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At least 253 records · Page 14

Nutrient Restoration of a Large, Impounded, Ultra-Oligotrophic Western River to Recover Declining Native Fishes

Abstract Declines in many fish populations in large, western rivers have been primarily attributed to the anthropogenic reduction of nutrient inputs and subsequent impacts to the food web. The largest known river fertilization program was implemented starting in 2005 on the Kootenai River in northern Idaho to restore resident fisheries. Annual electrofishing surveys were conducted at multiple sites in Idaho and Montana before and during nutrient addition to evaluate assemblage and population-level responses. Although few responses in fish assemblage structure were observed, the addition of liquid ammonium polyphosphate fertilizer (3 μg/L) to the Kootenai River increased fish abundance and biomass over the 20-km stretch of river downstream of the treatment site. Increases were most notable in Largescale Suckers Catostomus macrocheilus, Mountain Whitefish Prosopium williamsoni, and Rainbow Trout Oncorhynchus mykiss populations, although increases in catch and biomass were detected for nearly all fish species. The Kootenai River is approximately 30 times larger in discharge than other rivers that have been experimentally fertilized and provides compelling evidence that the mitigation of nutrient declines in rivers of similar size can result in positive influences on the fish populations where primary and secondary production are limiting growth, survival, and recruitment. However, results from our study also highlight the importance of completing evaluations across varying levels of biological organization (e.g., assemblage and population) and over biologically relevant timeframes.

Hardy, Ryan S.↗

Non-equilibrium states and interactions in the topological insulator and topological crystalline insulator phases of NaCd4As3

Topological materials are of great interest because they can support metallic edge or surface states that are robust against perturbations, with the potential for technological applications. Here, we experimentally explore the light-induced non-equilibrium properties of two distinct topological phases in NaCd4As3: a topological crystalline insulator (TCI) phase and a topological insulator (TI) phase. This material has surface states that are protected by mirror symmetry in the TCI phase at room temperature, while it undergoes a structural phase transition to a TI phase below 200 K. After exciting the TI phase by an ultrafast laser pulse, we observe a leading band edge shift of >150 meV that slowly builds up and reaches a maximum after ∼0.6 ps and that persists for ∼8 ps. The slow rise time of the excited electron population and electron temperature suggests that the electronic and structural orders are strongly coupled in this TI phase. It also suggests that the directly excited electronic states and the probed electronic states are weakly coupled. Both couplings are likely due to a partial relaxation of the lattice distortion, which is known to be associated with the TI phase. In contrast, no distinct excited state is observed in the TCI phase immediately or after photoexcitation, which we attribute to the low density of states and phase space available near the Fermi level. Our results show how ultrafast laser excitation can reveal the distinct excited states and interactions in phase-rich topological materials.

Angle-resolved photoemission spectroscopy↗

Enhanced thermoelectric performance of SnSe by controlled vacancy population

Abstract The thermoelectric performance of SnSe strongly depends on its low-energy electron band structure that provides high density of states in a narrow energy window due to the multi-valley valence band maximum (VBM). Angle-resolved photoemission spectroscopy measurements, in conjunction with first-principles calculations, reveal that the binding energy of the VBM of SnSe is tuned by the population of Sn vacancy, which is determined by the cooling rate during the sample growth. The VBM shift follows precisely the behavior of the thermoelectric power factor, while the effective mass is barely modified upon changing the population of Sn vacancies. These findings indicate that the low-energy electron band structure is closely correlated with the high thermoelectric performance of hole-doped SnSe, providing a viable route toward engineering the intrinsic defect-induced thermoelectric performance via the sample growth condition without an additional ex-situ process. Graphical Abstract

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Global overview and major challenges of host prediction methods for uncultivated phages

Bacterial communities play critical roles across all of Earth’s biomes, affecting human health and global ecosystem functioning. They do so under strong constraints exerted by viruses, i.e., bacteriophages or “phages”. Phages can reshape bacterial communities’ structure, influence long-term evolution of bacterial populations, and alter host cell metabolism during infection. Metagenomics approaches, i.e., shotgun sequencing of environmental DNA or RNA, recently enabled large-scale exploration of phage genomic diversity, yielding several millions of phage genomes now to be further analyzed and characterized. One major challenge however is the lack of direct host information for these phages. Several methods and tools have been proposed to bioinformatically predict the potential host(s) of uncultivated phages based only on genome sequence information. Here we review these different approaches and highlight their distinct strengths and limitations. We also outline complementary experimental assays which are being proposed to validate and refine these bioinformatic predictions.

