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DOE OSTI2024

Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation

Protein turnover is critical for proteostasis, but turnover quantification is challenging, and even in well-studied E. coli, proteome-wide measurements remain scarce. Here, we quantify the turnover rates of ~3200 E. coli proteins under 13 conditions by combining heavy isotope labeling with complement reporter ion quantification and find that cytoplasmic proteins are recycled when nitrogen is limited. We use knockout experiments to assign substrates to the known cytoplasmic ATP-dependent proteases. Surprisingly, none of these proteases are responsible for the observed cytoplasmic protein degradation in nitrogen limitation, suggesting that a major proteolysis pathway in E. coli remains to be discovered. Lastly, we show that protein degradation rates are generally independent of cell division rates. Thus, we present broadly applicable technology for protein turnover measurements and provide a rich resource for protein half-lives and protease substrates in E. coli, complementary to genomics data, that will allow researchers to study the control of proteostasis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Unidirectional ray polaritons in twisted asymmetric stacks

Abstract The vast repository of van der Waals (vdW) materials supporting polaritons offers numerous possibilities to tailor electromagnetic waves at the nanoscale. The development of twistoptics—the modulation of the optical properties by twisting stacks of vdW materials—enables directional propagation of phonon polaritons (PhPs) along a single spatial direction, known as canalization. Here we demonstrate a complementary type of directional propagation of polaritons by reporting the visualization of unidirectional ray polaritons (URPs). They arise naturally in twisted hyperbolic stacks with very different thicknesses of their constituents, demonstrated for homostructures of$$\alpha$$ α -MoO 3 and heterostructures of$$\alpha$$ α -MoO 3 and$$\beta$$ β -Ga 2 O 3 . Importantly, their ray-like propagation, characterized by large momenta and constant phase, is tunable by both the twist angle and the illumination frequency. Apart from their fundamental importance, our findings introduce twisted asymmetric stacks as efficient platforms for nanoscale directional polariton propagation, opening the door for applications in nanoimaging, (bio)-sensing, or polaritonic thermal management.

Science & Technology - Other Topics↗

DOE OSTI2024

Highly multiplexed design of an allosteric transcription factor to sense new ligands

Allosteric transcription factors (aTF) regulate gene expression through conformational changes induced by small molecule binding. Although widely used as biosensors, aTFs have proven challenging to design for detecting new molecules because mutation of ligand-binding residues often disrupts allostery. Here, we develop Sensor-seq, a high-throughput platform to design and identify aTF biosensors that bind to non-native ligands. We screen a library of 17,737 variants of the aTF TtgR, a regulator of a multidrug exporter, against six non-native ligands of diverse chemical structures – four derivatives of the cancer therapeutic tamoxifen, the antimalarial drug quinine, and the opiate analog naltrexone – as well as two native flavonoid ligands, naringenin and phloretin. Sensor-seq identifies biosensors for each of these ligands with high dynamic range and diverse specificity profiles. The structure of a naltrexone-bound design shows shape-complementary methionine-aromatic interactions driving ligand specificity. To demonstrate practical utility, we develop cell-free detection systems for naltrexone and quinine. Sensor-seq enables rapid and scalable design of new biosensors, overcoming constraints of natural biosensors.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Direct observation of ultrafast cluster dynamics in supercritical carbon dioxide using X-ray Photon Correlation Spectroscopy

Supercritical fluids exhibit distinct thermodynamic and transport properties, making them of particular interest for a wide range of scientific and engineering applications. These anomalous properties emerge from structural heterogeneities due to the formation of molecular clusters at conditions above the critical point. While the static behavior of these clusters and their effects on the thermodynamic response functions have been recognized, the relation between the ultrafast cluster dynamics and transport properties remains elusive. By measuring the intermediate scattering function in carbon dioxide at conditions near the critical point with X-ray photon correlation spectroscopy, we directly capture the cross-over dynamics between 4 and 13 picoseconds, revealing the transition between ballistic and diffusive motion. Complementary analysis using large-scale molecular dynamics simulations reveals that this behavior arises from collisions between unbound molecules and clusters. This study provides direct evidence of the ultrafast momentum exchange between clusters, which has significant impact on transport properties, solvation processes, and reaction kinetics in supercritical fluids.

