Understanding the chemistry of atmospheric aerosol particle formation via observations of physical properties

It is widely accepted that the global climate is heating up due to human activities, such as burning of fossil fuels. Therefore we find ourselves forced to make decisions on what measures, if any, need to be taken to decrease our warming effect on the planet before any irrevocable damage occurs. Research is being conducted in a variety of fields to better understand all relevant processes governing Earth s climate, and to assess the relative roles of anthropogenic and biogenic emissions into the atmosphere. One of the least well quantified problems is the impact of small aerosol particles (both of anthropogenic and biogenic origin) on climate, through reflecting solar radiation and their ability to act as condensation nuclei for cloud droplets. In this thesis, the compounds driving the biogenic formation of new particles in the atmosphere have been examined through detailed measurements. As directly measuring the composition of these newly formed particles is extremely difficult, the approach was to indirectly study their different characteristics by measuring the hygroscopicity (water uptake) and volatility (evaporation) of particles between 10 and 50 nm. To study the first steps of the formation process in the sub-3 nm range, the nucleation of gaseous precursors to small clusters, the chemical composition of ambient naturally charged ions were measured. The ion measurements were performed with a newly developed mass spectrometer, which was first characterized in the laboratory before being deployed at a boreal forest measurement site. It was also successfully compared to similar, low-resolution instruments. The ambient measurements showed that sulfuric acid clusters dominate the negative ion spectrum during new particle formation events. Sulfuric acid/ammonia clusters were detected in ambient air for the first time in this work. Even though sulfuric acid is believed to be the most important gas phase precursor driving the initial cluster formation, measurements of the hygroscopicity and volatility of growing 10-50 nm particles in Hyytiälä showed an increasing role of organic vapors of a variety of oxidation levels. This work has provided additional insights into the compounds participating both in the initial formation and subsequent growth of atmospheric new aerosol particles. It will hopefully prove an important step in understanding atmospheric gas-to-particle conversion, which, by influencing cloud properties, can have important climate impacts. All available knowledge needs to be constantly updated, summarized, and brought to the attention of our decision-makers. Only by increasing our understanding of all the relevant processes can we build reliable models to predict the long-term effects of decisions made today.

Observations on the first steps of atmospheric particle formation and growth

Atmospheric aerosol particles have a significant impact on air quality, human health and global climate. The climatic effects of secondary aerosol are currently among the largest uncertainties limiting the scientific understanding of future and past climate changes. To better estimate the climatic importance of secondary aerosol particles, detailed information on atmospheric particle formation mechanisms and the vapours forming the aerosol is required. In this thesis we studied these issues by applying novel instrumentation in a boreal forest to obtain direct information on the very first steps of atmospheric nucleation and particle growth. Additionally, we used detailed laboratory experiments and process modelling to determine condensational growth properties, such as saturation vapour pressures, of dicarboxylic acids, which are organic acids often found in atmospheric samples. Based on our studies, we came to four main conclusions: 1) In the boreal forest region, both sulphurous compounds and organics are needed for secondary particle formation, the previous contributing mainly to particle formation and latter to growth; 2) A persistent pool of molecular clusters, both neutral and charged, is present and participates in atmospheric nucleation processes in boreal forests; 3) Neutral particle formation seems to dominate over ion-mediated mechanisms, at least in the boreal forest boundary layer; 4) The subcooled liquid phase saturation vapour pressures of C3-C9 dicarboxylic acids are of the order of 1e-5 1e-3 Pa at atmospheric temperatures, indicating that a mixed pre-existing particulate phase is required for their condensation in atmospheric conditions. The work presented in this thesis gives tools to better quantify the aerosol source provided by secondary aerosol formation. The results are particularly useful when estimating, for instance, anthropogenic versus biogenic influences and the fractions of secondary aerosol formation explained by neutral or ion-mediated nucleation mechanisms, at least in environments where the average particle formation rates are of the order of some tens of particles per cubic centimeter or lower. However, as the factors driving secondary particle formation are likely to vary depending on the environment, measurements on atmospheric nucleation and particle growth are needed from around the world to be able to better describe the secondary particle formation, and assess its climatic effects on a global scale.

