ContinuousMultimodal Global Optimization with Differential Evolution-Based Methods

Metaheuristic methods have become increasingly popular approaches in solving global optimization problems. From a practical viewpoint, it is often desirable to perform multimodal optimization which, enables the search of more than one optimal solution to the task at hand. Population-based metaheuristic methods offer a natural basis for multimodal optimization. The topic has received increasing interest especially in the evolutionary computation community. Several niching approaches have been suggested to allow multimodal optimization using evolutionary algorithms. Most global optimization approaches, including metaheuristics, contain global and local search phases. The requirement to locate several optima sets additional requirements for the design of algorithms to be effective in both respects in the context of multimodal optimization. In this thesis, several different multimodal optimization algorithms are studied in regard to how their implementation in the global and local search phases affect their performance in different problems. The study concentrates especially on variations of the Differential Evolution algorithm and their capabilities in multimodal optimization. To separate the global and local search search phases, three multimodal optimization algorithms are proposed, two of which hybridize the Differential Evolution with a local search method. As the theoretical background behind the operation of metaheuristics is not generally thoroughly understood, the research relies heavily on experimental studies in finding out the properties of different approaches. To achieve reliable experimental information, the experimental environment must be carefully chosen to contain appropriate and adequately varying problems. The available selection of multimodal test problems is, however, rather limited, and no general framework exists. As a part of this thesis, such a framework for generating tunable test functions for evaluating different methods of multimodal optimization experimentally is provided and used for testing the algorithms. The results demonstrate that an efficient local phase is essential for creating efficient multimodal optimization algorithms. Adding a suitable global phase has the potential to boost the performance significantly, but the weak local phase may invalidate the advantages gained from the global phase.

Evaluation of liver regeneration diet supplemented with omega-3 fatty acids: experimental study in rats

Objective: to evaluate liver regeneration in rats after partial hepatectomy of 60% with and without action diet supplemented with fatty acids through the study of the regenerated liver weight, laboratory parameters of liver function and histological study. Methods: thirty-six Wistar rats, males, adults were used, weighing between 195 and 330 g assigned to control and groups. The supplementation group received the diet by gavage and were killed after 24h, 72h and seven days. Evaluation of regeneration occurred through analysis of weight gain liver, serum aspartate aminotransferase, alanine aminotransferase, gamma-glutamyltranspeptidase, and mitosis of the liver stained with H&E. Results: the diet supplemented group showed no statistical difference (p>0.05) on the evolution of weights. Administration of fatty acids post-hepatectomy had significant reduction in gamma glutamyltransferase levels and may reflect liver regeneration. Referring to mitotic index, it did not differ between period of times among the groups. Conclusion: supplementation with fatty acids in rats undergoing 60% hepatic resection showed no significant interference related to liver regeneration.

IgE expression on the surface of B1 and B2 lymphocytes in experimental murine schistosomiasis

In a previous study we monitored the distribution and phenotype expression of B1 cells during the evolution of experimental murine schistosomiasis mansoni and we proposed that the B1 cells were heterogeneous: a fraction which originated in the spleen and followed the migratory pathway to mesenteric ganglia, while the other was the resident peritoneal B1-cell pool. In the present study, we have addressed the question of whether these two B1-lymphocyte populations are involved in the production of the late Ig isotype IgE, which is present in high levels in schistosomal infection. Lymphocyte expression of surface markers and immunoglobulins were monitored by immunofluorescence flow cytometry. Both in the spleen and mesenteric ganglia, the B1 and B2 cells were induced to switch from IgM to IgE in the early Th2-dominated phase of the disease, with an increase of IgE in its later phases. Conversely, peritoneal B1-IgM+ switched to the remaining IgE+ present in high numbers in the peritoneal cavity throughout the disease. We correlated the efficient induction of the expression of late Ig isotypes by B1 cells with high levels of inflammatory cytokines due to the intense host response to the presence of worms and their eggs in the abdominal cavity. In conclusion, B1 cells have a different switch behavior from IgM to IgE indicating that these cell sub-populations depend on the microenvironment.