carbon capture and storage↗

DOE OSTI2024

Small-angle scattering interferometry with neutron orbital angular momentum states

Methods to prepare and characterize neutron helical waves carrying orbital angular momentum (OAM) were recently demonstrated at small-angle neutron scattering (SANS) facilities. These methods enable access to the neutron orbital degree of freedom which provides new avenues of exploration in fundamental science experiments as well as in material characterization applications. However, it remains a challenge to recover phase profiles from SANS measurements. We introduce and demonstrate a novel neutron interferometry technique for extracting phase information that is typically lost in SANS measurements. An array of reference beams, with complementary structured phase profiles, are put into a coherent superposition with the array of object beams, thereby manifesting the phase information in the far-field intensity profile. We demonstrate this by resolving petal-structure signatures of helical wave interference for the first time: an implementation of the long-sought recovery of phase information from small-angle scattering measurements.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Advanced multi-modal mass spectrometry imaging reveals functional differences of placental villous compartments at microscale resolution

The placenta is a complex and heterogeneous organ that links the mother and fetus, playing a crucial role in nourishing and protecting the fetus throughout pregnancy. Integrative spatial multi-omics approaches can provide a systems-level understanding of molecular changes underlying the mechanisms leading to the histological variations of the placenta during healthy pregnancy and pregnancy complications. Herein, we advance our metabolome-informed proteome imaging (MIPI) workflow to include lipidomic imaging, while also expanding the molecular coverage of metabolomic imaging by incorporating on-tissue chemical derivatization (OTCD). The improved MIPI workflow advances biomedical investigations by leveraging state-of-the-art molecular imaging technologies. Lipidome imaging identifies molecular differences between two morphologically distinct compartments of a placental villous functional unit, syncytiotrophoblast (STB) and villous core. Next, our advanced metabolome imaging maps villous functional units with enriched metabolomic activities related to steroid and lipid metabolism, outlining distinct molecular distributions across morphologically different villous compartments. Complementary proteome imaging on these villous functional units reveals a plethora of fatty acid- and steroid-related enzymes uniquely distributed in STB and villous core compartments. Integration across our advanced MIPI imaging modalities enables the reconstruction of active biological pathways of molecular synthesis and maternal-fetal signaling across morphologically distinct placental villous compartments with micrometer-scale resolution.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Best practices for in-situ and operando techniques within electrocatalytic systems

In-situ and operando techniques in heterogeneous electrocatalysis are a powerful tool used to elucidate reaction mechanisms. Ultimately, they are key in determining concrete links between a catalyst’s physical/electronic structure and its activity en route to designing next-generation systems. To this end, the exact execution and interpretation of these lines of experiments is critical as this determines the strength of conclusions that can be drawn and what uncertainties remain. Instead of focusing on how techniques were used to understand systems, as is the case with most reviews on the topic, this work instead initiates a nuanced discussion of 1) how to best carry out each technique and 2) initiate a nuanced analysis of which level of insights can be drawn from the set of in-situ or operando experiments/controls carried out. We focus on several commonly used techniques, including vibrational (IR, Raman) spectroscopy, X-ray absorption spectroscopy and electrochemical mass spectrometry. In addition to this, we include sections of reactor design and the link with theoretical modelling that are applicable across all techniques. While we focus on heterogeneous electrocatalysis, we make links when appropriate to the areas of photo- and thermo-catalytic systems. We highlight common pitfalls in the field, how to avoid them, and what sets of complementary experiments may be used to strengthen the analysis. We end with an overview of what gaps remain in in-situ and operando techniques and what innovations must be made to overcome them.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

High-fidelity topochemical polymerization in single crystals, polycrystals, and solution aggregates

