USGS ScienceSearch

SEARCH · USGS Science

Results for “Journal of Computational Physics”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

1,659 records · Page 88Linked to original sources

Preventing overfitting when using tree-based methods for mapping hydrothermal favorability

Ensemble tree-based algorithms are robust tools for estimating sparsely distributed resources with non-linear dependencies (e.g., hydrothermal systems). These algorithms naturally accommodate the threshold conditions necessary to enable and support hydrothermal systems (e.g., having sufficient heat and permeability) and are simpler than many other non-linear machine learning strategies (e.g., artificial neural networks), which is an advantage when working with few labeled examples from which to learn. In previous work, we used eXtreme Gradient Boosting (XGBoost) to produce regional prediction and uncertainty maps of hydrothermal favorability; however, recent studies suggest that, even when properly applied, XGBoost has some risk of overfitting when there are few labeled examples from which to learn. To evaluate overfitting when constructing hydrothermal favorability maps with tree-based methods, we compare XGBoost with Extremely Randomized Trees (ExtraTrees), another ensemble tree-based algorithm that has the potential to underfit when using few labeled examples. We hold all other modeling parameters constant, resulting in two contrasting favorability maps of conventional geothermal resources for the Great Basin. Our results indicate that ExtraTrees demonstrably reduces overfitting compared with XGBoost. After considering overall performance, we conclude that ExtraTrees provides a more suitable modeling approach than XGBoost for the purposes of conventional hydrothermal resource assessments.

Conference Paper

A practical framework for identifying genetic subpopulations and ESUs: Insights for IUCN assessments and broader management

Species conservation assessments evaluate extinction risk, and recovery potential, advancing species persistence through guiding resource prioritization and planning. Assessment frameworks, including the International Union for Conservation of Nature Red List and Green Status of Species, typically focus on species as a whole. Importantly, they do not routinely account for genetically distinct units or do not have standardized methods of unit delineation. This limits the representation of genetically distinct components, including adaptive genetic diversity that underpins long-term resilience and recovery. Incorporating standardized within-species units like subpopulations and Evolutionarily Significant Units (ESUs) into species assessments could help address this oversight. However, identifying and delineating such units remain challenging, particularly when molecular data are limited. Here, we propose a flexible framework that integrates molecular and non-molecular evidence to identify both subpopulations and ESUs across taxa, providing a practical tool to incorporate within-species diversity into conservation assessments.

BioScience

Land-based nutrient flux to a fringing reef: Insights from Ofu Island, American Samoa

Submarine groundwater discharge (SGD) is a critical driver of nutrient transport in coral reef ecosystems, shaping water quality, primary productivity, and overall reef health. This study quantifies SGD fluxes and associated nutrient dynamics in two reef flat pools within the Ofu Unit of the National Park of American Samoa: Papaloloa and Fatuana. A multi-method approach integrating unoccupied aerial system-based thermal infrared (UAS-TIR) surveys, radon-based SGD measurements, multichannel electrical resistivity tomography (ERT), and discrete water sampling was used to assess SGD rates and nutrient contributions. UAS-TIR imagery revealed cooler sea surface temperatures in both pools, indicative of SGD, with the higher fluxes observed in Papaloloa. Radon measurements revealed a strong inverse correlation between SGD rates and tidal stage, with a more immediate SGD response at Papaloloa due to its highly permeable calcareous sand and gravel substrate. In contrast, a 2–3-hour lag in SGD response at Fatuana suggests discharge from a more inland aquifer that has lower diffusivity. Nutrient concentrations correlated with temperature and salinity, confirming SGD as the dominant nutrient transport mechanism, whereas isotopic analyses indicated inputs from both groundwater and potential anthropogenic sources. Despite lower SGD flux at Fatuana, higher algal cover suggests additional factors influencing algal proliferation, including substrate availability and hydrodynamic conditions. Excess nutrient inputs from SGD may contribute to algal overgrowth, which threatens Ofu’s thermally tolerant corals by increasing competition for space and light. These findings underscore the complexity of SGD-mediated nutrient dynamics in reef environments and emphasize the need for integrated hydrological and ecological assessments to support effective reef conservation and management strategies.