59 BASIC BIOLOGICAL SCIENCES↗

Prediction of Transition-State Scaling Relationships and Universal Transition-State Vibrational and Entropic Correlations for Dehydrogenations

Linear scaling relationships (LSRs) and Brønsted–Evans–Polanyi (BEP) or transition-state scaling (TSS) relations aid with the prediction of electronic energies. However, temperature effects and pre-exponentials are often taken as constants across metal surfaces or a homologous series. Vibrational scaling relationships (VSRs) offer a way to determine such parameters. Transition-state VSRs (TSVSRs) between local minima and transition states of AH X (A = C, N, O) surface diffusions correlate with BEP relations and broaden to thermochemical property scaling. Using density functional theory, we extend TSVSRs to AHX dehydrogenation reactions on transition-metal surfaces, relating vibrational modes of local minima to transition states. We first predict the slopes of the TSS relations by incorporating bond angles using the Slater–Koster structure factors and hybridization through crystal orbital overlap population analysis and energy overlap integrals between adsorbates and metal surfaces. Additionally, we uncover universal thermochemical property scaling, enabling the estimation of entropies and temperature corrections to enthalpies across a homologous series. Here, we demonstrate both significant vibrational corrections in reactions with low intrinsic electronic barriers and considerable variation in the pre-exponential of a simple dehydrogenation reaction across metals and AH X adsorbates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spectroscopic Probe Molecule Selection Using Quantum Theory, First-Principles Calculations, and Machine Learning

Probe molecule vibrational spectra have a long history of being used to characterize materials including metals, oxides, metal-organic frameworks, and even human proteins. Furthermore, recent advances in machine learning have enabled computationally generated spectra to aid in detailed characterization of complex surfaces with probe molecules. Despite widespread use of probe molecules, the science of probe molecule selection is underdeveloped. Here, we develop physical concepts, including orbital interaction energy and the energy overlap integral, to explain and predict the ability of probe molecules to discriminate structural descriptors. We resolve the crystal orbital overlap population (COOP) to specific molecular orbitals and quantify their bonding character, which directly influences vibrational frequencies. Using only a single adsorbate calculation from density function theory (DFT), we compute the interaction energy of individual adsorbate molecular orbitals with adsorption site atomic orbitals across many different sites. Combining the molecular orbital resolved COOP and changes in orbital interaction energy enables probe molecule selection for improved discrimination of various sites. We demonstrate these concepts by comparing the predicted effectiveness of carbon monoxide (CO), nitric oxide (NO), and ethylene (C 2 H 4 ) to probe Pt adsorption sites. Finally, using a previously developed machine learning framework, we show that models trained on hundreds of thousand C 2 H 4 spectra, computed from DFT, which regress surface binding-type and generalized coordination number (GCN), outperform those trained using CO and NO spectra. Lastly, a python package, pDOS_overlap, for implementing the electron density based analysis on any combination of adsorbates and materials, is also made available.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Ultrafast Carrier Self-Trapping Driven by Strong Exciton–Phonon Coupling in 2D MA 3 Bi 2 I 6 Cl 3 Perovskite