Topochemical polymerization (TCP) emerges as a leading approach for synthesizing single crystalline polymers, but is traditionally restricted to transformations in solid-medium. The complexity in achieving single-crystal-to-single-crystal (SCSC) transformations due to lattice disparities and the untapped potential of performing TCP in a liquid medium with solid-state structural fidelity present unsolved challenges. Herein, by using X-rays as the primary means to overcome crystal disintegration, we reveal the details of SCSC transformation during the TCP of chiral azaquinodimethane (AQM) monomers through in situ crystallographic analysis while spotlighting a rare metastable crystalline phase. Complementary in situ investigations of powders and thin films provide critical insights into the side-chain dependent polymerization kinetics of solid-state reactions. Furthermore, we enable TCP of AQM monomers in a liquid medium via an antisolvent-reinforced aggregated state, yielding polymer nanofibers with high crystallinity akin to that of solid-state. This study testifies high structural precision of TCP performed in different states and media, offering critical insights into the synthesis of processable nanostructured polymers with desired structural integrity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Optical imaging of flavor order in flat band graphene

Abstract Spin- and valley flavor polarization plays a central role in the many-body physics of flat band graphene, with Fermi surface reconstruction — often accompanied by quantized anomalous Hall and superconducting state — observed in a variety of experimental systems. Here we describe an optical technique that sensitively and selectively detects flavor textures via the exciton response of a proximal transition metal dichalcogenide layer. Through a systematic study of rhombohedral and rotationally faulted graphene bilayers and trilayers, we show that when the semiconducting dichalcogenide is in direct contact with the graphene, the exciton response is most sensitive to the large momentum rearrangement of the Fermi surface, providing information that is distinct from and complementary to electrical compressibility measurements. The wide-field imaging capability of optical probes allows us to obtain spatial maps of flavor order with high throughput, and with broad temperature and device compatibility. Our work helps pave the way for optical probing and imaging of flavor orders in flat band graphene systems.

Science & Technology - Other Topics↗

DOE OSTI2025

Merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis

Synthetic biology offers the promise of manufacturing chemicals more sustainably than petrochemistry. Yet, both the rate at which biomanufacturing can synthesize these molecules and the net chemical accessible space are limited by existing pathway discovery methods, which can often rely on arduous literature searches. Here, we introduce BioPKS pipeline, an automated retrobiosynthesis tool combining multifunctional type I polyketide synthases (PKSs) and monofunctional enzymes via two complementary tools: RetroTide and DORAnet. Monofunctional enzymes are valuable for carefully decorating a substrate’s carbon backbone while PKSs are unique in their ability to iteratively catalyze carbon-carbon bond formation reactions, thereby expanding carbon backbones in a predictable fashion. We evaluate the performance of BioPKS pipeline using a previously reported set of 155 biomanufacturing candidates, achieving exact synthetic designs for 93 compounds and generating chemically similar pathways for most remaining targets. Furthermore, BioPKS pipeline can propose pathways for the complex therapeutic natural products cryptofolione and basidalin.

Chainani, Yash↗

DOE OSTI2025

Emergent topological polarization textures in relaxor ferroelectrics

Relaxor ferroelectrics underpin high-performance actuators and sensors, yet the nature of polar heterogeneities driving their broadband dielectric response remains debated. Using a unified, multimodal structural refinement framework— simultaneously fitting complementary X-ray and neutron total scattering, X-ray absorption spectra, and diffuse scattering—we reconstruct 3D mesoscale polarization maps in the classic relaxor system PbMg 1/3 Nb 2/3 O 3 –PbTiO 3 . We uncover self-organized swirling polarization textures with half-skyrmion (meron) vortices, challenging models of independent polar nanoregions. These textures, characterized by smooth changes in the polarization direction, originate from overlapping volumes in which the projections of locally correlated polarization vectors onto each volume’s long axis share the same sign. Vortex cores correlate strongly with local charge and strain gradients imposed by compositional heterogeneities. In this work, our results suggest that chemical disorder, acting via depolarizing and strain fields, stabilizes topological vortex textures of the polarization field, offering a route for engineering new dielectric and ferroelectric functionalities.