American Samoa, Ofu Island, Olosega Island

Reduced injection rates and shallower depths mitigated induced seismicity in Oklahoma

The proximity of wastewater disposal to the Precambrian basement is a critical factor influencing induced earthquake rates in the Central United States, but the impact of reducing injection depths has not been widely demonstrated. Beginning in 2015, state regulatory efforts in Oklahoma and Kansas mandated that wells injecting into the lower Arbuckle Group, a basal sedimentary unit, be backfilled with cement (i.e. “plugged back”) so that they inject into shallower formations. This plug back activity gives us a unique opportunity to investigate the relationship between injection depth and induced seismicity rate. To evaluate the impact that decreased injection rates and plug backs had on the seismicity rates, we create a suite of rate-state earthquake models. Observed seismicity rates are best fit when only lower Arbuckle volumes are considered, suggesting the lower Arbuckle injectors were primarily responsible for the seismicity and that plug backs were effective at isolating the injected volumes to shallower formations. Our models demonstrate that if these wells had not been plugged back, seismicity rates would be multiple times larger than they are today. We find that the combination of well plug backs and injection volume decreases can be effective strategies for reducing induced seismicity rates.

Oklahoma

Correction to A regime shift in sediment export from a coastal watershed during a record wet winter, California: Implications for landscape response to hydroclimatic extremes

In the referenced article, the authors would like to correct text in the first paragraph on page 2571, Figure 9 and its caption. The changes reflect an error made in the processing of the rainfall intensity-duration data used to compare storms to published debris flow triggering thresholds. The correctly processed data does not change the interpretations made in the paper but does correctly indicate that the investigated storms did not exceed the rainfall intensity – duration threshold of Cannon (1988) but did significantly exceed the debris flow triggering threshold of Wieczorek (1987).

Earth Surface Processes and Landforms

Comparative crop yield forecasting using satellite-derived biophysical and agro-climatic predictors in Sub-Saharan Africa

Timely and accurate crop yield forecasting is central to food security early warning systems, particularly in climate-vulnerable regions. While operational forecasting frameworks commonly rely on precipitation and vegetation indices such as NDVI, their ability to provide actionable lead time remains limited. Here, we evaluate the added value of satellite-derived biophysical Essential Climate Variables (ECVs): Leaf Area Index (LAI) and Fraction of Photosynthetically Active Radiation (FAPAR), for forecasting millet yield in Burkina Faso (BF) and maize yield in South Africa (ZA) and Malawi (MW). Using Random Forest models, we quantify forecast skill across the growing season at both national and sub-national scales. Results show that LAI and FAPAR provide effective forecast lead times of approximately 4 months in BF, 2 months in ZA, and up to 6 months in MW relative to harvest. At peak performance, Mean Absolute Percentage Error (MAPE) reaches 19.8% (LAI) and 23.8% (FAPAR) in BF, 12.0% and 9.8% in ZA, and 21.8% and 20.8% in MW, respectively. Across countries, biophysical parameters often outperform NDVI and precipitation, particularly in arid and semi-arid regions. At the sub-national level, LAI and FAPAR enable classification of administrative units into high and moderate-skill forecast units, revealing strong spatial heterogeneity linked to crop dominance. However, forecast skill declines where the target crop is not the dominant type, highlighting an important limitation for operational deployment. Overall, the findings suggest that satellite-derived biophysical parameters can provide earlier and more spatially resolved yield signals than commonly used predictors, with potential to improve the timeliness and effectiveness of food security early warning systems.

Remote Sensing Applications: Society and Environme

USGS addresses needs for lithium calibration and quality control materials for pLIBS analysis

Lithium (Li) is a globally important commodity used for energy storage, national defense, human health, and advanced technologies. Lithium resource development requires identifying deposits with elevated concentrations and optimal mineralogy, typically associated with select clays and pegmatites. Lithium is a light, highly reactive alkali metal with low atomic mass that is difficult to detect and quantify using conventional portable geochemical techniques such as X-ray fluorescence (XRF). However, portable laser-induced breakdown spectroscopy (pLIBS) is a powerful analytical technique for lithium exploration due to its ability to analyze solids quickly with minimal preparation. The expanded utility of pLIBS is hampered by the lack of matrix-matched calibration and quality control (QC) materials. The United States Geological Survey (USGS) has developed in-house lithium calibration and QC materials for lithium in clay and pegmatite matrices to address this limitation. We present the workflow and implementation of a custom-built matrix specific calibration on a SciAps Z-300 pLIBS, using proprietary Profile Builder software. The implementation of the custom calibration and quality control standards enables us to collect semiquantitative results directly from the pLIBS while in the field. Ultimately, this calibration has improved confidence in sample selection and collection in the field, providing more efficient site characterization.

