Nucleation Scheme Research Articles

An integrated modeling study on the effects of mineral dust and sea salt particles on clouds and precipitation

Abstract. This report addresses the effects of pollution on the development of precipitation in clean ("pristine") and polluted ("hazy") environments in the Eastern Mediterranean by using the Integrated Community Limited Area Modeling System (ICLAMS) (an extended version of the Regional Atmospheric Modeling System, RAMS). The use of this model allows one to investigate the interactions of the aerosols with cloud development. The simulations show that the onset of precipitation in hazy clouds is delayed compared to pristine conditions. Adding small concentrations of GCCN to polluted clouds promotes early-stage rain. The addition of GCCN to pristine clouds has no effect on precipitation amounts. Topography was found to be more important for the distribution of precipitation than aerosol properties. Increasing by 15% the concentration of hygroscopic dust particles for a case study over the Eastern Mediterranean resulted in more vigorous convection and more intense updrafts. The clouds that were formed extended about three kilometers higher, delaying the initiation of precipitation by one hour. Prognostic treatment of the aerosol concentrations in the explicit cloud droplet nucleation scheme of the model, improved the model performance for the twenty-four hour accumulated precipitation. The spatial distribution and the amounts of precipitation were found to vary greatly between the different aerosol scenarios. These results indicate the large uncertainty that remains and the need for more accurate description of aerosol feedbacks in atmospheric models and climate change predictions.

A new flexible multicomponent model for the study of aerosol dynamics in the marine boundary layer

A new sectional aerosol dynamics model, MAFOR, was developed with the focus to study nucleation in the marine boundary layer. Novel aspects of the model are (1) flexibility in the treatment of gas phase chemistry, (2) treatment of liquid phase chemistry, which can be extended according to needs and (3) simultaneous calculation of number and mass concentration distributions of a multicomponent aerosol as functions of time. Comparison with well-documented aerosol models (MONO32 and AEROFOR), a comprehensive data set on gas phase compounds, aerosol size distribution and chemical composition obtained during theA OE-96 (Arctic Ocean Expedition, 1996)was used to evaluate the model. Dimethyl sulphide decay during advection of an air parcel over the Arctic pack ice was well captured by the applied models and predicted concentrations of gaseous sulphuric acid and methane sulphonic acid range up to 1.0 × 106 cm−3 and 1.8 × 106 cm−3, respectively. Different nucleation schemes were implemented in MAFOR which allow the simulation of new particle formation. Modelled nucleation rates from sulphuric acid nucleation via cluster activation were up to 0.21 cm−3 s−1 while those from ion-mediated nucleationwere below 10−2 cm−3 s−1. Classical homogeneous binary and ternary nucleation theories failed to predict nucleation over the central Arctic Ocean in summer.

Aerosol nucleation and its role for clouds and Earth's radiative forcing in the aerosol-climate model ECHAM5-HAM

Abstract. Nucleation from the gas phase is an important source of aerosol particles in the Earth's atmosphere, contributing to the number of cloud condensation nuclei, which form cloud droplets. We have implemented in the aerosol-climate model ECHAM5-HAM a new scheme for neutral and charged nucleation of sulfuric acid and water based on laboratory data, and nucleation of an organic compound and sulfuric acid using a parametrization of cluster activation based on field measurements. We give details of the implementation, compare results with observations, and investigate the role of the individual aerosol nucleation mechanisms for clouds and the Earth's radiative forcing. The results of our simulations are most consistent with observations when neutral and charged nucleation of sulfuric acid proceed throughout the troposphere and nucleation due to cluster activation is limited to the forested boundary layer. The globally averaged annual mean contributions of the individual nucleation processes to total absorbed solar short-wave radiation via the direct, semi-direct, indirect cloud-albedo and cloud-lifetime effects in our simulations are −1.15 W/m2 for charged H2SO4/H2O nucleation, −0.235 W/m2 for cluster activation, and −0.05 W/m2 for neutral H2SO4/H2O nucleation. The overall effect of nucleation is −2.55 W/m2, which exceeds the sum of the individual terms due to feedbacks and interactions in the model. Aerosol nucleation contributes over the oceans with −2.18 W/m2 to total absorbed solar short-wave radiation, compared to −0.37 W/m2 over land. We explain the higher effect of aerosol nucleation on Earth's radiative forcing over the oceans with the larger area covered by ocean clouds, due to the larger contrast in albedo between clouds and the ocean surface compared to continents, and the larger susceptibility of pristine clouds owing to the saturation of effects. The large effect of charged nucleation in our simulations is not in contradiction with small effects seen in local measurements: over southern Finland, where cluster activation proceeds efficiently, we find that charged nucleation of sulfuric acid and water contributes on average less than 10% to ultrafine aerosol concentrations, in good agreement with observations.