Towards reverse engineering of Photosystem II: Synergistic Computational and Experimental Approaches

ABSTRACT Photosystem II (PSII) of oxygenic photosynthesis has the unique ability to photochemically oxidize water, extracting electrons from water to result in the evolution of oxygen gas while depositing these electrons to the rest of the photosynthetic machinery which in turn reduces CO2 to carbohydrate molecules acting as fuel for the cell. Unfortunately, native PSII is unstable and not suitable to be used in industrial applications. Consequently, there is a need to reverse-engineer the water oxidation photochemical reactions of PSII using solution-stable proteins. But what does it take to reverse-engineer PSII’s reactions? PSII has the pigment with the highest oxidation potential in nature known as P680. The high oxidation of P680 is in fact the driving force for water oxidation. P680 is made up of a chlorophyll a dimer embedded inside the relatively hydrophobic transmembrane environment of PSII. In this thesis, the electrostatic factors contributing to the high oxidation potential of P680 are described. PSII oxidizes water in a specialized metal cluster known as the Oxygen Evolving Complex (OEC). The pathways that water can take to enter the relatively hydrophobic region of PSII are described as well. A previous attempt to reverse engineer PSII’s reactions using the protein scaffold of E. coli’s Bacterioferritin (BFR) existed. The oxidation potential of the pigment used for the BFR ‘reaction centre’ was measured and the protein effects calculated in a similar fashion to how P680 potentials were calculated in PSII. The BFR-RC’s pigment oxidation potential was found to be 0.57 V, too low to oxidize water or tyrosine like PSII. We suggest that the observed tyrosine oxidation in BRF-RC could be driven by the ZnCe6 di-cation. In order to increase the efficiency of iii tyrosine oxidation, and ultimately oxidize water, the first potential of ZnCe6 would have to attain a value in excess of 0.8 V. The results were used to develop a second generation of BFR-RC using a high oxidation pigment. The hypervalent phosphorous porphyrin forms a radical pair that can be observed using Transient Electron Paramagnetic Resonance (TR-EPR). Finally, the results from this thesis are discussed in light of the development of solar fuel producing systems.

Modeling Metal Protein Complexes from Experimental Extended X-ray Absorption Fine Structure using Computational Intelligence

Experimental Extended X-ray Absorption Fine Structure (EXAFS) spectra carry information about the chemical structure of metal protein complexes. However, pre- dicting the structure of such complexes from EXAFS spectra is not a simple task. Currently methods such as Monte Carlo optimization or simulated annealing are used in structure refinement of EXAFS. These methods have proven somewhat successful in structure refinement but have not been successful in finding the global minima. Multiple population based algorithms, including a genetic algorithm, a restarting ge- netic algorithm, differential evolution, and particle swarm optimization, are studied for their effectiveness in structure refinement of EXAFS. The oxygen-evolving com- plex in S1 is used as a benchmark for comparing the algorithms. These algorithms were successful in finding new atomic structures that produced improved calculated EXAFS spectra over atomic structures previously found.

Systematics and floral evolution of the Dialiinae (Caesalpinioideae), a diverse lineage of tropical legumes

