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At least 127 records · Page 7

From oxide epitaxy to freestanding membranes: Opportunities and challenges

Motivated by the growing demand to integrate functional oxides with dissimilar materials, numerous studies have been undertaken to detach a functional oxide film from its original substrate, effectively forming a membrane, which can then be affixed to the desired host material. This review article is centered on the synthesis of functional oxide membranes, encompassing various approaches to their synthesis, exfoliation, and transfer techniques. First, we explore the characteristics of thin-film growth techniques with emphasis on molecular beam epitaxy. We then examine the fundamental principles and pivotal factors underlying three key approaches of creating membranes: (i) chemical lift-off, (ii) the two-dimensional layer–assisted lift-off, and (iii) spalling. We review the methods of exfoliation and transfer for each approach. Last, we provide an outlook into the future of oxide membranes, highlighting their applications and emerging properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Superstructural phase transitions in polymer-grafted nanooctahedra

Superlattices of polyhedral nanocrystals exhibit emergent properties defined by their structural arrangements, but native nanocrystal ligands often limit their programmability. Polymeric ligands address this limitation by enabling tunable nanocrystal softness through modifications of polymer molecular weight and grafting density. Here, we investigate phase transitions in polymer-grafted nanooctahedra by varying polymer length, nanocrystal size, truncation, and ligand density. In two-dimensional superlattices, longer polymers or smaller nanooctahedra induce a transition from orientationally ordered to hexagonal rotator lattices. In three-dimensional superlattices, increasing polymer length drives transitions from Minkowski to body-centered cubic and plastic hexagonal close-packed phases, while higher grafting densities further enable transitions to simple hexagonal phases. Polymer brush and thermodynamic perturbation theories, supported by Monte Carlo simulations, uncover the entropic and enthalpic forces that govern these transitions. This work highlights the versatility of polymer-grafted anisotropic nanocrystals as building blocks for designing hierarchical superstructures and metamaterials with customizable properties.

36 MATERIALS SCIENCE↗

From breaking rules to making rules in materials science

This editorial is a perspective article discussing the broader philosophy of synthesis science, emphasizing how techniques such as MBE allow researchers to manipulate bonding, structure, and defects beyond equilibrium thermodynamics, enabling the design of new materials and emergent properties through controlled growth and epitaxial engineering.

Jalan, Bharat [Univ. of Minnesota, Minneapolis, MN↗

Impact of Polymicrobial Infection on Fitness of Streptococcus gordonii In Vivo

Pathogenic microbial ecosystems are often polymicrobial, and interbacterial interactions drive emergent properties of these communities. In the oral cavity, Streptococcus gordonii is a foundational species in the development of plaque biofilms, which can contribute to periodontal disease and, after gaining access to the bloodstream, target remote sites such as heart valves. Here, we used a transposon sequencing (Tn-Seq) library of S. gordonii to identify genes that influence fitness in a murine abscess model, both as a monoinfection and as a coinfection with an oral partner species, Porphyromonas gingivalis. In the context of a monoinfection, conditionally essential genes were widely distributed among functional pathways. Coinfection with P. gingivalis almost completely changed the nature of in vivo gene essentiality. Community-dependent essential (CoDE) genes under the coinfection condition were primarily related to DNA replication, transcription, and translation, indicating that robust growth and replication are required to survive with P. gingivalis in vivo. Interestingly, a group of genes in an operon encoding streptococcal receptor polysaccharide (RPS) were associated with decreased fitness of S. gordonii in a coinfection with P. gingivalis. Individual deletion of two of these genes (SGO_2020 and SGO_2024) resulted in the loss of RPS production by S. gordonii and increased susceptibility to killing by neutrophils. P. gingivalis protected the RPS mutants by inhibiting neutrophil recruitment, degranulation, and neutrophil extracellular trap (NET) formation. These results provide insight into genes and functions that are important for S. gordonii survival in vivo and the nature of polymicrobial synergy with P. gingivalis. Furthermore, we show that RPS-mediated immune protection in S. gordonii is dispensable and detrimental in the presence of a synergistic partner species that can interfere with neutrophil killing mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗

A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index

In recent decades, the taxonomy of Bacteria and Archaea , and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology community because the emergent properties of Bacteria and Archaea that are identified in this study will help assign genera with higher taxonomic resolution.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamics of Three-Dimensional Shock-Wave/Boundary-Layer Interactions