Conference Paper

A diatom-based quantitative sea-ice proxy for the Bering and Chukchi seas

Sea ice affects Earth's climate system on both regional and global scales. Its incorporation into climate can be used to achieve more accurate predictions of future climate. However, instrumental records of sea-ice concentration do not extend earlier than 1978. In an effort to extend this record, we constructed a proxy using the generalized additive model based on relative abundances of five easy-to-identify diatom species found in sediment samples across the Bering and Chukchi seas. Here we present the first quantitative diatom-based sea-ice proxy developed for Beringia. The developed proxy has been applied to two sediment cores in the Bering Sea ranging from 0 to 25.7 ka (HLY0204 51JPC) and 369 to 430 ka (IODP Exp 323 Site U1345) and one in the Chukchi Sea ranging from 2.7 to 10 ka (HLY0204 24JPC). The obtained reconstructions of sea-ice concentrations are similar, but not identical to previously published qualitative and nearby records based on other proxies. Because our results are quantitative, they can be incorporated into regional climate models. The proxy is publicly available as an R Shiny application (app) and can be applied to any diatom count from marine sediments in the region.

Bering Sea, Chukchi Sea

Tracing mercury from land to river: Global sources, retention, and implications for sustainability

Mercury (Hg) pollution in river systems is a global sustainability challenge. Yet the transport, transformation, and retention of Hg within global rivers remain poorly quantified, particularly in regions with sparse observations such as Southeast Asia and Africa, hindering effective pollution mitigation and reinforcing geographic inequities in scientific knowledge and environmental governance. Here, we present the first global, high-resolution simulation of riverine Hg dynamics using a process-based model that traces Hg from land-based sources through river networks to the ocean. Under a realistic scenario, we estimate that ~1,900 megagrams per year (Mg/yr) of Hg enters global rivers, including 1,500 Mg/yr from human-induced sources and 400 Mg/yr from soil erosion. Nearly half of this flux (~1,000 Mg/yr) is retained in reservoirs and dams, which act as major sinks. While such retention limits downstream delivery to the oceans, it also heightens in-reservoir Hg methylation risks. By bridging the gap between Hg releases and observed riverine exports, our framework offers a scalable tool for data-limited regions, promotes data access, and supports global freshwater and pollution-management strategies.

EarthArXiv

Tracing mercury from land to river: Global sources, retention, and implications for sustainability

Mercury (Hg) pollution in river systems is a global sustainability challenge. Yet the transport, transformation, and retention of Hg within global rivers remain poorly quantified, particularly in regions with sparse observations such as Southeast Asia and Africa, hindering effective pollution mitigation and reinforcing geographic inequities in scientific knowledge and environmental governance. Here, we present the first global, high-resolution simulation of riverine Hg dynamics using a process-based model that traces Hg from land-based sources through river networks to the ocean. Under a realistic scenario, we estimate that ∼1900 megagrams per year (Mg/yr) of Hg enters global rivers, including 1500 Mg/yr from human-induced sources and 400 Mg/yr from soil erosion. Nearly half of this flux (∼1000 Mg/yr) is retained in reservoirs and dams, which act as major sinks. While such retention limits downstream delivery to the oceans, it also heightens in-reservoir Hg methylation risks. By bridging the gap between Hg releases and observed riverine exports, our framework offers a scalable tool for data-limited regions, promotes data access, and supports global freshwater and pollution-management strategies.

Environmental Science & Technology

New developments at the Center for Engineering Strong-Motion Data (CESMD)

The Center for Engineering Strong-Motion Data (CESMD), an internationally utilized joint center of the U.S. Geological Survey (USGS) and the California Geological Survey (CGS), provides a single access point for earthquake strong-motion records and station metadata from the CGS California Strong-Motion Instrumentation Program (CSMIP), the USGS National Strong-Motion Project (NSMP), the USGS Advanced National Seismic System, and other affiliates. The CESMD has been continuously improving its webtools to facilitate the access of strong-motion data and metadata for use in post-earthquake response and for scientific and engineering research applications. The Center provides raw and processed strong-motion data via the Engineering Data Center (EDC) and the Virtual Data Center (VDC) web portals. This paper focuses on the strong-motion products provided by the EDC where more than 48,000 records with peak ground accelerations greater than 0.1% g from over 2400 earthquakes are currently hosted. and on the ongoing efforts to develop data access tools and applications. The new developments and ongoing efforts in the EDC include: 1) enhancements to the CESMD webservices to facilitate access to station metadata, earthquake information, and strong motion records 2) new features to the interactive map interface, improving the visualization and access to earthquake, station, and record information, 3) efforts to develop a new web application tool for data format conversion from a number of data formats, 4) efforts to unify varying waveform data formats into a consistent format, 5) ongoing efforts to compile seismic station site geology, measured or inferred Vs30 values, shear-wave profiles, NEHRP site class, and available structural instrument deployment schematics, and 6) a special studies pages for research topic-specific ground motion datasets that offer uniform processing of records from a variety of sources.

