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DOE OSTI2021

A Binomial Stochastic Framework for Efficiently Modeling Discrete Statistics of Convective Populations

Abstract Understanding the coupling between convective clouds and the general circulation, as well as addressing the gray zone problem in convective parameterization, requires insight into the genesis and maintenance of spatial patterns in cumulus cloud populations. In this study, a simple toy model for recreating populations of interacting convective objects as distributed over a two‐dimensional Eulerian grid is formulated to this purpose. Key elements at the foundation of the model include i) a fully discrete formulation for capturing discrete behavior in convective properties at small population sample sizes, ii) object age‐dependence for representing life‐cycle effects, and iii) a prognostic number budget allowing for object interactions and co‐existence of multiple species. A primary goal is to optimize the computational efficiency of this system. To this purpose the object birth rate is represented stochastically through a spatially aware Bernoulli process. The same binomial stochastic operator is applied to horizontal advection of objects, conserving discreteness in object number. The applicability to atmospheric convection as well as behavior implied by the formulation is assessed. Various simple applications of the BiOMi model (Binomial Objects on Microgrids) are explored, suggesting that important convective behavior can be captured at low computational cost. This includes i) subsampling effects and associated powerlaw scaling in the convective gray zone, ii) stochastic predator‐prey behavior, iii) the downscale turbulent energy cascade, and iv) simple forms of spatial organization and convective memory. Consequences and opportunities for convective parameterization in next‐generation weather and climate models are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Sensor-Equipped Unmanned Surface Vehicle for High-Resolution Mapping of Water Quality in Low- to Mid-Order Streams

Longitudinal profiling of water quality via the deployment of sensors from watercraft has advanced the understanding of spatial patterns in large rivers and lakes; however, a similar approach in low- to mid-order streams is lacking. To fill this gap, we developed an unmanned surface vehicle (USV)-water quality measurement platform (the “AquaBOT”). The components of the AquaBOT included a nitrate sensor, multiparameter sonde (temperature, conductivity, turbidity, dissolved oxygen, chlorophyll), quantum sensor, and global positioning system (GPS) mounted to a small pontoon-style USV. The AquaBOT was tested in four streams and rivers in Iowa and Tennessee. All measured water quality parameters varied longitudinally, and greater ranges were generally observed along the low-order, agriculturally influenced streams in Iowa. Nitrate, in particular, was spatially heterogeneous. For example, during one run in early June, concentrations ranged from 10.5 to 12.5 mg N L –1 along a 2.3 km reach and hotspots were observed directly downstream of some tile drains. The spatial resolution of AquaBOT data collected in June was 10× higher than grab sampling data, and measurements were collected in less time and at a comparable cost. Here, the AquaBOT can complement existing measurement approaches and will lead to advancements in understanding the processes driving water quality along the stream-to-river continuum.

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

Daily, 30 m Resolution NDSI Data for the East River Watershed, CO for 2000-2020

This dataset contains daily Normalized Difference Snow Index (NDSI) values at 30 m spatial resolution for the East River watershed in Colorado, USA. The temporal range of these data includes water years 2001-2020. These data were created using the Spatial and Temporal Adaptive Reflectance Fusion Model (STARFM). This model fuses low spatial and high temporal resolution data from MODIS (500 m, daily) with high spatial and low temporal resolution data from Landsat (30 m, 16 days) to create a 30m synthetic daily snow product. This product allows for the analysis of historical snow covered area trends in the East River Watershed at fine spatiotemporal resolutions where it was not available previously. This research was performed as a part of the Department of Energy’s Subsurface Biogeochemical Research Program with the primary intent of better understanding the timing and spatial patterns of water delivery to the Critical Zone in mountain watersheds. Each .zip file contains one "water year" of data (October 1 - September 30; i.e., water year 2010 starts October 1, 2010 and ends September 30, 2011). Each zip file contains the following: STARFM daily Normalized Difference Snow Index (NDSI) fusion data files in GeoTiff format with one layer for each day between Landsat data acquisition dates (i.e., for dates of Landsat acquisition, the Landsat image is included for that date). The study area is located in an area of Landsat path overlap, so Landsat dates acquisitions are every 7-9 days. Landsat NDSI files containing the high spatial (30m), low temporal (7-9 days due to Landsat path overlap) resolution data used as input to STARFM in GeoTiff format with one layer for each day. Dates for which no Landsat data were obtained are included as NoData layers. MODIS NDSI files containing the high temporal (daily), low spatial (500m) resolution data used as input to STARFM in GeoTiff format with one layer for each day. Please note the MODIS data were resampled to 30m pixels for input into the STARFM model. The data have a scale factor of 10,000 and a no data value of -32767. The projection of all datasets is WGS 84 (EPSG: 4326), which has a latitude/longitude based degree resolution of 0.0002694946 X 0.0002694946, and approximates to the 30 m spatial resolution mentioned above. The Layer Index files in .csv format. They contain information for each layer in the above GeoTiff files regarding the corresponding date for each layer, the fraction of pixels in the image that contain valid data (missing data is due to either cloud cover or poor data quality; these values are not percent snow cover). Dates of Landsat overpass are indicated in these files. If no Landsat data were able to be obtained due to cloud cover or lack of Landsat Tier 1 data available on Google Earth Engine, this is also noted.