Quantum Chemical Studies on Tropospheric Nucleation Mechanisms Involving Sulfuric Acid

Nucleation is the first step of the process by which gas molecules in the atmosphere condense to form liquid or solid particles. Despite the importance of atmospheric new-particle formation for both climate and health-related issues, little information exists on its precise molecular-level mechanisms. In this thesis, potential nucleation mechanisms involving sulfuric acid together with either water and ammonia or reactive biogenic molecules are studied using quantum chemical methods. Quantum chemistry calculations are based on the numerical solution of Schrödinger's equation for a system of atoms and electrons subject to various sets of approximations, the precise details of which give rise to a large number of model chemistries. A comparison of several different model chemistries indicates that the computational method must be chosen with care if accurate results for sulfuric acid - water - ammonia clusters are desired. Specifically, binding energies are incorrectly predicted by some popular density functionals, and vibrational anharmonicity must be accounted for if quantitatively reliable formation free energies are desired. The calculations reported in this thesis show that a combination of different high-level energy corrections and advanced thermochemical analysis can quantitatively replicate experimental results concerning the hydration of sulfuric acid. The role of ammonia in sulfuric acid - water nucleation was revealed by a series of calculations on molecular clusters of increasing size with respect to all three co-ordinates; sulfuric acid, water and ammonia. As indicated by experimental measurements, ammonia significantly assists the growth of clusters in the sulfuric acid - co-ordinate. The calculations presented in this thesis predict that in atmospheric conditions, this effect becomes important as the number of acid molecules increases from two to three. On the other hand, small molecular clusters are unlikely to contain more than one ammonia molecule per sulfuric acid. This implies that the average NH3:H2SO4 mole ratio of small molecular clusters in atmospheric conditions is likely to be between 1:3 and 1:1. Calculations on charged clusters confirm the experimental result that the HSO4- ion is much more strongly hydrated than neutral sulfuric acid. Preliminary calculations on HSO4- NH3 clusters indicate that ammonia is likely to play at most a minor role in ion-induced nucleation in the sulfuric acid - water system. Calculations of thermodynamic and kinetic parameters for the reaction of stabilized Criegee Intermediates with sulfuric acid demonstrate that quantum chemistry is a powerful tool for investigating chemically complicated nucleation mechanisms. The calculations indicate that if the biogenic Criegee Intermediates have sufficiently long lifetimes in atmospheric conditions, the studied reaction may be an important source of nucleation precursors.

Observations of production and transport of NOx formed by energetic particle precipitation in the polar night atmosphere

This work is focused on the effects of energetic particle precipitation of solar or magnetospheric origin on the polar middle atmosphere. The energetic charged particles have access to the atmosphere in the polar areas, where they are guided by the Earth's magnetic field. The particles penetrate down to 20-100 km altitudes (stratosphere and mesosphere) ionising the ambient air. This ionisation leads to production of odd nitrogen (NOx) and odd hydrogen species, which take part in catalytic ozone destruction. NOx has a very long chemical lifetime during polar night conditions. Therefore NOx produced at high altitudes during polar night can be transported to lower stratospheric altitudes. Particular emphasis in this work is in the use of both space and ground based observations: ozone and NO2 measurements from the GOMOS instrument on board the European Space Agency's Envisat-satellite are used together with subionospheric VLF radio wave observations from ground stations. Combining the two observation techniques enabled detection of NOx enhancements throughout the middle atmosphere, including tracking the descent of NOx enhancements of high altitude origin down to the stratosphere. GOMOS observations of the large Solar Proton Events of October-November 2003 showed the progression of the SPE initiated NOx enhancements through the polar winter. In the upper stratosphere, nighttime NO2 increased by an order of magnitude, and the effect was observed to last for several weeks after the SPEs. Ozone decreases up to 60 % from the pre-SPE values were observed in the upper stratosphere nearly a month after the events. Over several weeks the GOMOS observations showed the gradual descent of the NOx enhancements to lower altitudes. Measurements from years 2002-2006 were used to study polar winter NOx increases and their connection to energetic particle precipitation. NOx enhancements were found to occur in a good correlation with both increased high-energy particle precipitation and increased geomagnetic activity. The average wintertime polar NOx was found to have a nearly linear relationship with the average wintertime geomagnetic activity. The results from this thesis work show how important energetic particle precipitation from outside the atmosphere is as a source of NOx in the middle atmosphere, and thus its importance to the chemical balance of the atmosphere.