Advances in measuring and understanding separated, nominally two-dimensional (2D) shock-wave/turbulent-boundary-layer interactions (STBLI) have triggered recent campaigns focused on three-dimensional (3D) STBLI, which display far greater configuration diversity. Nonetheless, unifying properties emerge for semi-infinite interactions, taking the form of conical asymptotic behavior where shock-generator specifics become insignificant. The contrast between 2D and 3D separation is substantial; the skewed vortical structure of 3D STBLI reflects the essentially 2D influence of the boundary layer on the 3D character of the swept shock. As with 2D STBLI, conical interactions engender prominent spectral content below that of the turbulent boundary layer. However, the uniform separation length scale, which is crucial to normalizing the lowest-frequency dynamics in 2D STBLI, is absent. Comparatively, the spectra of 3D STBLI are more representative of the mid-frequency, convective, shear-layer dynamics in 2D, while phenomena associated with 2D separation-shock breathing are muted. Asymptotic behavior breaks down in many regions important to 3D-STBLI dynamics, occurring in a configuration-dependent manner. Aspects of inceptive regions near shock generators and symmetry planes are reviewed. Focused efforts toward 3D modal and nonmodalanalyses, moving-shock/boundary-layer interactions, fluid/structure interactions, and flow control are suggested as directions for future work.

42 ENGINEERING↗

Big Advances at the Nano Scale in the Nanocarbons Division

In this issue of ECS Interface, we highlight some exciting success stories for low-dimensional materials in technologically critical fields. These are areas where emergent properties and processes within quantum-confined low-dimensional materials (and heterostructures) enable novel applications beyond what can be achieved in bulk materials.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Breast-Specific Molecular Clocks Comprised of ELF5 Expression and Promoter Methylation Identify Individuals Susceptible to Cancer Initiation

A robust breast cancer prevention strategy requires risk assessment biomarkers for early detection. We show that expression of ELF5, a transcription factor critical for normal mammary development, is downregulated in mammary luminal epithelia with age. DNA methylation of the ELF5 promoter is negatively correlated with expression in an age-dependent manner. Both ELF5 methylation and gene expression were used to build biological clocks to estimate chronological ages of mammary epithelia. ELF5 clock-based estimates of biological age in luminal epithelia from average-risk women were within three years of chronological age. Biological ages of breast epithelia from BRCA1 or BRCA2 mutation carriers, who were high risk for developing breast cancer, suggested they were accelerated by two decades relative to chronological age. The ELF5 DNA methylation clock had better performance at predicting biological age in luminal epithelial cells as compared with two other epigenetic clocks based on whole tissues. We propose that the changes in ELF5 expression or ELF5-proximal DNA methylation in luminal epithelia are emergent properties of at-risk breast tissue and constitute breast-specific biological clocks.

60 APPLIED LIFE SCIENCES↗

A Bimodal Diagnostic Cloud Fraction Parameterization. Part I: Motivating Analysis and Scheme Description

Cloud fraction parameterizations are beneficial to regional, convection-permitting numerical weather prediction. For its operational regional midlatitude forecasts, the Met Office uses a diagnostic cloud fraction scheme that relies on a unimodal, symmetric subgrid saturation-departure distribution. This scheme has been shown before to underestimate cloud cover and hence an empirically based bias correction is used operationally to improve performance. This first of a series of two papers proposes a new diagnostic cloud scheme as a more physically based alternative to the operational bias correction. The new cloud scheme identifies entrainment zones associated with strong temperature inversions. Additionally, for model grid boxes located in this entrainment zone, collocated moist and dry Gaussian modes are used to represent the subgrid conditions. The mean and width of the Gaussian modes, inferred from the turbulent characteristics, are then used to diagnose cloud water content and cloud fraction. It is shown that the new scheme diagnoses enhanced cloud cover for a given gridbox mean humidity, similar to the current operational approach. It does so, however, in a physically meaningful way. Using observed aircraft data and ground-based retrievals over the southern Great Plains in the United States, it is shown that the new scheme improves the relation between cloud fraction, relative humidity, and liquid water content. An emergent property of the scheme is its ability to infer skewed and bimodal distributions from the large-scale state that qualitatively compare well against observations. A detailed evaluation and resolution sensitivity study will follow in Part II.