EARTH SCIENCE > CRYOSPHERE > SNOW/ICE↗

DOE OSTI2025

Harnessing the Power of Machine Learning and Omics to Identify Environmental Regulation on Microbial Functional Composition for Soil C, N, and P Cycling

Microbial enzyme-mediated soil organic matter (SOM) decomposition regulates many key ecosystem functions, such as elemental cycling, soil carbon sequestration, and soil fertility. However, representing microbial processes in Earth system models (ESMs) remains challenging due to a limited understanding of the spatial patterns of diverse microbial functions responsible for soil carbon (C), nitrogen (N), and phosphorus (P) cycling as well as the underlying mechanisms regulating their relative abundances across various environments. We collected published metagenomics data across the continental US (CONUS) to identify hundreds of microbial genes involved in soil C, N, and P cycling and grouped them into eight enzyme functional classes (EFCs). Each EFC represented a group of gene-encoded potential enzymes that decompose similar soil compounds. By integrating the abundances of omics-informed EFCs with the corresponding environmental information, we trained a machine learning (ML) model to identify key edaphic, climate, and vegetation factors regulating the abundances of each EFC. Quantitative analysis of effects of these factors revealed that the spatial distribution of eight EFCs for soil C, N, and P cycling across CONUS reflected potential resource optimization strategies of microbial communities under nutrient limitation, preferential organic-mineral associations, and climatological stresses. This insight, together with the interpreted ML tool and the CONUS-level benchmark for EFCs abundances, paves the way for parameterizing environmental-regulated microbial functional dynamics in biogeochemical models.

machine learning↗

DOE OSTI2023

Accelerated Stress Testing of Perovskite Photovoltaic Modules: Differentiating Degradation Modes with Electroluminescence Imaging

Herein, electroluminescence (EL) and thermal imaging are used to examine p–i–n metal halide perovskite (MHP) photovoltaic (PV) mini-modules (MA0.6FA0.4PbI3, 20 cells, 78 cm2) before and after indoor-accelerated stress testing or outdoor deployment. Distinct spatial patterns in the EL images emerge, which depend on the external stress conditions experienced by the mini-module. Imaging results highlight a distribution of dark speckle features that dominate after UV stress, attributed to widespread interfacial contact degradation. Lateral intensity gradients across cells dominate after thermal cycling (TC) stress, attributed to current crowding near scribe defects. While current–voltage analysis alone does not give full insight on the degradation process, this study shows that distinct degradation modes can be further defined by multimodal electro-optical imaging (i.e., EL combined with photoluminescence and dark lock-in thermography). Neither UV exposure nor TC-accelerated stress testing alone replicates the same degradation signatures observed after outdoor deployment, suggesting that multiple degradation modes occur under concurrent stressors outdoors. Finally, spatial characterization of degradation modes in MHP PV mini-modules before and after accelerated stress testing lays the groundwork for developing targeted accelerated stress testing procedures through comparison with outdoor aging.

