ALBERT

Description: Based on a given time series, the data-driven Langevin equation (dLE) estimates the drift and the diffusion field of the dynamics, which are then employed to reproduce the essential statistical and dynamical features of the original time series. Because the propagation of the dLE requires only local information, the input data are neither required to be Boltzmann weighted nor to be a continuous trajectory. Similar to a Markov state model, the dLE approach therefore holds the promise of predicting the long-time dynamics of a biomolecular system from relatively short trajectories which can be run in parallel. The practical applicability of the approach is shown to be mainly limited by the initial sampling of the system’s conformational space obtained from the short trajectories. Adopting extensive molecular dynamics simulations of the unfolding and refolding of a short peptide helix, it is shown that the dLE approach is able to describe microsecond conformational dynamics from a few hundred nanosecond trajectories. In particular, the dLE quantitatively reproduces the free energy landscape and the associated conformational dynamics along the chosen five-dimensional reaction coordinate.

Description: Principal component analysis of molecular dynamics simulations is a popular method to account for the essential dynamics of the system on a low-dimensional free energy landscape. Using Cartesian coordinates, first the translation and overall rotation need to be removed from the trajectory. Since the rotation depends via the moment of inertia on the molecule's structure, this separation is only straightforward for relatively rigid systems. Adopting millisecond molecular dynamics simulations of the folding of villin headpiece and the functional dynamics of BPTI provided by D. E. Shaw Research, it is demonstrated via a comparison of local and global rotational fitting that the structural dynamics of flexible molecules necessarily results in a mixing of overall and internal motion. Even for the small-amplitude functional motion of BPTI, the conformational distribution obtained from a Cartesian principal component analysis therefore reflects to some extend the dominant overall motion rather than the much smaller internal motion of the protein. Internal coordinates such as backbone dihedral angles, on the other hand, are found to yield correct and well-resolved energy landscapes for both examples. The virtues and shortcomings of the choice of various fitting schemes and coordinate sets as well as the generality of these results are discussed in some detail.

Description: Principal component analysis of molecular dynamics simulations is a popular method to account for the essential dynamics of the system on a low-dimensional free energy landscape. Using Cartesian coordinates, first the translation and overall rotation need to be removed from the trajectory. Since the rotation depends via the moment of inertia on the molecule's structure, this separation is only straightforward for relatively rigid systems. Adopting millisecond molecular dynamics simulations of the folding of villin headpiece and the functional dynamics of BPTI provided by D. E. Shaw Research, it is demonstrated via a comparison of local and global rotational fitting that the structural dynamics of flexible molecules necessarily results in a mixing of overall and internal motion. Even for the small-amplitude functional motion of BPTI, the conformational distribution obtained from a Cartesian principal component analysis therefore reflects to some extend the dominant overall motion rather than the much smaller internal motion of the protein. Internal coordinates such as backbone dihedral angles, on the other hand, are found to yield correct and well-resolved energy landscapes for both examples. The virtues and shortcomings of the choice of various fitting schemes and coordinate sets as well as the generality of these results are discussed in some detail.

Description: During the "African Monsoon Multidisciplinary Analysis" (AMMA) field phase in August 2006, a variety of measurements focusing on deep convection were performed over West Africa. The German research aircraft Falcon based in Ouagadougou (Burkina Faso) investigated the chemical composition in the outflow of large mesoscale convective systems (MCS). Here we analyse two different types of MCS originating north and south of the intertropical convergence zone (ITCZ, ~10° N), respectively. In addition to the airborne trace gas measurements, stroke measurements from the Lightning Location Network (LINET), set up in Northern Benin, are analysed. The main focus of the present study is 1) to analyse the trace gas composition (CO, O3, NO, NOx, NOy, and HCHO) in the convective outflow as a function of distance from the convective core, 2) to investigate how different trace gas compositions in the boundary layer (BL) and ambient air may influence the O3 concentration in the convective outflow, and 3) to estimate the rate of lightning-produced nitrogen oxides per flash in selected thunderstorms and compare it to our previous results for the tropics. The MCS outflow was probed at different altitudes (~10–12 km) and distances from the convective core (

