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At least 307 records · Page 17

Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination

Abstract In eukaryotes, fine-scale maps of meiotic recombination events have greatly advanced our understanding of the factors that affect genomic variation patterns and evolution of traits. However, in bacteria that lack natural systems for sexual reproduction, unbiased characterization of recombination landscapes has remained challenging due to variable rates of genetic exchange and influence of natural selection. Here, to overcome these limitations and to gain a genome-wide view on recombination, we crossed Bacillus strains with different genetic distances using protoplast fusion. The offspring displayed complex inheritance patterns with one of the parents consistently contributing the major part of the chromosome backbone and multiple unselected fragments originating from the second parent. Our results demonstrate that this bias was in part due to the action of restriction–modification systems, whereas genome features like GC content and local nucleotide identity did not affect distribution of recombination events around the chromosome. Furthermore, we found that recombination occurred uniformly across the genome without concentration into hotspots. Notably, our results show that species-level genetic distance did not affect genome-wide recombination. This study provides a new insight into the dynamics of recombination in bacteria and a platform for studying recombination patterns in diverse bacterial species.

59 BASIC BIOLOGICAL SCIENCES↗

Inverse design of two-dimensional materials with invertible neural networks

The ability to readily design novel materials with chosen functional properties on-demand represents a next frontier in materials discovery. However, thoroughly and efficiently sampling the entire design space in a computationally tractable manner remains a highly challenging task. To tackle this problem, we propose an inverse design framework (MatDesINNe) utilizing invertible neural networks which can map both forward and reverse processes between the design space and target property. This approach can be used to generate materials candidates for a designated property, thereby satisfying the highly sought-after goal of inverse design. We then apply this framework to the task of band gap engineering in two-dimensional materials, starting with MoS 2 . Within the design space encompassing six degrees of freedom in applied tensile, compressive and shear strain plus an external electric field, we show the framework can generate novel, high fidelity, and diverse candidates with near-chemical accuracy. We extend this generative capability further to provide insights regarding metal-insulator transition in MoS 2 which are important for memristive neuromorphic applications, among others. This approach is general and can be directly extended to other materials and their corresponding design spaces and target properties.

36 MATERIALS SCIENCE↗

Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates

The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies.

59 BASIC BIOLOGICAL SCIENCES↗

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 ↗

Site specific N- and O-glycosylation mapping of the spike proteins of SARS-CoV-2 variants of concern

Abstract The glycosylation on the spike (S) protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, modulates the viral infection by altering conformational dynamics, receptor interaction and host immune responses. Several variants of concern (VOCs) of SARS-CoV-2 have evolved during the pandemic, and crucial mutations on the S protein of the virus have led to increased transmissibility and immune escape. In this study, we compare the site-specific glycosylation and overall glycomic profiles of the wild type Wuhan-Hu-1 strain (WT) S protein and five VOCs of SARS-CoV-2: Alpha, Beta, Gamma, Delta and Omicron. Interestingly, both N- and O-glycosylation sites on the S protein are highly conserved among the spike mutant variants, particularly at the sites on the receptor-binding domain (RBD). The conservation of glycosylation sites is noteworthy, as over 2 million SARS-CoV-2 S protein sequences have been reported with various amino acid mutations. Our detailed profiling of the glycosylation at each of the individual sites of the S protein across the variants revealed intriguing possible association of glycosylation pattern on the variants and their previously reported infectivity. While the sites are conserved, we observed changes in the N- and O-glycosylation profile across the variants. The newly emerged variants, which showed higher resistance to neutralizing antibodies and vaccines, displayed a decrease in the overall abundance of complex-type glycans with both fucosylation and sialylation and an increase in the oligomannose-type glycans across the sites. Among the variants, the glycosylation sites with significant changes in glycan profile were observed at both the N -terminal domain and RBD of S protein, with Omicron showing the highest deviation. The increase in oligomannose-type happens sequentially from Alpha through Delta. Interestingly, Omicron does not contain more oligomannose-type glycans compared to Delta but does contain more compared to the WT and other VOCs. O-glycosylation at the RBD showed lower occupancy in the VOCs in comparison to the WT. Our study on the sites and pattern of glycosylation on the SARS-CoV-2 S proteins across the VOCs may help to understand how the virus evolved to trick the host immune system. Our study also highlights how the SARS-CoV-2 virus has conserved both N - and O - glycosylation sites on the S protein of the most successful variants even after undergoing extensive mutations, suggesting a correlation between infectivity/ transmissibility and glycosylation.