14 SOLAR ENERGY↗

DOE OSTI2025

Tracing the impacts of Mount Pinatubo eruption on regional climate using spatially-varying changepoint detection

Significant events, such as volcanic eruptions, can have global and long-lasting impacts on climate. These global impacts, however, are not uniform across space and time. Understanding how the Mt. Pinatubo eruption affects global and regional climate is of great interest for predicting the impact on climate due to similar events as well as understanding the possible effect of the stratospheric aerosol injections proposed to combat climate change. While many studies illustrated the impact of the Pinatubo eruption on a global scale, studies at a fine regional scale are scarce. Here, we propose a Bayesian spatially-varying changepoint detection and estimation method to trace the impact of Mt. Pinatubo eruption on regional climate. Our approach takes into account the diffusing nature and spatial correlation of the climate changes attributed to the volcanic eruption. We illustrate our method and demonstrate its advantages over an existing changepoint detection method through simulations. Finally, we apply our method to monthly stratospheric aerosol optical depth and surface temperature data from 1985 to 1995 to detect and estimate changepoints following the 1991 Mt. Pinatubo eruption. Our results quantitatively characterize the spatial pattern of the eruption’s impact on regional climate, complementing the previous studies on the global impact of the Pinatubo eruption.

Aerosol optical depth↗

DOE OSTI2020

Modeling the smoky troposphere of the southeast Atlantic: a comparison to ORACLES airborne observations from September of 2016

The southeast Atlantic is home to well-defined smoke outflow from Africa coinciding vertically with extensive marine boundary-layer cloud decks, both reaching their climatological maxima in spatial extent around September. A framework is put forth for evaluating the performance of a range of global and regional aerosol models against observations made during the NASA ORACLES (ObseRvations of Aerosols above CLouds and their intEractionS) airborne mission in September 2016. The sparse airborne observations are first aggregated into 2o grid boxes and into three vertical layers: the cloud-topped marine boundary layer (MBL), the layer from cloud top to 3 km, and the 3-6 km layer. Aerosol extensive properties simulated for the entire study region for all September suggest that the 2016 ORACLES observations are reasonably representative of the regional monthly average, with systematic deviations of 30% or less. All six models typically place the bottom of the smoke layer at lower altitudes than do the airborne lidar observations by 300-1400 m, whereas model aerosol top heights are within 0-500 m of the observations. All but one of the models that report carbonaceous aerosol masses underestimate the ratio of particulate extinction to the masses, a proxy for mass extinction efficiency, in 3-6 km. Notable findings on individual models include that WRF-CAM5 predicts the mass of black carbon and organic aerosols with minor (~10% or less) biases. GEOS-5 overestimates the carbonaceous particle masses in the MBL by a factor of 3-6. Extinction coefficients in the free troposphere (FT) and above-cloud aerosol optical depth (ACAOD) are 10-30% lower in WRF-CAM5, 30-50% lower in GEOS-5, 10-40% higher in GEOS-Chem, 10-20% higher in EAM-E3SM except for the practically unbiased 3-6 km extinction, and 20-70% lower in the Unified Model, than the airborne in situ, lidar and sunphotometer measurements. ALADIN-Climate also underestimates the ACAOD, by 30%. GEOS-5 and GEOS-Chem predict carbon monoxide in the MBL with small (10% or less) negative biases, despite their overestimates of carbonaceous aerosol masses. Overall, this study highlights a new approach to utilizing airborne aerosol measurements for model diagnosis.

Shinozuka, Yohei↗

DOE OSTI2026

Nematic cell alignment directs calcium waves in an epithelial monolayer

Tissues rely on supracellular signals to coordinate their cells over a long range. Two such tissuescale cues are calcium waves and patterns of cell-cell alignment or nematic order. During wound healing, for example, calcium waves propagate across a tissue to guide directed cell migration and reepithelialization. Defects in long-range cell-cell alignment, or nematic orientation, can act to localize morphogenetic events in a tissue. Although these two cues have been considered in isolation, we demonstrate a relationship in epithelial tissue between long-range calcium signaling and the cell’s nematic order: The speed of a wound-induced calcium wave depends monotonically on the angle between the wave vector and cell axis, with maximal wave speed occurring perpendicular to the tissue’s orientation. Including anisotropic di↵usive coupling between cells in a canonical reactiondi↵usion model recapitulates our measured calcium wave dynamics. Our model demonstrates how orientation defects can desynchronize information propagation across a tissue. A calcium wave front is bent around nematic defects, therefore cells the same distance from a wound can receive the calcium signal at di↵erent times. Our work elucidates how spatial patterns in global cell alignment can control collective communication via calcium signaling during development, wound healing, and disease.