Description: This paper presents a general concept and mathematical framework of particle hygroscopicity distribution for the analysis and modeling of aerosol hygroscopic growth and cloud condensation nucleus (CCN) activity. The cumulative distribution function of particle hygroscopicity, H(κ, Dd) is defined as the number fraction of particles with a given dry diameter, Dd, and with an effective hygroscopicity parameter smaller than the parameter κ. From hygroscopicity tandem differential mobility analyzer (HTDMA) and size-resolved CCN measurement data, H(κ, Dd) can be derived by solving the κ-Köhler model equation. Alternatively, H(κ, Dd) can be predicted from measurement or model data resolving the chemical composition of single particles. A range of model scenarios are used to explain and illustrate the concept, and exemplary practical applications are shown with HTDMA and CCN measurement data from polluted megacity and pristine rainforest air. Lognormal distribution functions are found to be suitable for approximately describing the hygroscopicity distributions of the investigated atmospheric aerosol samples. For detailed characterization of aerosol hygroscopicity distributions, including externally mixed particles of low hygroscopicity such as freshly emitted soot, we suggest that size-resolved CCN measurements with a wide range and high resolution of water vapor supersaturation and dry particle diameter should be combined with comprehensive HTDMA measurements and size-resolved or single-particle measurements of aerosol chemical composition, including refractory components. In field and laboratory experiments, hygroscopicity distribution data from HTDMA and CCN measurements can complement mixing state information from optical, chemical and volatility-based techniques. Moreover, we propose and intend to use hygroscopicity distribution functions in model studies investigating the influence of aerosol mixing state on the formation of cloud droplets.

Description: We examine the effects of ozone precursor emissions from megacities on present-day air quality using the global chemistry–climate model UM-UKCA (UK Met Office Unified Model coupled to the UK Chemistry and Aerosols model). The sensitivity of megacity and regional ozone to local emissions, both from within the megacity and from surrounding regions, is important for determining air quality across many scales, which in turn is key for reducing human exposure to high levels of pollutants. We use two methods, perturbation and tagging, to quantify the impact of megacity emissions on global ozone. We also completely redistribute the anthropogenic emissions from megacities, to compare changes in local air quality going from centralised, densely populated megacities to decentralised, lower density urban areas. Focus is placed not only on how changes to megacity emissions affect regional and global NOx and O3, but also on changes to NOy deposition and to local chemical environments which are perturbed by the emission changes. The perturbation and tagging methods show broadly similar megacity impacts on total ozone, with the perturbation method underestimating the contribution partially because it perturbs the background chemical environment. The total redistribution of megacity emissions locally shifts the chemical environment towards more NOx-limited conditions in the megacities, which is more conducive to ozone production, and monthly mean surface ozone is found to increase up to 30% in megacities, depending on latitude and season. However, the displacement of emissions has little effect on the global annual ozone burden (0.12% change). Globally, megacity emissions are shown to contribute ~3% of total NOy deposition. The changes in O3, NOx and NOy deposition described here are useful for quantifying megacity impacts and for understanding the sensitivity of megacity regions to local emissions. The small global effects of the 100% redistribution carried out in this study suggest that the distribution of emissions on the local scale is unlikely to have large implications for chemistry–climate processes on the global scale.

Description: During the "African Monsoon Multidisciplinary Analysis" (AMMA) field phase in August 2006, a variety of measurements focusing on deep convection were performed over West Africa. The German research aircraft Falcon based in Ouagadougou (Burkina Faso) investigated the chemical composition in the outflow of large mesoscale convective systems (MCS). Here we analyse two different types of MCS originating north and south of the intertropical convergence zone (ITCZ, ~10° N), respectively. In addition to the airborne trace gas measurements, stroke measurements from the Lightning Location Network (LINET), set up in Northern Benin, are analysed. The main focus of the present study is (1) to analyse the trace gas composition (CO, O3, NO, NOx, NOy, and HCHO) in the convective outflow as a function of distance from the convective core, (2) to investigate how different trace gas compositions in the boundary layer (BL) and ambient air may influence the O3 concentration in the convective outflow, and (3) to estimate the rate of lightning-produced nitrogen oxides per flash in selected thunderstorms and compare it to our previous results for the tropics. The MCS outflow was probed at different altitudes (~10–12 km) and distances from the convective core (

Description: Airborne lidar and in-situ measurements of aerosols and trace gases were performed in volcanic ash plumes over Europe between Southern Germany and Iceland with the Falcon aircraft during the eruption period of the Eyjafjalla volcano between 19 April and 18 May 2010. Flight planning and measurement analyses were supported by a refined Meteosat ash product and trajectory model analysis. The volcanic ash plume was observed with lidar directly over the volcano and up to a distance of 2700 km downwind, and up to 120 h plume ages. Aged ash layers were between a few 100 m to 3 km deep, occurred between 1 and 7 km altitude, and were typically 100 to 300 km wide. Particles collected by impactors had diameters up to 20 μm diameter, with size and age dependent composition. Ash mass concentrations were derived from optical particle spectrometers for a particle density of 2.6 g cm−3 and various values of the refractive index (RI, real part: 1.59; 3 values for the imaginary part: 0, 0.004 and 0.008). The mass concentrations, effective diameters and related optical properties were compared with ground-based lidar observations. Theoretical considerations of particle sedimentation constrain the particle diameters to those obtained for the lower RI values. The ash mass concentration results have an uncertainty of a factor of two. The maximum ash mass concentration encountered during the 17 flights with 34 ash plume penetrations was below 1 mg m−3. The Falcon flew in ash clouds up to about 0.8 mg m−3 for a few minutes and in an ash cloud with approximately 0.2 mg m−3 mean-concentration for about one hour without engine damage. The ash plumes were rather dry and correlated with considerable CO and SO2 increases and O3 decreases. To first order, ash concentration and SO2 mixing ratio in the plumes decreased by a factor of two within less than a day. In fresh plumes, the SO2 and CO concentration increases were correlated with the ash mass concentration. The ash plumes were often visible slantwise as faint dark layers, even for concentrations below 0.1 mg m−3. The large abundance of volatile Aitken mode particles suggests previous nucleation of sulfuric acid droplets. The effective diameters range between 0.2 and 3 μm with considerable surface and volume contributions from the Aitken and coarse mode aerosol, respectively. The distal ash mass flux on 2 May was of the order of 500 (240–1600) kg s−1. The volcano induced about 10 (2.5–50) Tg of distal ash mass and about 3 (0.6–23) Tg of SO2 during the whole eruption period. The results of the Falcon flights were used to support the responsible agencies in their decisions concerning air traffic in the presence of volcanic ash.

