water for nucleophilic attack, thus explaining the significantly improved rate of ertapenem deacylation by ADC-1 TM . In this study, we showed for the first time that a class C β-lactamase can produce high-level resistance to carbapenem antibiotics, which underlines the potential for enzymes of this class to evolve such resistance and could further exacerbate the problem of antibiotic resistance in bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Hidden orders and phase transitions for the fully packed quantum loop model on the triangular lattice

Abstract Quantum loop and dimer models are prototypical correlated systems with local constraints, which are not only intimately connected to lattice gauge theories and topological orders but are also widely applicable to the broad research areas of quantum materials and quantum simulation. Employing our sweeping cluster quantum Monte Carlo algorithm, we reveal the complete phase diagram of the triangular-lattice fully packed quantum loop model. Apart from the known lattice nematic (LN) solid and the even$${{\mathbb{Z}}}_{2}$$ Z 2 quantum spin liquid (QSL) phases, we discover a hidden vison plaquette (VP) phase, which had been overlooked and misinterpreted as a QSL for more than a decade. Moreover, the VP-to-QSL continuous transition belongs to the (2 + 1)D cubic * universality class, which offers a lattice realization of the (fractionalized) cubic fixed point that had long been considered as irrelevant towards the O(3) symmetry until corrected recently by conformal bootstrap calculations. Our results are therefore of relevance to recent developments in both experiments and theory, and facilitate further investigations of hidden phases and transitions.

Physics↗
DOE OSTI2024

Effect of Acid Etching Time in Ti 3 C 2 MXene’s Interlayer Spacing and Conductivity

Materials with sheet-like morphologies often form interconnected networks of layers or flakes, offering continuous channels for electron and ion transport in electrochemical energy storage applications. One such material is the recently discovered class of 2-D transition metal carbides/nitrides, called MXene, whose general formula is M n+1 X n T x (where M = transition metal; n = 1, 2, or 3; X = carbon or nitrogen; and T x = termination group such as –F, –OH, and/or =O). Ti 3 C 2 , one of the most studied MXene, can be synthesized by selectively etching the aluminum layer in Ti 3 AlC 2 (also called MAX phase). The most straightforward technique to exfoliate this layer is by wet-chemical etching with high-concentration hydrofluoric acid (HF). In this study, the effect of etching time on the morphology, interlayer spacing, and electrical conductivity of the resultant MXene was studied.

25 ENERGY STORAGE↗
DOE OSTI2026

Collins asymmetries for pion-in-jet production in polarized ℓp collisions at the EIC

We study Collins azimuthal asymmetries for pion-in-jet production in polarized lepton-proton collisions, extending previous analyses of polarized pp scattering to a complementary and theoretically simpler process. We keep adopting a simplified transverse momentum dependent (TMD) approach, with a collinear configuration for the initial state, and employ the transversity and Collins fragmentation functions as extracted from semi-inclusive deep inelastic scattering and $e^{+}e^{-}$ annihilation processes. We then compute azimuthal asymmetries for the Electron-Ion Collider (EIC) kinematics, both within a leading order (LO) approach and by including quasireal photon exchange in the Weizsäcker-Williams approximation. Although this contribution is relevant in the whole kinematical range explored, it does not spoil the dominance of quark-initiated channels, leaving only a marginal role to their gluon counterparts. In this respect, Collins asymmetries in lepton-proton processes allow for a much clearer access to the transversity distribution, including its sea-quark component. As we will argue, a comparison with future EIC data could represent a further step in testing the hypothesis of the universality of the Collins function as well as of the TMD factorization for this class of processes.

