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At least 1,189 records · Page 66

Dissecting the contributions to non-photochemical quenching in a land plant under fluctuating light

Photosynthetic organisms have evolved multiple non-photochemical quenching (NPQ) processes, providing photoprotection by safely dissipating excess excitation energy. These processes involve various molecular players functioning on overlapping timescales from seconds to days, making it challenging to isolate and quantify their individual kinetics. In this study, we perform whole-leaf chlorophyll fluorescence lifetime and xanthophyll concentration measurements on wild-type and various newly characterized NPQ mutants of Nicotiana benthamiana, a vascular land plant. Based on these measurements, we construct a fluorescence lifetime-based quantitative kinetic model that disentangles individual photoprotection components and, when integrated additively, accurately predicts wild-type and mutant NPQ behaviors under various light-dark regimes. Additionally, the model quantifies the per-molecule quenching effectiveness of various xanthophylls and the contributions of six quenching components (qE V , qE A , qE Z , qE L , qZ, and qI) across different genotypes. It also suggests improved overall quenching efficiency at specific VDE:ZEP:PsbS overexpression stoichiometries, aligning with previous studies and supporting translational efforts to optimize photoprotection and enhance crop yields under dynamic light environments.

Lam, Lam [University of California, Berkeley, CA (↗

Genome resources for three modern cotton lines guide future breeding efforts

Cotton ( Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars (‘UGA230’, ‘UA48’ and ‘CSX8308’) and updating the ‘TM-1’ cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from ‘Pima’ cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.

59 BASIC BIOLOGICAL SCIENCES↗

Accelerating charge estimation in molecular dynamics simulations using physics-informed neural networks: corrosion applications

Molecular Dynamics (MD) simulations are used to understand the effects of corrosion on metallic materials in salt brine. Reactive force fields in classical MD enable accurate modeling of bond formation and breakage in the aqueous medium and at the metal-electrolyte interface, while also facilitating dynamic partial charge equilibration. However, MD simulations are computationally intensive and unsuitable for modeling the long time scales characteristic of corrosive phenomena. To address this, we develop reduced-order machine learning models that provide accurate and efficient predictions of charge density in corrosive environments. Specifically, we use Long Short-Term Memory (LSTM) networks to forecast charge density evolution based on atomic environments represented by Smooth Overlap of Atomic Positions (SOAP) descriptors. A physics-informed loss function enforces charge neutrality and electronegativity equivalence. The atomic charges predicted by the deep learning model trained on this work were obtained two orders of magnitude faster than those from molecular dynamics (MD) simulations, with an error of less than 3% compared to the MD-obtained charges, even in extrapolative scenarios, while adhering to physical constraints. This demonstrates the excellent accuracy, computational efficiency, and validity of the developed model. Lastly, even though developed for corrosion, these protocols are formulated in a phenomenon-agnostic manner, allowing application to various variable-charge interatomic potentials and related fields.

Atomistic models↗

High-efficiency microwave-optical quantum transduction based on a cavity electro-optic superconducting system with long coherence time

Abstract Frequency conversion between microwave and optical photons is a key enabling technology to create links between superconducting quantum processors and to realize distributed quantum networks. We propose a microwave-optical transduction platform based on long-coherence time superconducting radio-frequency (SRF) cavities coupled to electro-optic optical cavities to mitigate the loss mechanisms that limit the attainment of high conversion efficiency. We optimize the microwave-optical field overlap and optical coupling losses in the design while achieving long microwave and optical photon lifetime at milli-Kelvin temperatures. This represents a significant enhancement of the transduction efficiency up to 50% under incoming pump power of 140 μW, which allows the conversion of few-photon quantum signals. Furthermore, this scheme exhibits high resolution for optically reading out the dispersive shift induced by a superconducting transmon qubit coupled to the SRF cavity. We also show that low microwave losses enhance the fidelity of heralded entanglement generation between two remote quantum systems. Finally, high precision in quantum sensing can be reached below the standard quantum limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quantum Zeno Monte Carlo for computing observables

The recent development of logical quantum processors marks a pivotal transition from the noisy intermediate-scale quantum (NISQ) era to the fault-tolerant quantum computing (FTQC) era. These devices have the potential to address classically challenging problems with polynomial computational time using quantum properties. However, they remain susceptible to noise, necessitating noise resilient algorithms. We introduce Quantum Zeno Monte Carlo (QZMC), a classical-quantum hybrid algorithm that demonstrates resilience to device noise and Trotter errors while showing polynomial computational cost for a gapped system. QZMC computes static and dynamic properties without requiring initial state overlap or variational parameters, offering reduced quantum circuit depth.

