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At least 109 records · Page 6

A new approach for simulating inhomogeneous chemical kinetics

Abstract In this paper, inhomogeneous chemical kinetics are simulated by describing the concentrations of interacting chemical species by a linear expansion of basis functions in such a manner that the coupled reaction and diffusion processes are propagated through time efficiently by tailor-made numerical methods. The approach is illustrated through modelling $$\alpha$$ α - and $$\gamma$$ γ -radiolysis in thin layers of water and at their solid interfaces from the start of the chemical phase until equilibrium was established. The method’s efficiency is such that hundreds of such systems can be modelled in a few hours using a single core of a typical laptop, allowing the investigation of the effects of the underlying parameter space. Illustrative calculations showing the effects of changing dose-rate and water-layer thickness are presented. Other simulations are presented which show the approach’s capability to solve problems with spherical symmetry (an approximation to an isolated radiolytic spur), where the hollowing out of an initial Gaussian distribution is observed, in line with previous calculations. These illustrative simulations show the generality and the computational efficiency of this approach to solving reaction-diffusion problems. Furthermore, these example simulations illustrate the method’s suitability for simulating solid-fluid interfaces, which have received a lot of experimental attention in contrast to the lack of computational studies.

97 MATHEMATICS AND COMPUTING↗

Non-Contact Vapor Detection of Illicit Drugs via Atmospheric Flow Tube-Mass Spectrometry

Real-time, non-contact detection of illicit drugs is a desirable goal for the interdiction of these controlled substances, but the relatively low vapor pressures of such species present a challenge for trace vapor detection technologies. The introduction of atmospheric flow tube-mass spectrometry (AFT-MS), which has previously been demonstrated to detect gas-phase analytes at low parts-per-quadrillion levels for explosives and organophosphorus compounds, also enables the potential for non-contact drug detection. With AFT-MS, direct vapor detection of cocaine and methamphetamine from ~5 µg residues at room temperature is demonstrated herein. Furthermore, thermal desorption of low- to sub-picogram levels of cocaine, methamphetamine, fentanyl, and heroin is observed via AFT-MS using a carrier flow rate of several L/min of air. These low levels can permit non-contact sampling through collection of vapor, effectively preconcentrating the analyte before desorption and analysis. Quantitative evaluation of the thermal desorption approach has yielded limits of detection (LODs) on order of 10 fg for cocaine and fentanyl, 100 fg for methamphetamine, and 1.6 pg for heroin. The LOD for heroin was lowered to 200 fg by using tributyl phosphate as a dopant to form a proton-bound heterodimer with heroin. When used with AFT-MS, the intentional formation of specific drug-dopant adducts has the potential to enhance detection limits and selectivity of additional drug species. Species that are prone to form adducts present a challenge to analysis, but that difficulty can be overcome by the intentional addition of a dopant. Molecules unlikely to form adducts will remain essentially unimpacted, but the adduct-forming species will interact with the dopant to compress the analyte signal into a single peak. This approach would be valuable in the application of non-contact screening for illicit substances via vapor collection followed by thermal desorption for analysis.

methamphetamine, cocaine, heroin, fentanyl, atmosp↗

Landscape fragmentation overturns classical metapopulation thinking

Habitat loss and isolation caused by landscape fragmentation represent a growing threat to global biodiversity. Existing theory suggests that the process will lead to a decline in metapopulation viability. However, since most metapopulation models are restricted to simple networks of discrete habitat patches, the effects of real landscape fragmentation, particularly in stochastic environments, are not well understood. To close this major gap in ecological theory, we developed a spatially explicit, individual-based model applicable to realistic landscape structures, bridging metapopulation ecology and landscape ecology. This model reproduced classical metapopulation dynamics under conventional model assumptions, but on fragmented landscapes, it uncovered general dynamics that are in stark contradiction to the prevailing views in the ecological and conservation literature. Notably, fragmentation can give rise to a series of dualities: a) positive and negative responses to environmental noise, b) relative slowdown and acceleration in density decline, and c) synchronization and desynchronization of local population dynamics. Furthermore, counter to common intuition, species that interact locally (“residents”) were often more resilient to fragmentation than long-ranging “migrants.” This set of findings signals a need to fundamentally reconsider our approach to ecosystem management in a noisy and fragmented world.