Winterstrain, Annemarie C. [Brandeis University, W↗

DOE OSTI2022

Simulation of ENSO Teleconnections to Precipitation Extremes over the United States in the High-Resolution Version of E3SM

Abstract We evaluate the simulated teleconnection of El Niño–Southern Oscillation (ENSO) to winter season precipitation extremes over the United States in a long (98 years) 1950 control high-resolution version (HR; 25-km nominal atmosphere model horizontal resolution) of the U.S. Department of Energy’s (DOE) Energy Exascale Earth System Model version 1 (E3SMv1). The model bias and spatial pattern of ENSO teleconnections to mean and extreme precipitation in HR overall are similar to the low-resolution model’s (LR; 110 km) historical simulation (four-member ensemble, 1925–59). However, over the southeastern United States (SE-U.S.), HR produces stronger El Niño–associated extremes, reducing LR’s model bias. Both LR and HR produce weaker than observed increase in storm track activity during El Niño events there, but HR improves the ENSO-associated variability of moisture transport over SE-U.S. During El Niño, stronger vertical velocities in HR produce stronger large-scale precipitation, causing larger latent heating of the troposphere that pulls in more moisture from the Gulf of Mexico into the SE-U.S. This positive feedback also contributes to the stronger mean and extreme precipitation response in HR. Over the Pacific Northwest, LR’s bias of stronger than observed La Niña associated extremes is amplified in HR. Both models simulate stronger than observed moisture transport from the Pacific Ocean into the region during La Niña years. The amplified HR bias there is due to stronger orographically driven vertical updrafts that create stronger large-scale precipitation, despite weaker La Niña–induced storm track activity. Significance Statement New high-resolution Earth system models (ESMs) solve mathematical equations of fluid flow at much smaller spatial scales than prevalent ESMs, and thus are prohibitively expensive to compute. However, they can be useful for simulating accurate details of regional climate extremes that are driven by naturally occurring climate oscillations like El Niño–Southern Oscillation (ENSO). Here, we evaluate the simulation of ENSO-driven precipitation extremes over the United States in the high-resolution version of the U.S. Department of Energy’s new Energy Exascale Earth System Model version 1. We find that the high-resolution model improves upon its low-resolution counterpart over the southeastern United States by producing a better transport of moisture into the region from the Gulf of Mexico during El Niño. Over the U.S. Pacific Northwest, the high-resolution model simulates the atmospheric flow in more detail over the complex mountainous terrain. However, it also brings in more moisture from the Pacific Ocean just like the low-resolution model. This causes it to produce precipitation extremes during La Niña years there that are stronger than that observed in the real world.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Linking transportation agent-based model ($\mathrm{ABM}$) outputs with micro-urban social types ($\mathrm{MUSTs}$) via typology transfer for improved community relevance

The human relationship with transportation is shaped by social, economic, demographic, and urban form variables, or socio-spatial factors. The spatial dynamics of these are key to generating and interpreting outputs of transportation models that are most relevant for a community and the diverse mobility needs of its members. Here we present a typology transfer framework, grounded in socio-spatial dynamics shaping people's mobility, to take transportation-themed regional mobility model outcomes, in this case from two agent-based models (ABMs), and extrapolate them to other cities, with less time and resource intensity than new ABM development. The typology transfer process first identifies micro-urban social types (MUSTs) using socio-spatial factors, then defines city types based on spatial patterns of MUSTs to assess across which cities transfer results are likely to best hold. Lastly, a typology transfer multiplier matrix extrapolates a given variable, in our case the Mobility Energy Productivity (MEP) metric, to another city. The full process demonstration uses ABM results from Chicago (POLARIS model) and San Francisco (BEAM model), applying them to New York City. We discuss how MEP or other outputs can be appropriately estimated and used for integrated, human-centered mobility analysis. Key findings include that this MUST framework of user-defined dependent and independent variables allows tailoring ABM results and interpretations to specific community needs and data availability. Findings clarify that positive outcomes can be targeted towards user groups, based on sociospatial characteristics, using a typology approach, such as inclusive access to mobility choices, transportation affordability, and greater efficiency in resource use.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2025

