Articles | Volume 18, issue 19
https://doi.org/10.5194/gmd-18-6647-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-18-6647-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Development and technical paper
| 
01 Oct 2025
Development and technical paper |
| 01 Oct 2025
| 01 Oct 2025
Implementation of a dry deposition module (DEPAC v3.11_ext) in a large eddy simulation code (DALES v4.4)
Leon Geers
TNO, Department of Air quality and Emissions Research, Utrecht, the Netherlands
TNO, Department of Air quality and Emissions Research, Utrecht, the Netherlands
Gudrun Thorkelsdottir
TNO, Department of Air quality and Emissions Research, Utrecht, the Netherlands
Meteorology and Air Quality Section, Wageningen University, Wageningen, the Netherlands
now at: RIVM National Institute for Public Health and the Environment, Center for Environmental Quality, Bilthoven, the Netherlands
Jordi Vilà-Guerau de Arellano
Meteorology and Air Quality Section, Wageningen University, Wageningen, the Netherlands
Martijn Schaap
TNO, Department of Air quality and Emissions Research, Utrecht, the Netherlands
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Atmos. Chem. Phys., 25, 4943–4963, https://doi.org/10.5194/acp-25-4943-2025, https://doi.org/10.5194/acp-25-4943-2025, 2025
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This article compares three ammonia (NH3) deposition models in a dune ecosystem and investigates the uncertainty of these models. The Zhang model aligned best with the measurements, whereas the DEPAC (DEPosition of Acidifying Compounds) and Massad models overestimated and underestimated the NH3 deposition respectively. The study found that NH3 exchange with wet plant leaves was an important but uncertain process. It offers recommendations to improve future models and suggests measurements to lower the existing uncertainty.
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Atmos. Chem. Phys., 25, 8959–8981, https://doi.org/10.5194/acp-25-8959-2025, https://doi.org/10.5194/acp-25-8959-2025, 2025
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Analysis of CH4 data (2010–2021) from ZOTTO in Central Siberia shows an increase in the summer diurnal amplitude, driven by nighttime emissions. These trends correlate with rising soil temperature and moisture, especially in late summer. Peaks in 2012, 2016, and 2019 emission link to wildfires and wetland activity. Findings suggest wetlands as key CH4 sources and underscore the need for ongoing high-resolution monitoring in this region.
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Geosci. Model Dev., 18, 4571–4599, https://doi.org/10.5194/gmd-18-4571-2025, https://doi.org/10.5194/gmd-18-4571-2025, 2025
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Aircraft measurements are used to investigate high-altitude downdrafts in tropical deep convective clouds. The cloud water present in the downdrafts and its intensity do not show any correlation. Surprisingly, downdrafts occurred in supersaturated regions, contradicting the classical view of subsaturated downdrafts. Up- and downdrafts of similar strength show similar particle size distributions. These findings shed new light on the interplay between deep convection dynamics and microphysics.
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Felipe Lobos-Roco, Jordi Vilà-Guerau de Arellano, and Camilo del Río
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Atmos. Chem. Phys., 24, 8893–8910, https://doi.org/10.5194/acp-24-8893-2024, https://doi.org/10.5194/acp-24-8893-2024, 2024
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Composite analysis of gas concentration before and after rainfall, during the day and night, gives insight into the complex relationship between trace gas variability and precipitation. The analysis helps us to understand the sources and sinks of trace gases within a forest ecosystem. It elucidates processes that are not discernible under undisturbed conditions and contributes to a deeper understanding of the trace gas life cycle and its intricate interactions with cloud dynamics in the Amazon.
Kim A. P. Faassen, Jordi Vilà-Guerau de Arellano, Raquel González-Armas, Bert G. Heusinkveld, Ivan Mammarella, Wouter Peters, and Ingrid T. Luijkx
Biogeosciences, 21, 3015–3039, https://doi.org/10.5194/bg-21-3015-2024, https://doi.org/10.5194/bg-21-3015-2024, 2024
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The ratio between atmospheric O2 and CO2 can be used to characterize the carbon balance at the surface. By combining a model and observations from the Hyytiälä forest (Finland), we show that using atmospheric O2 and CO2 measurements from a single height provides a weak constraint on the surface CO2 exchange because large-scale processes such as entrainment confound this signal. We therefore recommend always using multiple heights of O2 and CO2 measurements to study surface CO2 exchange.