Azimuthal asymmetries↗
DOE OSTI2025

La 2 ⁢O 3 ⁢Mn 2 ⁢Se 2 : A correlated insulating layered d-wave altermagnet

Altermagnets represent a new class of magnetic phases without net magnetization, invariant under a combination of rotation and time reversal. Unlike conventional collinear antiferromagnets (AFM), altermagnets could lead to new correlated states and important material properties deriving from their nonrelativistic spin-split band structure. Indeed, they serve as the magnetic analogue of unconventional superconductors and can yield spin-polarized electrical currents in the absence of external magnetic fields, making them promising candidates for next-generation spintronics. Here, we report altermagnetism in the correlated insulator, magnetically ordered tetragonal oxychalcogenide, L⁢a 2 ⁢O 3⁢ M⁢n 2 ⁢S⁢e 2 . Symmetry analysis reveals a 𝑑 𝑥 2 −𝑦 2 -wave-like spin-momentum locking arising from the M⁢n 2 ⁢O Lieb lattice, supported by density functional theory (DFT) calculations. Magnetic measurements confirm the AFM transition below ∼166K while neutron pair distribution function analysis reveals a 2D short-range magnetic order that persists above the Néel temperature. Single crystals are grown and characterized using x-ray diffraction, optical and electron microscopy, and micro-Raman spectroscopy to confirm the crystal structure, stoichiometry, and uniformity. Furthermore, our findings establish L⁢a 2⁢ O 3 ⁢M⁢n 2⁢ S⁢e 2 as a model altermagnetic system realized on a Lieb lattice.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Predictions of m/n = 2/1 neoclassical tearing mode stabilization via high field side lower hybrid current drive on the DIII-D tokamak

Neoclassical tearing modes (NTMs) are a class of resistive instabilities that arise in tokamaks at rational surfaces and form magnetic islands. These islands flatten the pressure gradient, reducing plasma performance and may lead to disruptions if they grow large enough. Driving current within the island can stabilize the NTM, which has been achieved with electron cyclotron current drive (ECCD) on multiple devices. An alternative to ECCD is lower hybrid current drive (LHCD), which offers the advantages of increased current drive efficiency and reduced system cost. LHCD has been viewed as poorly suited for NTM suppression due to the large spatial extent of the driven current when in the multi-pass absorption regime (as has been the case in all past LHCD experiments). However, the driven current is more localized when in the single pass absorption regime, as is predicted for the DIII-D high field side (HFS) LHCD experiment. This work evaluates the feasibility of NTM suppression with HFS LHCD on DIII-D by predicting the island growth rate for a set of representative DIII-D plasmas via the modified Rutherford equation with and without the application of LHCD. In these plasmas, NTM suppression is achieved at reasonable power levels, even with finite misalignment between LH current and the island. The effect of current condensation was included and found to be most significant at smaller island sizes, assuming an experimentally typical temperature perturbation amplitude of 10%.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Multiplicity dependence of charm baryon and charm meson production in pPb collisions at $\sqrt{s_{NN}} = 8.16$ TeV

Measurements of the production yields of charm baryons (Λ$^+_c$ ) and charm mesons (D 0 ) in proton-lead collisions at a nucleon-nucleon center-of-mass energy of 8.16 TeV are presented. The data were collected in 2016 with the CMS experiment and correspond to an integrated luminosity of 186 nb -1 . The Λ$^+_c$ baryon is reconstructed from the decay channel Λ$^+_c$ → K$^0_S$p , while the D 0 meson is reconstructed via D 0 → K - π + . The Λ$^+_c$ baryon and D 0 meson yields are extracted in several charged-particle multiplicity classes. No strong multiplicity dependence of the Λ$^+_c$-to-D 0 yield ratio is observed, unlike the observed strange baryon to strange meson yield ratio of $Λ/\bar{Λ}$to K$^0_S$, which shows a strong multiplicity dependence. This observation indicates different mechanisms for the multiplicity evolution of hadronization processes for charm and strange quarks and provides new constraints to the understanding of heavy flavor production and collectivity in small collision systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Progress in the development of the community Particle Accelerator Lattice Standard (PALS)

The Particle Accelerator Lattice Standard (PALS) is a community effort to create an open standard to promote lattice information exchange for particle accelerators. PALS development is a community-wide international effort involving accelerator physicists from multiple institutions. While it started as a lattice standard for beam dynamics simulations, it is now being extended to support other particle accelerator activities, in particular accelerator operation. With new accelerators that are becoming more complex, larger collaborations and the increasing imprint of artificial intelligence in all accelerator activities (from design to operation to workforce development), the imperative for a common, standardized accelerator ontology has been transitioning from “nice-to-have” to “must-have”. We will present the status of the project, its relations to other projects, including to two of the particle accelerator projects of the newly announced US DOE Genesis Mission: the Multi-Office Accelerator Team (MOAT) project and the Nuclear physics AI-Ready Accelerator Data (NARAD) project.