Drivers of Historical and Future Coastal Runoff Across the Arctic and Sub‐Arctic Subregions of Alaska, USA

This study investigates historical and future coastal runoff across the Arctic and sub-Arctic subregions of Alaska, USA, emphasising changes in terrestrial hydrology and their implications for coastal discharge. Using the physically based SnowModel-HydroFlow framework, historical (1991–2020) and future (2071–2100) coastal discharge climatologies were simulated, incorporating meteorological, topographic, and land cover inputs. Results reveal distinct seasonal and spatial patterns in temperature, precipitation, and snow dynamics across the Beaufort, Chukchi, Yukon, and Bristol subregions. Future projections suggest significant warming and shifts in hydrological regimes, such as increased annual precipitation and coastal discharge totals. Following a high emissions, business as usual pathway (SSP5-8.5), coastal discharge hydrographs in the Beaufort and Yukon subregions remain snow dominated with increases in discharge in nearly all months, while Chukchi and Bristol subregions shift from snow dominated to rain dominated. These changes are linked to rising temperatures, decreasing snow precipitation fractions, and altered freezing levels, with implications for water storage, timing, and availability. This research provides insights into the drivers and consequences of hydrological changes in a rapidly warming Arctic, supporting efforts to predict and mitigate the impacts on coastal and marine ecosystems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

What causes the spread of model projections of ocean dynamic sea-level change in response to greenhouse gas forcing?

Abstract Sea levels of different atmosphere–ocean general circulation models (AOGCMs) respond to climate change forcing in different ways, representing a crucial uncertainty in climate change research. We isolate the role of the ocean dynamics in setting the spatial pattern of dynamic sea-level ( ζ ) change by forcing several AOGCMs with prescribed identical heat, momentum (wind) and freshwater flux perturbations. This method produces a ζ projection spread comparable in magnitude to the spread that results from greenhouse gas forcing, indicating that the differences in ocean model formulation are the cause, rather than diversity in surface flux change. The heat flux change drives most of the global pattern of ζ change, while the momentum and water flux changes cause locally confined features. North Atlantic heat uptake causes large temperature and salinity driven density changes, altering local ocean transport and ζ . The spread between AOGCMs here is caused largely by differences in their regional transport adjustment, which redistributes heat that was already in the ocean prior to perturbation. The geographic details of the ζ change in the North Atlantic are diverse across models, but the underlying dynamic change is similar. In contrast, the heat absorbed by the Southern Ocean does not strongly alter the vertically coherent circulation. The Arctic ζ change is dissimilar across models, owing to differences in passive heat uptake and circulation change. Only the Arctic is strongly affected by nonlinear interactions between the three air-sea flux changes, and these are model specific.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

The substantial role of May soil temperature over Central Asia for summer surface air temperature variation and prediction over Northeastern China

The slowly varying soil temperature can exert local and nonlocal influences on regional climate system, and may thus provide a critical source of subseasonal-to-seasonal climate prediction. In this study, we identify that soil temperature in May over the key region of Central Asia (42 °N–50 °N, 62 °E–80 °E, KRCA) from Noah, Mosaic, CLM and ERA-interim datasets is closely linked to variations of the surface air temperature, daily maximum temperature and hot days over Northeastern China in summer (June-July-August), with correlation coefficients of regional average detrended time series ranging from 0.42 to 0.54, and all significant at the 99% confidence level for the period of 1979-2018. The possible physical mechanism behind the substantial downstream impacts of soil temperature over Central Asia are explored via diagnostical analysis combined with regional climate model experiments. Warmer soil temperature in May over the KRCA tends to cause positive anomalies of geopotential height in summer over Northeastern China through the Rossby wave propagation, and associated stronger subsidence warming, less cloud cover, more solar radiation reaching the surface, higher planetary boundary layer, and stronger thermal advection at 850 hPa, which provide favorable conditions for warmer surface air temperature particularly in the daytime as well as more hot days. Here this study further reveals that soil temperature over Central Asia in May makes important contribution to prediction of summer surface air temperature, daily maximum temperature and hot days over Northeastern China in terms of regional average time series and spatial patterns. Our findings highlight the previously-unknown substantial role of antecedent soil temperature condition over Central Asia for summer surface air temperature variation and prediction over Northeastern China.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Greenhouse-gas forced changes in the Atlantic meridional overturning circulation and related worldwide sea-level change