Two-dimensional (2D) hybrid bismuth halide perovskites have emerged as promising lead-free materials for optoelectronic applications due to their solution processability and tunable structures. Here, in this study, we investigate 2D layered hybrid perovskite MA 3 Bi 2 I 6 Cl 3 using temperature-dependent photoluminescence (PL) and femtosecond transient absorption spectroscopy. Our results reveal strong coupling between excitons and phonons, evidenced by giant Huang–Rhys factors, coherent phonon oscillations, and ultrafast carrier self-trapping into small-polaron and self-trapped exciton (STE) states. These processes appear as time-dependent ground-state bleach and photoinduced absorption features, highlighting the influence of the lattice in carrier dynamics. Wavelength- and time-resolved measurements reveal that PL emission is dominated by STEs, while free exciton emission is weak and short-lived. By comparing 2D MA 3 Bi 2 I 6 Cl 3 with 0D MA 3 Bi 2 I 9 , which contains molecularly isolated [BiI 6 ] 3− octahedra and 2D MA 3 Bi 2 Br 9 perovskites, we demonstrate how halide composition and structural dimensionality influence the balance between free exciton populations and carrier localization. These insights uncover the intrinsic kinetic landscape of photoexcited states in MA 3 Bi 2 I 6 Cl 3 . Overall, our study contributes to a mechanistic understanding of exciton–phonon interactions in lead-free 2D perovskites.

Pradeep, Kodimana Ramakrishnan [Northwestern Univ.↗

Increasing freshwater supply to sustainably address global water security at scale

While significant parts of the globe are already facing significant freshwater scarcity, the need for more freshwater is projected to increase in order to sustain the increasing global population and economic growth, and adapt to climate change. Current approaches for addressing this challenge, which has the potential to result in catastrophic outcomes for consumptive needs and economic growth, rely on increasing the efficient use of existing resources. However, the availability of freshwater resources is rapidly declining due to over-exploitation and climate change and, therefore, is unlikely to sustainably address future needs, which requires a rethink of our solutions and associated investments. Here we present a bold departure from existing approaches by establishing the viability of significantly increasing freshwater through the capture of humid air over oceans. We show that the atmosphere above the oceans proximal to the land can yield substantial freshwater, sufficient to support large population centers across the globe, using appropriately engineered structures. Due to the practically limitless supply of water vapor from the oceans, this approach is sustainable under climate change and can transform our ability to address present and future water security concerns. This approach is envisioned to be transformative in establishing a mechanism for sustainably providing freshwater security to the present and future generations that is economically viable.

54 ENVIRONMENTAL SCIENCES↗

The differences between mass- and light-derived structural parameters over time for MaNGA elliptical galaxies

ABSTRACT We apply stellar population synthesis analysis to obtain spatially resolved archaeological inferences for a large sample of ‘red and dead’ Elliptical galaxies (Classical Ellipticals, CLEs) from the MaNGA/SDSS-IV DR15 survey. From their 2D stellar light and mass maps, we explore the differences between the radial mass and light distributions in the rest-frame bands g, r, and i as functions of look-back time, tlb, or redshift, z. We characterize these differences through the ratios between the following mass- and light-derived global properties: sizes, concentrations, and effective surface densities. We find that the mass-to-light ratios of these properties change with tlb, more the more massive the galaxies are. The CLE galaxy archaeological progenitors are, on average, less compact, concentrated, and dense in light than in mass as z decreases. However, at later times, when also the evolution of the progenitors becomes passive at all radii, there is an upturn in these trends and the differences between mass and light in compactness/concentration decrease towards z ∼ 0. The trends in the ratios of mass-to-light sizes agree qualitatively with results from direct observations in galaxy surveys at different redshifts. We discuss the caveats and interpretations of our results, and speculate that the strong structural evolution found in some previous studies for early-type galaxies could be explained partially by photometric changes rather than by intrinsic structural changes.

Ibarra-Medel, H. (ORCID:0000000297906313)↗

Demographic Microsimulator for Integrated Urban Systems: Adapting Panel Survey of Income Dynamics to Capture the Continuum of Life