Eremenko, Maksim [National Institute of Standards ↗

DOE OSTI2025

Multimodal super-resolution: discovering hidden physics and its application to fusion plasmas

Understanding complex physical systems often requires integrating data from multiple diagnostics, each with limited resolution or coverage. We present a machine learning framework that reconstructs synthetic high-temporal-resolution data for a target diagnostic using information from other diagnostics, without direct target measurements during the inference. This multimodal super-resolution technique improves diagnostic robustness and enables monitoring even in case of measurement failures or degradation. Applied to fusion plasmas, our method targets edge-localized modes (ELMs), which can damage plasma-facing materials. By reconstructing super-resolution Thomson Scattering data from complementary diagnostics, we uncover fine-scale plasma dynamics and validate the role of resonant magnetic perturbations (RMPs) in ELM suppression through magnetic island formation. The approach provides new observation supporting the plasma profile flattening due to these islands. Our results demonstrate the framework’s ability to generate high-fidelity synthetic diagnostics, offering a powerful tool for ELM control development in future reactors like ITER. The approach is broadly transferable to other domains facing sparse, incomplete, or degraded diagnostic data, opening new avenues for discovery.

Jalalvand, Azarakhsh [Princeton Univ., NJ (United ↗

DOE OSTI2025

Extending quantum-mechanical benchmark accuracy to biological ligand-pocket interactions

Predicting the binding affinity of ligands to protein pockets is key in the drug design pipeline. The flexibility of ligand-pocket motifs arises from a range of attractive and repulsive electronic interactions during binding. Accurately accounting for all interactions requires robust quantum-mechanical (QM) benchmarks, which are scarce for ligand-pocket systems. Additionally, disagreement between “gold standard” Coupled Cluster (CC) and Quantum Monte Carlo (QMC) methods casts doubt on many benchmarks for larger non-covalent systems. We introduce the “QUantum Interacting Dimer” (QUID) benchmark framework containing 170 non-covalent (non-)equilibrium systems modeling chemically and structurally diverse ligand-pocket motifs. Symmetry-adapted perturbation theory shows that QUID broadly covers non-covalent binding motifs and energetic contributions. Robust binding energies are obtained using complementary CC and QMC methods, achieving agreement of 0.5 kcal/mol. The benchmark data analysis reveals that several dispersion-inclusive density functional approximations provide accurate energy predictions, though their atomic van der Waals forces differ in magnitude and orientation. Contrarily, semiempirical methods and empirical force fields require improvements in capturing non-covalent interactions (NCIs) for out-of-equilibrium geometries. The wide span of NCIs, highly accurate interaction energies, and analysis of molecular properties take QUID beyond the “gold standard” for QM benchmarks of ligand-protein systems.

Puleva, Mirela [University of Luxembourg, Luxembou↗

DOE OSTI2025

Moiré-controllable exciton localization and dynamics through spatially-modulated inter- and intralayer excitons in a MoSe 2 /WS 2 heterobilayer

Moiré heterobilayers exhibiting spatially varying exciton localization that can be precisely controlled through the twist angle have emerged as exciting platforms for studying complex quantum phenomena. Here, we study the exciton landscape in MoSe 2 /WS 2 heterobilayers through synergistic first-principles GW plus Bethe Salpeter equation (GW-BSE) calculations and complementary time- and angle-resolved photoemission spectroscopy (tr-ARPES). We find that the MoSe 2 /WS 2 heterobilayer has a type I band alignment at large twist angles. In contrast, at small twist angles, there exist simultaneous spatially modulated regions of local type I band alignment, hosting bright intralayer excitons, and local type II band alignment, hosting long-lived interlayer excitons, due to lattice reconstruction in different high-symmetry regions. In tr-ARPES this manifests in the observation of long-lived excitons with electron population in only MoSe 2 at large twist angles, while in samples with small twist angles, signals from two distinct long-lived exciton states with electron population in both layers are observed. Contrary to earlier studies, we find no excitonic hybridization near the low-energy absorption peaks in MoSe 2 /WS 2 , whose splitting can, instead, be explained by the lattice reconstruction.

