Normaalijakaumaan perustuva mutaatio-operaatio differentiaalievoluutioalgoritmiin

Evoluutioalgoritmit ovat viime vuosina osoittautuneet tehokkaiksi menetelmiksi globaalien optimointitehtävien ratkaisuun. Niiden vahvuutena on etenkin yleiskäyttöisyys ja kyky löytää globaali ratkaisu juuttumatta optimoitavan tavoitefunktion paikallisiin optimikohtiin. Tässä työssä on tavoitteena kehittää uusi, normaalijakaumaan perustuva mutaatio-operaatio differentiaalievoluutioalgoritmiin, joka on eräs uusimmista evoluutiopohjaisista optimointialgoritmeista. Menetelmän oletetaan vähentävän entisestään sekä populaation ennenaikaisen suppenemisen, että algoritmin tilojen juuttumisen riskiä ja se on teoreettisesti osoitettavissa suppenevaksi. Tämä ei päde alkuperäisen differentiaalievoluution tapauksessa, koska on voitu osoittaa, että sen tilanmuutokset voivat pienellä todennäköisyydellä juuttua. Työssä uuden menetelmän toimintaa tarkastellaan kokeellisesti käyttäen testiongelmina monirajoiteongelmia. Rajoitefunktioiden käsittelyyn käytetään Jouni Lampisen kehittämää, Pareto-optimaalisuuden periaatteeseen perustuvaa menetelmää. Samalla saadaan kerättyä lisää kokeellista näyttöä myös tämän menetelmän toiminnasta. Kaikki käytetyt testiongelmat kyettiin ratkaisemaan sekä alkuperäisellä differentiaalievoluutiolla, että uutta mutaatio-operaatiota käyttävällä versiolla. Uusi menetelmä osoittautui kuitenkin luotettavammaksi sellaisissa tapauksissa, joissa alkuperäisellä algoritmilla oli vaikeuksia. Lisäksi useimmat ongelmat kyettiin ratkaisemaan luotettavasti pienemmällä populaation koolla kuin alkuperäistä differentiaalievoluutiota käytettäessä. Uuden menetelmän käyttö myös mahdollistaa paremmin sellaisten kontrolliparametrien käytön, joilla hausta saadaan rotaatioinvariantti. Laskennallisesti uusi menetelmä on hieman alkuperäistä differentiaalievoluutiota raskaampi ja se tarvitsee yhden kontrolliparametrin enemmän. Uusille kontrolliparametreille määritettiin kuitenkin mahdollisimman yleiskäyttöiset arvot, joita käyttämällä on mahdollista ratkaista suuri joukko erilaisia ongelmia.

Populaation monimuotoisuuden mittaaminen liukulukukoodatuissa evoluutioalgoritmeissa

Diplomityössä esitetään menetelmä populaation monimuotoisuuden mittaamiseen liukulukukoodatuissa evoluutioalgoritmeissa, ja tarkastellaan kokeellisesti sen toimintaa. Evoluutioalgoritmit ovat populaatiopohjaisia menetelmiä, joilla pyritään ratkaisemaan optimointiongelmia. Evoluutioalgoritmeissa populaation monimuotoisuuden hallinta on välttämätöntä, jotta suoritettu haku olisi riittävän luotettavaa ja toisaalta riittävän nopeaa. Monimuotoisuuden mittaaminen on erityisen tarpeellista tutkittaessa evoluutioalgoritmien dynaamista käyttäytymistä. Työssä tarkastellaan haku- ja tavoitefunktioavaruuden monimuotoisuuden mittaamista. Toistaiseksi ei ole ollut olemassa täysin tyydyttäviä monimuotoisuuden mittareita, ja työn tavoitteena on kehittää yleiskäyttöinen menetelmä liukulukukoodattujen evoluutioalgoritmien suhteellisen ja absoluuttisen monimuotoisuuden mittaamiseen hakuavaruudessa. Kehitettyjen mittareiden toimintaa ja käyttökelpoisuutta tarkastellaan kokeellisesti ratkaisemalla optimointiongelmia differentiaalievoluutioalgoritmilla. Toteutettujen mittareiden toiminta perustuu keskihajontojen laskemiseen populaatiosta. Keskihajonnoille suoritetaan skaalaus, joko alkupopulaation tai nykyisen populaation suhteen, riippuen lasketaanko absoluuttista vai suhteellista monimuotoisuutta. Kokeellisessa tarkastelussa havaittiin kehitetyt mittarit toimiviksi ja käyttökelpoisiksi. Tavoitefunktion venyttäminen koordinaattiakseleiden suunnassa ei vaikuta mittarin toimintaan. Myöskään tavoitefunktion kiertäminen koordinaatistossa ei vaikuta mittareiden tuloksiin. Esitetyn menetelmän aikakompleksisuus riippuu lineaarisesti populaation koosta, ja mittarin toiminta on siten nopeaa suuriakin populaatioita käytettäessä. Suhteellinen monimuotoisuus antaa vertailukelpoisia tuloksia riippumatta parametrien lukumäärästä tai populaation koosta.