60 APPLIED LIFE SCIENCES↗

Multitask graph neural networks for elastoplastic response prediction in dual-phase polycrystals

Microstructure-sensitive prediction of elastoplastic response remains a recurring bottleneck in multiscale damage and fatigue modeling, where large ensembles of statistically distinct polycrystals are required to quantify variability and extreme-value behavior. In this work, we develop a multitask graph neural network (GNN) surrogate that maps dual-phase ferrite–martensite polycrystal microstructures to Statistical Volume Element (SVE)-level elastoplastic Quantities of Interest (QoIs). Each SVE is represented as a grain-adjacency graph, with node features encoding phase, geometry, and crystallographic orientation, and edge features encoding relative misorientation. A message-passing graph convolution generates node embeddings, which are pooled into a graph representation and passed to a multitask regression head that jointly predicts 10 scalar QoIs and vector-valued stress–strain responses in orthogonal loading directions across multiple martensite volume fractions and SVE sizes. Results show high accuracy for scalar QoIs and strong agreement for full stress–strain trajectories, with population envelopes reproducing both median behavior and finite-SVE variability across compositions and partition scales. A unified model trained on pooled volume-fraction data preserves most within-regime accuracy relative to regime-specific models while also capturing the broader cross-regime variation reflected in the pooled test set. Distributional comparisons further demonstrate that the surrogate preserves heterogeneity under SVE partitioning, enabling statistically consistent block-wise random-field construction for mesoscale analyses. Overall, the proposed grain-graph surrogate provides a practical pathway to accelerate ensemble-based studies of SVE-level constitutive variability in dual-phase polycrystals.

Crystal plasticity↗

Electrode Modification by Laser Ablation to Overcome Mechanical and Scalability Limitations of Solid-State Prealkylation of Electrode Architectures

In this work, laser ablation of Si electrode surfaces is utilized to provide localized strain relief during the Solid State Prealkylation of Electrode Architectures (SPEAR) process, in addition to volumetric expansion relief in the form of free volume channels across the electrode. A hexagonal mesh patterning was employed via laser ablation, where the hexagonal diameter (pitch) was varied from 250 to 1000 µm. It was demonstrated that these channels serve as expansion voids, accommodating the increase in electrode thickness observed during SPEAR and preventing cracking at the electrode surface. Optical microscopy and Raman mapping confirm that Li diffusion is the rate-limiting solid-state process, requiring a 24 h rest period to achieve homogeneous LixSi alloying through the electrode bulk. Electrochemical evaluations in full cells show that a 1000 μm pitch pattern yields a high initial discharge capacity of 2485 mA h g–1 and 86.4% capacity retention after 80 cycles, whereas smaller pitches (<500 μm) result in lithium plating at 4.1 V in full cells paired with NMC 811 due to excessive current collector exposure from the ablation process. XPS analysis reveals that the laser treatment modifies the electrode surface by increasing the Si–O and C–O species, changing the SEI composition observed via an increase in fluorophosphates upon cycling.

Musgrove, Amanda [ORNL] (ORCID:0009000220910389)↗

Mapping the structural–mechanical landscape of amorphous carbon with ReaxFF molecular dynamics

We use ReaxFF molecular dynamics (MD) to investigate the relationship between structural and mechanical properties in bulk and nanostructured amorphous carbon (a-C). The liquid-quench MD method is used to generate isotropic bulk samples with mass densities ranging from 0.96 to 3.29 g/cm3. Structural analysis identifies two types of structures with distinct short- and medium-range order: lower-density sp2-dominated a-C, which is characterized by a bimodal ring-size distribution, and higher-density sp3-dominated tetrahedral amorphous carbon (ta-C), exhibiting a unimodal ring-size distribution. Stress–strain MD simulations and analysis reveal how an atomistic structure impacts elastic properties and post-yield atomic rearrangements. All stretched structures demonstrate elastic isotropy and plasticity driven by a ring-size expansion mechanism reflected in changes in ring statistics. The plastic region is substantially larger in ta-C than in a-C due to the post-yield shift from sp3 to sp2 C dominant bonding. In both a-C and ta-C, ultimate failure occurs when a reactive crack, traversed by long sp chains, forms and propagates predominantly perpendicular to the direction of the applied strain. Oxygen infiltration into the fractured region significantly reduces stress resistance, primarily through the early rupture of long sp chains. MD simulations and analysis are extended to a-C slabs, a-C nanotubes, and partially a-C nanotubes. The latter nanostructure highlights the differences between the elastically isotropic a-C walls, which develop circumferential cracking, and the crystalline walls, which tear along crystallographic directions. These results provide a strong foundation for further computational characterization of a-C materials.