54 ENVIRONMENTAL SCIENCES↗

Skyrmion dynamics and topological sorting on periodic obstacle arrays

Abstract We examine skyrmions under a dc drive interacting with a square array of obstacles for varied obstacle size and damping. When the drive is applied in a fixed direction, we find that the skyrmions are initially guided in the drive direction but also move transverse to the drive due to the Magnus force. The skyrmion Hall angle, which indicates the difference between the skyrmion direction of motion and the drive direction, increases with drive in a series of quantized steps as a result of the locking of the skyrmion motion to specific symmetry directions of the obstacle array. On these steps, the skyrmions collide with an integer number of obstacles to create a periodic motion. The transitions between the different locking steps are associated with jumps or dips in the velocity–force curves. In some regimes, the skyrmion Hall angle is actually higher than the intrinsic skyrmion Hall angle that would appear in the absence of obstacles. In the limit of zero damping, the skyrmion Hall angle is 90°, and we find that it decreases as the damping increases. For multiple interacting skyrmion species in the collective regime, we find jammed behavior at low drives where the different skyrmion species are strongly coupled and move in the same direction. As the drive increases, the species decouple and each can lock to a different symmetry direction of the obstacle lattice, making it possible to perform topological sorting in analogy to the particle sorting methods used to fractionate different species of colloidal particles moving over two-dimensional obstacle arrays.

36 MATERIALS SCIENCE↗

Numerical discreteness errors in multispecies cosmological N -body simulations

ABSTRACT We present a detailed analysis of numerical discreteness errors in two-species, gravity-only, cosmological simulations using the density power spectrum as a diagnostic probe. In a simple set-up where both species are initialized with the same total matter transfer function, biased growth of power forms on small scales when the solver force resolution is finer than the mean interparticle separation. The artificial bias is more severe when individual density and velocity transfer functions are applied. In particular, significant large-scale offsets in power are measured between simulations with conventional offset grid initial conditions when compared against converged high-resolution results where the force resolution scale is matched to the interparticle separation. These offsets persist even when the cosmology is chosen so that the two particle species have the same mass, indicating that the error is sourced from discreteness in the total matter field as opposed to unequal particle mass. We further investigate two mitigation strategies to address discreteness errors: the frozen potential method and softened interspecies short-range forces. The former evolves particles under the approximately ‘frozen’ total matter potential in linear theory at early times, while the latter filters cross-species gravitational interactions on small scales in low-density regions. By modelling closer to the continuum limit, both mitigation strategies demonstrate considerable reductions in large-scale power spectrum offsets.

79 ASTRONOMY AND ASTROPHYSICS↗

Correlating confinement to topological fluctuations near the crossover transition in QCD

We show the existence of strong (anti)correlations between the topological hot spots and the local values of the trace of the Polyakov loop in 2 + 1 flavor QCD with physical quark mass, in the vicinity of the crossover transition corresponding to the simultaneous restoration of chiral symmetry and deconfinement. Using sophisticated lattice techniques, we have carefully identified the topological hot spots using quark zero modes and measured the short-distance fluctuations of the Polyakov loop about them, showing how the latter is repelled quite strongly around the peak of the zero modes. Though we could explain some aspects of these correlations within the instanton-dyon picture, our work sets the stage for a larger goal towards a systematic study of the role of different topological species that interact with the Polyakov loop, establishing the strong connection between topology and confinement.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Microbes display broad diversity in cobamide preferences