Le clade Dialiinae représente l’une des premières lignées de la sous-famille Caesalpinioideae des Leguminosae. Il se compose de 17 genres (environ 90 espèces), avec des taxons qui sont répandus dans toutes les régions tropicales du monde. Morphologiquement, le groupe comprend un assemblage divers de taxons qui peut représenter une «phase expérimentale» dans l’évolution florale des légumineuses. Différents représentants du clade présentent de la poly-, mono-, et asymétrie, et semblent avoir subi un haut degré de perte d’organe, produisant, dans certains cas, des fleurs extrêmement réduites qui sont à peine reconnaissables comme appartenant à la famille des légumineuses. Afin d’obtenir une image plus claire de l’évolution florale du clade Dialiinae, une phylogénie bien résolue et bien soutenue est nécessaire. Dans le but de créer une telle phylogénie, un total de 37 échantillons d’ADN des Dialiinae a été séquencé pour deux régions chloroplastiques, soit rps16 et trnL. De plus, une étude morphologique complète a été réalisée. Un total de 135 caractères végétatifs et reproductifs a été évalué pour 79 espèces de Dialiinae et pour quatre groupes externes. Les analyses phylogénétiques ont d’abord été effectuées sur un groupe restreint de taxons pour lesquels les trois types de données étaient disponibles. Les nœuds fortement soutenus de cette phylogénie ont ensuite été utilisés comme contrainte pour une seconde analyse de parcimonie avec les données morphologiques d’un ensemble plus important de taxons. Les caractères morphologiques ont été optimisés sur l’un des arbres les plus parcimonieux de cette seconde analyse. Un certain nombre de nouvelles relations au niveau de l’espèce ont été résolues, créant une image plus claire quant à l’évolution de la forme florale dans le temps, particulièrement pour les genres Labichea et Dialium. En plus de leur morphologie florale mature diverse, les Dialiinae sont également très variables dans leur ontogénèse florale, affichant à la fois la perte et la suppression des organes, et présentant une variété de modes d’initiation d’organes. Afin de construire une image plus complète du développement floral et de l’évolution dans ce clade, l’ontogénèse florale de plusieurs espèces non documentées à ce jour a été étudiée. La série complète du développement a été compilée pour six espèces de Dialiinae; quatre de Dialium, ainsi que Poeppigia procera et Mendoravia dumaziana. Le mode et le moment de l’initiation des organes étaient pour la plupart uniforme pour toutes les espèces de Dialium étudiés. Tant pour ce qui est des gains ou des pertes d’organes chez Dialium, une tendance est apparente – l’absence d’organe abaxial. Que ce soit pour les sépales ou les étamines, les gains se produisent toujours en position médiane adaxiale, tandis que les étamines et les pétales perdus sont toujours les organes les plus ventraux. Les taxons étudiés ici illustrent le manque apparent de canalisation du développement observé chez les Caesalpinioideae. Cette plasticité ontogénétique est le reflet de la diversité morphologique au niveau des fleurs tel qu’observée dans l’ensemble de la sous-famille. Une des espèces de Dialiinae, Apuleia leiocarpa, produit une inflorescence andromonoïque, une caractéristique qui est unique en son clade et rare dans les légumineuses dans son ensemble. La microscopie optique et électronique ont été utilisées pour entreprendre une étude détaillée de la morphologie florale de ce taxon. On a constaté que tandis que les fleurs hermaphrodites produisent un seul carpelle et deux étamines, les fleurs staminées produisent trois étamines sans toutefois montrer signe de développement du carpelle. Les inflorescences semblent produire près de quatre fois plus de fleurs staminées que de fleurs hermaphrodites, lesquelles occupent toujours la position centrale de l’inflorescence cymeuse. Ce ratio élevé mâle/bisexuel et la détermination précoce du sexe chez Apuleia sont rares chez les Caesalpinioideae, ce qui suggère que l’andromonoecie se développe dans ce genre comme un moyen d’accroître la dispersion du pollen plutôt qu’en réponse à des limitations de ressources.

Microstructural evolution of primary crystallization in diffusion-controlled grain growth

A model has been developed for evaluating grain size distributions in primary crystallizations where the grain growth is diffusion controlled. The body of the model is grounded in a recently presented mean-field integration of the nucleation and growth kinetic equations, modified conveniently in order to take into account a radius-dependent growth rate, as occurs in diffusion-controlled growth. The classical diffusion theory is considered, and a modification of this is proposed to take into account interference of the diffusion profiles between neighbor grains. The potentiality of the mean-field model to give detailed information on the grain size distribution and transformed volume fraction for transformations driven by nucleation and either interface- or diffusion-controlled growth processes is demonstrated. The model is evaluated for the primary crystallization of an amorphous alloy, giving an excellent agreement with experimental data. Grain size distributions are computed, and their properties are discussed.

