The nonplanar peptide unit III. Quantum chemical calculations for related compounds and experimental X-ray diffraction data

The possible nonplanar distortions of the amide group in formamide, acetamide, N-methylacetamide, and N-ethylacetamide have been examined using CNDO/2 and INDO methods. The predictions from these methods are compared with the results obtained from X-ray and neutron diffraction studies on crystals of small open peptides, cyclic peptides, and amides. It is shown that the INDO results are in good agreement with observations, and that the dihedral angles N and defining the nonplanarity of the amide unit are correlated approximately by the relation N = -2, while C is small and uncorrelated with . The present study indicates that the nonplanar distortions at the nitrogen atom of the peptide unit may have to be taken into consideration, in addition to the variation in the dihedral angles (,), in working out polypeptide and protein structures.

Application of ab initio molecular orbital calculations to the structural moieties of carbohydrates. 3

Ab initio RHF/4-31G level molecular orbital calculations have been carried out on dimethoxymethane as a model compound for the acetal moiety in methyl pyranosides. The calculations are consistent with the predictions of the anomeric effect and the exo-anomeric effect. They reproduce very successfully the differences in molecular geometry observed by x-ray and neutron diffraction of single crystals of the methyl cy-D- and methyl 0-D-pyranosides. Calculations carried out at the 6-3 1G* level for methanediol confirm the earlier calculations at the 4-31G level, with smaller energy differences between the four staggered conformations.

The problem of liquid droplet combustion-reexamination

The simple quasi-steady analysis of the combustion of a liquid fuel droplet in an oxidising atmosphere provides unsatisfactory explanations for several experimental observations. It's prediction of values for the burning constant (K), the flame-to-droplet diameter ratio ( ) and the flame temperature (Tf) have been found to be amgibuous if not completely inaccurate. A critical survey of the literature has led us to a detailed examination of the effects of unsteadiness and variable properties. The work published to date indicates that the gas-phase unsteadiness is relatively short and therefore quite insignificant.A new theoretical analysis based on heat transfer within the droplet is presented here. It shows that the condensed-phase unsteadiness lasts for about 20â??25% of the total burning time. It is concluded that the discrepancies between experimental observations and the predictions of the constant-property quasi-steady analysis cannot be attributed either to gas-phase or condensed-phase unsteadiness.An analytical model of quasi-steady droplet combustion with variable thermodynamic and transport properties and non-unity Lewis numbers will be examined. Further findings reveal a significant improvement in the prediction of combustion parameters, particularly of K, when consideration is given to variations of cp and λ with the temperature and concentrations of several species. Tf is accurately predicted when the required conditions of incomplete combustion or low ( ) at the flame are met. Further refinement through realistic Lewis numbers predicts ( ) meaningfully.

Evaluation of k-epsilon and RNG turbulence models for confined swirling and non-swirling flow

In a very recent study [1] the Renormalisation Group (RNG) turbulence model was used to obtain flow predictions in a strongly swirling quarl burner, and was found to perform well in predicting certain features that are not well captured using less sophisticated models of turbulence. The implication is that the RNG approach should provide an economical and reliable tool for the prediction of swirling flows in combustor and furnace geometries commonly encountered in technological applications. To test this hypothesis the present work considers flow in a model furnace for which experimental data is available [2]. The essential features of the flow which differentiate it from the previous study [1] are that the annular air jet entry is relatively narrow and the base wall of the cylindrical furnace is at 90 degrees to the inlet pipe. For swirl numbers of order 1 the resulting flow is highly complex with significant inner and outer recirculation regions. The RNG and standard k-epsilon models are used to model the flow for both swirling and non-swirling entry jets and the results compared with experimental data [2]. Near wall viscous effects are accounted for in both models via the standard wall function formulation [3]. For the RNG model, additional computations with grid placement extending well inside the near wall viscous-affected sublayer are performed in order to assess the low Reynolds number capabilities of the model.