Dernov, A. (ORCID:0009000004220973)↗

Tailoring Piezoelectricity of 3D Printing PVDF-MoS 2 Nanocomposite via In Situ Induced Shear Stress

3D printing of unique structures with tunable properties offers significant advantages in the fabrication of complex and customized electronic devices. Here, this study introduces a process-microstructure–property-guided manufacturing route to fabricate PVDF-2D MoS 2 piezoelectric nanocomposites with tunable piezoelectric properties without having a postprocess. We control PVDF’s microstructure through direct ink writing (DIW) 3D printing while tuning PVDF-MoS 2 interfacial strain by controlling rheology and 3D printing parameters, such as nozzle size and printing speed. Our approach demonstrates tunable piezoelectricity in PVDF-MoS 2 , achieving a 15-fold increase in the piezoelectric coefficient (d 33 ) at a printing-induced shear stress of 6685 Pa. This enhancement arises from the electrostatic interactions between PVDF and MoS 2 and the filler distribution and alignment caused by the in situ shear stress in 3D printing, as confirmed by XPS and Raman mapping analyses. Our findings advance the understanding of piezoelectric mechanisms in PVDF-based nanocomposites, laying the foundation for 3D printing of piezoelectric sensors in wearable device applications with enhanced performance and customization capabilities.

2D MoS2↗

Assessing the Viability of Geothermal Microgrid Deployment: A Geospatial Analysis Across the United States

Geothermal microgrids hold a potential of supplying clean and dependable power to communities throughout the United States (US), all while sidestepping the expenses associated with connecting to strained or isolated power grids. Nonetheless, their implementation is still in its early stages in the country. The objective of this analysis is to leverage available data to pinpoint regions across the US that exhibit favorable conditions for the development of geothermal microgrids. Drawing from a variety of sources, including estimates of geothermal resources, the costs associated with geothermal energy generation and electricity transmission, existing microgrid locations, and subsidy programs, we aim to identify promising areas for further exploration. By mapping out the contiguous US, Alaska, and Hawaii, we delineate regions with high relative favorability for geothermal microgrid deployment. Our findings reveal the presence of highly favorable regions across the Western states of the contiguous US, as well as isolated areas in Alaska and Hawaii. Furthermore, we delve into a discussion on state policies and incentive programs, considering their role in fostering favorable conditions or posing barriers to geothermal microgrid development.

Alaska↗

A finite micro-rotation material point method for micropolar solid and fluid dynamics with three-dimensional evolving contacts and free surfaces

This paper introduces an explicit material point method designed specifically for simulating the micropolar continuum dynamics in the finite deformation and finite microrotation regime. The material point method enables us to simulate large deformation problems while circumventing the potential mesh distortion without remeshing. To eliminate rotational motion damping and loss of angular momentum during the projection, we introduce the mapping for microinertia and angular momentum between particles and grids through the affine particle-in-cell approach. The microrotation and the curvature at each particle are updated through zero-order forward integration of the microgyration and its spatial gradient. We show that the microinertia and the angular momentum are conserved during the projections between particles and grids in our formulation. We verify the formulation and implementation by comparing with the analytical dispersion relation of micropolar waves under the small strain and small microrotation, as well as the analytical soliton solution for solids undergoing large deformation and large microrotation. Additionally we also demonstrate the capacity of the proposed computational framework to handle a wide spectrum of simulations that exhibit size effects in the geometrical nonlinear regime through three representative numerical examples, i.e., a cantilever beam torsion problem, a fragment-impact penetration problem, and a micropolar fluid discharging problem.