Spatial distributions of particle number concentrations in the global troposphere: Simulations, observations, and implications for nucleation mechanisms

Particle number concentration in the troposphere is an important parameter controlling the climate and health impacts of atmospheric aerosols. We show that nucleation rates and total particle number concentrations in the troposphere, predicted by different nucleation schemes, differ significantly. Our extensive comparisons of simulated results with land‐, ship‐, and aircraft‐based measurements indicate that, among six widely used nucleation schemes involving sulfuric acid, only the ion‐mediated nucleation (IMN) scheme can reasonably account for both absolute values (within a factor of ∼2) and spatial distributions of particle number concentrations in the whole troposphere. Binary homogeneous nucleation (BHN) schemes significantly underpredict particle number concentration in the lower troposphere (below ∼500 mbar), especially in the boundary layer over major continents (by a factor of up to ∼10). BHN is also insignificant in the upper troposphere based on a recent kinetically self‐consistent nucleation model constrained by multiple independent laboratory data. Previous conclusions about the importance of BHN in the upper troposphere should be revisited. Empirical activation and kinetic nucleation formulas significantly overpredict the particle number concentrations over tropical and subtropical oceans (by a factor of up to ∼10 in the boundary layer), and the overpredictions extend from ocean surface to around ∼400 mbar. This study represents the first comprehensive comparison of global particle number simulations with relevant measurements that have a 3‐D global spatial coverage. Our results suggest that ion‐mediated H2SO4‐H2O nucleation appears to dominate over neutral H2SO4‐H2O nucleation, not only in the lower troposphere but also in the middle and upper troposphere.

The Role of Error Covariances in Estimation of Aerosol Number Concentrations

The evolution of error covariance and its impact in Kalman Filtering are examined. A synthetic aerosol size distribution and an associated error covariance matrix are used as an input for a tangent-linear box model simulating aerosol microphysics. The evolution of the error correlation structures are found to be robust with respect to changes in ambient vapor conditions and nucleation schemes. The near-diagonal error correlations evolve only modestly for particles larger than ∼20–30 nm, and the nucleation and condensation processes cause strong correlations between number density errors of small (below 10 nm) and large (above 100 nm) particles. The evolving error covariances significantly improve the estimation accuracy of the Kalman Filter in case of synthetic observations.

Simulating Marine New Particle Formation and Growth Using the M7 Modal Aerosol Dynamics Modal

A modal atmospheric aerosol model (M7) is evaluated in terms of predicting marine new particle formation and growth. Simulations were carried out for three different nucleation schemes involving (1) kinetic self‐nucleation of OIO (2) nucleation via OIO activation by H2SO4 and (3) nucleation via OIO activation by H2SO4 plus condensation of a low‐volatility organic vapour. Peak OIO and H2SO4 vapour concentrations were both limited to 6 × 106 molecules cm-3 at noontime while the peak organic vapour concentration was limited to 12 × 106 molecules cm-3. All simulations produced significant concentrations of new particles in the Aitken mode. From a base case particle concentration of 222 cm-3 at radii >15 nm, increases in concentrations to 366 cm-3 were predicted from the OIO‐OIO case, 722 cm-3 for the OIO‐H2SO4 case, and 1584 cm-3 for the OIO‐H2SO4 case with additional condensing organic vapours. The results indicate that open ocean new particle production is feasible for clean conditions; however, new particle production becomes most significant when an additional condensable organic vapour is available to grow the newly formed particles to larger sizes. Comparison to sectional model for a typical case study demonstrated good agreement and the validity of using the modal model.