Structure and assembly of Sesbania mosaic virus

Sesbania mosaic virus (SeMV) is a ss-RNA (4149 nt) plant sobemovirus isolated from farmer's field around Tirupathi, Andhra Pradesh. The viral capsid (30 nm diameter) consists of 180 copies of protein subunits (MW 29 kDa) organized with icosahedral symmetry. In order to understand the mechanism of assembly of SeMV, a large number of deletion and substitution mutants of the coat protein (CP) were constructed. Recombinant SeMV CP (rCP) as well as the N-terminal rCP deletion mutant Delta N22 were found to assemble in E. coli into virus-like particles (VLPs). Delta N36 and Delta N65 mostly formed smaller particles consisting of 60 protein subunits. Although particlem assembly was not affected due to the substitution of aspartates (D14 and D149) that coordinate calcium ions by asparagines, the stability of the resulting capsids was drastically reduced. Deletion of residues forming a characteristic beta-annulus at the icosahedral 3-folds did not affect the assembly of VLPs. Mutation of a single tryptophan, which occurs near the icosahedral fivefold axis to glutamate or lysine, resulted in the disruption of the capsid leading to soluble dimers that resembled the quasi-dimer structure of the native virus. Replacement of positively charged residues in the amino terminal segment of CP resulted in the formation of empty shells. Based on these observations, a plausible mechanism of assembly is proposed.

Dimensional Reduction Near the Deconfinement Transition

When ordinary nuclear matter is heated to a high temperature of ~ 10^12 K, it undergoes a deconfinement transition to a new phase, strongly interacting quark-gluon plasma. While the color charged fundamental constituents of the nuclei, the quarks and gluons, are at low temperatures permanently confined inside color neutral hadrons, in the plasma the color degrees of freedom become dominant over nuclear, rather than merely nucleonic, volumes. Quantum Chromodynamics (QCD) is the accepted theory of the strong interactions, and confines quarks and gluons inside hadrons. The theory was formulated in early seventies, but deriving first principles predictions from it still remains a challenge, and novel methods of studying it are needed. One such method is dimensional reduction, in which the high temperature dynamics of static observables of the full four-dimensional theory are described using a simpler three-dimensional effective theory, having only the static modes of the various fields as its degrees of freedom. A perturbatively constructed effective theory is known to provide a good description of the plasma at high temperatures, where asymptotic freedom makes the gauge coupling small. In addition to this, numerical lattice simulations have, however, shown that the perturbatively constructed theory gives a surprisingly good description of the plasma all the way down to temperatures a few times the transition temperature. Near the critical temperature, the effective theory, however, ceases to give a valid description of the physics, since it fails to respect the approximate center symmetry of the full theory. The symmetry plays a key role in the dynamics near the phase transition, and thus one expects that the regime of validity of the dimensionally reduced theories can be significantly extended towards the deconfinement transition by incorporating the center symmetry in them. In the introductory part of the thesis, the status of dimensionally reduced effective theories of high temperature QCD is reviewed, placing emphasis on the phase structure of the theories. In the first research paper included in the thesis, the non-perturbative input required in computing the g^6 term in the weak coupling expansion of the pressure of QCD is computed in the effective theory framework at an arbitrary number of colors. The two last papers on the other hand focus on the construction of the center-symmetric effective theories, and subsequently the first non-perturbative studies of these theories are presented. Non-perturbative lattice simulations of a center-symmetric effective theory for SU(2) Yang-Mills theory show --- in sharp contrast to the perturbative setup --- that the effective theory accommodates a phase transition in the correct universality class of the full theory. This transition is seen to take place at a value of the effective theory coupling constant that is consistent with the full theory coupling at the critical temperature.