Electronic properties and materials↗

DOE OSTI2025

Multi-messenger dynamic imaging of laser-driven shocks in water using a plasma wakefield accelerator

Understanding dense matter hydrodynamics is critical for predicting plasma behavior in environments relevant to laser-driven inertial confinement fusion. Traditional diagnostic sources face limitations in brightness, spatiotemporal resolution, and in their ability to detect relevant electromagnetic fields. In this work, we present a dual-probe, multi-messenger laser wakefield accelerator platform combining ultrafast X-rays and relativistic electron beams at 1 Hz, to interrogate a free-flowing water target in vacuum, heated by an intense 200 ps laser pulse. This scheme enables high-repetition-rate tracking the evolution of the interaction using both particle types. Betatron X-rays reveal a cylindrically symmetric shock compression morphology assisted by low-density vapor, resembling foam-layer-assisted fusion targets. The synchronized electron beam detects time-evolving electromagnetic fields, uncovering charge separation and ion species differentiation during plasma expansion – phenomena not captured by photons or hydrodynamic simulations. We show that combining both probes provides complementary insights spanning kinetic to hydrodynamic regimes, highlighting the need for hybrid physics models to accurately predict fusion-relevant plasma behavior.

imaging techniques↗

DOE OSTI2026

Citywide indoor air sampling mirrors wastewater and clinical for environmental surveillance of respiratory viruses

Wastewater surveillance of respiratory pathogens can provide timely estimates of viral activity and disease trends in a population. Indoor air surveillance could be used similarly with some advantages but remains largely unvalidated at the community -scale. Here, an indoor air surveillance program was employed as part of public health environmental surveillance in Chicago, Illinois, USA. Ten air samplers were placed in healthcare and congregate living settings across the city. Weekly air samples were evaluated for influenza A, influenza B, respiratory syncytial virus, and SARS -CoV-2 over two respiratory virus seasons (2023 -2025). Citywide, aggregated air sample positivity and viral load were closely correlated with local clinical case and wastewater surveillance data across all respiratory viruses. Virus trends in air data often preceded clinical and wastewater, although this varied across pathogens and respiratory virus seasons. Further, whole -genome sequencing of SARS -CoV-2 showed close correlation of variant proportions across all datasets. At the building -scale, air samples obtained from a single sampling device provided efficient respiratory virus surveillance, with respiratory pathogen levels mirroring citywide clinical surveillance data. These data demonstrate that air surveillance can provide respiratory virus case and variant trend data at a building or community -scale, serving as an alternative or complementary tool for public health environmental surveillance.

Wilton, Rosemarie↗

DOE OSTI2021

A phononic interface between a superconducting quantum processor and quantum networked spin memories

We introduce a method for high-fidelity quantum state transduction between a superconducting microwave qubit and the ground state spin system of a solid-state artificial atom, mediated via an acoustic bus connected by piezoelectric transducers. Applied to present-day experimental parameters for superconducting circuit qubits and diamond silicon-vacancy centers in an optimized phononic cavity, we estimate quantum state transduction with fidelity exceeding 99% at a MHz-scale bandwidth. By combining the complementary strengths of superconducting circuit quantum computing and artificial atoms, the hybrid architecture provides high-fidelity qubit gates with long-lived quantum memory, high-fidelity measurement, large qubit number, reconfigurable qubit connectivity, and high-fidelity state and gate teleportation through optical quantum networks.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Nematic fluctuations in iron-oxychalcogenide Mott insulators

Nematic fluctuations occur in a wide range physical systems from biological molecules to cuprates and iron pnictide high- T c superconductors. It is unclear whether nematicity in pnictides arises from electronic spin or orbital degrees of freedom. We studied the iron-based Mott insulators La 2 O 2 Fe 2 OM 2 M = (S, Se), which are structurally similar to pnictides. Nuclear magnetic resonance revealed a critical slowing down of nematic fluctuations and complementary Mössbauerr spectroscopy data showed a change of electrical field gradient. The neutron pair distribution function technique detected local C 2 fluctuations while neutron diffraction indicates that global C 4 symmetry is preserved. A geometrically frustrated Heisenberg model with biquadratic and single-ion anisotropic terms provides the interpretation of the low temperature magnetic fluctuations. The nematicity is not due to spontaneous orbital order, instead it is linked to geometrically frustrated magnetism based on orbital selectivity. This study highlights the interplay between orbital order and spin fluctuations in nematicity.

36 MATERIALS SCIENCE↗