Conservation Genetics of Exploited Finnish Salmonid Fishes

Genetic diversity is one of the levels of biodiversity that the World Conservation Union (IUCN) has recognized as being important to preserve. This is because genetic diversity is fundamental to the future evolution and to the adaptive flexibility of a species to respond to the inherently dynamic nature of the natural world. Therefore, the key to maintaining biodiversity and healthy ecosystems is to identify, monitor and maintain locally-adapted populations, along with their unique gene pools, upon which future adaptation depends. Thus, conservation genetics deals with the genetic factors that affect extinction risk and the genetic management regimes required to minimize the risk. The conservation of exploited species, such as salmonid fishes, is particularly challenging due to the conflicts between different interest groups. In this thesis, I conduct a series of conservation genetic studies on primarily Finnish populations of two salmonid fish species (European grayling, Thymallus thymallus, and lake-run brown trout, Salmo trutta) which are popular recreational game fishes in Finland. The general aim of these studies was to apply and develop population genetic approaches to assist conservation and sustainable harvest of these populations. The approaches applied included: i) the characterization of population genetic structure at national and local scales; ii) the identification of management units and the prioritization of populations for conservation based on evolutionary forces shaping indigenous gene pools; iii) the detection of population declines and the testing of the assumptions underlying these tests; and iv) the evaluation of the contribution of natural populations to a mixed stock fishery. Based on microsatellite analyses, clear genetic structuring of exploited Finnish grayling and brown trout populations was detected at both national and local scales. Finnish grayling were clustered into three genetically distinct groups, corresponding to northern, Baltic and south-eastern geographic areas of Finland. The genetic differentiation among and within population groups of grayling ranged from moderate to high levels. Such strong genetic structuring combined with low genetic diversity strongly indicates that genetic drift plays a major role in the evolution of grayling populations. Further analyses of European grayling covering the majority of the species’ distribution range indicated a strong global footprint of population decline. Using a coalescent approach the beginning of population reduction was dated back to 1 000-10 000 years ago (ca. 200-2 000 generations). Forward simulations demonstrated that the bottleneck footprints measured using the M ratio can persist within small populations much longer than previously anticipated in the face of low levels of gene flow. In contrast to the M ratio, two alternative methods for genetic bottleneck detection identified recent bottlenecks in six grayling populations that warrant future monitoring. Consistent with the predominant role of random genetic drift, the effective population size (N_e) estimates of all grayling populations were very low with the majority of N_e estimates below 50. Taken together, highly structured local populations, limited gene flow and the small N_e of grayling populations indicates that grayling populations are vulnerable to overexploitation and, hence, monitoring and careful management using the precautionary principles is required not only in Finland but throughout Europe. Population genetic analyses of lake-run brown trout populations in the Inari basin (northernmost Finland) revealed hierarchical population structure where individual populations were clustered into three population groups largely corresponding to different geographic regions of the basin. Similar to my earlier work with European grayling, the genetic differentiation among and within population groups of lake-run brown trout was relatively high. Such strong differentiation indicated that the power to determine the relative contribution of populations in mixed fisheries should be relatively high. Consistent with these expectations, high accuracy and precision in mixed stock analysis (MSA) simulations were observed. Application of MSA to indigenous fish caught in the Inari basin identified altogether twelve populations that contributed significantly to mixed stock fisheries with the Ivalojoki river system being the major contributor (70%) to the total catch. When the contribution of wild trout populations to the fisheries was evaluated regionally, geographically nearby populations were the main contributors to the local catches. MSA also revealed a clear separation between the lower and upper reaches of Ivalojoki river system – in contrast to lower reaches of the Ivalojoki river that contributed considerably to the catch, populations from the upper reaches of the Ivalojoki river system (>140 km from the river mouth) did not contribute significantly to the fishery. This could be related to the available habitat size but also associated with a resident type life history and increased cost of migration. The studies in my thesis highlight the importance of dense sampling and wide population coverage at the scale being studied and also demonstrate the importance of critical evaluation of the underlying assumptions of the population genetic models and methods used. These results have important implications for conservation and sustainable fisheries management of Finnish populations of European grayling and brown trout in the Inari basin.