42 ENGINEERING↗

Boron Nitride-Driven Strengthening of Aluminum Composites via Friction Stir Processing

Friction stir welding and processing (FSW/P) has emerged as an effective solid-state joining technique for fabricating metal matrix composites (MMCs), offering improved mechanical properties through refined microstructural evolution. In this study, an aluminum-boron nitride nanoparticle (Al-BNNP) composite was synthesized via FSW, and its indentation-based mechanical properties were systematically evaluated. Microhardness mapping across the weld cross-section revealed a progressive increase in hardness toward the stir zone (SZ), attributed to severe plastic deformation, dynamic recrystallization (DRX), and the reinforcing effect of BNNPs. Profilometry-based indentation plastometry (PIP) inferred yield strength (YS) demonstrates a 47.8% increase compared to the base metal (BM) and a 75% improvement compared to FSP pure aluminum reported in literature. This enhancement is attributed to strengthening mechanisms, including grain boundary pinning, load transfer, and increased dislocation density. The strain rate sensitivity (SRS) measurements at the nanoscale demonstrated a substantial decrease in the SZ, correlated with ultrafine grain structures and strong BNNP-matrix interactions. Activation volume analysis revealed a significant reduction in the SZ, suggesting that dislocation motion is increasingly restricted by dislocation-dislocation and dislocation-particle interactions. These findings suggest that incorporating BNNPs in FSW/P enables tailoring the microstructure without thermal degradation of the secondary particles, thereby significantly enhancing the mechanical performance of aluminum composites, particularly for structural applications in aerospace and automotive industries.

Aluminum↗

Improved Vertical Carrier Transport for Green III-Nitride LEDs Using ( In , Ga ) N Alloy Quantum Barriers

We report on experimental and simulation-based results using ( In , Ga ) N alloy quantum barriers in c -plane green light-emitting diode (LED) structures as a means to improve vertical carrier transport and reduce forward voltage ( V F ) . Three-dimensional device simulations that include random alloy fluctuations are used to understand carrier behavior in a disordered potential. The simulated current density–voltage ( J - V ) characteristics and modified electron-hole overlap | F mod | 2 indicate that increasing the indium fraction in the ( In , Ga ) N quantum barriers leads to a reduced polarization discontinuity at the interface between the quantum barrier and quantum well, thereby reducing V F and improving | F mod | 2 . Maps of electron and hole current through the device show a relatively homogenous distribution in the X Y plane for structures using Ga N quantum barriers; in contrast, preferential pathways for vertical transport are identified in structures with ( In , Ga ) N barriers as regions of high and low current. A positive correlation between hole (electron) current in the p -side ( n -side) barrier and indium fraction reveals that preferential pathways exist in regions of high indium content. Furthermore, a negative correlation between the strain ε z z and indium fraction shows that high indium content regions have reduced strain-induced piezoelectric polarization in the Z direction due to the mechanical constraint of the surrounding lower indium content regions. Experimentally, multiple quantum well green LEDs with ( In , Ga ) N quantum barriers exhibit lower V F and blue-shifted wavelengths relative to LEDs with Ga N quantum barriers, consistent with simulation data. These results can be used to inform heterostructure design of low V F , long-wavelength LEDs and provide important insight into the nature of carrier transport in III-nitride alloy materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

High-quality Acinetobacter genomes recovered from combat wounds via metagenomic sequencing resemble cultured isolate genomes

The ability to accurately characterize wound pathogens is critical to informing clinical decisions for wound infections with complex treatment requirements. Acinetobacter baumannii is an impactful nosocomial pathogen in combat wounds and civilian hospital-acquired infections. An informed understanding of the phylogenetics and epidemiology of A. baumannii infections in military and civilian environments could guide approaches that improve antibiotic treatment regimens for both military and civilian patients. Whole-genome data for bacterial strains can be difficult to obtain due to challenges in culturing isolates from preserved military specimens. Metagenomic sequencing and assembly create opportunities for genomic analysis of pathogens directly from clinical specimens. The ability to perform comparative analyses between metagenome-derived genomes and culture-derived genomes would support a range of comparative bacterial genomic studies. Wound tissue biopsy and effluent samples from combat injuries were subjected to metagenomic sequencing and assembly. In total, 42 microbial metagenome-assembled genomes (MAGs) were obtained directly from metagenomic sequence data, 36 of which were designated “high” quality. Thirty of these genomes corresponded to Acinetobacter, with 29 mapping specifically to A. baumannii. Other observed genera included Bordetella, Citrobacter, Escherichia, and Pseudomonas. Single-copy and multi-copy orthologs were identified across Acinetobacter MAGs and publicly available isolate genomes derived from military and civilian sources. Both MAG and military isolate genomes were annotated with antimicrobial resistance data, and MAG genomes were statistically comparable to genomes obtained from isolates. Our results highlight the potential of de novo metagenome assembly for enabling high-resolution characterization directly from clinical specimens, thereby improving diagnostic precision, guiding antimicrobial stewardship, and enhancing understanding of pathogen evolution across diverse healthcare and battlefield environments.