ABSTRACT Cobamides, the vitamin B 12 (cobalamin) family of cofactors, are used by most organisms but produced by only a fraction of prokaryotes, and are thus considered key shared nutrients among microbes. Cobamides are structurally diverse, with multiple different cobamides found in most microbial communities. The ability to use different cobamides has been tested for several bacteria and microalgae, and nearly all show preferences for certain cobamides. This approach is limited by the commercial unavailability of cobamides other than cobalamin. Here, we have extracted and purified seven commercially unavailable cobamides to characterize bacterial cobamide preferences based on growth in specific cobamide-dependent conditions. The tested bacteria include engineered strains of Escherichia coli , Sinorhizobium meliloti , and Bacillus subtilis expressing native or heterologous cobamide-dependent enzymes, cultured under conditions that functionally isolate specific cobamide-dependent processes such as methionine synthesis. Comparison of these results to those of previous studies of diverse bacteria and microalgae revealed that a broad diversity of cobamide preferences exists not only across different organisms but also between different cobamide-dependent metabolic pathways within the same organism. The microbes differed in the cobamides that support growth most efficiently, cobamides that do not support growth, and the minimum cobamide concentrations required for growth. The latter differ by up to four orders of magnitude across organisms from different environments and by up to 20-fold between cobamide-dependent enzymes within the same organism. Given that cobamides are shared, required for use of specific growth substrates, and essential for central metabolism in certain organisms, cobamide preferences likely impact community structure and function. IMPORTANCE Nearly all bacteria are found in microbial communities with tens to thousands of other species. Molecular interactions such as metabolic cooperation and competition are key factors underlying community assembly and structure. Cobamides, the vitamin B 12 family of enzyme cofactors, are one such class of nutrients, produced by only a minority of prokaryotes but required by most microbes. A unique aspect of cobamides is their broad diversity, with nearly 20 structural forms identified in nature. Importantly, this structural diversity impacts growth as most bacteria that have been tested show preferences for specific cobamide forms. We measured cobamide-dependent growth in several model bacteria and compared the results to those of previous analyses of cobamide preference. We found that cobamide preferences vary widely across bacteria, showing the importance of characterizing these aspects of cobamide biology to understand the impact of cobamides on microbial communities.

Mok, Kenny C. (ORCID:0000000252276987)↗

Simulation of the dynamics of gas mixtures during plasma processing in the C75 Cavity

Plasma processing using a mixture of noble gas and oxygen is a technique that is currently being used to reduce field emission and multipacting in accelerating cavities. Plasma is created inside the cavity when the gas mixture is exposed to an electromagnetic field that is generated by applying RF power through the fundamental power or higher-order mode couplers. Oxygen ions and atomic oxygen are created in the plasma which breaks down the hydrocarbons on the surface of the cavity and the residuals from this process are removed as part of the process gas flow. Removal of hydrocarbons from the surface increases the work function and reduces the secondary emission coefficient. This work describes the initial results of plasma simulation, which provides insight into the ignition process, distribution of different species, and interactions of free oxygen and oxygen ions with the cavity surfaces. The simulations have been done with an Ar/?2 plasma using COMSOL® multiphysics. These simulations help in understanding the dynamics and control of plasma inside the cavity and the exploration of different gas mixtures.

Dhakal, Pashupati↗

Thermodynamics of Tritium Trapping by Point Defects at Interfacial Cr-based Phases of the Al Coating

Density functional theory (DFT) simulations have been carried out to evaluate the potential for tritium trapping by metal vacancies in four phases Cr-containing phases (i.e., Cr3Si, Al0.3Cr0.7, Al8Cr5-HT, and Al8Cr5) identified near the interface between the Al coating and 316 stainless steel (316 SS) cladding. In addition, an ab initio thermodynamics approach has been employed to predict the temperature and T2-partial pressure dependence on the thermodynamics of singly tritiated defects. Key results in this work suggest that metal vacancies in the four phases have the potential to favorably trap tritium species, especially Si vacancies in Cr3Si phase. This overall thermodynamic trend can be correlated to the energy cost of having an interstitial tritium in the lattice, which has been calculated to range from 0.17 eV in Al8Cr5-HT to 0.89 eV in Cr3Si. A comparison of the results from this study with previous theoretical works investigating tritium behavior in other Fe-Al phases identified in the aluminide coating, suggests that metal vacancies are generally able to trap tritium in various Fe-Al aluminide phases. Especially, it was found that Si and Al vacancies would be the most efficient to trap for tritium, followed by Cr vacancies, then Fe and Ni vacancies. In the four Cr-based material phases investigated in this work, it is interesting to note that, in the absences of Fe or Ni species, strong interactions between tritium and the metal vacancies are always occurring by the formation of preferential Cr—T bonds (i.e., no Si—T or Al—T bonds were formed).