Verbal proficiency as fitness indicator: Experimental and comparative research on the evolutionary psychology of language and verbal displays

Summary: Recent research on the evolution of language and verbal displays (e.g., Miller, 1999, 2000a, 2000b, 2002) indicated that language is not only the result of natural selection but serves as a sexually-selected fitness indicator that is an adaptation showing an individual’s suitability as a reproductive mate. Thus, language could be placed within the framework of concepts such as the handicap principle (Zahavi, 1975). There are several reasons for this position: Many linguistic traits are highly heritable (Stromswold, 2001, 2005), while naturally-selected traits are only marginally heritable (Miller, 2000a); men are more prone to verbal displays than women, who in turn judge the displays (Dunbar, 1996; Locke & Bogin, 2006; Lange, in press; Miller, 2000a; Rosenberg & Tunney, 2008); verbal proficiency universally raises especially male status (Brown, 1991); many linguistic features are handicaps (Miller, 2000a) in the Zahavian sense; most literature is produced by men at reproduction-relevant age (Miller, 1999). However, neither an experimental study investigating the causal relation between verbal proficiency and attractiveness, nor a study showing a correlation between markers of literary and mating success existed. In the current studies, it was aimed to fill these gaps. In the first one, I conducted a laboratory experiment. Videos in which an actor and an actress performed verbal self-presentations were the stimuli for counter-sex participants. Content was always alike, but the videos differed on three levels of verbal proficiency. Predictions were, among others, that (1) verbal proficiency increases mate value, but that (2) this applies more to male than to female mate value due to assumed past sex-different selection pressures causing women to be very demanding in mate choice (Trivers, 1972). After running a two-factorial analysis of variance with the variables sex and verbal proficiency as factors, the first hypothesis was supported with high effect size. For the second hypothesis, there was only a trend going in the predicted direction. Furthermore, it became evident that verbal proficiency affects long-term more than short-term mate value. In the second study, verbal proficiency as a menstrual cycle-dependent mate choice criterion was investigated. Basically the same materials as in the former study were used with only marginal changes in the used questionnaire. The hypothesis was that fertile women rate high verbal proficiency in men higher than non-fertile women because of verbal proficiency being a potential indicator of “good genes”. However, no significant result could be obtained in support of the hypothesis in the current study. In the third study, the hypotheses were: (1) most literature is produced by men at reproduction-relevant age. (2) The more works of high literary quality a male writer produces, the more mates and children he has. (3) Lyricists have higher mating success than non-lyric writers because of poetic language being a larger handicap than other forms of language. (4) Writing literature increases a man’s status insofar that his offspring shows a significantly higher male-to-female sex ratio than in the general population, as the Trivers-Willard hypothesis (Trivers & Willard, 1973) applied to literature predicts. In order to test these hypotheses, two famous literary canons were chosen. Extensive biographical research was conducted on the writers’ mating successes. The first hypothesis was confirmed; the second one, controlling for life age, only for number of mates but not entirely regarding number of children. The latter finding was discussed with respect to, among others, the availability of effective contraception especially in the 20th century. The third hypothesis was not satisfactorily supported. The fourth hypothesis was partially supported. For the 20th century part of the German list, the secondary sex ratio differed with high statistical significance from the ratio assumed to be valid for a general population.

