Räumliche und jahreszeitliche Verteilung von OH- und HO 2-Radikalen in der Troposphäre über Europa

Durch geologische Prozesse freigesetzte sowie biogen und anthropogen emittierte Gase werden hauptsächlich von der untersten Atmosphärenschicht, der Troposphäre, aufgenommen und abgebaut. Durch in die Troposphä¬re einfallende solare Strahlung wird ein Abbau des Großteils der emittierten Spurengase durch reaktive Radikale initiiert. Der wichtigste Vertreter dieser reaktiven Radikale in der Troposphäre ist das Hydroxylradikal (OH-Radikal), welches im schnellen Gleichgewicht mit Hydroperoxyradikalen (HO2-Radikal) vorliegt, sodass die Summe aus OH- und HO2-Radikalen oft als HOx zusammengefasst wird. HOx-Radikale bilden tagsüber den Hauptteil der Oxidationskapazität der Troposphäre und sind somit verantwortlich für den oxidativen Abbau vieler, auch chemisch und photolytisch stabiler, Spurengase. Daher wird die Oxidationskapazität als Selbstreinigungskraft der Troposphäre verstanden. rnIm Rahmen meiner Arbeit wurde die wissenschaftliche Fragestellung auf die Oxidationskapazität der Troposphäre über Europa fokussiert. Die Höhen- und Breitenverteilung der OH- und HO2-Mischungsverhältnisse und ihre jahreszeitliche Variation wurde während der flugzeuggestützten HOOVER-Kampagnen (HOOVER 1 & 2) charakterisiert, wobei ein Fokus auf der oberen Troposphäre lag. Es wird gezeigt, welchen Einfluss die einfallende Strahlung, die Variation von HOx-Vorläufersubstanzen (wie z. B. Ozon) und die Variation von Substanzen, die das HOx-Gleichgewicht beeinflussen (z. B. Stickstoffmonoxid), auf das HOx-Budget haben. rnEs wird beispielhaft für den Höhenbereich zwischen 8 und 9.5 km gezeigt, dass die Oxidationskapazität in der oberen Troposphäre des Sommers im Ver¬gleich zu der des Herbstes aufgrund von einer verstärkten HO2-Zyklierung im Mittel deutlich erhöht ist (500 %). rnDurch konvektiven Transport werden im Sommer im Gegensatz zum Herbst regelmäßig Luftmassen aus der planetaren Grenzschicht in die obere Troposphäre eingemischt. Daher wurden der konvektive Luftmassentransport und der Einfluss der eingemischten Spurengase auf die Oxidationskapazität der oberen Troposphäre anhand eines konvektiven Elements über Südostdeutschland untersucht. Wie in dieser Arbeit berichtet wird, wurden in den Luftmassen der Ausströmregion mit bis zu 3.5 pmol/mol (Maximum 10 s-Mittelwert) sehr hohe OH-Mischungsverhältnisse gefunden, die aus der HO2-Konversion mit NO gebildet wurden. Das modellierte HOx-Budget zeigt, dass die HOx-Chemie - unter den beobachteten Bedingungen in der Ausströmregion - durch HOx-Zyklierungsreaktionen beherrscht wird. rnDie gemessenen OH-Mischungsverhältnisse in der Ausströmregion liegen etwa um einen Faktor fünf höher, als die während dieses Fluges in der konvektiv unbeeinflussten oberen Troposphäre gemessenen OH-Mischungsverhältnisse. Am Beispiel der NO2- und CH4-Lebensdauer wird ein schnellerer Abbau von Spurengasen aufgrund der erhöhten Oxidationskapazität nachgewiesen. Aus der NO2-Lebensdauer wird abgeschätzt, wie lange die Oxidationskapazität aufgrund des konvektiven Transports von NOx in den Luftmassen des Ausströmgebietes erhöht ist.rnDie während den Kampagnen durchgeführten Messungen wurden genutzt, um Modellberechnungen des vertikalen HOx-Budgets (über Südschweden) und des meridionalen HOx-Budgets zwischen Nordeuropa und Korsika durchzuführen. Es wurde gezeigt, dass das Modell die OH- und HO2-Mischungsverhältnisse im Allgemeinen gut reproduziert (Modell/Messung: OH im Sommer 94 %, HO2 im Sommer 93 % im Herbst 95 %), wohingegen die vergleichsweise kleinen OH-Mischungsverhältnisse im Herbst aufgrund von einer überschätzten H2O2 abhängigen OH-Produktion stark überschätzt wurden (Modell/Messung: 147 %). rnZur Charakterisierung der Oxidationskapazität innerhalb der planetaren Grenzschicht wurden die DOMINO-Kampagnen durchgeführt. Dabei wurde die Zusammensetzung unterschiedlicher Luftmassen untersucht, die aus verschiedenen Herkunftsorten zum Messort transportiert wurden und aufgrund ihres Ursprungs kaum prozessierte bis prozessierte anthropogen emittierte Spurengase enthielten. Zusätzlich enthielt ein Teil der Luftmassen biogen emittierte Spurengase. Komplementäre Messungen ermöglichen die Berechnung der totalen OH-Produktion und den Vergleich mit den bekannten OH-Quellen. Der Vergleich zeigt, dass offenbar wichtige OH-Produktionskanäle durch die gemessenen Spurengase oder die durchgeführten Berechnungen nicht abgebildet werden. Es wird gezeigt, dass die Stärke der unbekannten OH-Quellen, vor allem unter niedrigen NO-Bedingungen, groß ist und mit den Isopren-, RO2- und HO2-Mischungsverhältnissen korreliert.rn