Han, Mancheon [Korea Institute for Advanced Study ↗

Vacancy defect control of colossal thermopower in FeSb2

Abstract Iron diantimonide is a material with the highest known thermoelectric power. By combining scanning transmission electron microscopic study with electronic transport neutron, X-ray scattering, and first principle calculation, we identify atomic defects that control colossal thermopower magnitude and nanoprecipitate clusters with Sb vacancy ordering, which induce additional phonon scattering and substantially reduce thermal conductivity. Defects are found to cause rather weak but important monoclinic distortion of the unit cell P n n m → P m . The absence of Sb along [010] for high defect concentration forms conducting path due to Fe d orbital overlap. The connection between atomic defect anisotropy and colossal thermopower in FeSb 2 paves the way for the understanding and tailoring of giant thermopower in related materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quantum Monte Carlo study of lattice polarons in the two-dimensional three-orbital Su–Schrieffer–Heeger model

The electron–lattice interaction gives rise to a rich set of phenomena in quantum materials. Microscopically, this interaction often arises from the modulation of orbital overlaps; however, many theoretical studies neglect such couplings. Here, we present an exact diagonalization and determinant quantum Monte Carlo study of a three-orbital Su–Schrieffer–Heeger (SSH) model, on a two-dimensional Lieb lattice and in the negative charge transfer regime. At half-filling (one hole/unit cell), we observe a bipolaron insulating phase with a bond-disproportionate lattice. This phase is robust against moderate hole doping but is suppressed at large hole concentrations, leading to a metallic polaron-liquid-like state with fluctuating patches of local distortions. We also find an s-wave superconducting state at large hole doping that primarily appears on the oxygen sublattice. Our work provides a non-perturbative view of SSH-type couplings in two dimensions with implications for materials where such couplings are dominant.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quasi-particle interference of the van Hove singularity in Sr2RuO4

Abstract The single-layered ruthenate Sr 2 RuO 4 is one of the most enigmatic unconventional superconductors. While for many years it was thought to be the best candidate for a chiral p -wave superconducting ground state, desirable for topological quantum computations, recent experiments suggest a singlet state, ruling out the original p -wave scenario. The superconductivity as well as the properties of the multi-layered compounds of the ruthenate perovskites are strongly influenced by a van Hove singularity in proximity of the Fermi energy. Tiny structural distortions move the van Hove singularity across the Fermi energy with dramatic consequences for the physical properties. Here, we determine the electronic structure of the van Hove singularity in the surface layer of Sr 2 RuO 4 by quasi-particle interference imaging. We trace its dispersion and demonstrate from a model calculation accounting for the full vacuum overlap of the wave functions that its detection is facilitated through the octahedral rotations in the surface layer.

36 MATERIALS SCIENCE↗

Contribution of Ryugu-like material to Earth’s volatile inventory by Cu and Zn isotopic analysis

We report initial analyses showed that asteroid Ryugu’s composition is close to CI (Ivuna-like) carbonaceous chondrites (CCs) – the chemically most primitive meteorites, characterized by near-solar abundances for most elements. However, some isotopic signatures (for example, Ti, Cr) overlap with other CC groups, so the details of the link between Ryugu and the CI chondrites are not yet fully clear. Here we show that Ryugu and CI chondrites have the same zinc and copper isotopic composition. As the various chondrite groups have very distinct Zn and Cu isotopic signatures, our results point at a common genetic heritage between Ryugu and CI chondrites, ruling out any affinity with other CC groups. Since Ryugu’s pristine samples match the solar elemental composition for many elements, their Zn and Cu isotopic compositions likely represent the best estimates of the solar composition. Earth’s mass-independent Zn isotopic composition is intermediate between Ryugu/CC and non-carbonaceous chondrites (NCs), suggesting a contribution of Ryugu-like material to Earth’s budgets of Zn and other moderately volatile elements.

