About

Jose D. Fuentes is a Professor of Meteorology at Penn State University, with a research specialty in the Atmospheric Boundary Layer and Turbulence, Atmospheric Chemistry and Pollution, and Climate Earth-Atmosphere Interactions. He earned his Ph.D. from the University of Guelph in 1992. His research interests include biogenic hydrocarbons, pollutant deposition processes, carbon sequestration, and the atmospheric boundary layer. He is a Fellow of the American Meteorological Society and a member of the American Geophysical Union. His work involves studying the interactions between atmospheric chemistry and physical processes, contributing to our understanding of air quality, climate, and environmental change.

Research topics

• Environmental science
• Physics
• Chemistry
• Atmospheric sciences
• Geology
• Ecology
• Meteorology
• Geography
• Environmental chemistry
• Political Science
• Computer Science
• Climatology
• Organic chemistry
• Botany
• Engineering
• Environmental resource management
• Environmental engineering
• Biology
• Civil engineering
• Photochemistry

Selected publications

• Long-Term Trends and Interannual Variability in Tidal Wetland Gross Primary Production Across the Conterminous United States

  2026-01-20

  articleOpen access

  Tidal wetlands are critical carbon sinks, yet their response to ongoing environmental change remains uncertain across the conterminous United States. To address this gap, we quantified long-term trends and interannual variability in tidal wetland gross primary production (GPP; g C m⁻² d⁻¹) using a 20-year (2001–2020) satellite-based dataset. We also examined regional differences and the relative influence of climate drivers versus vegetation canopy on GPP dynamics. At the continental scale, GPP increased by approximately 6% over two decades, with the strongest gains in the South Atlantic and Gulf regions. Gulf wetlands exhibited the highest productivity, while Pacific and northern Atlantic wetlands were substantially lower, reflecting climatic gradients. Decomposition analysis indicates that rising shortwave radiation and air temperature are the primary drivers of productivity increases, outweighing declines in vegetative canopy coverage and apparent greenness. Interannual variability was modest overall but greatest in the Western Gulf, where episodic disturbances such as hurricanes and drought exert strong influence. These findings suggest that recent productivity gains are driven largely by climate forcing rather than vegetation changes, underscoring the need to incorporate climatic drivers into tidal wetland carbon models and management strategies.

  PublisherOA PDFDOI

• A concept of a convection-cloud chamber to study aerosol-cloud-drizzle interactions

  Bulletin of the American Meteorological Society · 2026-04-28

  article

  Abstract Understanding and quantifying the full chain of processes from aerosol activation to drizzle formation, and the associated feedbacks to the aerosol chemical and physical properties, all within a turbulent cloud are some of the toughest challenges in atmospheric chemistry and physics and are keys to the cloud-precipitation puzzle. This paper describes a concept for a new type of research facility consisting of a cloud chamber plus associated instrumentation and computational models, to explore aerosol-cloud interactions and processing, cloud optical properties, entrainment-cloud interactions, and quantitative assessment of drizzle onset. The envisioned design is for a 3-m by 3-m by 9-meter chamber, such that the height is sufficient to achieve long lifetimes for aerosol processing and for significant drizzle growth by collision and coalescence. A suite of computational tools for simulating microphysical properties in the chamber provides a digital twin for designing the chamber and a range of example experiments. Theory and test results from novel remote sensing systems for exploring chemical and physical interactions and evolution of aerosols, cloud droplets, and drizzle within turbulent clouds are described. Testing of technology needed for operation of a large-volume chamber, including aerosol generation methods and novel materials for water-vapor boundary conditions are described. Simulations suggest that spatially uniform turbulence and microphysical properties can be sustained in steady-state, with reasonable aerosol and water vapor fluxes, and that substantial drizzle can be produced through collision and coalescence of cloud droplets. Remaining challenges for more detailed engineering design, and a discussion of possible first-light experiments are described.