Stima dei parametri di modelli idrologici mediante ottimizzazione dell’utilità

Tradizionalmente, l'obiettivo della calibrazione di un modello afflussi-deflussi è sempre stato quello di ottenere un set di parametri (o una distribuzione di probabilità dei parametri) che massimizzasse l'adattamento dei dati simulati alla realtà osservata, trattando parzialmente le finalità applicative del modello. Nel lavoro di tesi viene proposta una metodologia di calibrazione che trae spunto dell'evidenza che non sempre la corrispondenza tra dati osservati e simulati rappresenti il criterio più appropriato per calibrare un modello idrologico. Ai fini applicativi infatti, può risultare maggiormente utile una miglior rappresentazione di un determinato aspetto dell'idrogramma piuttosto che un altro. Il metodo di calibrazione che viene proposto mira a valutare le prestazioni del modello stimandone l'utilità nell'applicazione prevista. Tramite l'utilizzo di opportune funzioni, ad ogni passo temporale viene valutata l'utilità della simulazione ottenuta. La calibrazione viene quindi eseguita attraverso la massimizzazione di una funzione obiettivo costituita dalla somma delle utilità stimate nei singoli passi temporali. Le analisi mostrano come attraverso l'impiego di tali funzioni obiettivo sia possibile migliorare le prestazioni del modello laddove ritenute di maggior interesse per per le finalità applicative previste.

Numerical modelling of fluid-structure interaction with application in hemodynamics

The thesis deals with numerical algorithms for fluid-structure interaction problems with application in blood flow modelling. It starts with a short introduction on the mathematical description of incompressible viscous flow with non-Newtonian viscosity and a moving linear viscoelastic structure. The mathematical model consists of the generalized Navier-Stokes equation used for the description of fluid flow and the generalized string model for structure movement. The arbitrary Lagrangian-Eulerian approach is used in order to take into account moving computational domain. A part of the thesis is devoted to the discussion on the non-Newtonian behaviour of shear-thinning fluids, which is in our case blood, and derivation of two non-Newtonian models frequently used in the blood flow modelling. Further we give a brief overview on recent fluid-structure interaction schemes with discussion about the difficulties arising in numerical modelling of blood flow. Our main contribution lies in numerical and experimental study of a new loosely-coupled partitioned scheme called the kinematic splitting fluid-structure interaction algorithm. We present stability analysis for a coupled problem of non-Newtonian shear-dependent fluids in moving domains with viscoelastic boundaries. Here, we assume both, the nonlinearity in convective as well is diffusive term. We analyse the convergence of proposed numerical scheme for a simplified fluid model of the Oseen type. Moreover, we present series of experiments including numerical error analysis, comparison of hemodynamic parameters for the Newtonian and non-Newtonian fluids and comparison of several physiologically relevant computational geometries in terms of wall displacement and wall shear stress. Numerical analysis and extensive experimental study for several standard geometries confirm reliability and accuracy of the proposed kinematic splitting scheme in order to approximate fluid-structure interaction problems.