Brynes, A. [Science and Technology Facilities Coun↗
DOE OSTI2025

Spectroscopy of the Hamburg Meteorite, Michigan H4

Spectroscopic studies of the Hamburg (Michigan H4) meteorite using visible–near-infrared (VNIR), mid-infrared (MIR), Raman, and Mössbauer data reproduce the results of more conventional laboratory measurements of petrology and geochemistry. This combination provides general information on the mineral modes of silicates, although spectroscopy was performed on different splits of this meteorite, and varying results may be explained by heterogeneity that is typical of ordinary chondrites. Raman also detects small features assigned to first-order D and G carbon bands, while Mössbauer data show the presence of Fe oxides and carbides. The electron microprobe (EMPA) composition of olivine in this meteorite is accurately measured to be Fo 81.3 , while MIR and Raman closely agree with Fo 80 and Fo 82 , respectively, and Mössbauer, at Fo 60 − Fo 70 , is in the ballpark. Similarly, P. R. Heck et al. report pyroxenes with compositions of Fs 16 Wo 1 , while Raman suggests a somewhat similar composition of Fs 28 Wo 0 . Both VNIR and MIR detect the presence of small amounts of feldspar, while EMPA identifies its composition as An 14 Ab 8 Or 5 . VNIR data were matched to spectral libraries of meteorite and asteroid data and shown to closely match other L and H meteorites. The best spectral matches to the Michigan H4 meteorite are to asteroid classes L/H/LL/URE, EH/EL/AUB, and CO/CV from M. D. Dyar et al.; objects in this group are intermediate in semimajor axis lengths for their orbits. The results highlight the strengths and weaknesses of each technique and show their collective strength when applied together to a single meteorite sample.

58 GEOSCIENCES↗
DOE OSTI2026

Spectro-Microscopic Analysis of Soot Particle Composition and Source Attribution

Ambient soot particles significantly impact Earth’s radiative balance, human health, and atmospheric visibility. Their microstructural properties depend on formation and aging mechanisms, which vary by emission source and atmospheric processes. Hence, accurately identifying sources of soot enhances our understanding of their physicochemical properties and atmospheric implications. This study used a multi-modal approach to characterize and attribute sources of submicron soot particles collected in Israel during new particle formation events, biomass burning episodes, and background atmospheric conditions. Synchrotron-based X-ray microscopy was used to map soot (elemental carbon), organic carbon, and inorganic species. Implemented atomic force microscopy showed highly diverse phase states, with soot consistently exhibiting a solid-like phase. Automated µ-Raman analysis was subsequently performed on ~690 particles, identifying three soot classes based on spectral features corresponding to the "Defect" (D) and "Graphite" (G) bands of soot. We applied two-peak and five-peak fitting approaches to deconvolute the “Defect” peaks (D1, D2, D3, and D4) and G band from average Raman, revealing varying degrees of graphitic order. The degree of graphitic order was determined from metrics such as the D3 peak area, often observed when soot was internally mixed with organic material. Raman spectral features, along with temporal variations in particle classes contributions, suggest that Particle Type 1 corresponds to traffic related soot and Particle Type 2 to less graphitic soot from biomass burning, while Particle Type 3 is associated with more heterogeneous particulate representative of soot-OC mixtures emitted during new particle formation and biomass burning episodes.

Rivera-Adorno, Felipe (ORCID:0000000273557999)↗
DOE OSTI2024

High-Entropy Alloy R&D for Accelerator Beam Window Applications

High-Entropy Alloys are a class of novel material that can offer improved resistance to beam-induced radiation damage and thermal shock. Development of these new alloys to serve as beam windows in multi-megawatt accelerator target applications is ongoing at Fermilab. Currently we are investigating AlCoCrMnTiV alloy systems of 4-6 components for service as beam windows; these compositions are predicted by CALPHAD simulation to have a low density and single-phase BCC crystal structure. The microstructures of these systems are being studied by electron microscopy techniques such as energy dispersive X-ray spectroscopy (EDS) to determine elemental homogeneity and composition, electron backscatter diffraction (EBSD) to quantify grain structure and orientation, and transmission electron microscopy (TEM) to observe defect structures and precipitate formation; nanoindentation is used to probe microstructural mechanical properties. Initial bulk property characterization utilizes differential scanning calorimetry to quantify specific heat capacity (cp), dilatometry to determine the coefficient of thermal expansion (CTE), and time-domain thermoreflectance (TDTR) to measure thermal conductivity (K). A miniature tensile testing apparatus is also being developed to test tensile properties. Post-irradiation examination is currently ongoing for several of these compositions that have been irradiated by low-energy ions to damage levels and at a temperature relevant to beam window applications at future next-generation accelerator facilities. This talk will briefly describe the alloy design and synthesis before going into more depth covering microstructural pre-characterization, and post-irradiation examination results from low-energy ion irradiated specimens. This will be followed by the plans for alloy down selection and future prototypic proton irradiations.

43 PARTICLE ACCELERATORS↗