Raquel González-Armas, Jordi Vilà-Guerau de Arellano, Mary Rose Mangan, Oscar Hartogensis, and Hugo de Boer
Biogeosciences, 21, 2425–2445, https://doi.org/10.5194/bg-21-2425-2024, https://doi.org/10.5194/bg-21-2425-2024, 2024
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This paper investigates the water and CO2 exchange for an alfalfa field with observations and a model with spatial scales ranging from the stomata to the atmospheric boundary layer. To relate the environmental factors to the leaf gas exchange, we developed three equations that quantify how many of the temporal changes of the leaf gas exchange occur due to changes in the environmental variables. The novelty of the research resides in the capacity to dissect the dynamics of the leaf gas exchange.
Ruben B. Schulte, Jordi Vilà-Guerau de Arellano, Susanna Rutledge-Jonker, Shelley van der Graaf, Jun Zhang, and Margreet C. van Zanten
Biogeosciences, 21, 557–574, https://doi.org/10.5194/bg-21-557-2024, https://doi.org/10.5194/bg-21-557-2024, 2024
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We analyzed measurements with the aim of finding relations between the surface atmosphere exchange of NH3 and the CO2 uptake and transpiration by vegetation. We found a high correlation of daytime NH3 emissions with both latent heat flux and photosynthetically active radiation. Very few simultaneous measurements of NH3, CO2 fluxes and meteorological variables exist at sub-diurnal timescales. This study paves the way to finding more robust relations between the NH3 exchange flux and CO2 uptake.
Robbert P. J. Moonen, Getachew A. Adnew, Oscar K. Hartogensis, Jordi Vilà-Guerau de Arellano, David J. Bonell Fontas, and Thomas Röckmann
Atmos. Meas. Tech., 16, 5787–5810, https://doi.org/10.5194/amt-16-5787-2023, https://doi.org/10.5194/amt-16-5787-2023, 2023
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Isotope fluxes allow for net ecosystem gas exchange fluxes to be partitioned into sub-components like plant assimilation, respiration and transpiration, which can help us better understand the environmental drivers of each partial flux. We share the results of a field campaign isotope fluxes were derived using a combination of laser spectroscopy and eddy covariance. We found lag times and high frequency signal loss in the isotope fluxes we derived and present methods to correct for both.
Kim A. P. Faassen, Linh N. T. Nguyen, Eadin R. Broekema, Bert A. M. Kers, Ivan Mammarella, Timo Vesala, Penelope A. Pickers, Andrew C. Manning, Jordi Vilà-Guerau de Arellano, Harro A. J. Meijer, Wouter Peters, and Ingrid T. Luijkx
Atmos. Chem. Phys., 23, 851–876, https://doi.org/10.5194/acp-23-851-2023, https://doi.org/10.5194/acp-23-851-2023, 2023
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The exchange ratio (ER) between atmospheric O2 and CO2 provides a useful tracer for separately estimating photosynthesis and respiration processes in the forest carbon balance. This is highly relevant to better understand the expected biosphere sink, which determines future atmospheric CO2 levels. We therefore measured O2, CO2, and their ER above a boreal forest in Finland and investigated their diurnal behaviour for a representative day, and we show the most suitable way to determine the ER.
Pascal Wintjen, Frederik Schrader, Martijn Schaap, Burkhard Beudert, Richard Kranenburg, and Christian Brümmer
Biogeosciences, 19, 5287–5311, https://doi.org/10.5194/bg-19-5287-2022, https://doi.org/10.5194/bg-19-5287-2022, 2022
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For the first time, we compared four methods for estimating the annual dry deposition of total reactive nitrogen into a low-polluted forest ecosystem. In our analysis, we used 2.5 years of flux measurements, an in situ modeling approach, a large-scale chemical transport model (CTM), and canopy budget models. Annual nitrogen dry deposition budgets ranged between 4.3 and 6.7 kg N ha−1 a−1, depending on the applied method.