Description: This work examines the effect of direct radiative forcing of aerosols in the eastern Mediterranean troposphere as a function of air mass composition, particle size distribution and hygroscopicity, and relative humidity (RH). During intensive field measurements on the island of Crete, Greece, the hygroscopic properties of atmospheric particles were determined using a Hygroscopicity Tandem Differential Mobility Analyzer (H-TDMA) and a Hygroscopicity Differential Mobility Analyzer-Aerodynamic Particle Sizer (H-DMA-APS). Similar to former studies, the H-TDMA identified three hygroscopic sub-fractions of particles in the sub-μm range: a more hygroscopic group, a less hygroscopic group and a nearly hydrophobic particle group. The average hygroscopic particle growth factors at 90 % RH were a significant function of particle mobility diameter (Dp): 1.42 (± 0.05) at 30 nm compared to 1.63 (± 0.07) at 250 nm. The H-DMA-APS identified up to three hygroscopic sub-fractions at mobility diameters of 1.0 and 1.2 μm. The data recorded between 12 August and 20 October 2005 were classified into four distinct synoptic-scale air mass types distinguishing between different regions of origin (western Mediterranean vs. the Aegean Sea) as well as the degree of continental pollution (marine vs. continentally influenced). The hygroscopic properties of particles with diameter Dp≥150 nm showed the most pronounced dependency on air mass origin, with growth factors in marine air masses exceeding those in continentally influenced air masses. Particle size distributions and hygroscopic growth factors were used to calculate aerosol light scattering coefficients at ambient RH using a Mie model. A main result was the pronounced enhancement of particle scattering over the eastern Mediterranean due to hygroscopic growth, both in the marine and continentally influenced air masses. When RH reached its summer daytime values around 70–80 %, up to 50–70 % of the calculated visibility reduction was due to the hygroscopic growth of the particles by water compared to the effect of the dry particles alone. The estimated aerosol direct radiative forcings for both, marine and continentally influenced air masses were negative indicating a net cooling of the atmosphere due to the aerosol. The radiative forcing ΔFr was nevertheless governed by the total aerosol concentration most of the time: ΔFr was typically more negative for continentally influenced aerosols (ca. −4 W m−2) compared to rather clean marine aerosols (ca. −1.5 W m−2). When RH occasionally reached 90 % in marine air masses, ΔFr even reached values down to −7 W m−2. Our results emphasize, on the basis of explicit particle hygroscopicity measurements, the relevance of ambient RH for the radiative forcing of regional atmospheres.

Description: The impact of the megacities of the world on global tropospheric ozone, and conversely, the extent to which megacities are influenced by emissions of ozone precursors from outside of the megacities is examined under the four alternative RCP ("Representative Concentration Pathway") emissions scenarios. Despite accounting for about 6% of present-day anthropogenic emissions of ozone precursor species, the contribution of emissions from megacities to global tropospheric ozone is calculated to be 0.84%. By 2100 this contribution falls to between 0.18% and 0.62% depending on the scenario, with the lower value being for the most-polluting of the four future emissions scenarios due to stringent controls on ozone precursor emissions from highly populated areas combined with a stronger tropospheric background ozone field. The higher end of this range is from the least-polluting of the four emissions scenarios, due to lower background tropospheric ozone combined with the use of a simpler downscaling methodology in the construction of the scenario, which results in higher emissions from megacities. Although the absolute impact of megacities on global ozone is small, an important result of this study is that under all future scenarios, future air quality in megacities is expected to be less influenced by local emissions within the cities, but instead more influenced by emission sources outside of the cities, with mixing ratios of background ozone projected to play an increasing role in megacity air quality throughout the 21st century. Assumptions made when downscaling the emissions scenarios onto the grids used in such modelling studies can have a large influence on these results; future generations of emissions scenarios should include spatially explicit representations or urban development suitable for air quality studies using global chemical transport models.