Computation of confined swirling flow using RNG and k-epsilon turbulence models

In this work we numerically model isothermal turbulent swirling flow in a cylindrical burner. Three versions of the RNG k-epsilon model are assessed against performance of the standard k-epsilon model. Sensitivity of numerical predictions to grid refinement, differing convective differencing schemes and choice of (unknown) inlet dissipation rate, were closely scrutinised to ensure accuracy. Particular attention is paid to modelling the inlet conditions to within the range of uncertainty of the experimental data, as model predictions proved to be significantly sensitive to relatively small changes in upstream flow conditions. We also examine the characteristics of the swirl--induced recirculation zone predicted by the models over an extended range of inlet conditions. Our main findings are: - (i) the standard k-epsilon model performed best compared with experiment; - (ii) no one inlet specification can simultaneously optimize the performance of the models considered; - (iii) the RNG models predict both single-cell and double-cell IRZ characteristics, the latter both with and without additional internal stagnation points. The first finding indicates that the examined RNG modifications to the standard k-e model do not result in an improved eddy viscosity based model for the prediction of swirl flows. The second finding suggests that tuning established models for optimal performance in swirl flows a priori is not straightforward. The third finding indicates that the RNG based models exhibit a greater variety of structural behaviour, despite being of the same level of complexity as the standard k-e model. The plausibility of the predicted IRZ features are discussed in terms of known vortex breakdown phenomena.

Computation of turbulent flow in an IFRF quarl burner

A computational model for isothermal axisymmetric turbulent flow in a quarl burner is set up using the CFD package FLUENT, and numerical solutions obtained from the model are compared with available experimental data. A standard k-e model and and two versions of the RNG k-e model are used to model the turbulence. One of the aims of the computational study is to investigate whether the RNG based k-e turbulence models are capable of yielding improved flow predictions compared with the standard k-e turbulence model. A difficulty is that the flow considered here features a confined vortex breakdown which can be highly sensitive to flow behaviour both upstream and downstream of the breakdown zone. Nevertheless, the relatively simple confining geometry allows us to undertake a systematic study so that both grid-independent and domain-independent results can be reported. The systematic study includes a detailed investigation of the effects of upstream and downstream conditions on the predictions, in addition to grid refinement and other tests to ensure that numerical error is not significant. Another important aim is to determine to what extent the turbulence model predictions can provide us with new insights into the physics of confined vortex breakdown flows. To this end, the computations are discussed in detail with reference to known vortex breakdown phenomena and existing theories. A major conclusion is that one of the RNG k-e models investigated here is able to correctly capture the complex forward flow region inside the recirculating breakdown zone. This apparently pathological result is in stark contrast to the findings of previous studies, most of which have concluded that either algebraic or differential Reynolds stress modelling is needed to correctly predict the observed flow features. Arguments are given as to why an isotropic eddy-viscosity turbulence model may well be able to capture the complex flow structure within the recirculating zone for this flow setup. With regard to the flow physics, a major finding is that the results obtained here are more consistent with the view that confined vortex breakdown is a type of axisymmetric boundary layer separation, rather than a manifestation of a subcritical flow state.

Analysis of turbulent confined highly swirling flow

We report here a CFD model of highly swirling flow in a quarl burner using three versions of the k-epsilon model. Results for the recirculating zone, the bounding shear layer and the downstream flow are presented. We discuss, with suitable qualifications, how the model predictions can inform our understanding of this class of flows.