Sassi, Michel J.↗

Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

59 BASIC BIOLOGICAL SCIENCES↗

A novel open-source cultivation system helps establish the first full cycle chemosynthetic symbiosis model system involving the giant ciliate Zoothamnium niveum

Symbiotic interactions drive species evolution, with nutritional symbioses playing vital roles across ecosystems. Chemosynthetic symbioses are globally distributed and ecologically significant, yet the lack of model systems has hindered research progress. The giant ciliate Zoothamnium niveum and its sulfur-oxidizing symbionts represent the only known chemosynthetic symbiosis with a short life span that has been transiently cultivated in the laboratory. While it is experimentally tractable and presents a promising model system, it currently lacks an open-source, simple, and standardized cultivation setup. Following the FABricated Ecosystems (EcoFABs) model, we leveraged 3D printing and polydimethylsiloxane (PDMS) casting to develop simple flow-through cultivation chambers that can be produced and adopted by any laboratory. The streamlined manufacturing process reduces production time by 86% and cuts cost by tenfold compared to the previous system. Benchmarking using previously established optimal growth conditions, the new open-source cultivation system proves stable, efficient, more autonomous, and promotes a more prolific growth of the symbiosis. For the first time, starting from single cells, we successfully cultivated the symbiosis in flow-through chambers for 20 days, spanning multiple generations of colonies that remained symbiotic. They were transferred from chamber to chamber enabling long-term cultivation and eliminating the need for continuous field sampling. The chambers, optimized for live imaging, allowed detailed observation of the synchronized growth between the host and symbiont. Highlighting the benefit of this new system, we here describe a new step in the first hours of development where the host pauses growth, expels a coat, before resuming growth, hinting at a putative symbiont selection mechanism early in the colony life cycle. With this simple, open-source, cultivation setup, Z. niveum holds promises for comparative studies, standardization of research and wide adoption by the symbiosis research community.

59 BASIC BIOLOGICAL SCIENCES↗

Mapping Post-Climate Change Biogeographical Regions with Deep Latent Variable Models

Forecasting future changes to biodiversity due to shifts in climate is challenging due to nonlinear interactions between species as recorded in their presence/absence data. This work proposes using variational autoencoders with environmental covariates to identify low-dimensional structure in species’ joint co-occurrence patterns and leveraging this simplified representation to provide multivariate predictions of their habitat extent under future climate scenarios. We pursue a latent space clustering approach to map biogeographical regions of frequently co-occurring species and apply this methodology to a dataset from northern Belgium, generating predictive maps illustrating how these regions may expand or contract with changing temperature under a future climate scenario.

Krapu, Chris↗

Interactive effects of elevated CO 2 , warming, reduced rainfall, and nitrogen on leaf gas exchange in five perennial grassland species

Abstract Global changes can interact to affect photosynthesis and thus ecosystem carbon capture, yet few multi‐factor field studies exist to examine such interactions. Here, we evaluate leaf gas exchange responses of five perennial grassland species from four functional groups to individual and interactive global changes in an open‐air experiment in Minnesota, USA, including elevated CO 2 (eCO 2 ), warming, reduced rainfall and increased soil nitrogen supply. All four factors influenced leaf net photosynthesis and/or stomatal conductance, but almost all effects were context‐dependent, i.e. they differed among species, varied with levels of other treatments and/or depended on environmental conditions. Firstly, the response of photosynthesis to eCO 2 depended on species and nitrogen, became more positive as vapour pressure deficit increased and, for a C 4 grass and a legume, was more positive under reduced rainfall. Secondly, reduced rainfall increased photosynthesis in three functionally distinct species, potentially via acclimation to low soil moisture. Thirdly, warming had positive, neutral or negative effects on photosynthesis depending on species and rainfall. Overall, our results show that interactions among global changes and environmental conditions may complicate predictions based on simple theoretical expectations of main effects, and that the factors and interactions influencing photosynthesis vary among herbaceous species.