Caratterizzazione e simulazione di processi di colata in sabbia di ghise sferoidali

L’oggetto principale delle attività di tesi è la caratterizzazione numerico-sperimentale di processi di colata in sabbia di ghisa sferoidale. Inizialmente è stata effettuata un’approfondita indagine bibliografica per comprendere appieno le problematiche relative all’influenza dei parametri del processo fusorio (composizione chimica, trattamento del bagno, velocità di raffreddamento) sulle proprietà microstrutturali e meccaniche di getti ottenuti e per valutare lo stato dell’arte degli strumenti numerici di simulazione delle dinamiche di solidificazione e di previsione delle microstrutture. Sono state definite, realizzate ed impiegate attrezzature sperimentali di colata per la caratterizzazione di leghe rivolte alla misura ed alla differenziazione delle condizioni di processo, in particolare le velocità di raffreddamento, ed atte a validare strumenti di simulazione numerica e modelli previsionali. Inoltre sono stati progettati ed impiegati diversi sistemi per l’acquisizione ed analisi delle temperature all’interno di getti anche di grandi dimensioni. Lo studio, mediante analisi metallografica, di campioni di materiale ottenuto in condizioni differenziate ha confermato l’effetto dei parametri di processo considerati sulle proprietà microstrutturali quali dimensioni dei noduli di grafite e contenuto di ferrite e perlite. In getti di grandi dimensioni si è riscontrata anche una forte influenza dei fenomeni di macrosegregazione e convezione della lega su microstrutture e difettologie dei getti. Le attività si sono concentrate principalmente nella simulazione numerica FEM dei processi fusori studiati e nell’impiego di modelli empirico-analitici per la previsione delle microstrutture. I dati misurati di temperature di processo e di microstrutture sono stati impiegati per la validazione ed ottimizzazione degli strumenti numerici previsionali impiegati su un ampio intervallo di condizioni di processo. L’impiego di strumenti affidabili di simulazione del processo fusorio, attraverso l’implementazione di correlazioni sperimentali microstrutture-proprietà meccaniche, permette la valutazione di proprietà e difettologie dei getti, fornendo un valido aiuto nell’ottimizzazione del prodotto finito e del relativo processo produttivo.

Kollineare Laserspektroskopie an radioaktiven Praseodymionen und Cadmiumatomen

Die Analyse optischer Spektren liefert einen kernmodellunabhängigen Zugang zur Bestimmung der Kernspins, Ladungsradien und elektromagnetischen Momente von Atomkernen im Grundzustand und von langlebigen Isomeren. Eine der vielseitigsten Methoden zur optischen Spektroskopie an kurzlebigen Isotopen ist die kollineare Laserspektroskopie. Im Rahmen dieser Arbeit wurde zum einen die TRIGA-LASER Strahlstrecke am Institut für Kernchemie der Universität Mainz durch die Implementierung einer neuen offline Oberflächenionenquelle für hohe Verdampfungstemperaturen und eines Strahlanalysesystems weiterentwickelt. Zum anderen wurde kollineare Laserspektroskopie an kurzlebigen Praseodym- und Cadmiumisotopen an ISOLDE/CERN durchgeführt. Die neue Ionenquelle ermöglichte dabei den Test der kollinearen Laserspektroskopie an Praseodymionen am TRIGA-LASER Experiment. Die Spektroskopie der Prasdeodymionen motivierte sich aus der Beobachtung einer zeitlichen Modulation der EC-Zerfallsrate von wasserstoffähnlichem 140Pr58+. Für die Erklärung dieser sogenannten GSI Oszillationen wird unter anderem das magnetische Moment des Kerns benötigt, welches bislang noch nicht experimentell bestimmt wurde. Zudem wurde für wasserstoffähnliches 140Pr58+ überraschenderweise eine kleinere EC-Zerfallskonstante gemessen als für heliumähnliches 140Pr57+. Die Erklärung dieses Phänomens setzt ein positives magnetisches Moment voraus. Bei der Spektroskopie am COLLAPS Experiment wurden erstmals die magnetischen Momente von 135Pr, 136Pr und 137Pr vermessen. Aufgrund zu geringer Produktionsraten war die Spektroskopie des gewünschten Isotops 140Pr jedoch nicht erfolgreich. Die Untersuchung der Cadmiumisotope ist kernphysikalisch motiviert. In der Zinnregion erstrecken sich die Isotope über die beiden magischen Zahlen N=50 und N=82 bei gleichzeitiger Nähe des Z=50 Schalenabschlusses. Hier können verschiedene Kernmodelle getestet werden, die sich beispielsweise hinsichtlich der Stärke des N=82 Schalenabschlusses widersprechen. Diese Arbeit berichtet über erste Ergebnisse der Spektroskopie an Cadmiumatomen, die sich über die Isotope 106−124,126Cd sowie die zugehörigen langlebigen I=11/2− Isomere erstreckt. Die zuvor experimentell bekannten oder aus dem erweiterten Schalenmodell abgeleiteten Kernspins konnten für alle Isotope bis auf 119Cd bestätigt werden. Der Kernspin von 119Cd wurde eindeutig zu I=1/2 bestimmt. Die elektrischen Quadrupolmomente der Isomere zeigen ein bemerkenswert lineares Verhalten in Abhängigkeit von der Neutronenzahl und dies über die eigentliche Kapazität der 1h11/2 Unterschale hinaus. Die Änderungen der mittleren quadratischen Ladungsradien zeigen den auch an Indium- und Zinnisotopen beobachteten stetigen Verlauf. Der lineare Anteil passt sehr gut zu den Berechnung des Tröpfchenmodells in der Parametrisierung nach Berchidevsky und Tondeur. Die Differenzen der mittleren quadratischen Ladungsradien zwischen Grund- und isomeren Zustand der ungeraden Cadmiumisotope zeigen einen interessanten parabolischen Verlauf mit einem Minimum zwischen A=117 und A=119.