Studies on the Effects of Property Taxation, Rent Control and Housing Allowances

Tämä väitöskirja koostuu asuntomarkkinoiden taloustieteellistä analyysia esittelevästä johdantoluvusta ja kolmesta tutkimuksesta, joissa analysoidaan asuntomarkkinoihin vaikuttavia politiikkatoimenpiteitä. Luvussa 2 tutkitaan Suomen kiinteistöverojärjestelmän vaikutusta asuntorakentamiseen. Vuonna 2001 tehtiin uudistus, jonka myötä kunnat voivat verottaa rakentamatonta asuintonttia korkeammalla veroasteella kuin rakennettua tonttia. Maanomistajan rakentamispäätöksen teoreettisen mallin mukaan rakentamattoman tontin korotettu kiinteistöveron pitäisi nopeuttaa rakentamista, mutta toisaalta myös rakentamiseen investoitu rahamäärä saattaa muuttua. Asuintonttien kiinteistöverojen yleinen taso ei vaikuta maanomistajan käyttäytymiseen, sillä tontin verotusarvo ei riipu rakentamispäätöksestä. Vain rakentamattoman ja rakennetun tontin veroasteiden erolla on merkitystä. Empiiriset tulokset ovat sopusoinnussa teorian kanssa. Tulosten mukaan prosenttiyksikön nousu rakentamattoman ja rakennetun tontin veroasteiden erossa lisää omakotialoitusten määrää viidellä prosentilla lyhyellä aikavälillä. Luvussa 3 analysoidaan vuokrasääntelystä vuokralaisille aiheutuvia hyötyjä ja haittoja. Vuokrasäännellyissä asunnoissa asuvat kotitaloudet hyötyvät vuokrasääntelystä alhaisen vuokran muodossa. Heille saattaa kuitenkin koitua myös haittaa siitä, että toiveita vastaavan asunnon löytäminen on vuokrasääntelytilanteessa vaikeaa, koska vapaille asunnoille on suuri määrä ottajia. Vapaarahoitteisen vuokra-asuntokannan vuokrien sääntely purettiin Suomessa asteittain vuosina 1992–1995. Tutkimuksen empiiriset tulokset viittaavat siihen, että vuokrasääntelyn aiheuttamista suurista eroista halutun ja todellisen asuntokulutuksen välillä koituvat hyvinvointitappiot kumosivat merkittävän osan matalien vuokrien hyödyistä vuokralaisille. Luvussa 4 tutkitaan Suomen asumistukijärjestelmän kannustinvaikutuksia. Asumistuen määrää rajoittavat asunnon pinta-alalle ja neliövuokralle asetetut ylärajat. Neliövuokrarajoite voidaan tulkita asumisen laatua rajoittavana tekijänä. Tutkimuksen teoreettisessa osassa osoitetaan, että asumistukijärjestelmä luo vahvat kannustimet muuttaa asuntoihin, joissa pinta-ala- ja laaturajoitteet purevat. Empiiristen tulosten mukaan asumistukeen oikeutetut kotitaloudet eivät näytä reagoivan kannusteisiin. Tukeen oikeutettujen kotitalouksien asumisvalinnat suhteessa pinta-ala ja laaturajoitteisiin vastaavat muiden kotitalouksien valintoja ja asunnonvaihdon mahdollistama potentiaalinen asumistuen lisäys ei nosta muuttotodennäköisyyttä. Muuttamiseen liittyvät kustannukset ja vajavaiset tiedot tukijärjestelmästä saattavat selittää heikkoa reagointia asumistuen luomiin kannustimiin. Toinen mahdollinen selitys on asumistuen vajaakäyttö. Tutkimuksen mukaan vain 70–80 prosenttia asumistukeen oikeutetuista kotitalouksista nostaa tukea. Asumistuen hyödyntämisen todennäköisyys riippuu koulutustasosta, tuen määrästä ja tulo-odotuksista.