  PublisherDOI

• Similarity of Wind Speed in the Roughness Sublayer Above Vegetation

  Agricultural and Forest Meteorology · 2025-01-01

  articleOpen access

  In fluid dynamics, the theory of similarity states that, under certain conditions, the statistical characteristics of turbulent flows remain invariant when normalized by dimensionless parameters. Above irregular surfaces, an atmospheric layer called the Roughness Sublayer (RS) is formed. Various measurements of turbulent fluxes are made within the RS. However, there is still no unified similarity theory that properly captures the turbulence characteristics in this layer. Contextually, we propose using characteristic scales defined at the inflection point of the vertical wind speed profile as normalization parameters, enabling the formulation of a similarity theory for wind speed over dense vegetation. These scales are: the height of the inflection point in the wind profile (zi), the wind speed at that point (ui), and the shear length scale (Ls). Wind speed profiles measured in three dense forest areas in the Brazilian Amazon and in a cornfield in the United States were used. The results indicated that the normalization of wind profiles using zi, ui and Ls showed significantly lower statistical errors compared to normalization by "classical" parameters, such as wind speed at canopy height (uh) and average canopy height (h). In addition, this normalization made it possible to model the vertical wind speed profile using the equation U/ui = 1 + arctan[(z - zi)/Ls], which can be applied even with a limited number of measurement heights, provided that ui, zi and Ls are properly parameterized. Moreover, this model performs better than exponential models in simulating wind in the air layer between h/2 and h, which is critically important for accurately representing turbulent exchanges between vegetated surfaces and the atmosphere. These findings represent an advance in the formulation of more realistic parameterizations of turbulent exchange processes in the RS and constitute an essential step towards the development of a similarity theory specific to this layer.

  PublisherDOI

• Integrated Analysis of Airborne In-situ Cloud and Aerosol Microphysics Data during the 2022 Chemistry in the Arctic: Clouds, Halogens, and Aerosols (CHACHA) Field Campaign

  2025-03-14

  preprintOpen access

  The Chemistry in the Arctic: Clouds, Halogens, and Aerosols (CHACHA) field project featured a wide collaboration from six universities to enhance the scientific understanding of multiphase halogen chemistry in the Arctic that took place in Utqiaġvik, Alaska during February-April 2022. This project was spurred by the pursuit of strengthening our understanding of how Arctic Sea ice loss and fossil fuel extraction affects atmospheric halogen chemistry.In this study, cloud flights from the University of Wyoming King Air are evaluated closely to assess the ambient conditions relevant to the Arctic boundary layer during flights targeting clouds emanating from open leads in the Arctic sea ice. During these flights, the Particle into Liquid Sampler (PILS) was utilized using a Roger’s inlet and Counterflow Virtual Impactor (CVI) with low volume (1.5 mL) samples being collected. This study aims to introduce a methodological basis for prioritizing samples and identifying samples that can be safely grouped together to maximize the chemical analysis possible. Instruments are used for this method include Aerosol microphysics data from instruments including Condensation Particle Counters (CPC), Portable Optical Particle Spectrometer (POPS), and Passive Cavity Aerosol Spectrometer Probe (PCASP) and cloud microphysics data from a Cloud Droplet Probe (CDP) and Two-Dimensional Stereo (2D-S). Ultimately, this work is a key step in chemical analysis of cloud flights that will be used to better understand multiphase Arctic halogen chemistry by constraining a Lagrangian chemical box model and cloud parcel modeling.

  PublisherDOI

• Discrepancies in precipitation trends between observational and reanalysis datasets in the Amazon Basin

  Scientific Reports · 2025-03-01 · 11 citations

  articleOpen accessSenior author

  The Amazon rainforest is a region of global importance as it accounts for 10% of terrestrial biodiversity and stores at least 10 years' worth of global anthropogenic carbon dioxide ([Formula: see text]) emissions. However, the rainforest is currently under tremendous pressure from deforestation and the impacts of climate change, leading to rainforest degradation and perturbations of the regional carbon and water cycles. Using data sets from various sources, we produce spatial and temporal analyses of precipitation for the Amazon Basin from 1980 to 2022. Results demonstrate substantial seasonal and regional variations across the Amazon Basin, indicating that while some regions are experiencing increasing trends in precipitation, others are undergoing declines. These trends are not consistent among available datasets, with substantial differences between observational, reanalysis, and climate model data. For example, precipitation data from reanalyses for 1980-2022 reveal significant drying patterns in the southern and central Amazon during the dry season, which are not present in the observational datasets.