Hybrid Modelling of Titan's Interaction with the Magnetosphere of Saturn

In this dissertation we study the interaction between Saturn's moon Titan and the magnetospheric plasma and magnetic field. The method of research is a three-dimensional computer simulation model, that is used to simulate this interaction. The simulation model used is a hybrid model. Hybrid models enable individual tracking or tracing of ions and also take into account the particle motion in the propagation of the electromagnetic fields. The hybrid model has been developed at the Finnish Meteorological Institute. This thesis gives a general description of the effects that the solar wind has on Earth and other planets of our solar system. Planetary satellites can also have similar interactions with the solar wind but also with the plasma flows of planetary magnetospheres. Titan is clearly the largest among the satellites of Saturn and also the only known satellite with a dense atmosphere. It is the atmosphere that makes Titan's plasma interaction with the magnetosphere of Saturn so unique. Nevertheless, comparisons with the plasma interactions of other solar system bodies are valuable. Detecting charged plasma particles requires in situ measurements obtainable through scientific spacecraft. The Cassini mission has been one of the most remarkable international efforts in space science. Since 2004 the measurements and images obtained from instruments onboard the Cassini spacecraft have increased the scientific knowledge of Saturn as well as its satellites and magnetosphere in a way no one was probably able to predict. The current level of science on Titan is practically unthinkable without the Cassini mission. Many of the observations by Cassini instrument teams have influenced this research both the direct measurements of Titan as well as observations of its plasma environment. The theoretical principles of the hybrid modelling approach are presented in connection to the broader context of plasma simulations. The developed hybrid model is described in detail: e.g. the way the equations of the hybrid model are solved is shown explicitly. Several simulation techniques, such as the grid structure and various boundary conditions, are discussed in detail as well. The testing and monitoring of simulation runs is presented as an essential routine when running sophisticated and complex models. Several significant improvements of the model, that are in preparation, are also discussed. A main part of this dissertation are four scientific articles based on the results of the Titan model. The Titan model developed during the course of the Ph.D. research has been shown to be an important tool to understand Titan's plasma interaction. One reason for this is that the structures of the magnetic field around Titan are very much three-dimensional. The simulation results give a general picture of the magnetic fields in the vicinity of Titan. The magnetic fine structure of Titan's wake as seen in the simulations seems connected to Alfvén waves an important wave mode in space plasmas. The particle escape from Titan is also a major part of these studies. Our simulations show a bending or turning of Titan's ionotail that we have shown to be a direct result of the basic principles in plasma physics. Furthermore, the ion flux from the magnetosphere of Saturn into Titan's upper atmosphere has been studied. The modelled ion flux has asymmetries that would likely have a large impact in the heating in different parts of Titan's upper atmosphere.

Sukupolvien ongelma : Tutkielmia sukupolven käsitteestä, sukupolvitietoisuudesta ja suurista ikäluokista

The aims of the thesis are (1) to present a systematic evaluation of generation and its relevance as a sociological concept, (2) to reflect on how generational consciousness, i.e. generation as an object of collective identification that has social significance, can emerge and take shape, (3) to analyze empirically the generational experiences and consciousness of one specific generation, namely Finnish baby boomers (b. 1945 1950). The thesis contributes to the discussion on the social (as distinct from its genealogical) meaning of the concept of generation, launched by Karl Mannheim s classic Das Problem der Generationen (1928), in which the central idea is that a certain group of people is bonded together by a shared experience and that this bonding can result in a distinct self-consciousness. The thesis is comprised of six original articles and an extensive summarizing chapter. In the empirical articles, the baby boomers are studied on the basis of nationally representative survey data (N = 2628) and narrative life-story interviews (N = 38). In the article that discusses the connection of generations and social movements, the analysis is based on the member survey of Attac Finland (N = 1096). Three main themes were clarified in the thesis. (1) In the social sense the concept of generation is a modern, problematic, and ultimately a political concept. It served the interests of the intellectuals who developed the concept in the early 20th century and provided them, as an alternative to the concept of social class, a new way of think about social change and progress. The concept of generation is always coupled with the concept of Zeitgeist or some other controversial way of defining what is essential, i.e. what creates generations, in a given culture. Thus generation is, as a product of definition and classification struggles, a contested concept. The concept also clearly implies elitist connotations; the idea of some kind of vanguard (the elite) that represents an entire generation by proclaiming itself as its spokesman automatically creates a counterpart, namely the others in the peer group who are thought to be represented (the masses). (2) Generational consciousness cannot emerge as a result of any kind of automatic process or endogenously; it must be made. There has to be somebody who represents the generation in order for that generation to exist in people s minds and as an object of identification; generational experiences and their meanings must be articulated. Hence, social generations are, in a fundamental manner, discursively constructed. The articulations of generational experiences (speeches, writings, manifests, labels etc.) can be called as the discursive dimension of social generations, and through this notion, how public discourse shapes people s generational consciousness can be seen. Another important element in the process is collective memory, as generational consciousness often takes form only retrospectively. (3) Finnish baby boomers are not a united or homogeneous generation but are divided into many smaller sections with specific generational experiences and consciousnesses. The content of the generational consciousness of the baby boomers is heavily politically charged. A salient dividing line inside the age group is formed by individual attitudes towards so-called 1960s radicalism. Identification with the 1960s generation functions today as a positive self-definition of a certain small leftist elite group, and the values and characteristics usually connected with the idea of the 1960s generation do not represent the whole age group. On the contrary, among some of the members of the baby boomers, the generational identification is still directed by the experience of how traditional values were disgraced in the 1960s. As objects of identification, the neutral term baby boomers and the charged 1960s generation are totally different things, and therefore they should not be used as synonyms. Although the significance of the group of the 1960s generation is often overestimated, they are however special with respect to generational consciousness because they have presented themselves as the voice of the entire generation. Their generational interpretations have spread through the media with the help of certain iconic images of the generation insomuch that 1960s radicalism has become an indirect generational experience for other parts of the baby boom cohort as well.