Conference Paper

Wildfire, extreme precipitation and debris flows, oh my! Channel response to compounding disturbances in a mountain stream in the Upper Colorado Basin, USA

Compounding changes in climate and human activities stand to increase sediment input to rivers in many landscapes, including via discrete perturbations such as post-fire debris flows. Because sediment supply is a dominant control on river morphology, understanding mountain river responses to sediment regime perturbations is critical to predicting and addressing downstream effects to infrastructure, water security and aquatic habitat. A growing body of literature explores the causes, likelihood, size and composition of post-fire debris flows, but the channel response to these disturbances remains poorly studied. This study used repeat field surveys, time-lapse photographs and pre- and post-disturbance remote sensing datasets to document and analyse space- and time-varying channel response to post-fire debris flows along a steep mountain stream in the Upper Colorado River Basin, USA. Specifically, we evaluated channel morphology and bed composition changes, correlations between channel changes and valley and channel attributes, and the relative importance of spring snowmelt versus summer monsoon events. Several cross-sectional channel change types were observed from lidar a month after post-fire debris-flow events, including channelized and braided incision into deposits, incision into the pre-fire channel bed, bank erosion and no change. Channel changes were most correlated with pre-fire channel width, valley width and unit stream power, and these relationships could be tested in other burned locations to evaluate their transferability. Repeat channel surveys before and after snowmelt indicate rapid recovery and channel narrowing following major sediment disturbances, although sediment deposits remained in the channel margins. Together, these results highlight the importance of field and remote sensing-based channel surveys to improve understanding of, and potential to predict, mountain channel response to compounding climate disturbances.

Earth Surface Processes and Landforms

Combining scanning electron microscopy, X-ray diffraction, and X-ray fluorescence to characterize shear zones at the Pogo gold deposit, Alaska

This study employs a multi-method analytical approach to characterize the mineralogical, geochemical, and textural properties of fault rocks from the Pogo gold mine in the Yukon-Tanana Upland, central Alaska. Specifically, we examine cataclasites, to document the structural and geochemical evolution of shear zones and their associations with gold mineralization. To investigate the shear zone, we integrate portable X-ray fluorescence (pXRF), scanning electron microscopy-based automated mineralogy (SEM-AM), X-ray diffraction (XRD), and high-resolution micro-X-ray fluorescence (micro-XRF) mapping. These methods collectively provide insights into bulk and trace element chemistry, mineralogical composition, and deformation-related textures across multiple scales. Handheld pXRF enables rapid geochemical screening, guiding SEM-AM and XRD analyses to ensure consistent mineralogical interpretation. X-ray diffraction identifies and quantifies crystalline phases, while SEM-AM produces high-resolution mineral maps, revealing mineral abundances, grain-scale textures, and gold associations. Micro-XRF mapping further refines our understanding by showing visual trace element distributions at sub-millimetre resolution. By integrating these techniques, we improve our understanding of the nature and geochemistry of Pogo shear zones, their role in gold mineralization, and support metallurgical processing strategies. This approach enhances exploration models and resource characterization for structurally complex gold deposits.

Alaska

Preparing for today's and tomorrow's water-resources challenges in eastern Long Island, New York

Freshwater is a vital natural resource. Although New York is a water-rich State, the wise and economical use of water resources is needed to ensure that there is enough water of adequate quality for both human and ecological needs—both for today and for tomorrow. Nowhere in New York is this more evident than in Nassau and Suffolk Counties on Long Island, where the public water supply is obtained from the sole-source aquifers located directly beneath the nearly 3 million people who live there. In 2023, in eastern Long Island’s Suffolk County, groundwater was pumped from these aquifers by more than 1,100 public water-supply wells to meet the needs of about 1.5 million people.