Agent-based models (ABMs) simulate activity and travel decisions at the disaggregate level of households, and individuals. To do this, ABMs require detailed information pertaining to socioeconomic and demographic characteristics of individuals. Various synthetic population generators (SPGs) have been proposed to address this need. However, most of the SPGs currently in practice are cross-sectional in nature, and do not account for the interrelationships among household's or individual's life progression. This is a major shortcoming of SPGs as literature has shown that transportation decisions are impacted by lifecycle events that unfold over a span of time. While some demographic evolution simulators have been proposed to address this shortcoming, they: i) are developed using cross-sectional data, ii) do not capture the full spectrum of lifecycle events and their interdependency. Overcoming these drawbacks, this paper proposes a Demographic Microsimulator (DEMOS) which captures the 'continuum of life' by accounting for a range of household-, and individual-level lifecycle events. DEMOS is developed using the Panel Survey of Income Dynamics, which is one of the world's longest running longitudinal surveys. DEMOS sub-models consider key lifecycle events which are influenced by a host of demographic variables. The whole framework is applied to evolve the population of San Francisco Bay Area over a 9-year horizon. Results indicate that the household and individual evolution are tightly connected, and that the structural framework (i.e., model sequencing) is a key element in capturing the population trend accurately.

ADVANCED PROPULSION SYSTEMS,ENERGY PLANNING, POLIC↗

Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unveiling the star formation history of the Upper Scorpius association through its kinematics

ABSTRACT Stellar associations can be discerned as overdensities of sources not only in the physical space but also in the velocity space. The common motion of their members, gradually eroded by the galactic tidal field, is partially reminiscent of the initial kinematic structure. Using recent data from Gaia EDR3, combined with radial velocities from GALAH and APOGEE, we traced back the present positions of stars belonging to Upper Scorpius (USCO), a subgroup of Scorpius–Centaurus, the nearest OB association. About one half of the subgroup (the ‘clustered’ population) appears composed of many smaller entities, which were in a more compact configuration in the past. The presence of a kinematic duality is reflected into an age spread between this younger clustered population and an older diffuse population, in turn confirmed by a different fraction fD of disc-bearing stars (fD = 0.24 ± 0.02 versus fD = 0.10 ± 0.01). Star formation in USCO appears to have lasted more than 10 Myr and proceeded in small groups that, after a few Myr, dissolve in the field of the older population but retain for some time memory of their initial structure. The difference of ages inferred through isochrones and kinematics, in this regard, could provide a powerful tool to quantify the time-scale of gas removal.

79 ASTRONOMY AND ASTROPHYSICS↗

Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China

Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments.

59 BASIC BIOLOGICAL SCIENCES↗

Distance Estimate Method for Asymptotic Giant Branch Stars Using Infrared Spectral Energy Distributions

We present a method to estimate distances to asymptotic giant branch (AGB) stars in the Galaxy, using spectral energy distributions (SEDs) in the near- and mid-infrared. By assuming that a given set of source properties (initial mass, stellar temperature, composition, and evolutionary stage) will provide a typical SED shape and brightness, sources are color matched to a distance-calibrated template and thereafter scaled to extract the distance. The method is tested by comparing the distances obtained to those estimated from very long baseline interferometry or Gaia parallax measurements, yielding a strong correlation in both cases. Additional templates are formed by constructing a source sample likely to be close to the Galactic center, and thus with a common, typical distance for calibration of the templates. These first results provide statistical distance estimates to a set of almost 15,000 Milky Way AGB stars belonging to the Bulge Asymmetries and Dynamical Evolution (BAaDE) survey, with typical distance errors of ±35%. With these statistical distances, a map of the intermediate-age population of stars traced by AGBs is formed, and a clear bar structure can be discerned, consistent with the previously reported inclination angle of 30° to the GC–Sun direction vector. These results motivate deeper studies of the AGB population to tease out the intermediate-age stellar distribution throughout the Galaxy, as well as determining statistical properties of the AGB population luminosity and mass-loss-rate distributions.