Aerosol size distribution modeling with the Community Multiscale Air Quality modeling system in the Pacific Northwest: 2. Parameterizations for ternary nucleation and nucleation mode processes

In order to test Community Multiscale Air Quality (CMAQ) model performance for ultrafine particle concentrations in the Pacific Northwest, CMAQ v4.4 was modified for ternary NH3‐H2SO4‐H2O nucleation and for atmospheric processing of ultrafine particles. Sulfuric acid from sulfur dioxide oxidation is iteratively partitioned into gaseous sulfuric acid, newly condensed aerosol sulfate, and aerosol sulfuric acid contained in new 1 nm particles. Freshly nucleated particles are either coagulated to larger particles or grown by sulfuric acid condensation to 10 nm at which point they are included in CMAQ's existing Aitken mode. Multiple nucleation parameterizations were implemented into CMAQ, and one other was investigated in a sensitivity analysis. For a case study in the Pacific Northwest where aerosol number concentration and size distributions were measured, standard binary nucleation in CMAQ produces nearly no particles for this case study. Ternary nucleation can produce millions of 1 nm particles per cm3, but few of these particles survive coagulation loss and grow to 10 nm and into the Aitken mode. There are occasions when the additions to CMAQ increase the number of particles to within an order of magnitude of observations, but it is more common for number concentrations to remain underpredicted by, on average, one order of magnitude. Significant particle nucleation in CMAQ successfully produces a distinct Aitken and accumulation mode and an Aitken mode that is more prominent than the accumulation mode, although errors in the size distribution remain. A more recent ternary nucleation scheme including ammonium bisulfate clusters does not nucleate an appreciable number of particles.

Ice formation in Arctic mixed‐phase clouds: Insights from a 3‐D cloud‐resolving model with size‐resolved aerosol and cloud microphysics

The single‐layer mixed‐phase clouds observed during the Atmospheric Radiation Measurement (ARM) program's Mixed‐Phase Arctic Cloud Experiment (MPACE) are simulated with a three‐dimensional cloud‐resolving model, the System for Atmospheric Modeling (SAM), coupled with an explicit bin microphysics scheme and a radar simulator. By implementing an aerosol‐dependent and a temperature‐ and supersaturation‐dependent ice nucleation scheme and treating IN size distribution prognostically, the link between ice crystal and aerosol properties is established to study aerosol indirect effects. Two possible ice enhancement mechanisms, activation of droplet evaporation residues by condensation followed by freezing and droplet evaporation freezing by contact freezing inside out, are scrutinized by extensive comparisons with the in situ and remote sensing measurements. Simulations with either mechanism agree well with the in situ and remote sensing measurements of ice microphysical properties but liquid water content is slightly underpredicted. These two mechanisms give similar cloud properties, although ice nucleation occurs at very different rates and locations. Ice nucleation from activation of evaporation nuclei occurs mostly near cloud top areas, while ice nucleation from the drop freezing during evaporation has no significant location preference. Both ice enhancement mechanisms contribute dramatically to ice formation with ice particle concentration of 10–15 times higher relative to the simulation without either of them. Ice nuclei (IN) recycling from ice sublimation contributes significantly to maintaining concentrations of IN and ice particles in this case, implying an important role to maintain the observed long‐term existence of mixed‐phase clouds. Cloud can be very sensitive to IN initially but become much less sensitive as cloud evolves to a steady mixed‐phase condition.