New York

GRAPES: Earthquake early warning by passing seismic vectors through the grapevine

Estimating an earthquake's magnitude and location may not be necessary to predict shaking in real time; instead, wavefield-based approaches predict shaking with few assumptions about the seismic source. Here, we introduce GRAph Prediction of Earthquake Shaking (GRAPES), a deep learning model trained to characterize and propagate earthquake shaking across a seismic network. We show that GRAPES’ internal activations, which we call “seismic vectors”, correspond to the arrival of distinct seismic phases. GRAPES builds upon recent deep learning models applied to earthquake early warning by allowing for continuous ground motion prediction with seismic networks of all sizes. While trained on earthquakes recorded in Japan, we show that GRAPES, without modification, outperforms the ShakeAlert earthquake early warning system on the 2019 M7.1 Ridgecrest, CA earthquake.

Shimane/HiroshimaPrefectures

Incorporating location uncertainty improves inference with stop-level North American Breeding Bird Survey data

Ecological models should account for uncertainty to be most effective and useful. Yet, uncertainty from model covariates—unlike that from other sources, such as sampling error or process variability—is seldom explicitly incorporated. This can cause underestimates of uncertainty to cascade through model parameter estimates, predictions, and downstream uses. Burner et al. proposed a method for quantifying uncertainty in covariates and incorporating it into models using informative Bayesian priors. This method was applied to stop-level Breeding Bird Survey (BBS) analyses, where land cover uncertainty at each stop arises from substantial stop location uncertainty. A limited validation of model-estimated land cover, using stops with known locations, indicated the method’s potential effectiveness, but it was not rigorously evaluated. We conduct a robust simulation-based test, generating stop locations, extracting land cover, and simulating bird communities across 210 BBS routes in the upper Midwest. We compare 3 models: a “known” model with true land cover, a “naive” model assuming consistent 800-m stop spacing, and a “full” model using informative priors to estimate land cover. Species parameter estimates and predicted prevalence patterns across gradients in land cover from the full model approached those of the known model and were substantially closer to the true values used in simulations relative to those from the naive model. Naive model parameters were more biased relative to the other models, and credible intervals of predicted species prevalence rarely included the true simulated values. The full model also produced land cover covariate estimates closer to true simulation values relative to the mean informative priors. Our results show that, for the BBS, informative priors enable more accurate stop-level analyses despite location uncertainty. In contrast, naive models that ignore this uncertainty yield poor inferences. More broadly, we demonstrate empirically the utility of informative priors to account for covariate uncertainty in ecological models.

Michigan, Minnesota, Wisconson

Groundwater flow model for the Des Moines River alluvial aquifer near Des Moines, Iowa

Des Moines Water Works (DMWW) is a regional municipal water utility that provides residential and commercial water resources to about 600,000 customers in Des Moines, Iowa, and surrounding municipalities in central Iowa. DMWW has identified a need for increased water supply and is exploring the potential for expanding groundwater production capabilities in the Des Moines River alluvial aquifer, where it operates two radial collector wells (RCWs). The U.S. Geological Survey, in cooperation with DMWW, completed a study of the Des Moines River alluvial aquifer and interactions of the RCWs with the aquifer; no previously published model has included the existing well locations, which is the focus of this model. A conceptual and numerical groundwater flow model have been developed to characterize the Des Moines River alluvial aquifer under existing conditions, to simulate water levels observed in the RCWs, and to provide publicly accessible hydrologic data and research that advance understanding of the regional hydrologic system and can potentially be used in the future to evaluate groundwater production scenarios. Model performance was assessed by comparing observed and simulated groundwater levels that included water level elevations, water level changes, water level inequality observations, surface water streamflow, and change in surface water volume from upstream to downstream. Water table elevation in the aquifer layers is on average slightly overestimated with average absolute value error less than 1.5 meters at both RCWs and less than 2.5 meters for all observation wells in the alluvial aquifer layers. The model also accurately simulated water tables greater than the RCW design minimum (a water level threshold at which RCW pumping is reduced) in all timesteps for which water level observation data existed. Water table elevation error was higher in other model layers that were not the focus of the study, and the model did not accurately match streamflow targets.

Iowa

State shifts in the deep Critical Zone drive landscape evolution in volcanic terrains

Understanding the near-surface environment where atmospheric and solid earth processes interact, often termed the “Critical Zone,” is important for assessing resources and building resilient societies. Here, we examine a volcanic landscape in the Oregon Cascade Range, an understudied Critical Zone setting that is host to major regional water resources, pervasive silicate weathering, and significant geohazards. We leverage a bedrock age chronosequence to show that the volcanic Critical Zone undergoes a structural shift, from depth extents of >1 km to meters, over timescales of ~1 My. We map an active groundwater volume comparable to major continental lakes, stored at the Cascade Range crest. This state shift makes volcanic landscape evolution a unique probe of deep coupling between Earth systems.

PNAS