The main philosophy underlying this research is that a model should constitute a representation of both what we know and what we do not know about the structure and behavior of a system. In other words it should summarize, as far as possible, both our degree of certainty and degree of uncertainty, so that it facilitates statements about prediction uncertainty arising from model structural uncertainty. Based on this philosophy, the following issues were explored in the dissertation: Identification of a hydrologic system model based on assumption about perceptual and conceptual models structure only, without strong additional assumptions about its mathematical structure Development of a novel data assimilation method for extraction of mathematical relationships between modeled variables using a Bayesian probabilistic framework as an alternative to up-scaling of governing equations Evaluation of the uncertainty in predicted system response arising from three uncertainty types: o uncertainty caused by initial conditions, o uncertainty caused by inputs, o uncertainty caused by mathematical structure Merging of theory and data to identify a system as an alternative to parameter calibration and state-updating approaches Possibility of correcting existing models and including descriptions of uncertainty about their mapping relationships using the proposed method Investigation of a simple hydrological conceptual mass balance model with two-dimensional input, one-dimensional state and two-dimensional output at watershed scale and different temporal scales using the method

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As the expression of the genetic blueprint, proteins are at the heart of all biological systems. The ever increasing set of available protein structures has taught us that diversity is the hallmark of their architecture, a fundamental characteristic that enables them to perform the vast array of functionality upon which all of life depends. This diversity, however, is central to one of the most challenging problems in molecular biology: how does a folding polypeptide chain navigate its way through all of the myriad of possible conformations to find its own particular biologically active form? With few overarching structural principles to draw upon that can be applied to all protein architecture, the search for a solution to the protein folding problem has yet to produce an algorithm that can explain and duplicate this fundamental biological process. In this thesis, we take a two-pronged approach for investigating the protein folding process. Our initial statistical studies of the distributions of hydrophobic and hydrophilic residues within α-helices and β-sheets suggest (i) that hydrophobicity plays a critical role in helix and sheet formation; and (ii) that the nucleation of these motifs may result in largely unidirectional growth. Most tellingly, from an examination of the amino acids found in the smallest β-sheets, we do not find any evidence of a β-nucleating code in the primary protein sequence. Complementing these statistical analyses, we have analyzed the structural environments of several ever-widening aspects of protein topology. Our examination of the gaps between strands in the smallest β-sheets reveals a common organizational principle underlying β-formation involving strands separated by large sequential gaps: with very few exceptions, these large gaps fold into single, compact structural modules, bringing the β-strands that are otherwise far apart in the sequence close together in space. We conclude, therefore, that β-nucleation in the smallest sheets results from the co-location of two strands that are either local in sequence, or local in space following prior folding events. A second study of larger β-sheets both corroborates and extends these findings: virtually all large sequential gaps between pairs of β-strands organize themselves into an hierarchical arrangement, creating a bread-crumb model of go-and-come-back structural organization that ultimately juxtaposes two strands of a parental β-structure that are far apart in the sequence in close spatial proximity. In a final study, we have formalized this go-and-come-back notion into the concept of anti-parallel double-strandedness (DS), and measure this property across protein architecture in general. With over 90% of all residues in a large, non-redundant set of protein structures classified as DS, we conclude that DS is a unifying structural principle that underpins all globular proteins. We postulate, moreover, that this one simple principle, anti-parallel double-strandedness, unites protein structure, protein folding and protein evolution. / Thesis (Ph.D, Biochemistry) -- Queen's University, 2011-09-30 12:32:41.379

One approach to protein structure prediction is to first predict from sequence, a thresholded and binary 2D representation of a protein's topology known as a contact map. Then, the predicted contact map can be used as distance constraints to construct a 3D structure. We focus on the latter half of the process and aim to obtain a set of non-binary distance constraints from contacts maps. This thesis proposes an approach to extend the traditional binary definition of “in contact” by incorporating fuzzy logic to construct fuzzy contact maps from a set of contact maps at different thresholds, providing a vehicle for error handling. Then, a novel template-based similarity search and distance geometry methods were applied to predict distance constraints in the form of a distance map. The three-dimensional coordinates were then calculated from the predicted distance constraints. Experiments were conducted to test our approach for various levels of noise. As well, we compare the performance of fuzzy contact maps to binary contact maps in the framework of our methodology. Our results showed that fuzzy contact map similarity was indicative of distance map similarity. Thus, we were able to retrieved similar distance map regions using fuzzy contact map similarity. The retrieved distance map regions provided a good starting point for adaptation and allowed for the extrapolation of missing distance values. We were thus able to predict distance maps from which, the three-dimensional coordinates were able to be calculated. Testing of this framework on binary contact maps revealed that fuzzy contact maps had better performance with or without noise due to a stronger correlation between fuzzy contact map similarity and distance map similarity. Thus, the methodology described in this thesis is able to predict good distance maps from fuzzy contact maps in the presence of noise and the resulting coordinates were highly correlated to the performance of the predicted distance maps. / Thesis (Ph.D, Computing) -- Queen's University, 2012-05-23 13:59:28.12

