A single-point modeling approach for the intercomparison and evaluation of ozone dry deposition across chemical transport models (Activity 2 of AQMEII4).

A primary sink of air pollutants and their precursors is dry deposition. Dry deposition estimates differ across chemical transport models, yet an understanding of the model spread is incomplete. Here, we introduce Activity 2 of the Air Quality Model Evaluation International Initiative Phase 4 (AQMEII4). We examine 18 dry deposition schemes from regional and global chemical transport models as well as standalone models used for impact assessments or process understanding. We configure the schemes as single-point models at eight Northern Hemisphere locations with observed ozone fluxes. Single-point models are driven by a common set of site-specific meteorological and environmental conditions. Five of eight sites have at least 3 years and up to 12 years of ozone fluxes. The interquartile range across models in multiyear mean ozone deposition velocities ranges from a factor of 1.2 to 1.9 annually across sites and tends to be highest during winter compared with summer. No model is within 50 % of observed multiyear averages across all sites and seasons, but some models perform well for some sites and seasons. For the first time, we demonstrate how contributions from depositional pathways vary across models. Models can disagree with respect to relative contributions from the pathways, even when they predict similar deposition velocities, or agree with respect to the relative contributions but predict different deposition velocities. Both stomatal and nonstomatal uptake contribute to the large model spread across sites. Our findings are the beginning of results from AQMEII4 Activity 2, which brings scientists who model air quality and dry deposition together with scientists who measure ozone fluxes to evaluate and improve dry deposition schemes in the chemical transport models used for research, planning, and regulatory purposes.

Assessing the potential risk and relationship between microplastics and phthalates in surface seawater of a heavily human-impacted metropolitan bay in northern China.

The impacts of microplastics (MPs) and phthalates (PAEs), a class of MP-associated contaminants, on the marine environment are not thoroughly understood despite concern over their adverse effects on humans and ecosystems. Field studies linking MPs and PAEs in seawater have not yet been reported. We investigate for the first time the correlation between MPs contamination and the presence of PAEs in the surface seawater of Jiaozhou Bay (JZB), a semi-enclosed metropolitan bay in northern China heavily impacted by human activity. The abundance of MPs, dominated by polyethylene and polyethylene terephthalate mostly smaller than 2 mm, ranged between 24.44 items/m3 and 180.23 items/m3, with the majority being black and transparent fibers and fragments. Concentrations of PAEs varied from 129.96 ng/L to 921.22 ng/L. Relatively higher abundances of MPs and higher concentrations of PAEs were generally found in areas near riverine inputs and sewage treatment plants. There was a strong correlation between PAEs concentration and MPs abundance, suggesting that they are closely linked. In a risk assessment combining PAEs and MPs, the risk quotients (RQs) indicated that the ecological risk of di-n-butyl phthalate in JZB was relatively high (0.046

A 3D numerical model to Track Marine Plastic Debris (TrackMPD): Sensitivity of microplastic trajectories and fates to particle dynamical properties and physical processes.

Numerical modelling is a key tool in understanding and determining the sources, trajectories and fates of micro-plastic debris (MPD). In this study, we introduce TrackMPD, a new modelling framework for the 3D transport of marine debris. TrackMPD fills the gaps in previous models by: (1) using a three-dimensional approach; (2) providing compatibility with a variety of ocean models; and (3) including a wide range of physical processes (advection, dispersion, windage, sinking, settling, beaching and re-floating) and MPD behaviours that depend on particle dynamical properties, and the fouling and degradation states. We implement a sensitivity analysis based on 44 scenarios to assess the relative importance of the different processes and behaviours on the MPD trajectories and fates. Results show that the MPD dynamical properties that impact their sinking, in particular plastic density and biofilm thickness and density, have the biggest effect on the MPD transport, followed by turbulent dispersion and washing-off.

Central place foragers select ocean surface convergent features despite differing foraging strategies.