54 ENVIRONMENTAL SCIENCES↗

Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

Abstract Background Microbe-microbe interactions between members of the plant rhizosphere are important but remain poorly understood. A more comprehensive understanding of the molecular mechanisms used by microbes to cooperate, compete, and persist has been challenging because of the complexity of natural ecosystems and the limited control over environmental factors. One strategy to address this challenge relies on studying complexity in a progressive manner, by first building a detailed understanding of relatively simple subsets of the community and then achieving high predictive power through combining different building blocks (e.g., hosts, community members) for different environments. Herein, we coupled this reductionist approach with high-resolution mass spectrometry-based metaproteomics to study molecular mechanisms driving community assembly, adaptation, and functionality for a defined community of ten taxonomically diverse bacterial members of Populus deltoides rhizosphere co-cultured either in a complex or defined medium. Results Metaproteomics showed this defined community assembled into distinct microbiomes based on growth media that eventually exhibit composition and functional stability over time. The community grown in two different media showed variation in composition, yet both were dominated by only a few microbial strains. Proteome-wide interrogation provided detailed insights into the functional behavior of each dominant member as they adjust to changing community compositions and environments. The emergence and persistence of select microbes in these communities were driven by specialization in strategies including motility, antibiotic production, altered metabolism, and dormancy. Protein-level interrogation identified post-translational modifications that provided additional insights into regulatory mechanisms influencing microbial adaptation in the changing environments. Conclusions This study provides high-resolution proteome-level insights into our understanding of microbe-microbe interactions and highlights specialized biological processes carried out by specific members of assembled microbiomes to compete and persist in changing environmental conditions. Emergent properties observed in these lower complexity communities can then be re-evaluated as more complex systems are studied and, when a particular property becomes less relevant, higher-order interactions can be identified.

59 BASIC BIOLOGICAL SCIENCES↗

Data for Soil Oxygen Dynamics: A Key Mediator of Tile Drainage Impacts on Coupled Hydrological, Biogeochemical, and Crop Systems

Tile drainage removes excess water and is an essential, widely adopted management practice to enhance crop productivity in the US Midwest and throughout the world. Tile drainage has been shown to significantly change hydrological and biogeochemical cycles by lowering the water table and reducing the residence time of soil water, although examining the complex interactions and feedbacks in an integrated hydrology–biogeochemistry–crop system remains elusive. Oxygen dynamics are critical to unraveling these interactions and have been ignored or oversimplified in existing models. Understanding these impacts is essential, particularly so because tile drainage has been highlighted as an adaptation under projected wetter springs and drier summers in the changing climate in the US Midwest. We used the ecosys model that uniquely incorporates first-principle soil oxygen dynamics and crop oxygen uptake mechanisms to quantify the impacts of tile drainage on hydrological and biogeochemical cycles and crop growth in corn–soybean rotation fields. The model was validated with data from a multi-treatment, multi-year experiment in Washington, IA. The relative root mean square error (rRMSE) for the corn and soybean yield in validation is 5.66 % and 12.57 %, respectively. The Pearson coefficient (r) of the monthly tile flow during the growing season is 0.78. Plant oxygen stress turns out as an emergent property of the equilibrium between the soil oxygen supply and biological demand. The impact of tile drainage on the system is achieved through a series of coupled feedback mechanisms. The model results show that tile drainage reduces the soil water content and enhances soil oxygenation. It additionally increases the subsurface discharge and elevates inorganic nitrogen leaching, with seasonal variations influenced by climate and crop phenology. The improved aerobic condition alleviates crop oxygen stress during wet springs, thereby promoting crop root growth during the early growth stage. The development of greater root density, in turn, mitigates water stress during dry summers, leading to an overall increase in the crop yield by ∼6 %. These functions indicate the potential of tile drainage in bolstering crop resilience to climate change and the use of this modeling tool for large-scale assessments of tile drainage. The model reveals the underlying causal mechanisms that drive the agroecosystem response to drainage on the coupled hydrology, biogeochemistry, and crop system dynamics.