Stable isotope composition of atmospheric carbon monoxide : a modelling study

Stable isotope composition of atmospheric carbon monoxide: A modelling study.rnrnThis study aims at an improved understanding of the stable carbon and oxygen isotope composition of the carbon monoxide (CO) in the global atmosphere by means of numerical simulations. At first, a new kinetic chemistry tagging technique for the most complete parameterisation of isotope effects has been introduced into the Modular Earth Submodel System (MESSy) framework. Incorporated into the ECHAM/MESSy Atmospheric Chemistry (EMAC) general circulation model, an explicit treatment of the isotope effects on the global scale is now possible. The expanded model system has been applied to simulate the chemical system containing up to five isotopologues of all carbon- and oxygen-bearing species, which ultimately determine the δ13C, δ18O and Δ17O isotopic signatures of atmospheric CO. As model input, a new stable isotope-inclusive emission inventory for the relevant trace gases has been compiled. The uncertainties of the emission estimates and of the resulting simulated mixing and isotope ratios have been analysed. The simulated CO mixing and stable isotope ratios have been compared to in-situ measurements from ground-based observatories and from the civil-aircraft-mounted CARIBIC−1 measurement platform.rnrnThe systematically underestimated 13CO/12CO ratios of earlier, simplified modelling studies can now be partly explained. The EMAC simulations do not support the inferences of those studies, which suggest for CO a reduced input of the highly depleted in 13C methane oxidation source. In particular, a high average yield of 0.94 CO per reacted methane (CH4) molecule is simulated in the troposphere, to a large extent due to the competition between the deposition and convective transport processes affecting the CH4 to CO reaction chain intermediates. None of the other factors, assumed or disregarded in previous studies, however hypothesised to have the potential in enriching tropospheric CO in 13C, were found significant when explicitly simulated. The inaccurate surface emissions, likely underestimated over East Asia, are responsible for roughly half of the discrepancies between the simulated and observed 13CO in the northern hemisphere (NH), whereas the remote southern hemisphere (SH) compositions suggest an underestimated fractionation during the oxidation of CO by the hydroxyl radical (OH). A reanalysis of the kinetic isotope effect (KIE) in this reaction contrasts the conventional assumption of a mere pressure dependence, and instead suggests an additional temperature dependence of the 13C KIE, which is driven by changes in the partitioning of the reaction exit channels. This result is yet to be confirmed in the laboratory.rnrnApart from 13CO, for the first time the atmospheric distribution of the oxygen mass-independent fractionation (MIF) in CO, Δ17O, has been consistently simulated on the global scale with EMAC. The applicability of Δ17O(CO) observations to unravelling changes in the tropospheric CH4-CO-OH system has been scrutinised, as well as the implications of the ozone (O3) input to the CO isotope oxygen budget. The Δ17O(CO) is confirmed to be the principal signal for the CO photochemical age, thus providing a measure for the OH chiefly involved in the sink of CO. The highly mass-independently fractionated O3 oxygen is estimated to comprise around 2% of the overall tropospheric CO source, which has implications for the δ18O, but less likely for the Δ17O CO budgets. Finally, additional sensitivity simulations with EMAC corroborate the nearly equal net effects of the present-day CH4 and CO burdens in removing tropospheric OH, as well as the large turnover and stability of the abundance of the latter. The simulated CO isotopologues nonetheless hint at a likely insufficient OH regeneration in the NH high latitudes and the upper troposphere / lower stratosphere (UTLS).rn

Volatile organic compounds at the air-sea interface : gas exchange rates, oceanic emissions and the effect of ocean acidification