Discovering the predictors of foraging locations can be challenging, and is often the critical missing piece for interpreting the ecological significance of observed movement patterns of predators. This is especially true in dynamic coastal marine systems, where planktonic food resources are diffuse and must be either physically or biologically concentrated to support upper trophic levels. In the Western Antarctic Peninsula, recent climate change has created new foraging sympatry between Adélie (Pygoscelis adeliae) and gentoo (P. papua) penguins in a known biological hotspot near Palmer Deep canyon. We used this recent sympatry as an opportunity to investigate how dynamic local oceanographic features affect aspects of the foraging ecology of these two species. Simulated particle trajectories from measured surface currents were used to investigate the co-occurrence of convergent ocean features and penguin foraging locations. Adélie penguin diving activity was restricted to the upper mixed layer, while gentoo penguins often foraged much deeper than the mixed layer, suggesting that Adélie penguins may be more responsive to dynamic surface convergent features compared to gentoo penguins. We found that, despite large differences in diving and foraging behavior, both shallow-diving Adélie and deeper-diving gentoo penguins strongly selected for surface convergent features. Furthermore, there was no difference in selectivity for shallow- versus deep-diving gentoo penguins. Our results suggest that these two mesopredators are selecting surface convergent features, however, how these surface signals are related to subsurface prey fields is unknown.

Investigation of ozone deposition to vegetation under warm and dry conditions near the Eastern Mediterranean coast.

Dry deposition of ozone (O3) to vegetation is an important removal pathway for tropospheric O3, while O3 uptake through plant stomata negatively affects vegetation and leads to climate change. Both processes are controlled by vegetation characteristics and ambient conditions via complex mechanisms. Recent studies have revealed that these processes can be fundamentally impacted by coastal effects, and by dry and warm conditions in ways that have not been fully characterized, largely due to lack of measurements under such conditions. Hence, we hypothesized that measuring dry deposition of O3 to vegetation along a sharp spatial climate gradient, and at different distances from the coast, can offer new insights into the characterization of these effects on O3 deposition to vegetation and stomatal uptake, providing important information for afforestation management and for climate and air-quality model improvement. To address these hypotheses, several measurement campaigns were performed at different sites, including pine, oak, and mixed Mediterranean forests, at distances of 20-59 km from the Eastern Mediterranean coast, under semiarid, Mediterranean and humid Mediterranean climate conditions. The eddy covariance technique was used to quantify vertical O3 flux (Ftot) and its partitioning to stomatal flux (Fst) and non-stomatal flux (Fns). Whereas Fst tended to peak around noon under humid Mediterranean and Mediterranean conditions in summer, it was strongly limited by drought under semiarid conditions from spring to early winter, with minimum average Fst/Ftot of 8-11% during the summer. Fns in the area was predominantly controlled by relative humidity (RH), whereas increasing Fns with RH for RH < 70% indicated enhancement of Fns by aerosols, via surface wetness stimulation. At night, efficient turbulence due to sea and land breezes, together with increased RH, resulted in strong enhancement of Ftot. Extreme dry surface events, some induced by dry intrusion from the upper troposphere, resulted in positive Fns events.

Measurement-based investigation of ozone deposition to vegetation under the effects of coastal and photochemical air pollution in the Eastern Mediterranean.