Modeling↗

Physics Division Strategic Plan Fiscal Years 2020-2024

The vision of the Physics Division (PHY) at Argonne National Laboratory is to continue enhancing its role as a world-leading institution in basic nuclear physics research and its applications. Key to this vision is for PHY to continue to safely and effectively operate and evolve the capabilities of the Argonne Tandem Linac Accelerator System (ATLAS) facility to best serve its users. ATLAS is the Department of Energy (DOE) accelerator facility for low-energy nuclear physics research. The research carried out by PHY covers many themes in contemporary science but can be distilled into five areas of focus. These themes are interconnected, with continuously evolving synergies between the various groups and facilities in PHY and the broader Laboratory. This five-year strategic plan serves to illustrate our current capabilities and new directions related to these five areas of focus (ATLAS also develops an independent strategic plan): Accelerator research and design. The goal of this theme is to design, fabricate, test, and implement novel accelerator systems, with a focus on high-intensity ion and electron systems. These R&D activities have led to enhancements in the ATLAS accelerator system. Among others, the division’s accelerator systems are in use or planned for use at Fermilab, the Advanced Photon Source, and in a broad variety of applications at the Facility for Rare Isotope Beams (FRIB). Atom trapping and fundamental symmetries. The goal of this theme is to explore and exploit the uses of advanced laser cooling and trapping techniques to manipulate atoms. There are three main areas of focus. First is in the application of the atom trap trace analysis (ATTA) technique for age determination of groundwater and ice by using radio-krypton dating. The next two trapping-based programs involve tests of fundamental symmetries in nature: the cooling and trapping of radium-225 with the aim of determining limits on an observation of its electric dipole moment and precision measurements of the beta decay properties of helium-6 to set limits on the tensor coupling constant. This is complemented by measurements of similar properties in lithium-8 and boron-8. Nuclear astrophysics. The goal of this theme is to enhance our understanding of how elements are created in the universe via explosive nucleosynthesis and how stars evolve. To meet the challenges of this theme, many of the capabilities of ATLAS are being enhanced, including the development of new beams through a new in-flight separator (RAISOR) and the anticipated neutron-generator upgrade of the Californium Rare Isotope Breeder Upgrade facility (nuCARIBU). These are coupled to state-of-the-art instruments such as the Canadian Penning Trap, Helical Orbit Spectrometer, Gammasphere, GRETINA, Multi-Sampling Ionization Chamber, the Fragment Mass Analyzer, and Argonne Gas-filled Fragment Analyzer, and a new low-background experimental area for decay studies. Nuclear structure. The goal of this theme is to understand the structure of nuclei, both stable and radioactive, in terms of single-particle properties, their shapes, and the dynamics governing reactions between them. These include questions such as what are the limits of nuclear stability and what are the properties of super heavy nuclei. As with the nuclear astrophysics theme, the capabilities of ATLAS, guided by the ATLAS user community, are continuously being enhanced to this end. The Division has strategic initiatives to play a leading role in the development of instrumentation and research programs at the FRIB. Quantum chromodynamics (QCD) and hadron physics. The goal of this theme is to lead major research programs focused on revealing the quark and gluon structure of protons, neutrons, nuclei, and short-lived mesons and baryons. These involve major programs at Jefferson Lab, Fermilab, and smaller facilities. They are complemented by theoretical endeavors centered on the question of how hadrons and their properties emerge from QCD. Out of these activities arise strategic initiatives to play a major role in the forthcoming Electron-Ion Collider (EIC).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The Electron-Ion Collider at Brookhaven National Laboratory

The Electron-Ion Collider (EIC), designed by a BNL-TJNAF partnership, will uniquely address three profound questions about nucleons - neutrons and protons, and how they are assembled to form the nuclei of atoms: How does the mass of the nucleon arise? How does the spin of the nucleon arise? What are the emergent properties of dense systems of gluons?

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Institute for Quantum Matter

The mission of the Institute for Quantum Matter (IQM) Energy Frontier Research Center was to discover and understand emergent properties in material systems with the potential for transformative impacts on energy and information technologies.

36 MATERIALS SCIENCE↗

Zentropy Theory for Transformative Functionalities of Magnetic and Superconducting Materials

The proposed research developed the zentropy theory through applications to complex magnetic materials and superconductors under the hypothesis that the emergent properties of complex magnetic materials and superconductors can be predicted by statistical mechanics of ergodic microstates with their partition functions computed from DFT-predicted free energies. The key objective is to develop approaches to systematically determine the types and number of microstates and the supercell size in DFT-based calculations through convergency of macroscopic functionalities, with the incorporation of our mixed-space approach accounting for the interactions between periodic supercells. In addition to use scientific intuitions to guide the design of important microstates, the key innovation of the proposed research is to integrate the domain knowledge and the material-property-descriptor database (MPDD) with 4 million microstates, which is supported by our deep neural network machine learning models (SIPFENN: structure-informed prediction of formation energy using neural networks) and integrated with our high throughput DFT Tool Kit (DFTTK). For complex magnetic materials, one of the objectives is to develop approaches to calculate short-range ordering from the statistical distribution of each microstate. For superconductors, the divergency of quasiparticle effective mass at a quantum critical point will be investigated, and the superconducting and non-superconducting microstates will be delineated through analysis of electronic band structure, density of states, charge density, and Fermi surface.