Oceans are key sources and sinks in the global budgets of significant atmospheric trace gases, termed Volatile Organic Compounds (VOCs). Despite their low concentrations, these species have an important role in the atmosphere, influencing ozone photochemistry and aerosol physics. Surprisingly, little work has been done on assessing their emissions or transport mechanisms and rates between ocean and atmosphere, all of which are important when modelling the atmosphere accurately.rnA new Needle Trap Device (NTD) - GC-MS method was developed for the effective sampling and analysis of VOCs in seawater. Good repeatability (RSDs <16 %), linearity (R2 = 0.96 - 0.99) and limits of detection in the range of pM were obtained for DMS, isoprene, benzene, toluene, p-xylene, (+)-α-pinene and (-)-α-pinene. Laboratory evaluation and subsequent field application indicated that the proposed method can be used successfully in place of the more usually applied extraction techniques (P&T, SPME) to extend the suite of species typically measured in the ocean and improve detection limits. rnDuring a mesocosm CO2 enrichment study, DMS, isoprene and α-pinene were identified and quantified in seawater samples, using the above mentioned method. Based on correlations with available biological datasets, the effects of ocean acidification as well as possible ocean biological sources were investigated for all examined compounds. Future ocean's acidity was shown to decrease oceanic DMS production, possibly impact isoprene emissions but not affect the production of α-pinene. rnIn a separate activity, ocean - atmosphere interactions were simulated in a large scale wind-wave canal facility, in order to investigate the gas exchange process and its controlling mechanisms. Air-water exchange rates of 14 chemical species (of which 11 VOCs) spanning a wide range of solubility (dimensionless solubility, α = 0:4 to 5470) and diffusivity (Schmidt number in water, Scw = 594 to 1194) were obtained under various turbulent (wind speed at ten meters height, u10 = 0:8 to 15ms-1) and surfactant modulated (two different sized Triton X-100 layers) surface conditions. Reliable and reproducible total gas transfer velocities were obtained and the derived values and trends were comparable to previous investigations. Through this study, a much better and more comprehensive understanding of the gas exchange process was accomplished. The role of friction velocity, uw* and mean square slope, σs2 in defining phenomena such as waves and wave breaking, near surface turbulence, bubbles and surface films was recognized as very significant. uw* was determined as the ideal turbulent parameter while σs2 described best the related surface conditions. A combination of both uw* and σs2 variables, was found to reproduce faithfully the air-water gas exchange process. rnA Total Transfer Velocity (TTV) model provided by a compilation of 14 tracers and a combination of both uw* and σs2 parameters, is proposed for the first time. Through the proposed TTV parameterization, a new physical perspective is presented which provides an accurate TTV for any tracer within the examined solubility range. rnThe development of such a comprehensive air-sea gas exchange parameterization represents a highly useful tool for regional and global models, providing accurate total transfer velocity estimations for any tracer and any sea-surface status, simplifying the calculation process and eliminating inevitable calculation uncertainty connected with the selection or combination of different parameterizations.rnrn