Aerosol indirect forcing in a global model with particle nucleation

Abstract. The number concentration of cloud condensation nuclei (CCN) formed as a result of anthropogenic emissions is a key uncertainty in the study of aerosol indirect forcing and global climate change. Here, we use a global aerosol model that includes an empirical boundary layer nucleation mechanism, the use of primary-emitted sulfate particles to represent sub-grid scale nucleation, as well as binary homogeneous nucleation to explore how nucleation affects the CCN concentration and the first aerosol indirect effect (AIE). The inclusion of the boundary layer nucleation scheme increases the global average CCN concentrations in the boundary layer by 31.4% when no primary-emitted sulfate particles are included and by 5.3% when they are included. Particle formation with the boundary layer nucleation scheme decreases the first indirect forcing over ocean, and increases the first indirect forcing over land when primary sulfate particles are included. This suggests that whether particle formation from aerosol nucleation increases or decreases aerosol indirect effects largely depends on the relative change of primary particles and SO2 emissions from the preindustrial to the present day atmosphere. Including primary-emitted sulfate particle significantly increases both the anthropogenic fraction of CCN concentrations and the first aerosol indirect forcing. The forcing from various treatments of aerosol nucleation ranges from −1.22 to −2.03 w/m2. This large variation shows the importance of better quantifying aerosol nucleation mechanisms for the prediction of CCN concentrations and aerosol indirect effects.

Inclusion of Ice Microphysics in the NCAR Community Atmospheric Model Version 3 (CAM3)

AbstractA prognostic equation for ice crystal number concentration together with an ice nucleation scheme are implemented in the National Center for Atmospheric Research (NCAR) Community Atmospheric Model version 3 (CAM3) with the aim of studying the indirect effect of aerosols on cold clouds. The effective radius of ice crystals, which is used in the radiation and gravitational settlement calculations, is now calculated from model-predicted mass and number of ice crystals rather than diagnosed as a function of temperature. A water vapor deposition scheme is added to replace the condensation and evaporation (C–E) in the standard CAM3 for ice clouds. The repartitioning of total water into liquid and ice in mixed-phase clouds as a function of temperature is removed, and ice supersaturation is allowed. The predicted ice water content in the modified CAM3 is in better agreement with the Aura Microwave Limb Sounder (MLS) data than that in the standard CAM3. The cirrus cloud fraction near the tropical tropopause, which is underestimated in the standard CAM3 as revealed through comparison with the Stratospheric Aerosol and Gas Experiment II (SAGE II) data, is increased by 20%–30%, and the cold temperature bias there is reduced by 1–2 K. However, an increase in the cloud fraction in polar regions makes the underestimation (by ∼20 W m−2) of downwelling shortwave radiation in the standard CAM3 even worse. A sensitivity test reducing the threshold relative humidity with respect to ice (RHi) for heterogeneous ice nucleation from 120% to 105% (representing nearly perfect ice nuclei) increases the global cloud cover by 1.4%, temperature near the tropical tropopause by 4–5 K, and water vapor in the stratosphere by 50%–80%.

Numerical solution of population balance equations for nucleation, growth and aggregation processes

This article focuses on the derivation of numerical schemes for solving population balance models (PBMs) with simultaneous nucleation, growth and aggregation processes. Two numerical methods are proposed for this purpose. The first method combines a method of characteristics (MOC) for growth process with a finite volume scheme (FVS) for aggregation process. For handling nucleation terms, a cell of nuclei size is added at a given time level. The second method purely uses a semi-discrete finite volume scheme for nucleation, growth and aggregation of particles. Note that both schemes use the same finite volume scheme for aggregation process. On one hand, the method of characteristics offers a technique which is in general a powerful tool for solving linear growth processes, has the capability to overcome numerical diffusion and dispersion, is computationally efficient, as well as give highly resolved solutions. On the other hand, the finite volume schemes which were derived for a general system in divergence form, are applicable to any grid to control resolution, and are also computationally not expensive. In the first method a combination of finite volume scheme and the method of characteristics gives a highly accurate and efficient scheme for simultaneous nucleation, growth and aggregation processes. The second method demonstrates the applicability, generality, robustness and efficiency of high-resolution schemes. The proposed techniques are tested for pure growth, simultaneous growth and aggregation, nucleation and growth, as well as simultaneous nucleation, growth and aggregation processes. The numerical results of both schemes are compared with each other and are also validated against available analytical solutions. The numerical results of the schemes are in good agreement with the analytical solutions.