Dry deposition of ozone (O3) to vegetation is an important pathway for its removal from the troposphere, and it can lead to adverse effects in plants and changes in climate. However, our mechanistic understanding of O3 dry deposition is insufficient to adequately account for it in global and regional models, primarily because this process is highly complicated by feedback mechanisms and sensitivity to specific characteristics of vegetative environment and atmospheric dynamics and composition. We hypothesized that measuring dry deposition of O3 to vegetation near the Eastern Mediterranean (EM) coast, where large variations in meteorological conditions and photochemical air pollution frequently occur, would enable identifying the mechanisms controlling O3 deposition to vegetation. Moreover, we have only limited knowledge of O3 deposition to vegetation occurring near a coastline, under air pollution, or in the EM. This study investigated O3 deposition to mixed Mediterranean vegetation between the summers of 2015 and 2017, 3.6 km away from the EM coast, using the eddy covariance technique to quantify vertical flux of O3 and its partitioning to stomatal and non-stomatal flux, concurrent with nitrogen oxide (NOx), sulfur dioxide and carbon monoxide. Surprisingly, nighttime O3-deposition velocity (Vd) was smaller than daytime Vd by only ~20-37% on average for all measurement periods, primarily related to moderate nighttime atmospheric stability due to proximity to the seashore. We provide evidence for the role of sea-salt aerosols in enhancing O3 deposition via surface-wetness buildup at low relative humidity near the coast, and for daytime enhancement of O3 deposition by the combined effects of biogenic volatile organic compound emission and surface-wetness buildup. We further show that NOx emitted from elevated emission sources can reduce O3 deposition, and even lead to a positive O3 flux, demonstrating the importance of adequately taking into account the impact of air pollution on O3 deposition to vegetation.

Variability in summer surface residence time within a West Antarctic Peninsula biological hotspot.

Palmer Deep canyon along the central West Antarctic Peninsula is known to have higher phytoplankton biomass than the surrounding non-canyon regions, but the circulation mechanisms that transport and locally concentrate phytoplankton and Antarctic krill, potentially increasing prey availability to upper-trophic-level predators such as penguins and cetaceans, are currently unknown. We deployed a three-site high-frequency radar network that provided hourly surface circulation maps over the Palmer Deep hotspot. A series of particle release experiments were used to estimate surface residence time and connectivity across the canyon. The majority of residence times fell between 1.0 and 3.5 days, with a mean of 2 days and a maximum of 5 days. We found a highly significant negative relationship between wind speed and residence time. Our residence time analysis indicates that the elevated phytoplankton biomass over the central canyon is transported into and out of the hotspot on time scales much shorter than the observed phytoplankton growth rate, suggesting that the canyon may not act as an incubator of phytoplankton productivity as previously suggested. It may instead serve more as a conveyor belt of phytoplankton biomass produced elsewhere, continually replenishing the phytoplankton biomass for the local Antarctic krill community, which in turn supports numerous top predators.This article is part of the theme issue 'The marine system of the West Antarctic Peninsula: status and strategy for progress in a region of rapid change'.

Auto-correlated directional swimming can enhance settlement success and connectivity in fish larvae.

Larvae of coastal-marine fishes have been shown repeatedly to swim directionally in the pelagic environment. Yet, biophysical models of larval dispersal typically impose a Simple Random Walk (SRW) algorithm to simulate non-directional movement in the open ocean. Here we investigate the use of a Correlated Random Walk (CRW) algorithm; imposing auto-correlated directional swimming onto simulated larvae within a high-resolution 3D biophysical model of the Gulf of Aqaba, the Red Sea. Our findings demonstrate that implementation of auto-correlated directional swimming can result in an increase of up to ×2.7 in the estimated success rate of larval-settlement, as well as an increase in the extent of connectivity. With accumulating empirical support for the capacity for directional-swimming during the pelagic phase, we propose that CRW should be applied in biophysical models of dispersal by coastal marine fish-larvae.

A new hybrid algorithm for finding the lowest minima of potential surfaces: approach and application to peptides.

A new algorithm is presented for finding the global minimum, and other low-lying minima, of a potential energy surface (PES) of biological molecules. The algorithm synergetically combines three well-known global optimization methods: the diffusion equation method (DEM), which involves smoothing the PES; a simulated annealing (SA) algorithm; and evolutionary programming (EP), whose population-oriented approach allows for a parallel search over different regions of the PES. Tests on five peptides having between 6 and 9 residues show that the code implementing the new combined algorithm is efficient and is found to outperform the constituent methods, DEM and SA. Results of the algorithm, in the gas phase and with the GBSA implicit solvent model, are compared with crystallographic data for the test peptides; good accord is found in all cases. Also, for all but one of the examples, our hybrid algorithm finds a minimum deeper than those obtained by a very extensive scan. TINKERs implementation of the OPLS-AA force field is employed for the structure prediction. The results show that the new algorithm is a powerful structure predictor, when a reliable potential function is available. Our implementation of the algorithm is time-efficient, and requires only modest computational resources. Work is underway on applications of the new algorithm to structural prediction of proteins and other biological macro-molecules.