Aerosol-cloud interactions studied with a chemistry-climate model

This study aims at a comprehensive understanding of the effects of aerosol-cloud interactions and their effects on cloud properties and climate using the chemistry-climate model EMAC. In this study, CCN activation is regarded as the dominant driver in aerosol-cloud feedback loops in warm clouds. The CCN activation is calculated prognostically using two different cloud droplet nucleation parameterizations, the STN and HYB CDN schemes. Both CDN schemes account for size and chemistry effects on the droplet formation based on the same aerosol properties. The calculation of the solute effect (hygroscopicity) is the main difference between the CDN schemes. The kappa-method is for the first time incorporated into Abdul-Razzak and Ghan activation scheme (ARG) to calculate hygroscopicity and critical supersaturation of aerosols (HYB), and the performance of the modied scheme is compared with the osmotic coefficient model (STN), which is the standard in the ARG scheme. Reference simulations (REF) with the prescribed cloud droplet number concentration have also been carried out in order to understand the effects of aerosol-cloud feedbacks. In addition, since the calculated cloud coverage is an important determinant of cloud radiative effects and is influencing the nucleation process two cloud cover parameterizations (i.e., a relative humidity threshold; RH-CLC and a statistical cloud cover scheme; ST-CLC) have been examined together with the CDN schemes, and their effects on the simulated cloud properties and relevant climate parameters have been investigated. The distinct cloud droplet spectra show strong sensitivity to aerosol composition effects on cloud droplet formation in all particle sizes, especially for the Aitken mode. As Aitken particles are the major component of the total aerosol number concentration and CCN, and are most sensitive to aerosol chemical composition effect (solute effect) on droplet formation, the activation of Aitken particles strongly contribute to total cloud droplet formation and thereby providing different cloud droplet spectra. These different spectra influence cloud structure, cloud properties, and climate, and show regionally varying sensitivity to meteorological and geographical condition as well as the spatiotemporal aerosol properties (i.e., particle size, number, and composition). The changes responding to different CDN schemes are more pronounced at lower altitudes than higher altitudes. Among regions, the subarctic regions show the strongest changes, as the lower surface temperature amplifies the effects of the activated aerosols; in contrast, the Sahara desert, where is an extremely dry area, is less influenced by changes in CCN number concentration. The aerosol-cloud coupling effects have been examined by comparing the prognostic CDN simulations (STN, HYB) with the reference simulation (REF). Most pronounced effects are found in the cloud droplet number concentration, cloud water distribution, and cloud radiative effect. The aerosol-cloud coupling generally increases cloud droplet number concentration; this decreases the efficiency of the formation of weak stratiform precipitation, and increases the cloud water loading. These large-scale changes lead to larger cloud cover and longer cloud lifetime, and contribute to high optical thickness and strong cloud cooling effects. This cools the Earth's surface, increases atmospheric stability, and reduces convective activity. These changes corresponding to aerosol-cloud feedbacks are also differently simulated depending on the cloud cover scheme. The ST-CLC scheme is more sensitive to aerosol-cloud coupling, since this scheme uses a tighter linkage of local dynamics and cloud water distributions in cloud formation process than the RH-CLC scheme. For the calculated total cloud cover, the RH-CLC scheme simulates relatively similar pattern to observations than the ST-CLC scheme does, but the overall properties (e.g., total cloud cover, cloud water content) in the RH simulations are overestimated, particularly over ocean. This is mainly originated from the difference in simulated skewness in each scheme: the RH simulations calculate negatively skewed distributions of cloud cover and relevant cloud water, which is similar to that of the observations, while the ST simulations yield positively skewed distributions resulting in lower mean values than the RH-CLC scheme does. The underestimation of total cloud cover over ocean, particularly over the intertropical convergence zone (ITCZ) relates to systematic defficiency of the prognostic calculation of skewness in the current set-ups of the ST-CLC scheme.rnOverall, the current EMAC model set-ups perform better over continents for all combinations of the cloud droplet nucleation and cloud cover schemes. To consider aerosol-cloud feedbacks, the HYB scheme is a better method for predicting cloud and climate parameters for both cloud cover schemes than the STN scheme. The RH-CLC scheme offers a better simulation of total cloud cover and the relevant parameters with the HYB scheme and single-moment microphysics (REF) than the ST-CLC does, but is not very sensitive to aerosol-cloud interactions.

Hydrogen bonding of nucleotide base pairs: Application of the PM3 method

The ability of the pm3 semiempirical quantum mechanical method to reproduce hydrogen bonding in nucleotide base pairs was assessed. Results of pm3 calculations on the nucleotides 2′-deoxyadenosine 5′-monophosphate (pdA), 2′-deoxyguanosine 5′-monophosphate (pdG), 2′-deoxycytidine 5′-monophosphate (pdC), and 2′-deoxythymidine 5′-monophosphate (pdT) and the base pairs pdA–pdT, pdG–pdC, and pdG(syn)–pdC are presented and discussed. The pm3 method is the first of the parameterized nddo quantum mechanical models with any ability to reproduce hydrogen bonding between nucleotide base pairs. Intermolecular hydrogen bond lengths between nucleotides displaying Watson–Crick base pairing are 0.1–0.2 Å less than experimental results. Nucleotide bond distances, bond angles, and torsion angles about the glycosyl bond (χ), the C4′C5′ bond (γ), and the C5′O5′ bond (β) agree with experimental results. There are many possible conformations of nucleotides. pm3 calculations reveal that many of the most stable conformations are stabilized by intramolecular CHO hydrogen bonds. These interactions disrupt the usual sugar puckering. The stacking interactions of a dT–pdA duplex are examined at different levels of gradient optimization. The intramolecular hydrogen bonds found in the nucleotide base pairs disappear in the duplex, as a result of the additional constraints on the phosphate group when part of a DNA backbone. Sugar puckering is reproduced by the pm3 method for the four bases in the dT–pdA duplex. pm3 underestimates the attractive stacking interactions of base pairs in a B-DNA helical conformation. The performance of the pm3 method implemented in SPARTAN is contrasted with that implemented in MOPAC. At present, accurate ab initio calculations are too timeconsuming to be of practical use, and molecular mechanics methods cannot be used to determine quantum mechanical properties such as reaction-path calculations, transition-state structures, and activation energies. The pm3 method should be used with extreme caution for examination of small DNA systems. Future parameterizations of semiempirical methods should incorporate base stacking interactions into the parameterization data set to enhance the ability of these methods.