Optical properties of nonpolar -plane GaN layers

We have studied optical properties of nonpolar a -plane GaN layers grown on r -plane sapphire by metalorganic chemical vapor deposition and hydride vapor phase epitaxy using different nucleation schemes. Several emission bands, which are not typical for c -plane GaN, are observed in the photoluminescence spectra and their excitation-intensity, temperature, and polarization dependencies are examined. In addition, the spatial distribution of the emissions was examined by cathodoluminescence imaging and relations of the different emissions with particular structural features in the layers are revealed. The results are discussed with emphasis on the origin of the emission line and particular recombination mechanisms.

Contribution of secondary condensable organics to new particle formation: A case study in Houston, Texas

We report aerosol simulations using the EPA's Models‐3 Community Multiscale Air Quality model (CMAQ) and ground‐based and aircraft aerosol measurements to investigate new particle formation in Houston, Texas. The aerosol measurements reveal elevated ultrafine particles that reach the highest value in the afternoon, indicating prominent new particle formation. Simulations of the binary H2SO4‐H2O nucleation predict an order of magnitude lower concentrations for aerosols near 10 nm than the measurements. A parameterized nucleation scheme that accounts for the enhanced nucleation effect of secondary condensable organics is incorporated into the Models‐3/CMAQ. The organic nucleation scheme predicts the number concentrations in agreement with the measurements during the daytime. The diurnal variation is well reproduced in the simulations including the organic nucleation scheme. Comparison with the aircraft measurements also shows that the organic nucleation scheme produces good predictions of the altitude‐dependent number size distributions of the ultrafine particles. The results corroborate the importance of secondary condensable organics in new particle formation when sulfate and organics are abundant.

Numerical simulation of polymeric foaming processes using modified nucleation theory

This paper develops a modified nucleation theory and examines its application to simulate the bubble nucleating phenomena in polymeric foaming processes. Bubbles typically nucleate homogeneously in the bulk phase of the polymer/gas solution and heterogeneously at the boundaries between the bulk phase and the nucleating agents. Although past research had attempted to consider the heterogeneous nucleation to simulate the plastic foaming process, the assumption of a flat nucleating surface might not be realistic. In this context, the authors have modified the heterogeneous nucleation theory by considering random surface geometries, and have developed a computer simulation program to predict the cell nuclei density based on this heterogeneous nucleation scheme with random surface geometries. Homogeneous cell nucleation was also included in the simulation. The simulation results obtained in this study are compared with the experimentally observed data from a batch foaming process to evaluate the validity of the theory proposed herein. It is found that the modified theory does in fact account for the quantitative aspects of the experimental observations when an iterative approach is used to determine the contact angle θc. Although the appropriateness of the values selected for θc requires further investigation from both experimental and theoretical points of view, this study illustrated that the modified nucleation theory can represent a new access point for exploring the cell nucleating phenomena in plastic foaming processes.

Synthesis of Lead Chalcogenide Nanocrystals by Sequential Ion Implantation in Silica