Disallowed Ramachandran Conformations of Amino Acid Residues in Protein Structures

An analysis of the nature and distribution of disallowed Ramachandran conformations of amino acid residues observed in high resolution protein crystal structures has been carried out. A data set consisting of 110 high resolution, non-homologous, protein crystal structures from the Brookhaven Protein Data Bank was examined. The data set consisted of a total of 18,708 non-Gly residues, which were characterized on the basis of their backbone dihedral angles (φ, ψ). Residues falling outside the defined “broad allowed limits” on the Ramachandran map were chosen and the reportedB-factor value of the α-carbon atom was used to further select well defined disallowed conformations. The conformations of the selected 66 disallowed residues clustered in distinct regions of the Ramachandran map indicating that specific φ, ψ angle distortions are preferred under compulsions imposed by local constraints. The distribution of various amino acid residues in the disallowed residue data set showed a predominance of small polar/charged residues, with bulky hydrophobic residues being infrequent. As a further check, for all the 66 cases non-hydrogen van der Waals short contacts in the protein structures were evaluated and compared with the ideal “Ala-dipeptide” constructed using disallowed dihedral angle (φ, ψ) values. The analysis reveals that short contacts are eliminated in most cases by local distortions of bond angles. An analysis of the conformation of the identified disallowed residues in related protein structures reveals instances of conservation of unusual stereochemistry.

Triosephosphate isomerase from Plasmodium falciparum:. the crystal structure provides insights into antimalarial drug design

Background: Malaria caused by the parasite Plasmodium falciparum is a major public health concern. The parasite lacks a functional tricarboxylic acid cycle, making glycolysis its sole energy source. Although parasite enzymes have been considered as potential antimalarial drug targets, little is known about their structural biology. Here we report the crystal structure of triosephosphate isomerase (TIM) from P. falciparum at 2.2 Angstrom resolution. Results: The crystal structure of P. falciparum TIM (PfTIM), expressed in Escherichia coli, was determined by the molecular replacement method using the structure of trypanosomal TIM as the starting model. Comparison of the PfTIM structure with other TIM structures, particularly human TIM, revealed several differences, In most TIMs the residue at position 183 is a glutamate but in PtTIM it is a leucine, This leucine residue is completely exposed and together with the surrounding positively charged patch, may be responsible for binding TIM to the erythrocyte membrane. Another interesting feature is the occurrence of a cysteine residue at the dimer interface of PfTIM (Cys13), in contrast to human TIM where this residue is a methionine. Finally, residue 96 of human TIM (Ser96), which occurs near the active site, has been replaced by phenylalanine in PfTIM.