Ability of the PM3 Quantum Mechanical Method to Model Intermolecular Hydrogen Bonding between Neutral Molecules

The PM3 semiempirical quantum-mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02-0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol-' suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol-' imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high-resolution spectroscopic observations, gas electron diffraction data, and high-level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1-0.2 for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1-2 kcal mol-l. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and 0 predict that donor strength follows the order F > 0 > N and acceptor strength follows the order N > 0 > F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F-H- - -N bond to be the strongest and the N-H- - -F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two-center repulsive forces brought about by the parameterization of the Gaussian core-core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum-mechanical calculations can be applied to small biologic systems.

PM(10) remote sensing from geostationary SEVIRI and polar-orbiting MODIS sensors over the complex terrain of the European Alpine region

The subject of this study is to investigate the capability of spaceborne remote sensing data to predict ground concentrations of PM10 over the European Alpine region using satellite derived Aerosol Optical Depth (AOD) from the geostationary Spinning Enhanced Visible and InfraRed Imager (SEVIRI) and the polar-orbiting MODerate resolution Imaging Spectroradiometer (MODIS). The spatial and temporal resolutions of these aerosol products (10 km and 2 measurements per day for MODIS, ∼ 25 km and observation intervals of 15 min for SEVIRI) permit an evaluation of PM estimation from space at different spatial and temporal scales. Different empirical linear relationships between coincident AOD and PM10 observations are evaluated at 13 ground-based PM measurement sites, with the assumption that aerosols are vertically homogeneously distributed below the planetary Boundary Layer Height (BLH). The BLH and Relative Humidity (RH) variability are assessed, as well as their impact on the parameterization. The BLH has a strong influence on the correlation of daily and hourly time series, whilst RH effects are less clear and smaller in magnitude. Despite its lower spatial resolution and AOD accuracy, SEVIRI shows higher correlations than MODIS (rSEV∼ 0.7, rMOD∼ 0.6) with regard to daily averaged PM10. Advantages from MODIS arise only at hourly time scales in mountainous locations but lower correlations were found for both sensors at this time scale (r∼ 0.45). Moreover, the fraction of days in 2008 with at least one satellite observation was 27% for SEVIRI and 17% for MODIS. These results suggest that the frequency of observations plays an important role in PM monitoring, while higher spatial resolution does not generally improve the PM estimation. Ground-based Sun Photometer (SP) measurements are used to validate the satellite-based AOD in the study region and to discuss the impact of aerosols' micro-physical properties in the empirical models. A lower error limit of 30 to 60% in the PM10 assessment from space is estimated in the study area as a result of AOD uncertainties, variability of aerosols properties and the heterogeneity of ground measurement sites. It is concluded that SEVIRI has a similar capacity to map PM as sensors on board polar-orbiting platforms, with the advantage of a higher number of observations. However, the accuracy represents a serious limitation to the applicability of satellites for ground PM mapping, especially in mountainous areas.

The simultaneous role of an alveolus as flow mixer and flow feeder for the deposition of inhaled submicron particles

In an effort to understand the fate of inhaled submicron particles in the small sacs, or alveoli, comprising the gas-exchange region of the lung, we calculated the flow in three-dimensional (3D) rhythmically expanding models of alveolated ducts. Since convection toward the alveolar walls is a precursor to particle deposition, it was the goal of this paper to investigate the streamline maps' dependence upon alveoli location along the acinar tree. On the alveolar midplane, the recirculating flow pattern exhibited closed streamlines with a stagnation saddle point. Off the midplane we found no closed streamlines but nested, funnel-like, spiral, structures (reminiscent of Russian nesting dolls) that were directed towards the expanding walls in inspiration, and away from the contracting walls in expiration. These nested, funnel-like, structures were surrounded by air that flowed into the cavity from the central channel over inspiration and flowed from the cavity to the central channel over expiration. We also found that fluid particle tracks exhibited similar nested funnel-like spiral structures. We conclude that these unique alveolar flow structures may be of importance in enhancing deposition. In addition, due to inertia, the nested, funnel-like, structures change shape and position slightly during a breathing cycle, resulting in flow mixing. Also, each inspiration feeds a fresh supply of particle-laden air from the central channel to the region surrounding the mixing region. Thus, this combination of flow mixer and flow feeder makes each individual alveolus an effective mixing unit, which is likely to play an important role in determining the overall efficiency of convective mixing in the acinus.