  PublisherOA PDFDOI

• Measurements of the Emission Rates of Nitrogen Oxides and Greenhouse Gases From the Prudhoe Bay Oil Field

  Journal of Geophysical Research Atmospheres · 2025-08-06 · 1 citations

  article

  Abstract Oil and gas production regions are significant sources of greenhouse gases and reactive pollutants such as nitrogen oxides (NO x ) and volatile organic compounds. Research has also shown that methane (CH 4 ) emissions reported to the Environmental Protection Agency's (EPA) Greenhouse Gas Reporting Program (GHGRP) are generally underestimated. The Arctic accounted for 5.5% of global oil and gas production in 2022 but is estimated to contain significant undiscovered resources. The emitted NO x and volatile organic compounds can impact the composition and chemistry of the Arctic atmosphere. The Prudhoe Bay Oil Field in Alaska is one of the 10 largest oil fields in the US and has been approved for significant development expansion. However, only one recent study has reported measurements of its greenhouse gas emissions. We estimate the emission rates for carbon dioxide (CO 2 ), CH 4 , and NO x from the Prudhoe Bay Oil Field during the spring of 2022 using airborne mass balance methods and emission ratios. We also discuss emissions per energy produced and show an increase over time, with values higher than the national average for oil and gas producing regions, though within uncertainties. Our estimates are lower than the NO x emission estimate reported in the National Emissions Inventory (NEI), as seen in other oil and gas studies, but fall within the uncertainty range of the greenhouse gases reported in the GHGRP. This work provides a valuable snapshot of emissions before further expansion of extraction activities.

  PublisherDOI

• Estimating scalar turbulent fluxes with slow response sensors in the stable atmospheric boundary layer

  arXiv (Cornell University) · 2024-01-22

  preprintOpen access

  Conventional and recently developed approaches for estimating turbulent scalar fluxes under stable conditions are evaluated. The focus is on methods that do not require fast scalar sensors such as the relaxed eddy accumulation (REA) approach, the disjunct eddy-covariance (DEC) approach, and a novel mixing length parametrization labelled as A22. Using high-frequency measurements collected from two contrasting sites (Utqiagvik, Alaska and Wendell, Idaho "during winter"), it is shown that the REA and A22 models outperform the conventional Monin-Obukhov Similarity Theory (MOST) utilized in Earth System Models. With slow trace gas sensors used in disjunct eddy-covariance (DEC) approaches and the more complex signal filtering associated with REA devices (here simulated using filtered signals from fast-response sensors), A22 outperforms REA and DEC in predicting the observed unfiltered (total) eddy-covariance (EC) fluxes. However, REA and DEC can still capture the observed filtered EC fluxes computed with the filtered scalar signal. This finding motivates the development of a correction, blending the REA and DEC methods, for the underestimated net averaged fluxes to incorporate the effect of sensor filtering. The only needed parameter for this correction is the mean velocity at the instrument height, a surrogate of the advective timescale.

  PublisherOA PDFDOI

• Critical thermal maxima differ between groups of insect pollinators and their foraging times: Implications for their responses to climate change

  Journal of Melittology · 2024-10-11 · 2 citations

  articleOpen access

  Insects perform essential roles within ecosystems and can be vulnerable to climate change because of their small body size and limited capacity to regulate body temperature. Several groups of insects, such as bees and flies, are important pollinators of wild and cultivated plants. However, aspects of their thermal biology remain poorly studied, which limits predictions of their responses to climate change. We assessed the critical thermal maximum (CTMax) of bees and flies visiting flowers in urban and periurban areas in tropical and subtropical regions of the Americas. We also assessed the effect of the foraging time of the day on CTMax. Overall, we found that bees displayed higher CTMax than flies. Flies foraging in the morning and afternoon displayed similar CTMax while bees in the morning displayed a higher CTMax than in the afternoon. The results of this study suggest differences in the vulnerability to climate change between these two major groups of pollinators, with flies being more at risk.