58 GEOSCIENCES↗

Asymmetric magnetic proximity interactions in MoSe 2 /CrBr 3 van der Waals heterostructures

Magnetic proximity interactions between atomically thin semiconductors and two-dimensional magnets provide a means to manipulate spin and valley degrees of freedom in non-magnetic monolayers, without using applied magnetic fields. In such van der Waals heterostructures, magnetic proximity interactions originate in the nanometre-scale coupling between spin-dependent electronic wavefunctions in the two materials, and typically their overall effect is regarded as an effective magnetic field acting on the semiconductor monolayer. Here we demonstrate that magnetic proximity interactions in van der Waals heterostructures can in fact be markedly asymmetric. Valley-resolved reflection spectroscopy of MoSe2/CrBr3 van der Waals structures reveals strikingly different energy shifts in the K and K' valleys of the MoSe2 due to ferromagnetism in the CrBr3 layer. Density functional calculations indicate that valley-asymmetric magnetic proximity interactions depend sensitively on the spin-dependent hybridization of overlapping bands and as such are likely a general feature of hybrid van der Waals structures. Here, these studies suggest routes to control specific spin and valley states in monolayer semiconductors.

36 MATERIALS SCIENCE↗

Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

Abstract Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.

59 BASIC BIOLOGICAL SCIENCES↗

$\mathrm{COBRA}$ improves the completeness and contiguity of viral genomes assembled from metagenomes

Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.

54 ENVIRONMENTAL SCIENCES↗

Layer-resolved magnetic proximity effect in van der Waals heterostructures

Magnetic proximity effects are integral to manipulating spintronic, superconducting, excitonic and topological phenomena in heterostructures. These effects are highly sensitive to the interfacial electronic properties, such as electron wavefunction overlap and band alignment. The recent emergence of magnetic two-dimensional materials opens new possibilities for exploring proximity effects in van der Waals heterostructures. In particular, atomically thin CrI 3 exhibits layered antiferromagnetism, in which adjacent ferromagnetic monolayers are antiferromagnetically coupled. In this paper, we report a layer-resolved magnetic proximity effect in heterostructures formed by monolayer WSe 2 and bi/trilayer CrI 3 . By controlling the individual layer magnetization in CrI 3 with a magnetic field, we show that the spin-dependent charge transfer between WSe 2 and CrI 3 is dominated by the interfacial CrI 3 layer, while the proximity exchange field is highly sensitive to the layered magnetic structure as a whole. In combination with reflective magnetic circular dichroism measurements, these properties allow the use of monolayer WSe 2 as a spatially sensitive magnetic sensor to map out layered antiferromagnetic domain structures at zero magnetic field as well as antiferromagnetic/ferromagnetic domains at finite magnetic fields. Our work reveals a way to control proximity effects and probe interfacial magnetic order via van der Waals engineering.

36 MATERIALS SCIENCE↗

Poincaré beams from a free electron laser

Poincaré beams are light beams that have spatially inhomogeneous polarization structure that spans a finite portion of the Poincaré sphere. This feature bestows the beams with intriguing topological properties and has led to a surge in research on their fundamental characteristics, their controlled generation and on emerging applications. Here we present an experimental demonstration of a Poincaré beam generated in the extreme ultraviolet (16.7 nm) at the FERMI free electron laser (FEL). The ‘star’ type Poincaré beam is generated by exploiting the phase and intensity structure intrinsic to FEL radiation without relying on optical elements. Here, we controlled the spatial polarization distribution through a precise overlap and power balance between two FEL pulses, each with different transverse phase distributions and orthogonal circular polarizations. The spatial polarization structure was mapped in detail and shows extensive coverage of the Poincaré sphere, in agreement with analytic predictions. This method of in situ Poincaré beam production in FELs enables straightforward flexibility in the orientation and balance of polarization states, and can readily be extended to other vector beams and to shorter wavelengths enabling novel science applications in modern light sources.