79 ASTRONOMY AND ASTROPHYSICS↗

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition

ABSTRACT Understanding the organizational principles of microbial communities is essential for interpreting ecosystem stability. Previous studies have investigated the formation of bacterial communities under nutrient-poor conditions or obligate relationships to observe cooperative interactions among different species. How microorganisms form stabilized communities in nutrient-rich environments, without obligate metabolic interdependency for growth, is still not fully disclosed. In this study, three bacterial strains isolated from the Populus deltoides rhizosphere were co-cultured in complex medium, and their growth behavior was tracked. These strains co-exist in mixed culture over serial transfer for multiple growth-dilution cycles. Competition is proposed as an emergent interaction relationship among the three bacteria based on their significantly decreased growth levels. The effects of different initial inoculum ratios, up to three orders of magnitude, on community structure were investigated, and the final compositions of the mixed communities with various starting composition indicate that community structure is not dependent on the initial inoculum ratio. Furthermore, the competitive relationships within the community were not altered by different initial inoculum ratios. The community structure was simulated by generalized Lotka-Volterra and dynamic flux balance analysis to provide mechanistic predictions into emergence of community structure under a nutrient-rich environment. Metaproteomic analyses provide support for the metabolite exchanges predicted by computational modeling and for highly altered physiologies when microbes are grown in co-culture. These findings broaden our understanding of bacterial community dynamics and metabolic diversity in higher-order interactions and could be significant in the management of rhizospheric bacterial communities. IMPORTANCE Bacteria naturally co-exist in multispecies consortia, and the ability to engineer such systems can be useful in biotechnology. Despite this, few studies have been performed to understand how bacteria form a stable community and interact with each other under nutrient-rich conditions. In this study, we investigated the effects of initial inoculum ratios on bacterial community structure using a complex medium and found that the initial inoculum ratio has no significant impact on resultant community structure or on interaction patterns between community members. The microbial population profiles were simulated using computational tools in order to understand intermicrobial relationships and to identify potential metabolic exchanges that occur during stabilization of the bacterial community. Studying microbial community assembly processes is essential for understanding fundamental ecological principles in microbial ecosystems and can be critical in predicting microbial community structure and function.

59 BASIC BIOLOGICAL SCIENCES↗

Deep Learning Scene Classification Experiments in Automatic Detection of Slums on Planetscope Imagery

Population growth is increasingly happening in slum settlements of the large urban centers in the Global South. The term "slum" encompasses a wide range of communities, located mostly in underserved areas, and often exhibiting distinct structural and functional informalities with a relatively high concentration of marginalized populations. To address the issues confronting slums for effective planning and development, including the realistic estimation of the resident population, identifying them accurately is fundamental. Given the disagreements over a universal definition, diverse characteristic features, and socio-political limitations, global detection of slums is a veritable challenge. In this paper, we present experiments in slum detection using a scene classification algorithm and 3-meter spatial resolution satellite imagery. We train and evaluate the model for slum detection in Mumbai, India for the year 2023 and test the temporal generalization of the trained model on Mumbai in 2020 and 2018. In addition, we explore the pathways toward geographic generalization to Kolkata and Delhi (India). We discuss several limitations in the workflow and model, situate our findings in the existing literature, and suggest improvements and alternatives. With this, we establish baseline methods and experiments as a first step towards developing an image-based global slum detection framework and algorithm. This work adds to the community discussion on methods, data challenges, and open questions related to the detection of slums globally. With this research, we hope to improve our understanding of human settlements, especially in critical areas, improve population estimates, and help measure progress towards the sustainable development goals.

Arndt, Jacob↗

Electron emission from bromouracil and uracil induced by protons and radiosensitization

Absolute double differential cross sections (DDCS) of electrons emitted from uracil and 5-bromouracil (BrU) in collisions with protons of energy 200 keV have been measured for various forward and backward emission angles over wide range of electron energies. The measured DDCS are compared with the continuum distorted wave-eikonal initial state (CDW-EIS) calculations. The optimized structure of the BrU was estimated along with the population analysis of all the occupied orbitals using a self-consistent field density. A comparison between the measured DDCS data for the two molecules show that the cross section of low energy electrons emitted from BrU is substantially larger than that for uracil. The BrU-to-uracil DDCS ratios obtained from the present measurements indicate an enhancement of the electron emission by a factor which is as large as 2.0 to 2.5. These electrons being the major agent for damaging the DNA/RNA of the malignant tissues, the present results are expected to provide an important input for the radiosensitization effect in hadron therapy. It is noteworthy to mention that the CDW-EIS calculations for Coulomb ionization cannot predict such enhancement. A large angular asymmetry is observed for uracil with a broad structure, which is absent in case of BrU.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