Pastore, Melissa A.↗

Allometric relationships and trade‐offs in 11 common M editerranean‐climate grasses

Abstract Biomass allocation in plants is the foundation for understanding dynamics in ecosystem carbon balance, species competition, and plant–environment interactions. However, existing work on plant allometry has mainly focused on trees, with fewer studies having developed allometric equations for grasses. Grasses with different life histories can vary in their carbon investment by prioritizing the growth of specific organs to survive, outcompete co‐occurring plants, and ensure population persistence. Further, because grasses are important fuels for wildfire, the lack of grass allocation data adds uncertainty to process‐based models that relate plant physiology to wildfire dynamics. To fill this gap, we conducted a greenhouse experiment with 11 common California grasses varying in photosynthetic pathway and growth form. We measured plant sizes and harvested above‐ and belowground biomass throughout the life cycle of annual species, while for the establishment stage of perennial grasses to quantify allometric relationships for leaf, stem, and root biomass, as well as plant height and canopy area. We used basal diameter as a reference measure of plant size. Overall, basal diameter is the best predictor for leaf and stem biomass, height, and canopy area. Including height as another predictor can improve model accuracy in predicting leaf and stem biomass and canopy area. Fine root biomass is a function of leaf biomass alone. Species vary in their allometric relationships, with most variation occurring for plant height, canopy area, and stem biomass. We further explored potential trade‐offs in biomass allocation across species between leaf and fine root, leaf and stem, and allocation to reproduction. Consistent with our expectation, we found that fast‐growing plants allocated a greater fraction to reproduction. Additionally, plant height and specific leaf area negatively influenced the leaf‐to‐stem ratio. However, contrary to our hypothesis, there were no differences in root‐to‐leaf ratio between perennial and annual or C 4 and C 3 plants. Our study provides species‐specific and functional‐type‐specific allometry equations for both above‐ and belowground organs of 11 common California grass species, enabling nondestructive biomass assessment in California grasslands. These allometric relationships and trade‐offs in carbon allocation across species can improve ecosystem model predictions of grassland species interactions and environmental responses through differences in morphology.

54 ENVIRONMENTAL SCIENCES↗

Nitrogen addition alters soil fungal communities, but root fungal communities are resistant to change

Plants are colonized by numerous microorganisms serving important symbiotic functions that are vital to plant growth and success. Understanding and harnessing these interactions will be useful in both managed and natural ecosystems faced with global change, but it is still unclear how variation in environmental conditions and soils influence the trajectory of these interactions. In this study, we examine how nitrogen addition alters plant-fungal interactions within two species of Populus - Populus deltoides and P. trichocarpa. In this experiment, we manipulated plant host, starting soil (native vs. away for each tree species), and nitrogen addition in a fully factorial replicated design. After ~10 weeks of growth, we destructively harvested the plants and characterized plant growth factors and the soil and root endosphere fungal communities using targeted amplicon sequencing of the ITS2 gene region. Overall, we found nitrogen addition altered plant growth factors, e.g., plant height, chlorophyll density, and plant N content. Interestingly, nitrogen addition resulted in a lower fungal alpha diversity in soils but not plant roots. Further, there was an interactive effect of tree species, soil origin, and nitrogen addition on soil fungal community composition. Starting soils collected from Oregon and West Virginia were dominated by the ectomycorrhizal fungi Inocybe (55.8% relative abundance), but interestingly when P. deltoides was grown in its native West Virginia soil, the roots selected for a high abundance of the arbuscular mycorrhizal fungi, Rhizophagus. These results highlight the importance of soil origin and plant species on establishing plant-fungal interactions.