36 MATERIALS SCIENCE↗

Local chiral EFT potentials in nuclei and neutron matter: results and issues

In recent years, the combination of advanced quantum Monte Carlo (QMC) methods and local interactions derived from chiral effective field theory (EFT) has been shown to provide a versatile and systematic approach to nuclear systems. Calculations at next-to-next-to-leading order in chiral EFT have lead to fascinating results for nuclei and nucleonic matter. On the one hand, ground-state properties of nuclei are well reproduced up to A $≤$ 16, even though these potentials have been fit to nucleon-nucleon scattering and few-body observables only. On the other hand, a reasonable description of neutron-matter properties emerges. While regulator functions applied to two- and three-nucleon forces are a necessary ingredient in these many-body calculations, the use of local regulators leads to a substantial residual regulator and cutoff dependence that increases current theoretical uncertainties. In this contribution, we review local chiral interactions, their applications, and QMC results for nuclei and neutron matter. In addition, we address regulator issues for such potentials and present a possible path forward.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Quantifying the structural uncertainty of the aerosol mixing state representation in a modal model

Abstract. Aerosol mixing state is an important emergent property that affects aerosol radiative forcing and aerosol–cloud interactions, but it has not been easy to constrain this property globally. This study aims to verify the global distribution of aerosol mixing state represented by modal models. To quantify the aerosol mixing state, we used the aerosol mixing state indices for submicron aerosol based on the mixing of optically absorbing and non-absorbing species (χo), the mixing of primary carbonaceous and non-primary carbonaceous species (χc), and the mixing of hygroscopic and non-hygroscopic species (χh). To achieve a spatiotemporal comparison, we calculated the mixing state indices using output from the Community Earth System Model with the four-mode version of the Modal Aerosol Module (MAM4) and compared the results with the mixing state indices from a benchmark machine-learned model trained on high-detail particle-resolved simulations from the particle-resolved stochastic aerosol model PartMC-MOSAIC. The two methods yielded very different spatial patterns of the mixing state indices. In some regions, the yearly averaged χ value computed by the MAM4 model differed by up to 70 percentage points from the benchmark values. These errors tended to be zonally structured, with the MAM4 model predicting a more internally mixed aerosol at low latitudes and a more externally mixed aerosol at high latitudes compared to the benchmark. Our study quantifies potential model bias in simulating mixing state in different regions and provides insights into potential improvements to model process representation for a more realistic simulation of aerosols towards better quantification of radiative forcing and aerosol–cloud interactions.

54 ENVIRONMENTAL SCIENCES↗

Development of a plant carbon–nitrogen interface coupling framework in a coupled biophysical-ecosystem–biogeochemical model (SSiB5/TRIFFID/DayCent-SOM v1.0)

Plant and microbial nitrogen (N) dynamics and N availability regulate the photosynthetic capacity and capture, allocation, and turnover of carbon (C) in terrestrial ecosystems. Studies have shown that a wide divergence in representations of N dynamics in land surface models leads to large uncertainties in the biogeochemical cycle of terrestrial ecosystems and then in climate simulations as well as the projections of future trajectories. In this study, a plant C–N interface coupling framework is developed and implemented in a coupled biophysical-ecosystem–biogeochemical model (SSiB5/TRIFFID/DayCent-SOM v1.0). The main concept and structure of this plant C–N framework and its coupling strategy are presented in this study. This framework takes more plant N-related processes into account. The dynamic ratio (CNR) for each plant functional type (PFT) is introduced to consider plant resistance and adaptation to N availability to better evaluate the plant response to N limitation. Furthermore, when available N is less than plant N demand, plant growth is restricted by a lower maximum carboxylation capacity of RuBisCO (V c,max ), reducing gross primary productivity (GPP). In addition, a module for plant respiration rates is introduced by adjusting the respiration with different rates for different plant components at the same N concentration. Since insufficient N can potentially give rise to lags in plant phenology, the phenological scheme is also adjusted in response to N availability. All these considerations ensure a more comprehensive incorporation of N regulations to plant growth and C cycling. This new approach has been tested systematically to assess the effects of this coupling framework and N limitation on the terrestrial carbon cycle. Long-term measurements from flux tower sites with different PFTs and global satellite-derived products are employed as references to assess these effects. The results show a general improvement with the new plant C–N coupling framework, with more consistent emergent properties, such as GPP and leaf area index (LAI), compared to the observations. The main improvements occur in tropical Africa and boreal regions, accompanied by a decrease in the bias in global GPP and LAI by 16.3 % and 27.1 %, respectively.

54 ENVIRONMENTAL SCIENCES↗