Morgan, Jenny [SLAC National Accelerator Laborator↗

Hybridized quadrupolar excitations in the spin-anisotropic frustrated magnet FeI 2

Magnetic order is usually associated with well-defined magnon excitations. Exotic magnetic fluctuations with fractional, topological or multipolar character, have been proposed for radically different forms of magnetic matter such as spin-liquids. As a result, considerable efforts have searched for, and uncovered, low-spin materials with suppressed dipolar order at low temperatures. In this work, we report neutron-scattering experiments and quantitative theoretical modeling of an exceptional spin-1 system – the uniaxial triangular magnet FeI 2 – where a bright and dispersive band of mixed dipolarquadrupolar fluctuations emerges just above a dipolar ordered ground-state. This excitation arises from anisotropic exchange interactions that hybridize overlapping modes carrying fundamentally different quantum numbers. Remarkably, a generalization of spin-wave theory to local SU(3) degrees of freedom accounts for all details of the low-energy dynamical response of FeI 2 without going beyond quadratic order. Our work highlights that quantum excitations without classical counterparts can be realized even in presence of fully developed magnetic order.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Visualization of bulk and edge photocurrent flow in anisotropic Weyl semimetals

Materials that rectify light into current in their bulk are desired for optoelectronic applications. In Weyl semimetals that break inversion symmetry, bulk photocurrents may arise due to nonlinear optical processes that are enhanced near the Weyl nodes. However, the photoresponse of these materials is commonly studied by scanning photocurrent microscopy, which convolves the effects of photocurrent generation and collection. Here we directly image the photocurrent flow inside the type-II Weyl semimetals WTe 2 and TaIrTe 4 using high-sensitivity quantum magnetometry with nitrogen-vacancy centre spins. We elucidate a mechanism for bulk photocurrent generation, which we call the anisotropic photothermoelectric effect, where unequal thermopowers along different crystal axes drive intricate circulations of photocurrent around the photoexcitation. Using overlapping scanning photocurrent microscopy and magnetic imaging at the interior and edges of the sample, we visualize how the anisotropic photothermoelectric effect stimulates the long-range photocurrent collected in our WTe 2 and TaIrTe 4 devices through the Shockley–Ramo mechanism. Furthermore, our results highlight a widely relevant source of current flow and will inspire photodetectors that utilize bulk materials with thermoelectric anisotropy.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Intrinsic glassy-metallic transport in an amorphous coordination polymer

Conducting organic materials, such as doped organic polymers, molecular conductors and emerging coordination polymers4, underpin technologies ranging from displays to flexible electronics. Realizing high electrical conductivity in traditionally insulating organic materials necessitates tuning their electronic structure through chemical doping6. Furthermore, even organic materials that are intrinsically conductive, such as single-component molecular conductors, require crystallinity for metallic behavior. However, conducting polymers are often amorphous to aid durability and processability. Using molecular design to produce high conductivity in undoped amorphous materials would enable tunable and robust conductivity in many applications, but there are no intrinsically conducting organic materials that maintain high conductivity when disordered. Here we report an amorphous coordination polymer, Ni tetrathiafulvalene tetrathiolate, which displays markedly high electronic conductivity (up to 1,200 S cm –1 ) and intrinsic glassy-metallic behavior. Theory shows that these properties are enabled by molecular overlap that is robust to structural perturbations. This unusual set of features results in high conductivity that is stable to humid air for weeks, pH 0–14 and temperatures up to 140 °C. Furthermore, these findings demonstrate that molecular design can enable metallic conductivity even in heavily disordered materials, raising fundamental questions about how metallic transport can exist without periodic structure and indicating exciting new applications for these materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The importance of trait selection in ecology

Two recent publications have explored the importance of roots for understanding plant form and function but reached opposite conclusions on the basis of largely overlapping data. Carmona et al. concluded that their results “do not confirm the strong covariation between leaf and fine-root traits predicted by the plant economics spectrum hypothesis”. By contrast, Weigelt et al. concluded that “key leaf and fine-root traits were aligned along the expected [fast–slow] ‘conservation’ gradient of plant economic investment”. Furthermore, here we reflect on the causes for the apparent discrepancies of these studies and show that the rationale behind trait selection is vital for the conclusions.

59 BASIC BIOLOGICAL SCIENCES↗