Institutions, Behavior and Evolution

The three articles constituting this thesis are for reasons of content or method related to the following three fields in economics: Behavioral Economics, Evolutionary Game Theory and Formal Institutional Economics. A core element of these fields is the concept of individual preferences. Preferences are of central importance for the conceptional framework to analyze human behavior. They form the foundation for the theory of rational choice which is defined by the determination of the choice set and the selection of the most preferred alternative according to some consistency requirements. The theory of rational choice is based on a very simplified description of the problem of choice (object function and constraints). However, that choices depend on many more factors is for instance propagated by psychological theories and is supported by many empirical and experimental studies. This thesis adds to a better understanding of individual behavior to the extent that the evolution of certain characteristics of preferences and their consequences on human behavior forms the overarching theme of the dissertation. The long-term effect of evolutionary forces on a particular characteristic of importance in the theoretical, empirical and experimental economic literature, the concept of inequality aversion, is subject of the article “The evolution of inequality aversion in a simplified game of life” (Chapter 4). The contribution of the article is the overcoming of a restriction of former approaches to analyze the evolution of preferences in very simple environments. By classifying human interaction into three central economic games, the article provides a first step towards a simplified and sufficiently complete description of the interaction environment. Within such an environment the article characterizes the evolutionary stable preference distribution. One result shows, that the interaction of the aforementioned three classes can stabilize a preference of inequality aversion in the subpopulation which is favored in the problem of redistribution. The two remaining articles are concerned with social norms, which dissemination is determined by medium-run forces of cultural evolution. The article “The impact of market innovations on the evolution of social norms: the sustainability case.“ (Chapter 2) studies the interrelation between product innovations which are relevant from a sustainability perspective and an according social norm in consumption. This relation is based on a conformity bias in consumption and the attempt to avoid cognitive dissonances resulting from non-compliant consumption. Among others, it is shown that a conformity bias on the consumption side can lead to multiple equilibria on the side of norm adoption. The article “Evolution of cooperation in social dilemmas: signaling internalized norms.” (Chapter 3) studies the emergence of cooperation in social dilemmas based on the signaling of social norms. The article provides a potential explanation of cooperative behavior, which does not rely on the assumption of structured populations or on the unmotivated ability of social norms to restrict individual actions or strategy spaces. A comprehensive result of the single articles is the explanation of the phenomenon of partial norm adaption or dissemination of preferences. The plurality of the applied approaches with respect to the proximity to the rational choice approach and regarding the underlying evolutionary mechanics is a particular strength of the thesis. It shows the equality of these approaches in their potential to explain the phenomenon of cooperation in environments that provide material incentives for defective behavior. This also points to the need of a unified framework considering the biological and cultural coevolution of preference patterns.

Experimental crop growing in Jordan to develop methodology for the identification of ancient crop irrigation

Crop irrigation has long been recognized as having been important for the evolution of social complexity in several parts of the world. Structural evidence for water management, as in the form of wells, ditches and dams, is often difficult to interpret and may be a poor indicator of past irrigation that may have had no need for such constructions. It would be of considerable value, therefore, to be able to infer past irrigation directly from archaeo-botanical remains, and especially the type of archaeo-botanical remains that are relatively abundant in the archaeological record, such as phytoliths. Building on the pioneering work of Rosen and Wiener (1994), this paper describes a crop-growing experiment designed to explore the impact of irrigation on the formation of phytoliths within cereals. If it can be shown that a systemic and consistent relationship exists between phytolith size, structure and the intensity of irrigation, and if various taphonomic and palaeoenvironmental processes can be controlled for, then the presence of past irrigation can feasibly be inferred from the phytoliths recovered from the archaeological record.

Population genetic models can be used to study the evolution of the interacting behaviours of parents and their progeny

An example of the evolution of the interacting behaviours of parents and progeny is studied using iterative equations linking the frequencies of the gametes produced by the progeny to the frequencies of the gametes in the parental generation. This population genetics approach shows that a model in which both behaviours are determined by a single locus can lead to a stable equilibrium in which the two behaviours continue to segregate. A model in which the behaviours are determined by genes at two separate loci leads eventually to fixation of the alleles at both loci but this can take many generations of selection. Models of the type described in this paper will be needed to understand the evolution of complex behaviour when genomic or experimental information is available about the genetic determinants of behaviour and the selective values of different genomes. (c) 2007 Elsevier Inc. All rights reserved.