Plant-Herbivore Interaction in a Fragmented Landscape: Local Adaptation and Inbreeding

Reciprocal selection between interacting species is a major driver of biodiversity at both the genetic and the species level. This reciprocal selection, or coevolution, has led to the diversification of two highly diverse and abundant groups of organisms, flowering plants and their insect herbivores. In heterogeneous environments, the outcome of coevolved species interactions is influenced by the surrounding community and/or the abiotic environment. The process of adaptation allows species to adapt to their local conditions and to local populations of interacting species. However, adaptation can be disrupted or slowed down by an absence of genetic variation or by increased inbreeding, together with the following inbreeding depression, both of which are common in small and isolated populations that occur in fragmented environments. I studied the interaction between a long-lived plant Vincetoxicum hirundinaria and its specialist herbivore Abrostola asclepiadis in the southwestern archipelago of Finland. I focused on mutual local adaptation of plants and herbivores, which is a demonstration of reciprocal selection between species, a prerequisite for coevolution. I then proceeded to investigate the processes that could potentially hamper local adaptation, or species interaction in general, when the population size is small. I did this by examining how inbreeding of both plants and herbivores affects traits that are important for interaction, as well as among-population variation in the effects of inbreeding. In addition to bi-parental inbreeding, in plants inbreeding can arise from self-fertilization which has important implications for mating system evolution. I found that local adaptation of the plant to its herbivores varied among populations. Local adaptation of the herbivore varied among populations and years, being weaker in populations that were most connected. Inbreeding caused inbreeding depression in both plants and herbivores. In some populations inbreeding depression in herbivore biomass was stronger in herbivores feeding on inbred plants than in those feeding on outbred ones. For plants it was the other way around: inbreeding depression in anti-herbivore resistance decreased when the herbivores were inbred. Underlying some of the among-population variation in the effects of inbreeding is variation in plant phenolic compounds. However, variation in the modification of phenolic compounds in the digestive tract of the herbivore did not explain the inbreeding depression in herbivore biomass. Finally, adult herbivores had a preference for outbred host plants for egg deposition, and herbivore inbreeding had a positive effect on egg survival when the eggs were exposed to predators and parasitoids. These results suggest that plants and herbivores indeed exert reciprocal selection, as demonstrated by the significant local adaptation of V. hirundinaria and A. asclepiadis to one another. The most significant cause of disruption of the local adaptation of herbivore populations was population connectivity, and thus probably gene flow. In plants local adaptation tended to increase with increasing genetic variation. Whether or not inbreeding depression occurred varied according to the life-history stage of the herbivore and/or the plant trait in question. In addition, the effects of inbreeding strongly depended on the population. Taken together, inbreeding modified plant-herbivore interactions at several different levels, and can thus affect the strength of reciprocal selection between species. Thus inbreeding has the potential to affect the outcome of coevolution.

Implementation of population balances in simulation of gas-liquid reactors using a CFD-PBM coupled approach

In bubbly flow simulations, bubble size distribution is an important factor in determination of hydrodynamics. Beside hydrodynamics, it is crucial in the prediction of interfacial area available for mass transfer and in the prediction of reaction rate in gas-liquid reactors such as bubble columns. Solution of population balance equations is a method which can help to model the size distribution by considering continuous bubble coalescence and breakage. Therefore, in Computational Fluid Dynamic simulations it is necessary to couple CFD and Population Balance Model (CFD-PBM) to get reliable distribution. In the current work a CFD-PBM coupled model is implemented as FORTRAN subroutines in ANSYS CFX 10 and it has been tested for bubbly flow. This model uses the idea of Multi Phase Multi Size Group approach which was previously presented by Sha et al. (2006) [18]. The current CFD-PBM coupled method considers inhomogeneous flow field for different bubble size groups in the Eulerian multi-dispersed phase systems. Considering different velocity field for bubbles can give the advantageof more accurate solution of hydrodynamics. It is also an improved method for prediction of bubble size distribution in multiphase flow compared to available commercial packages.