Lead chalcogenide (PbS, PbSe, and PbTe) nanocrystals were synthesized by sequential implantation of Pb and one of the chalcogen species into pure silica. The implantation energy and fluence were chosen so that the implantation profiles practically overlap at a depth approximately 150 nm with a maximum concentration of about 0.3 atom %. Annealing for 1-8 h at 850-900 degrees C triggers nanocrystal growth, which is monitored by high-resolution (HRTEM) and conventional transmission electron microscopy (TEM), secondary-ion mass spectrometry (SIMS), and Rutherford backscattering spectrometry (RBS). Striking differences are found in the depth distributions and microstructures of the resulting nanocrystals. We show that the differing chemical interactions of Pb and chalcogens (between each other and with silica) play a crucial role in chalcogenide nucleation and growth. Using available information on chalcogen redox states in silicate glass, we propose a nonclassical nucleation and growth mechanism consistent with our experimental results. The complex chemistry involved at the microscopic level is shown to impair control over the nanocrystal size distribution. Finally, PbS nanocrystal-doped silica is shown to emit intense photoluminescence (PL) in the 1.5-2 microm wavelength range, an effect that we relate to the above nucleation and growth scheme.

Simulation of atmospheric nucleation mode: A comparison of nucleation models and size distribution representations

Atmospheric particle formation and growth were investigated using different nucleation models and size distribution representations. Nucleation was modeled using recently developed parameterizations for binary nucleation of water and sulphuric acid and ternary nucleation of water, sulphuric acid, and ammonia. A comparison with older nucleation parameterizations, combined with full aerosol dynamics, demonstrated that the difference in nucleation rate (1–2 orders of magnitude) is clearly reflected in the resulting total particle concentration. A comparison of binary and ternary nucleation schemes showed that above 240 K the ternary nucleation rate exceeds the binary by over 10 orders of magnitude, indicating that in most cases, at lower tropospheric conditions, only ternary nucleation can be relevant. In addition, the performance of aerosol dynamics models applying either a multimodal monodisperse or a fixed sectional size distribution representation was evaluated against a molecular resolution model, which follows the changes in the nucleation mode particle size distribution molecule by molecule. Regarding total number concentration, the sectional method converged to the molecular resolution approach when increasing the number of size sections. With strong condensational growth, however, numerical diffusion problems were evident. Overall, the performance of the sectional method with low number of sections was not satisfactory. The monodisperse method gave very good results, at least in terms of total number, when the background modes were set to match the condensation sinks of respective lognormal modes. On the basis of our study the multimodal monodisperse method seems to be a possible candidate when selecting the size distribution approach for large‐scale atmospheric models.

A springtime cloud over the Beaufort Sea polynya: Three‐dimensional simulation with explicit spectral microphysics and comparison with observations

This paper addresses the formation of a cloud system associated with an arctic polynya in Beaufort Sea during springtime. Data were obtained as a part of the First International Satellite Cloud Climatology Project (ISCCP) Regional Experiment (FIRE) Arctic Clouds Experiment from the Canadian Convair 580 aircraft during 25 April 1998. These data include in situ observations of cloud microphysics and meteorological variables and remote measurements from satellite and airborne lidar. A three‐dimensional cloud‐resolving model with explicit bin‐resolving cloud microphysics is used to simulate the atmospheric boundary layer and cloud evolution associated with the polynya. After initialization with the aircraft sounding profiles, a quasi‐steady polynya‐induced atmospheric boundary layer (ABL) and a cloud system form. Strong turbulence in the ABL occurs above the polynya, the internal thermal boundary layer (ITBL) develops and grows upward in the downwind direction, and the ABL downwind of the polynya is separated into two decoupled layers. The cloud forms in the middle of the polynya, and its upper boundary lifts downwind while the lower boundary lowers and reaches the surface beyond the polynya southern boundary as a light fog. Farther to the south, the fog evaporates and transforms into an elevated cloud plume that extends for several tens of kilometers downwind. This cloud morphology is in good agreement with the lidar observations, which showed a cloud layer extending for more than 100 km downwind, and with the numerous previous observations. The simulated microphysical properties of a mixed cloud are similar to those observed. A new ice nucleation scheme resulted in cloud plume gradual crystallization along the wind and eventual transformation into diamond dust. Detailed evaluation of the water budget, supersaturation, and crystal size spectra showed that the ice crystal supersaturation relaxation times are 10–60 min; thus deposition on the crystals is rather slow, and only 1–5% of the available vapor is deposited on the crystals. The large ice crystal supersaturation relaxation time explains the relatively slow growth and gravitational fallout of the ice crystals, as well as the extensive propagation downwind of the plume.