A knowledge-based evolution strategy for the multi-objective minimum spanning tree problem

A fast Knowledge-based Evolution Strategy, KES, for the multi-objective minimum spanning tree, is presented. The proposed algorithm is validated, for the bi-objective case, with an exhaustive search for small problems (4-10 nodes), and compared with a deterministic algorithm, EPDA and NSGA-II for larger problems (up to 100 nodes) using benchmark hard instances. Experimental results show that KES finds the true Pareto fronts for small instances of the problem and calculates good approximation Pareto sets for larger instances tested. It is shown that the fronts calculated by YES are superior to NSGA-II fronts and almost as good as those established by EPDA. KES is designed to be scalable to multi-objective problems and fast due to its small complexity.

Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus

We provide experimental evidence of a replication enhancer element (REE) within the capsid gene of tick-borne encephalitis virus (TBEV, genus Flavivirus). Thermodynamic and phylogenetic analyses predicted that the REE folds as a long stable stem–loop (designated SL6), conserved among all tick-borne flaviviruses (TBFV). Homologous sequences and potential base pairing were found in the corresponding regions of mosquito-borne flaviviruses, but not in more genetically distant flaviviruses. To investigate the role of SL6, nucleotide substitutions were introduced which changed a conserved hexanucleotide motif, the conformation of the terminal loop and the base-paired dsRNA stacking. Substitutions were made within a TBEV reverse genetic system and recovered mutants were compared for plaque morphology, single-step replication kinetics and cytopathic effect. The greatest phenotypic changes were observed in mutants with a destabilized stem. Point mutations in the conserved hexanucleotide motif of the terminal loop caused moderate virus attenuation. However, all mutants eventually reached the titre of wild-type virus late post-infection. Thus, although not essential for growth in tissue culture, the SL6 REE acts to up-regulate virus replication. We hypothesize that this modulatory role may be important for TBEV survival in nature, where the virus circulates by non-viraemic transmission between infected and non-infected ticks, during co-feeding on local rodents.

Amphioxus type I keratin cDNA and the evolution of intermediate filament genes

We report the cloning of an intermediate filament (IF) cDNA from the cephalochordate amphioxus that encodes a protein assignable to the type I keratin group. This is the first type I keratin reported from an invertebrate. Molecular phylogenetic analyses reveal that amphioxus also possesses a type II keratin, and that the genes encoding short-rod IF proteins underwent different patterns of duplication in vertebrates and their closest relatives, the cephalochordates. Extensive IF gene duplication and divergence may have facilitated the origin of new specialised cell types in vertebrates.

Structure variation and evolution in microphase-separated grafted diblock copolymer films

The phase behavior of grafted d-polystyrene-block-poly(methyl methacrylate) diblock copolymer films is examined, with particular focus on the effect of solvent and annealing time. It was observed that the films undergo a two-step transformation from an initially disordered state, through an ordered metastable state, to the final equilibrium configuration. It was also found that altering the solvent used to wash the films, or complete removal of the solvent prior to thermal annealing using supercritical CO2, could influence the structure of the films in the metastable state, though the final equilibrium state was unaffected. To aid in the understanding to these experimental results, a series of self-consistent field theory calculations were done on a model diblock copolymer brush containing solvent. Of the different models examined, those which contained a solvent selective for the grafted polymer block most accurately matched the observed experimental behavior. We hypothesize that the structure of the films in the metastable state results from solvent enrichment of the film near the film/substrate interface in the case of films washed with solvent or faster relaxation of the nongrafted block for supercritical CO2 treated (solvent free) films. The persistence of the metastable structures was attributed to the slow reorganization of the polymer chains in the absence of solvent.