Correspondence establishment in statistical modeling of shapes with arbitrary topology

Correspondence establishment is a key step in statistical shape model building. There are several automated methods for solving this problem in 3D, but they usually can only handle objects with simple topology, like that of a sphere or a disc. We propose an extension to correspondence establishment over a population based on the optimization of the minimal description length function, allowing considering objects with arbitrary topology. Instead of using a fixed structure of kernel placement on a sphere for the systematic manipulation of point landmark positions, we rely on an adaptive, hierarchical organization of surface patches. This hierarchy can be built on surfaces of arbitrary topology and the resulting patches are used as a basis for a consistent, multi-scale modification of the surfaces' parameterization, based on point distribution models. The feasibility of the approach is demonstrated on synthetic models with different topologies.

Implementation of monotonic higher order upwind scheme in KIVA 4

KIVA is a FORTRAN code developed by Los Alamos national lab to simulate complete engine cycle. KIVA is a flow solver code which is used to perform calculation of properties in a fluid flow field. It involves using various numerical schemes and methods to solve the Navier-Stokes equation. This project involves improving the accuracy of one such scheme by upgrading it to a higher order scheme. The numerical scheme to be modified is used in the critical final stage calculation called as rezoning phase. The primitive objective of this project is to implement a higher order numerical scheme, to validate and verify that the new scheme is better than the existing scheme. The latest version of the KIVA family (KIVA 4) is used for implementing the higher order scheme to support handling the unstructured mesh. The code is validated using the traditional shock tube problem and the results are verified to be more accurate than the existing schemes in reference with the analytical result. The convection test is performed to compare the computational accuracy on convective transfer; it is found that the new scheme has less numerical diffusion compared to the existing schemes. A four valve pentroof engine, an example case of KIVA package is used as application to ensure the stability of the scheme in practical application. The results are compared for the temperature profile. In spite of all the positive results, the numerical scheme implemented has a downside of consuming more CPU time for the computational analysis. The detailed comparison is provided. However, in an overview, the implementation of the higher order scheme in the latest code KIVA 4 is verified to be successful and it gives better results than the existing scheme which satisfies the objective of this project.

Predicting the Mechanical Properties of Carbon-Based Materials Using Molecular Dynamics

The development of innovative carbon-based materials can be greatly facilitated by molecular modeling techniques. Although molecular modeling has been used extensively to predict elastic properties of materials, modeling of more complex phenomenon such as fracture has only recently been possible with the development of new force fields such as ReaxFF, which is used in this work. It is not fully understood what molecular modeling parameters such as thermostat type, thermostat coupling, time step, system size, and strain rate are required for accurate modeling of fracture. Selection of modeling parameters to model fracture can be difficult and non-intuitive compared to modeling elastic properties using traditional force fields, and the errors generated by incorrect parameters may be non-obvious. These molecular modeling parameters are systematically investigated and their effects on the fracture of well-known carbon materials are analyzed. It is determined that for coupling coefficients of 250 fs and greater do not result in substantial differences in the stress-strain response of the materials using any thermostat type. A time step of 0.5 fs of smaller is required for accurate results. Strain rates greater than 2.2 ns-1 are sufficient to obtain repeatable results with slower strain rates for the materials studied. The results of this study indicate that further refinement of the Chenoweth parameter set is required to accurately predict the mechanical response of carbon-based systems. The ReaxFF has been used extensively to model systems in which bond breaking and formation occur. In particular ReaxFF has been used to model reactions of small molecules. Some elastic and fracture properties have been successfully modeled using ReaxFF in materials such as silicon and some metals. However, it is not clear if current parameterizations for ReaxFF are able to accurately reproduce the elastic and fracture properties of carbon materials. The stress-strain response of a new ReaxFF parameterization is compared to the previous parameterization and density functional theory results for well-known carbon materials. The new ReaxFF parameterization makes xv substantial improvements to the predicted mechanical response of carbon materials, and is found to be suitable for modeling the mechanical response of carbon materials. Finally, a new material composed of carbon nanotubes within an amorphous carbon (AC) matrix is modeled using the ReaxFF. Various parameters that may be experimentally controlled are investigated such as nanotube bundling, comparing multi-walled nanotube with single-walled nanotubes, and degree of functionalization of the nanotubes. Elastic and fracture properties are investigated for the composite systems and compared to results of pure-nanotube and pure-AC models. It is found that the arrangement of the nanotubes and degree of crosslinking may substantially affect the properties of the systems, particularly in the transverse directions.