The Macroeconomic Effects of Fiscal Policy in a Small Open Economy under a Flexible Exchange Rate Regime

This licentiate's thesis analyzes the macroeconomic effects of fiscal policy in a small open economy under a flexible exchange rate regime, assuming that the government spends exclusively on domestically produced goods. The motivation for this research comes from the observation that the literature on the new open economy macroeconomics (NOEM) has focused almost exclusively on two-country global models and the analyses of the effects of fiscal policy on small economies are almost completely ignored. This thesis aims at filling in the gap in the NOEM literature and illustrates how the macroeconomic effects of fiscal policy in a small open economy depend on the specification of preferences. The research method is to present two theoretical model that are extensions to the model contained in the Appendix to Obstfeld and Rogoff (1995). The first model analyzes the macroeconomic effects of fiscal policy, making use of a model that exploits the idea of modelling private and government consumption as substitutes in private utility. The model offers intuitive predictions on how the effects of fiscal policy depend on the marginal rate of substitution between private and government consumption. The findings illustrate that the higher the substitutability between private and government consumption, (i) the bigger is the crowding out effect on private consumption (ii) and the smaller is the positive effect on output. The welfare analysis shows that the less fiscal policy decreases welfare the higher is the marginal rate of substitution between private and government consumption. The second model of this thesis studies how the macroeconomic effects of fiscal policy depend on the elasticity of substitution between traded and nontraded goods. This model reveals that this elasticity a key variable to explain the exchange rate, current account and output response to a permanent rise in government spending. Finally, the model demonstrates that temporary changes in government spending are an effective stabilization tool when used wisely and timely in response to undesired fluctuations in output. Undesired fluctuations in output can be perfectly offset by an opposite change in government spending without causing any side-effects.

The Population Consequences of Sex and Conflict

Natural selection generally operates at the level of the individual, or more specifically at the level of the gene. As a result, individual selection does not always favour traits which benefit the population or species as a whole. The spread of an individual gene may even act to the detriment of the organism in which it finds. Thus selection at the level of the individual can affect processes at the level of the organism, group or even at the level of the species. As most behaviours ultimately affect births, deaths and the distribution of individuals, it seems inevitable that behavioural decisions will have an impact on population dynamics and population densities. Behavioural decisions can often involve costs through allocation of energy into behavioural strategies, such as the investment into armaments involved in fighting over resources or increased mortality due to injury or increased predation risk. Similarly, behaviour may act o to benefit the population, in terms of higher survival and increased fecundity. Examples include increased investment through parental care, choosing a mate based on the nuptial gifts they may supply and choosing territories in the face of competition. Investigating the impact of behaviour on population ecology may seem like a trivial task, but it is likely to have important consequences at different levels. For example, antagonistic behaviour may occasionally become so extreme that it increases the risk of extinction, and such extinction risk may have important implications for conservation. As a corollary, any such behaviour may also act as a macroevolutionary force, weeding out populations with traits which, whilst beneficial to the individuals in the short term, ultimately result in population extinction. In this thesis, I examine how behaviours, specifically conflict and competition over a resource and aspects of behaviour involved in sexual selection, can affect population densities, and what the implications are for the evolution and ecology of the populations in question. It is found that both behaviours related to individual conflict and mating strategies can have an effect at the level of the population, but that various factors, such as a feedback between selection and population densities or macroevolution caused by species extinctions, may act to limit the intensity of conflicts that we observe in nature.

Phytoplankton quantity as an indicator of eutrophication in Finnish coastal waters : Applications within the Water Framework Directive