  PublisherOA PDFDOI

• Estimating scalar turbulent fluxes with slow-response sensors in the stable atmospheric boundary layer

  Atmospheric chemistry and physics · 2024-08-30 · 2 citations

  articleOpen accessCorresponding

  Abstract. Conventional and recently developed approaches for estimating turbulent scalar fluxes under stable atmospheric conditions are evaluated, with a focus on gases for which fast sensors are not readily available. First, the relaxed eddy accumulation (REA) classical approach and a recently proposed mixing length parameterization, labeled A22, are tested against eddy-covariance computations. Using high-frequency measurements collected from two contrasting sites (the frozen tundra near Utqiaġvik, Alaska, and a sparsely vegetated grassland in Wendell, Idaho, during winter), it is shown that the REA and A22 models outperform the conventional Monin–Obukhov similarity theory (MOST) utilized widely to infer fluxes from mean gradients. Second, scenarios where slow trace gas sensors are the only viable option in field measurements are investigated using digital filtering applied to fast-response sensors to simulate their slow-response counterparts. With a filtered scalar signal, the observed filtered eddy-covariance fluxes are referred to here as large-eddy-covariance (LEC) fluxes. A virtual eddy accumulation (VEA) approach, akin to the REA model but not requiring a mechanical apparatus to separate the gas flows, is also formulated and tested. A22 outperforms VEA and LEC in predicting the observed unfiltered (total) eddy-covariance (EC) fluxes; however, VEA can still capture the LEC fluxes well. This finding motivates the introduction of a sensor response time correction into the VEA formulation to offset the effect of sensor filtering on the underestimated net averaged fluxes. The only needed parameter for this correction is the mean velocity at the instrument height, a surrogate of the advective timescale. The VEA approach is very suitable and simple to use with gas sensors of intermediate speed (∼ 0.5 to 1 Hz) and with conventional open- or closed-path setups.

  PublisherDOI

• Evaluating Numerical Methods to Investigate Spectral Solar Radiative Transfer in Plant Canopies

  Journal of Advances in Modeling Earth Systems · 2024-06-29

  articleOpen accessSenior authorCorresponding

  Abstract The disposition of spectral solar irradiance in plant canopies is crucially important to understand processes such as photolysis of molecules amenable to absorbing actinic light. Thus, one objective of this study is to evaluate the most commonly applied radiative transfer approaches to estimate spectral irradiance as a function of plant canopy depth. Eight radiative transfer approaches are ascertained. Another objective is to determine the impacts of the spectral resolution assumed in radiative transfer calculations and model choice on key processes such as canopy absorption and reflection of irradiance. By comparing results from broadband‐only and spectrally‐resolved canopy radiative transfer, we aim to quantitatively determine the uncertainties associated with failing to resolve the sunlight spectra. We determine the optimal spectral resolution required to estimate canopy radiative transfer results such as air‐chemistry‐specific quantities related to photolysis of a select group of molecules. In addition, we evaluate techniques for binning leaf and soil optical properties. Results showed that high spectral resolution is ideally desired to compute photolysis of molecules such as ozone, nitrogen dioxide, nitrate radical, nitrous acid, and formaldehyde. For in‐canopy photolysis of molecules, a waveband resolution of at least 10 nm is sufficient to obtain accurate estimates for most photochemical reactions. Positive reaction‐dependent uncertainties in canopy‐mean relative photolysis values for individual molecules can be as high as 30% compared to estimates derived with broad‐band solar irradiance.

  PublisherOA PDFDOI

Recent grants

• Collaborative proposal: Track 1 Increasing Diversity in the Geosciences Through Experiential Learning

  NSF · $100k · 2010–2013

• REU Site: Climate Science Research at the Pennsylvania State University

  NSF · $360k · 2013–2017

• Collaborative Research: CHemistry in the Arctic: Clouds, Halogens, and Aerosols (CHACHA)

  NSF · $316k · 2020–2025

• EAGER: Do Air Pollutants Modify the Strength and Quality of Floral Scents?

  NSF · $161k · 2009–2012

• WSC-Category 2 Collaborative: Robust decision-making for South Florida water resources by ecosystem service valuation, hydro-economic optimization, and conflict resolution modeling

  NSF · $301k · 2013–2018

Frequent coauthors

• Marcelo Chamecki

  University of California, Los Angeles

  50 shared

• Tobias Gerken

  48 shared

• Gabriel G. Katul

  Duke University

  44 shared

• Gilberto Fisch

  Universidade de Taubaté

  37 shared

• Nelson Luı́s Dias

  Universidade Federal do Paraná

  35 shared

• Paul C. Stoy

  University of Wisconsin–Madison

  35 shared

• Jesus Ruiz‐Plancarte

  Naval Postgraduate School

  34 shared

• Amy M. Trowbridge

  University of Wisconsin–Madison

  33 shared

Awards & honors

• Fellow, American Meteorological Society
• American Geophysical Union Fellow