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This thesis examines the determinants of a strong rule of law in post-colonial societies by comparing Jamaica and Barbados, two countries with many similarities, but with divergent outcomes concerning the rule of law. The research takes a comparative historical approach, specifically investigating the origins of the divergence of the rule of law between Jamaica and Barbados during the transition to independence. The analysis suggests that the extent of communal divisions influenced the political culture of the masses during the transition to universal suffrage in the late colonial period. This proved to be the critical factor that determined whether political violence and patronage politics were institutionalized, which ultimately led to the deterioration in the capacity of the state to promote the rule of law. Differences along four key dimensions (the extent of a race-class correlation, the extent to which the Afro-Caribbean population viewed themselves as members of the national community, the orientation of the religion of the lower classes towards the established order, and the structural conditions that facilitated the cultural autonomy of the lower classes) developed between the two islands during the early colonial period that influenced the formation of communal divisions along class lines, which in turn influenced the political culture of the masses. In Jamaica, the ethnic division between the lower and middle classes led the former to adopt a political culture that challenged the authority of the colonial state, which, combined with the inaction of colonial authorities, ultimately resulted in the establishment of a democratic political system based on violence, lawlessness and patronage that emerged during a critical period of instability on the island (the transition to both universal suffrage and independence). In Barbados, the absence of communal divisions resulted in the adoption of the dominant political culture by the masses. As such, there was broad-based acceptance of the legitimacy of legal state authority, with all major political parties appealing to the electorate on a rational basis, thereby hindering the escalation and institutionalization of political violence and clientelism. Moreover, the compatibility between the political culture and the state authority structure in Barbados provided the foundation for a strong rule of law during the post-colonial period. / Cette thèse examine les déterminants de la légitimité de la loi dans les sociétés post-coloniales à travers la comparaison entre la Barbade et la Jamaique, deux pays similaires à plusieurs niveaux, mais dont la légitimité de la loi s'exerce on ne peut plus différemment. Ce projet de recherche propose une comparaison historique, ayant pour angle une recherche des origines de cette divergence de la légitimité de la loi entre ces deux pays pendant leur transition vers l'indépendance. L'analyse propose que le degré des divisions ethniques à influencer la culture politique de la masse lors de la transition au suffrage universel vers la fin de la période coloniale. C'était le facteur critique qui a déterminé si la violence et le favoritisme politiques étaient institutionnalisés, ce qui a conduit à la détérioration de la capacité de l'état à promouvoir la légitimité de la loi. Des divergences entourant quatre éléments-clés (la présence d'une corrélation race-classe sociale, le niveau d'identification de la population Afro-Antillaise à la communauté nationale, l'orientation de la religion de la classe inférieure envers l'ordre établi, et les conditions qui ont facilité l'autonomie culturelle des classes inférieures) se sont développés entre les deux îles pendant le début de l'ère coloniale et ont influencé le développement des divisions ethniques entre les classes, entraînant une influence de la culture politique de la masse. En Jamaique, la division ethnique entre les classes moyennes et inférieures ont poussé ces dernières à adopter une culture politique qui défiait l'autorité de l'état colonial, qui, combiné avec l'inaction des autorités coloniales, a eu pour résultat l'établissement d'un système politique démocratique basé sur la violence, l'absence de lois et le patronage durant cette période critique d'instabilité sur l'île (la transition vers le suffrage universel et l'indépendance). À la Barbade, l'absence de divisions ethniques a entraîné l'adoption de la culture politique par la masse. Il y avait une large acceptation de la légitimité de l'autorité judiciaire de l'État, avec tous les principaux partis politiques faisant appel à l'électorat sur une base rationnelle, ce qui a empêché l'escalade et l'institutionnalisation de la violence politique et du favoritisme. Par ailleurs, la compatibilité entre la culture politique et la structure d'autorité de l'État à la Barbade a constitué le fondement d'une légitimité de la loi forte pendant la période post-coloniale.