The role of polar and facial amphipathic character in determining lipopolysaccharide-binding properties in synthetic cationic peptides

Two series of peptides, designated K and NK were synthesized and tested for lipid A binding and neutralizing properties. K-2, which has an 11-residue amphiphilic core, and a branched N-terminus bearing two branched lysinyl residues does not bind lipid A, while NK2, also with an 11-residue amphiphilic core comprised entirely of non-ionizable residues, and a similarly branched, cationic N-terminus, binds lipid A very weakly. Both peptides do not inhibit lipopolysaccharide (LPS) activity in the Limulus assay, nor do they inhibit LPS-induced TNF-alpha and NO production in 5774 cells. These results are entirely unlike a homologous peptide with an exclusively hydrophobic core whose LPS-binding and neutralizing properties are very similar to that of polymyxin B [David SA, Awasthi SK, Wiese A et al. Characterization of the interactions of a polycationic, amphiphilic, terminally branched oligopeptide with lipid A and lipopolysaccharide from the deep rough mutant of Salmonella minnesota. J Endotoxin Res 1996; 3: 369-379]. These data suggest that a clear segregation of charged and apolar domains is crucial in molecules designed for purposes of LPS sequestration and that head-tail (polar) orientation of the cationic/hydrophobic regions is preferable to molecules with mixed or facial cationic/amphipathic character.

Search for Higgs bosons predicted in two-Higgs-doublet models via decays to tau lepton pairs in 1.96 TeV proton-antiproton collisions

We present the results of a search for Higgs bosons predicted in two-Higgs-doublet models, in the case where the Higgs bosons decay to tau lepton pairs, using 1.8 inverse fb of integrated luminosity of proton-antiproton collisions recorded by the CDF II experiment at the Fermilab Tevatron. Studying the observed mass distribution in events where one or both tau leptons decay leptonically, no evidence for a Higgs boson signal is observed. The result is used to infer exclusion limits in the two-dimensional parameter space of tan beta versus m(A).

Observation of exclusive charmonium production and gamma+gamma to mu+mu- in p+pbar collisions at sqrt{s} = 1.96 TeV

We have observed the reactions p+pbar --> p+X+pbar, with X being a centrally produced J/psi, psi(2S) or chi_c0, and gamma+gamma --> mu+mu-, in proton- antiproton collisions at sqrt{s} = 1.96 TeV using the Run II Collider Detector at Fermilab. The event signature requires two oppositely charged muons, each with pseudorapidity |eta| mu+mu-. Events with a J/psi and an associated photon candidate are consistent with exclusive chi_c0 production through double pomeron exchange. The exclusive vector meson production is as expected for elastic photo- production, gamma+p --> J/psi(psi(2S)) + p, which is observed here for the first time in hadron-hadron collisions. The cross sections ds/dy(y=0) for p + pbar --> p + X + pbar with X = J/psi, psi(2S) orchi_c0 are 3.92+/-0.62 nb, 0.53+/-0.14 nb, and 75+/-14 nb respectively. The cross section for the continuum, with |eta(mu+/-)|

Search for Higgs bosons predicted in two-Higgs-doublet models via decays to tau lepton pairs in 1.96 TeV proton-antiproton collisions

We present the results of a search for Higgs bosons predicted in two-Higgs-doublet models, in the case where the Higgs bosons decay to tau lepton pairs, using 1.8 inverse fb of integrated luminosity of proton-antiproton collisions recorded by the CDF II experiment at the Fermilab Tevatron. Studying the observed mass distribution in events where one or both tau leptons decay leptonically, no evidence for a Higgs boson signal is observed. The result is used to infer exclusion limits in the two-dimensional parameter space of tan beta versus m(A).

Measurement of Particle Production and Inclusive Differential Cross Sections in pbar{p} Collisions at sqrt{s}=1.96 TeV

We report a set of measurements of particle production in inelastic pbar{p} collisions collected with a minimum-bias trigger at the Tevatron Collider with the CDF II experiment. The inclusive charged particle transverse momentum differential cross section is measured, with improved precision, over a range about ten times wider than in previous measurements. The former modeling of the spectrum appears to be incompatible with the high particle momenta observed. The dependence of the charged particle transverse momentum on the event particle multiplicity is analyzed to study the various components of hadron interactions. This is one of the observable variables most poorly reproduced by the available Monte Carlo generators. A first measurement of the event transverse energy sum differential cross section is also reported. A comparison with a Pythia prediction at the hadron level is performed. The inclusive charged particle differential production cross section is fairly well reproduced only in the transverse momentum range available from previous measurements. At higher momentum the agreement is poor. The transverse energy sum is poorly reproduced over the whole spectrum. The dependence of the charged particle transverse momentum on the particle multiplicity needs the introduction of more sophisticated particle production mechanisms, such as multiple parton interactions, in order to be better explained.