Micael Amore Cecchini, Marco de Bruine, Jordi Vilà-Guerau de Arellano, and Paulo Artaxo
Atmos. Chem. Phys., 22, 11867–11888, https://doi.org/10.5194/acp-22-11867-2022, https://doi.org/10.5194/acp-22-11867-2022, 2022
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Shallow clouds (vertical extent up to 3 km height) are ubiquitous throughout the Amazon and are responsible for redistributing the solar heat and moisture vertically and horizontally. They are a key component of the water cycle because they can grow past the shallow phase to contribute significantly to the precipitation formation. However, they need favourable environmental conditions to grow. In this study, we analyse how changing wind patterns affect the development of such shallow clouds.
Felipe Lobos-Roco, Oscar Hartogensis, Francisco Suárez, Ariadna Huerta-Viso, Imme Benedict, Alberto de la Fuente, and Jordi Vilà-Guerau de Arellano
Hydrol. Earth Syst. Sci., 26, 3709–3729, https://doi.org/10.5194/hess-26-3709-2022, https://doi.org/10.5194/hess-26-3709-2022, 2022
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This research brings a multi-scale temporal analysis of evaporation in a saline lake of the Atacama Desert. Our findings reveal that evaporation is controlled differently depending on the timescale. Evaporation is controlled sub-diurnally by wind speed, regulated seasonally by radiation and modulated interannually by ENSO. Our research extends our understanding of evaporation, contributing to improving the climate change assessment and efficiency of water management in arid regions.
Ruben B. Schulte, Margreet C. van Zanten, Bart J. H. van Stratum, and Jordi Vilà-Guerau de Arellano
Atmos. Chem. Phys., 22, 8241–8257, https://doi.org/10.5194/acp-22-8241-2022, https://doi.org/10.5194/acp-22-8241-2022, 2022
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We present a fine-scale simulation framework, utilizing large-eddy simulations, to assess NH3 measurements influenced by boundary-layer dynamics and turbulent dispersion of a nearby emission source. The minimum required distance from an emission source differs for concentration and flux measurements, from 0.5–3.0 km and 0.75–4.5 km, respectively. The simulation framework presented here proves to be a powerful and versatile tool for future NH3 research at high spatio-temporal resolutions.
Christian Brümmer, Jeremy J. Rüffer, Jean-Pierre Delorme, Pascal Wintjen, Frederik Schrader, Burkhard Beudert, Martijn Schaap, and Christof Ammann
Earth Syst. Sci. Data, 14, 743–761, https://doi.org/10.5194/essd-14-743-2022, https://doi.org/10.5194/essd-14-743-2022, 2022
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Field campaigns were carried out to investigate the biosphere–atmosphere exchange of selected reactive nitrogen compounds over different land surfaces using two different analytical devices for ammonia and total reactive nitrogen. The datasets improve our understanding of the temporal variability of surface–atmosphere exchange in different ecosystems, thereby providing validation opportunities for inferential models simulating the exchange of reactive nitrogen.
Pascal Wintjen, Frederik Schrader, Martijn Schaap, Burkhard Beudert, and Christian Brümmer
Biogeosciences, 19, 389–413, https://doi.org/10.5194/bg-19-389-2022, https://doi.org/10.5194/bg-19-389-2022, 2022
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Fluxes of total reactive nitrogen (∑Nr) over a low polluted forest were analyzed with regard to their temporal dynamics. Mostly deposition was observed with median fluxes ranging from −15 to −5 ng N m−2 s−1, corresponding to a range of deposition velocities from 0.2 to 0.5 cm s−1. While seasonally changing contributions of NH3 and NOx to the ∑Nr signal were found, we estimate an annual total N deposition (dry+wet) of 12.2 and 10.9 kg N ha−1 a−1 in the 2 years of observation.
Shelley van der Graaf, Enrico Dammers, Arjo Segers, Richard Kranenburg, Martijn Schaap, Mark W. Shephard, and Jan Willem Erisman
Atmos. Chem. Phys., 22, 951–972, https://doi.org/10.5194/acp-22-951-2022, https://doi.org/10.5194/acp-22-951-2022, 2022
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CrIS NH3 satellite observations are assimilated into the LOTOS-EUROS model using two different methods. In the first method the data are used to fit spatially varying NH3 emission time factors. In the second method a local ensemble transform Kalman filter is used. Compared to in situ observations, combining both methods led to the most significant improvements in the modeled concentrations and deposition, illustrating the usefulness of CrIS NH3 to improve the spatiotemporal distribution of NH3.