The tackling of coastal eutrophication requires water protection measures based on status assessments of water quality. The main purpose of this thesis was to evaluate whether it is possible both scientifically and within the terms of the European Union Water Framework Directive (WFD) to assess the status of coastal marine waters reliably by using phytoplankton biomass (ww) and chlorophyll a (Chl) as indicators of eutrophication in Finnish coastal waters. Empirical approaches were used to study whether the criteria, established for determining an indicator, are fulfilled. The first criterion (i) was that an indicator should respond to anthropogenic stresses in a predictable manner and has low variability in its response. Summertime Chl could be predicted accurately by nutrient concentrations, but not from the external annual loads alone, because of the rapid affect of primary production and sedimentation close to the loading sources in summer. The most accurate predictions were achieved in the Archipelago Sea, where total phosphorus (TP) and total nitrogen (TN) alone accounted for 87% and 78% of the variation in Chl, respectively. In river estuaries, the TP mass-balance regression model predicted Chl most accurately when nutrients originated from point-sources, whereas land-use regression models were most accurate in cases when nutrients originated mainly from diffuse sources. The inclusion of morphometry (e.g. mean depth) into nutrient models improved accuracy of the predictions. The second criterion (ii) was associated with the WFD. It requires that an indicator should have type-specific reference conditions, which are defined as "conditions where the values of the biological quality elements are at high ecological status". In establishing reference conditions, the empirical approach could only be used in the outer coastal water types, where historical observations of Secchi depth of the early 1900s are available. The most accurate prediction was achieved in the Quark. In the inner coastal water types, reference Chl, estimated from present monitoring data, are imprecise - not only because of the less accurate estimation method but also because the intrinsic characteristics, described for instance by morphometry, vary considerably inside these extensive inner coastal types. As for phytoplankton biomass, the reference values were less accurate than in the case of Chl, because it was possible to estimate reference conditions for biomass only by using the reconstructed Chl values, not the historical Secchi observations. An paleoecological approach was also applied to estimate annual average reference conditions for Chl. In Laajalahti, an urban embayment off Helsinki, strongly loaded by municipal waste waters in the 1960s and 1970s, reference conditions prevailed in the mid- and late 1800s. The recovery of the bay from pollution has been delayed as a consequence of benthic release of nutrients. Laajalahti will probably not achieve the good quality objectives of the WFD on time.    The third criterion (iii) was associated with coastal management including the resources it has available. Analyses of Chl are cheap and fast to carry out compared to the analyses of phytoplankton biomass and species composition; the fact which has an effect on number of samples to be taken and thereby on the reliability of assessments. However, analyses on phytoplankton biomass and species composition provide more metrics for ecological classification, the metrics which reveal various aspects of eutrophication contrary to what Chl alone does.

Effects of environmental variation on ecological and evolutionary dynamics

Environmental variation is a fact of life for all the species on earth: for any population of any particular species, the local environmental conditions are liable to vary in both time and space. In today's world, anthropogenic activity is causing habitat loss and fragmentation for many species, which may profoundly alter the characteristics of environmental variation in remaining habitat. Previous research indicates that, as habitat is lost, the spatial configuration of remaining habitat will increasingly affect the dynamics by which populations are governed. Through the use of mathematical models, this thesis asks how environmental variation interacts with species properties to influence population dynamics, local adaptation, and dispersal evolution. More specifically, we couple continuous-time continuous-space stochastic population dynamic models to landscape models. We manipulate environmental variation via parameters such as mean patch size, patch density, and patch longevity. Among other findings, we show that a mixture of high and low quality habitat is commonly better for a population than uniformly mediocre habitat. This conclusion is justified by purely ecological arguments, yet the positive effects of landscape heterogeneity may be enhanced further by local adaptation, and by the evolution of short-ranged dispersal. The predicted evolutionary responses to environmental variation are complex, however, since they involve numerous conflicting factors. We discuss why the species that have high levels of local adaptation within their ranges may not be the same species that benefit from local adaptation during range expansion. We show how habitat loss can lead to either increased or decreased selection for dispersal depending on the type of habitat and the manner in which it is lost. To study the models, we develop a recent analytical method, Perturbation expansion, to enable the incorporation of environmental variation. Within this context, we use two methods to address evolutionary dynamics: Adaptive dynamics, which assumes mutations occur infrequently so that the ecological and evolutionary timescales can be separated, and via Genotype distributions, which assume mutations are more frequent. The two approaches generally lead to similar predictions yet, exceptionally, we show how the evolutionary response of dispersal behaviour to habitat turnover may qualitatively depend on the mutation rate.