Anharmonic vibrational calculations modeling the raman spectra of intermediates in the photoactive yellow protein (PYP) photocycle.

The role of anharmonic effects in the vibrational spectroscopy of the dark state and two major chromophore intermediates of the photoactive yellow protein (PYP) photocycle is examined via ab initio vibrational self-consistent field (VSCF) calculations and time-resolved resonance Raman spectroscopy. For the first time, anharmonicity is considered explicitly in calculating the vibrational spectra of an ensemble consisting of the PYP chromophore surrounded by model compounds used as mimics of the important active-site residues. Predictions of vibrational frequencies on an ab initio corrected semiempirical potential energy surface show remarkable agreement with experimental frequencies for all three states, thus shedding light on the potential along the reaction path. For example, calculated frequencies for vibrational modes of the red-shifted intermediate, PYPL, exhibit an overall average error of 0.82% from experiment. Upon analysis of anharmonicity patterns in the PYP modes we observe a decrease in anharmonicity in the C8-C9 stretching mode nu29 (trans-cis isomerization marker mode) with the onset of the cis configuration in PYPL. This can be attributed to the loss of the hydrogen-bonding character of the adjacent C9-O2 to the methylamine (Cys69 backbone). For several of the modes, the anharmonicity is mostly due to mode-mode coupling, while for others it is mostly intrinsic. This study shows the importance of the inclusion of anharmonicity in theoretical spectroscopic calculations, and the sensitivity of experiments to anharmonicity. The characterization of protein active-site residues by small molecular mimics provides an acceptable chemical structural representation for biomolecular spectroscopy calculations.

Simulation of vibrational dephasing of I(2) in solid Kr using the semiclassical Liouville method.

In this paper, we present simulations of the decay of quantum coherence between vibrational states of I(2) in its ground (X) electronic state embedded in a cryogenic Kr matrix. We employ a numerical method based on the semiclassical limit of the quantum Liouville equation, which allows the simulation of the evolution and decay of quantum vibrational coherence using classical trajectories and ensemble averaging. The vibrational level-dependent interaction of the I(2)(X) oscillator with the rare-gas environment is modeled using a recently developed method for constructing state-dependent many-body potentials for quantum vibrations in a many-body classical environment [J. M. Riga, E. Fredj, and C. C. Martens, J. Chem. Phys. 122, 174107 (2005)]. The vibrational dephasing rates gamma(0n) for coherences prepared between the ground vibrational state mid R:0 and excited vibrational state mid R:n are calculated as a function of n and lattice temperature T. Excellent agreement with recent experiments performed by Karavitis et al. [Phys. Chem. Chem. Phys. 7, 791 (2005)] is obtained.

Quantum vibrational state-dependent potentials for classical many-body simulations.

In this paper, we present a method for constructing simple state-dependent many-body potentials for quantum vibrations in a classical bath. The approach is based on an adiabatic separation between high-frequency quantum vibrational modes of the solute and the lower frequency classical motion of the solvent, and on a first-order perturbation theory description of the dependence of the quantum energies on bath configuration. In the simplest realization of the method, the delocalized quantum probability density of the vibrational mode is approximated by a sum of two delta functions, with positions and weights chosen to represent the lowest three moments of the exact distribution. Thus, in the many-body description of the system, each atom describing the quantum vibration is represented by a pair of particles. These quantum particles are held in rigid relative position and interact with the bath via potentials the magnitudes of which are modified by the delta-function weights. The resulting approach allows the classical molecular dynamics of molecules in arbitrary quantum vibrational states to be simulated with a little more effort than a purely classical description. The applicability of the method is illustrated in many-body simulations of the dephasing of vibrational superposition states of I(2) in a cryogenic krypton matrix, yielding results in good agreement with experiment.