59 BASIC BIOLOGICAL SCIENCES↗

TiO x -supported Na-Mn-W oxides for the oxidative coupling of methane

Supported Na-Mn-W oxides are among the most studied catalysts for the oxidative coupling of methane (OCM) because of their superior thermal stability and relatively high C 2+ product yields. However, because of the structural complexity, the roles of each component in these catalysts have been controversial. In this work, WO x and MnO x sites were supported on titanate nanowires and employed in OCM studies. Compared to the commonly studied silica support, which is subject to severe restructuring due to the Na-induced crystallization, titanate support not only serves as a reservoir for alkali metals (e.g., Na), but also stabilizes isolated MnO x species. The catalytic performance of the titanate-based catalyst is similar to that of reference catalyst, MnO x /Na 2 WO 4 /SiO 2 , with a synergistic effect between MnO x and WO x sites. Further, advanced electron microscopy, X-ray diffraction, infrared spectroscopy, and X-ray absorption near edge structure spectroscopy suggest that the basic NaO x and MnO x species have strong interactions with the acidic WO x and TiO x species, which might contribute to the high selectivity toward C 2+ products and suppressed CO x formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simultaneous Discovery of Positive and Negative Interactions Among Rhizosphere Bacteria Using Microwell Recovery Arrays

Understanding microbe-microbe interactions is critical to predict microbiome function and to construct communities for desired outcomes. Investigation of these interactions poses a significant challenge due to the lack of suitable experimental tools available. Here we present the microwell recovery array (MRA), a new technology platform that screens interactions across a microbiome to uncover higher-order strain combinations that inhibit or promote the function of a focal species. One experimental trial generates 10 4 microbial communities that contain the focal species and a distinct random sample of uncharacterized cells from plant rhizosphere. Cells are sequentially recovered from individual wells that display highest or lowest levels of focal species growth using a high-resolution photopolymer extraction system. Interacting species are then identified and putative interactions are validated. Using this approach, we screen the poplar rhizosphere for strains affecting the growth of Pantoea sp. YR343, a plant growth promoting bacteria isolated from Populus deltoides rhizosphere. In one screen, we montiored 3,600 microwells within the array to uncover multiple antagonistic Stenotrophomonas strains and a set of Enterobacter strains that promoted YR343 growth. The later demonstrates the unique ability of the platform to discover multi-membered consortia that generate emergent outcomes, thereby expanding the range of phenotypes that can be characterized from microbiomes. This knowledge will aid in the development of consortia for Populus production, while the platform offers a new approach for screening and discovery of microbial interactions, applicable to any microbiome.

59 BASIC BIOLOGICAL SCIENCES↗

Genetic identification of avian samples recovered from solar energy installations

Renewable energy production and development will drastically affect how we meet global energy demands, while simultaneously reducing the impact of climate change. Although the possible effects of renewable energy production (mainly from solar- and wind-energy facilities) on wildlife have been explored, knowledge gaps still exist, and collecting data from wildlife remains (when negative interactions occur) at energy installations can act as a first step regarding the study of species and communities interacting with facilities. In the case of avian species, samples can be collected relatively easily (as compared to other sampling methods), but may only be able to be identified when morphological characteristics are diagnostic for a species. Therefore, many samples that appear as partial remains, or “feather spots”—known to be of avian origin but not readily assignable to species via morphology—may remain unidentified, reducing the efficiency of sample collection and the accuracy of patterns observed. To obtain data from these samples and ensure their identification and inclusion in subsequent analyses, we applied, for the first time, a DNA barcoding approach that uses mitochondrial genetic data to identify unknown avian samples collected at solar facilities to species. We also verified and compared identifications obtained by our genetic method to traditional morphological identifications using a blind test, and discuss discrepancies observed. Our results suggest that this genetic tool can be used to verify, correct, and supplement identifications made in the field and can produce data that allow accurate comparisons of avian interactions across facilities, locations, or technology types. We recommend implementing this genetic approach to ensure that unknown samples collected are efficiently identified and contribute to a better understanding of wildlife impacts at renewable energy projects.

14 SOLAR ENERGY↗