Assessing uncertainty in pollutant build-up and wash-off processes

Assessing build-up and wash-off process uncertainty is important for accurate interpretation of model outcomes to facilitate informed decision making for developing effective stormwater pollution mitigation strategies. Uncertainty inherent to pollutant build-up and wash-off processes influences the variations in pollutant loads entrained in stormwater runoff from urban catchments. However, build-up and wash-off predictions from stormwater quality models do not adequately represent such variations due to poor characterisation of the variability of these processes in mathematical models. The changes to the mathematical form of current models with the incorporation of process variability, facilitates accounting for process uncertainty without significantly affecting the model prediction performance. Moreover, the investigation of uncertainty propagation from build-up to wash-off confirmed that uncertainty in build-up process significantly influences wash-off process uncertainty. Specifically, the behaviour of particles <150µm during build-up primarily influences uncertainty propagation, resulting in appreciable variations in the pollutant load and composition during a wash-off event.

Influence of uncertainty inherent to heavy metal build-up and wash-off on stormwater quality

Uncertainty inherent to heavy metal build-up and wash-off stems from process variability. This results in inaccurate interpretation of stormwater quality model predictions. The research study has characterised the variability in heavy metal build-up and wash-off processes based on the temporal variations in particle-bound heavy metals commonly found on urban roads. The study outcomes found that the distribution of Al, Cr, Mn, Fe, Ni, Cu, Zn, Cd and Pb were consistent over particle size fractions <150µm and >150µm, with most metals concentrated in the particle size fraction <150µm. When build-up and wash-off are considered as independent processes, the temporal variations in these processes in relation to the heavy metals load are consistent with variations in the particulate load. However, the temporal variations in the load in build-up and wash-off of heavy metals and particulates are not consistent for consecutive build-up and wash-off events that occur on a continuous timeline. These inconsistencies are attributed to interactions between heavy metals and particulates <150µm and >150µm, which are influenced by particle characteristics such as organic matter content. The behavioural variability of particles determines the variations in the heavy metals load entrained in stormwater runoff. Accordingly, the variability in build-up and wash-off of particle-bound pollutants needs to be characterised in the description of pollutant attachment to particulates in stormwater quality modelling. This will ensure the accounting of process uncertainty, and thereby enhancing the interpretation of the outcomes derived from modelling studies.

Genomic approach to organ-specific growth control

Growth is a fundamental aspect of life cycle of all organisms. Body size varies highly in most animal groups, such as mammals. Moreover, growth of a multicellular organism is not uniform enlargement of size, but different body parts and organs grow to their characteristic sizes at different times. Currently very little is known about the molecular mechanisms governing this organ-specific growth. The genome sequencing projects have provided complete genomic DNA sequences of several species over the past decade. The amount of genomic sequence information, including sequence variants within species, is constantly increasing. Based on the universal genetic code, we can make sense of this sequence information as far as it codes proteins. However, less is known about the molecular mechanisms that control expression of genes, and about the variations in gene expression that underlie many pathological states in humans. This is caused in part by lack of information about the second genetic code that consists of the binding specificities of transcription factors and the combinatorial code by which transcription factor binding sites are assembled to form tissue-specific and/or ligand-regulated enhancer elements. This thesis presents a high-throughput assay for identification of transcription factor binding specificities, which were then used to measure the DNA binding profiles of transcription factors involved in growth control. We developed ‘enhancer element locator’, a computational tool, which can be used to predict functional enhancer elements. A genome-wide prediction of human and mouse enhancer elements generated a large database of enhancer elements. This database can be used to identify target genes of signaling pathways, and to predict activated transcription factors based on changes in gene expression. Predictions validated in transgenic mouse embryos revealed the presence of multiple tissue-specific enhancers in mouse c- and N-Myc genes, which has implications to organ specific growth control and tumor type specificity of oncogenes. Furthermore, we were able to locate a variation in a single nucleotide, which carries a susceptibility to colorectal cancer, to an enhancer element and propose a mechanism by which this SNP might be involved in generation of colorectal cancer.