Carlos Román-Cascón, Marie Lothon, Fabienne Lohou, Oscar Hartogensis, Jordi Vila-Guerau de Arellano, David Pino, Carlos Yagüe, and Eric R. Pardyjak
Geosci. Model Dev., 14, 3939–3967, https://doi.org/10.5194/gmd-14-3939-2021, https://doi.org/10.5194/gmd-14-3939-2021, 2021
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The type of vegetation (or land cover) and its status influence the heat and water transfers between the surface and the air, affecting the processes that develop in the atmosphere at different (but connected) spatiotemporal scales. In this work, we investigate how these transfers are affected by the way the surface is represented in a widely used weather model. The results encourage including realistic high-resolution and updated land cover databases in models to improve their predictions.
Felipe Lobos-Roco, Oscar Hartogensis, Jordi Vilà-Guerau de Arellano, Alberto de la Fuente, Ricardo Muñoz, José Rutllant, and Francisco Suárez
Atmos. Chem. Phys., 21, 9125–9150, https://doi.org/10.5194/acp-21-9125-2021, https://doi.org/10.5194/acp-21-9125-2021, 2021
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We investigate the influence of regional atmospheric circulation on the evaporation of a saline lake in the Altiplano region of the Atacama Desert through a field experiment and regional modeling. Our results show that evaporation is controlled by two regimes: (1) in the morning by local conditions with low evaporation rates and low wind speed and (2) in the afternoon with high evaporation rates and high wind speed. Afternoon winds are connected to the regional Pacific Ocean–Andes flow.
Ruud H. H. Janssen, Colette L. Heald, Allison L. Steiner, Anne E. Perring, J. Alex Huffman, Ellis S. Robinson, Cynthia H. Twohy, and Luke D. Ziemba
Atmos. Chem. Phys., 21, 4381–4401, https://doi.org/10.5194/acp-21-4381-2021, https://doi.org/10.5194/acp-21-4381-2021, 2021
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Bioaerosols are ubiquitous in the atmosphere and have the potential to affect cloud formation, as well as human and ecosystem health. However, their emissions are not well quantified, which hinders the assessment of their role in atmospheric processes. Here, we develop two new emission schemes for fungal spores based on multi-annual datasets of spore counts. We find that our modeled global emissions and burden are an order of magnitude lower than previous estimates.
Xinrui Ge, Martijn Schaap, Richard Kranenburg, Arjo Segers, Gert Jan Reinds, Hans Kros, and Wim de Vries
Atmos. Chem. Phys., 20, 16055–16087, https://doi.org/10.5194/acp-20-16055-2020, https://doi.org/10.5194/acp-20-16055-2020, 2020
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This article is about improving the modeling of agricultural ammonia emissions. By considering land use, meteorology and agricultural practices, ammonia emission totals officially reported by countries are distributed in space and time. We illustrated the first step for a better understanding of the variability of ammonia emission, with the possibility of being applied at a European scale, which is of great significance for ammonia budget research and future policy-making.
Emmanuele Russo, Silje Lund Sørland, Ingo Kirchner, Martijn Schaap, Christoph C. Raible, and Ulrich Cubasch
Geosci. Model Dev., 13, 5779–5797, https://doi.org/10.5194/gmd-13-5779-2020, https://doi.org/10.5194/gmd-13-5779-2020, 2020
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The parameter space of the COSMO-CLM RCM is investigated for the Central Asia CORDEX domain using a perturbed physics ensemble (PPE) with different parameter values. Results show that only a subset of model parameters presents relevant changes in model performance and these changes depend on the considered region and variable: objective calibration methods are highly necessary in this case. Additionally, the results suggest the need for calibrating an RCM when targeting different domains.
Cited articles
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Short summary
High-resolution data on reactive nitrogen deposition are needed to inform cost-effective policies. Here, we describe the implementation of a dry deposition module in a large eddy simulation code. With this model, we are able to represent the turbulent exchange of tracers at the hectometer resolution. The model calculates the dispersion and deposition of NOx and NH3 in great spatial detail, clearly showing the influence of local land use patterns.
High-resolution data on reactive nitrogen deposition are needed to inform cost-effective...