Acinetobacter baumannii↗

Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping

N 4 -acetylcytidine (ac 4 C) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA. However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated. In this work, we report ac 4 C-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of ac 4 C at single-nucleotide resolution. In human and yeast mRNAs, ac 4 C sites are not detected but can be induced—at a conserved sequence motif—via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of ac 4 C across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. Ac 4 C is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of ac 4 C and its potential thermoadaptive role. Our studies quantitatively define the ac 4 C landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease.

59 BASIC BIOLOGICAL SCIENCES↗

Imaging Charged Exciton Localization in van der Waals WSe 2 /MoSe 2 Heterobilayers

Exciton localization in transition-metal dichalcogenide monolayers is behind a variety of interesting phenomena and applications, including broad-spectrum solar cells and singlephoton emissions. Strain fields at the periphery of topographically distinct features such as nanoscopic bubbles were recently associated with localized charge-neutral excitons. Here, we use tip-enhanced photoluminescence (PL) to visualize excitons in WSe 2 /MoSe 2 heterobilayers (HBL). We find strong optical emission from charged excitons, particularly positively charged trions, in HBL supported by interlayer charge transfer. Our results reveal strong trion confinement, with a localization length scale comparable to the trion size, at the apex region inside individual nanoscopic bubbles. Nano-PL mapping also shows sub-10 nm spatial variations in the localized trion emission spectra, which stem from atomic-scale potential energy fluctuations. These findings demonstrate the possibility of confining charged exciton complexes that are electrically tunable, opening up further opportunities to probe many-body exciton physics, and to explore additional possible sites for strong exciton localization that can lead to quantum emissions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Strength-ductility synergy through microstructural and compositional heterogeneity in directed energy deposition additive manufacturing of face-centered cubic materials

Directed energy deposition (DED) is an additive manufacturing (AM) process based on welding technology and offers the advantages of large build volume, high deposition rate, and ability to fabricate multi-material parts. Epitaxial continuous columnar grain growth is a characteristic microstructural feature of DED processed alloys. In this study, a bamboo-like microstructure (periodic alternation of equiaxed and columnar structure) was produced by adopting an intermittent deposition strategy in 316L stainless steel and Inconel 625. The formation of a bamboo-like alternating microstructure was confirmed through electron backscattered diffraction (EBSD) analysis. Hardness mapping showed that the columnar to equiaxed transition (CET) occurred at the region right below the fusion line. A finite element (FE) model was used to investigate the relationship between the temperature gradient (G) and the solidification rate (R). The FE model showed a low G/R ratio at the region right below the interface promoting the CET. The grain size and material-dependent deformation behaviors are analyzed using digital image correlation (DIC). The lower deformation on the fine-grain regions observed in DIC analysis is attributed to a higher strain hardening rate, which is confirmed through dislocation density analysis on a tensile-interrupted specimen. The periodically alternating grain size coupled with the microstructural changes caused by intermittent deposition strategy result in a better strength-ductility synergy in both single-material and bimetallic specimens.

36 MATERIALS SCIENCE↗

Mapping the Path Forward to Next Generation Algal Technologies: Workshop on Understanding the Rules of Life and Complexity in Algal Systems

Algal technology offers enormous potential as a source of renewable biomass and bioproducts for fuels, biochemicals, nutrients, and numerous other applications. While tremendous opportunities exist, significant challenges are also present in harnessing and utilizing this valuable and potentially sustainable bioproduction platform. Funded by a joint partnership between the Bioenergy Technologies Office (BETO) at the Department of Energy (DOE) and the National Science Foundation (NSF), the recent virtual workshop, "Understanding the Rules of Life: Complexity in Algal Systems Workshop," was organized to bring together thought leaders from academia, national laboratories and other government agencies, and industry to identify key challenges and propose research strategies to overcome these barriers. Two parallel sessions were undertaken: 1) algae strain and toolkit development and 2) algal ecosystem and microbiome dynamics, in order to advance algae engineering and cultivation efforts. In each session, attendees discussed the most pressing challenges from the perspective of model systems and omics analysis. Themes such as genetic engineering toolboxes, translation from the laboratory to outdoor cultivation, functional genomics, metabolomics, algal ecology, consortial design, microbiome dynamics, mathematical models, and data analytics emerged from the discussion. Overall, this workshop has served to elucidate the key hurdles and many opportunities present as we continue to advance algal science and technology from the laboratory and into the commercial realm.

09 BIOMASS FUELS↗