Influence of a pre-deposited carbon submonolayer on the Ge island nucleation on Si(001)

Si surfaces manipulated by a carbon (C) pre-deposition have been used to modify the growth morphology of Ge islands. In situ reflection high-energy electron diffraction and x-ray photoelectron diffraction and ex situ atomic force microscopy studies have been conducted for constant C seeding and varying growth temperatures and Ge coverages, with the aim of deepening the understanding of the relevant Ge quantum dot formation. With temperatures ranging from 400 to 600 °C, well structured Ge islands grow in a Volmer–Weber mode as soon as 0.4 ML of C and 1 ML of Ge are deposited. Strongly modified behaviors are nevertheless observed by changing the Ge growth temperature from 500 to 600 °C. By increasing the Ge coverage from 1 to 6 ML at 500 °C, the island height increases at constant density, whereas, at 600 °C, a strong reduction of the density is observed, with a three-dimensional-two-dimensional transition probably due to a partial Ge intermixing in the Si matrix. These different nucleation schemes are connected with varying evolutions of the initial C-related c(4×4) reconstruction.

Particle formation at a continental background site: comparison of model results with observations

Abstract. At Hohenpeissenberg (47° 48' N, 11° 07' E, 988 m asl), a rural site 200--300~m higher than the surrounding terrain, sulphuric acid concentrations, particle size distributions, and other trace gas concentrations were measured over a two and a half year period. Measured particle number concentrations and inferred particle surface area concentrations were compared with box-model simulations for 12 carefully selected data sets collected during the HAFEX experiment (Birmili et al., 2003). The 12 cases were selected after meteorological and aerosol dynamical criteria in order to justify the use of a box-model. The aerosol model included a binary sulphuric acid water nucleation scheme. Calculated nucleation rates were corrected with a factor to match measured and calculated particle number concentrations. For the investigated 12 data sets, the correction factors were smallest for measurements made under stable thermal stratification and low wind conditions, i.e. conditions that are frequently encountered during winter. Correction factors were largest for measurements made under strong convective conditions. Our comparison of measured and simulated particle size distributions suggests that the particle formation process maybe strongly influenced by mixing processes driven by thermal convection and/or wind sheer.

Sequence and Structure Patterns in Proteins from an Analysis of the Shortest Helices: Implications for Helix Nucleation

The shortest helices (three-length 3 10 and four-length α), most abundant among helices of different lengths, have been analyzed from a database of protein structures. A characteristic feature of three-length 3 10-helices is the shifted backbone conformation for the C-terminal residue (φ,ψ angles: −95°,0°), compared to the rest of the helix (−62°,−24°). The deviation can be attributed to the release of electrostatic repulsion between the carbonyl oxygen atoms at the two C-terminal residues and further stabilization (due to a more linear geometry) of an intrahelical hydrogen bond. A consequence of this non-canonical C-terminal backbone conformation can be a potential origin of helix kinks when a 3 10-helix is sequence-contiguous at the α-helix N-terminal. An analysis of hydrogen bonding, as well as hydrophobic interactions in the shortest helices shows that capping interactions, some of them not observed for longer helices, dominate at the N termini. Further, consideration of the distribution of amino acid residues indicates that the shortest helices resemble the N-terminal end of α-helices rather than the C terminus, implying that the folding of helices may be initiated at the N-terminal end, which does not get propagated in the case of the shortest helices. Finally, pairwise comparison of β-turns and the shortest helices, based on correlation matrices of site-specific amino acid composition, and the relative abundance of these short secondary structural elements, leads to a helix nucleation scheme that considers the formation of an isolated β-turn (and not an α-turn) as the helix nucleation step, with shortest 3 10-helices as intermediates between the shortest α-helix and the β-turn. Our results ascribe an important role played by shortest 3 10-helices in proteins with important structural and folding implications.