Abstract The effect of anthropogenic climate change in the ocean is challenging to project because atmosphere-ocean general circulation models (AOGCMs) respond differently to forcing. This study focuses on changes in the Atlantic Meridional Overturning Circulation (AMOC), ocean heat content ( $$\Delta$$ Δ OHC), and the spatial pattern of ocean dynamic sea level ( $$\Delta \zeta$$ Δ ζ ). We analyse experiments following the FAFMIP protocol, in which AOGCMs are forced at the ocean surface with standardised heat, freshwater and momentum flux perturbations, typical of those produced by doubling $$\hbox {CO}_{{2}}$$ CO 2 . Using two new heat-flux-forced experiments, we find that the AMOC weakening is mainly caused by and linearly related to the North Atlantic heat flux perturbation, and further weakened by a positive coupled heat flux feedback. The quantitative relationships are model-dependent, but few models show significant AMOC change due to freshwater or momentum forcing, or to heat flux forcing outside the North Atlantic. AMOC decline causes warming at the South Atlantic-Southern Ocean interface. It does not strongly affect the global-mean vertical distribution of $$\Delta$$ Δ OHC, which is dominated by the Southern Ocean. AMOC decline strongly affects $$\Delta \zeta$$ Δ ζ in the North Atlantic, with smaller effects in the Southern Ocean and North Pacific. The ensemble-mean $$\Delta \zeta$$ Δ ζ and $$\Delta$$ Δ OHC patterns are mostly attributable to the heat added by the flux perturbation, with smaller effects from ocean heat and salinity redistribution. The ensemble spread, on the other hand, is largely due to redistribution, with pronounced disagreement among the AOGCMs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Evaluating skill in predicting the Interdecadal Pacific Oscillation in initialized decadal climate prediction hindcasts in E3SMv1 and CESM1 using two different initialization methods and a small set of start years

Abstract It is a daunting challenge to conduct initialized hindcasts with enough ensemble members and associated start years to form a drifted climatology from which to compute the anomalies necessary to quantify the skill of the hindcasts when compared to observations. This limits the ability to experiment with case studies and other applications where only a few initial years are needed. Here we run a set of hindcasts with CESM1 and E3SMv1 using two different initialization methods for a limited set of start years and use the respective uninitialized free-running historical simulations to form the model climatologies. Since the drifts from the observed initial states in the hindcasts toward the uninitialized model state are large and rapid, after a few years the drifted initialized models approach the uninitialized model climatological errors. Therefore, hindcasts from the limited start years can use the uninitialized climatology to represent the drifted model states after about lead year 3, providing a means to compute forecast anomalies in the absence of a large hindcast sample. There is comparable skill for predicting spatial patterns of multi-year Pacific sea surface temperature anomalies in the domain of the Interdecadal Pacific Oscillation using this method compared to the conventional methodology with a large hindcast data set, though there is a model dependence to the drifts in the two initialization methods.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Food web dynamics drive variation in Smallmouth Bass Micropterus dolomieu mercury contamination in protected Southern Appalachian streams