Gas-liquid mass transfer in bubbly flow: Estimation of mass transfer, bubble size and reactor performance in various applications

Gas-liquid mass transfer is an important issue in the design and operation of many chemical unit operations. Despite its importance, the evaluation of gas-liquid mass transfer is not straightforward due to the complex nature of the phenomena involved. In this thesis gas-liquid mass transfer was evaluated in three different gas-liquid reactors in a traditional way by measuring the volumetric mass transfer coefficient (kLa). The studied reactors were a bubble column with a T-junction two-phase nozzle for gas dispersion, an industrial scale bubble column reactor for the oxidation of tetrahydroanthrahydroquinone and a concurrent downflow structured bed.The main drawback of this approach is that the obtained correlations give only the average volumetric mass transfer coefficient, which is dependent on average conditions. Moreover, the obtained correlations are valid only for the studied geometry and for the chemical system used in the measurements. In principle, a more fundamental approach is to estimate the interfacial area available for mass transfer from bubble size distributions obtained by solution of population balance equations. This approach has been used in this thesis by developing a population balance model for a bubble column together with phenomenological models for bubble breakage and coalescence. The parameters of the bubble breakage rate and coalescence rate models were estimated by comparing the measured and calculated bubble sizes. The coalescence models always have at least one experimental parameter. This is because the bubble coalescence depends on liquid composition in a way which is difficult to evaluate using known physical properties. The coalescence properties of some model solutions were evaluated by measuring the time that a bubble rests at the free liquid-gas interface before coalescing (the so-calledpersistence time or rest time). The measured persistence times range from 10 msup to 15 s depending on the solution. The coalescence was never found to be instantaneous. The bubble oscillates up and down at the interface at least a coupleof times before coalescence takes place. The measured persistence times were compared to coalescence times obtained by parameter fitting using measured bubble size distributions in a bubble column and a bubble column population balance model. For short persistence times, the persistence and coalescence times are in good agreement. For longer persistence times, however, the persistence times are at least an order of magnitude longer than the corresponding coalescence times from parameter fitting. This discrepancy may be attributed to the uncertainties concerning the estimation of energy dissipation rates, collision rates and mechanisms and contact times of the bubbles.

Size Effect and Notch Size Effect in Metal Fatigue

It is a well known phenomenon that the constant amplitude fatigue limit of a large component is lower than the fatigue limit of a small specimen made of the same material. In notched components the opposite occurs: the fatigue limit defined as the maximum stress at the notch is higher than that achieved with smooth specimens. These two effects have been taken into account in most design handbooks with the help of experimental formulas or design curves. The basic idea of this study is that the size effect can mainly be explained by the statistical size effect. A component subjected to an alternating load can be assumed to form a sample of initiated cracks at the end of the crack initiation phase. The size of the sample depends on the size of the specimen in question. The main objective of this study is to develop a statistical model for the estimation of this kind of size effect. It was shown that the size of a sample of initiated cracks shall be based on the stressed surface area of the specimen. In case of varying stress distribution, an effective stress area must be calculated. It is based on the decreasing probability of equally sized initiated cracks at lower stress level. If the distribution function of the parent population of cracks is known, the distribution of the maximum crack size in a sample can be defined. This makes it possible to calculate an estimate of the largest expected crack in any sample size. The estimate of the fatigue limit can now be calculated with the help of the linear elastic fracture mechanics. In notched components another source of size effect has to be taken into account. If we think about two specimens which have similar shape, but the size is different, it can be seen that the stress gradient in the smaller specimen is steeper. If there is an initiated crack in both of them, the stress intensity factor at the crack in the larger specimen is higher. The second goal of this thesis is to create a calculation method for this factor which is called the geometric size effect. The proposed method for the calculation of the geometric size effect is also based on the use of the linear elastic fracture mechanics. It is possible to calculate an accurate value of the stress intensity factor in a non linear stress field using weight functions. The calculated stress intensity factor values at the initiated crack can be compared to the corresponding stress intensity factor due to constant stress. The notch size effect is calculated as the ratio of these stress intensity factors. The presented methods were tested against experimental results taken from three German doctoral works. Two candidates for the parent population of initiated cracks were found: the Weibull distribution and the log normal distribution. Both of them can be used successfully for the prediction of the statistical size effect for smooth specimens. In case of notched components the geometric size effect due to the stress gradient shall be combined with the statistical size effect. The proposed method gives good results as long as the notch in question is blunt enough. For very sharp notches, stress concentration factor about 5 or higher, the method does not give sufficient results. It was shown that the plastic portion of the strain becomes quite high at the root of this kind of notches. The use of the linear elastic fracture mechanics becomes therefore questionable.