Mercury is a global pollutant that threatens otherwise protected aquatic ecosystems. Mercury food web dynamics are not well understood in streams with no point sources of contamination but have the potential to concentrate this dangerous pollutant in upper trophic level consumers. A 2016 study revealed that mercury concentrations of Smallmouth Bass Micropterus dolomieu varied between three streams in Great Smoky Mountains National Park (GSMNP), Tennessee, USA. We tested the hypothesis that food web interactions drive spatial variation in mercury concentrations of the apex predator of protected stream ecosystems. We measured carbon and nitrogen stable isotope ratios, and mercury concentrations of eight food web components of GSMNP streams including basal resources, intermediate consumers, and Smallmouth Bass, the apex predator. Mean THg concentrations of basal resources did not differ between streams, but the spatial pattern of concentrations of intermediate consumers mirrored Smallmouth Bass. Relationships between organismal contaminant concentrations and trophic level were positive in all three streams, indicating biomagnification is occurring in the protected streams of GSMNP. Furthermore, our findings indicate that mercury dynamics in intermediate trophic levels, rather than differences in basal resource concentrations, may drive differences in mercury contamination of apex predators of the protected stream ecosystems of GSMNP.

Bioaccumulation↗

DOE OSTI2024

Inferring Stochastic Rates from Heterogeneous Snapshots of Particle Positions

Many imaging techniques for biological systems—like fixation of cells coupled with fluorescence microscopy—provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics they intend to capture. In this study, these snapshot observations contain no information about individual trajectories, but still encode information about movement and demographic dynamics, especially when combined with a well-motivated biophysical model. The relationship between spatially evolving populations and single-moment representations of their collective locations is well-established with partial differential equations (PDEs) and their inverse problems. However, experimental data is commonly a set of locations whose number is insufficient to approximate a continuous-in-space PDE solution. Here, motivated by popular subcellular imaging data of gene expression, we embrace the stochastic nature of the data and investigate the mathematical foundations of parametrically inferring demographic rates from snapshots of particles undergoing birth, diffusion, and death in a nuclear or cellular domain. Toward inference, we rigorously derive a connection between individual particle paths and their presentation as a Poisson spatial process. Using this framework, we investigate the properties of the resulting inverse problem and study factors that affect quality of inference. One pervasive feature of this experimental regime is the presence of cell-to-cell heterogeneity. Rather than being a hindrance, we show that cell-to-cell geometric heterogeneity can increase the quality of inference on dynamics for certain parameter regimes. Altogether, the results serve as a basis for more detailed investigations of subcellular spatial patterns of RNA molecules and other stochastically evolving populations that can only be observed for single instants in their time evolution.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Photosynthesis phenology, as defined by solar-induced chlorophyll fluorescence, is overestimated by vegetation indices in the extratropical Northern Hemisphere

Vegetation phenology is highly sensitive to climate change, although the data and methods used to estimate key phenological states can influence this sensitivity. Because of its direct relation to leaf photosynthetic carbon uptake, remotely sensed solar-induced chlorophyll fluorescence (SIF) can provide new insight assessing changes in vegetation phenology. In this work, we investigated the potential of using a SIF time series product named contiguous SIF (CSIF) to estimate spring, summer, and autumn phenology in the extratropical Northern Hemisphere (>30°N) and compared the results with those based on Moderate Resolution Imaging Spectroradiometer (MODIS) Normalized Difference Vegetation Index (NDVI) for the period 2001–2018. Overall, we found similar spatial patterns in phenological states. However, specific dates of key phenological events differed when using CSIF vs. MODIS NDVI data. NDVI data indicated that the growing season started earlier (by 10.1 days on average) and ended later (11.5 days on average) relative to CSIF data. This implies that actual periods for photosynthetic activity are shorter (by 21.6 days on average) than those estimated from vegetation indices more directly related to changes in canopy structure. These large differences between results from NDVI and that from CSIF suggest that vegetation indices such as NDVI seem to overestimate the period for active photosynthesis over the extratropical Northern Hemisphere. Furthermore, while phenology of the early growing season is dominated by temperature for both NDVI and CSIF data, phenology of the late growing season is mainly controlled by temperature for NDVI but by precipitation for CSIF. Our findings were further confirmed by other SIF (GOME-2 SIF) and vegetation index (MODIS EVI) datasets. Phenology modes in Earth system modelling are often parameterized using leaf unfolding and senescence from either station or satellite observations. Our results imply that canopy structure-based parameterization schemes may have overestimated photosynthesis active period, and thus productivity responses. We conclude that SIF data offers a novel and unique approach for assessing phenological change - one that is more directly tied to the carbon cycle and how it is being influenced by climate change.

54 ENVIRONMENTAL SCIENCES↗